From 6a4d53751f9f66d9c3efe08373631002368ef35f Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 23 Jun 2020 14:25:06 -0700 Subject: [PATCH 01/30] changed name of parameters in Crossover, add_half_crossover, and add_full_crossover --- ...helix_origami_rectangle_twist_corrected.py | 4 +- examples/6_helix_bundle_honeycomb.py | 22 ++--- scadnano/scadnano.py | 84 +++++++++---------- tests/scadnano_tests.py | 54 ++++++------ ...st_16_helix_origami_rectangle_no_twist.dna | 2 +- ...e_2_helix_origami_deletions_insertions.dna | 2 +- ...stape_2_helix_origami_extremely_simple.dna | 2 +- ...ape_2_helix_origami_extremely_simple_2.dna | 2 +- .../test_6_helix_origami_rectangle.dna | 2 +- tutorial/tutorial.md | 6 +- 10 files changed, 91 insertions(+), 89 deletions(-) diff --git a/examples/24_helix_origami_rectangle_twist_corrected.py b/examples/24_helix_origami_rectangle_twist_corrected.py index cc880eb8..002dbe3b 100644 --- a/examples/24_helix_origami_rectangle_twist_corrected.py +++ b/examples/24_helix_origami_rectangle_twist_corrected.py @@ -34,8 +34,8 @@ def add_staple_crossovers(design: sc.DNADesign): start_offset = 24 if helix % 2 == 0 else 40 for offset in range(start_offset, 296, 32): if offset != 152: # skip crossover near seam - design.add_full_crossover(helix1=helix, helix2=helix + 1, offset1=offset, - forward1=helix % 2 == 1) + design.add_full_crossover(helix=helix, helix2=helix + 1, offset=offset, + forward=helix % 2 == 1) def add_staple_nicks(design: sc.DNADesign): diff --git a/examples/6_helix_bundle_honeycomb.py b/examples/6_helix_bundle_honeycomb.py index cd70acb3..7e3bdf24 100644 --- a/examples/6_helix_bundle_honeycomb.py +++ b/examples/6_helix_bundle_honeycomb.py @@ -97,22 +97,22 @@ def add_nicks(design: sc.DNADesign): def add_crossovers(design: sc.DNADesign): # staples interior for offset in range(84, 1246, 42): - design.add_full_crossover(helix1=0, helix2=1, offset1=offset, forward1=False) - design.add_full_crossover(helix1=3, helix2=4, offset1=offset, forward1=True) + design.add_full_crossover(helix=0, helix2=1, offset=offset, forward=False) + design.add_full_crossover(helix=3, helix2=4, offset=offset, forward=True) for offset in range(56, 1246, 42): - design.add_full_crossover(helix1=1, helix2=2, offset1=offset, forward1=True) - design.add_full_crossover(helix1=4, helix2=5, offset1=offset, forward1=False) + design.add_full_crossover(helix=1, helix2=2, offset=offset, forward=True) + design.add_full_crossover(helix=4, helix2=5, offset=offset, forward=False) for offset in range(70, 1246, 42): - design.add_full_crossover(helix1=2, helix2=3, offset1=offset, forward1=False) - design.add_full_crossover(helix1=5, helix2=0, offset1=offset, forward1=True) + design.add_full_crossover(helix=2, helix2=3, offset=offset, forward=False) + design.add_full_crossover(helix=5, helix2=0, offset=offset, forward=True) for offset in range(49, 1245, 42): # extra crossovers 5 - 0 for some reason - design.add_full_crossover(helix1=5, helix2=0, offset1=offset, forward1=True) + design.add_full_crossover(helix=5, helix2=0, offset=offset, forward=True) # staples edges - design.add_half_crossover(helix1=0, helix2=1, offset1=42, forward1=False) - design.add_half_crossover(helix1=3, helix2=4, offset1=42, forward1=True) - design.add_half_crossover(helix1=0, helix2=5, offset1=1245, forward1=False) - design.add_half_crossover(helix1=2, helix2=3, offset1=1245, forward1=False) + design.add_half_crossover(helix=0, helix2=1, offset=42, forward=False) + design.add_half_crossover(helix=3, helix2=4, offset=42, forward=True) + design.add_half_crossover(helix=0, helix2=5, offset=1245, forward=False) + design.add_half_crossover(helix=2, helix2=3, offset=1245, forward=False) # scaffold interior crossovers = [] diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 8bf71621..3d04cbcf 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -3741,35 +3741,34 @@ def add_nick(self, helix: int, offset: int, forward: bool): self.strands.extend([strand_before, strand_after]) - def add_half_crossover(self, helix1: int, helix2: int, offset1: int, forward1: bool, + def add_half_crossover(self, helix: int, helix2: int, offset: int, forward: bool, offset2: int = None, forward2: bool = None): """ - Add a half crossover from helix `helix1` at offset `offset1` to `helix2`, on the strand + Add a half crossover from helix `helix` at offset `offset` to `helix2`, on the strand with :py:data:`Strand.forward` = `forward`. Unlike :py:meth:`DNADesign.add_full_crossover`, which automatically adds a nick between the two half-crossovers, to call this method, there must *already* be nicks adjacent to the given offsets on the given helices. (either on the left or right side) - :param helix1: index of one helix of half crossover + :param helix: index of one helix of half crossover :param helix2: index of other helix of half crossover - :param offset1: offset on `helix1` at which to add half crossover - :param forward1: direction of :any:`Strand` on `helix1` to which to add half crossover + :param offset: offset on `helix` at which to add half crossover + :param forward: direction of :any:`Strand` on `helix` to which to add half crossover :param offset2: offset on `helix2` at which to add half crossover. - If not specified, defaults to `offset1` + If not specified, defaults to `offset` :param forward2: direction of :any:`Strand` on `helix2` to which to add half crossover. - If not specified, defaults to the negation of `forward1` - + If not specified, defaults to the negation of `forward` """ if offset2 is None: - offset2 = offset1 + offset2 = offset if forward2 is None: - forward2 = not forward1 - domain1 = self.domain_at(helix1, offset1, forward1) + forward2 = not forward + domain1 = self.domain_at(helix, offset, forward) domain2 = self.domain_at(helix2, offset2, forward2) if domain1 is None: raise IllegalDNADesignError( - f"Cannot add half crossover at (helix={helix1}, offset={offset1}). " + f"Cannot add half crossover at (helix={helix}, offset={offset}). " f"There is no Domain there.") if domain2 is None: raise IllegalDNADesignError( @@ -3780,7 +3779,7 @@ def add_half_crossover(self, helix1: int, helix2: int, offset1: int, forward1: b if strand1 == strand2: raise IllegalDNADesignError(f"Cannot add crossover from " - f"(helix={helix1}, offset={offset1}) to " + f"(helix={helix}, offset={offset}) to " f"(helix={helix2}, offset={offset2}) " f"because that would join two Domains " f"already on the same Strand! " @@ -3789,10 +3788,10 @@ def add_half_crossover(self, helix1: int, helix2: int, offset1: int, forward1: b f"crossover addition, to ensure that all strands are " f"non-circular, even in intermediate stages.") - if domain1.offset_3p() == offset1 and domain2.offset_5p() == offset2: + if domain1.offset_3p() == offset and domain2.offset_5p() == offset2: strand_first = strand1 strand_last = strand2 - elif domain1.offset_5p() == offset1 and domain2.offset_3p() == offset2: + elif domain1.offset_5p() == offset and domain2.offset_3p() == offset2: strand_first = strand2 strand_last = strand1 else: @@ -3816,25 +3815,25 @@ def add_half_crossover(self, helix1: int, helix2: int, offset1: int, forward1: b self.strands.remove(strand_last) self.strands.append(new_strand) - def add_full_crossover(self, helix1: int, helix2: int, offset1: int, forward1: bool, + def add_full_crossover(self, helix: int, helix2: int, offset: int, forward: bool, offset2: int = None, forward2: bool = None): """ - Adds two half-crossovers, one at `offset1` and another at `offset1`-1. + Adds two half-crossovers, one at `offset` and another at `offset`-1. Other arguments have the same meaning as in :py:meth:`DNADesign.add_half_crossover`. - A nick is automatically added on helix `helix1` between - `offset1` and `offset1`-1 if one is not already present, + A nick is automatically added on helix `helix` between + `offset` and `offset`-1 if one is not already present, and similarly for `offset2` on helix `helix2`. """ if offset2 is None: - offset2 = offset1 + offset2 = offset if forward2 is None: - forward2 = not forward1 - for helix, forward, offset in [(helix1, forward1, offset1), (helix2, forward2, offset2)]: + forward2 = not forward + for helix, forward, offset in [(helix, forward, offset), (helix2, forward2, offset2)]: self._prepare_nicks_for_full_crossover(helix, forward, offset) - self.add_half_crossover(helix1=helix1, helix2=helix2, offset1=offset1 - 1, offset2=offset2 - 1, - forward1=forward1, forward2=forward2) - self.add_half_crossover(helix1=helix1, helix2=helix2, offset1=offset1, offset2=offset2, - forward1=forward1, forward2=forward2) + self.add_half_crossover(helix=helix, helix2=helix2, offset=offset - 1, offset2=offset2 - 1, + forward=forward, forward2=forward2) + self.add_half_crossover(helix=helix, helix2=helix2, offset=offset, offset2=offset2, + forward=forward, forward2=forward2) def add_crossovers(self, crossovers: List[Crossover]): """ @@ -3852,19 +3851,19 @@ def add_crossovers(self, crossovers: List[Crossover]): """ for crossover in crossovers: if not crossover.half: - for helix, forward, offset in [(crossover.helix1, crossover.forward1, crossover.offset1), + for helix, forward, offset in [(crossover.helix, crossover.forward, crossover.offset), (crossover.helix2, crossover.forward2, crossover.offset2)]: self._prepare_nicks_for_full_crossover(helix, forward, offset) for crossover in crossovers: if crossover.half: - self.add_half_crossover(helix1=crossover.helix1, helix2=crossover.helix2, - forward1=crossover.forward1, forward2=crossover.forward2, - offset1=crossover.offset1, offset2=crossover.offset2) + self.add_half_crossover(helix=crossover.helix, helix2=crossover.helix2, + forward=crossover.forward, forward2=crossover.forward2, + offset=crossover.offset, offset2=crossover.offset2) else: - self.add_full_crossover(helix1=crossover.helix1, helix2=crossover.helix2, - forward1=crossover.forward1, forward2=crossover.forward2, - offset1=crossover.offset1, offset2=crossover.offset2) + self.add_full_crossover(helix=crossover.helix, helix2=crossover.helix2, + forward=crossover.forward, forward2=crossover.forward2, + offset=crossover.offset, offset2=crossover.offset2) def _prepare_nicks_for_full_crossover(self, helix, forward, offset): domain_right = self.domain_at(helix, offset, forward) @@ -4033,27 +4032,28 @@ class Crossover: :any:`DNADesign` with circular strands, which are currently unsupported. """ - helix1: int + helix: int """index of one helix of half crossover""" helix2: int """index of other helix of half crossover""" - offset1: int - """offset on `helix1` at which to add half crossover""" + offset: int + """offset on `helix` at which to add half crossover""" - forward1: bool - """direction of :any:`Strand` on `helix1` to which to add half crossover""" + forward: bool + """direction of :any:`Strand` on `helix` to which to add half crossover""" offset2: int = None """ - offset on `helix2` at which to add half crossover. If not specified, defaults to `offset1` + offset on `helix2` at which to add half crossover. + If not specified, defaults to `offset` """ forward2: bool = None """ direction of :any:`Strand` on `helix2` to which to add half crossover. - If not specified, defaults to the negation of `forward1` + If not specified, defaults to the negation of `forward` """ half: bool = False @@ -4064,6 +4064,6 @@ class Crossover: def __post_init__(self): if self.offset2 is None: - self.offset2 = self.offset1 + self.offset2 = self.offset if self.forward2 is None: - self.forward2 = not self.forward1 + self.forward2 = not self.forward diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index c46678ef..3e559243 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -1335,7 +1335,7 @@ def test_add_full_crossover__small_design_H0_forward(self): <------+ +------] TTTGGGCC AAACCCGG """ - self.small_design.add_full_crossover(helix1=0, helix2=1, offset1=8, forward1=True) + self.small_design.add_full_crossover(helix=0, helix2=1, offset=8, forward=True) self.assertEqual(4, len(self.small_design.strands)) # two new Strands self.assertIn(sc.Strand([ @@ -1372,7 +1372,7 @@ def test_add_full_crossover__small_design_H0_reverse(self): <------- -------] TTTGGGCC AAACCCGG """ - self.small_design.add_full_crossover(helix1=0, helix2=1, offset1=8, forward1=False) + self.small_design.add_full_crossover(helix=0, helix2=1, offset=8, forward=False) self.assertEqual(4, len(self.small_design.strands)) # two new Strands self.assertIn(sc.Strand([ @@ -1411,7 +1411,7 @@ def test_add_half_crossover__small_design_H0_reverse_8(self): """ self.small_design.add_nick(helix=0, offset=8, forward=False) self.small_design.add_nick(helix=1, offset=8, forward=True) - self.small_design.add_half_crossover(helix1=0, helix2=1, offset1=8, forward1=False) + self.small_design.add_half_crossover(helix=0, helix2=1, offset=8, forward=False) self.assertEqual(5, len(self.small_design.strands)) # three new Strands self.assertIn(sc.Strand([ @@ -1452,7 +1452,7 @@ def test_add_half_crossover__small_design_H0_reverse_0(self): <------- -------] TTTGGGCC AAACCCGG """ - self.small_design.add_half_crossover(helix1=0, helix2=1, offset1=0, forward1=False) + self.small_design.add_half_crossover(helix=0, helix2=1, offset=0, forward=False) self.assertEqual(3, len(self.small_design.strands)) # one new Strand self.assertIn(sc.Strand([ @@ -1483,7 +1483,7 @@ def test_add_half_crossover__small_design_H0_reverse_15(self): <------- -------] TTTGGGCC AAACCCGG """ - self.small_design.add_half_crossover(helix1=0, helix2=1, offset1=15, forward1=False) + self.small_design.add_half_crossover(helix=0, helix2=1, offset=15, forward=False) self.assertEqual(3, len(self.small_design.strands)) # one new Strand self.assertIn(sc.Strand([ @@ -1511,7 +1511,7 @@ def test_add_half_crossover__small_design_illegal(self): <------- -------] """ with self.assertRaises(sc.IllegalDNADesignError): - self.small_design.add_half_crossover(helix1=0, helix2=1, offset1=16, forward1=False) + self.small_design.add_half_crossover(helix=0, helix2=1, offset=16, forward=False) def test_add_full_crossover__small_design_illegal(self): """ @@ -1523,7 +1523,7 @@ def test_add_full_crossover__small_design_illegal(self): <------- -------] """ with self.assertRaises(sc.IllegalDNADesignError): - self.small_design.add_full_crossover(helix1=0, helix2=1, offset1=16, forward1=False) + self.small_design.add_full_crossover(helix=0, helix2=1, offset=16, forward=False) def test_add_full_crossover__small_design_illegal_only_one_helix_has_domain(self): """ @@ -1541,7 +1541,7 @@ def test_add_full_crossover__small_design_illegal_only_one_helix_has_domain(self sc.Strand([sc.Domain(1, False, 0, 5)]), ], grid=sc.square) with self.assertRaises(sc.IllegalDNADesignError): - design.add_full_crossover(helix1=0, helix2=1, offset1=10, forward1=False) + design.add_full_crossover(helix=0, helix2=1, offset=10, forward=False) r""" 0 8 16 24 32 40 48 56 64 72 80 88 96 @@ -1625,33 +1625,33 @@ def test_add_nick__6_helix_rectangle(self): def add_crossovers_after_nicks(self, design: sc.DNADesign): # scaffold seam crossovers - design.add_full_crossover(helix1=1, helix2=2, offset1=48, forward1=False) - design.add_full_crossover(helix1=3, helix2=4, offset1=48, forward1=False) + design.add_full_crossover(helix=1, helix2=2, offset=48, forward=False) + design.add_full_crossover(helix=3, helix2=4, offset=48, forward=False) # staple crossovers - design.add_full_crossover(helix1=0, helix2=1, offset1=16, forward1=False) - design.add_full_crossover(helix1=0, helix2=1, offset1=80, forward1=False) - design.add_full_crossover(helix1=1, helix2=2, offset1=32, forward1=True) - design.add_full_crossover(helix1=1, helix2=2, offset1=64, forward1=True) - design.add_full_crossover(helix1=2, helix2=3, offset1=16, forward1=False) - design.add_full_crossover(helix1=2, helix2=3, offset1=80, forward1=False) - design.add_full_crossover(helix1=3, helix2=4, offset1=32, forward1=True) - design.add_full_crossover(helix1=3, helix2=4, offset1=64, forward1=True) - design.add_full_crossover(helix1=4, helix2=5, offset1=16, forward1=False) - design.add_full_crossover(helix1=4, helix2=5, offset1=80, forward1=False) + design.add_full_crossover(helix=0, helix2=1, offset=16, forward=False) + design.add_full_crossover(helix=0, helix2=1, offset=80, forward=False) + design.add_full_crossover(helix=1, helix2=2, offset=32, forward=True) + design.add_full_crossover(helix=1, helix2=2, offset=64, forward=True) + design.add_full_crossover(helix=2, helix2=3, offset=16, forward=False) + design.add_full_crossover(helix=2, helix2=3, offset=80, forward=False) + design.add_full_crossover(helix=3, helix2=4, offset=32, forward=True) + design.add_full_crossover(helix=3, helix2=4, offset=64, forward=True) + design.add_full_crossover(helix=4, helix2=5, offset=16, forward=False) + design.add_full_crossover(helix=4, helix2=5, offset=80, forward=False) # The left and right edge crossovers need to be added last to ensure the Strands remain # non-circular during all intermediate stages. # scaffold left crossovers - design.add_half_crossover(helix1=0, helix2=1, offset1=0, forward1=True) - design.add_half_crossover(helix1=2, helix2=3, offset1=0, forward1=True) - design.add_half_crossover(helix1=4, helix2=5, offset1=0, forward1=True) + design.add_half_crossover(helix=0, helix2=1, offset=0, forward=True) + design.add_half_crossover(helix=2, helix2=3, offset=0, forward=True) + design.add_half_crossover(helix=4, helix2=5, offset=0, forward=True) # scaffold right crossovers - design.add_half_crossover(helix1=0, helix2=1, offset1=95, forward1=True) - design.add_half_crossover(helix1=2, helix2=3, offset1=95, forward1=True) - design.add_half_crossover(helix1=4, helix2=5, offset1=95, forward1=True) + design.add_half_crossover(helix=0, helix2=1, offset=95, forward=True) + design.add_half_crossover(helix=2, helix2=3, offset=95, forward=True) + design.add_half_crossover(helix=4, helix2=5, offset=95, forward=True) def test_add_nick_then_add_crossovers__6_helix_rectangle(self): self.add_nicks(self.design) @@ -2445,6 +2445,8 @@ def test_add_strand__with_loopout(self): self.assertEqual(ss2, design.domain_at(1, 0, False)) + + class TestAssignDNA(unittest.TestCase): def test_assign_dna__hairpin(self): diff --git a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna index b4f44a0b..85d2d644 100644 --- a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna +++ b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna index 5ef2048d..2844cbb4 100644 --- a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.dna b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.dna index bb701927..b41270a6 100644 --- a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.dna +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.dna b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.dna index d3b0da59..db9cd2bd 100644 --- a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.dna +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_extremely_simple_2.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna index eb6d0e2c..f7c10441 100644 --- a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna +++ b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 192, "grid_position": [0, 0]}, diff --git a/tutorial/tutorial.md b/tutorial/tutorial.md index 81ed5b82..92153e58 100644 --- a/tutorial/tutorial.md +++ b/tutorial/tutorial.md @@ -417,7 +417,7 @@ def add_staple_crossovers(design: sc.DNADesign): start_offset = 24 if helix % 2 == 0 else 40 for offset in range(start_offset, 296, 32): if offset != 152: # skip crossover near seam - design.add_full_crossover(helix1=helix, helix2=helix+1, offset1=offset, forward1=helix%2==1) + design.add_full_crossover(helix=helix, helix2=helix+1, offset=offset, forward=helix%2==1) ``` The design is now mostly complete: @@ -576,8 +576,8 @@ def add_staple_crossovers(design: sc.DNADesign): start_offset = 24 if helix % 2 == 0 else 40 for offset in range(start_offset, 296, 32): if offset != 152: # skip crossover near seam - design.add_full_crossover(helix1=helix, helix2=helix + 1, offset1=offset, - forward1=helix % 2 == 1) + design.add_full_crossover(helix=helix, helix2=helix + 1, offset=offset, + forward=helix % 2 == 1) def add_staple_nicks(design: sc.DNADesign): From 0a93dbdd74a201b8f9d17739df4c11873a6c4653 Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 23 Jun 2020 14:27:43 -0700 Subject: [PATCH 02/30] fixed name shadowing bug --- scadnano/scadnano.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 3d04cbcf..a5731fdf 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -3828,8 +3828,8 @@ def add_full_crossover(self, helix: int, helix2: int, offset: int, forward: bool offset2 = offset if forward2 is None: forward2 = not forward - for helix, forward, offset in [(helix, forward, offset), (helix2, forward2, offset2)]: - self._prepare_nicks_for_full_crossover(helix, forward, offset) + for helix_, forward_, offset_ in [(helix, forward, offset), (helix2, forward2, offset2)]: + self._prepare_nicks_for_full_crossover(helix_, forward_, offset_) self.add_half_crossover(helix=helix, helix2=helix2, offset=offset - 1, offset2=offset2 - 1, forward=forward, forward2=forward2) self.add_half_crossover(helix=helix, helix2=helix2, offset=offset, offset2=offset2, From ffdd62fbc18e2fa42ebf073383866de67a23ff53 Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 23 Jun 2020 14:32:50 -0700 Subject: [PATCH 03/30] cleaned up docstrings --- scadnano/scadnano.py | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index a5731fdf..ca8feb7a 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -3823,6 +3823,15 @@ def add_full_crossover(self, helix: int, helix2: int, offset: int, forward: bool A nick is automatically added on helix `helix` between `offset` and `offset`-1 if one is not already present, and similarly for `offset2` on helix `helix2`. + + :param helix: index of one helix of half crossover + :param helix2: index of other helix of half crossover + :param offset: offset on `helix` at which to add half crossover + :param forward: direction of :any:`Strand` on `helix` to which to add half crossover + :param offset2: offset on `helix2` at which to add half crossover. + If not specified, defaults to `offset` + :param forward2: direction of :any:`Strand` on `helix2` to which to add half crossover. + If not specified, defaults to the negation of `forward` """ if offset2 is None: offset2 = offset @@ -3839,7 +3848,10 @@ def add_crossovers(self, crossovers: List[Crossover]): """ Adds a list of :any:`Crossover`'s in batch. - This helps to avoid problems where adding them one at a time + This helps to avoid problems where adding them one at a time using + :py:meth:`DNADesign.add_half_crossover` + or + :py:meth:`DNADesign.add_full_crossover` creates an intermediate design with circular strands. :param crossovers: list of :any:`Crossover`'s to add. Its fields have the same meaning as in From d33dbae1c1a682d70440dd53ad039c89350886ac Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 23 Jun 2020 14:43:46 -0700 Subject: [PATCH 04/30] cleaned up docstrings --- scadnano/scadnano.py | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index ca8feb7a..fc903847 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -3859,7 +3859,6 @@ def add_crossovers(self, crossovers: List[Crossover]): and :py:meth:`DNADesign.add_full_crossover`, with the extra field `Crossover.half` indicating whether it represents a half or full crossover. - """ for crossover in crossovers: if not crossover.half: @@ -3898,10 +3897,21 @@ def inline_deletions_insertions(self): Converts deletions and insertions by "inlining" them. Insertions and deletions are removed, and their domains have their lengths altered. Also, major tick marks on the helices will be shifted to preserve their adjacency to bases already present. For example, if there are major - tick marks at 0, 8, 18, 24, and a deletion between 0 and 8, then - the domain is shortened by 1, + tick marks at 0, 8, 18, 24, and a deletion between 0 and 8: + + .. code-block:: none + + 0 8 18 24 30 + |--X---|---------|-----|------ + + then the domain is shortened by 1, the tick marks become 0, 7, 15, 23, - and the helix's maximum offset is shrunk by 1. + and the helix's maximum offset is shrunk by 1: + + .. code-block:: none + + 0 7 17 23 29 + |-----|---------|-----|------ We assume that a major tick mark appears just to the LEFT of the offset it encodes, so the minimum and maximum offsets for tick marks are respectively the helix's minimum offset From 9dc504f6afdc2e8a4227d35acea337082db26ffb Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 23 Jun 2020 14:45:35 -0700 Subject: [PATCH 05/30] replaced parameter names in calls to add_*_crossover --- ...helix_origami_rectangle_twist_corrected.py | 6 ++-- examples/6_helix_bundle_honeycomb.py | 20 +++++------ ...elix_origami_barrel_from_algoSST_paper.dna | 2 +- .../16_helix_origami_rectangle.dna | 2 +- .../16_helix_origami_rectangle_idt.dna | 2 +- .../16_helix_origami_rectangle_no_seq.dna | 2 +- ...elix_origami_rectangle_no_seq_no_twist.dna | 2 +- .../16_helix_origami_rectangle_no_twist.dna | 2 +- ...ami_rectangle_seed_tiles_grow_from_top.dna | 2 +- ..._origami_rectangle_shifted_seam_no_seq.dna | 2 +- .../1_staple_1_helix_origami.dna | 2 +- .../1_staple_1_helix_origami_mismatches.dna | 2 +- ...le_1_helix_origami_position_nondefault.dna | 2 +- .../1_staple_1_helix_origami_roll.dna | 2 +- ...elix_origami_rectangle_twist_corrected.dna | 2 +- ...x_2_strands_multiple_substrands_no_seq.dna | 2 +- .../2_staple_2_helix_modifications.dna | 34 +++++++++---------- .../2_staple_2_helix_origami_6bases_wide.dna | 2 +- .../2_staple_2_helix_origami_deletions.dna | 2 +- ...e_2_helix_origami_deletions_insertions.dna | 2 +- ...elix_origami_deletions_insertions_mods.dna | 2 +- ...ix_origami_deletions_insertions_no_seq.dna | 2 +- .../3_helix_deletions_insertions.dna | 2 +- examples/output_designs/4_helix_grid_none.dna | 2 +- ..._none_min_offset_position_x_nondefault.dna | 2 +- .../4_helix_min_offsets_nonzero.dna | 2 +- .../56_helix_origami_rectangle.dna | 2 +- .../64_helix_origami_rectangle.dna | 2 +- .../6_helix_6_col_origami_rectangle.dna | 2 +- .../6_helix_bundle_honeycomb.dna | 2 +- .../6_helix_origami_rectangle.dna | 2 +- ...origami_rectangle_helices_out_of_order.dna | 2 +- .../add_deletions_to_24_helix_rectangle.dna | 2 +- examples/output_designs/empty.dna | 2 +- examples/output_designs/hairpin.dna | 2 +- .../helices_out_of_order_nonconsecutive.dna | 2 +- examples/output_designs/hex_lattice_10x10.dna | 2 +- .../hex_lattice_10x10_with_negative.dna | 2 +- .../honeycomb_lattice_10x10.dna | 2 +- .../honeycomb_lattice_10x10_with_negative.dna | 2 +- .../output_designs/idt-plates-explicit.dna | 2 +- .../output_designs/long_range_crossovers.dna | 2 +- .../output_designs/loopouts_all_types.dna | 2 +- examples/output_designs/many_big_helices.dna | 2 +- .../many_helices_modifications.dna | 28 +++++++-------- examples/output_designs/proposal.dna | 2 +- examples/output_designs/sst-motif-3_2.dna | 2 +- examples/output_designs/sst-motif-4_1.dna | 2 +- 48 files changed, 88 insertions(+), 88 deletions(-) diff --git a/examples/24_helix_origami_rectangle_twist_corrected.py b/examples/24_helix_origami_rectangle_twist_corrected.py index 002dbe3b..96c42264 100644 --- a/examples/24_helix_origami_rectangle_twist_corrected.py +++ b/examples/24_helix_origami_rectangle_twist_corrected.py @@ -69,13 +69,13 @@ def add_scaffold_crossovers(design: sc.DNADesign): # scaffold interior for helix in range(1, 23, 2): - crossovers.append(sc.Crossover(helix1=helix, helix2=helix + 1, offset1=152, forward1=False)) + crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, offset=152, forward=False)) # scaffold edges for helix in range(0, 23, 2): - crossovers.append(sc.Crossover(helix1=helix, helix2=helix + 1, offset1=8, forward1=True, half=True)) + crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, offset=8, forward=True, half=True)) crossovers.append( - sc.Crossover(helix1=helix, helix2=helix + 1, offset1=295, forward1=True, half=True)) + sc.Crossover(helix=helix, helix2=helix + 1, offset=295, forward=True, half=True)) design.add_crossovers(crossovers) diff --git a/examples/6_helix_bundle_honeycomb.py b/examples/6_helix_bundle_honeycomb.py index 7e3bdf24..4e347ce6 100644 --- a/examples/6_helix_bundle_honeycomb.py +++ b/examples/6_helix_bundle_honeycomb.py @@ -117,21 +117,21 @@ def add_crossovers(design: sc.DNADesign): # scaffold interior crossovers = [] for offset in range(58, 1250, 42): - crossovers.append(sc.Crossover(helix1=0, helix2=1, offset1=offset, forward1=True)) + crossovers.append(sc.Crossover(helix=0, helix2=1, offset=offset, forward=True)) for offset in range(30, 1250, 42): - crossovers.append(sc.Crossover(helix1=1, helix2=2, offset1=offset, forward1=False)) + crossovers.append(sc.Crossover(helix=1, helix2=2, offset=offset, forward=False)) for offset in range(54, 1250, 42): - crossovers.append(sc.Crossover(helix1=2, helix2=3, offset1=offset, forward1=True)) + crossovers.append(sc.Crossover(helix=2, helix2=3, offset=offset, forward=True)) for offset in range(26, 1250, 42): - crossovers.append(sc.Crossover(helix1=3, helix2=4, offset1=offset, forward1=False)) + crossovers.append(sc.Crossover(helix=3, helix2=4, offset=offset, forward=False)) # scaffold edges - crossovers.append(sc.Crossover(helix1=0, helix2=1, offset1=16, forward1=True, half=True)) - crossovers.append(sc.Crossover(helix1=2, helix2=3, offset1=12, forward1=True, half=True)) - crossovers.append(sc.Crossover(helix1=4, helix2=5, offset1=19, forward1=True, half=True)) - crossovers.append(sc.Crossover(helix1=0, helix2=1, offset1=1275, forward1=True, half=True)) - crossovers.append(sc.Crossover(helix1=2, helix2=3, offset1=1271, forward1=True, half=True)) - crossovers.append(sc.Crossover(helix1=4, helix2=5, offset1=1278, forward1=True, half=True)) + crossovers.append(sc.Crossover(helix=0, helix2=1, offset=16, forward=True, half=True)) + crossovers.append(sc.Crossover(helix=2, helix2=3, offset=12, forward=True, half=True)) + crossovers.append(sc.Crossover(helix=4, helix2=5, offset=19, forward=True, half=True)) + crossovers.append(sc.Crossover(helix=0, helix2=1, offset=1275, forward=True, half=True)) + crossovers.append(sc.Crossover(helix=2, helix2=3, offset=1271, forward=True, half=True)) + crossovers.append(sc.Crossover(helix=4, helix2=5, offset=1278, forward=True, half=True)) design.add_crossovers(crossovers) diff --git a/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna b/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna index b8bdd4ad..c06acb18 100644 --- a/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna +++ b/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ { diff --git a/examples/output_designs/16_helix_origami_rectangle.dna b/examples/output_designs/16_helix_origami_rectangle.dna index a95abf44..bdc835fa 100644 --- a/examples/output_designs/16_helix_origami_rectangle.dna +++ b/examples/output_designs/16_helix_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/examples/output_designs/16_helix_origami_rectangle_idt.dna b/examples/output_designs/16_helix_origami_rectangle_idt.dna index be2a60b9..f1e11f96 100644 --- a/examples/output_designs/16_helix_origami_rectangle_idt.dna +++ b/examples/output_designs/16_helix_origami_rectangle_idt.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq.dna b/examples/output_designs/16_helix_origami_rectangle_no_seq.dna index 1ce37cbf..369f9431 100644 --- a/examples/output_designs/16_helix_origami_rectangle_no_seq.dna +++ b/examples/output_designs/16_helix_origami_rectangle_no_seq.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna b/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna index 60a2f617..af114c70 100644 --- a/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna +++ b/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/examples/output_designs/16_helix_origami_rectangle_no_twist.dna b/examples/output_designs/16_helix_origami_rectangle_no_twist.dna index 121420bf..04374c03 100644 --- a/examples/output_designs/16_helix_origami_rectangle_no_twist.dna +++ b/examples/output_designs/16_helix_origami_rectangle_no_twist.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna b/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna index f39f6607..c2fb2406 100644 --- a/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna +++ b/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ { diff --git a/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna b/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna index cd6403ba..a25df6b1 100644 --- a/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna +++ b/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 448, "grid_position": [0, 0]}, diff --git a/examples/output_designs/1_staple_1_helix_origami.dna b/examples/output_designs/1_staple_1_helix_origami.dna index 3e513592..5c06a41e 100644 --- a/examples/output_designs/1_staple_1_helix_origami.dna +++ b/examples/output_designs/1_staple_1_helix_origami.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ { diff --git a/examples/output_designs/1_staple_1_helix_origami_mismatches.dna b/examples/output_designs/1_staple_1_helix_origami_mismatches.dna index 0e41471f..b0c3a6c1 100644 --- a/examples/output_designs/1_staple_1_helix_origami_mismatches.dna +++ b/examples/output_designs/1_staple_1_helix_origami_mismatches.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]} diff --git a/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna b/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna index 30ed934f..5c0ba069 100644 --- a/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna +++ b/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ { diff --git a/examples/output_designs/1_staple_1_helix_origami_roll.dna b/examples/output_designs/1_staple_1_helix_origami_roll.dna index e9ed78bc..3c186cb5 100644 --- a/examples/output_designs/1_staple_1_helix_origami_roll.dna +++ b/examples/output_designs/1_staple_1_helix_origami_roll.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0], "roll": 90} diff --git a/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna b/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna index 07f249b9..04a8d593 100644 --- a/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna +++ b/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 304, "grid_position": [0, 0]}, diff --git a/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna b/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna index 157c8f1d..e5d9d70f 100644 --- a/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna +++ b/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/2_staple_2_helix_modifications.dna b/examples/output_designs/2_staple_2_helix_modifications.dna index c91b538a..09610211 100644 --- a/examples/output_designs/2_staple_2_helix_modifications.dna +++ b/examples/output_designs/2_staple_2_helix_modifications.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, @@ -12,18 +12,12 @@ "display_connector": false, "location": "5'" }, - "/3Cy3Sp/": { - "display_text": "Cy3", - "idt_text": "/3Cy3Sp/", + "/3Bio/": { + "display_text": "B", + "idt_text": "/3Bio/", "display_connector": false, "location": "3'" }, - "/iCy3/": { - "display_text": "Cy3", - "idt_text": "/iCy3/", - "display_connector": false, - "location": "internal" - }, "/iBiodT/": { "display_text": "B", "idt_text": "/iBiodT/", @@ -31,11 +25,11 @@ "location": "internal", "allowed_bases": ["T"] }, - "/3Bio/": { - "display_text": "B", - "idt_text": "/3Bio/", + "/iCy5/": { + "display_text": "Cy5", + "idt_text": "/iCy5/", "display_connector": false, - "location": "3'" + "location": "internal" }, "/5Biosg/": { "display_text": "B", @@ -43,9 +37,15 @@ "display_connector": false, "location": "5'" }, - "/iCy5/": { - "display_text": "Cy5", - "idt_text": "/iCy5/", + "/3Cy3Sp/": { + "display_text": "Cy3", + "idt_text": "/3Cy3Sp/", + "display_connector": false, + "location": "3'" + }, + "/iCy3/": { + "display_text": "Cy3", + "idt_text": "/iCy3/", "display_connector": false, "location": "internal" } diff --git a/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna b/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna index 40609b3e..46798974 100644 --- a/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna +++ b/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions.dna b/examples/output_designs/2_staple_2_helix_origami_deletions.dna index e3e7f4cb..c438c557 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna index f2eb167f..29295ec1 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 48, "grid_position": [0, 0]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna index 591daced..dcaee9aa 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 48, "grid_position": [0, 0]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna index fb6c9262..d774e313 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/3_helix_deletions_insertions.dna b/examples/output_designs/3_helix_deletions_insertions.dna index a99db8c1..62824fa1 100644 --- a/examples/output_designs/3_helix_deletions_insertions.dna +++ b/examples/output_designs/3_helix_deletions_insertions.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 64, "grid_position": [0, 0]}, diff --git a/examples/output_designs/4_helix_grid_none.dna b/examples/output_designs/4_helix_grid_none.dna index 7b9798d6..5165a279 100644 --- a/examples/output_designs/4_helix_grid_none.dna +++ b/examples/output_designs/4_helix_grid_none.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "none", "helices": [ { diff --git a/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna b/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna index 95bc60c4..f48c0f27 100644 --- a/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna +++ b/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "none", "helices": [ { diff --git a/examples/output_designs/4_helix_min_offsets_nonzero.dna b/examples/output_designs/4_helix_min_offsets_nonzero.dna index 086dda0b..2989e9f5 100644 --- a/examples/output_designs/4_helix_min_offsets_nonzero.dna +++ b/examples/output_designs/4_helix_min_offsets_nonzero.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 30, "grid_position": [0, 0]}, diff --git a/examples/output_designs/56_helix_origami_rectangle.dna b/examples/output_designs/56_helix_origami_rectangle.dna index 4309e3a9..2afa7d30 100644 --- a/examples/output_designs/56_helix_origami_rectangle.dna +++ b/examples/output_designs/56_helix_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 160, "grid_position": [0, 0]}, diff --git a/examples/output_designs/64_helix_origami_rectangle.dna b/examples/output_designs/64_helix_origami_rectangle.dna index e8fbdb88..7da9f394 100644 --- a/examples/output_designs/64_helix_origami_rectangle.dna +++ b/examples/output_designs/64_helix_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 128, "grid_position": [0, 0]}, diff --git a/examples/output_designs/6_helix_6_col_origami_rectangle.dna b/examples/output_designs/6_helix_6_col_origami_rectangle.dna index d7ea78c1..c79dc893 100644 --- a/examples/output_designs/6_helix_6_col_origami_rectangle.dna +++ b/examples/output_designs/6_helix_6_col_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/6_helix_bundle_honeycomb.dna b/examples/output_designs/6_helix_bundle_honeycomb.dna index 01306a72..0b2682de 100644 --- a/examples/output_designs/6_helix_bundle_honeycomb.dna +++ b/examples/output_designs/6_helix_bundle_honeycomb.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "honeycomb", "helices": [ {"max_offset": 1295, "grid_position": [1, 1, 0]}, diff --git a/examples/output_designs/6_helix_origami_rectangle.dna b/examples/output_designs/6_helix_origami_rectangle.dna index bcbe97ba..909a8e13 100644 --- a/examples/output_designs/6_helix_origami_rectangle.dna +++ b/examples/output_designs/6_helix_origami_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 192, "grid_position": [0, 0]}, diff --git a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna index d2ef4834..a2166a2f 100644 --- a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna +++ b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 192, "grid_position": [0, 0]}, diff --git a/examples/output_designs/add_deletions_to_24_helix_rectangle.dna b/examples/output_designs/add_deletions_to_24_helix_rectangle.dna index 56947ab6..d2875005 100644 --- a/examples/output_designs/add_deletions_to_24_helix_rectangle.dna +++ b/examples/output_designs/add_deletions_to_24_helix_rectangle.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "e", "helices": [ {"max_offset": 304, "grid_position": [0, -3]}, diff --git a/examples/output_designs/empty.dna b/examples/output_designs/empty.dna index 2ff8f165..13fe4dfd 100644 --- a/examples/output_designs/empty.dna +++ b/examples/output_designs/empty.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [], "strands": [] diff --git a/examples/output_designs/hairpin.dna b/examples/output_designs/hairpin.dna index c36e8aea..9a1af2e1 100644 --- a/examples/output_designs/hairpin.dna +++ b/examples/output_designs/hairpin.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]} diff --git a/examples/output_designs/helices_out_of_order_nonconsecutive.dna b/examples/output_designs/helices_out_of_order_nonconsecutive.dna index ca6c937d..10a971a3 100644 --- a/examples/output_designs/helices_out_of_order_nonconsecutive.dna +++ b/examples/output_designs/helices_out_of_order_nonconsecutive.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "none", "helices": [ {"max_offset": 20, "grid_position": [0, 2], "idx": 2}, diff --git a/examples/output_designs/hex_lattice_10x10.dna b/examples/output_designs/hex_lattice_10x10.dna index a87ab6b8..629d3227 100644 --- a/examples/output_designs/hex_lattice_10x10.dna +++ b/examples/output_designs/hex_lattice_10x10.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "hex", "helices": [ {"max_offset": 16, "grid_position": [0, 0, 0]}, diff --git a/examples/output_designs/hex_lattice_10x10_with_negative.dna b/examples/output_designs/hex_lattice_10x10_with_negative.dna index 2d305f15..cfc61094 100644 --- a/examples/output_designs/hex_lattice_10x10_with_negative.dna +++ b/examples/output_designs/hex_lattice_10x10_with_negative.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "hex", "helices": [ {"max_offset": 16, "grid_position": [-4, -4, 0]}, diff --git a/examples/output_designs/honeycomb_lattice_10x10.dna b/examples/output_designs/honeycomb_lattice_10x10.dna index 9bec2064..a24f2649 100644 --- a/examples/output_designs/honeycomb_lattice_10x10.dna +++ b/examples/output_designs/honeycomb_lattice_10x10.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "honeycomb", "helices": [ {"max_offset": 16, "grid_position": [0, 0, 0]}, diff --git a/examples/output_designs/honeycomb_lattice_10x10_with_negative.dna b/examples/output_designs/honeycomb_lattice_10x10_with_negative.dna index a811c7a7..c7426ac3 100644 --- a/examples/output_designs/honeycomb_lattice_10x10_with_negative.dna +++ b/examples/output_designs/honeycomb_lattice_10x10_with_negative.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "honeycomb", "helices": [ {"max_offset": 16, "grid_position": [-4, -4, 0]}, diff --git a/examples/output_designs/idt-plates-explicit.dna b/examples/output_designs/idt-plates-explicit.dna index c20408ce..6782b63c 100644 --- a/examples/output_designs/idt-plates-explicit.dna +++ b/examples/output_designs/idt-plates-explicit.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/long_range_crossovers.dna b/examples/output_designs/long_range_crossovers.dna index d3d848bc..96f21359 100644 --- a/examples/output_designs/long_range_crossovers.dna +++ b/examples/output_designs/long_range_crossovers.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/loopouts_all_types.dna b/examples/output_designs/loopouts_all_types.dna index 94860ec6..c54f3f0d 100644 --- a/examples/output_designs/loopouts_all_types.dna +++ b/examples/output_designs/loopouts_all_types.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, diff --git a/examples/output_designs/many_big_helices.dna b/examples/output_designs/many_big_helices.dna index 8ee0a079..38d7035c 100644 --- a/examples/output_designs/many_big_helices.dna +++ b/examples/output_designs/many_big_helices.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"max_offset": 2000, "grid_position": [0, 0]}, diff --git a/examples/output_designs/many_helices_modifications.dna b/examples/output_designs/many_helices_modifications.dna index d41343ef..31eb5071 100644 --- a/examples/output_designs/many_helices_modifications.dna +++ b/examples/output_designs/many_helices_modifications.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "helices": [ {"grid_position": [0, 0]}, @@ -12,6 +12,19 @@ {"grid_position": [0, 7]} ], "modifications_in_design": { + "/5Biosg/": { + "display_text": "B", + "idt_text": "/5Biosg/", + "display_connector": false, + "location": "5'" + }, + "/iBiodT/": { + "display_text": "B", + "idt_text": "/iBiodT/", + "display_connector": false, + "location": "internal", + "allowed_bases": ["T"] + }, "/3Cy3Sp/": { "display_text": "Cy3", "idt_text": "/3Cy3Sp/", @@ -23,19 +36,6 @@ "idt_text": "/iCy3/", "display_connector": false, "location": "internal" - }, - "/iBiodT/": { - "display_text": "B", - "idt_text": "/iBiodT/", - "display_connector": false, - "location": "internal", - "allowed_bases": ["T"] - }, - "/5Biosg/": { - "display_text": "B", - "idt_text": "/5Biosg/", - "display_connector": false, - "location": "5'" } }, "strands": [ diff --git a/examples/output_designs/proposal.dna b/examples/output_designs/proposal.dna index cfd8ef6c..c03a732a 100644 --- a/examples/output_designs/proposal.dna +++ b/examples/output_designs/proposal.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "none", "helices": [ { diff --git a/examples/output_designs/sst-motif-3_2.dna b/examples/output_designs/sst-motif-3_2.dna index 55fefc73..477375f2 100644 --- a/examples/output_designs/sst-motif-3_2.dna +++ b/examples/output_designs/sst-motif-3_2.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "major_tick_distance": 10, "helices": [ diff --git a/examples/output_designs/sst-motif-4_1.dna b/examples/output_designs/sst-motif-4_1.dna index 08b7a678..fc358406 100644 --- a/examples/output_designs/sst-motif-4_1.dna +++ b/examples/output_designs/sst-motif-4_1.dna @@ -1,5 +1,5 @@ { - "version": "0.9.0", + "version": "0.9.1", "grid": "square", "major_tick_distance": 10, "helices": [ From 0426e10921bb0f3b5ee2a480af8a6892b1c4bcd5 Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 23 Jun 2020 14:57:17 -0700 Subject: [PATCH 06/30] added code to check for overlapping domains in post_init of Strand --- scadnano/scadnano.py | 10 + tests/scadnano_tests.py | 23 +- ...st_16_helix_origami_rectangle_no_twist.dna | 416 +++++++++--------- ...e_2_helix_origami_deletions_insertions.dna | 4 +- .../test_6_helix_origami_rectangle.dna | 60 +-- 5 files changed, 260 insertions(+), 253 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index fc903847..28807245 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1764,6 +1764,7 @@ def __post_init__(self): self.set_default_idt(True) self._ensure_modifications_legal() + self._ensure_domains_nonoverlapping() def __eq__(self, other: Strand) -> bool: if not isinstance(other, Strand): @@ -2116,6 +2117,14 @@ def _ensure_modifications_legal(self, check_offsets_legal=False): f"{len(self.dna_sequence)}: " f"{self.modifications_int}") + + def _ensure_domains_nonoverlapping(self): + for d1,d2 in itertools.combinations(self.domains, 2): + if isinstance(d1, Domain) and isinstance(d2, Domain) and d1.overlaps_illegally(d2): + raise StrandError(self, f'two domains on strand overlap:' + f'\n{d1}' + f'\n{d2}') + def idt_dna_sequence(self): self._ensure_modifications_legal(check_offsets_legal=True) @@ -2146,6 +2155,7 @@ def unmodified_version(self): return strand_nomods + def _string_merge_wildcard(s1: str, s2: str, wildcard: str) -> str: """Takes a "union" of two equal-length strings `s1` and `s2`. Whenever one has a symbol `wildcard` and the other does not, the result has the non-wildcard symbol. diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 3e559243..5302b365 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -12,18 +12,6 @@ import scadnano.modifications as mod -# TODO: add tests for mutation methods on DNADesign - -# TODO: mutator methods let me create this strand (which should be illegal); add a test for it -# { -# "color": {"r": 51, "g": 51, "b": 51}, -# "domains": [ -# {"helix": 2, "forward": false, "start": 40, "end": 48}, -# {"helix": 2, "forward": false, "start": 32, "end": 48, "deletions": [44]}, -# {"helix": 3, "forward": true, "start": 32, "end": 40} -# ] -# } - def strand_matching(strands: Iterable[sc.Strand], helix: int, forward: bool, start: int, end: int): """ Finds strand whose first bound domain matches the given parameters. @@ -2444,7 +2432,16 @@ def test_add_strand__with_loopout(self): self.assertEqual(ss1, design.domain_at(0, 0, True)) self.assertEqual(ss2, design.domain_at(1, 0, False)) - + def test_add_strand__illegal_overlapping_domains(self): + helices = [sc.Helix(max_offset=50)] * 2 + design = sc.DNADesign(helices=helices, strands=[], grid=sc.square) + with self.assertRaises(sc.StrandError): + strand = sc.Strand([ + sc.Domain(0, False, 40, 48), + sc.Domain(0, False, 32, 48, deletions=[44]), + sc.Domain(1, True, 32, 40), + ]) + design.add_strand(strand) class TestAssignDNA(unittest.TestCase): diff --git a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna index 85d2d644..fb93dc4b 100644 --- a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna +++ b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna @@ -59,7 +59,7 @@ "is_scaffold": true }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GCCGCTTTTGCGGGATTTGCAGGGAGTTAAAG", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -67,7 +67,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CAAGAGTAATCTTGACGCTGGCTGACCTTCAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -75,7 +75,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "TGCAAAAGAAGTTTTGAATAGCGAGAGGCTTT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -83,7 +83,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "ACGGTGTCTGGAAGTTAATATGCAACTAAAGT", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, @@ -91,7 +91,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AGTCAAATCACCATCAGAGAAAGGCCGGAGAC", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, @@ -99,7 +99,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GGCGGATTGACCGTAACTCCGTGGGAACAAAC", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, @@ -107,7 +107,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "AAATTGTTATCCGCTCAGCTGTTTCCTGTGTG", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, @@ -115,7 +115,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GAGTCCACTATTAAAGTTCCAGTTTGGAACAA", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, @@ -123,7 +123,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "AACCCATGTACCGTAAGCAAGCCCAATAGG", "domains": [ {"helix": 0, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "AGCCAGAATGGAAAGATAAATCCTCATTAA", "domains": [ {"helix": 2, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -139,7 +139,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "ACTTGAGCCATTTGGTTATCACCGTCACCG", "domains": [ {"helix": 4, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -147,7 +147,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AACCCACAAGAATTGTAATATCAGAGAGAT", "domains": [ {"helix": 6, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -155,7 +155,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CATCGTAGGAATCATAGCCGTTTTTATTTT", "domains": [ {"helix": 8, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -163,7 +163,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "TAATTACTAGAAAAATAAACACCGGAATCA", "domains": [ {"helix": 10, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -171,7 +171,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "TTAATTACATTTAACATCAAGAAAACAAAA", "domains": [ {"helix": 12, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -179,7 +179,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CTTTGCCCGAACGTTAACTCGTATTAAATC", "domains": [ {"helix": 14, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -187,14 +187,14 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AGAATAGAAAGGAACAACTAAAGGAATTGCG", "domains": [ {"helix": 0, "forward": false, "start": 216, "end": 248, "deletions": [225]} ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "TACCAAGCCTCATCTTTGACCCCCTCAAGAG", "domains": [ {"helix": 2, "forward": false, "start": 208, "end": 216}, @@ -202,7 +202,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AAGGATTAAGAGGCTGAGACTCCAGCGATTA", "domains": [ {"helix": 1, "forward": true, "start": 232, "end": 240}, @@ -210,7 +210,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AATCTACGACCAGTCAGGACGTTGTTCATAA", "domains": [ {"helix": 4, "forward": false, "start": 208, "end": 216}, @@ -218,7 +218,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "TCAAAATCAGCGTTTGCCATCTTGGAAGAAA", "domains": [ {"helix": 3, "forward": true, "start": 232, "end": 240}, @@ -226,7 +226,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GCCCGAAATTGCATCAAAAAGATTACGTAGA", "domains": [ {"helix": 6, "forward": false, "start": 208, "end": 216}, @@ -234,7 +234,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "AAATACATGCAGTATGTTAGCAAAAGAGGAA", "domains": [ {"helix": 5, "forward": true, "start": 232, "end": 240}, @@ -242,7 +242,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "CAAAATTACATACAGGCAAGGCAACCTAATT", "domains": [ {"helix": 8, "forward": false, "start": 208, "end": 216}, @@ -250,7 +250,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "TGCCAGTTAGCGTCTTTCCAGAGAGAATTAG", "domains": [ {"helix": 7, "forward": true, "start": 232, "end": 240}, @@ -258,7 +258,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TTGTATAAAGAAAAGCCCCAAAAAACAATAA", "domains": [ {"helix": 10, "forward": false, "start": 208, "end": 216}, @@ -266,7 +266,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "ACAACATGTCTGTCCAGACGACGCAGGAAGA", "domains": [ {"helix": 9, "forward": true, "start": 232, "end": 240}, @@ -274,7 +274,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CTCTTCGCTTGGGAAGGGCGATCGAGACTAC", "domains": [ {"helix": 12, "forward": false, "start": 208, "end": 216}, @@ -282,7 +282,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CTTTTTAAAATCATAGGTCTGAGGTGCGGGC", "domains": [ {"helix": 11, "forward": true, "start": 232, "end": 240}, @@ -290,7 +290,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CTTTTCACGTATTGGGCGCCAGGGAAACAGA", "domains": [ {"helix": 14, "forward": false, "start": 208, "end": 216}, @@ -298,7 +298,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "AATAAAGAAATTATTTGCACGTATGGTTTTT", "domains": [ {"helix": 13, "forward": true, "start": 232, "end": 240}, @@ -306,14 +306,14 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GAACGTGGCGAGAAAGGAAGGGAATCACCTT", "domains": [ {"helix": 15, "forward": true, "start": 200, "end": 232, "deletions": [225]} ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CCGATATATTCGGTCGCTGAGGCCGTCACC", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -321,7 +321,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CTCAGCAGAGACCAGGCGCATAGAAGAACC", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -330,7 +330,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "GGATATTCGACGATAAAAACCAACCAGAGG", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -339,7 +339,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GGGTAATAGCTCAACATGTTTTATCATTCC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 48}, @@ -348,7 +348,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "ATATAACAAAGATTCAAAAGGGTATATGAT", "domains": [ {"helix": 7, "forward": true, "start": 40, "end": 48}, @@ -357,7 +357,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "ATTCAACCACAACCCGTCGGATTTGGGATA", "domains": [ {"helix": 9, "forward": true, "start": 40, "end": 48}, @@ -366,7 +366,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "GGTCACGTCGTAATCATGGTCATACAATTC", "domains": [ {"helix": 11, "forward": true, "start": 40, "end": 48}, @@ -375,7 +375,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CACACAACTAGGGTTGAGTGTTGAACGTGG", "domains": [ {"helix": 13, "forward": true, "start": 40, "end": 48}, @@ -384,7 +384,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "ACTCCAACGTCAAAGGGCGAAAAAAAAGAATA", "domains": [ {"helix": 15, "forward": true, "start": 40, "end": 64}, @@ -392,7 +392,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CGGTGTACCGAAAGACAGCATCGGACGCATAA", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -401,7 +401,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "TACCAGACATTACCCAAATCAACGCAGATGAA", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -410,7 +410,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "ATGCTGTAGTAAAATGTTTAGACTCCCTCGTT", "domains": [ {"helix": 6, "forward": false, "start": 48, "end": 56}, @@ -419,7 +419,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "TGTAGGTAGTTGATTCCCAATTCTTGAATATA", "domains": [ {"helix": 8, "forward": false, "start": 48, "end": 56}, @@ -428,7 +428,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "AGCGAGTAGTTCTAGCTGATAAATGAGTAATG", "domains": [ {"helix": 10, "forward": false, "start": 48, "end": 56}, @@ -437,7 +437,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CTCGAATTTGGTGTAGATGGGCGCTAAATGTG", "domains": [ {"helix": 12, "forward": false, "start": 48, "end": 56}, @@ -446,7 +446,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "GCCCGAGAATACGAGCCGGAAGCAGTACCGAG", "domains": [ {"helix": 14, "forward": false, "start": 48, "end": 56}, @@ -455,7 +455,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GACAATGACAACAACCATCGCCCAACGAGGG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -463,7 +463,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "TAGCAACGCAACTTTGAAAGAGGATAACAAAG", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -472,7 +472,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "CTGCTCATAGCAACACTATCATAAGGATAGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -481,7 +481,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "TCCAATACCTTAGAGCTTAATTGCGCGAACGA", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 80}, @@ -490,7 +490,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GTAGATTTTTTAAATGCAATGCCTTAATGCCG", "domains": [ {"helix": 7, "forward": true, "start": 72, "end": 80}, @@ -499,7 +499,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "GAGAGGGTCAGCTTTCATCAACATATCGTAAC", "domains": [ {"helix": 9, "forward": true, "start": 72, "end": 80}, @@ -508,7 +508,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CGTGCATCTCTAGAGGATCCCCGGTAAAGTGT", "domains": [ {"helix": 11, "forward": true, "start": 72, "end": 80}, @@ -517,7 +517,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "AAAGCCTGAATCCCTTATAAATCACCGTCTAT", "domains": [ {"helix": 13, "forward": true, "start": 72, "end": 80}, @@ -526,7 +526,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "CAGGGCGATGGCCCACTACGTGATTCCGAAA", "domains": [ {"helix": 15, "forward": true, "start": 72, "end": 96, "deletions": [81]}, @@ -534,7 +534,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AACTGACGCTACAGAGGCTTTGGTTGCGCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -543,7 +543,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "TAGTAAGTCAGTGAATAAGGCTGGGAACCG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -552,7 +552,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CGGATGGTGCGGAATCGTCATAACGAGGCA", "domains": [ {"helix": 6, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -561,7 +561,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CATATATAGTTTGACCATTAGACATTTTTG", "domains": [ {"helix": 8, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -570,7 +570,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "CTGTAGCAGCTATTTTTGAGAGAGAACCCT", "domains": [ {"helix": 10, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -579,7 +579,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "GGTCGACTGCCAGTTTGAGGGGTGGCCTTC", "domains": [ {"helix": 12, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -588,7 +588,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TCGGCAAGGGTGCCTAATGAGTTGCCTGCA", "domains": [ {"helix": 14, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -597,7 +597,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "TTCTTAAACAGCTTGATACCGATAAGGACTAA", "domains": [ {"helix": 0, "forward": false, "start": 96, "end": 120}, @@ -605,7 +605,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "AGACTTTTAGACGGTCAATCATAATGCCCTGA", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -614,7 +614,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CGAGAAACAACGCCAAAAGGAATTAATATTCA", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -623,7 +623,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "TTGAATCCCCTTTTGATAAGAGGTTACATTTC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 112}, @@ -632,7 +632,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "GCAAATGGAAGGATAAAAATTTTTATCTACAA", "domains": [ {"helix": 7, "forward": true, "start": 104, "end": 112}, @@ -641,7 +641,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AGGCTATCAAAAATAATTCGCGTCACGACGAC", "domains": [ {"helix": 9, "forward": true, "start": 104, "end": 112}, @@ -650,7 +650,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AGTATCGGCAGTGCCAAGCTTGCAGAGCTAAC", "domains": [ {"helix": 11, "forward": true, "start": 104, "end": 112}, @@ -659,7 +659,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "TCACATTATCCTGTTTGATGGTGGACCATCAC", "domains": [ {"helix": 13, "forward": true, "start": 104, "end": 112}, @@ -668,7 +668,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CCAAATCAAGTTTTTTGGGGTCGACCCCAGCA", "domains": [ {"helix": 15, "forward": true, "start": 104, "end": 128}, @@ -676,7 +676,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CGAGGCGCTCATGAGGAAGTTTCCAGGTGAAT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -685,7 +685,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "AGATACATACCAGAACGAGTAGTAAGCCGGAA", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -694,7 +694,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "TAATTGCTCCCTCAAATGCTTTAAACTAATGC", "domains": [ {"helix": 6, "forward": false, "start": 112, "end": 120}, @@ -703,7 +703,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TTCAACGCTCAATAACCTGTTTAGAGTACCTT", "domains": [ {"helix": 8, "forward": false, "start": 112, "end": 120}, @@ -712,7 +712,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "ACGCCATCAGGTCATTGCCTGAGAGCCTTTAT", "domains": [ {"helix": 10, "forward": false, "start": 112, "end": 120}, @@ -721,7 +721,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "ACGACGGCCCTCAGGAAGATCGCACAATAGGA", "domains": [ {"helix": 12, "forward": false, "start": 112, "end": 120}, @@ -730,7 +730,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "GGCGAAAAATTGCGTTGCGCTCACGTTGTAAA", "domains": [ {"helix": 14, "forward": false, "start": 112, "end": 120}, @@ -739,7 +739,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "ATCGGTTTATCAGCTTGCTTTCGATTAAAC", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -747,7 +747,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "GGGTAAAATGCTCCATGTTACTTAATTGGG", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -756,7 +756,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "CTTGAGATGGAATACCACATTCAACAGTTC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -765,7 +765,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AGAAAACGAGGTCAGGATTAGAGCTATATT", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 144}, @@ -774,7 +774,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "TTCATTTGACTTTTGCGGGAGAAGTCTGGA", "domains": [ {"helix": 7, "forward": true, "start": 136, "end": 144}, @@ -783,7 +783,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GCAAACAAAGCTCATTTTTTAACCTCCAGC", "domains": [ {"helix": 9, "forward": true, "start": 136, "end": 144}, @@ -792,7 +792,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CAGCTTTCTTTCCCAGTCACGACTGCCCGC", "domains": [ {"helix": 11, "forward": true, "start": 136, "end": 144}, @@ -801,7 +801,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "TTTCCAGTGTCCACGCTGGTTTGGGTGCCG", "domains": [ {"helix": 13, "forward": true, "start": 136, "end": 144}, @@ -810,7 +810,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "TAAAGCACTAAATCGGAACCCTAAAGAGTTGC", "domains": [ {"helix": 15, "forward": true, "start": 136, "end": 160}, @@ -818,7 +818,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "CCGCGACCTACGTAATGCCACTACTTAATTGT", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -827,7 +827,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "GAGATTTAGGTTTAATTTCAACTTGTCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, @@ -836,7 +836,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "ACTCCAACAGAATGACCATAAATCCATCAGTT", "domains": [ {"helix": 6, "forward": false, "start": 144, "end": 152}, @@ -845,7 +845,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CCTGTAATGGGCGCGAGCTGAAAAGGAAGCAA", "domains": [ {"helix": 8, "forward": false, "start": 144, "end": 152}, @@ -854,7 +854,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GTTAAATCGAGAATCGATGAACGGATTATGAC", "domains": [ {"helix": 10, "forward": false, "start": 144, "end": 152}, @@ -863,7 +863,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "GCCAGGGTCGGCACCGCTTCTGGTAAATTTTT", "domains": [ {"helix": 12, "forward": false, "start": 144, "end": 152}, @@ -872,7 +872,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AGCAAGCGCGGGAAACCTGTCGTGTGGGTAAC", "domains": [ {"helix": 14, "forward": false, "start": 144, "end": 152}, @@ -881,7 +881,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AAAAAAGGCTCCAAAAGGAGCCTGAAGGCAC", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 184, "deletions": [177]}, @@ -889,7 +889,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CAACCTAATCGCCTGATAAATTGTTAATCATT", "domains": [ {"helix": 1, "forward": true, "start": 168, "end": 176}, @@ -898,7 +898,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GTGAATTATACAGGTAGAAAGATTAAAAATCA", "domains": [ {"helix": 3, "forward": true, "start": 168, "end": 176}, @@ -907,7 +907,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "GGTCTTTACAAAGCGAACCAGACCGGTGGCAT", "domains": [ {"helix": 5, "forward": true, "start": 168, "end": 176}, @@ -916,7 +916,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "CAATTCTACGGTTGTACCAAAAACTAATCGTA", "domains": [ {"helix": 7, "forward": true, "start": 168, "end": 176}, @@ -925,7 +925,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AAACTAGCTGTTAAAATTCGCATTGCCGGAAA", "domains": [ {"helix": 9, "forward": true, "start": 168, "end": 176}, @@ -934,7 +934,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "CCAGGCAATGCAAGGCGATTAAGTCCAGCTGC", "domains": [ {"helix": 11, "forward": true, "start": 168, "end": 176}, @@ -943,7 +943,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "ATTAATGAACCGCCTGGCCCTGAGAGGGAGCC", "domains": [ {"helix": 13, "forward": true, "start": 168, "end": 176}, @@ -952,7 +952,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CCCGATTTAGAGCTTGACGGGGAAGCTGATT", "domains": [ {"helix": 15, "forward": true, "start": 168, "end": 192, "deletions": [177]}, @@ -960,7 +960,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "TGTATCAAACGAAAGAGGCAAAATCTCCAA", "domains": [ {"helix": 2, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -969,7 +969,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "ACATTATCCTTATGCGATTTTACGGAGATT", "domains": [ {"helix": 4, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -978,7 +978,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CGAGCTTCCCTGACTATTATAGACGGAACA", "domains": [ {"helix": 6, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -987,7 +987,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GCTAAATCTAATAGTAGTAGCATTTTAATT", "domains": [ {"helix": 8, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -996,7 +996,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AATATTTATGTCAATCATATGTAGCATAAA", "domains": [ {"helix": 10, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1005,7 +1005,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "GATGTGCAGCGCCATTCGCCATTAAACGTT", "domains": [ {"helix": 12, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1014,7 +1014,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GCCCTTCATCGGCCAACGCGCGGAAAGGGG", "domains": [ {"helix": 14, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1023,7 +1023,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "AATAATAATTTTTTCACGTTGAAAAGAATACA", "domains": [ {"helix": 0, "forward": false, "start": 192, "end": 216}, @@ -1031,7 +1031,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "CTAAAACAGCGAAACAAAGTACAAAGAACTGG", "domains": [ {"helix": 1, "forward": true, "start": 200, "end": 208}, @@ -1040,7 +1040,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CTCATTATTTAATAAAACGAACTATCAGAAGC", "domains": [ {"helix": 3, "forward": true, "start": 200, "end": 208}, @@ -1049,7 +1049,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AAAGCGGAGACTTCAAATATCGCGTTAACATC", "domains": [ {"helix": 5, "forward": true, "start": 200, "end": 208}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CAATAAATAGCAATAAAGCCTCAGACCCCGGT", "domains": [ {"helix": 7, "forward": true, "start": 200, "end": 208}, @@ -1067,7 +1067,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "TGATAATCGCAAATATTTAAATTGTCAGGCTG", "domains": [ {"helix": 9, "forward": true, "start": 200, "end": 208}, @@ -1076,7 +1076,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CGCAACTGTATTACGCCAGCTGGCGGGAGAGG", "domains": [ {"helix": 11, "forward": true, "start": 200, "end": 208}, @@ -1085,7 +1085,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CGGTTTGCCAGTGAGACGGGCAACAAGCCGGC", "domains": [ {"helix": 13, "forward": true, "start": 200, "end": 208}, @@ -1094,7 +1094,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "GCTGAACCTCAAATATCAAACCCTGAACCTAC", "domains": [ {"helix": 15, "forward": true, "start": 232, "end": 256}, @@ -1102,7 +1102,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AAGTATTAGGATTAGCGGGGTTTTGCGGAGTG", "domains": [ {"helix": 2, "forward": false, "start": 240, "end": 248}, @@ -1111,7 +1111,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "CCCTTATTACCGGAACCAGAGCCAAAACATGA", "domains": [ {"helix": 4, "forward": false, "start": 240, "end": 248}, @@ -1120,7 +1120,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CTTATTACACATAAAGGTGGCAACTCATAGCC", "domains": [ {"helix": 6, "forward": false, "start": 240, "end": 248}, @@ -1129,7 +1129,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CGCTAACGACAAAATAAACAGCCATAAGACTC", "domains": [ {"helix": 8, "forward": false, "start": 240, "end": 248}, @@ -1138,7 +1138,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "AAAGTAATTTCAGCTAATGCAGAACTTACCAA", "domains": [ {"helix": 10, "forward": false, "start": 240, "end": 248}, @@ -1147,7 +1147,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "TTTATCAACCTCCGGCTTAGGTTGCAAAAGGT", "domains": [ {"helix": 12, "forward": false, "start": 240, "end": 248}, @@ -1156,7 +1156,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CATATCAAAATTGCGTAGATTTTCATAGTGAA", "domains": [ {"helix": 14, "forward": false, "start": 240, "end": 248}, @@ -1165,7 +1165,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "CTAAACAACTTTCAACAGTTTCAGCTCAGTA", "domains": [ {"helix": 0, "forward": false, "start": 256, "end": 280, "deletions": [273]}, @@ -1173,7 +1173,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CCAGGCGGGGAACCTATTATTCTGCCACCGGA", "domains": [ {"helix": 1, "forward": true, "start": 264, "end": 272}, @@ -1182,7 +1182,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "ACCGCCTCTCATCGGCATTTTCGGATATAAAA", "domains": [ {"helix": 3, "forward": true, "start": 264, "end": 272}, @@ -1191,7 +1191,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "GAAACGCAAAAGAACTGGCATGATTATTATTT", "domains": [ {"helix": 5, "forward": true, "start": 264, "end": 272}, @@ -1200,7 +1200,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "ATCCCAATCAATTTTATCCTGAATCGCGCCTG", "domains": [ {"helix": 7, "forward": true, "start": 264, "end": 272}, @@ -1209,7 +1209,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "TTTATCAAGAATATAAAGTACCGAGGTTATAT", "domains": [ {"helix": 9, "forward": true, "start": 264, "end": 272}, @@ -1218,7 +1218,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AACTATATACGCTGAGAAGAGTCAAGGTTTAA", "domains": [ {"helix": 11, "forward": true, "start": 264, "end": 272}, @@ -1227,7 +1227,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "CGTCAGATAATAATGGAAGGGTTACAATCAAT", "domains": [ {"helix": 13, "forward": true, "start": 264, "end": 272}, @@ -1236,7 +1236,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "ATCTGGTCAGTTGGCAAATCAACTGGATTAT", "domains": [ {"helix": 15, "forward": true, "start": 264, "end": 288, "deletions": [273]}, @@ -1244,7 +1244,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CTATTTCATAAGTGCCGTCGAGGGATTTTG", "domains": [ {"helix": 2, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1253,7 +1253,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CGCGTTTCCTCAGAGCCGCCACCCCCCTGC", "domains": [ {"helix": 4, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1262,7 +1262,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "ATACCCAAAGACACCACGGAATGACTGTAG", "domains": [ {"helix": 6, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1271,7 +1271,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CCAGCTACCAAATAAGAAACGAATAACGGA", "domains": [ {"helix": 8, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1280,7 +1280,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AATAAGACAATAGATAAGTCCTTTTTGCAC", "domains": [ {"helix": 10, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1289,7 +1289,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "GATTAAGGTAAATGCTGATGCAGAGCCAGT", "domains": [ {"helix": 12, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1298,7 +1298,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "ACTTCTGGAATATACAGTAACAATAGCTTA", "domains": [ {"helix": 14, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1307,7 +1307,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "GTTAGTAAATGAATTTTCTGTATGAGGGTTGA", "domains": [ {"helix": 0, "forward": false, "start": 288, "end": 312}, @@ -1315,7 +1315,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "TATAAGTAGTATAAACAGTTAATGCCTCAGAA", "domains": [ {"helix": 1, "forward": true, "start": 296, "end": 304}, @@ -1324,7 +1324,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CCGCCACCTTTGCCTTTAGCGTCAAAGTTTAT", "domains": [ {"helix": 3, "forward": true, "start": 296, "end": 304}, @@ -1333,7 +1333,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "TTTGTCACCCGAGGAAACGCAATATTTTTTGT", "domains": [ {"helix": 5, "forward": true, "start": 296, "end": 304}, @@ -1342,7 +1342,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "TTAACGTCTCAAGATTAGTTGCTAGAACAAGA", "domains": [ {"helix": 7, "forward": true, "start": 296, "end": 304}, @@ -1351,7 +1351,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "AAAATAATAGGCAGAGGCATTTTCAATCCAAT", "domains": [ {"helix": 9, "forward": true, "start": 296, "end": 304}, @@ -1360,7 +1360,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CGCAAGACCCTTGAAAACATAGCGGTACCTTT", "domains": [ {"helix": 11, "forward": true, "start": 296, "end": 304}, @@ -1369,7 +1369,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TACATCGGTATAATCCTGATTGTTAGTTGAAA", "domains": [ {"helix": 13, "forward": true, "start": 296, "end": 304}, @@ -1378,7 +1378,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GGAATTGAGGAAGGTTATCTAAAAGATGGCAA", "domains": [ {"helix": 15, "forward": true, "start": 296, "end": 320}, @@ -1386,7 +1386,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CAGTGCCCTAGCCCGGAATAGGTGTTCCAGAC", "domains": [ {"helix": 2, "forward": false, "start": 304, "end": 312}, @@ -1395,7 +1395,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "GAATCAAGCTCAGAGCCACCACCCTTGAGTAA", "domains": [ {"helix": 4, "forward": false, "start": 304, "end": 312}, @@ -1404,7 +1404,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "GAAGGAAAAATCAATAGAAAATTCTAGCGACA", "domains": [ {"helix": 6, "forward": false, "start": 304, "end": 312}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GCCTTAAAAAAAATGAAAATAGCAAGTTACCA", "domains": [ {"helix": 8, "forward": false, "start": 304, "end": 312}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "TGTAATTTATCCCATCCTAATTTAGTTTTGAA", "domains": [ {"helix": 10, "forward": false, "start": 304, "end": 312}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CTTAGAATAAAGAACGCGAGAAAACGCCAACA", "domains": [ {"helix": 12, "forward": false, "start": 304, "end": 312}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "TTCATCAAGAGAAACAATAACGGAAATTTTCC", "domains": [ {"helix": 14, "forward": false, "start": 304, "end": 312}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AACGATCTAAAGTTTTGTCGTCTTATCACC", "domains": [ {"helix": 0, "forward": false, "start": 320, "end": 344, "deletions": [321]}, @@ -1457,7 +1457,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GTACTCAGAACGGGGTCAGTGCCTCAGAGC", "domains": [ {"helix": 1, "forward": true, "start": 328, "end": 336}, @@ -1466,7 +1466,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CGCCACCACAGCACCGTAATCAGATATGGT", "domains": [ {"helix": 3, "forward": true, "start": 328, "end": 336}, @@ -1475,7 +1475,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "TTACCAGCCAGATAGCCGAACAAGCCTTTA", "domains": [ {"helix": 5, "forward": true, "start": 328, "end": 336}, @@ -1484,7 +1484,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CAGAGAGACCCGACTTGCGGGAGCGAGCAT", "domains": [ {"helix": 7, "forward": true, "start": 328, "end": 336}, @@ -1493,7 +1493,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GTAGAAACCGCCATATTTAACAACTTTTTC", "domains": [ {"helix": 9, "forward": true, "start": 328, "end": 336}, @@ -1502,7 +1502,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AAATATATTCGTCGCTATTAATTTTCGCCT", "domains": [ {"helix": 11, "forward": true, "start": 328, "end": 336}, @@ -1511,7 +1511,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "GATTGCTTTCCTGATTATCAGATTATCTTT", "domains": [ {"helix": 13, "forward": true, "start": 328, "end": 336}, @@ -1520,7 +1520,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "AGGAGCACTAACAACTAATAGATTGGAATTAT", "domains": [ {"helix": 15, "forward": true, "start": 328, "end": 352}, @@ -1528,7 +1528,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "TAAGTTTTGAGGTTTAGTACCGCCGTTAGCGT", "domains": [ {"helix": 2, "forward": false, "start": 336, "end": 344}, @@ -1537,7 +1537,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "ATCGATAGGAACCACCACCAGAGCACTGGTAA", "domains": [ {"helix": 4, "forward": false, "start": 336, "end": 344}, @@ -1546,7 +1546,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "AAAGTAAGGCCAAAGACAAAAGGGATGAAACC", "domains": [ {"helix": 6, "forward": false, "start": 336, "end": 344}, @@ -1555,7 +1555,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "GCGAACCTATAACATAAAAACAGGTTTTAAGA", "domains": [ {"helix": 8, "forward": false, "start": 336, "end": 344}, @@ -1564,7 +1564,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "TTGAGAATCAATCAATAATCGGCTGCGTTTTA", "domains": [ {"helix": 10, "forward": false, "start": 336, "end": 344}, @@ -1573,7 +1573,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "TCTGTAAATTTAGTTAATTTCATCGGGCTTAA", "domains": [ {"helix": 12, "forward": false, "start": 336, "end": 344}, @@ -1582,7 +1582,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CATCATATTGAATACCAAGTTACAACCTTGCT", "domains": [ {"helix": 14, "forward": false, "start": 336, "end": 344}, @@ -1591,7 +1591,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GCATTCCACAGACAGCCCTCATAACCCTCAG", "domains": [ {"helix": 0, "forward": false, "start": 352, "end": 376, "deletions": [369]}, @@ -1599,7 +1599,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "AACCGCCAGATGATACAGGAGTGTCGCCGCCA", "domains": [ {"helix": 1, "forward": true, "start": 360, "end": 368}, @@ -1608,7 +1608,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GCATTGACGCCGGAAACGTCACCACGACATTC", "domains": [ {"helix": 3, "forward": true, "start": 360, "end": 368}, @@ -1617,7 +1617,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AACCGATTATCTTACCGAAGCCCTGAAGCGCA", "domains": [ {"helix": 5, "forward": true, "start": 360, "end": 368}, @@ -1626,7 +1626,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TTAGACGGATTCTAAGAACGCGAGGTCTTTCC", "domains": [ {"helix": 7, "forward": true, "start": 360, "end": 368}, @@ -1635,7 +1635,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "TTATCATTCCAACGCTCAACAGTATTCTGACC", "domains": [ {"helix": 9, "forward": true, "start": 360, "end": 368}, @@ -1644,7 +1644,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "TAAATTTATATATGTGAGTGAATAAAATCGCG", "domains": [ {"helix": 11, "forward": true, "start": 360, "end": 368}, @@ -1653,7 +1653,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CAGAGGCGAACCACCAGAAGGAGCAGAGCCGT", "domains": [ {"helix": 13, "forward": true, "start": 360, "end": 368}, @@ -1662,7 +1662,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CAATAGATAATACATTTGAGGATTTTGCGGA", "domains": [ {"helix": 15, "forward": true, "start": 360, "end": 384, "deletions": [369]}, @@ -1670,7 +1670,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "GGCTTTTCCCTCAGAACCGCCACGCCTGTA", "domains": [ {"helix": 2, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1679,7 +1679,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "TAGCAAGAGGAGGTTGAGGCAGTCATACAT", "domains": [ {"helix": 4, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1688,7 +1688,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AATAGCTGAGGGAGGGAAGGTAATTACCAT", "domains": [ {"helix": 6, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1697,7 +1697,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "ATCCGGTGAGAATTAACTGAACGAAATAGC", "domains": [ {"helix": 8, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1706,7 +1706,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "TATAAAGCCAAGAACGGGTATTGAAGGCTT", "domains": [ {"helix": 10, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1715,7 +1715,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "AAATCAAATGGTTTGAAATACCCTTACCAG", "domains": [ {"helix": 12, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1724,7 +1724,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "ACAAAGAAATTATTCATTTCAACAGTACAT", "domains": [ {"helix": 14, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1733,7 +1733,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "TTTCGTCACCAGTACAAACTACAACCCTCAGA", "domains": [ {"helix": 0, "forward": false, "start": 384, "end": 408}, @@ -1741,7 +1741,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "GCCACCACACCGTTCCAGTAAGCGGTCAGACG", "domains": [ {"helix": 1, "forward": true, "start": 392, "end": 400}, @@ -1750,7 +1750,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "ATTGGCCTAATCACCAGTAGCACCAATATTGA", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 400}, @@ -1759,7 +1759,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CGGAAATTAAGAGCAAGAAACAATACCCTGAA", "domains": [ {"helix": 5, "forward": true, "start": 392, "end": 400}, @@ -1768,7 +1768,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CAAAGTCAAAGCAAATCAGATATAAAACCAAG", "domains": [ {"helix": 7, "forward": true, "start": 392, "end": 400}, @@ -1777,7 +1777,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "TACCGCACATGCGTTATACAAATTGACCGTGT", "domains": [ {"helix": 9, "forward": true, "start": 392, "end": 400}, @@ -1786,7 +1786,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "GATAAATACCTTTTTTAATGGAAATTACCTGA", "domains": [ {"helix": 11, "forward": true, "start": 392, "end": 400}, @@ -1795,7 +1795,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GCAAAAGATGAGTAACATTATCATTTAGAAGT", "domains": [ {"helix": 13, "forward": true, "start": 392, "end": 400}, @@ -1804,7 +1804,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "ATTAGACTTTACAAACAATTCGACATTAATTT", "domains": [ {"helix": 15, "forward": true, "start": 392, "end": 416}, @@ -1812,7 +1812,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CTGAATTTCCTCATTTTCAGGGATACACTGAG", "domains": [ {"helix": 2, "forward": false, "start": 400, "end": 408}, @@ -1821,7 +1821,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GCCAGCAATGATATTCACAAACAACGCAGTCT", "domains": [ {"helix": 4, "forward": false, "start": 400, "end": 408}, @@ -1830,7 +1830,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CCAATAATATTCATTAAAGGTGAAGAATTAGA", "domains": [ {"helix": 6, "forward": false, "start": 400, "end": 408}, @@ -1839,7 +1839,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "CCAATAGCGAGGGTAATTGAGCGCAGTTAAGC", "domains": [ {"helix": 8, "forward": false, "start": 400, "end": 408}, @@ -1848,7 +1848,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AGTATCATTCATCGAGAACAAGCATACCGCGC", "domains": [ {"helix": 10, "forward": false, "start": 400, "end": 408}, @@ -1857,7 +1857,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TTGAATTAAGGCGTTAAATAAGAAGCCTGTTT", "domains": [ {"helix": 12, "forward": false, "start": 400, "end": 408}, @@ -1866,7 +1866,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "TAAAAGTTAGATGATGAAACAAACAATTTCAT", "domains": [ {"helix": 14, "forward": false, "start": 400, "end": 408}, diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna index 2844cbb4..d3df6edc 100644 --- a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna @@ -17,7 +17,7 @@ "is_scaffold": true }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GTTACGTTACGTTACGTTGTTACGTTACGTTAC", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, @@ -25,7 +25,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "ACGTTACGTTACGTTACCGTTACGTTACGTTACGTT", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, diff --git a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna index f7c10441..6fa68a22 100644 --- a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna +++ b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna @@ -29,7 +29,7 @@ "is_scaffold": true }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -37,7 +37,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -45,7 +45,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -53,7 +53,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 176}, @@ -61,7 +61,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", "domains": [ {"helix": 2, "forward": false, "start": 160, "end": 176}, @@ -69,7 +69,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", "domains": [ {"helix": 4, "forward": false, "start": 160, "end": 176}, @@ -77,14 +77,14 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", "domains": [ {"helix": 0, "forward": false, "start": 88, "end": 120} ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -92,7 +92,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -100,7 +100,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -108,7 +108,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -116,14 +116,14 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -140,7 +140,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -149,7 +149,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 64}, @@ -157,7 +157,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -166,7 +166,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -175,7 +175,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "AATGAATCGGCCAACGCGCGGGGAGTTGCAG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -183,7 +183,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CAAGCGGTCCTGTTTGATGGTGGTACGTGGAC", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -192,7 +192,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "TCCAACGTTGGCCCACTACGTGAAAGCCGGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -201,7 +201,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AGTATCGGCCTCAGGAAGATCGCAGTGCGGGC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 128}, @@ -209,7 +209,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -218,7 +218,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -227,7 +227,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -235,7 +235,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -244,7 +244,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GCCAGGGTTGGGAAGGGCGATCGCTCCAGC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -253,7 +253,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CAGCTTTCCGGCACCGCTTCTGGTCAGGCTGC", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 160}, @@ -261,7 +261,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GTCGACTCACGAGCCGGAAGCATACTAACTCA", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -270,7 +270,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, From f36d223da2c26fa79b116e7914f5d623eb07e4c9 Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 23 Jun 2020 17:52:21 -0700 Subject: [PATCH 07/30] fixes #85 --- scadnano/scadnano.py | 191 +++++++- tests/scadnano_tests.py | 175 +++++++- ...st_16_helix_origami_rectangle_no_twist.dna | 416 +++++++++--------- ...e_2_helix_origami_deletions_insertions.dna | 4 +- .../test_6_helix_origami_rectangle.dna | 60 +-- 5 files changed, 601 insertions(+), 245 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 28807245..9c3d13f2 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1606,6 +1606,94 @@ def _check_idt_string_not_none_or_empty(value: str, field_name: str): raise IllegalDNADesignError(f'field {field_name} in IDTFields cannot be empty') +class StrandBuilder: + """ + Represents a :any:`Strand` that is being built in an existing :any:`DNADesign`. + + This is an intermediate object created when using "literal" chained method building by calling + :py:meth:`DNADesign.strand`, for example + + .. code-block:: Python + + design.strand(0, 0).to(10).cross(1).to(5) + """ + + def __init__(self, design: DNADesign, helix: int, offset: int): + self.design = design + self.current_helix = helix + self.current_offset = offset + self.strand_created_already = False + self.loopout_length = None + + def cross(self, helix: int, offset: int = None) -> StrandBuilder: + """ + Add crossover. Must be followed by call to :py:meth:`StrandBuilder.to` to have any effect. + + :param helix: :any:`Helix` to crossover to + :param offset: new offset on `helix`. If not specified, defaults to current offset. + (i.e., a "vertical" crossover) + :return: self + """ + self.current_helix = helix + if offset is not None: + self.current_offset = offset + return self + + def loopout(self, helix: int, length: int, offset: int = None) -> StrandBuilder: + """ + Like :py:meth:`StrandBuilder.cross`, but creates a :any:`Loopout` instead of a crossover. + + :param helix: :any:`Helix` to crossover to + :param length: length of :any:`Loopout` to add + :return: self + """ + self.current_helix = helix + self.loopout_length = length + if offset is not None: + self.current_offset = offset + return self + + def to(self, offset: int) -> StrandBuilder: + """ + Extends this :any:`StrandBuilder` on the current helix to offset `offset`, + which adds a new :any:`Domain` to the :any:`Strand` being built. + + This updates the underlying :any:`DNADesign` with a new :any:`Domain`, + and if :py:meth:`StrandBuilder.loopout` was last called on this :any:`StrandBuilder`, + also a new :any:`Loopout`. + + :param offset: new offset to extend to. If less than current offset, + the new :any:`Domain` is reverse, otherwise it is forward. + :return: self + """ + if offset > self.current_offset: + forward = True + start = self.current_offset + end = offset + elif offset < self.current_offset: + forward = False + start = offset + end = self.current_offset + else: + raise IllegalDNADesignError(f'offset {offset} cannot be equal to current offset') + + domain = Domain(helix=self.current_helix, forward=forward, start=start, end=end) + if self.strand_created_already: + strand = self.design.strands[-1] + if self.loopout_length is not None: + self.design.append_domain(strand, Loopout(self.loopout_length)) + self.design.append_domain(strand, domain) + self.loopout_length = None + else: + self.strand_created_already = True + strand = Strand(domains=[domain]) + self.design.add_strand(strand) + + self.current_offset = offset + + return self + + @dataclass class Strand(_JSONSerializable): """ @@ -2117,9 +2205,8 @@ def _ensure_modifications_legal(self, check_offsets_legal=False): f"{len(self.dna_sequence)}: " f"{self.modifications_int}") - def _ensure_domains_nonoverlapping(self): - for d1,d2 in itertools.combinations(self.domains, 2): + for d1, d2 in itertools.combinations(self.domains, 2): if isinstance(d1, Domain) and isinstance(d2, Domain) and d1.overlaps_illegally(d2): raise StrandError(self, f'two domains on strand overlap:' f'\n{d1}' @@ -2155,7 +2242,6 @@ def unmodified_version(self): return strand_nomods - def _string_merge_wildcard(s1: str, s2: str, wildcard: str) -> str: """Takes a "union" of two equal-length strings `s1` and `s2`. Whenever one has a symbol `wildcard` and the other does not, the result has the non-wildcard symbol. @@ -2395,6 +2481,8 @@ def __init__(self, *, def __post_init__(self): # XXX: exact order of these calls is important + self._ensure_helices_distinct_objects() + self._ensure_strands_distinct_objects() self._set_helices_idxs() self._set_helices_grid_positions() self._build_domains_on_helix_lists() @@ -2788,6 +2876,59 @@ def _all_modifications(self) -> Set[Modification]: mods_int = {mod for strand in self.strands for mod in strand.modifications_int.values()} return mods_5p | mods_3p | mods_int + def strand(self, helix: int, offset: int) -> StrandBuilder: + """Used for "literal" chained method building by calling + :py:meth:`DNADesign.strand` to build the :any:`Strand` domain by domain, in order from 5' to 3'. + For example + + .. code-block:: Python + + design.strand(0, 7).to(10).cross(1).to(5).cross(2).to(15) + + This creates a :any:`Strand` in this :any:`DNADesign` equivalent to + + .. code-block:: Python + + design.add_strand(Strand([ + sc.Domain(0, True, 7, 10), + sc.Domain(1, False, 5, 10), + sc.Domain(2, True, 5, 15), + ])) + + Loopouts can also be included: + + .. code-block:: Python + + design.strand(0, 7).to(10).cross(1).to(5).loopout(2, 3).to(15) + + This creates a :any:`Strand` in this :any:`DNADesign` equivalent to + + .. code-block:: Python + + design.add_strand(Strand([ + sc.Domain(0, True, 7, 10), + sc.Domain(1, False, 5, 10), + sc.Loopout(3), + sc.Domain(2, True, 5, 15), + ])) + + It returns an each call to + :py:meth:`DNADesign.strand`, + :py:meth:`DNADesign.cross`, + :py:meth:`DNADesign.loopout`, + :py:meth:`DNADesign.to` + returns a :any:`StrandBuilder` object. + + Each call to + :py:meth:`DNADesign.to` + modifies the :any:`DNADesign` by replacing the Strand with an updated version. + + :param helix: starting :any:`Helix` + :param offset: starting offset on `helix` + :return: :any:`StrandBuilder` object representing the partially completed :any:`Strand` + """ + return StrandBuilder(self, helix, offset) + def assign_m13_to_scaffold(self, rotation: int = 5588, variant: M13Variant = M13Variant.p7249): """Assigns the scaffold to be the sequence of M13: :py:func:`m13` with the given `rotation`. @@ -3226,6 +3367,7 @@ def add_strand(self, strand: Strand): for domain in strand.domains: if domain.is_domain(): self.helices[domain.helix].domains.append(domain) + self._check_strands_overlap_legally(domain_to_check=domain) def remove_strand(self, strand: Strand): """Remove `strand` from this design.""" @@ -3234,15 +3376,31 @@ def remove_strand(self, strand: Strand): if domain.is_domain(): self.helices[domain.helix].domains.remove(domain) + def append_domain(self, strand: Strand, domain: Union[Domain, Loopout]): + """ + Same as :any:`DNADesign.insert_domain`, but inserts at end. + + :param strand: strand to append `domain` to + :param domain: :any:`Domain` or :any:`Loopout` to append to :any:`Strand` + """ + self.insert_domain(strand, len(strand.domains), domain) + def insert_domain(self, strand: Strand, order: int, domain: Union[Domain, Loopout]): """Insert `Domain` into `strand` at index given by `order`. Uses same indexing as Python lists, - e.g., ``strand.insert_domain(domain, 0)`` inserts ``domain`` as the new first :any:`Domain`.""" + e.g., ``design.insert_domain(strand, domain, 0)`` + inserts ``domain`` as the new first :any:`Domain`.""" + if domain.is_domain() and domain.helix not in self.helices: + err_msg = f"domain {domain} refers to nonexistent Helix index {domain.helix}; " \ + f"here is the list of valid helices: {self._helices_to_string()}" + raise StrandError(strand, err_msg) + assert strand in self.strands strand.insert_domain(order, domain) self._check_strand_references_legal_helices(strand) self._check_loopouts_not_consecutive_or_singletons_or_zero_length() if domain.is_domain(): self.helices[domain.helix].domains.append(domain) + self._check_strands_overlap_legally(domain_to_check=domain) def remove_domain(self, strand: Strand, domain: Union[Domain, Loopout]): """Remove `Domain` from `strand`.""" @@ -3999,6 +4157,31 @@ def reverse_all(self): def set_major_tick_distance(self, major_tick_distance: int): self.major_tick_distance = major_tick_distance + def _ensure_helices_distinct_objects(self): + pair = _find_index_pair_same_object(self.helices) + if pair: + i, j = pair + raise IllegalDNADesignError('helices must all be distinct objects, but those at indices ' + f'{i} and {j} are the same object') + + def _ensure_strands_distinct_objects(self): + pair = _find_index_pair_same_object(self.strands) + if pair: + i, j = pair + raise IllegalDNADesignError('strands must all be distinct objects, but those at indices ' + f'{i} and {j} are the same object') + + +def _find_index_pair_same_object(elts: Union[List,Dict]) -> Optional[Tuple]: + # return pair of indices representing same object in elts, or None if they do not exist + # input can be list or dict; if dict, returns pair of keys mapping to same object + if isinstance(elts, list): + elts = dict(enumerate(elts)) + for i, j in itertools.combinations(elts.keys(), 2): + if elts[i] is elts[j]: + return i, j + return None + def _name_of_this_script() -> str: """Return name of the currently running script, WITHOUT the .py extension.""" diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 5302b365..6b65dded 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -28,6 +28,179 @@ def remove_whitespace(sequence): return sequence +class TestCreateStrandLiterate(unittest.TestCase): + # tests methods for creating strands using chained "literate" notation as in this issue: + # https://github.com/UC-Davis-molecular-computing/scadnano-python-package/issues/85 + + def setUp(self): + helices = [sc.Helix(max_offset=100) for _ in range(6)] + self.design_6helix = sc.DNADesign(helices=helices, strands=[], grid=sc.square) + + def test_strand__0_0_to_10_cross_1_to_5(self): + design = self.design_6helix + sb = design.strand(0, 0) + sb.to(10) + sb.cross(1) + sb.to(5) + expected_strand = sc.Strand([ + sc.Domain(0, True, 0, 10), + sc.Domain(1, False, 5, 10), + ]) + self.assertEqual(1, len(design.strands)) + self.assertEqual(expected_strand, design.strands[0]) + self.assertEqual(1, len(design.helices[0].domains)) + self.assertEqual(1, len(design.helices[1].domains)) + self.assertEqual(0, len(design.helices[2].domains)) + self.assertEqual(0, len(design.helices[3].domains)) + self.assertEqual(0, len(design.helices[4].domains)) + self.assertEqual(0, len(design.helices[5].domains)) + + def test_strand__0_0_to_10_cross_1_to_5__reverse(self): + design = self.design_6helix + design.strand(1, 5).to(10).cross(0).to(0) + expected_strand = sc.Strand([ + sc.Domain(1, True, 5, 10), + sc.Domain(0, False, 0, 10), + ]) + self.assertEqual(1, len(design.strands)) + self.assertEqual(expected_strand, design.strands[0]) + self.assertEqual(1, len(design.helices[0].domains)) + self.assertEqual(1, len(design.helices[1].domains)) + self.assertEqual(0, len(design.helices[2].domains)) + self.assertEqual(0, len(design.helices[3].domains)) + self.assertEqual(0, len(design.helices[4].domains)) + self.assertEqual(0, len(design.helices[5].domains)) + + def test_strand__h0_off0_to_off10_cross_h1_to_off5_loopout_length3_h2_to_off15(self): + design = self.design_6helix + sb = design.strand(0, 0) + sb.to(10) + sb.cross(1) + sb.to(5) + sb.loopout(2, 3) + sb.to(15) + expected_strand = sc.Strand([ + sc.Domain(0, True, 0, 10), + sc.Domain(1, False, 5, 10), + sc.Loopout(3), + sc.Domain(2, True, 5, 15), + ]) + self.assertEqual(1, len(design.strands)) + self.assertEqual(expected_strand, design.strands[0]) + self.assertEqual(1, len(design.helices[0].domains)) + self.assertEqual(1, len(design.helices[1].domains)) + self.assertEqual(1, len(design.helices[2].domains)) + self.assertEqual(0, len(design.helices[3].domains)) + self.assertEqual(0, len(design.helices[4].domains)) + self.assertEqual(0, len(design.helices[5].domains)) + + def test_strand__two_forward_paranemic_crossovers(self): + design = self.design_6helix + design.strand(0, 0).to(10).cross(1).to(15).cross(2).to(20) + expected_strand = sc.Strand([ + sc.Domain(0, True, 0, 10), + sc.Domain(1, True, 10, 15), + sc.Domain(2, True, 15, 20), + ]) + self.assertEqual(1, len(design.strands)) + self.assertEqual(expected_strand, design.strands[0]) + self.assertEqual(1, len(design.helices[0].domains)) + self.assertEqual(1, len(design.helices[1].domains)) + self.assertEqual(1, len(design.helices[2].domains)) + self.assertEqual(0, len(design.helices[3].domains)) + self.assertEqual(0, len(design.helices[4].domains)) + self.assertEqual(0, len(design.helices[5].domains)) + + def test_strand__two_reverse_paranemic_crossovers(self): + design = self.design_6helix + design.strand(0, 20).to(10).cross(1).to(5).cross(2).to(0) + expected_strand = sc.Strand([ + sc.Domain(0, False, 10, 20), + sc.Domain(1, False, 5, 10), + sc.Domain(2, False, 0, 5), + ]) + self.assertEqual(1, len(design.strands)) + self.assertEqual(expected_strand, design.strands[0]) + self.assertEqual(1, len(design.helices[0].domains)) + self.assertEqual(1, len(design.helices[1].domains)) + self.assertEqual(1, len(design.helices[2].domains)) + self.assertEqual(0, len(design.helices[3].domains)) + self.assertEqual(0, len(design.helices[4].domains)) + self.assertEqual(0, len(design.helices[5].domains)) + + def test_strand__multiple_strands(self): + design = self.design_6helix + design.strand(0, 0).to(10).cross(1).to(0) + design.strand(0, 20).to(10).cross(1).to(20) + expected_strand0 = sc.Strand([ + sc.Domain(0, True, 0, 10), + sc.Domain(1, False, 0, 10), + ]) + expected_strand1 = sc.Strand([ + sc.Domain(0, False, 10, 20), + sc.Domain(1, True, 10, 20), + ]) + self.assertEqual(2, len(design.strands)) + self.assertEqual(expected_strand0, design.strands[0]) + self.assertEqual(expected_strand1, design.strands[1]) + self.assertEqual(2, len(design.helices[0].domains)) + self.assertEqual(2, len(design.helices[1].domains)) + self.assertEqual(0, len(design.helices[2].domains)) + self.assertEqual(0, len(design.helices[3].domains)) + self.assertEqual(0, len(design.helices[4].domains)) + self.assertEqual(0, len(design.helices[5].domains)) + + def test_strand__multiple_strands_other_order(self): + design = self.design_6helix + design.strand(0, 20).to(10).cross(1).to(20) + design.strand(0, 0).to(10).cross(1).to(0) + expected_strand0 = sc.Strand([ + sc.Domain(0, False, 10, 20), + sc.Domain(1, True, 10, 20), + ]) + expected_strand1 = sc.Strand([ + sc.Domain(0, True, 0, 10), + sc.Domain(1, False, 0, 10), + ]) + self.assertEqual(2, len(design.strands)) + self.assertEqual(expected_strand0, design.strands[0]) + self.assertEqual(expected_strand1, design.strands[1]) + self.assertEqual(2, len(design.helices[0].domains)) + self.assertEqual(2, len(design.helices[1].domains)) + self.assertEqual(0, len(design.helices[2].domains)) + self.assertEqual(0, len(design.helices[3].domains)) + self.assertEqual(0, len(design.helices[4].domains)) + self.assertEqual(0, len(design.helices[5].domains)) + + def test_strand__multiple_strands_overlap_no_error(self): + design = self.design_6helix + design.strand(0, 0).to(10).cross(1).to(0) + design.strand(0, 10).to(0).cross(1).to(10) + expected_strand0 = sc.Strand([ + sc.Domain(0, True, 0, 10), + sc.Domain(1, False, 0, 10), + ]) + expected_strand1 = sc.Strand([ + sc.Domain(0, False, 0, 10), + sc.Domain(1, True, 0, 10), + ]) + self.assertEqual(2, len(design.strands)) + self.assertEqual(expected_strand0, design.strands[0]) + self.assertEqual(expected_strand1, design.strands[1]) + self.assertEqual(2, len(design.helices[0].domains)) + self.assertEqual(2, len(design.helices[1].domains)) + self.assertEqual(0, len(design.helices[2].domains)) + self.assertEqual(0, len(design.helices[3].domains)) + self.assertEqual(0, len(design.helices[4].domains)) + self.assertEqual(0, len(design.helices[5].domains)) + + def test_strand__multiple_strands_overlap_error(self): + design = self.design_6helix + design.strand(0, 0).to(10).cross(1).to(0) + with self.assertRaises(sc.IllegalDNADesignError): + design.strand(0, 2).to(8) + + class TestCreateHelix(unittest.TestCase): def test_helix_constructor_no_max_offset_with_major_ticks(self): @@ -2433,7 +2606,7 @@ def test_add_strand__with_loopout(self): self.assertEqual(ss2, design.domain_at(1, 0, False)) def test_add_strand__illegal_overlapping_domains(self): - helices = [sc.Helix(max_offset=50)] * 2 + helices = [sc.Helix(max_offset=50), sc.Helix(max_offset=50)] design = sc.DNADesign(helices=helices, strands=[], grid=sc.square) with self.assertRaises(sc.StrandError): strand = sc.Strand([ diff --git a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna index fb93dc4b..5e13c176 100644 --- a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna +++ b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna @@ -59,7 +59,7 @@ "is_scaffold": true }, { - "color": "#7300de", + "color": "#320096", "sequence": "GCCGCTTTTGCGGGATTTGCAGGGAGTTAAAG", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -67,7 +67,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CAAGAGTAATCTTGACGCTGGCTGACCTTCAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -75,7 +75,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TGCAAAAGAAGTTTTGAATAGCGAGAGGCTTT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -83,7 +83,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "ACGGTGTCTGGAAGTTAATATGCAACTAAAGT", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, @@ -91,7 +91,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "AGTCAAATCACCATCAGAGAAAGGCCGGAGAC", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, @@ -99,7 +99,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "GGCGGATTGACCGTAACTCCGTGGGAACAAAC", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, @@ -107,7 +107,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "AAATTGTTATCCGCTCAGCTGTTTCCTGTGTG", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, @@ -115,7 +115,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "GAGTCCACTATTAAAGTTCCAGTTTGGAACAA", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, @@ -123,7 +123,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "AACCCATGTACCGTAAGCAAGCCCAATAGG", "domains": [ {"helix": 0, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "AGCCAGAATGGAAAGATAAATCCTCATTAA", "domains": [ {"helix": 2, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -139,7 +139,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "ACTTGAGCCATTTGGTTATCACCGTCACCG", "domains": [ {"helix": 4, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -147,7 +147,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "AACCCACAAGAATTGTAATATCAGAGAGAT", "domains": [ {"helix": 6, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -155,7 +155,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CATCGTAGGAATCATAGCCGTTTTTATTTT", "domains": [ {"helix": 8, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -163,7 +163,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "TAATTACTAGAAAAATAAACACCGGAATCA", "domains": [ {"helix": 10, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -171,7 +171,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "TTAATTACATTTAACATCAAGAAAACAAAA", "domains": [ {"helix": 12, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -179,7 +179,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CTTTGCCCGAACGTTAACTCGTATTAAATC", "domains": [ {"helix": 14, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -187,14 +187,14 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "AGAATAGAAAGGAACAACTAAAGGAATTGCG", "domains": [ {"helix": 0, "forward": false, "start": 216, "end": 248, "deletions": [225]} ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "TACCAAGCCTCATCTTTGACCCCCTCAAGAG", "domains": [ {"helix": 2, "forward": false, "start": 208, "end": 216}, @@ -202,7 +202,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "AAGGATTAAGAGGCTGAGACTCCAGCGATTA", "domains": [ {"helix": 1, "forward": true, "start": 232, "end": 240}, @@ -210,7 +210,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "AATCTACGACCAGTCAGGACGTTGTTCATAA", "domains": [ {"helix": 4, "forward": false, "start": 208, "end": 216}, @@ -218,7 +218,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "TCAAAATCAGCGTTTGCCATCTTGGAAGAAA", "domains": [ {"helix": 3, "forward": true, "start": 232, "end": 240}, @@ -226,7 +226,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "GCCCGAAATTGCATCAAAAAGATTACGTAGA", "domains": [ {"helix": 6, "forward": false, "start": 208, "end": 216}, @@ -234,7 +234,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "AAATACATGCAGTATGTTAGCAAAAGAGGAA", "domains": [ {"helix": 5, "forward": true, "start": 232, "end": 240}, @@ -242,7 +242,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CAAAATTACATACAGGCAAGGCAACCTAATT", "domains": [ {"helix": 8, "forward": false, "start": 208, "end": 216}, @@ -250,7 +250,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "TGCCAGTTAGCGTCTTTCCAGAGAGAATTAG", "domains": [ {"helix": 7, "forward": true, "start": 232, "end": 240}, @@ -258,7 +258,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "TTGTATAAAGAAAAGCCCCAAAAAACAATAA", "domains": [ {"helix": 10, "forward": false, "start": 208, "end": 216}, @@ -266,7 +266,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "ACAACATGTCTGTCCAGACGACGCAGGAAGA", "domains": [ {"helix": 9, "forward": true, "start": 232, "end": 240}, @@ -274,7 +274,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "CTCTTCGCTTGGGAAGGGCGATCGAGACTAC", "domains": [ {"helix": 12, "forward": false, "start": 208, "end": 216}, @@ -282,7 +282,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CTTTTTAAAATCATAGGTCTGAGGTGCGGGC", "domains": [ {"helix": 11, "forward": true, "start": 232, "end": 240}, @@ -290,7 +290,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CTTTTCACGTATTGGGCGCCAGGGAAACAGA", "domains": [ {"helix": 14, "forward": false, "start": 208, "end": 216}, @@ -298,7 +298,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "AATAAAGAAATTATTTGCACGTATGGTTTTT", "domains": [ {"helix": 13, "forward": true, "start": 232, "end": 240}, @@ -306,14 +306,14 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "GAACGTGGCGAGAAAGGAAGGGAATCACCTT", "domains": [ {"helix": 15, "forward": true, "start": 200, "end": 232, "deletions": [225]} ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "CCGATATATTCGGTCGCTGAGGCCGTCACC", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -321,7 +321,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "CTCAGCAGAGACCAGGCGCATAGAAGAACC", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -330,7 +330,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "GGATATTCGACGATAAAAACCAACCAGAGG", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -339,7 +339,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "GGGTAATAGCTCAACATGTTTTATCATTCC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 48}, @@ -348,7 +348,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "ATATAACAAAGATTCAAAAGGGTATATGAT", "domains": [ {"helix": 7, "forward": true, "start": 40, "end": 48}, @@ -357,7 +357,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "ATTCAACCACAACCCGTCGGATTTGGGATA", "domains": [ {"helix": 9, "forward": true, "start": 40, "end": 48}, @@ -366,7 +366,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "GGTCACGTCGTAATCATGGTCATACAATTC", "domains": [ {"helix": 11, "forward": true, "start": 40, "end": 48}, @@ -375,7 +375,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "CACACAACTAGGGTTGAGTGTTGAACGTGG", "domains": [ {"helix": 13, "forward": true, "start": 40, "end": 48}, @@ -384,7 +384,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "ACTCCAACGTCAAAGGGCGAAAAAAAAGAATA", "domains": [ {"helix": 15, "forward": true, "start": 40, "end": 64}, @@ -392,7 +392,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CGGTGTACCGAAAGACAGCATCGGACGCATAA", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -401,7 +401,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "TACCAGACATTACCCAAATCAACGCAGATGAA", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -410,7 +410,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "ATGCTGTAGTAAAATGTTTAGACTCCCTCGTT", "domains": [ {"helix": 6, "forward": false, "start": 48, "end": 56}, @@ -419,7 +419,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "TGTAGGTAGTTGATTCCCAATTCTTGAATATA", "domains": [ {"helix": 8, "forward": false, "start": 48, "end": 56}, @@ -428,7 +428,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "AGCGAGTAGTTCTAGCTGATAAATGAGTAATG", "domains": [ {"helix": 10, "forward": false, "start": 48, "end": 56}, @@ -437,7 +437,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "CTCGAATTTGGTGTAGATGGGCGCTAAATGTG", "domains": [ {"helix": 12, "forward": false, "start": 48, "end": 56}, @@ -446,7 +446,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "GCCCGAGAATACGAGCCGGAAGCAGTACCGAG", "domains": [ {"helix": 14, "forward": false, "start": 48, "end": 56}, @@ -455,7 +455,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "GACAATGACAACAACCATCGCCCAACGAGGG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -463,7 +463,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "TAGCAACGCAACTTTGAAAGAGGATAACAAAG", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -472,7 +472,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "CTGCTCATAGCAACACTATCATAAGGATAGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -481,7 +481,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "TCCAATACCTTAGAGCTTAATTGCGCGAACGA", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 80}, @@ -490,7 +490,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "GTAGATTTTTTAAATGCAATGCCTTAATGCCG", "domains": [ {"helix": 7, "forward": true, "start": 72, "end": 80}, @@ -499,7 +499,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "GAGAGGGTCAGCTTTCATCAACATATCGTAAC", "domains": [ {"helix": 9, "forward": true, "start": 72, "end": 80}, @@ -508,7 +508,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CGTGCATCTCTAGAGGATCCCCGGTAAAGTGT", "domains": [ {"helix": 11, "forward": true, "start": 72, "end": 80}, @@ -517,7 +517,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "AAAGCCTGAATCCCTTATAAATCACCGTCTAT", "domains": [ {"helix": 13, "forward": true, "start": 72, "end": 80}, @@ -526,7 +526,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "CAGGGCGATGGCCCACTACGTGATTCCGAAA", "domains": [ {"helix": 15, "forward": true, "start": 72, "end": 96, "deletions": [81]}, @@ -534,7 +534,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "AACTGACGCTACAGAGGCTTTGGTTGCGCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -543,7 +543,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "TAGTAAGTCAGTGAATAAGGCTGGGAACCG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -552,7 +552,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "CGGATGGTGCGGAATCGTCATAACGAGGCA", "domains": [ {"helix": 6, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -561,7 +561,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CATATATAGTTTGACCATTAGACATTTTTG", "domains": [ {"helix": 8, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -570,7 +570,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CTGTAGCAGCTATTTTTGAGAGAGAACCCT", "domains": [ {"helix": 10, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -579,7 +579,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "GGTCGACTGCCAGTTTGAGGGGTGGCCTTC", "domains": [ {"helix": 12, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -588,7 +588,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "TCGGCAAGGGTGCCTAATGAGTTGCCTGCA", "domains": [ {"helix": 14, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -597,7 +597,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "TTCTTAAACAGCTTGATACCGATAAGGACTAA", "domains": [ {"helix": 0, "forward": false, "start": 96, "end": 120}, @@ -605,7 +605,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "AGACTTTTAGACGGTCAATCATAATGCCCTGA", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -614,7 +614,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CGAGAAACAACGCCAAAAGGAATTAATATTCA", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -623,7 +623,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TTGAATCCCCTTTTGATAAGAGGTTACATTTC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 112}, @@ -632,7 +632,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GCAAATGGAAGGATAAAAATTTTTATCTACAA", "domains": [ {"helix": 7, "forward": true, "start": 104, "end": 112}, @@ -641,7 +641,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "AGGCTATCAAAAATAATTCGCGTCACGACGAC", "domains": [ {"helix": 9, "forward": true, "start": 104, "end": 112}, @@ -650,7 +650,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "AGTATCGGCAGTGCCAAGCTTGCAGAGCTAAC", "domains": [ {"helix": 11, "forward": true, "start": 104, "end": 112}, @@ -659,7 +659,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "TCACATTATCCTGTTTGATGGTGGACCATCAC", "domains": [ {"helix": 13, "forward": true, "start": 104, "end": 112}, @@ -668,7 +668,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "CCAAATCAAGTTTTTTGGGGTCGACCCCAGCA", "domains": [ {"helix": 15, "forward": true, "start": 104, "end": 128}, @@ -676,7 +676,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CGAGGCGCTCATGAGGAAGTTTCCAGGTGAAT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -685,7 +685,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "AGATACATACCAGAACGAGTAGTAAGCCGGAA", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -694,7 +694,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "TAATTGCTCCCTCAAATGCTTTAAACTAATGC", "domains": [ {"helix": 6, "forward": false, "start": 112, "end": 120}, @@ -703,7 +703,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "TTCAACGCTCAATAACCTGTTTAGAGTACCTT", "domains": [ {"helix": 8, "forward": false, "start": 112, "end": 120}, @@ -712,7 +712,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "ACGCCATCAGGTCATTGCCTGAGAGCCTTTAT", "domains": [ {"helix": 10, "forward": false, "start": 112, "end": 120}, @@ -721,7 +721,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "ACGACGGCCCTCAGGAAGATCGCACAATAGGA", "domains": [ {"helix": 12, "forward": false, "start": 112, "end": 120}, @@ -730,7 +730,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "GGCGAAAAATTGCGTTGCGCTCACGTTGTAAA", "domains": [ {"helix": 14, "forward": false, "start": 112, "end": 120}, @@ -739,7 +739,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "ATCGGTTTATCAGCTTGCTTTCGATTAAAC", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -747,7 +747,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GGGTAAAATGCTCCATGTTACTTAATTGGG", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -756,7 +756,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "CTTGAGATGGAATACCACATTCAACAGTTC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -765,7 +765,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "AGAAAACGAGGTCAGGATTAGAGCTATATT", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 144}, @@ -774,7 +774,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "TTCATTTGACTTTTGCGGGAGAAGTCTGGA", "domains": [ {"helix": 7, "forward": true, "start": 136, "end": 144}, @@ -783,7 +783,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "GCAAACAAAGCTCATTTTTTAACCTCCAGC", "domains": [ {"helix": 9, "forward": true, "start": 136, "end": 144}, @@ -792,7 +792,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CAGCTTTCTTTCCCAGTCACGACTGCCCGC", "domains": [ {"helix": 11, "forward": true, "start": 136, "end": 144}, @@ -801,7 +801,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "TTTCCAGTGTCCACGCTGGTTTGGGTGCCG", "domains": [ {"helix": 13, "forward": true, "start": 136, "end": 144}, @@ -810,7 +810,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "TAAAGCACTAAATCGGAACCCTAAAGAGTTGC", "domains": [ {"helix": 15, "forward": true, "start": 136, "end": 160}, @@ -818,7 +818,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "CCGCGACCTACGTAATGCCACTACTTAATTGT", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -827,7 +827,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "GAGATTTAGGTTTAATTTCAACTTGTCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, @@ -836,7 +836,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "ACTCCAACAGAATGACCATAAATCCATCAGTT", "domains": [ {"helix": 6, "forward": false, "start": 144, "end": 152}, @@ -845,7 +845,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CCTGTAATGGGCGCGAGCTGAAAAGGAAGCAA", "domains": [ {"helix": 8, "forward": false, "start": 144, "end": 152}, @@ -854,7 +854,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "GTTAAATCGAGAATCGATGAACGGATTATGAC", "domains": [ {"helix": 10, "forward": false, "start": 144, "end": 152}, @@ -863,7 +863,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GCCAGGGTCGGCACCGCTTCTGGTAAATTTTT", "domains": [ {"helix": 12, "forward": false, "start": 144, "end": 152}, @@ -872,7 +872,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "AGCAAGCGCGGGAAACCTGTCGTGTGGGTAAC", "domains": [ {"helix": 14, "forward": false, "start": 144, "end": 152}, @@ -881,7 +881,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "AAAAAAGGCTCCAAAAGGAGCCTGAAGGCAC", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 184, "deletions": [177]}, @@ -889,7 +889,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "CAACCTAATCGCCTGATAAATTGTTAATCATT", "domains": [ {"helix": 1, "forward": true, "start": 168, "end": 176}, @@ -898,7 +898,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "GTGAATTATACAGGTAGAAAGATTAAAAATCA", "domains": [ {"helix": 3, "forward": true, "start": 168, "end": 176}, @@ -907,7 +907,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "GGTCTTTACAAAGCGAACCAGACCGGTGGCAT", "domains": [ {"helix": 5, "forward": true, "start": 168, "end": 176}, @@ -916,7 +916,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CAATTCTACGGTTGTACCAAAAACTAATCGTA", "domains": [ {"helix": 7, "forward": true, "start": 168, "end": 176}, @@ -925,7 +925,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "AAACTAGCTGTTAAAATTCGCATTGCCGGAAA", "domains": [ {"helix": 9, "forward": true, "start": 168, "end": 176}, @@ -934,7 +934,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "CCAGGCAATGCAAGGCGATTAAGTCCAGCTGC", "domains": [ {"helix": 11, "forward": true, "start": 168, "end": 176}, @@ -943,7 +943,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "ATTAATGAACCGCCTGGCCCTGAGAGGGAGCC", "domains": [ {"helix": 13, "forward": true, "start": 168, "end": 176}, @@ -952,7 +952,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "CCCGATTTAGAGCTTGACGGGGAAGCTGATT", "domains": [ {"helix": 15, "forward": true, "start": 168, "end": 192, "deletions": [177]}, @@ -960,7 +960,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "TGTATCAAACGAAAGAGGCAAAATCTCCAA", "domains": [ {"helix": 2, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -969,7 +969,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "ACATTATCCTTATGCGATTTTACGGAGATT", "domains": [ {"helix": 4, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -978,7 +978,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "CGAGCTTCCCTGACTATTATAGACGGAACA", "domains": [ {"helix": 6, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -987,7 +987,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "GCTAAATCTAATAGTAGTAGCATTTTAATT", "domains": [ {"helix": 8, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -996,7 +996,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "AATATTTATGTCAATCATATGTAGCATAAA", "domains": [ {"helix": 10, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1005,7 +1005,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "GATGTGCAGCGCCATTCGCCATTAAACGTT", "domains": [ {"helix": 12, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1014,7 +1014,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "GCCCTTCATCGGCCAACGCGCGGAAAGGGG", "domains": [ {"helix": 14, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1023,7 +1023,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "AATAATAATTTTTTCACGTTGAAAAGAATACA", "domains": [ {"helix": 0, "forward": false, "start": 192, "end": 216}, @@ -1031,7 +1031,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CTAAAACAGCGAAACAAAGTACAAAGAACTGG", "domains": [ {"helix": 1, "forward": true, "start": 200, "end": 208}, @@ -1040,7 +1040,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "CTCATTATTTAATAAAACGAACTATCAGAAGC", "domains": [ {"helix": 3, "forward": true, "start": 200, "end": 208}, @@ -1049,7 +1049,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "AAAGCGGAGACTTCAAATATCGCGTTAACATC", "domains": [ {"helix": 5, "forward": true, "start": 200, "end": 208}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CAATAAATAGCAATAAAGCCTCAGACCCCGGT", "domains": [ {"helix": 7, "forward": true, "start": 200, "end": 208}, @@ -1067,7 +1067,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "TGATAATCGCAAATATTTAAATTGTCAGGCTG", "domains": [ {"helix": 9, "forward": true, "start": 200, "end": 208}, @@ -1076,7 +1076,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CGCAACTGTATTACGCCAGCTGGCGGGAGAGG", "domains": [ {"helix": 11, "forward": true, "start": 200, "end": 208}, @@ -1085,7 +1085,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CGGTTTGCCAGTGAGACGGGCAACAAGCCGGC", "domains": [ {"helix": 13, "forward": true, "start": 200, "end": 208}, @@ -1094,7 +1094,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GCTGAACCTCAAATATCAAACCCTGAACCTAC", "domains": [ {"helix": 15, "forward": true, "start": 232, "end": 256}, @@ -1102,7 +1102,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "AAGTATTAGGATTAGCGGGGTTTTGCGGAGTG", "domains": [ {"helix": 2, "forward": false, "start": 240, "end": 248}, @@ -1111,7 +1111,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "CCCTTATTACCGGAACCAGAGCCAAAACATGA", "domains": [ {"helix": 4, "forward": false, "start": 240, "end": 248}, @@ -1120,7 +1120,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "CTTATTACACATAAAGGTGGCAACTCATAGCC", "domains": [ {"helix": 6, "forward": false, "start": 240, "end": 248}, @@ -1129,7 +1129,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "CGCTAACGACAAAATAAACAGCCATAAGACTC", "domains": [ {"helix": 8, "forward": false, "start": 240, "end": 248}, @@ -1138,7 +1138,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "AAAGTAATTTCAGCTAATGCAGAACTTACCAA", "domains": [ {"helix": 10, "forward": false, "start": 240, "end": 248}, @@ -1147,7 +1147,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "TTTATCAACCTCCGGCTTAGGTTGCAAAAGGT", "domains": [ {"helix": 12, "forward": false, "start": 240, "end": 248}, @@ -1156,7 +1156,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "CATATCAAAATTGCGTAGATTTTCATAGTGAA", "domains": [ {"helix": 14, "forward": false, "start": 240, "end": 248}, @@ -1165,7 +1165,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "CTAAACAACTTTCAACAGTTTCAGCTCAGTA", "domains": [ {"helix": 0, "forward": false, "start": 256, "end": 280, "deletions": [273]}, @@ -1173,7 +1173,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CCAGGCGGGGAACCTATTATTCTGCCACCGGA", "domains": [ {"helix": 1, "forward": true, "start": 264, "end": 272}, @@ -1182,7 +1182,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "ACCGCCTCTCATCGGCATTTTCGGATATAAAA", "domains": [ {"helix": 3, "forward": true, "start": 264, "end": 272}, @@ -1191,7 +1191,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "GAAACGCAAAAGAACTGGCATGATTATTATTT", "domains": [ {"helix": 5, "forward": true, "start": 264, "end": 272}, @@ -1200,7 +1200,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "ATCCCAATCAATTTTATCCTGAATCGCGCCTG", "domains": [ {"helix": 7, "forward": true, "start": 264, "end": 272}, @@ -1209,7 +1209,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "TTTATCAAGAATATAAAGTACCGAGGTTATAT", "domains": [ {"helix": 9, "forward": true, "start": 264, "end": 272}, @@ -1218,7 +1218,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "AACTATATACGCTGAGAAGAGTCAAGGTTTAA", "domains": [ {"helix": 11, "forward": true, "start": 264, "end": 272}, @@ -1227,7 +1227,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "CGTCAGATAATAATGGAAGGGTTACAATCAAT", "domains": [ {"helix": 13, "forward": true, "start": 264, "end": 272}, @@ -1236,7 +1236,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "ATCTGGTCAGTTGGCAAATCAACTGGATTAT", "domains": [ {"helix": 15, "forward": true, "start": 264, "end": 288, "deletions": [273]}, @@ -1244,7 +1244,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "CTATTTCATAAGTGCCGTCGAGGGATTTTG", "domains": [ {"helix": 2, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1253,7 +1253,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CGCGTTTCCTCAGAGCCGCCACCCCCCTGC", "domains": [ {"helix": 4, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1262,7 +1262,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "ATACCCAAAGACACCACGGAATGACTGTAG", "domains": [ {"helix": 6, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1271,7 +1271,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "CCAGCTACCAAATAAGAAACGAATAACGGA", "domains": [ {"helix": 8, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1280,7 +1280,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "AATAAGACAATAGATAAGTCCTTTTTGCAC", "domains": [ {"helix": 10, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1289,7 +1289,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "GATTAAGGTAAATGCTGATGCAGAGCCAGT", "domains": [ {"helix": 12, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1298,7 +1298,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "ACTTCTGGAATATACAGTAACAATAGCTTA", "domains": [ {"helix": 14, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1307,7 +1307,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "GTTAGTAAATGAATTTTCTGTATGAGGGTTGA", "domains": [ {"helix": 0, "forward": false, "start": 288, "end": 312}, @@ -1315,7 +1315,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TATAAGTAGTATAAACAGTTAATGCCTCAGAA", "domains": [ {"helix": 1, "forward": true, "start": 296, "end": 304}, @@ -1324,7 +1324,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "CCGCCACCTTTGCCTTTAGCGTCAAAGTTTAT", "domains": [ {"helix": 3, "forward": true, "start": 296, "end": 304}, @@ -1333,7 +1333,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "TTTGTCACCCGAGGAAACGCAATATTTTTTGT", "domains": [ {"helix": 5, "forward": true, "start": 296, "end": 304}, @@ -1342,7 +1342,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "TTAACGTCTCAAGATTAGTTGCTAGAACAAGA", "domains": [ {"helix": 7, "forward": true, "start": 296, "end": 304}, @@ -1351,7 +1351,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "AAAATAATAGGCAGAGGCATTTTCAATCCAAT", "domains": [ {"helix": 9, "forward": true, "start": 296, "end": 304}, @@ -1360,7 +1360,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "CGCAAGACCCTTGAAAACATAGCGGTACCTTT", "domains": [ {"helix": 11, "forward": true, "start": 296, "end": 304}, @@ -1369,7 +1369,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "TACATCGGTATAATCCTGATTGTTAGTTGAAA", "domains": [ {"helix": 13, "forward": true, "start": 296, "end": 304}, @@ -1378,7 +1378,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "GGAATTGAGGAAGGTTATCTAAAAGATGGCAA", "domains": [ {"helix": 15, "forward": true, "start": 296, "end": 320}, @@ -1386,7 +1386,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "CAGTGCCCTAGCCCGGAATAGGTGTTCCAGAC", "domains": [ {"helix": 2, "forward": false, "start": 304, "end": 312}, @@ -1395,7 +1395,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "GAATCAAGCTCAGAGCCACCACCCTTGAGTAA", "domains": [ {"helix": 4, "forward": false, "start": 304, "end": 312}, @@ -1404,7 +1404,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "GAAGGAAAAATCAATAGAAAATTCTAGCGACA", "domains": [ {"helix": 6, "forward": false, "start": 304, "end": 312}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "GCCTTAAAAAAAATGAAAATAGCAAGTTACCA", "domains": [ {"helix": 8, "forward": false, "start": 304, "end": 312}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "TGTAATTTATCCCATCCTAATTTAGTTTTGAA", "domains": [ {"helix": 10, "forward": false, "start": 304, "end": 312}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CTTAGAATAAAGAACGCGAGAAAACGCCAACA", "domains": [ {"helix": 12, "forward": false, "start": 304, "end": 312}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "TTCATCAAGAGAAACAATAACGGAAATTTTCC", "domains": [ {"helix": 14, "forward": false, "start": 304, "end": 312}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "AACGATCTAAAGTTTTGTCGTCTTATCACC", "domains": [ {"helix": 0, "forward": false, "start": 320, "end": 344, "deletions": [321]}, @@ -1457,7 +1457,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "GTACTCAGAACGGGGTCAGTGCCTCAGAGC", "domains": [ {"helix": 1, "forward": true, "start": 328, "end": 336}, @@ -1466,7 +1466,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "CGCCACCACAGCACCGTAATCAGATATGGT", "domains": [ {"helix": 3, "forward": true, "start": 328, "end": 336}, @@ -1475,7 +1475,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "TTACCAGCCAGATAGCCGAACAAGCCTTTA", "domains": [ {"helix": 5, "forward": true, "start": 328, "end": 336}, @@ -1484,7 +1484,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CAGAGAGACCCGACTTGCGGGAGCGAGCAT", "domains": [ {"helix": 7, "forward": true, "start": 328, "end": 336}, @@ -1493,7 +1493,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "GTAGAAACCGCCATATTTAACAACTTTTTC", "domains": [ {"helix": 9, "forward": true, "start": 328, "end": 336}, @@ -1502,7 +1502,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "AAATATATTCGTCGCTATTAATTTTCGCCT", "domains": [ {"helix": 11, "forward": true, "start": 328, "end": 336}, @@ -1511,7 +1511,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "GATTGCTTTCCTGATTATCAGATTATCTTT", "domains": [ {"helix": 13, "forward": true, "start": 328, "end": 336}, @@ -1520,7 +1520,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "AGGAGCACTAACAACTAATAGATTGGAATTAT", "domains": [ {"helix": 15, "forward": true, "start": 328, "end": 352}, @@ -1528,7 +1528,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "TAAGTTTTGAGGTTTAGTACCGCCGTTAGCGT", "domains": [ {"helix": 2, "forward": false, "start": 336, "end": 344}, @@ -1537,7 +1537,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "ATCGATAGGAACCACCACCAGAGCACTGGTAA", "domains": [ {"helix": 4, "forward": false, "start": 336, "end": 344}, @@ -1546,7 +1546,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "AAAGTAAGGCCAAAGACAAAAGGGATGAAACC", "domains": [ {"helix": 6, "forward": false, "start": 336, "end": 344}, @@ -1555,7 +1555,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GCGAACCTATAACATAAAAACAGGTTTTAAGA", "domains": [ {"helix": 8, "forward": false, "start": 336, "end": 344}, @@ -1564,7 +1564,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "TTGAGAATCAATCAATAATCGGCTGCGTTTTA", "domains": [ {"helix": 10, "forward": false, "start": 336, "end": 344}, @@ -1573,7 +1573,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "TCTGTAAATTTAGTTAATTTCATCGGGCTTAA", "domains": [ {"helix": 12, "forward": false, "start": 336, "end": 344}, @@ -1582,7 +1582,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "CATCATATTGAATACCAAGTTACAACCTTGCT", "domains": [ {"helix": 14, "forward": false, "start": 336, "end": 344}, @@ -1591,7 +1591,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "GCATTCCACAGACAGCCCTCATAACCCTCAG", "domains": [ {"helix": 0, "forward": false, "start": 352, "end": 376, "deletions": [369]}, @@ -1599,7 +1599,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "AACCGCCAGATGATACAGGAGTGTCGCCGCCA", "domains": [ {"helix": 1, "forward": true, "start": 360, "end": 368}, @@ -1608,7 +1608,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "GCATTGACGCCGGAAACGTCACCACGACATTC", "domains": [ {"helix": 3, "forward": true, "start": 360, "end": 368}, @@ -1617,7 +1617,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "AACCGATTATCTTACCGAAGCCCTGAAGCGCA", "domains": [ {"helix": 5, "forward": true, "start": 360, "end": 368}, @@ -1626,7 +1626,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "TTAGACGGATTCTAAGAACGCGAGGTCTTTCC", "domains": [ {"helix": 7, "forward": true, "start": 360, "end": 368}, @@ -1635,7 +1635,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "TTATCATTCCAACGCTCAACAGTATTCTGACC", "domains": [ {"helix": 9, "forward": true, "start": 360, "end": 368}, @@ -1644,7 +1644,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "TAAATTTATATATGTGAGTGAATAAAATCGCG", "domains": [ {"helix": 11, "forward": true, "start": 360, "end": 368}, @@ -1653,7 +1653,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CAGAGGCGAACCACCAGAAGGAGCAGAGCCGT", "domains": [ {"helix": 13, "forward": true, "start": 360, "end": 368}, @@ -1662,7 +1662,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CAATAGATAATACATTTGAGGATTTTGCGGA", "domains": [ {"helix": 15, "forward": true, "start": 360, "end": 384, "deletions": [369]}, @@ -1670,7 +1670,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GGCTTTTCCCTCAGAACCGCCACGCCTGTA", "domains": [ {"helix": 2, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1679,7 +1679,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "TAGCAAGAGGAGGTTGAGGCAGTCATACAT", "domains": [ {"helix": 4, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1688,7 +1688,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "AATAGCTGAGGGAGGGAAGGTAATTACCAT", "domains": [ {"helix": 6, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1697,7 +1697,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "ATCCGGTGAGAATTAACTGAACGAAATAGC", "domains": [ {"helix": 8, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1706,7 +1706,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "TATAAAGCCAAGAACGGGTATTGAAGGCTT", "domains": [ {"helix": 10, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1715,7 +1715,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "AAATCAAATGGTTTGAAATACCCTTACCAG", "domains": [ {"helix": 12, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1724,7 +1724,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "ACAAAGAAATTATTCATTTCAACAGTACAT", "domains": [ {"helix": 14, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1733,7 +1733,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "TTTCGTCACCAGTACAAACTACAACCCTCAGA", "domains": [ {"helix": 0, "forward": false, "start": 384, "end": 408}, @@ -1741,7 +1741,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "GCCACCACACCGTTCCAGTAAGCGGTCAGACG", "domains": [ {"helix": 1, "forward": true, "start": 392, "end": 400}, @@ -1750,7 +1750,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "ATTGGCCTAATCACCAGTAGCACCAATATTGA", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 400}, @@ -1759,7 +1759,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "CGGAAATTAAGAGCAAGAAACAATACCCTGAA", "domains": [ {"helix": 5, "forward": true, "start": 392, "end": 400}, @@ -1768,7 +1768,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CAAAGTCAAAGCAAATCAGATATAAAACCAAG", "domains": [ {"helix": 7, "forward": true, "start": 392, "end": 400}, @@ -1777,7 +1777,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TACCGCACATGCGTTATACAAATTGACCGTGT", "domains": [ {"helix": 9, "forward": true, "start": 392, "end": 400}, @@ -1786,7 +1786,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GATAAATACCTTTTTTAATGGAAATTACCTGA", "domains": [ {"helix": 11, "forward": true, "start": 392, "end": 400}, @@ -1795,7 +1795,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "GCAAAAGATGAGTAACATTATCATTTAGAAGT", "domains": [ {"helix": 13, "forward": true, "start": 392, "end": 400}, @@ -1804,7 +1804,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "ATTAGACTTTACAAACAATTCGACATTAATTT", "domains": [ {"helix": 15, "forward": true, "start": 392, "end": 416}, @@ -1812,7 +1812,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "CTGAATTTCCTCATTTTCAGGGATACACTGAG", "domains": [ {"helix": 2, "forward": false, "start": 400, "end": 408}, @@ -1821,7 +1821,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "GCCAGCAATGATATTCACAAACAACGCAGTCT", "domains": [ {"helix": 4, "forward": false, "start": 400, "end": 408}, @@ -1830,7 +1830,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CCAATAATATTCATTAAAGGTGAAGAATTAGA", "domains": [ {"helix": 6, "forward": false, "start": 400, "end": 408}, @@ -1839,7 +1839,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CCAATAGCGAGGGTAATTGAGCGCAGTTAAGC", "domains": [ {"helix": 8, "forward": false, "start": 400, "end": 408}, @@ -1848,7 +1848,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "AGTATCATTCATCGAGAACAAGCATACCGCGC", "domains": [ {"helix": 10, "forward": false, "start": 400, "end": 408}, @@ -1857,7 +1857,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "TTGAATTAAGGCGTTAAATAAGAAGCCTGTTT", "domains": [ {"helix": 12, "forward": false, "start": 400, "end": 408}, @@ -1866,7 +1866,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "TAAAAGTTAGATGATGAAACAAACAATTTCAT", "domains": [ {"helix": 14, "forward": false, "start": 400, "end": 408}, diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna index d3df6edc..933fa3c6 100644 --- a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna @@ -17,7 +17,7 @@ "is_scaffold": true }, { - "color": "#7300de", + "color": "#320096", "sequence": "GTTACGTTACGTTACGTTGTTACGTTACGTTAC", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, @@ -25,7 +25,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "ACGTTACGTTACGTTACCGTTACGTTACGTTACGTT", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, diff --git a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna index 6fa68a22..d9092bd5 100644 --- a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna +++ b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna @@ -29,7 +29,7 @@ "is_scaffold": true }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -37,7 +37,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -45,7 +45,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -53,7 +53,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 176}, @@ -61,7 +61,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", "domains": [ {"helix": 2, "forward": false, "start": 160, "end": 176}, @@ -69,7 +69,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", "domains": [ {"helix": 4, "forward": false, "start": 160, "end": 176}, @@ -77,14 +77,14 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", "domains": [ {"helix": 0, "forward": false, "start": 88, "end": 120} ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -92,7 +92,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -100,7 +100,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -108,7 +108,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -116,14 +116,14 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -140,7 +140,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -149,7 +149,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 64}, @@ -157,7 +157,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -166,7 +166,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -175,7 +175,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "AATGAATCGGCCAACGCGCGGGGAGTTGCAG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -183,7 +183,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CAAGCGGTCCTGTTTGATGGTGGTACGTGGAC", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -192,7 +192,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "TCCAACGTTGGCCCACTACGTGAAAGCCGGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -201,7 +201,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "AGTATCGGCCTCAGGAAGATCGCAGTGCGGGC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 128}, @@ -209,7 +209,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -218,7 +218,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -227,7 +227,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -235,7 +235,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -244,7 +244,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "GCCAGGGTTGGGAAGGGCGATCGCTCCAGC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -253,7 +253,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "CAGCTTTCCGGCACCGCTTCTGGTCAGGCTGC", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 160}, @@ -261,7 +261,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "GTCGACTCACGAGCCGGAAGCATACTAACTCA", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -270,7 +270,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, From 534fc8a155e832808aaba4b7b12e1c145dc7f32b Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 23 Jun 2020 18:13:30 -0700 Subject: [PATCH 08/30] added a few chained methods for modifying strands --- scadnano/scadnano.py | 63 ++- tests/scadnano_tests.py | 21 +- ...st_16_helix_origami_rectangle_no_twist.dna | 416 +++++++++--------- ...e_2_helix_origami_deletions_insertions.dna | 4 +- .../test_6_helix_origami_rectangle.dna | 60 +-- 5 files changed, 314 insertions(+), 250 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 9c3d13f2..154c9567 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1622,8 +1622,8 @@ def __init__(self, design: DNADesign, helix: int, offset: int): self.design = design self.current_helix = helix self.current_offset = offset - self.strand_created_already = False self.loopout_length = None + self.strand = None def cross(self, helix: int, offset: int = None) -> StrandBuilder: """ @@ -1678,21 +1678,70 @@ def to(self, offset: int) -> StrandBuilder: raise IllegalDNADesignError(f'offset {offset} cannot be equal to current offset') domain = Domain(helix=self.current_helix, forward=forward, start=start, end=end) - if self.strand_created_already: - strand = self.design.strands[-1] + if self.strand: if self.loopout_length is not None: - self.design.append_domain(strand, Loopout(self.loopout_length)) - self.design.append_domain(strand, domain) + self.design.append_domain(self.strand, Loopout(self.loopout_length)) + self.design.append_domain(self.strand, domain) self.loopout_length = None else: self.strand_created_already = True - strand = Strand(domains=[domain]) - self.design.add_strand(strand) + self.strand = Strand(domains=[domain]) + self.design.add_strand(self.strand) self.current_offset = offset return self + def as_scaffold(self) -> StrandBuilder: + """ + Makes Strand being built a scaffold. + + :return: self + """ + self.strand.set_scaffold(True) + return self + + def with_modification_5p(self, mod: Modification5Prime) -> StrandBuilder: + """ + Sets Strand being built to have given 5' modification. + + :param mod: 5' modification + :return: self + """ + self.strand.set_modification_5p(mod) + return self + + def with_modification_3p(self, mod: Modification3Prime) -> StrandBuilder: + """ + Sets Strand being built to have given 3' modification. + + :param mod: 3' modification + :return: self + """ + self.strand.set_modification_3p(mod) + return self + + def with_modification_internal(self, idx: int, mod: ModificationInternal, warn_on_no_dna: bool ) -> StrandBuilder: + """ + Sets Strand being built to have given internal modification. + + :param idx: idx along DNA sequence of internal modification + :param mod: internal modification + :param warn_on_no_dna: whether to print warning to screen if DNA has not been assigned + :return: self + """ + self.strand.set_modification_internal(idx, mod, warn_on_no_dna) + return self + + def with_color(self, color: Color) -> StrandBuilder: + + """ + Sets Strand being built to have given color. + + :return: self + """ + self.strand.set_color(color) + @dataclass class Strand(_JSONSerializable): diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 6b65dded..9d2a97a0 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -174,19 +174,34 @@ def test_strand__multiple_strands_other_order(self): def test_strand__multiple_strands_overlap_no_error(self): design = self.design_6helix - design.strand(0, 0).to(10).cross(1).to(0) - design.strand(0, 10).to(0).cross(1).to(10) + design.strand(0, 0).to(10).cross(1).to(0) \ + .as_scaffold() \ + .with_modification_internal(5, mod.cy3_int, warn_on_no_dna=False) + design.strand(0, 10).to(0).cross(1).to(10).with_modification_5p(mod.biotin_5p) expected_strand0 = sc.Strand([ sc.Domain(0, True, 0, 10), sc.Domain(1, False, 0, 10), - ]) + ], is_scaffold=True) expected_strand1 = sc.Strand([ sc.Domain(0, False, 0, 10), sc.Domain(1, True, 0, 10), ]) + + expected_strand0.set_modification_internal(5, mod.cy3_int, warn_on_no_dna=False) + expected_strand1.set_modification_5p(mod.biotin_5p) + self.assertEqual(2, len(design.strands)) + self.assertEqual(expected_strand0, design.strands[0]) + self.assertEqual(None, design.strands[0].modification_5p) + self.assertEqual(None, design.strands[0].modification_3p) + self.assertDictEqual({5: mod.cy3_int}, design.strands[0].modifications_int) + self.assertEqual(expected_strand1, design.strands[1]) + self.assertEqual(mod.biotin_5p, design.strands[1].modification_5p) + self.assertEqual(None, design.strands[1].modification_3p) + self.assertDictEqual({}, design.strands[1].modifications_int) + self.assertEqual(2, len(design.helices[0].domains)) self.assertEqual(2, len(design.helices[1].domains)) self.assertEqual(0, len(design.helices[2].domains)) diff --git a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna index 5e13c176..e7744f8a 100644 --- a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna +++ b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna @@ -59,7 +59,7 @@ "is_scaffold": true }, { - "color": "#320096", + "color": "#333333", "sequence": "GCCGCTTTTGCGGGATTTGCAGGGAGTTAAAG", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -67,7 +67,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "CAAGAGTAATCTTGACGCTGGCTGACCTTCAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -75,7 +75,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "TGCAAAAGAAGTTTTGAATAGCGAGAGGCTTT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -83,7 +83,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "ACGGTGTCTGGAAGTTAATATGCAACTAAAGT", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, @@ -91,7 +91,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "AGTCAAATCACCATCAGAGAAAGGCCGGAGAC", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, @@ -99,7 +99,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "GGCGGATTGACCGTAACTCCGTGGGAACAAAC", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, @@ -107,7 +107,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "AAATTGTTATCCGCTCAGCTGTTTCCTGTGTG", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, @@ -115,7 +115,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "GAGTCCACTATTAAAGTTCCAGTTTGGAACAA", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, @@ -123,7 +123,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "AACCCATGTACCGTAAGCAAGCCCAATAGG", "domains": [ {"helix": 0, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "AGCCAGAATGGAAAGATAAATCCTCATTAA", "domains": [ {"helix": 2, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -139,7 +139,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "ACTTGAGCCATTTGGTTATCACCGTCACCG", "domains": [ {"helix": 4, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -147,7 +147,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "AACCCACAAGAATTGTAATATCAGAGAGAT", "domains": [ {"helix": 6, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -155,7 +155,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "CATCGTAGGAATCATAGCCGTTTTTATTTT", "domains": [ {"helix": 8, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -163,7 +163,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "TAATTACTAGAAAAATAAACACCGGAATCA", "domains": [ {"helix": 10, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -171,7 +171,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "TTAATTACATTTAACATCAAGAAAACAAAA", "domains": [ {"helix": 12, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -179,7 +179,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "CTTTGCCCGAACGTTAACTCGTATTAAATC", "domains": [ {"helix": 14, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -187,14 +187,14 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "AGAATAGAAAGGAACAACTAAAGGAATTGCG", "domains": [ {"helix": 0, "forward": false, "start": 216, "end": 248, "deletions": [225]} ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "TACCAAGCCTCATCTTTGACCCCCTCAAGAG", "domains": [ {"helix": 2, "forward": false, "start": 208, "end": 216}, @@ -202,7 +202,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "AAGGATTAAGAGGCTGAGACTCCAGCGATTA", "domains": [ {"helix": 1, "forward": true, "start": 232, "end": 240}, @@ -210,7 +210,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "AATCTACGACCAGTCAGGACGTTGTTCATAA", "domains": [ {"helix": 4, "forward": false, "start": 208, "end": 216}, @@ -218,7 +218,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "TCAAAATCAGCGTTTGCCATCTTGGAAGAAA", "domains": [ {"helix": 3, "forward": true, "start": 232, "end": 240}, @@ -226,7 +226,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "GCCCGAAATTGCATCAAAAAGATTACGTAGA", "domains": [ {"helix": 6, "forward": false, "start": 208, "end": 216}, @@ -234,7 +234,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "AAATACATGCAGTATGTTAGCAAAAGAGGAA", "domains": [ {"helix": 5, "forward": true, "start": 232, "end": 240}, @@ -242,7 +242,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "CAAAATTACATACAGGCAAGGCAACCTAATT", "domains": [ {"helix": 8, "forward": false, "start": 208, "end": 216}, @@ -250,7 +250,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "TGCCAGTTAGCGTCTTTCCAGAGAGAATTAG", "domains": [ {"helix": 7, "forward": true, "start": 232, "end": 240}, @@ -258,7 +258,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "TTGTATAAAGAAAAGCCCCAAAAAACAATAA", "domains": [ {"helix": 10, "forward": false, "start": 208, "end": 216}, @@ -266,7 +266,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "ACAACATGTCTGTCCAGACGACGCAGGAAGA", "domains": [ {"helix": 9, "forward": true, "start": 232, "end": 240}, @@ -274,7 +274,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "CTCTTCGCTTGGGAAGGGCGATCGAGACTAC", "domains": [ {"helix": 12, "forward": false, "start": 208, "end": 216}, @@ -282,7 +282,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "CTTTTTAAAATCATAGGTCTGAGGTGCGGGC", "domains": [ {"helix": 11, "forward": true, "start": 232, "end": 240}, @@ -290,7 +290,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "CTTTTCACGTATTGGGCGCCAGGGAAACAGA", "domains": [ {"helix": 14, "forward": false, "start": 208, "end": 216}, @@ -298,7 +298,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "AATAAAGAAATTATTTGCACGTATGGTTTTT", "domains": [ {"helix": 13, "forward": true, "start": 232, "end": 240}, @@ -306,14 +306,14 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "GAACGTGGCGAGAAAGGAAGGGAATCACCTT", "domains": [ {"helix": 15, "forward": true, "start": 200, "end": 232, "deletions": [225]} ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "CCGATATATTCGGTCGCTGAGGCCGTCACC", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -321,7 +321,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "CTCAGCAGAGACCAGGCGCATAGAAGAACC", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -330,7 +330,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "GGATATTCGACGATAAAAACCAACCAGAGG", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -339,7 +339,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "GGGTAATAGCTCAACATGTTTTATCATTCC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 48}, @@ -348,7 +348,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "ATATAACAAAGATTCAAAAGGGTATATGAT", "domains": [ {"helix": 7, "forward": true, "start": 40, "end": 48}, @@ -357,7 +357,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "ATTCAACCACAACCCGTCGGATTTGGGATA", "domains": [ {"helix": 9, "forward": true, "start": 40, "end": 48}, @@ -366,7 +366,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "GGTCACGTCGTAATCATGGTCATACAATTC", "domains": [ {"helix": 11, "forward": true, "start": 40, "end": 48}, @@ -375,7 +375,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "CACACAACTAGGGTTGAGTGTTGAACGTGG", "domains": [ {"helix": 13, "forward": true, "start": 40, "end": 48}, @@ -384,7 +384,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "ACTCCAACGTCAAAGGGCGAAAAAAAAGAATA", "domains": [ {"helix": 15, "forward": true, "start": 40, "end": 64}, @@ -392,7 +392,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "CGGTGTACCGAAAGACAGCATCGGACGCATAA", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -401,7 +401,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "TACCAGACATTACCCAAATCAACGCAGATGAA", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -410,7 +410,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "ATGCTGTAGTAAAATGTTTAGACTCCCTCGTT", "domains": [ {"helix": 6, "forward": false, "start": 48, "end": 56}, @@ -419,7 +419,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "TGTAGGTAGTTGATTCCCAATTCTTGAATATA", "domains": [ {"helix": 8, "forward": false, "start": 48, "end": 56}, @@ -428,7 +428,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "AGCGAGTAGTTCTAGCTGATAAATGAGTAATG", "domains": [ {"helix": 10, "forward": false, "start": 48, "end": 56}, @@ -437,7 +437,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "CTCGAATTTGGTGTAGATGGGCGCTAAATGTG", "domains": [ {"helix": 12, "forward": false, "start": 48, "end": 56}, @@ -446,7 +446,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "GCCCGAGAATACGAGCCGGAAGCAGTACCGAG", "domains": [ {"helix": 14, "forward": false, "start": 48, "end": 56}, @@ -455,7 +455,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "GACAATGACAACAACCATCGCCCAACGAGGG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -463,7 +463,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "TAGCAACGCAACTTTGAAAGAGGATAACAAAG", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -472,7 +472,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "CTGCTCATAGCAACACTATCATAAGGATAGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -481,7 +481,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "TCCAATACCTTAGAGCTTAATTGCGCGAACGA", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 80}, @@ -490,7 +490,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "GTAGATTTTTTAAATGCAATGCCTTAATGCCG", "domains": [ {"helix": 7, "forward": true, "start": 72, "end": 80}, @@ -499,7 +499,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "GAGAGGGTCAGCTTTCATCAACATATCGTAAC", "domains": [ {"helix": 9, "forward": true, "start": 72, "end": 80}, @@ -508,7 +508,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "CGTGCATCTCTAGAGGATCCCCGGTAAAGTGT", "domains": [ {"helix": 11, "forward": true, "start": 72, "end": 80}, @@ -517,7 +517,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "AAAGCCTGAATCCCTTATAAATCACCGTCTAT", "domains": [ {"helix": 13, "forward": true, "start": 72, "end": 80}, @@ -526,7 +526,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "CAGGGCGATGGCCCACTACGTGATTCCGAAA", "domains": [ {"helix": 15, "forward": true, "start": 72, "end": 96, "deletions": [81]}, @@ -534,7 +534,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "AACTGACGCTACAGAGGCTTTGGTTGCGCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -543,7 +543,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "TAGTAAGTCAGTGAATAAGGCTGGGAACCG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -552,7 +552,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "CGGATGGTGCGGAATCGTCATAACGAGGCA", "domains": [ {"helix": 6, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -561,7 +561,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "CATATATAGTTTGACCATTAGACATTTTTG", "domains": [ {"helix": 8, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -570,7 +570,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "CTGTAGCAGCTATTTTTGAGAGAGAACCCT", "domains": [ {"helix": 10, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -579,7 +579,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "GGTCGACTGCCAGTTTGAGGGGTGGCCTTC", "domains": [ {"helix": 12, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -588,7 +588,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "TCGGCAAGGGTGCCTAATGAGTTGCCTGCA", "domains": [ {"helix": 14, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -597,7 +597,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "TTCTTAAACAGCTTGATACCGATAAGGACTAA", "domains": [ {"helix": 0, "forward": false, "start": 96, "end": 120}, @@ -605,7 +605,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "AGACTTTTAGACGGTCAATCATAATGCCCTGA", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -614,7 +614,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "CGAGAAACAACGCCAAAAGGAATTAATATTCA", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -623,7 +623,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "TTGAATCCCCTTTTGATAAGAGGTTACATTTC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 112}, @@ -632,7 +632,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "GCAAATGGAAGGATAAAAATTTTTATCTACAA", "domains": [ {"helix": 7, "forward": true, "start": 104, "end": 112}, @@ -641,7 +641,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "AGGCTATCAAAAATAATTCGCGTCACGACGAC", "domains": [ {"helix": 9, "forward": true, "start": 104, "end": 112}, @@ -650,7 +650,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "AGTATCGGCAGTGCCAAGCTTGCAGAGCTAAC", "domains": [ {"helix": 11, "forward": true, "start": 104, "end": 112}, @@ -659,7 +659,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "TCACATTATCCTGTTTGATGGTGGACCATCAC", "domains": [ {"helix": 13, "forward": true, "start": 104, "end": 112}, @@ -668,7 +668,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "CCAAATCAAGTTTTTTGGGGTCGACCCCAGCA", "domains": [ {"helix": 15, "forward": true, "start": 104, "end": 128}, @@ -676,7 +676,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "CGAGGCGCTCATGAGGAAGTTTCCAGGTGAAT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -685,7 +685,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "AGATACATACCAGAACGAGTAGTAAGCCGGAA", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -694,7 +694,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "TAATTGCTCCCTCAAATGCTTTAAACTAATGC", "domains": [ {"helix": 6, "forward": false, "start": 112, "end": 120}, @@ -703,7 +703,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "TTCAACGCTCAATAACCTGTTTAGAGTACCTT", "domains": [ {"helix": 8, "forward": false, "start": 112, "end": 120}, @@ -712,7 +712,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "ACGCCATCAGGTCATTGCCTGAGAGCCTTTAT", "domains": [ {"helix": 10, "forward": false, "start": 112, "end": 120}, @@ -721,7 +721,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "ACGACGGCCCTCAGGAAGATCGCACAATAGGA", "domains": [ {"helix": 12, "forward": false, "start": 112, "end": 120}, @@ -730,7 +730,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "GGCGAAAAATTGCGTTGCGCTCACGTTGTAAA", "domains": [ {"helix": 14, "forward": false, "start": 112, "end": 120}, @@ -739,7 +739,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "ATCGGTTTATCAGCTTGCTTTCGATTAAAC", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -747,7 +747,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "GGGTAAAATGCTCCATGTTACTTAATTGGG", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -756,7 +756,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "CTTGAGATGGAATACCACATTCAACAGTTC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -765,7 +765,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "AGAAAACGAGGTCAGGATTAGAGCTATATT", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 144}, @@ -774,7 +774,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "TTCATTTGACTTTTGCGGGAGAAGTCTGGA", "domains": [ {"helix": 7, "forward": true, "start": 136, "end": 144}, @@ -783,7 +783,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "GCAAACAAAGCTCATTTTTTAACCTCCAGC", "domains": [ {"helix": 9, "forward": true, "start": 136, "end": 144}, @@ -792,7 +792,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "CAGCTTTCTTTCCCAGTCACGACTGCCCGC", "domains": [ {"helix": 11, "forward": true, "start": 136, "end": 144}, @@ -801,7 +801,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "TTTCCAGTGTCCACGCTGGTTTGGGTGCCG", "domains": [ {"helix": 13, "forward": true, "start": 136, "end": 144}, @@ -810,7 +810,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "TAAAGCACTAAATCGGAACCCTAAAGAGTTGC", "domains": [ {"helix": 15, "forward": true, "start": 136, "end": 160}, @@ -818,7 +818,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "CCGCGACCTACGTAATGCCACTACTTAATTGT", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -827,7 +827,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "GAGATTTAGGTTTAATTTCAACTTGTCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, @@ -836,7 +836,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "ACTCCAACAGAATGACCATAAATCCATCAGTT", "domains": [ {"helix": 6, "forward": false, "start": 144, "end": 152}, @@ -845,7 +845,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "CCTGTAATGGGCGCGAGCTGAAAAGGAAGCAA", "domains": [ {"helix": 8, "forward": false, "start": 144, "end": 152}, @@ -854,7 +854,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "GTTAAATCGAGAATCGATGAACGGATTATGAC", "domains": [ {"helix": 10, "forward": false, "start": 144, "end": 152}, @@ -863,7 +863,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "GCCAGGGTCGGCACCGCTTCTGGTAAATTTTT", "domains": [ {"helix": 12, "forward": false, "start": 144, "end": 152}, @@ -872,7 +872,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "AGCAAGCGCGGGAAACCTGTCGTGTGGGTAAC", "domains": [ {"helix": 14, "forward": false, "start": 144, "end": 152}, @@ -881,7 +881,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "AAAAAAGGCTCCAAAAGGAGCCTGAAGGCAC", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 184, "deletions": [177]}, @@ -889,7 +889,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "CAACCTAATCGCCTGATAAATTGTTAATCATT", "domains": [ {"helix": 1, "forward": true, "start": 168, "end": 176}, @@ -898,7 +898,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "GTGAATTATACAGGTAGAAAGATTAAAAATCA", "domains": [ {"helix": 3, "forward": true, "start": 168, "end": 176}, @@ -907,7 +907,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "GGTCTTTACAAAGCGAACCAGACCGGTGGCAT", "domains": [ {"helix": 5, "forward": true, "start": 168, "end": 176}, @@ -916,7 +916,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "CAATTCTACGGTTGTACCAAAAACTAATCGTA", "domains": [ {"helix": 7, "forward": true, "start": 168, "end": 176}, @@ -925,7 +925,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "AAACTAGCTGTTAAAATTCGCATTGCCGGAAA", "domains": [ {"helix": 9, "forward": true, "start": 168, "end": 176}, @@ -934,7 +934,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "CCAGGCAATGCAAGGCGATTAAGTCCAGCTGC", "domains": [ {"helix": 11, "forward": true, "start": 168, "end": 176}, @@ -943,7 +943,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "ATTAATGAACCGCCTGGCCCTGAGAGGGAGCC", "domains": [ {"helix": 13, "forward": true, "start": 168, "end": 176}, @@ -952,7 +952,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "CCCGATTTAGAGCTTGACGGGGAAGCTGATT", "domains": [ {"helix": 15, "forward": true, "start": 168, "end": 192, "deletions": [177]}, @@ -960,7 +960,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "TGTATCAAACGAAAGAGGCAAAATCTCCAA", "domains": [ {"helix": 2, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -969,7 +969,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "ACATTATCCTTATGCGATTTTACGGAGATT", "domains": [ {"helix": 4, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -978,7 +978,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "CGAGCTTCCCTGACTATTATAGACGGAACA", "domains": [ {"helix": 6, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -987,7 +987,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "GCTAAATCTAATAGTAGTAGCATTTTAATT", "domains": [ {"helix": 8, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -996,7 +996,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "AATATTTATGTCAATCATATGTAGCATAAA", "domains": [ {"helix": 10, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1005,7 +1005,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "GATGTGCAGCGCCATTCGCCATTAAACGTT", "domains": [ {"helix": 12, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1014,7 +1014,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "GCCCTTCATCGGCCAACGCGCGGAAAGGGG", "domains": [ {"helix": 14, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1023,7 +1023,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "AATAATAATTTTTTCACGTTGAAAAGAATACA", "domains": [ {"helix": 0, "forward": false, "start": 192, "end": 216}, @@ -1031,7 +1031,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "CTAAAACAGCGAAACAAAGTACAAAGAACTGG", "domains": [ {"helix": 1, "forward": true, "start": 200, "end": 208}, @@ -1040,7 +1040,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "CTCATTATTTAATAAAACGAACTATCAGAAGC", "domains": [ {"helix": 3, "forward": true, "start": 200, "end": 208}, @@ -1049,7 +1049,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "AAAGCGGAGACTTCAAATATCGCGTTAACATC", "domains": [ {"helix": 5, "forward": true, "start": 200, "end": 208}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "CAATAAATAGCAATAAAGCCTCAGACCCCGGT", "domains": [ {"helix": 7, "forward": true, "start": 200, "end": 208}, @@ -1067,7 +1067,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "TGATAATCGCAAATATTTAAATTGTCAGGCTG", "domains": [ {"helix": 9, "forward": true, "start": 200, "end": 208}, @@ -1076,7 +1076,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "CGCAACTGTATTACGCCAGCTGGCGGGAGAGG", "domains": [ {"helix": 11, "forward": true, "start": 200, "end": 208}, @@ -1085,7 +1085,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "CGGTTTGCCAGTGAGACGGGCAACAAGCCGGC", "domains": [ {"helix": 13, "forward": true, "start": 200, "end": 208}, @@ -1094,7 +1094,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "GCTGAACCTCAAATATCAAACCCTGAACCTAC", "domains": [ {"helix": 15, "forward": true, "start": 232, "end": 256}, @@ -1102,7 +1102,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "AAGTATTAGGATTAGCGGGGTTTTGCGGAGTG", "domains": [ {"helix": 2, "forward": false, "start": 240, "end": 248}, @@ -1111,7 +1111,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "CCCTTATTACCGGAACCAGAGCCAAAACATGA", "domains": [ {"helix": 4, "forward": false, "start": 240, "end": 248}, @@ -1120,7 +1120,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "CTTATTACACATAAAGGTGGCAACTCATAGCC", "domains": [ {"helix": 6, "forward": false, "start": 240, "end": 248}, @@ -1129,7 +1129,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "CGCTAACGACAAAATAAACAGCCATAAGACTC", "domains": [ {"helix": 8, "forward": false, "start": 240, "end": 248}, @@ -1138,7 +1138,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "AAAGTAATTTCAGCTAATGCAGAACTTACCAA", "domains": [ {"helix": 10, "forward": false, "start": 240, "end": 248}, @@ -1147,7 +1147,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "TTTATCAACCTCCGGCTTAGGTTGCAAAAGGT", "domains": [ {"helix": 12, "forward": false, "start": 240, "end": 248}, @@ -1156,7 +1156,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "CATATCAAAATTGCGTAGATTTTCATAGTGAA", "domains": [ {"helix": 14, "forward": false, "start": 240, "end": 248}, @@ -1165,7 +1165,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "CTAAACAACTTTCAACAGTTTCAGCTCAGTA", "domains": [ {"helix": 0, "forward": false, "start": 256, "end": 280, "deletions": [273]}, @@ -1173,7 +1173,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "CCAGGCGGGGAACCTATTATTCTGCCACCGGA", "domains": [ {"helix": 1, "forward": true, "start": 264, "end": 272}, @@ -1182,7 +1182,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "ACCGCCTCTCATCGGCATTTTCGGATATAAAA", "domains": [ {"helix": 3, "forward": true, "start": 264, "end": 272}, @@ -1191,7 +1191,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "GAAACGCAAAAGAACTGGCATGATTATTATTT", "domains": [ {"helix": 5, "forward": true, "start": 264, "end": 272}, @@ -1200,7 +1200,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "ATCCCAATCAATTTTATCCTGAATCGCGCCTG", "domains": [ {"helix": 7, "forward": true, "start": 264, "end": 272}, @@ -1209,7 +1209,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "TTTATCAAGAATATAAAGTACCGAGGTTATAT", "domains": [ {"helix": 9, "forward": true, "start": 264, "end": 272}, @@ -1218,7 +1218,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "AACTATATACGCTGAGAAGAGTCAAGGTTTAA", "domains": [ {"helix": 11, "forward": true, "start": 264, "end": 272}, @@ -1227,7 +1227,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "CGTCAGATAATAATGGAAGGGTTACAATCAAT", "domains": [ {"helix": 13, "forward": true, "start": 264, "end": 272}, @@ -1236,7 +1236,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "ATCTGGTCAGTTGGCAAATCAACTGGATTAT", "domains": [ {"helix": 15, "forward": true, "start": 264, "end": 288, "deletions": [273]}, @@ -1244,7 +1244,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "CTATTTCATAAGTGCCGTCGAGGGATTTTG", "domains": [ {"helix": 2, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1253,7 +1253,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "CGCGTTTCCTCAGAGCCGCCACCCCCCTGC", "domains": [ {"helix": 4, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1262,7 +1262,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "ATACCCAAAGACACCACGGAATGACTGTAG", "domains": [ {"helix": 6, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1271,7 +1271,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "CCAGCTACCAAATAAGAAACGAATAACGGA", "domains": [ {"helix": 8, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1280,7 +1280,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "AATAAGACAATAGATAAGTCCTTTTTGCAC", "domains": [ {"helix": 10, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1289,7 +1289,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "GATTAAGGTAAATGCTGATGCAGAGCCAGT", "domains": [ {"helix": 12, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1298,7 +1298,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "ACTTCTGGAATATACAGTAACAATAGCTTA", "domains": [ {"helix": 14, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1307,7 +1307,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "GTTAGTAAATGAATTTTCTGTATGAGGGTTGA", "domains": [ {"helix": 0, "forward": false, "start": 288, "end": 312}, @@ -1315,7 +1315,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "TATAAGTAGTATAAACAGTTAATGCCTCAGAA", "domains": [ {"helix": 1, "forward": true, "start": 296, "end": 304}, @@ -1324,7 +1324,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "CCGCCACCTTTGCCTTTAGCGTCAAAGTTTAT", "domains": [ {"helix": 3, "forward": true, "start": 296, "end": 304}, @@ -1333,7 +1333,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "TTTGTCACCCGAGGAAACGCAATATTTTTTGT", "domains": [ {"helix": 5, "forward": true, "start": 296, "end": 304}, @@ -1342,7 +1342,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "TTAACGTCTCAAGATTAGTTGCTAGAACAAGA", "domains": [ {"helix": 7, "forward": true, "start": 296, "end": 304}, @@ -1351,7 +1351,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "AAAATAATAGGCAGAGGCATTTTCAATCCAAT", "domains": [ {"helix": 9, "forward": true, "start": 296, "end": 304}, @@ -1360,7 +1360,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "CGCAAGACCCTTGAAAACATAGCGGTACCTTT", "domains": [ {"helix": 11, "forward": true, "start": 296, "end": 304}, @@ -1369,7 +1369,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "TACATCGGTATAATCCTGATTGTTAGTTGAAA", "domains": [ {"helix": 13, "forward": true, "start": 296, "end": 304}, @@ -1378,7 +1378,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "GGAATTGAGGAAGGTTATCTAAAAGATGGCAA", "domains": [ {"helix": 15, "forward": true, "start": 296, "end": 320}, @@ -1386,7 +1386,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "CAGTGCCCTAGCCCGGAATAGGTGTTCCAGAC", "domains": [ {"helix": 2, "forward": false, "start": 304, "end": 312}, @@ -1395,7 +1395,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "GAATCAAGCTCAGAGCCACCACCCTTGAGTAA", "domains": [ {"helix": 4, "forward": false, "start": 304, "end": 312}, @@ -1404,7 +1404,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "GAAGGAAAAATCAATAGAAAATTCTAGCGACA", "domains": [ {"helix": 6, "forward": false, "start": 304, "end": 312}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "GCCTTAAAAAAAATGAAAATAGCAAGTTACCA", "domains": [ {"helix": 8, "forward": false, "start": 304, "end": 312}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "TGTAATTTATCCCATCCTAATTTAGTTTTGAA", "domains": [ {"helix": 10, "forward": false, "start": 304, "end": 312}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "CTTAGAATAAAGAACGCGAGAAAACGCCAACA", "domains": [ {"helix": 12, "forward": false, "start": 304, "end": 312}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "TTCATCAAGAGAAACAATAACGGAAATTTTCC", "domains": [ {"helix": 14, "forward": false, "start": 304, "end": 312}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "AACGATCTAAAGTTTTGTCGTCTTATCACC", "domains": [ {"helix": 0, "forward": false, "start": 320, "end": 344, "deletions": [321]}, @@ -1457,7 +1457,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "GTACTCAGAACGGGGTCAGTGCCTCAGAGC", "domains": [ {"helix": 1, "forward": true, "start": 328, "end": 336}, @@ -1466,7 +1466,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "CGCCACCACAGCACCGTAATCAGATATGGT", "domains": [ {"helix": 3, "forward": true, "start": 328, "end": 336}, @@ -1475,7 +1475,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "TTACCAGCCAGATAGCCGAACAAGCCTTTA", "domains": [ {"helix": 5, "forward": true, "start": 328, "end": 336}, @@ -1484,7 +1484,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "CAGAGAGACCCGACTTGCGGGAGCGAGCAT", "domains": [ {"helix": 7, "forward": true, "start": 328, "end": 336}, @@ -1493,7 +1493,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "GTAGAAACCGCCATATTTAACAACTTTTTC", "domains": [ {"helix": 9, "forward": true, "start": 328, "end": 336}, @@ -1502,7 +1502,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "AAATATATTCGTCGCTATTAATTTTCGCCT", "domains": [ {"helix": 11, "forward": true, "start": 328, "end": 336}, @@ -1511,7 +1511,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "GATTGCTTTCCTGATTATCAGATTATCTTT", "domains": [ {"helix": 13, "forward": true, "start": 328, "end": 336}, @@ -1520,7 +1520,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "AGGAGCACTAACAACTAATAGATTGGAATTAT", "domains": [ {"helix": 15, "forward": true, "start": 328, "end": 352}, @@ -1528,7 +1528,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "TAAGTTTTGAGGTTTAGTACCGCCGTTAGCGT", "domains": [ {"helix": 2, "forward": false, "start": 336, "end": 344}, @@ -1537,7 +1537,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "ATCGATAGGAACCACCACCAGAGCACTGGTAA", "domains": [ {"helix": 4, "forward": false, "start": 336, "end": 344}, @@ -1546,7 +1546,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "AAAGTAAGGCCAAAGACAAAAGGGATGAAACC", "domains": [ {"helix": 6, "forward": false, "start": 336, "end": 344}, @@ -1555,7 +1555,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "GCGAACCTATAACATAAAAACAGGTTTTAAGA", "domains": [ {"helix": 8, "forward": false, "start": 336, "end": 344}, @@ -1564,7 +1564,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "TTGAGAATCAATCAATAATCGGCTGCGTTTTA", "domains": [ {"helix": 10, "forward": false, "start": 336, "end": 344}, @@ -1573,7 +1573,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "TCTGTAAATTTAGTTAATTTCATCGGGCTTAA", "domains": [ {"helix": 12, "forward": false, "start": 336, "end": 344}, @@ -1582,7 +1582,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "CATCATATTGAATACCAAGTTACAACCTTGCT", "domains": [ {"helix": 14, "forward": false, "start": 336, "end": 344}, @@ -1591,7 +1591,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "GCATTCCACAGACAGCCCTCATAACCCTCAG", "domains": [ {"helix": 0, "forward": false, "start": 352, "end": 376, "deletions": [369]}, @@ -1599,7 +1599,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "AACCGCCAGATGATACAGGAGTGTCGCCGCCA", "domains": [ {"helix": 1, "forward": true, "start": 360, "end": 368}, @@ -1608,7 +1608,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "GCATTGACGCCGGAAACGTCACCACGACATTC", "domains": [ {"helix": 3, "forward": true, "start": 360, "end": 368}, @@ -1617,7 +1617,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "AACCGATTATCTTACCGAAGCCCTGAAGCGCA", "domains": [ {"helix": 5, "forward": true, "start": 360, "end": 368}, @@ -1626,7 +1626,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "TTAGACGGATTCTAAGAACGCGAGGTCTTTCC", "domains": [ {"helix": 7, "forward": true, "start": 360, "end": 368}, @@ -1635,7 +1635,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "TTATCATTCCAACGCTCAACAGTATTCTGACC", "domains": [ {"helix": 9, "forward": true, "start": 360, "end": 368}, @@ -1644,7 +1644,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "TAAATTTATATATGTGAGTGAATAAAATCGCG", "domains": [ {"helix": 11, "forward": true, "start": 360, "end": 368}, @@ -1653,7 +1653,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "CAGAGGCGAACCACCAGAAGGAGCAGAGCCGT", "domains": [ {"helix": 13, "forward": true, "start": 360, "end": 368}, @@ -1662,7 +1662,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "CAATAGATAATACATTTGAGGATTTTGCGGA", "domains": [ {"helix": 15, "forward": true, "start": 360, "end": 384, "deletions": [369]}, @@ -1670,7 +1670,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "GGCTTTTCCCTCAGAACCGCCACGCCTGTA", "domains": [ {"helix": 2, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1679,7 +1679,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "TAGCAAGAGGAGGTTGAGGCAGTCATACAT", "domains": [ {"helix": 4, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1688,7 +1688,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "AATAGCTGAGGGAGGGAAGGTAATTACCAT", "domains": [ {"helix": 6, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1697,7 +1697,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "ATCCGGTGAGAATTAACTGAACGAAATAGC", "domains": [ {"helix": 8, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1706,7 +1706,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "TATAAAGCCAAGAACGGGTATTGAAGGCTT", "domains": [ {"helix": 10, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1715,7 +1715,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "AAATCAAATGGTTTGAAATACCCTTACCAG", "domains": [ {"helix": 12, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1724,7 +1724,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "ACAAAGAAATTATTCATTTCAACAGTACAT", "domains": [ {"helix": 14, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1733,7 +1733,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "TTTCGTCACCAGTACAAACTACAACCCTCAGA", "domains": [ {"helix": 0, "forward": false, "start": 384, "end": 408}, @@ -1741,7 +1741,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "GCCACCACACCGTTCCAGTAAGCGGTCAGACG", "domains": [ {"helix": 1, "forward": true, "start": 392, "end": 400}, @@ -1750,7 +1750,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "ATTGGCCTAATCACCAGTAGCACCAATATTGA", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 400}, @@ -1759,7 +1759,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "CGGAAATTAAGAGCAAGAAACAATACCCTGAA", "domains": [ {"helix": 5, "forward": true, "start": 392, "end": 400}, @@ -1768,7 +1768,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "CAAAGTCAAAGCAAATCAGATATAAAACCAAG", "domains": [ {"helix": 7, "forward": true, "start": 392, "end": 400}, @@ -1777,7 +1777,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "TACCGCACATGCGTTATACAAATTGACCGTGT", "domains": [ {"helix": 9, "forward": true, "start": 392, "end": 400}, @@ -1786,7 +1786,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "GATAAATACCTTTTTTAATGGAAATTACCTGA", "domains": [ {"helix": 11, "forward": true, "start": 392, "end": 400}, @@ -1795,7 +1795,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "GCAAAAGATGAGTAACATTATCATTTAGAAGT", "domains": [ {"helix": 13, "forward": true, "start": 392, "end": 400}, @@ -1804,7 +1804,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "ATTAGACTTTACAAACAATTCGACATTAATTT", "domains": [ {"helix": 15, "forward": true, "start": 392, "end": 416}, @@ -1812,7 +1812,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "CTGAATTTCCTCATTTTCAGGGATACACTGAG", "domains": [ {"helix": 2, "forward": false, "start": 400, "end": 408}, @@ -1821,7 +1821,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "GCCAGCAATGATATTCACAAACAACGCAGTCT", "domains": [ {"helix": 4, "forward": false, "start": 400, "end": 408}, @@ -1830,7 +1830,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "CCAATAATATTCATTAAAGGTGAAGAATTAGA", "domains": [ {"helix": 6, "forward": false, "start": 400, "end": 408}, @@ -1839,7 +1839,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "CCAATAGCGAGGGTAATTGAGCGCAGTTAAGC", "domains": [ {"helix": 8, "forward": false, "start": 400, "end": 408}, @@ -1848,7 +1848,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "AGTATCATTCATCGAGAACAAGCATACCGCGC", "domains": [ {"helix": 10, "forward": false, "start": 400, "end": 408}, @@ -1857,7 +1857,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "TTGAATTAAGGCGTTAAATAAGAAGCCTGTTT", "domains": [ {"helix": 12, "forward": false, "start": 400, "end": 408}, @@ -1866,7 +1866,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "TAAAAGTTAGATGATGAAACAAACAATTTCAT", "domains": [ {"helix": 14, "forward": false, "start": 400, "end": 408}, diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna index 933fa3c6..30a5f92e 100644 --- a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna @@ -17,7 +17,7 @@ "is_scaffold": true }, { - "color": "#320096", + "color": "#333333", "sequence": "GTTACGTTACGTTACGTTGTTACGTTACGTTAC", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, @@ -25,7 +25,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "ACGTTACGTTACGTTACCGTTACGTTACGTTACGTT", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, diff --git a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna index d9092bd5..a3f34eb8 100644 --- a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna +++ b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna @@ -29,7 +29,7 @@ "is_scaffold": true }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -37,7 +37,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -45,7 +45,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -53,7 +53,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 176}, @@ -61,7 +61,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", "domains": [ {"helix": 2, "forward": false, "start": 160, "end": 176}, @@ -69,7 +69,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", "domains": [ {"helix": 4, "forward": false, "start": 160, "end": 176}, @@ -77,14 +77,14 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", "domains": [ {"helix": 0, "forward": false, "start": 88, "end": 120} ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -92,7 +92,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -100,7 +100,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -108,7 +108,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -116,14 +116,14 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -140,7 +140,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -149,7 +149,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 64}, @@ -157,7 +157,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -166,7 +166,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -175,7 +175,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "AATGAATCGGCCAACGCGCGGGGAGTTGCAG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -183,7 +183,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "CAAGCGGTCCTGTTTGATGGTGGTACGTGGAC", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -192,7 +192,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "TCCAACGTTGGCCCACTACGTGAAAGCCGGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -201,7 +201,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "AGTATCGGCCTCAGGAAGATCGCAGTGCGGGC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 128}, @@ -209,7 +209,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -218,7 +218,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -227,7 +227,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -235,7 +235,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -244,7 +244,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "GCCAGGGTTGGGAAGGGCGATCGCTCCAGC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -253,7 +253,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "CAGCTTTCCGGCACCGCTTCTGGTCAGGCTGC", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 160}, @@ -261,7 +261,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "GTCGACTCACGAGCCGGAAGCATACTAACTCA", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -270,7 +270,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, From aa0e16d604ef52770b375501466046a975157119 Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 23 Jun 2020 18:24:03 -0700 Subject: [PATCH 09/30] updated docstrings --- scadnano/scadnano.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 154c9567..863efe9d 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1734,13 +1734,14 @@ def with_modification_internal(self, idx: int, mod: ModificationInternal, warn_o return self def with_color(self, color: Color) -> StrandBuilder: - """ Sets Strand being built to have given color. + :param color: color to set for Strand :return: self """ self.strand.set_color(color) + return self @dataclass From bfe6150de852e086d174dca71e1dcf8a8d262a82 Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 23 Jun 2020 19:48:59 -0700 Subject: [PATCH 10/30] cleaned up docstrings --- scadnano/scadnano.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 863efe9d..fbfbbda3 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1615,7 +1615,10 @@ class StrandBuilder: .. code-block:: Python - design.strand(0, 0).to(10).cross(1).to(5) + design.strand(0, 0).to(10).cross(1).to(5).with_modification_5p(mod.biotin_5p).as_scaffold() + + :any:`StrandBuilder` should generally not be created directly or manipulated in ways other than the kind + of method chaining described above, or else errors could result. """ def __init__(self, design: DNADesign, helix: int, offset: int): @@ -1647,8 +1650,8 @@ def loopout(self, helix: int, length: int, offset: int = None) -> StrandBuilder: :param length: length of :any:`Loopout` to add :return: self """ - self.current_helix = helix self.loopout_length = length + self.current_helix = helix if offset is not None: self.current_offset = offset return self From 7ef61cf901a59770808db3e32f528c7ab78e3cce Mon Sep 17 00:00:00 2001 From: David Doty Date: Wed, 24 Jun 2020 09:00:04 -0700 Subject: [PATCH 11/30] cleaned up some PEP warnings --- scadnano/scadnano.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index fbfbbda3..2b27dd68 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1648,6 +1648,8 @@ def loopout(self, helix: int, length: int, offset: int = None) -> StrandBuilder: :param helix: :any:`Helix` to crossover to :param length: length of :any:`Loopout` to add + :param offset: new offset on `helix`. If not specified, defaults to current offset. + (i.e., a "vertical" crossover) :return: self """ self.loopout_length = length @@ -1687,7 +1689,6 @@ def to(self, offset: int) -> StrandBuilder: self.design.append_domain(self.strand, domain) self.loopout_length = None else: - self.strand_created_already = True self.strand = Strand(domains=[domain]) self.design.add_strand(self.strand) @@ -1724,7 +1725,8 @@ def with_modification_3p(self, mod: Modification3Prime) -> StrandBuilder: self.strand.set_modification_3p(mod) return self - def with_modification_internal(self, idx: int, mod: ModificationInternal, warn_on_no_dna: bool ) -> StrandBuilder: + def with_modification_internal(self, idx: int, mod: ModificationInternal, + warn_on_no_dna: bool) -> StrandBuilder: """ Sets Strand being built to have given internal modification. @@ -4225,7 +4227,7 @@ def _ensure_strands_distinct_objects(self): f'{i} and {j} are the same object') -def _find_index_pair_same_object(elts: Union[List,Dict]) -> Optional[Tuple]: +def _find_index_pair_same_object(elts: Union[List, Dict]) -> Optional[Tuple]: # return pair of indices representing same object in elts, or None if they do not exist # input can be list or dict; if dict, returns pair of keys mapping to same object if isinstance(elts, list): From b10e6ee327adf7d473b318bb61347df366a0dca4 Mon Sep 17 00:00:00 2001 From: David Doty Date: Wed, 24 Jun 2020 14:09:37 -0700 Subject: [PATCH 12/30] closes #87 --- ...letions_insertions_mods_chained_methods.py | 29 ++ .../2_staple_2_helix_modifications.dna | 28 +- ...etions_insertions_mods_chained_methods.dna | 46 ++ ...ix_origami_deletions_insertions_no_seq.dna | 4 +- .../3_helix_deletions_insertions.dna | 20 +- examples/output_designs/4_helix_grid_none.dna | 2 +- ..._none_min_offset_position_x_nondefault.dna | 8 +- .../4_helix_min_offsets_nonzero.dna | 2 +- .../56_helix_origami_rectangle.dna | 448 +++++++++--------- .../64_helix_origami_rectangle.dna | 384 +++++++-------- .../6_helix_6_col_origami_rectangle.dna | 36 +- .../6_helix_bundle_honeycomb.dna | 344 +++++++------- .../6_helix_origami_rectangle.dna | 60 +-- ...origami_rectangle_helices_out_of_order.dna | 60 +-- examples/output_designs/hairpin.dna | 2 +- .../output_designs/idt-plates-explicit.dna | 416 ++++++++-------- .../output_designs/long_range_crossovers.dna | 48 +- .../output_designs/loopouts_all_types.dna | 2 +- .../many_helices_modifications.dna | 14 +- examples/output_designs/proposal.dna | 416 ++++++++-------- scadnano/scadnano.py | 63 ++- tests/scadnano_tests.py | 77 +++ ...st_16_helix_origami_rectangle_no_twist.dna | 416 ++++++++-------- ...e_2_helix_origami_deletions_insertions.dna | 4 +- .../test_6_helix_origami_rectangle.dna | 60 +-- 25 files changed, 1593 insertions(+), 1396 deletions(-) create mode 100644 examples/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.py create mode 100644 examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna diff --git a/examples/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.py b/examples/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.py new file mode 100644 index 00000000..8bddcd22 --- /dev/null +++ b/examples/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.py @@ -0,0 +1,29 @@ +import scadnano as sc +import modifications as mod + + +def main(): + # helices + helices = [sc.Helix(max_offset=48), sc.Helix(max_offset=48)] + + # whole design + design = sc.DNADesign(helices=helices, strands=[], grid=sc.square) + + design.strand(1, 8).to(24).cross(0).to(8) # left staple + design.strand(0, 40).to(24).cross(1).to(40).with_modification_5p(mod.biotin_5p) # right staple + design.strand(1, 24).to(8).cross(0).to(40).loopout(1, 3).to(24).as_scaffold() + + # deletions and insertions added to design are added to both strands on a helix + design.add_deletion(helix=1, offset=20) + design.add_insertion(helix=0, offset=14, length=1) + design.add_insertion(helix=0, offset=26, length=2) + + # also assigns complement to strands other than scaf bound to it + design.assign_dna(design.scaffold, 'AACGT' * 18) + + return design + + +if __name__ == '__main__': + design = main() + design.write_scadnano_file(directory='output_designs') diff --git a/examples/output_designs/2_staple_2_helix_modifications.dna b/examples/output_designs/2_staple_2_helix_modifications.dna index 09610211..72a00094 100644 --- a/examples/output_designs/2_staple_2_helix_modifications.dna +++ b/examples/output_designs/2_staple_2_helix_modifications.dna @@ -6,17 +6,23 @@ {"grid_position": [0, 1]} ], "modifications_in_design": { + "/iCy5/": { + "display_text": "Cy5", + "idt_text": "/iCy5/", + "display_connector": false, + "location": "internal" + }, "/5Cy5/": { "display_text": "Cy5", "idt_text": "/5Cy5/", "display_connector": false, "location": "5'" }, - "/3Bio/": { - "display_text": "B", - "idt_text": "/3Bio/", + "/iCy3/": { + "display_text": "Cy3", + "idt_text": "/iCy3/", "display_connector": false, - "location": "3'" + "location": "internal" }, "/iBiodT/": { "display_text": "B", @@ -25,12 +31,6 @@ "location": "internal", "allowed_bases": ["T"] }, - "/iCy5/": { - "display_text": "Cy5", - "idt_text": "/iCy5/", - "display_connector": false, - "location": "internal" - }, "/5Biosg/": { "display_text": "B", "idt_text": "/5Biosg/", @@ -43,11 +43,11 @@ "display_connector": false, "location": "3'" }, - "/iCy3/": { - "display_text": "Cy3", - "idt_text": "/iCy3/", + "/3Bio/": { + "display_text": "B", + "idt_text": "/3Bio/", "display_connector": false, - "location": "internal" + "location": "3'" } }, "strands": [ diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna new file mode 100644 index 00000000..e07fb076 --- /dev/null +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna @@ -0,0 +1,46 @@ +{ + "version": "0.9.1", + "grid": "square", + "helices": [ + {"max_offset": 48, "grid_position": [0, 0]}, + {"max_offset": 48, "grid_position": [0, 1]} + ], + "modifications_in_design": { + "/5Biosg/": { + "display_text": "B", + "idt_text": "/5Biosg/", + "display_connector": false, + "location": "5'" + } + }, + "strands": [ + { + "color": "#333333", + "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", + "domains": [ + {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} + ] + }, + { + "color": "#320096", + "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", + "domains": [ + {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, + {"helix": 1, "forward": true, "start": 24, "end": 40} + ], + "5prime_modification": "/5Biosg/" + }, + { + "color": "#0066cc", + "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", + "domains": [ + {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, + {"loopout": 3}, + {"helix": 1, "forward": false, "start": 24, "end": 40} + ], + "is_scaffold": true + } + ] +} \ No newline at end of file diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna index d774e313..42ad6256 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna @@ -17,14 +17,14 @@ "is_scaffold": true }, { - "color": "#333333", + "color": "#7300de", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, {"helix": 0, "forward": false, "start": 0, "end": 16, "deletions": [11, 12], "insertions": [[6, 1]]} ] }, { - "color": "#320096", + "color": "#aaaa00", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, {"helix": 1, "forward": true, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} diff --git a/examples/output_designs/3_helix_deletions_insertions.dna b/examples/output_designs/3_helix_deletions_insertions.dna index 62824fa1..ad5ae76e 100644 --- a/examples/output_designs/3_helix_deletions_insertions.dna +++ b/examples/output_designs/3_helix_deletions_insertions.dna @@ -19,7 +19,7 @@ "is_scaffold": true }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TTAGTTAGTTAGTTAGTTTAGTTAGTTAGTTAG", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, @@ -27,7 +27,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TTAGTTAGTTAGTTAGTAGTTAGTTAGTTAGTTAGT", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, @@ -35,53 +35,53 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AACTAACTAACTAACT", "domains": [ {"helix": 1, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GGTAGGTAGGTAGGTA", "domains": [ {"helix": 1, "forward": true, "start": 48, "end": 64} ] }, { - "color": "#007200", + "color": "#f74308", "domains": [ {"helix": 2, "forward": false, "start": 32, "end": 48} ] }, { - "color": "#cc0000", + "color": "#57bb00", "domains": [ {"helix": 2, "forward": true, "start": 16, "end": 32} ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AGTTAGTTAGTTAGTT", "domains": [ {"helix": 1, "forward": false, "start": 32, "end": 48} ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TACCTACCTACCTACC", "domains": [ {"helix": 1, "forward": false, "start": 48, "end": 64} ] }, { - "color": "#888888", + "color": "#320096", "domains": [ {"helix": 2, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#f7931e", + "color": "#888888", "domains": [ {"helix": 2, "forward": true, "start": 0, "end": 16} ] diff --git a/examples/output_designs/4_helix_grid_none.dna b/examples/output_designs/4_helix_grid_none.dna index 5165a279..18fb7f05 100644 --- a/examples/output_designs/4_helix_grid_none.dna +++ b/examples/output_designs/4_helix_grid_none.dna @@ -20,7 +20,7 @@ ], "strands": [ { - "color": "#32b86c", + "color": "#03b6a2", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 10} ] diff --git a/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna b/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna index f48c0f27..27b1c0f6 100644 --- a/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna +++ b/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna @@ -23,25 +23,25 @@ ], "strands": [ { - "color": "#333333", + "color": "#7300de", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#320096", + "color": "#aaaa00", "domains": [ {"helix": 1, "forward": true, "start": 8, "end": 16} ] }, { - "color": "#03b6a2", + "color": "#b8056c", "domains": [ {"helix": 2, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#7300de", + "color": "#007200", "domains": [ {"helix": 3, "forward": true, "start": 8, "end": 16} ] diff --git a/examples/output_designs/4_helix_min_offsets_nonzero.dna b/examples/output_designs/4_helix_min_offsets_nonzero.dna index 2989e9f5..1addab18 100644 --- a/examples/output_designs/4_helix_min_offsets_nonzero.dna +++ b/examples/output_designs/4_helix_min_offsets_nonzero.dna @@ -9,7 +9,7 @@ ], "strands": [ { - "color": "#aaaa00", + "color": "#cc0000", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 29} ] diff --git a/examples/output_designs/56_helix_origami_rectangle.dna b/examples/output_designs/56_helix_origami_rectangle.dna index 2afa7d30..205358d8 100644 --- a/examples/output_designs/56_helix_origami_rectangle.dna +++ b/examples/output_designs/56_helix_origami_rectangle.dna @@ -179,7 +179,7 @@ "is_scaffold": true }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AATAGAAAATTCATATTTATTTTGTCACAATC", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -187,7 +187,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GTAGCACCATTACCATGCCAGCAAAATCACCA", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -195,7 +195,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TCTTTTCATAATCAAATTATTAGCGTTTGCCA", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -203,7 +203,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GTCAGACGATTGGCCTCAGGAGGTTGAGGCAG", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, @@ -211,7 +211,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GTAACAGTGCCCGTATGGGGTCAGTGCCTTGA", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, @@ -219,7 +219,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TATAAGTATAGCCCGGCCGTCGAGAGGGTTGA", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, @@ -227,7 +227,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GTCACCAGTACAAACTCGTAACACTGAGTTTC", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, @@ -235,7 +235,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AAAGGAACAACTAAAGAGCGGAGTGAGAATAG", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, @@ -243,7 +243,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "ACAACCATCGCCCACGTGCGCCGACAATGACA", "domains": [ {"helix": 17, "forward": true, "start": 16, "end": 32}, @@ -251,7 +251,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GGAAGTTTCCATTAAAAAAGACTTTTTCATGA", "domains": [ {"helix": 19, "forward": true, "start": 16, "end": 32}, @@ -259,7 +259,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AAATTGTGTCGAAATCTGTATCATCGCCTGAT", "domains": [ {"helix": 21, "forward": true, "start": 16, "end": 32}, @@ -267,7 +267,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TGACAAGAACCGGATATCATCAAGAGTAATCT", "domains": [ {"helix": 23, "forward": true, "start": 16, "end": 32}, @@ -275,7 +275,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AGAACTGGCTCATTATACCTTATGCGATTTTA", "domains": [ {"helix": 25, "forward": true, "start": 16, "end": 32}, @@ -283,7 +283,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GAGGCATAGTAAGAGCCGCCAAAAGGAATTAC", "domains": [ {"helix": 27, "forward": true, "start": 16, "end": 32}, @@ -291,7 +291,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CATTGAATCCCCCTCAAATCGTCATAAATATT", "domains": [ {"helix": 29, "forward": true, "start": 16, "end": 32}, @@ -299,7 +299,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CGAGCTTCAAAGCGAAATATCGCGTTTTAATT", "domains": [ {"helix": 31, "forward": true, "start": 16, "end": 32}, @@ -307,7 +307,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AAGTACGGTGTCTGGATTTAAATATGCAACTA", "domains": [ {"helix": 33, "forward": true, "start": 16, "end": 32}, @@ -315,7 +315,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "ACTAATAGTAGTAGCAAGGTGGCATCAATTCT", "domains": [ {"helix": 35, "forward": true, "start": 16, "end": 32}, @@ -323,7 +323,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GGATAAAAATTTTTAGCTTTATTTCAACGCAA", "domains": [ {"helix": 37, "forward": true, "start": 16, "end": 32}, @@ -331,7 +331,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TTTTTGAGAGATCTACCCGGAGAGGGTAGCTA", "domains": [ {"helix": 39, "forward": true, "start": 16, "end": 32}, @@ -339,7 +339,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TTAAATTGTAAACGTTTTGTATAAGCAAATAT", "domains": [ {"helix": 41, "forward": true, "start": 16, "end": 32}, @@ -347,7 +347,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GATTCTCCGTGGGAACGAGTAACAACCCGTCG", "domains": [ {"helix": 43, "forward": true, "start": 16, "end": 32}, @@ -355,7 +355,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TGCCGGAAACCAGGCACCGGCACCGCTTCTGG", "domains": [ {"helix": 45, "forward": true, "start": 16, "end": 32}, @@ -363,7 +363,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TGTAAAACGACGGCCATTCCCAGTCACGACGT", "domains": [ {"helix": 47, "forward": true, "start": 16, "end": 32}, @@ -371,7 +371,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TGTAAAGCCTGGGGTGAGCCGGAAGCATAAAG", "domains": [ {"helix": 49, "forward": true, "start": 16, "end": 32}, @@ -379,7 +379,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CTTTTCACCAGTGAGACGCCAGGGTGGTTTTT", "domains": [ {"helix": 51, "forward": true, "start": 16, "end": 32}, @@ -387,7 +387,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CGAGATAGGGTTGAGTAATCAAAAGAATAGCC", "domains": [ {"helix": 53, "forward": true, "start": 16, "end": 32}, @@ -395,7 +395,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CTAAATCGGAACCCTAGAGGTGCCGTAAAGCA", "domains": [ {"helix": 55, "forward": true, "start": 16, "end": 32}, @@ -403,7 +403,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AAGAACTGGCATGATTATAACGGAATACCCAA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 144}, @@ -411,7 +411,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TATCTTACCGAAGCCCATGAAATAGCAATAGC", "domains": [ {"helix": 2, "forward": false, "start": 128, "end": 144}, @@ -419,7 +419,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GTCAGAGGGTAATTGAGAACACCCTGAACAAA", "domains": [ {"helix": 4, "forward": false, "start": 128, "end": 144}, @@ -427,7 +427,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AACGTCAAAAATGAAAAAACGATTTTTTGTTT", "domains": [ {"helix": 6, "forward": false, "start": 128, "end": 144}, @@ -435,7 +435,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ACGCTAACGAGCGTCTATCCTGAATCTTACCA", "domains": [ {"helix": 8, "forward": false, "start": 128, "end": 144}, @@ -443,7 +443,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TTAGCGAACCTCCCGAAAGAACGCGAGGCGTT", "domains": [ {"helix": 10, "forward": false, "start": 128, "end": 144}, @@ -451,7 +451,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "CCGTTTTTATTTTCATATCGAGAACAAGCAAG", "domains": [ {"helix": 12, "forward": false, "start": 128, "end": 144}, @@ -459,7 +459,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CGAGCATGTAGAAACCATCCCATCCTAATTTA", "domains": [ {"helix": 14, "forward": false, "start": 128, "end": 144}, @@ -467,7 +467,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CGACAATAAACAACATAATTCTGTCCAGACGA", "domains": [ {"helix": 16, "forward": false, "start": 128, "end": 144}, @@ -475,7 +475,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ACAACGCCAACATGTAAGAATCGCCATATTTA", "domains": [ {"helix": 18, "forward": false, "start": 128, "end": 144}, @@ -483,7 +483,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GAAAAAGCCTGTTTAGGGAATCATAATTACTA", "domains": [ {"helix": 20, "forward": false, "start": 128, "end": 144}, @@ -491,7 +491,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AATTTCATCTTCTGACCAAATATATTTTAGTT", "domains": [ {"helix": 22, "forward": false, "start": 128, "end": 144}, @@ -499,7 +499,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GGCTTAGGTTGGGTTATACCTTTTTAACCTCC", "domains": [ {"helix": 24, "forward": false, "start": 128, "end": 144}, @@ -507,7 +507,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TTGAAAACATAGCGATTTTTCCCTTAGAATCC", "domains": [ {"helix": 26, "forward": false, "start": 128, "end": 144}, @@ -515,7 +515,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CCTTTTTTAATGGAAAAATTTCATTTGAATTA", "domains": [ {"helix": 28, "forward": false, "start": 128, "end": 144}, @@ -523,7 +523,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GCGAATTATTCATTTCACAAAATCGCGCAGAG", "domains": [ {"helix": 30, "forward": false, "start": 128, "end": 144}, @@ -531,7 +531,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CAGATGAATATACAGTTTTTCAGGTTTAACGT", "domains": [ {"helix": 32, "forward": false, "start": 128, "end": 144}, @@ -539,7 +539,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ACTTCTGAATAATGGATGATTGTTTGGATTAT", "domains": [ {"helix": 34, "forward": false, "start": 128, "end": 144}, @@ -547,7 +547,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GAACAAAGAAACCACCACATTATCATTTTGCG", "domains": [ {"helix": 36, "forward": false, "start": 128, "end": 144}, @@ -555,7 +555,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AAGTATTAGACTTTACACATTTGAGGATTTAG", "domains": [ {"helix": 38, "forward": false, "start": 128, "end": 144}, @@ -563,7 +563,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TTGAAAGGAATTGAGGGTTGGCAAATCAACAG", "domains": [ {"helix": 40, "forward": false, "start": 128, "end": 144}, @@ -571,7 +571,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GAGAGCCAGCAGCAAAGCAACAGTGCCACGCT", "domains": [ {"helix": 42, "forward": false, "start": 128, "end": 144}, @@ -579,7 +579,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AAACATCGCCATTAAACGAACTGATAGCCCTA", "domains": [ {"helix": 44, "forward": false, "start": 128, "end": 144}, @@ -587,7 +587,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AGATAGAACCCTTCTGACATTCTGGCCAACAG", "domains": [ {"helix": 46, "forward": false, "start": 128, "end": 144}, @@ -595,7 +595,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CTACATTTTGACGCTCACGCTCATGGAAATAC", "domains": [ {"helix": 48, "forward": false, "start": 128, "end": 144}, @@ -603,7 +603,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CCTGAGTAGAAGAACTGTAATAACATCACTTG", "domains": [ {"helix": 50, "forward": false, "start": 128, "end": 144}, @@ -611,7 +611,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TTTTATAATCAGTGAGGAATCCTGAGAAGTGT", "domains": [ {"helix": 52, "forward": false, "start": 128, "end": 144}, @@ -619,7 +619,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ACGTGCTTTCCTCGTTTTGACGAGCACGTATA", "domains": [ {"helix": 54, "forward": false, "start": 128, "end": 144}, @@ -627,14 +627,14 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TTATTACGCAGTATGTTAGCAAACGTAGAAAA", "domains": [ {"helix": 0, "forward": false, "start": 88, "end": 120} ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TTATTCATAGGGAAGGTAAATATTAGTTACCA", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88}, @@ -642,7 +642,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GAAGGAAAGCAGATAGCCGAACAAGACGGAAA", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -650,7 +650,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TGCCTTTAAATCAGTAGCGACAGATGAGTTAA", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88}, @@ -658,7 +658,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GCCCAATAGATAACCCACAAGAATATCAAGTT", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -666,7 +666,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GCCACCACACCCTCAGAACCGCCAACAGGGAA", "domains": [ {"helix": 6, "forward": false, "start": 80, "end": 88}, @@ -674,7 +674,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GCGCATTAAGAGAATAACATAAAACCCTCAGA", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 112}, @@ -682,7 +682,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TAAGCGTCCAGTCTCTGAATTTACACAGCCAT", "domains": [ {"helix": 8, "forward": false, "start": 80, "end": 88}, @@ -690,7 +690,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ATTATTTAGCCAGTTACAAAATAACGTTCCAG", "domains": [ {"helix": 7, "forward": true, "start": 104, "end": 112}, @@ -698,7 +698,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CCTCAAGATGAAAGTATTAAGAGGTTAGTTGC", "domains": [ {"helix": 10, "forward": false, "start": 80, "end": 88}, @@ -706,7 +706,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TATTTTGCAAGCCTTAAATCAAGACTGAGACT", "domains": [ {"helix": 9, "forward": true, "start": 104, "end": 112}, @@ -714,7 +714,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CTCAGAGCACCGCCACCCTCAGAAAAATCAGA", "domains": [ {"helix": 12, "forward": false, "start": 80, "end": 88}, @@ -722,7 +722,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TATAGAAGGCGCCCAATAGCAAGCCCGCCACC", "domains": [ {"helix": 11, "forward": true, "start": 104, "end": 112}, @@ -730,7 +730,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ACGTTAGTTCTAAAGTTTTGTCGTCAAGAACG", "domains": [ {"helix": 14, "forward": false, "start": 80, "end": 88}, @@ -738,7 +738,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GGTATTAATCTTTCCTTATCATTCCTTTCCAG", "domains": [ {"helix": 13, "forward": true, "start": 104, "end": 112}, @@ -746,7 +746,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TCGGTTTACTCCAAAAGGAGCCTTACAATAGA", "domains": [ {"helix": 16, "forward": false, "start": 80, "end": 88}, @@ -754,7 +754,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TAAGTCCTACGCGCCTGTTTATCATAATTGTA", "domains": [ {"helix": 15, "forward": true, "start": 104, "end": 112}, @@ -762,7 +762,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CAGCGAAACTTTTGCGGGATCGTCAGAGAATA", "domains": [ {"helix": 18, "forward": false, "start": 80, "end": 88}, @@ -770,7 +770,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TAAAGTACTTTCGAGCCAGTAATAACCCTCAG", "domains": [ {"helix": 17, "forward": true, "start": 104, "end": 112}, @@ -778,7 +778,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CTCATCTTGAGGCAAAAGAATACATAAAGCCA", "domains": [ {"helix": 20, "forward": false, "start": 80, "end": 88}, @@ -786,7 +786,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "ACGCTCAACAAATTCTTACCAGTACTAAAACA", "domains": [ {"helix": 19, "forward": true, "start": 104, "end": 112}, @@ -794,7 +794,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CTTTGAAATCATAAGGGAACCGAAGATAAATA", "domains": [ {"helix": 22, "forward": false, "start": 80, "end": 88}, @@ -802,7 +802,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AGGCGTTAGAAATACCGACCGTGTCTGACCAA", "domains": [ {"helix": 21, "forward": true, "start": 104, "end": 112}, @@ -810,7 +810,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "ACGAGTAGCTTGCCCTGACGAGAAATCGCAAG", "domains": [ {"helix": 24, "forward": false, "start": 80, "end": 88}, @@ -818,7 +818,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "ACAAAGAATGCTGATGCAAATCCAACACCAGA", "domains": [ {"helix": 23, "forward": true, "start": 104, "end": 112}, @@ -826,7 +826,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AAAGATTCACGGAACAACATTATTGTGAATTT", "domains": [ {"helix": 26, "forward": false, "start": 80, "end": 88}, @@ -834,7 +834,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ATCAAAATCTGAGAAGAGTCAATAACAGGTAG", "domains": [ {"helix": 25, "forward": true, "start": 104, "end": 112}, @@ -842,7 +842,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TTTGCCAGGCGAGAGGCTTTTGCACCTTGCTT", "domains": [ {"helix": 28, "forward": false, "start": 80, "end": 88}, @@ -850,7 +850,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CTGTAAATATATGTGAGTGAATAAAAAGAAGT", "domains": [ {"helix": 27, "forward": true, "start": 104, "end": 112}, @@ -858,7 +858,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TCAGAAGCAGGTCTTTACCCTGACACATCAAG", "domains": [ {"helix": 30, "forward": false, "start": 80, "end": 88}, @@ -866,7 +866,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AAAACAAAGAAGATGATGAAACAATATTATAG", "domains": [ {"helix": 29, "forward": true, "start": 104, "end": 112}, @@ -874,7 +874,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TTTTTGCGATTGCTCCTTTTGATACGGATTCG", "domains": [ {"helix": 32, "forward": false, "start": 80, "end": 88}, @@ -882,7 +882,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CCTGATTGTCGGGAGAAACAATAAAGAGGTCA", "domains": [ {"helix": 31, "forward": true, "start": 104, "end": 112}, @@ -890,7 +890,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TCGCAAATTTTAGTTTGACCATTACACGTAAA", "domains": [ {"helix": 34, "forward": false, "start": 80, "end": 88}, @@ -898,7 +898,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ACAGAAATATATCAAAATTATTTGGATACATT", "domains": [ {"helix": 33, "forward": true, "start": 104, "end": 112}, @@ -906,7 +906,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GCTAAATCAGCAATAAAGCCTCAGTATCAGAT", "domains": [ {"helix": 36, "forward": false, "start": 80, "end": 88}, @@ -914,7 +914,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GATGGCAATCATCATATTCCTGATAGCATAAA", "domains": [ {"helix": 35, "forward": true, "start": 104, "end": 112}, @@ -922,7 +922,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AGACAGTCATTCAAAAGGGTGAGACCCGAACG", "domains": [ {"helix": 38, "forward": false, "start": 80, "end": 88}, @@ -930,7 +930,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TTATTAATCGTATTAAATCCTTTGAAGGCCGG", "domains": [ {"helix": 37, "forward": true, "start": 104, "end": 112}, @@ -938,7 +938,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CATGTCAAGATGAACGGTAATCGTCAACTAAT", "domains": [ {"helix": 40, "forward": false, "start": 80, "end": 88}, @@ -946,7 +946,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AGATTAGATCTTTAGGAGCACTAAAAAACTAG", "domains": [ {"helix": 39, "forward": true, "start": 104, "end": 112}, @@ -954,7 +954,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AAATAATTTTTAACCAATAGGAACCAAATATC", "domains": [ {"helix": 42, "forward": false, "start": 80, "end": 88}, @@ -962,7 +962,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AAACCCTCTCACCTTGCTGAACCTGCCATCAA", "domains": [ {"helix": 41, "forward": true, "start": 104, "end": 112}, @@ -970,7 +970,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GTTTGAGGCGCATCGTAACCGTGCCAGAGGTG", "domains": [ {"helix": 44, "forward": false, "start": 80, "end": 88}, @@ -978,7 +978,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AGGCGGTCCCAGCAGAAGATAAAAATCTGCCA", "domains": [ {"helix": 43, "forward": true, "start": 104, "end": 112}, @@ -986,7 +986,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CAGCTGGCGTGCGGGCCTCTTCGCATATTTTT", "domains": [ {"helix": 46, "forward": false, "start": 80, "end": 88}, @@ -994,7 +994,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GAATGGCTATACGTGGCACAGACATATTACGC", "domains": [ {"helix": 45, "forward": true, "start": 104, "end": 112}, @@ -1002,7 +1002,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TCATAGCTCCGAGCTCGAATTCGTATTCACCA", "domains": [ {"helix": 48, "forward": false, "start": 80, "end": 88}, @@ -1010,7 +1010,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GTCACACGTTATTTACATTGGCAGAATCATGG", "domains": [ {"helix": 47, "forward": true, "start": 104, "end": 112}, @@ -1018,7 +1018,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GCCAGCTGCTTTCCAGTCGGGAAACAATATTA", "domains": [ {"helix": 50, "forward": false, "start": 80, "end": 88}, @@ -1026,7 +1026,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CCGCCAGCCTGGTAATATCCAGAACCTGTCGT", "domains": [ {"helix": 49, "forward": true, "start": 104, "end": 112}, @@ -1034,7 +1034,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CCAGCAGGGCAAGCGGTCCACGCTAATTAACC", "domains": [ {"helix": 52, "forward": false, "start": 80, "end": 88}, @@ -1042,7 +1042,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GTTGTAGCGTCTGTCCATCACGCAGGTTTGCC", "domains": [ {"helix": 51, "forward": true, "start": 104, "end": 112}, @@ -1050,7 +1050,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TATCAGGGAACGTCAAAGGGCGAATTAAAGGG", "domains": [ {"helix": 54, "forward": false, "start": 80, "end": 88}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "ATTTTAGACTAAACAGGAGGCCGAAAACCGTC", "domains": [ {"helix": 53, "forward": true, "start": 104, "end": 112}, @@ -1066,14 +1066,14 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GAACGTGGCGAGAAAGGAAGGGAATGCGCCGC", "domains": [ {"helix": 55, "forward": true, "start": 72, "end": 104} ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "ACGCAAAGACACCACGGAATAAGTGGTTTACC", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56}, @@ -1081,7 +1081,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AGCGCCAACCATTTGGGAATTAGATAGCAAGG", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -1090,7 +1090,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CCGGAAACTTCGGTCATAGCCCCCATCACCGG", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -1099,7 +1099,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AACCAGAGCCGCCGCCAGCATTGATGATATTC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 48}, @@ -1108,7 +1108,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ACAAACAAGGTAATAAGTTTTAACAAACAGTT", "domains": [ {"helix": 7, "forward": true, "start": 40, "end": 48}, @@ -1117,7 +1117,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AATGCCCCACCAGGCGGATAAGTGAATAGGTG", "domains": [ {"helix": 9, "forward": true, "start": 40, "end": 48}, @@ -1126,7 +1126,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TATCACCGATAGGAACCCATGTACACAACGCC", "domains": [ {"helix": 11, "forward": true, "start": 40, "end": 48}, @@ -1135,7 +1135,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TGTAGCATAACTTTCAACAGTTTCGAATTGCG", "domains": [ {"helix": 13, "forward": true, "start": 40, "end": 48}, @@ -1144,7 +1144,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AATAATAAGCTTGATACCGATAGTCATAACCG", "domains": [ {"helix": 15, "forward": true, "start": 40, "end": 48}, @@ -1153,7 +1153,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "ATATATTCAGAGGCTTTGAGGACTCGGGTAAA", "domains": [ {"helix": 17, "forward": true, "start": 40, "end": 48}, @@ -1162,7 +1162,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "ATACGTAAAAGTACAACGGAGATTCGCGACCT", "domains": [ {"helix": 19, "forward": true, "start": 40, "end": 48}, @@ -1171,7 +1171,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GCTCCATGATAGGCTGGCTGACCTTTCATTAC", "domains": [ {"helix": 21, "forward": true, "start": 40, "end": 48}, @@ -1180,7 +1180,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CCAAATCATTAATCATTGTGAATTACCAGTCA", "domains": [ {"helix": 23, "forward": true, "start": 40, "end": 48}, @@ -1189,7 +1189,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GGACGTTGTAATGCAGATACATAAAACACTAT", "domains": [ {"helix": 25, "forward": true, "start": 40, "end": 48}, @@ -1198,7 +1198,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CATAACCCGCGTCCAATACTGCGGAATGCTTT", "domains": [ {"helix": 27, "forward": true, "start": 40, "end": 48}, @@ -1207,7 +1207,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AAACAGTTGCCCGAAAGACTTCAACCAGACCG", "domains": [ {"helix": 29, "forward": true, "start": 40, "end": 48}, @@ -1216,7 +1216,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GAAGCAAACTGTAGCTCAACATGTAGTTTCAT", "domains": [ {"helix": 31, "forward": true, "start": 40, "end": 48}, @@ -1225,7 +1225,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TCCATATAGGGGCGCGAGCTGAAATTAACATC", "domains": [ {"helix": 33, "forward": true, "start": 40, "end": 48}, @@ -1234,7 +1234,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CAATAAATCTTTTGCGGGAGAAGCAACCCTCA", "domains": [ {"helix": 35, "forward": true, "start": 40, "end": 48}, @@ -1243,7 +1243,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TATATTTTAGCTGATAAATTAATGAAAGGCTA", "domains": [ {"helix": 37, "forward": true, "start": 40, "end": 48}, @@ -1252,7 +1252,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TCAGGTCACCCAAAAACAGGAAGAAATATTTT", "domains": [ {"helix": 39, "forward": true, "start": 40, "end": 48}, @@ -1261,7 +1261,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GTTAAAATAACATTAAATGTGAGCAAACGGCG", "domains": [ {"helix": 41, "forward": true, "start": 40, "end": 48}, @@ -1270,7 +1270,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GATTGACCCACTCCAGCCAGCTTTAAGCGCCA", "domains": [ {"helix": 43, "forward": true, "start": 40, "end": 48}, @@ -1279,7 +1279,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TTCGCCATGGGTAACGCCAGGGTTGTGCCAAG", "domains": [ {"helix": 45, "forward": true, "start": 40, "end": 48}, @@ -1288,7 +1288,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CTTGCATGTTCCACACAACATACGCCTAATGA", "domains": [ {"helix": 47, "forward": true, "start": 40, "end": 48}, @@ -1297,7 +1297,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GTGAGCTACGGTTTGCGTATTGGGCGGGCAAC", "domains": [ {"helix": 49, "forward": true, "start": 40, "end": 48}, @@ -1306,7 +1306,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AGCTGATTGGCAAAATCCCTTATAGTTGTTCC", "domains": [ {"helix": 51, "forward": true, "start": 40, "end": 48}, @@ -1315,7 +1315,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AGTTTGGACAAGTTTTTTGGGGTCAAGGGAGC", "domains": [ {"helix": 53, "forward": true, "start": 40, "end": 48}, @@ -1324,7 +1324,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CCCCGATTTAGAGCTTGACGGGGAGAACCATC", "domains": [ {"helix": 55, "forward": true, "start": 40, "end": 64}, @@ -1332,7 +1332,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GACTTGAGAGACAAAAGGGCGACATAAAAGAA", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -1341,7 +1341,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TCGGCATTGTCACCAATGAAACCACCGTCACC", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -1350,7 +1350,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CACCAGAGCCACCACCGGAACCGCCGTTTTCA", "domains": [ {"helix": 6, "forward": false, "start": 48, "end": 56}, @@ -1359,7 +1359,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AGTGTACTATAAATCCTCATTAAAAGAACCAC", "domains": [ {"helix": 8, "forward": false, "start": 48, "end": 56}, @@ -1368,7 +1368,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TGCTCAGTCTGCCTATTTCGGAACGATACAGG", "domains": [ {"helix": 10, "forward": false, "start": 48, "end": 56}, @@ -1377,7 +1377,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CAAGCCCATACTCAGGAGGTTTAGCGGGGTTT", "domains": [ {"helix": 12, "forward": false, "start": 48, "end": 56}, @@ -1386,7 +1386,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TGCTAAACTCCACAGACAGCCCTCAGGGATAG", "domains": [ {"helix": 14, "forward": false, "start": 48, "end": 56}, @@ -1395,7 +1395,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CTTAAACATTTTTTCACGTTGAAATGGGATTT", "domains": [ {"helix": 16, "forward": false, "start": 48, "end": 56}, @@ -1404,7 +1404,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ACGGCTACGGTCGCTGAGGCTTGCGTGAATTT", "domains": [ {"helix": 18, "forward": false, "start": 48, "end": 56}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GCGAAACATGCCACTACGAAGGCAGGGTAGCA", "domains": [ {"helix": 20, "forward": false, "start": 48, "end": 56}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "CCAGGCGCTTACTTAGCCGGAACGTACCAAGC", "domains": [ {"helix": 22, "forward": false, "start": 48, "end": 56}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TTTCAACTACGTAACAAAGCTGCTTGTACAGA", "domains": [ {"helix": 24, "forward": false, "start": 48, "end": 56}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CATTCAACGGAAGAAAAATCTACGTGGTTTAA", "domains": [ {"helix": 26, "forward": false, "start": 48, "end": 56}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ACTGGATATCGTTTACCAGACGACGAATACCA", "domains": [ {"helix": 28, "forward": false, "start": 48, "end": 56}, @@ -1458,7 +1458,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AAGAGGAACAGAAAACGAGAATGAATGTTTAG", "domains": [ {"helix": 30, "forward": false, "start": 48, "end": 56}, @@ -1467,7 +1467,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "ATATAATGCTCCAACAGGTCAGGAAAAAGATT", "domains": [ {"helix": 32, "forward": false, "start": 48, "end": 56}, @@ -1476,7 +1476,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TTTCATTTACAGTTGATTCCCAATATTGCTGA", "domains": [ {"helix": 34, "forward": false, "start": 48, "end": 56}, @@ -1485,7 +1485,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CTGTAATACATACAGGCAAGGCAAAGCTATAT", "domains": [ {"helix": 36, "forward": false, "start": 48, "end": 56}, @@ -1494,7 +1494,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ACCGTTCTAAATGCAATGCCTGAGTTATGACC", "domains": [ {"helix": 38, "forward": false, "start": 48, "end": 56}, @@ -1503,7 +1503,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AGAAAAGCTTGCCTGAGAGTCTGGGATATTCA", "domains": [ {"helix": 40, "forward": false, "start": 48, "end": 56}, @@ -1512,7 +1512,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CTTTCATCTCGCATTAAATTTTTGTGATAATC", "domains": [ {"helix": 42, "forward": false, "start": 48, "end": 56}, @@ -1521,7 +1521,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GAAGATCGGTAATGGGATAGGTCAGTAGCCAG", "domains": [ {"helix": 44, "forward": false, "start": 48, "end": 56}, @@ -1530,7 +1530,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "ATTAAGTTTCAGGCTGCGCAACTGGGCCTCAG", "domains": [ {"helix": 46, "forward": false, "start": 48, "end": 56}, @@ -1539,7 +1539,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GCTCACAACCTGCAGGTCGACTCTGCAAGGCG", "domains": [ {"helix": 48, "forward": false, "start": 48, "end": 56}, @@ -1548,7 +1548,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GGGAGAGGACTCACATTAATTGCGTGTTATCC", "domains": [ {"helix": 50, "forward": false, "start": 48, "end": 56}, @@ -1557,7 +1557,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CCGAAATCGCCCTTCACCGCCTGGAACGCGCG", "domains": [ {"helix": 52, "forward": false, "start": 48, "end": 56}, @@ -1566,7 +1566,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ACCCAAATACAAGAGTCCACTATTTGGTGGTT", "domains": [ {"helix": 54, "forward": false, "start": 48, "end": 56}, @@ -1575,7 +1575,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TACATACATAAAGGTGGCAACATATTCAACCG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88}, @@ -1583,7 +1583,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "ATTGAGGGTAAAGGTGAATTATCATCGATAGC", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -1592,7 +1592,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AGCACCGTGCGTCAGACTGTAGCGCTCCCTCA", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -1601,7 +1601,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GAGCCGCCCCTCAGAGCCGCCACCGCCAGAAT", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 80}, @@ -1610,7 +1610,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GGAAAGCGATACATGGCTTTTGATCTATTATT", "domains": [ {"helix": 7, "forward": true, "start": 72, "end": 80}, @@ -1619,7 +1619,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CTGAAACAGAAGGATTAGGATTAGTACCGCCA", "domains": [ {"helix": 9, "forward": true, "start": 72, "end": 80}, @@ -1628,7 +1628,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CCCTCAGACACCACCCTCATTTTCATAGTTAG", "domains": [ {"helix": 11, "forward": true, "start": 72, "end": 80}, @@ -1637,7 +1637,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CGTAACGAAAATGAATTTTCTGTAATCTCCAA", "domains": [ {"helix": 13, "forward": true, "start": 72, "end": 80}, @@ -1646,7 +1646,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AAAAAAGGTCAGCTTGCTTTCGAGAGGGAGTT", "domains": [ {"helix": 15, "forward": true, "start": 72, "end": 80}, @@ -1655,7 +1655,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AAAGGCCGGACAGCATCGGAACGACCAACCTA", "domains": [ {"helix": 17, "forward": true, "start": 72, "end": 80}, @@ -1664,7 +1664,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AAACGAAATGACCCCCAGCGATTAAGGCGCAG", "domains": [ {"helix": 19, "forward": true, "start": 72, "end": 80}, @@ -1673,7 +1673,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "ACGGTCAAGAGGACAGATGAACGGCATTCAGT", "domains": [ {"helix": 21, "forward": true, "start": 72, "end": 80}, @@ -1682,7 +1682,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GAATAAGGTAAATTGGGCTTGAGATTAATAAA", "domains": [ {"helix": 23, "forward": true, "start": 72, "end": 80}, @@ -1691,7 +1691,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ACGAACTAATCAGTTGAGATTTAGGATAAAAA", "domains": [ {"helix": 25, "forward": true, "start": 72, "end": 80}, @@ -1700,7 +1700,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CCAAAATAAGGGGGTAATAGTAAACCATAAAT", "domains": [ {"helix": 27, "forward": true, "start": 72, "end": 80}, @@ -1709,7 +1709,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CAAAAATCAAAGCGGATTGCATCATTAGAGAG", "domains": [ {"helix": 29, "forward": true, "start": 72, "end": 80}, @@ -1718,7 +1718,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TACCTTTAGATGGCTTAGAGCTTATCTGCGAA", "domains": [ {"helix": 31, "forward": true, "start": 72, "end": 80}, @@ -1727,7 +1727,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CGAGTAGAGGTCAATAACCTGTTTAGAATTAG", "domains": [ {"helix": 33, "forward": true, "start": 72, "end": 80}, @@ -1736,7 +1736,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CAAAATTAGGTTGTACCAAAAACATAATGTGT", "domains": [ {"helix": 35, "forward": true, "start": 72, "end": 80}, @@ -1745,7 +1745,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AGGTAAAGAAATCACCATCAATATAGCAAACA", "domains": [ {"helix": 37, "forward": true, "start": 72, "end": 80}, @@ -1754,7 +1754,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AGAGAATCTCATATGTACCCCGGTTTAAATCA", "domains": [ {"helix": 39, "forward": true, "start": 72, "end": 80}, @@ -1763,7 +1763,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GCTCATTTCGCGTCTGGCCTTCCTCGTTGGTG", "domains": [ {"helix": 41, "forward": true, "start": 72, "end": 80}, @@ -1772,7 +1772,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TAGATGGGGGACGACGACAGTATCTTGGGAAG", "domains": [ {"helix": 43, "forward": true, "start": 72, "end": 80}, @@ -1781,7 +1781,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GGCGATCGGAAAGGGGGATGTGCTAGAGGATC", "domains": [ {"helix": 45, "forward": true, "start": 72, "end": 80}, @@ -1790,7 +1790,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CCCGGGTAGTTTCCTGTGTGAAATTTGCGCTC", "domains": [ {"helix": 47, "forward": true, "start": 72, "end": 80}, @@ -1799,7 +1799,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ACTGCCCGCATTAATGAATCGGCCCCCTGAGA", "domains": [ {"helix": 49, "forward": true, "start": 72, "end": 80}, @@ -1808,7 +1808,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GAGTTGCACGAAAATCCTGTTTGAAAAGAACG", "domains": [ {"helix": 51, "forward": true, "start": 72, "end": 80}, @@ -1817,7 +1817,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TGGACTCCCGATGGCCCACTACGTAAGCCGGC", "domains": [ {"helix": 53, "forward": true, "start": 72, "end": 80}, @@ -1826,7 +1826,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TACAGGGCGCGTACTATGGTTGCTAGAATCAG", "domains": [ {"helix": 55, "forward": true, "start": 104, "end": 128}, @@ -1834,7 +1834,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AAAAGTAACCGAGGAAACGCAATAAAGACTCC", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -1843,7 +1843,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ATCAGAGAATAAGAGCAAGAAACATTTTTAAG", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -1852,7 +1852,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CTTTACAGGACGGGAGAATTAACTGCGCTAAT", "domains": [ {"helix": 6, "forward": false, "start": 112, "end": 120}, @@ -1861,7 +1861,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CCTAATTTTCCCAATCCAAATAAGATAGCAGC", "domains": [ {"helix": 8, "forward": false, "start": 112, "end": 120}, @@ -1870,7 +1870,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AGGTTTTGACCCAGCTACAATTTTTTCCAGAG", "domains": [ {"helix": 10, "forward": false, "start": 112, "end": 120}, @@ -1879,7 +1879,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TCATTACCGCTTATCCGGTATTCTCTTGCGGG", "domains": [ {"helix": 12, "forward": false, "start": 112, "end": 120}, @@ -1888,7 +1888,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "ATCGGCTGACCAAGTACCGCACTCCGTAGGAA", "domains": [ {"helix": 14, "forward": false, "start": 112, "end": 120}, @@ -1897,7 +1897,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AATGCAGAGAACAAGAAAAATAATAATCAATA", "domains": [ {"helix": 16, "forward": false, "start": 112, "end": 120}, @@ -1906,7 +1906,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AGAGGCATCGACAAAAGGTAAAGTGTTCAGCT", "domains": [ {"helix": 18, "forward": false, "start": 112, "end": 120}, @@ -1915,7 +1915,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GCGTTATACAGTAGGGCTTAATTGATTTAGGC", "domains": [ {"helix": 20, "forward": false, "start": 112, "end": 120}, @@ -1924,7 +1924,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AATGGTTTAATAAGAATAAACACCTATCATAT", "domains": [ {"helix": 22, "forward": false, "start": 112, "end": 120}, @@ -1933,7 +1933,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TATGTAAACGCGAGAAAACTTTTTCTAAATTT", "domains": [ {"helix": 24, "forward": false, "start": 112, "end": 120}, @@ -1942,7 +1942,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TTAAGACGCATAGGTCTGAGAGACTATAACTA", "domains": [ {"helix": 26, "forward": false, "start": 112, "end": 120}, @@ -1951,7 +1951,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AAATCAATCGTCGCTATTAATTAAAGCTTAGA", "domains": [ {"helix": 28, "forward": false, "start": 112, "end": 120}, @@ -1960,7 +1960,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GAGCAAAAATTAATTACATTTAACCAGTACAT", "domains": [ {"helix": 30, "forward": false, "start": 112, "end": 120}, @@ -1969,7 +1969,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CTTTTACACTTTGAATACCAAGTTAATTACCT", "domains": [ {"helix": 32, "forward": false, "start": 112, "end": 120}, @@ -1978,7 +1978,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AACCTACCAAAGAAATTGCGTAGAAACAGTAC", "domains": [ {"helix": 34, "forward": false, "start": 112, "end": 120}, @@ -1987,7 +1987,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CGGAATTATTCATCAATATAATCCAGGGTTAG", "domains": [ {"helix": 36, "forward": false, "start": 112, "end": 120}, @@ -1996,7 +1996,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CGACAACTTTTAAAAGTTTGAGTAAGAAGGAG", "domains": [ {"helix": 38, "forward": false, "start": 112, "end": 120}, @@ -2005,7 +2005,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "CTAAAATAGCCGTCAATAGATAATAAACAATT", "domains": [ {"helix": 40, "forward": false, "start": 112, "end": 120}, @@ -2014,7 +2014,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CTAAAGCAAATCAATATCTGGTCAAAGGTTAT", "domains": [ {"helix": 42, "forward": false, "start": 112, "end": 120}, @@ -2023,7 +2023,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "ACGAACCAAGTATTAACACCGCCTTGAAAAAT", "domains": [ {"helix": 44, "forward": false, "start": 112, "end": 120}, @@ -2032,7 +2032,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GCGTAAGAATTAGTCTTTAATGCGAATACCGA", "domains": [ {"helix": 46, "forward": false, "start": 112, "end": 120}, @@ -2041,7 +2041,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GAAATGGAACCAGTAATAAAAGGGACCTGAAA", "domains": [ {"helix": 48, "forward": false, "start": 112, "end": 120}, @@ -2050,7 +2050,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CGGCCTTGCATTGCAACAGGAAAAAATCGTCT", "domains": [ {"helix": 50, "forward": false, "start": 112, "end": 120}, @@ -2059,7 +2059,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GTAAAAGAAATACTTCTTTGATTACAAACTAT", "domains": [ {"helix": 52, "forward": false, "start": 112, "end": 120}, @@ -2068,7 +2068,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AGCGGGAGCAGGAACGGTACGCCAGCCACCGA", "domains": [ {"helix": 54, "forward": false, "start": 112, "end": 120}, diff --git a/examples/output_designs/64_helix_origami_rectangle.dna b/examples/output_designs/64_helix_origami_rectangle.dna index 7da9f394..76ce6387 100644 --- a/examples/output_designs/64_helix_origami_rectangle.dna +++ b/examples/output_designs/64_helix_origami_rectangle.dna @@ -203,7 +203,7 @@ "is_scaffold": true }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GACAGCATCGGAACGAACCCTCAGCAGCGAAA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -211,7 +211,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TGCCACTACGAAGGCACGGGTAAAATACGTAA", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -219,7 +219,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AAGTACAACGGAGATTTACCAAGCGCGAAACA", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -227,7 +227,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TCATAAGGGAACCGAAAGGCGCAGACGGTCAA", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, @@ -235,7 +235,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TGACAAGAACCGGATATCATCAAGAGTAATCT", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, @@ -243,7 +243,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TAAATTGGGCTTGAGAACACCAGAACGAGTAG", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, @@ -251,7 +251,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GGAAGAAAAATCTACGACCAGTCAGGACGTTG", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, @@ -259,7 +259,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TAATGCAGATACATAAGAATACCACATTCAAC", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, @@ -267,7 +267,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GCGAGAGGCTTTTGCAGATAAAAACCAAAATA", "domains": [ {"helix": 17, "forward": true, "start": 16, "end": 32}, @@ -275,7 +275,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CATTGAATCCCCCTCAAATCGTCATAAATATT", "domains": [ {"helix": 19, "forward": true, "start": 16, "end": 32}, @@ -283,7 +283,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AAAGCGGATTGCATCATATTATAGTCAGAAGC", "domains": [ {"helix": 21, "forward": true, "start": 16, "end": 32}, @@ -291,7 +291,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CTCCAACAGGTCAGGACCAGACCGGAAGCAAA", "domains": [ {"helix": 23, "forward": true, "start": 16, "end": 32}, @@ -299,7 +299,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CTGTAGCTCAACATGTATTGCTGAATATAATG", "domains": [ {"helix": 25, "forward": true, "start": 16, "end": 32}, @@ -307,7 +307,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TTTAGTTTGACCATTATCTGCGAACGAGTAGA", "domains": [ {"helix": 27, "forward": true, "start": 16, "end": 32}, @@ -315,7 +315,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "ACTAATAGTAGTAGCAAGGTGGCATCAATTCT", "domains": [ {"helix": 29, "forward": true, "start": 16, "end": 32}, @@ -323,7 +323,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GGTTGTACCAAAAACAAGCATAAAGCTAAATC", "domains": [ {"helix": 31, "forward": true, "start": 16, "end": 32}, @@ -331,7 +331,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AAATGCAATGCCTGAGAACCCTCATATATTTT", "domains": [ {"helix": 33, "forward": true, "start": 16, "end": 32}, @@ -339,7 +339,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AGCTGATAAATTAATGGATATTCAACCGTTCT", "domains": [ {"helix": 35, "forward": true, "start": 16, "end": 32}, @@ -347,7 +347,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GATGAACGGTAATCGTAGCAAACAAGAGAATC", "domains": [ {"helix": 37, "forward": true, "start": 16, "end": 32}, @@ -355,7 +355,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TTAAATTGTAAACGTTTTGTATAAGCAAATAT", "domains": [ {"helix": 39, "forward": true, "start": 16, "end": 32}, @@ -363,7 +363,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CGCGTCTGGCCTTCCTGCCATCAAAAATAATT", "domains": [ {"helix": 41, "forward": true, "start": 16, "end": 32}, @@ -371,7 +371,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GTAATGGGATAGGTCAAAACGGCGGATTGACC", "domains": [ {"helix": 43, "forward": true, "start": 16, "end": 32}, @@ -379,7 +379,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CACTCCAGCCAGCTTTGGCCTCAGGAAGATCG", "domains": [ {"helix": 45, "forward": true, "start": 16, "end": 32}, @@ -387,7 +387,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GTGCGGGCCTCTTCGCTTGGGAAGGGCGATCG", "domains": [ {"helix": 47, "forward": true, "start": 16, "end": 32}, @@ -395,7 +395,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TGTAAAACGACGGCCATTCCCAGTCACGACGT", "domains": [ {"helix": 49, "forward": true, "start": 16, "end": 32}, @@ -403,7 +403,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GTTTCCTGTGTGAAATAATCATGGTCATAGCT", "domains": [ {"helix": 51, "forward": true, "start": 16, "end": 32}, @@ -411,7 +411,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ACTCACATTAATTGCGCCTAATGAGTGAGCTA", "domains": [ {"helix": 53, "forward": true, "start": 16, "end": 32}, @@ -419,7 +419,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CGGTTTGCGTATTGGGAACGCGCGGGGAGAGG", "domains": [ {"helix": 55, "forward": true, "start": 16, "end": 32}, @@ -427,7 +427,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GCAAGCGGTCCACGCTCCCTGAGAGAGTTGCA", "domains": [ {"helix": 57, "forward": true, "start": 16, "end": 32}, @@ -435,7 +435,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CGAGATAGGGTTGAGTAATCAAAAGAATAGCC", "domains": [ {"helix": 59, "forward": true, "start": 16, "end": 32}, @@ -443,7 +443,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CGATGGCCCACTACGTAAACCGTCTATCAGGG", "domains": [ {"helix": 61, "forward": true, "start": 16, "end": 32}, @@ -451,7 +451,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TAGAGCTTGACGGGGAAAGGGAGCCCCCGATT", "domains": [ {"helix": 63, "forward": true, "start": 16, "end": 32}, @@ -459,7 +459,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "ACAACCATCGCCCACGTGCGCCGACAATGACA", "domains": [ {"helix": 0, "forward": false, "start": 96, "end": 112}, @@ -467,7 +467,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CTCCAAAAGGAGCCTTATCTCCAAAAAAAAGG", "domains": [ {"helix": 2, "forward": false, "start": 96, "end": 112}, @@ -475,7 +475,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AACTTTCAACAGTTTCTGGGATTTTGCTAAAC", "domains": [ {"helix": 4, "forward": false, "start": 96, "end": 112}, @@ -483,7 +483,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TCCACAGACAGCCCTCACAACGCCTGTAGCAT", "domains": [ {"helix": 6, "forward": false, "start": 96, "end": 112}, @@ -491,7 +491,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CACCACCCTCATTTTCCCGCCACCCTCAGAGC", "domains": [ {"helix": 8, "forward": false, "start": 96, "end": 112}, @@ -499,7 +499,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TATAAGTATAGCCCGGCCGTCGAGAGGGTTGA", "domains": [ {"helix": 10, "forward": false, "start": 96, "end": 112}, @@ -507,7 +507,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TGAAAGTATTAAGAGGCTATTATTCTGAAACA", "domains": [ {"helix": 12, "forward": false, "start": 96, "end": 112}, @@ -515,7 +515,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GGTAATAAGTTTTAACGATACAGGAGTGTACT", "domains": [ {"helix": 14, "forward": false, "start": 96, "end": 112}, @@ -523,7 +523,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "ATAAATCCTCATTAAATGATATTCACAAACAA", "domains": [ {"helix": 16, "forward": false, "start": 96, "end": 112}, @@ -531,7 +531,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CCTCAGAGCCGCCACCCCCTCAGAGCCACCAC", "domains": [ {"helix": 18, "forward": false, "start": 96, "end": 112}, @@ -539,7 +539,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TCTTTTCATAATCAAATTATTAGCGTTTGCCA", "domains": [ {"helix": 20, "forward": false, "start": 96, "end": 112}, @@ -547,7 +547,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AATCAGTAGCGACAGATCGATAGCAGCACCGT", "domains": [ {"helix": 22, "forward": false, "start": 96, "end": 112}, @@ -555,7 +555,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "CCATTTGGGAATTAGACCGTCACCGACTTGAG", "domains": [ {"helix": 24, "forward": false, "start": 96, "end": 112}, @@ -563,7 +563,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AGACAAAAGGGCGACAGGTTTACCAGCGCCAA", "domains": [ {"helix": 26, "forward": false, "start": 96, "end": 112}, @@ -571,7 +571,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TAAAGGTGGCAACATAGTAGAAAATACATACA", "domains": [ {"helix": 28, "forward": false, "start": 96, "end": 112}, @@ -579,7 +579,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CCGAGGAAACGCAATAAGTTACCAGAAGGAAA", "domains": [ {"helix": 30, "forward": false, "start": 96, "end": 112}, @@ -587,7 +587,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ATAAGAGCAAGAAACATGAGTTAAGCCCAATA", "domains": [ {"helix": 32, "forward": false, "start": 96, "end": 112}, @@ -595,7 +595,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GACGGGAGAATTAACTACAGGGAAGCGCATTA", "domains": [ {"helix": 34, "forward": false, "start": 96, "end": 112}, @@ -603,7 +603,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TCCCAATCCAAATAAGACAGCCATATTATTTA", "domains": [ {"helix": 36, "forward": false, "start": 96, "end": 112}, @@ -611,7 +611,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "ACCCAGCTACAATTTTTTAGTTGCTATTTTGC", "domains": [ {"helix": 38, "forward": false, "start": 96, "end": 112}, @@ -619,7 +619,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GCTTATCCGGTATTCTAAATCAGATATAGAAG", "domains": [ {"helix": 40, "forward": false, "start": 96, "end": 112}, @@ -627,7 +627,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "ACCAAGTACCGCACTCCAAGAACGGGTATTAA", "domains": [ {"helix": 42, "forward": false, "start": 96, "end": 112}, @@ -635,7 +635,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GAACAAGAAAAATAATACAATAGATAAGTCCT", "domains": [ {"helix": 44, "forward": false, "start": 96, "end": 112}, @@ -643,7 +643,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CGACAAAAGGTAAAGTAGAGAATATAAAGTAC", "domains": [ {"helix": 46, "forward": false, "start": 96, "end": 112}, @@ -651,7 +651,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CAGTAGGGCTTAATTGTAAAGCCAACGCTCAA", "domains": [ {"helix": 48, "forward": false, "start": 96, "end": 112}, @@ -659,7 +659,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AATAAGAATAAACACCGATAAATAAGGCGTTA", "domains": [ {"helix": 50, "forward": false, "start": 96, "end": 112}, @@ -667,7 +667,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CGCGAGAAAACTTTTTATCGCAAGACAAAGAA", "domains": [ {"helix": 52, "forward": false, "start": 96, "end": 112}, @@ -675,7 +675,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CATAGGTCTGAGAGACGTGAATTTATCAAAAT", "domains": [ {"helix": 54, "forward": false, "start": 96, "end": 112}, @@ -683,7 +683,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CGTCGCTATTAATTAACCTTGCTTCTGTAAAT", "domains": [ {"helix": 56, "forward": false, "start": 96, "end": 112}, @@ -691,7 +691,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ATTAATTACATTTAACACATCAAGAAAACAAA", "domains": [ {"helix": 58, "forward": false, "start": 96, "end": 112}, @@ -699,7 +699,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CTTTGAATACCAAGTTCGGATTCGCCTGATTG", "domains": [ {"helix": 60, "forward": false, "start": 96, "end": 112}, @@ -707,7 +707,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AAAGAAATTGCGTAGACACGTAAAACAGAAAT", "domains": [ {"helix": 62, "forward": false, "start": 96, "end": 112}, @@ -715,14 +715,14 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ATATATTCGGTCGCTGAGGCTTGCAGGGAGTT", "domains": [ {"helix": 0, "forward": false, "start": 56, "end": 88} ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TTTCATGAAGAGGCTTTGAGGACTGTGAATTT", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -730,7 +730,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CTTAAACATCAGCTTGCTTTCGAGAAAGACTT", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -738,7 +738,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CTCATCTTGAGGCAAAAGAATACAGAATTGCG", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -746,7 +746,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AATAATAAAAAGGAACAACTAAAGCTAAAACA", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -754,7 +754,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GCTCCATGAAATTGTGTCGAAATCCTTTCCAG", "domains": [ {"helix": 6, "forward": false, "start": 48, "end": 56}, @@ -762,7 +762,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "ACGTTAGTTCTAAAGTTTTGTCGTCGCGACCT", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 80}, @@ -770,7 +770,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "CCAGGCGCGAGGACAGATGAACGGCGTAACAC", "domains": [ {"helix": 8, "forward": false, "start": 48, "end": 56}, @@ -778,7 +778,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TGAGTTTCATAGGAACCCATGTACTGTACAGA", "domains": [ {"helix": 7, "forward": true, "start": 72, "end": 80}, @@ -786,7 +786,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GAATAAGGACGTAACAAAGCTGCTTACCGCCA", "domains": [ {"helix": 10, "forward": false, "start": 48, "end": 56}, @@ -794,7 +794,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CCCTCAGATACTCAGGAGGTTTAGCATTCAGT", "domains": [ {"helix": 9, "forward": true, "start": 72, "end": 80}, @@ -802,7 +802,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CGATTTTATTAATCATTGTGAATTCGGGGTTT", "domains": [ {"helix": 12, "forward": false, "start": 48, "end": 56}, @@ -810,7 +810,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TGCTCAGTGAAGGATTAGGATTAGACCTTATG", "domains": [ {"helix": 11, "forward": true, "start": 72, "end": 80}, @@ -818,7 +818,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AAAGATTCACGGAACAACATTATTAAACAGTT", "domains": [ {"helix": 14, "forward": false, "start": 48, "end": 56}, @@ -826,7 +826,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AATGCCCCGTAACAGTGCCCGTATACAGGTAG", "domains": [ {"helix": 13, "forward": true, "start": 72, "end": 80}, @@ -834,7 +834,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CATAACCCGAGGCATAGTAAGAGCCGTTCCAG", "domains": [ {"helix": 16, "forward": false, "start": 48, "end": 56}, @@ -842,7 +842,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TAAGCGTCCAGTCTCTGAATTTACAACACTAT", "domains": [ {"helix": 15, "forward": true, "start": 72, "end": 80}, @@ -850,7 +850,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "ACTGGATAAGGGGGTAATAGTAAACAGGAGGT", "domains": [ {"helix": 18, "forward": false, "start": 48, "end": 56}, @@ -858,7 +858,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TGAGGCAGCCGCCGCCAGCATTGAATGTTTAG", "domains": [ {"helix": 17, "forward": true, "start": 72, "end": 80}, @@ -866,7 +866,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CAAAAATCCAGAAAACGAGAATGACTCCCTCA", "domains": [ {"helix": 20, "forward": false, "start": 48, "end": 56}, @@ -874,7 +874,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GAGCCGCCCCACCACCGGAACCGCCCATAAAT", "domains": [ {"helix": 19, "forward": true, "start": 72, "end": 80}, @@ -882,7 +882,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TTTTAATTGCCCGAAAGACTTCAACGTTTTCA", "domains": [ {"helix": 22, "forward": false, "start": 48, "end": 56}, @@ -890,7 +890,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TCGGCATTGCGTCAGACTGTAGCGATATCGCG", "domains": [ {"helix": 21, "forward": true, "start": 72, "end": 80}, @@ -898,7 +898,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TTTTTGCGATTGCTCCTTTTGATATAGCAAGG", "domains": [ {"helix": 24, "forward": false, "start": 48, "end": 56}, @@ -906,7 +906,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CCGGAAACGTAGCACCATTACCATAGAGGTCA", "domains": [ {"helix": 23, "forward": true, "start": 72, "end": 80}, @@ -914,7 +914,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TCCATATAAAGTACGGTGTCTGGAGACGGAAA", "domains": [ {"helix": 26, "forward": false, "start": 48, "end": 56}, @@ -922,7 +922,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TTATTCATAGGGAAGGTAAATATTAGTTTCAT", "domains": [ {"helix": 25, "forward": true, "start": 72, "end": 80}, @@ -930,7 +930,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TTTCATTTGGTCAATAACCTGTTTTTATTTTG", "domains": [ {"helix": 28, "forward": false, "start": 48, "end": 56}, @@ -938,7 +938,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TCACAATCACACCACGGAATAAGTAGCTATAT", "domains": [ {"helix": 27, "forward": true, "start": 72, "end": 80}, @@ -946,7 +946,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CAAAATTACATACAGGCAAGGCAAAAGACTCC", "domains": [ {"helix": 30, "forward": false, "start": 48, "end": 56}, @@ -954,7 +954,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TTATTACGAAGAACTGGCATGATTAGAATTAG", "domains": [ {"helix": 29, "forward": true, "start": 72, "end": 80}, @@ -962,7 +962,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CAACGCAACTTTTGCGGGAGAAGCTTTTTAAG", "domains": [ {"helix": 32, "forward": false, "start": 48, "end": 56}, @@ -970,7 +970,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AAAAGTAATATCTTACCGAAGCCCCTTTATTT", "domains": [ {"helix": 31, "forward": true, "start": 72, "end": 80}, @@ -978,7 +978,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AGACAGTCATTCAAAAGGGTGAGAGCGCTAAT", "domains": [ {"helix": 34, "forward": false, "start": 48, "end": 56}, @@ -986,7 +986,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "ATCAGAGAGTCAGAGGGTAATTGAAAGGCCGG", "domains": [ {"helix": 33, "forward": true, "start": 72, "end": 80}, @@ -994,7 +994,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TCAGGTCATTTTTGAGAGATCTACATAGCAGC", "domains": [ {"helix": 36, "forward": false, "start": 48, "end": 56}, @@ -1002,7 +1002,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CTTTACAGAACGTCAAAAATGAAAAAAGGCTA", "domains": [ {"helix": 35, "forward": true, "start": 72, "end": 80}, @@ -1010,7 +1010,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AGAAAAGCTCATATGTACCCCGGTTTCCAGAG", "domains": [ {"helix": 38, "forward": false, "start": 48, "end": 56}, @@ -1018,7 +1018,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CCTAATTTACGCTAACGAGCGTCTTGATAATC", "domains": [ {"helix": 37, "forward": true, "start": 72, "end": 80}, @@ -1026,7 +1026,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GCTCATTTTCGCATTAAATTTTTGCTTGCGGG", "domains": [ {"helix": 40, "forward": false, "start": 48, "end": 56}, @@ -1034,7 +1034,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AGGTTTTGTTAGCGAACCTCCCGATTAAATCA", "domains": [ {"helix": 39, "forward": true, "start": 72, "end": 80}, @@ -1042,7 +1042,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ACCCGTCGAACATTAAATGTGAGCCGTAGGAA", "domains": [ {"helix": 42, "forward": false, "start": 48, "end": 56}, @@ -1050,7 +1050,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TCATTACCCCGTTTTTATTTTCATGAGTAACA", "domains": [ {"helix": 41, "forward": true, "start": 72, "end": 80}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GTTTGAGGCGCATCGTAACCGTGCAATCAATA", "domains": [ {"helix": 44, "forward": false, "start": 48, "end": 56}, @@ -1066,7 +1066,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ATCGGCTGCGAGCATGTAGAAACCATCTGCCA", "domains": [ {"helix": 43, "forward": true, "start": 72, "end": 80}, @@ -1074,7 +1074,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TTCGCCATTGCCGGAAACCAGGCAGTTCAGCT", "domains": [ {"helix": 46, "forward": false, "start": 48, "end": 56}, @@ -1082,7 +1082,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AATGCAGACGACAATAAACAACATAAGCGCCA", "domains": [ {"helix": 45, "forward": true, "start": 72, "end": 80}, @@ -1090,7 +1090,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "ATTAAGTTGAAAGGGGGATGTGCTATTTAGGC", "domains": [ {"helix": 48, "forward": false, "start": 48, "end": 56}, @@ -1098,7 +1098,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AGAGGCATACAACGCCAACATGTAGCAAGGCG", "domains": [ {"helix": 47, "forward": true, "start": 72, "end": 80}, @@ -1106,7 +1106,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CCCGGGTACCTGCAGGTCGACTCTTATCATAT", "domains": [ {"helix": 50, "forward": false, "start": 48, "end": 56}, @@ -1114,7 +1114,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GCGTTATAGAAAAAGCCTGTTTAGAGAGGATC", "domains": [ {"helix": 49, "forward": true, "start": 72, "end": 80}, @@ -1122,7 +1122,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GCATAAAGTTCCACACAACATACGCTAAATTT", "domains": [ {"helix": 52, "forward": false, "start": 48, "end": 56}, @@ -1130,7 +1130,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AATGGTTTAATTTCATCTTCTGACAGCCGGAA", "domains": [ {"helix": 51, "forward": true, "start": 72, "end": 80}, @@ -1138,7 +1138,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GCCAGCTGCTTTCCAGTCGGGAAATATAACTA", "domains": [ {"helix": 54, "forward": false, "start": 48, "end": 56}, @@ -1146,7 +1146,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TATGTAAAGGCTTAGGTTGGGTTACCTGTCGT", "domains": [ {"helix": 53, "forward": true, "start": 72, "end": 80}, @@ -1154,7 +1154,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AGCTGATTCTTTTCACCAGTGAGAAGCTTAGA", "domains": [ {"helix": 56, "forward": false, "start": 48, "end": 56}, @@ -1162,7 +1162,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TTAAGACGTTGAAAACATAGCGATCGGGCAAC", "domains": [ {"helix": 55, "forward": true, "start": 72, "end": 80}, @@ -1170,7 +1170,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CCGAAATCCGAAAATCCTGTTTGACAGTACAT", "domains": [ {"helix": 58, "forward": false, "start": 48, "end": 56}, @@ -1178,7 +1178,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AAATCAATCCTTTTTTAATGGAAATGGTGGTT", "domains": [ {"helix": 57, "forward": true, "start": 72, "end": 80}, @@ -1186,7 +1186,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TGGACTCCACAAGAGTCCACTATTAATTACCT", "domains": [ {"helix": 60, "forward": false, "start": 48, "end": 56}, @@ -1194,7 +1194,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GAGCAAAAGCGAATTATTCATTTCAAAGAACG", "domains": [ {"helix": 59, "forward": true, "start": 72, "end": 80}, @@ -1202,7 +1202,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GTAAAGCACAAGTTTTTTGGGGTCAACAGTAC", "domains": [ {"helix": 62, "forward": false, "start": 48, "end": 56}, @@ -1210,7 +1210,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CTTTTACACAGATGAATATACAGTGAGGTGCC", "domains": [ {"helix": 61, "forward": true, "start": 72, "end": 80}, @@ -1218,14 +1218,14 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GAACGTGGCGAGAAAGGAAGGGAAAGGGTTAG", "domains": [ {"helix": 63, "forward": true, "start": 40, "end": 72} ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AAAGGCCGCTTTTGCGGGATCGTCGGGTAGCA", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56}, @@ -1233,7 +1233,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "ACGGCTACGGAAGTTTCCATTAAACCAACCTA", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -1242,7 +1242,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AAACGAAATGACCCCCAGCGATTATGTATCAT", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -1251,7 +1251,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CGCCTGATTTACTTAGCCGGAACGCTGACCAA", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 48}, @@ -1260,7 +1260,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CTTTGAAAATAGGCTGGCTGACCTTTCATTAC", "domains": [ {"helix": 7, "forward": true, "start": 40, "end": 48}, @@ -1269,7 +1269,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CCAAATCACTTGCCCTGACGAGAATGGTTTAA", "domains": [ {"helix": 9, "forward": true, "start": 40, "end": 48}, @@ -1278,7 +1278,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TTTCAACTAGAACTGGCTCATTATTTAATAAA", "domains": [ {"helix": 11, "forward": true, "start": 40, "end": 48}, @@ -1287,7 +1287,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "ACGAACTAATCAGTTGAGATTTAGCGCCAAAA", "domains": [ {"helix": 13, "forward": true, "start": 40, "end": 48}, @@ -1296,7 +1296,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GGAATTACTCGTTTACCAGACGACAAAGAAGT", "domains": [ {"helix": 15, "forward": true, "start": 40, "end": 48}, @@ -1305,7 +1305,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TTTGCCAGGCGTCCAATACTGCGGAATGCTTT", "domains": [ {"helix": 17, "forward": true, "start": 40, "end": 48}, @@ -1314,7 +1314,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AAACAGTTAGGTCTTTACCCTGACAAAAGATT", "domains": [ {"helix": 19, "forward": true, "start": 40, "end": 48}, @@ -1323,7 +1323,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AAGAGGAACGAGCTTCAAAGCGAATTAGAGAG", "domains": [ {"helix": 21, "forward": true, "start": 40, "end": 48}, @@ -1332,7 +1332,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TACCTTTAGATGGCTTAGAGCTTATTTAAATA", "domains": [ {"helix": 23, "forward": true, "start": 40, "end": 48}, @@ -1341,7 +1341,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TGCAACTAACAGTTGATTCCCAATGATACATT", "domains": [ {"helix": 25, "forward": true, "start": 40, "end": 48}, @@ -1350,7 +1350,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TCGCAAATGGGGCGCGAGCTGAAATTAACATC", "domains": [ {"helix": 27, "forward": true, "start": 40, "end": 48}, @@ -1359,7 +1359,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CAATAAATAGCAATAAAGCCTCAGTTATGACC", "domains": [ {"helix": 29, "forward": true, "start": 40, "end": 48}, @@ -1368,7 +1368,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CTGTAATAGGATAAAAATTTTTAGTAATGTGT", "domains": [ {"helix": 31, "forward": true, "start": 40, "end": 48}, @@ -1377,7 +1377,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AGGTAAAGAAATCACCATCAATATCCGGAGAG", "domains": [ {"helix": 33, "forward": true, "start": 40, "end": 48}, @@ -1386,7 +1386,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GGTAGCTATTGCCTGAGAGTCTGGAAAACTAG", "domains": [ {"helix": 35, "forward": true, "start": 40, "end": 48}, @@ -1395,7 +1395,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CATGTCAACCCAAAAACAGGAAGAAATATTTT", "domains": [ {"helix": 37, "forward": true, "start": 40, "end": 48}, @@ -1404,7 +1404,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GTTAAAATTTTAACCAATAGGAACGTAGCCAG", "domains": [ {"helix": 39, "forward": true, "start": 40, "end": 48}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CTTTCATCGATTCTCCGTGGGAACCGTTGGTG", "domains": [ {"helix": 41, "forward": true, "start": 40, "end": 48}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TAGATGGGGGACGACGACAGTATCCCGGCACC", "domains": [ {"helix": 43, "forward": true, "start": 40, "end": 48}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GCTTCTGGTCAGGCTGCGCAACTGTATTACGC", "domains": [ {"helix": 45, "forward": true, "start": 40, "end": 48}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CAGCTGGCGGGTAACGCCAGGGTTGTGCCAAG", "domains": [ {"helix": 47, "forward": true, "start": 40, "end": 48}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CTTGCATGCCGAGCTCGAATTCGTTGTTATCC", "domains": [ {"helix": 49, "forward": true, "start": 40, "end": 48}, @@ -1458,7 +1458,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GCTCACAATGTAAAGCCTGGGGTGTTGCGCTC", "domains": [ {"helix": 51, "forward": true, "start": 40, "end": 48}, @@ -1467,7 +1467,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "ACTGCCCGCATTAATGAATCGGCCCGCCAGGG", "domains": [ {"helix": 53, "forward": true, "start": 40, "end": 48}, @@ -1476,7 +1476,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TGGTTTTTGCCCTTCACCGCCTGGGGTTTGCC", "domains": [ {"helix": 55, "forward": true, "start": 40, "end": 48}, @@ -1485,7 +1485,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CCAGCAGGGGCAAAATCCCTTATAGTTGTTCC", "domains": [ {"helix": 57, "forward": true, "start": 40, "end": 48}, @@ -1494,7 +1494,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AGTTTGGAAACGTCAAAGGGCGAAGAACCATC", "domains": [ {"helix": 59, "forward": true, "start": 40, "end": 48}, @@ -1503,7 +1503,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ACCCAAATCTAAATCGGAACCCTAAAGCCGGC", "domains": [ {"helix": 61, "forward": true, "start": 40, "end": 48}, @@ -1512,7 +1512,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AACCTACCATATCAAAATTATTTGTTTTCAGG", "domains": [ {"helix": 63, "forward": true, "start": 72, "end": 96}, @@ -1520,7 +1520,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TCGGTTTAGCTTGATACCGATAGTCATAACCG", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88}, @@ -1529,7 +1529,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GAGAATAGTTTTTTCACGTTGAAATAATTGTA", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88}, @@ -1538,7 +1538,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CGTAACGAAAATGAATTTTCTGTAAGCGGAGT", "domains": [ {"helix": 6, "forward": false, "start": 80, "end": 88}, @@ -1547,7 +1547,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CAAGCCCAGTCACCAGTACAAACTATAGTTAG", "domains": [ {"helix": 8, "forward": false, "start": 80, "end": 88}, @@ -1556,7 +1556,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TATCACCGACCGCCACCCTCAGAAAGGGATAG", "domains": [ {"helix": 10, "forward": false, "start": 80, "end": 88}, @@ -1565,7 +1565,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CCTCAAGAACCAGGCGGATAAGTGAATAGGTG", "domains": [ {"helix": 12, "forward": false, "start": 80, "end": 88}, @@ -1574,7 +1574,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TGCCTTGACTGCCTATTTCGGAACCTGAGACT", "domains": [ {"helix": 14, "forward": false, "start": 80, "end": 88}, @@ -1583,7 +1583,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GGAAAGCGATACATGGCTTTTGATGGGGTCAG", "domains": [ {"helix": 16, "forward": false, "start": 80, "end": 88}, @@ -1592,7 +1592,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CACCAGAGGTCAGACGATTGGCCTGCCAGAAT", "domains": [ {"helix": 18, "forward": false, "start": 80, "end": 88}, @@ -1601,7 +1601,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AACCAGAGACCCTCAGAACCGCCAAGAACCAC", "domains": [ {"helix": 20, "forward": false, "start": 80, "end": 88}, @@ -1610,7 +1610,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TGCCTTTATTCGGTCATAGCCCCCATCACCGG", "domains": [ {"helix": 22, "forward": false, "start": 80, "end": 88}, @@ -1619,7 +1619,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AATCACCAGTCACCAATGAAACCAATCAAGTT", "domains": [ {"helix": 24, "forward": false, "start": 80, "end": 88}, @@ -1628,7 +1628,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "ATTGAGGGTAAAGGTGAATTATCAGCCAGCAA", "domains": [ {"helix": 26, "forward": false, "start": 80, "end": 88}, @@ -1637,7 +1637,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "ACGCAAAGAATAGAAAATTCATATTTCAACCG", "domains": [ {"helix": 28, "forward": false, "start": 80, "end": 88}, @@ -1646,7 +1646,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "ATACCCAACAGTATGTTAGCAAACTAAAAGAA", "domains": [ {"helix": 30, "forward": false, "start": 80, "end": 88}, @@ -1655,7 +1655,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GCAATAGCGCAGATAGCCGAACAAATAACGGA", "domains": [ {"helix": 32, "forward": false, "start": 80, "end": 88}, @@ -1664,7 +1664,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TGAACAAAGATAACCCACAAGAATATGAAATA", "domains": [ {"helix": 34, "forward": false, "start": 80, "end": 88}, @@ -1673,7 +1673,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TTTTGTTTAGAGAATAACATAAAAGAACACCC", "domains": [ {"helix": 36, "forward": false, "start": 80, "end": 88}, @@ -1682,7 +1682,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TCTTACCAGCCAGTTACAAAATAAAAACGATT", "domains": [ {"helix": 38, "forward": false, "start": 80, "end": 88}, @@ -1691,7 +1691,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GAGGCGTTAAGCCTTAAATCAAGAATCCTGAA", "domains": [ {"helix": 40, "forward": false, "start": 80, "end": 88}, @@ -1700,7 +1700,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CAAGCAAGGCGCCCAATAGCAAGCAAGAACGC", "domains": [ {"helix": 42, "forward": false, "start": 80, "end": 88}, @@ -1709,7 +1709,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CTAATTTATCTTTCCTTATCATTCATCGAGAA", "domains": [ {"helix": 44, "forward": false, "start": 80, "end": 88}, @@ -1718,7 +1718,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CCAGACGAACGCGCCTGTTTATCAATCCCATC", "domains": [ {"helix": 46, "forward": false, "start": 80, "end": 88}, @@ -1727,7 +1727,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CATATTTATTTCGAGCCAGTAATAAATTCTGT", "domains": [ {"helix": 48, "forward": false, "start": 80, "end": 88}, @@ -1736,7 +1736,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AATTACTACAAATTCTTACCAGTAAGAATCGC", "domains": [ {"helix": 50, "forward": false, "start": 80, "end": 88}, @@ -1745,7 +1745,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TTTTAGTTGAAATACCGACCGTGTGGAATCAT", "domains": [ {"helix": 52, "forward": false, "start": 80, "end": 88}, @@ -1754,7 +1754,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TAACCTCCTGCTGATGCAAATCCACAAATATA", "domains": [ {"helix": 54, "forward": false, "start": 80, "end": 88}, @@ -1763,7 +1763,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TAGAATCCCTGAGAAGAGTCAATATACCTTTT", "domains": [ {"helix": 56, "forward": false, "start": 80, "end": 88}, @@ -1772,7 +1772,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TTGAATTAATATGTGAGTGAATAATTTTCCCT", "domains": [ {"helix": 58, "forward": false, "start": 80, "end": 88}, @@ -1781,7 +1781,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GCGCAGAGGAAGATGATGAAACAAAATTTCAT", "domains": [ {"helix": 60, "forward": false, "start": 80, "end": 88}, @@ -1790,7 +1790,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TTTAACGTTCGGGAGAAACAATAAACAAAATC", "domains": [ {"helix": 62, "forward": false, "start": 80, "end": 88}, diff --git a/examples/output_designs/6_helix_6_col_origami_rectangle.dna b/examples/output_designs/6_helix_6_col_origami_rectangle.dna index c79dc893..b7753e3b 100644 --- a/examples/output_designs/6_helix_6_col_origami_rectangle.dna +++ b/examples/output_designs/6_helix_6_col_origami_rectangle.dna @@ -29,7 +29,7 @@ "is_scaffold": true }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CGAGATAGGGTTGAGTAATCAAAAGAATAGCC", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16}, @@ -37,7 +37,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CGATGGCCCACTACGTAAACCGTCTATCAGGG", "domains": [ {"helix": 3, "forward": true, "start": 0, "end": 16}, @@ -45,7 +45,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TAGAGCTTGACGGGGAAAGGGAGCCCCCGATT", "domains": [ {"helix": 5, "forward": true, "start": 0, "end": 16}, @@ -53,7 +53,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GCAAGCGGTCCACGCTCCCTGAGAGAGTTGCA", "domains": [ {"helix": 0, "forward": false, "start": 80, "end": 96}, @@ -61,7 +61,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CGGTTTGCGTATTGGGAACGCGCGGGGAGAGG", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 96}, @@ -69,7 +69,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "ACTCACATTAATTGCGCCTAATGAGTGAGCTA", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 96}, @@ -77,14 +77,14 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CCAGCAGGCGAAAATCCTGTTTGATGGTGGTT", "domains": [ {"helix": 0, "forward": false, "start": 40, "end": 72} ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TGGACTCCACAAGAGTCCACTATTCGGGCAAC", "domains": [ {"helix": 2, "forward": false, "start": 32, "end": 40}, @@ -92,7 +92,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AGCTGATTCTTTTCACCAGTGAGAAAAGAACG", "domains": [ {"helix": 1, "forward": true, "start": 56, "end": 64}, @@ -100,7 +100,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GTAAAGCACAAGTTTTTTGGGGTCCCTGTCGT", "domains": [ {"helix": 4, "forward": false, "start": 32, "end": 40}, @@ -108,7 +108,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GCCAGCTGCTTTCCAGTCGGGAAAGAGGTGCC", "domains": [ {"helix": 3, "forward": true, "start": 56, "end": 64}, @@ -116,14 +116,14 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GAACGTGGCGAGAAAGGAAGGGAAAGCCGGAA", "domains": [ {"helix": 5, "forward": true, "start": 24, "end": 56} ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CCGAAATCGGCAAAATCCCTTATAGTTGTTCC", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 40}, @@ -131,7 +131,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AGTTTGGAAACGTCAAAGGGCGAAGAACCATC", "domains": [ {"helix": 1, "forward": true, "start": 24, "end": 32}, @@ -140,7 +140,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "ACCCAAATCTAAATCGGAACCCTAAAGCCGGC", "domains": [ {"helix": 3, "forward": true, "start": 24, "end": 32}, @@ -149,7 +149,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GCATAAAGTGTAAAGCCTGGGGTGTTGCGCTC", "domains": [ {"helix": 5, "forward": true, "start": 56, "end": 80}, @@ -157,7 +157,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TGGTTTTTGCCCTTCACCGCCTGGGGTTTGCC", "domains": [ {"helix": 2, "forward": false, "start": 64, "end": 72}, @@ -166,7 +166,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "ACTGCCCGCATTAATGAATCGGCCCGCCAGGG", "domains": [ {"helix": 4, "forward": false, "start": 64, "end": 72}, diff --git a/examples/output_designs/6_helix_bundle_honeycomb.dna b/examples/output_designs/6_helix_bundle_honeycomb.dna index 0b2682de..62de1502 100644 --- a/examples/output_designs/6_helix_bundle_honeycomb.dna +++ b/examples/output_designs/6_helix_bundle_honeycomb.dna @@ -11,7 +11,7 @@ ], "strands": [ { - "color": "#888888", + "color": "#320096", "sequence": "CATTTCTCCGAAGAGACGCATTTCACATGTGGGCCTTGAATC", "domains": [ {"helix": 3, "forward": true, "start": 56, "end": 70}, @@ -20,7 +20,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "ACGCTCGCCCTGCTCAATGTCCCGCCAAGAATTGTCAACCTT", "domains": [ {"helix": 2, "forward": false, "start": 70, "end": 84}, @@ -29,7 +29,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ATCTCTGACCTCCTAGTCGGGAAACCTGGCACGAATATAGTT", "domains": [ {"helix": 4, "forward": false, "start": 56, "end": 70}, @@ -38,7 +38,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GGGAGTGACTCTATCAACTCGTCGGTGGTCGTGCCAGCTGCA", "domains": [ {"helix": 1, "forward": true, "start": 70, "end": 84}, @@ -47,7 +47,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TGTGAATTCATGGGGATGTTCTTCTAAGGGAGGAGAAGCCAG", "domains": [ {"helix": 3, "forward": true, "start": 98, "end": 112}, @@ -56,7 +56,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GCTGCAAGGCGATGCCTCTTCGCTATTAAAGGGCGATCGGTG", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 126}, @@ -65,7 +65,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CGCGCACGACTTAAAACGCGCGGGGAGACCAAGCTTTCTCCC", "domains": [ {"helix": 4, "forward": false, "start": 98, "end": 112}, @@ -74,7 +74,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GGTTAAGTTGGGTAAACGACGGCCAGTGGGCGGTTTGCGTAT", "domains": [ {"helix": 1, "forward": true, "start": 112, "end": 126}, @@ -83,7 +83,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AAAGCGCCATTCCGTGGTGCCGGAAACCCCTTTCCGGCACCG", "domains": [ {"helix": 3, "forward": true, "start": 140, "end": 154}, @@ -92,7 +92,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ATGGGCGCATCGTCGCGGATTGACCGTATCTCCGTGGGAACA", "domains": [ {"helix": 2, "forward": false, "start": 154, "end": 168}, @@ -101,7 +101,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AAGCCATTCAGGCTGTTTTTCTTTTCACACTCCAGCCAGCAG", "domains": [ {"helix": 4, "forward": false, "start": 140, "end": 154}, @@ -110,7 +110,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CTTAACCGTGCATCCTCAGGAAGATCGCCAGTGAGACGGGCA", "domains": [ {"helix": 1, "forward": true, "start": 154, "end": 168}, @@ -119,7 +119,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ATCAACATTAAACCTTCCTGTAGCCAGCGATAATTCGCGTCT", "domains": [ {"helix": 3, "forward": true, "start": 182, "end": 196}, @@ -128,7 +128,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AAACGTTAATATCCAAAAACAGGAAGATGATAATCAGAAAAG", "domains": [ {"helix": 2, "forward": false, "start": 196, "end": 210}, @@ -137,7 +137,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CCTGTGAGCGAGTATTCACCGCCTGGCCCGCCATCAAAAACG", "domains": [ {"helix": 4, "forward": false, "start": 182, "end": 196}, @@ -146,7 +146,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GGTTTGTTAAAATTTTAACCAATAGGAACTGAGAGAGTTGCA", "domains": [ {"helix": 1, "forward": true, "start": 196, "end": 210}, @@ -155,7 +155,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "ATCGTAAAACTAAAGAGAATCGATGAACGTAGTCTGGAGCAA", "domains": [ {"helix": 3, "forward": true, "start": 224, "end": 238}, @@ -164,7 +164,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AACCGTTCTAGCAAAGGCCGGAGACAGTGATTCAAAAGGGTG", "domains": [ {"helix": 2, "forward": false, "start": 238, "end": 252}, @@ -173,7 +173,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AGGCATGTCAATCACTGGTTTGCCCCAGTCATTGCCTGAGTA", "domains": [ {"helix": 4, "forward": false, "start": 224, "end": 238}, @@ -182,7 +182,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ACTGATAAATTAATCAAAGGCTATCAGGCAGGCGAAAATCCT", "domains": [ {"helix": 1, "forward": true, "start": 238, "end": 252}, @@ -191,7 +191,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ATATTTTAAATGAAAATTTTTAGAACCCCTTCAACGCAAGGA", "domains": [ {"helix": 3, "forward": true, "start": 266, "end": 280}, @@ -200,7 +200,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TAAAGCCTCAGAAATCATACAGGCAAGGGCATTAACATCCAA", "domains": [ {"helix": 2, "forward": false, "start": 280, "end": 294}, @@ -209,7 +209,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TACAATGCCTGAGTCCGAAATCGGCAAAGAAGCCTTTATTAT", "domains": [ {"helix": 4, "forward": false, "start": 266, "end": 280}, @@ -218,7 +218,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TAGCATAAAGCTAAATACTTTTGCGGGAATCCCTTATAAATC", "domains": [ {"helix": 1, "forward": true, "start": 280, "end": 294}, @@ -227,7 +227,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GAGCTGAAAAGGCATATTTTCATTTGGGAAATAACCTGTTTA", "domains": [ {"helix": 3, "forward": true, "start": 308, "end": 322}, @@ -236,7 +236,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TTCATTCCATATTATGTTTTAAATATGCTAATGCTGTAGCTC", "domains": [ {"helix": 2, "forward": false, "start": 322, "end": 336}, @@ -245,7 +245,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AATGGCATCAATTCAGATAGGGTTGAGTCGCAAATGGTCAAC", "domains": [ {"helix": 4, "forward": false, "start": 308, "end": 322}, @@ -254,7 +254,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GCAACAGTTGATTCCATTAGATACATTTGTTGTTCCAGTTTG", "domains": [ {"helix": 1, "forward": true, "start": 322, "end": 336}, @@ -263,7 +263,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TCATTTTTGCGGCAGCTCCTTTTGATAAGAGAGAGTACCTTT", "domains": [ {"helix": 3, "forward": true, "start": 350, "end": 364}, @@ -272,7 +272,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CCCGAAAGACTTTTGAAGCAAAGCGGATCCCTGACTATTATA", "domains": [ {"helix": 2, "forward": false, "start": 364, "end": 378}, @@ -281,7 +281,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GTATGGCTTAGAGCTATTAAAGAACGTGAGGTCAGGATTAGT", "domains": [ {"helix": 4, "forward": false, "start": 350, "end": 364}, @@ -290,7 +290,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AACAAATATCGCGTAAGCAAACTCCAACGACTCCAACGTCAA", "domains": [ {"helix": 1, "forward": true, "start": 364, "end": 378}, @@ -299,7 +299,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AAAACGAGAATGCCATGCTTTAAACAGTCAATTGAATCCCCC", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 406}, @@ -308,7 +308,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AAAAGAAGTTTTAAAGACGACGATAAAATCATAACCCTCGTT", "domains": [ {"helix": 2, "forward": false, "start": 406, "end": 420}, @@ -317,7 +317,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TAACCATAAATCAATCTATCAGGGCGATTCATAAATATTCAA", "domains": [ {"helix": 4, "forward": false, "start": 392, "end": 406}, @@ -326,7 +326,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TCGCCAGAGGGGGTATACTGCGGAATCGGGCCCACTACGTGA", "domains": [ {"helix": 1, "forward": true, "start": 406, "end": 420}, @@ -335,7 +335,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GCCAAAAGGAATATCTAATGCAGATACATAGGAATACCACAT", "domains": [ {"helix": 3, "forward": true, "start": 434, "end": 448}, @@ -344,7 +344,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TTGGGAAGAAAAAAGCGATTTTAAGAACCATTGTGAATTACC", "domains": [ {"helix": 2, "forward": false, "start": 448, "end": 462}, @@ -353,7 +353,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TTTACGAGGCATAGCAAGTTTTTTGGGGAGTTGAGATTTAGA", "domains": [ {"helix": 4, "forward": false, "start": 434, "end": 448}, @@ -362,7 +362,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TCATCTACGTTAATTAGAAAGATTCATCTCGAGGTGCCGTAA", "domains": [ {"helix": 1, "forward": true, "start": 448, "end": 462}, @@ -371,7 +371,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GTAAATTGGGCTGAGAAACACCAGAACGGAAGGCTTGCCCTG", "domains": [ {"helix": 3, "forward": true, "start": 476, "end": 490}, @@ -380,7 +380,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GACCTTCATCAAGACAGATGAACGGTGTACCAACTTTGAAAG", "domains": [ {"helix": 2, "forward": false, "start": 490, "end": 504}, @@ -389,7 +389,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AGTGAGATGGTTTAACCCTAAAGGGAGCATTCAGTGAATAAC", "domains": [ {"helix": 4, "forward": false, "start": 476, "end": 490}, @@ -398,7 +398,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "ACGAGTAATCTTGATAACAAAGCTGCTCCCCCGATTTAGAGC", "domains": [ {"helix": 1, "forward": true, "start": 490, "end": 504}, @@ -407,7 +407,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "ACGAGGCGCAGACACCATGTTACTTAGCTCAAATCCGCGACC", "domains": [ {"helix": 3, "forward": true, "start": 518, "end": 532}, @@ -416,7 +416,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TCATCTTTGACCCTACCTAAAACGAAAGGCCACTACGAAGGC", "domains": [ {"helix": 2, "forward": false, "start": 532, "end": 546}, @@ -425,7 +425,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "ACCGGTCAATCATACGGCGAACGTGGCGTAAATTGTGTCGAT", "domains": [ {"helix": 4, "forward": false, "start": 518, "end": 532}, @@ -434,7 +434,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TGCCCAGCGATTATGTATCATCGCCTGAAGAAAGGAAGGGAA", "domains": [ {"helix": 1, "forward": true, "start": 532, "end": 546}, @@ -443,7 +443,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CATGAGGAAGTTAAGAGGACTAAAGACTAACGGCTACAGAGG", "domains": [ {"helix": 3, "forward": true, "start": 560, "end": 574}, @@ -452,7 +452,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GAGGCTTGCAGGTTCAACCATCGCCCACTTGCGCCGACAATG", "domains": [ {"helix": 2, "forward": false, "start": 574, "end": 588}, @@ -461,7 +461,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "ACTCCATTAAACGGCGGGCGCTAGGGCGCGAGGGTAGCAAAG", "domains": [ {"helix": 4, "forward": false, "start": 560, "end": 574}, @@ -470,7 +470,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CTGAGTTAAAGGCCAGACAGCATCGGAACTGGCAAGTGTAGC", "domains": [ {"helix": 1, "forward": true, "start": 574, "end": 588}, @@ -479,7 +479,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TTTCGAGGTGAAGTATCGGTTTATCAGCGTAGGAGCCTTTAA", "domains": [ {"helix": 3, "forward": true, "start": 602, "end": 616}, @@ -488,7 +488,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AGTGAGAATAGAGTATGGGATTTTGCTAAGTAAATGAATTTT", "domains": [ {"helix": 2, "forward": false, "start": 616, "end": 630}, @@ -497,7 +497,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CTTTTCTTAAACAGTAACCACCACACCCAAAGGCTCCAAACA", "domains": [ {"helix": 4, "forward": false, "start": 602, "end": 616}, @@ -506,7 +506,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TTAAGGAACAACTAAAAATCTCCAAAAAGCCGCGCTTAATGC", "domains": [ {"helix": 1, "forward": true, "start": 616, "end": 630}, @@ -515,7 +515,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GCGTAACGATCTTCAGACAGCCCTCATAAAGCCTGTAGCATT", "domains": [ {"helix": 3, "forward": true, "start": 644, "end": 658}, @@ -524,7 +524,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CACCCTCATTTTACAGAACCGCCACCCTTTTAGTACCGCCAC", "domains": [ {"helix": 2, "forward": false, "start": 658, "end": 672}, @@ -533,7 +533,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CCAAAGTTTTGTCGCGTACTATGGTTGCACAAACTACAACTA", "domains": [ {"helix": 4, "forward": false, "start": 644, "end": 658}, @@ -542,7 +542,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CCCAGGGATAGCAAGTTTCGTCACCAGTTTTGACGAGCACGT", "domains": [ {"helix": 1, "forward": true, "start": 658, "end": 672}, @@ -551,7 +551,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GTATAGCCCGGACCTCGAGAGGGTTGATCAAGGCGGATAAGT", "domains": [ {"helix": 3, "forward": true, "start": 686, "end": 700}, @@ -560,7 +560,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TATTATTCTGAACGCGTATAAACAGTTAGCCTTGAGTAACAG", "domains": [ {"helix": 2, "forward": false, "start": 700, "end": 714}, @@ -569,7 +569,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TGATAGGTGTATCATCGTTAGAATCAGATTGCTCAGTACCTG", "domains": [ {"helix": 4, "forward": false, "start": 686, "end": 700}, @@ -578,7 +578,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GCACATGAAAGTATGGATTAGCGGGGTTGCGGGAGCTAAACA", "domains": [ {"helix": 1, "forward": true, "start": 700, "end": 714}, @@ -587,7 +587,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ACAGGAGTGTACCCTACATGGCTTTTGATCGTTCCAGTAAGC", "domains": [ {"helix": 3, "forward": true, "start": 728, "end": 742}, @@ -596,7 +596,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GGTCAGACGATTCAACCAGAGCCGCCGCGCCGCCACCAGAAC", "domains": [ {"helix": 2, "forward": false, "start": 742, "end": 756}, @@ -605,7 +605,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CATGGTAATAAGTTGGGATTTTAGACAGTCTGAATTTACCCT", "domains": [ {"helix": 4, "forward": false, "start": 728, "end": 742}, @@ -614,7 +614,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GTGGCCTTGATATTTGGAAAGCGCAGTCGAACGGTACGCCAG", "domains": [ {"helix": 1, "forward": true, "start": 742, "end": 756}, @@ -623,7 +623,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CCCTCAGAACCGGTCCTCCCTCAGAGCCTCGCCACCACCGGA", "domains": [ {"helix": 3, "forward": true, "start": 770, "end": 784}, @@ -632,7 +632,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GCGCGTTTTCATCGAGCGACAGAATCAAAGCAGCACCGTAAT", "domains": [ {"helix": 2, "forward": false, "start": 784, "end": 798}, @@ -641,7 +641,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CACCACCCTCAGAGTTTTTATAATCAGTACCGGAACCAGACT", "domains": [ {"helix": 4, "forward": false, "start": 770, "end": 784}, @@ -650,7 +650,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ACCGGCATTTTCGGTCATAATCAAAATCGAGGCCACCGAGTA", "domains": [ {"helix": 1, "forward": true, "start": 784, "end": 798}, @@ -659,7 +659,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TTAGCAAGGCCGTTCCAGTAGCACCATTTTAGAGCCAGCAAA", "domains": [ {"helix": 3, "forward": true, "start": 812, "end": 826}, @@ -668,7 +668,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GAGGGAGGGAAGCAACCAGCGCCAAAGAAGAAAATTCATATG", "domains": [ {"helix": 2, "forward": false, "start": 826, "end": 840}, @@ -677,7 +677,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GTGAAACGTCACCATCACGCAAATTAACCATTTGGGAATTAG", "domains": [ {"helix": 4, "forward": false, "start": 812, "end": 826}, @@ -686,7 +686,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "ATGTAAATATTGACTCACCGACTTGAGCCGTTGTAGCAATAC", "domains": [ {"helix": 1, "forward": true, "start": 826, "end": 840}, @@ -695,7 +695,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AAGACACCACGGCAACATATAAAAGAAAAAATACATAAAGGT", "domains": [ {"helix": 3, "forward": true, "start": 854, "end": 868}, @@ -704,7 +704,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CGCAATAATAACCAGATAGCCGAACAAATTTTAAGAAAAGTA", "domains": [ {"helix": 2, "forward": false, "start": 868, "end": 882}, @@ -713,7 +713,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AGAATAAGTTTATTATAACATCACTTGCCGTAGAAAATACAG", "domains": [ {"helix": 4, "forward": false, "start": 854, "end": 868}, @@ -722,7 +722,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GGGGAATACCCAAAAGTATGTTAGCAAACTGAGTAGAAGAAC", "domains": [ {"helix": 1, "forward": true, "start": 868, "end": 882}, @@ -731,7 +731,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AAACAATGAAATAACCCAATAATAAGAGTACAAGAATTGAGT", "domains": [ {"helix": 3, "forward": true, "start": 896, "end": 910}, @@ -740,7 +740,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AGCGCATTAGACAGTAGCAGCCTTTACATAACGTCAAAAATG", "domains": [ {"helix": 2, "forward": false, "start": 910, "end": 924}, @@ -749,7 +749,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AAAGCAATAGCTATTTGCTGGTAATATCAGAGATAACCCAAG", "domains": [ {"helix": 4, "forward": false, "start": 896, "end": 910}, @@ -758,7 +758,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TAGGGAGAATTAACAGCGCTAATATCAGCAGAACAATATTAC", "domains": [ {"helix": 1, "forward": true, "start": 910, "end": 924}, @@ -767,7 +767,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TTATTTATCCCAGTACAAAATAAACAGCAAGCCTAATTTGCC", "domains": [ {"helix": 3, "forward": true, "start": 938, "end": 952}, @@ -776,7 +776,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TTAAATCAAGATTTTTTAGCGAACCTCCTCTAAGAACGCGAG", "domains": [ {"helix": 2, "forward": false, "start": 952, "end": 966}, @@ -785,7 +785,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GCATCCAAATAAGAACAGGAAAAACGCTCGTCTTTCCAGAAG", "domains": [ {"helix": 4, "forward": false, "start": 938, "end": 952}, @@ -794,7 +794,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AGTAGTTGCTATTTCCAACGCTAACGAGCATGGAAATACCTA", "domains": [ {"helix": 1, "forward": true, "start": 952, "end": 966}, @@ -803,7 +803,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ATAGCAAGCAAAATGAATCATTACCGCGATTTTATTTTCATC", "domains": [ {"helix": 3, "forward": true, "start": 980, "end": 994}, @@ -812,7 +812,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CAATAATCGGCTAGAATATCCCATCCTAGTCCTGAACAAGAA", "domains": [ {"helix": 2, "forward": false, "start": 994, "end": 1008}, @@ -821,7 +821,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AATCAGATATAGAAATCGTCTGAAATGGAAGCAAGCCGTTTT", "domains": [ {"helix": 4, "forward": false, "start": 980, "end": 994}, @@ -830,7 +830,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GTGTCTTTCCTTATCACTCATCGAGAACATTATTTACATTGG", "domains": [ {"helix": 1, "forward": true, "start": 994, "end": 1008}, @@ -839,7 +839,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GCTAATGCAGAACGCAATAAACAACATGGTTCTGTCCAGACG", "domains": [ {"helix": 3, "forward": true, "start": 1022, "end": 1036}, @@ -848,7 +848,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CAACGCCAACATGACTCAACAGTAGGGCACCAGTATAAAGCC", "domains": [ {"helix": 2, "forward": false, "start": 1036, "end": 1050}, @@ -857,7 +857,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AACGCGCCTGTTTAACACGACCAGTAATAGGTAAAGTAATAT", "domains": [ {"helix": 4, "forward": false, "start": 1022, "end": 1036}, @@ -866,7 +866,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "ACGTAATTTAGGCAAAAGTACCGACAAAAAAAGGGACATTCT", "domains": [ {"helix": 1, "forward": true, "start": 1036, "end": 1050}, @@ -875,7 +875,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AAAGCCTGTTTAGCGAATCATAATTACTCCATAAGAATAAAC", "domains": [ {"helix": 3, "forward": true, "start": 1064, "end": 1078}, @@ -884,7 +884,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TCAAATATATTTCGAAATCCAATCGCAAATATGTAAATGCTG", "domains": [ {"helix": 2, "forward": false, "start": 1078, "end": 1092}, @@ -893,7 +893,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "ATGTATCATATGCGGAACCCTTCTGACCATAAGGCGTTAAAG", "domains": [ {"helix": 4, "forward": false, "start": 1064, "end": 1078}, @@ -902,7 +902,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "ACTAGTTAATTTCACGACCGTGTGATAATGAAAGCGTAAGAA", "domains": [ {"helix": 1, "forward": true, "start": 1078, "end": 1092}, @@ -911,7 +911,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "ACCTTTTTAACCCATCATAGGTCTGAGATTAGTGAATTTATC", "domains": [ {"helix": 3, "forward": true, "start": 1106, "end": 1120}, @@ -920,7 +920,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AATCGTCGCTATAATAAATCAATATATGTTTAATGGAAACAG", "domains": [ {"helix": 2, "forward": false, "start": 1120, "end": 1134}, @@ -929,7 +929,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TATCCGGCTTAGGTAATATTTTTGAATGAGAAGAGTCAATTA", "domains": [ {"helix": 4, "forward": false, "start": 1106, "end": 1120}, @@ -938,7 +938,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AATAATTAATTTTCAGATTAAGACGCTGGCTATTAGTCTTTA", "domains": [ {"helix": 1, "forward": true, "start": 1120, "end": 1134}, @@ -947,7 +947,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AATTAATTACATATCAAACATCAAGAAAAAAAAGAAGATGAT", "domains": [ {"helix": 3, "forward": true, "start": 1148, "end": 1162}, @@ -956,7 +956,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AATAACGGATTCAAGAATATACAGTAACTCAGGTTTAACGTC", "domains": [ {"helix": 2, "forward": false, "start": 1162, "end": 1176}, @@ -965,7 +965,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AGTTAACAATTTCAAGCCCTAAAACATCATTACCTGAGCAAA", "domains": [ {"helix": 4, "forward": false, "start": 1148, "end": 1162}, @@ -974,7 +974,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GAGCCTGATTGCTTAATTATTCATTTCAGCCATTAAAAATAC", "domains": [ {"helix": 1, "forward": true, "start": 1162, "end": 1176}, @@ -983,7 +983,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TTGCACGTAAAACACTACCATATCAAAACAATGGAAGGGTTA", "domains": [ {"helix": 3, "forward": true, "start": 1190, "end": 1204}, @@ -992,7 +992,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GGAATTATCATCACTTATCATTTTGCGGTTAAAAGTTTGAGT", "domains": [ {"helix": 2, "forward": false, "start": 1204, "end": 1218}, @@ -1001,7 +1001,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AACAGAAATAAAGAGCAGAAGATAAAACTACTTCTGAATAAA", "domains": [ {"helix": 4, "forward": false, "start": 1190, "end": 1204}, @@ -1010,7 +1010,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GAATATTCCTGATTGATTGTTTGGATTAAGAGGTGAGGCGGT", "domains": [ {"helix": 1, "forward": true, "start": 1204, "end": 1218}, @@ -1019,7 +1019,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TTAATGACTGTAAGGATACCGACAGTGCTGTCTAATCTATTT", "domains": [ {"helix": 5, "forward": true, "start": 84, "end": 91}, @@ -1029,7 +1029,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CTGCCATATCGGCCGTGTCCTTAGTGCTAATAACCCCGCTGT", "domains": [ {"helix": 0, "forward": false, "start": 91, "end": 98}, @@ -1039,7 +1039,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TGGGCGCGTTGTAAACGCCAGGGTTTTCAGAAAGGGGGATGT", "domains": [ {"helix": 5, "forward": true, "start": 126, "end": 133}, @@ -1049,7 +1049,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TCACGACCAGGGTGGCGCAACTGTTGGGCGCCAGCTGGCGGC", "domains": [ {"helix": 0, "forward": false, "start": 133, "end": 140}, @@ -1059,7 +1059,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "ACAGCTGTATCGGCTGCCAGTTTGAGGGTTACGTTGGTGTAG", "domains": [ {"helix": 5, "forward": true, "start": 168, "end": 175}, @@ -1069,7 +1069,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ACGACAGATTGCCCACAACCCGTCGGATATGGGATAGGTCTC", "domains": [ {"helix": 0, "forward": false, "start": 175, "end": 182}, @@ -1079,7 +1079,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GCAAGCGTCATTTTCGCATTAAATTTTTGGTATTTAAATTGT", "domains": [ {"helix": 5, "forward": true, "start": 210, "end": 217}, @@ -1089,7 +1089,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AATCAGCGTCCACGTATGTACCCCGGTTTGTATAAGCAAATA", "domains": [ {"helix": 0, "forward": false, "start": 217, "end": 224}, @@ -1099,7 +1099,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GTTTGATAGATCTAGCCGGAGAGGGTAGTCAATATGATATTC", "domains": [ {"helix": 5, "forward": true, "start": 252, "end": 259}, @@ -1109,7 +1109,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TTTTGAGGGTGGTTAATGTGTAGGTAAACAAATCACCATCAT", "domains": [ {"helix": 0, "forward": false, "start": 259, "end": 266}, @@ -1119,7 +1119,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AAAAGAACCCTGTAATCGGTTGTACCAAGCAAAATTAAGCAA", "domains": [ {"helix": 5, "forward": true, "start": 294, "end": 301}, @@ -1129,7 +1129,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "ATTATGATAGCCCGTACTAATAGTAGTACAAAGAATTAGCGC", "domains": [ {"helix": 0, "forward": false, "start": 301, "end": 308}, @@ -1139,7 +1139,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GAACAAGGTTTGACCCAATTCTGCGAACGAGTGTCTGGAAGT", "domains": [ {"helix": 5, "forward": true, "start": 336, "end": 343}, @@ -1149,7 +1149,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AGATTTAAGTCCACTTAATTGCTGAATAAACTAAAGTACGGG", "domains": [ {"helix": 0, "forward": false, "start": 343, "end": 350}, @@ -1159,7 +1159,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AGGGCGAAGACCGGTTTAATTCGAGCTTTCATTAAGAGGAAG", "domains": [ {"helix": 5, "forward": true, "start": 378, "end": 385}, @@ -1169,7 +1169,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GCGAACCAAAACCGAAATCAGGTCTTTATGCATCAAAAAGAG", "domains": [ {"helix": 0, "forward": false, "start": 385, "end": 392}, @@ -1179,7 +1179,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ACCATCAGCGTCCAAATAGTAAAATGTTTAAGAGGCTTTTGC", "domains": [ {"helix": 5, "forward": true, "start": 420, "end": 427}, @@ -1189,7 +1189,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CTGGATACCCAAATTAAGAGCAACACTAACCAAAATAGCGAC", "domains": [ {"helix": 0, "forward": false, "start": 427, "end": 434}, @@ -1199,7 +1199,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AGCACTATTACAGGAAAACGAACTAACGAGCCAGTCAGGACG", "domains": [ {"helix": 5, "forward": true, "start": 462, "end": 469}, @@ -1209,7 +1209,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AACATTAAATCGGAATTTCAACTTTAATTGGCTCATTATATA", "domains": [ {"helix": 0, "forward": false, "start": 469, "end": 476}, @@ -1219,7 +1219,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TTGACGGATCAACGCAAGAACCGGATATCGCATAGGCTGGCT", "domains": [ {"helix": 5, "forward": true, "start": 504, "end": 511}, @@ -1229,7 +1229,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TACCCAAGGAAAGCAGGGAACCGAACTGACAGACCAGGCGGA", "domains": [ {"helix": 0, "forward": false, "start": 511, "end": 518}, @@ -1239,7 +1239,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GAAAGCGGAGATTTACCAAGCGCGAAACTTACACTAAAACAC", "domains": [ {"helix": 5, "forward": true, "start": 546, "end": 553}, @@ -1249,7 +1249,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TACAACGAAAGGAGGTAAAATACGTAATAGGCAAAAGAATTT", "domains": [ {"helix": 0, "forward": false, "start": 553, "end": 560}, @@ -1259,7 +1259,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GGTCACGCAGCGAAGCTTTTGCGGGATCTTTATTCGGTCGCT", "domains": [ {"helix": 5, "forward": true, "start": 588, "end": 595}, @@ -1269,7 +1269,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CCCTCAGCTGCGCGCTTGATACCGATAGGCATAACCGATAGC", "domains": [ {"helix": 0, "forward": false, "start": 595, "end": 602}, @@ -1279,7 +1279,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GCCGCTACACGTTGAAGGAATTGCGAATGTCAGTTTCAGCGG", "domains": [ {"helix": 5, "forward": true, "start": 630, "end": 637}, @@ -1289,7 +1289,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "ATTTTTTCAGGGCGTCTTTCCAGACGTTAACAACTTTCAATA", "domains": [ {"helix": 0, "forward": false, "start": 637, "end": 644}, @@ -1299,7 +1299,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "ATAACGTACACTGAGCCCAATAGGAACCATCCTCAGAGCCAC", "domains": [ {"helix": 5, "forward": true, "start": 672, "end": 679}, @@ -1309,7 +1309,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TACCGTAGCTTTCCCCGTACTCAGGAGGCAGAACCGCCACAA", "domains": [ {"helix": 0, "forward": false, "start": 679, "end": 686}, @@ -1319,7 +1319,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GGAGGCCAGGATTATAAGAGGCTGAGACTGTATTTCGGAACC", "domains": [ {"helix": 5, "forward": true, "start": 714, "end": 721}, @@ -1329,7 +1329,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CAAGAGAGATTAAATTAACGGGGTCAGTATGCCCCCTGCCAT", "domains": [ {"helix": 0, "forward": false, "start": 721, "end": 728}, @@ -1339,7 +1339,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AATCCTGGCCAGAACACAAACAAATAAAGCGAGGTTGAGGCA", "domains": [ {"helix": 5, "forward": true, "start": 756, "end": 763}, @@ -1349,7 +1349,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CATTAAAAGAAGTGCCACCACCCTCAGACAGCATTGACAGCA", "domains": [ {"helix": 0, "forward": false, "start": 763, "end": 770}, @@ -1359,7 +1359,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AAAGAGTCATCTTTTCATAGCCCCCTTAACCGTCAGACTGTA", "domains": [ {"helix": 5, "forward": true, "start": 798, "end": 805}, @@ -1369,7 +1369,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CGTTTGCCTGTCCAATGAAACCATCGATGTTTGCCTTTAGCA", "domains": [ {"helix": 0, "forward": false, "start": 805, "end": 812}, @@ -1379,7 +1379,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TTCTTTGATCACCGGGAAATTATTCATTCGATTCAACCGATT", "domains": [ {"helix": 5, "forward": true, "start": 840, "end": 847}, @@ -1389,7 +1389,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GTGAATTATTAGTATTGTCACAATCAATCAAAAGGGCGACCA", "domains": [ {"helix": 0, "forward": false, "start": 847, "end": 854}, @@ -1399,7 +1399,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TCAAACTATTACGCAGAACTGGCATGATCAAAACCGAGGAAA", "domains": [ {"helix": 5, "forward": true, "start": 882, "end": 889}, @@ -1409,7 +1409,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ACTCCTTATCGGCCCTTACCGAAGCCCTGTTACCAGAAGGAG", "domains": [ {"helix": 0, "forward": false, "start": 889, "end": 896}, @@ -1419,7 +1419,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CGCCAGCGTAATTGTGAACACCCTGAACCATAAAAACAGGGA", "domains": [ {"helix": 5, "forward": true, "start": 924, "end": 931}, @@ -1429,7 +1429,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TCAGAGGCATTGCAAACGATTTTTTGTTGAGAGAATAACATA", "domains": [ {"helix": 0, "forward": false, "start": 931, "end": 938}, @@ -1439,7 +1439,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CATTTTGAATCTTATGCACCCAGCTACACCGGTTTTGAAGCC", "domains": [ {"helix": 5, "forward": true, "start": 966, "end": 973}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TATCCTGACGCTCAGGCTTATCCGGTATCGACTTGCGGGACA", "domains": [ {"helix": 0, "forward": false, "start": 973, "end": 980}, @@ -1459,7 +1459,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "CAGATTCAGTACCGCATTCCAAGAACGGTTGTAGAAACCAAT", "domains": [ {"helix": 5, "forward": true, "start": 1008, "end": 1015}, @@ -1469,7 +1469,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TAAACCAACCAGTCTCAACAATAGATAAATTTACGAGCATCA", "domains": [ {"helix": 0, "forward": false, "start": 1015, "end": 1022}, @@ -1479,7 +1479,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GGCCAACAGAATATGAGGCATTTTCGAGAGCGCCATATTTAA", "domains": [ {"helix": 5, "forward": true, "start": 1050, "end": 1057}, @@ -1489,7 +1489,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TAATAAGAGAGATATTATACAAATTCTTTTAATTGAGAATAA", "domains": [ {"helix": 0, "forward": false, "start": 1057, "end": 1064}, @@ -1499,7 +1499,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TACGTGGGAAATACTCTTCTGACCTAAAGAGAGAAAACTTTT", "domains": [ {"helix": 5, "forward": true, "start": 1092, "end": 1099}, @@ -1509,7 +1509,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ATGGTTTCACAGACTGGGTTATATAACTGACAAAGAACGCCT", "domains": [ {"helix": 0, "forward": false, "start": 1099, "end": 1106}, @@ -1519,7 +1519,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "ATGCGCGATAGCTTCCTTAGAATCCTTGACCTTGCTTCTGTA", "domains": [ {"helix": 5, "forward": true, "start": 1134, "end": 1141}, @@ -1529,7 +1529,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CATAGCGAACTGATTTTGAATTACCTTTTGAGTGAATAACAA", "domains": [ {"helix": 0, "forward": false, "start": 1141, "end": 1148}, @@ -1539,7 +1539,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CGAACGAAGAGGCGTGAATACCAAGTTATTATCGGGAGAAAC", "domains": [ {"helix": 5, "forward": true, "start": 1176, "end": 1183}, @@ -1549,7 +1549,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "ATCGCGCACCACCAAATTGCGTAGATTTAGTACCTTTTACAT", "domains": [ {"helix": 0, "forward": false, "start": 1183, "end": 1190}, @@ -1559,7 +1559,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CAGTATTTAATCCTATCAGATGATGGCATCACCAGAAGGAGC", "domains": [ {"helix": 5, "forward": true, "start": 1218, "end": 1225}, @@ -1569,7 +1569,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "ATCAATAAACACCGGAACGTTATTAATTAACAAAGAAACCGA", "domains": [ {"helix": 0, "forward": false, "start": 1225, "end": 1232}, @@ -1579,7 +1579,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ACTGCCCGAAATTGTCATGGTCATAGCTAAACGGAGGATCCC", "domains": [ {"helix": 5, "forward": true, "start": 42, "end": 49}, @@ -1589,7 +1589,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CCTGTGTGCTTTCCGGTTGGTGTAATGAACCTCGATAAAGAT", "domains": [ {"helix": 0, "forward": false, "start": 49, "end": 56}, @@ -1599,7 +1599,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CTAATCCTTTGCCCCCTGCAACAGTGCCAATACATTTGAGTC", "domains": [ {"helix": 4, "forward": false, "start": 1232, "end": 1246}, @@ -1608,7 +1608,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CAACTCGTATTACAACTTTACAAACAATATGATTTAGAAGTA", "domains": [ {"helix": 3, "forward": true, "start": 1232, "end": 1246}, diff --git a/examples/output_designs/6_helix_origami_rectangle.dna b/examples/output_designs/6_helix_origami_rectangle.dna index 909a8e13..07553463 100644 --- a/examples/output_designs/6_helix_origami_rectangle.dna +++ b/examples/output_designs/6_helix_origami_rectangle.dna @@ -29,7 +29,7 @@ "is_scaffold": true }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -37,7 +37,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -45,7 +45,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -53,7 +53,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 176}, @@ -61,7 +61,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", "domains": [ {"helix": 2, "forward": false, "start": 160, "end": 176}, @@ -69,7 +69,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", "domains": [ {"helix": 4, "forward": false, "start": 160, "end": 176}, @@ -77,14 +77,14 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", "domains": [ {"helix": 0, "forward": false, "start": 88, "end": 120} ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -92,7 +92,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -100,7 +100,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -108,7 +108,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -116,14 +116,14 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -140,7 +140,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -149,7 +149,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 64}, @@ -157,7 +157,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -166,7 +166,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -175,7 +175,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AATGAATCGGCCAACGCGCGGGGAGTTGCAG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -183,7 +183,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CAAGCGGTCCTGTTTGATGGTGGTACGTGGAC", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -192,7 +192,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TCCAACGTTGGCCCACTACGTGAAAGCCGGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -201,7 +201,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AGTATCGGCCTCAGGAAGATCGCAGTGCGGGC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 128}, @@ -209,7 +209,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -218,7 +218,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -227,7 +227,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -235,7 +235,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -244,7 +244,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GCCAGGGTTGGGAAGGGCGATCGCTCCAGC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -253,7 +253,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CAGCTTTCCGGCACCGCTTCTGGTCAGGCTGC", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 160}, @@ -261,7 +261,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GTCGACTCACGAGCCGGAAGCATACTAACTCA", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -270,7 +270,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, diff --git a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna index a2166a2f..c4630e16 100644 --- a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna +++ b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna @@ -30,7 +30,7 @@ "is_scaffold": true }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -38,7 +38,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -46,7 +46,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -54,7 +54,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 176}, @@ -62,7 +62,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", "domains": [ {"helix": 2, "forward": false, "start": 160, "end": 176}, @@ -70,7 +70,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", "domains": [ {"helix": 4, "forward": false, "start": 160, "end": 176}, @@ -78,14 +78,14 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", "domains": [ {"helix": 0, "forward": false, "start": 88, "end": 120} ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -93,7 +93,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -101,7 +101,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -109,7 +109,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -117,14 +117,14 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -132,7 +132,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -141,7 +141,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -150,7 +150,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 64}, @@ -158,7 +158,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -167,7 +167,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -176,7 +176,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AATGAATCGGCCAACGCGCGGGGAGTTGCAG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -184,7 +184,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CAAGCGGTCCTGTTTGATGGTGGTACGTGGAC", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -193,7 +193,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TCCAACGTTGGCCCACTACGTGAAAGCCGGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -202,7 +202,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AGTATCGGCCTCAGGAAGATCGCAGTGCGGGC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 128}, @@ -210,7 +210,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -219,7 +219,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -228,7 +228,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -236,7 +236,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -245,7 +245,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GCCAGGGTTGGGAAGGGCGATCGCTCCAGC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -254,7 +254,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "CAGCTTTCCGGCACCGCTTCTGGTCAGGCTGC", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 160}, @@ -262,7 +262,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GTCGACTCACGAGCCGGAAGCATACTAACTCA", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -271,7 +271,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, diff --git a/examples/output_designs/hairpin.dna b/examples/output_designs/hairpin.dna index 9a1af2e1..629c9951 100644 --- a/examples/output_designs/hairpin.dna +++ b/examples/output_designs/hairpin.dna @@ -6,7 +6,7 @@ ], "strands": [ { - "color": "#7300de", + "color": "#007200", "sequence": "AAAAACCCCCTGCATGGGGGTTTTT", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 10}, diff --git a/examples/output_designs/idt-plates-explicit.dna b/examples/output_designs/idt-plates-explicit.dna index 6782b63c..27024292 100644 --- a/examples/output_designs/idt-plates-explicit.dna +++ b/examples/output_designs/idt-plates-explicit.dna @@ -7,7 +7,7 @@ ], "strands": [ { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CTATTATAGTTTTACCCTGA", "idt": {"name": "staple1", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A1"}, "domains": [ @@ -16,7 +16,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CAGAAGCAAAAAATCAGGTC", "idt": {"name": "staple2", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B1"}, "domains": [ @@ -25,7 +25,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GCGGATTGCACATAAATCAA", "idt": {"name": "staple3", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C1"}, "domains": [ @@ -34,7 +34,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TCAAAAAGATCGAGAATGAC", "idt": {"name": "staple4", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D1"}, "domains": [ @@ -43,7 +43,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TAAGAGGAAGGTTCAGAAAA", "idt": {"name": "staple5", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E1"}, "domains": [ @@ -52,7 +52,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CCCGAAAGACGCTTTAAACA", "idt": {"name": "staple6", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F1"}, "domains": [ @@ -61,7 +61,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TTCAAATATCCCCCTCAAAT", "idt": {"name": "staple7", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G1"}, "domains": [ @@ -70,7 +70,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GCGTTTTAATTCATTGAATC", "idt": {"name": "staple8", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H1"}, "domains": [ @@ -79,7 +79,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TCGAGCTTCATCATAAATAT", "idt": {"name": "staple9", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A2"}, "domains": [ @@ -88,7 +88,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AAGCGAACCATGCGGAATCG", "idt": {"name": "staple10", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B2"}, "domains": [ @@ -97,7 +97,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GACCGGAAGCCGTCCAATAC", "idt": {"name": "staple11", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C2"}, "domains": [ @@ -106,7 +106,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AAACTCCAACGACTGGATAG", "idt": {"name": "staple12", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D2"}, "domains": [ @@ -115,7 +115,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AGGTCAGGATAAAATGTTTA", "idt": {"name": "staple13", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E2"}, "domains": [ @@ -124,7 +124,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TAGAGAGTACGGGTAATAGT", "idt": {"name": "staple14", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F2"}, "domains": [ @@ -133,7 +133,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CTTTAATTGCTTGCCAGAGG", "idt": {"name": "staple15", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G2"}, "domains": [ @@ -142,7 +142,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TCCTTTTGATAAAAGAAGTT", "idt": {"name": "staple16", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H2"}, "domains": [ @@ -151,7 +151,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AAGAGGTCATAGGCTTTTGC", "idt": {"name": "staple17", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A3"}, "domains": [ @@ -160,7 +160,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TTTTGCGGATAAATAGCGAG", "idt": {"name": "staple18", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B3"}, "domains": [ @@ -169,7 +169,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GGCTTAGAGCATAAAAACCA", "idt": {"name": "staple19", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C3"}, "domains": [ @@ -178,7 +178,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TTAATTGCTGCCAGACGACG", "idt": {"name": "staple20", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D3"}, "domains": [ @@ -187,7 +187,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AATATAATGCCCCTCGTTTA", "idt": {"name": "staple21", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E3"}, "domains": [ @@ -196,7 +196,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TGTAGCTCAAACTATCATAA", "idt": {"name": "staple22", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F3"}, "domains": [ @@ -205,7 +205,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "CATGTTTTAATAAGAGCAAC", "idt": {"name": "staple23", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G3"}, "domains": [ @@ -214,7 +214,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "ATATGCAACTCGAGGCATAG", "idt": {"name": "staple24", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H3"}, "domains": [ @@ -223,7 +223,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AAAGTACGGTAAAGGAATTA", "idt": {"name": "staple25", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A4"}, "domains": [ @@ -232,7 +232,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GTCTGGAAGTCATAACGCCA", "idt": {"name": "staple26", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B4"}, "domains": [ @@ -241,7 +241,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TTCATTCCATAATGCAGATA", "idt": {"name": "staple27", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C4"}, "domains": [ @@ -250,7 +250,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "ATAACAGTTGACATTCAACT", "idt": {"name": "staple28", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D4"}, "domains": [ @@ -259,7 +259,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "ATTCCCAATTTAGGAATACC", "idt": {"name": "staple29", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E4"}, "domains": [ @@ -268,7 +268,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CTGCGAACGAAGTTGAGATT", "idt": {"name": "staple30", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F4"}, "domains": [ @@ -277,7 +277,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GTAGATTTAGAAGATTCATC", "idt": {"name": "staple31", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G4"}, "domains": [ @@ -286,7 +286,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TTTGACCATTTACAGGTAGA", "idt": {"name": "staple32", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H4"}, "domains": [ @@ -295,7 +295,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AGATACATTTACAACATTAT", "idt": {"name": "staple33", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A5"}, "domains": [ @@ -304,7 +304,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CGCAAATGGTAACTAACGGA", "idt": {"name": "staple34", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B5"}, "domains": [ @@ -313,7 +313,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CAATAACCTGTAATAAAACG", "idt": {"name": "staple35", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C5"}, "domains": [ @@ -322,7 +322,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TTTAGCTATAAAATCTACGT", "idt": {"name": "staple36", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D5"}, "domains": [ @@ -331,7 +331,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TTTTCATTTGTTGGGAAGAA", "idt": {"name": "staple37", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E5"}, "domains": [ @@ -340,7 +340,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GGGCGCGAGCAGTCAGGACG", "idt": {"name": "staple38", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F5"}, "domains": [ @@ -349,7 +349,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TGAAAAGGTGTCATTATACC", "idt": {"name": "staple39", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G5"}, "domains": [ @@ -358,7 +358,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GCATCAATTCAAGAACTGGC", "idt": {"name": "staple40", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H5"}, "domains": [ @@ -367,7 +367,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TACTAATAGTATGCGATTTT", "idt": {"name": "staple41", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A6"}, "domains": [ @@ -376,7 +376,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AGTAGCATTAGAATTACCTT", "idt": {"name": "staple42", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B6"}, "domains": [ @@ -385,7 +385,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "ACATCCAATATAATCATTGT", "idt": {"name": "staple43", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C6"}, "domains": [ @@ -394,7 +394,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AATCATACAGATTTCAACTT", "idt": {"name": "staple44", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D6"}, "domains": [ @@ -403,7 +403,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GCAAGGCAAAAGATGGTTTA", "idt": {"name": "staple45", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E6"}, "domains": [ @@ -412,7 +412,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GAATTAGCAAATTGGGCTTG", "idt": {"name": "staple46", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F6"}, "domains": [ @@ -421,7 +421,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AATTAAGCAACGAGTAGTAA", "idt": {"name": "staple47", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G6"}, "domains": [ @@ -430,7 +430,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TAAAGCCTCAAACACCAGAA", "idt": {"name": "staple48", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H6"}, "domains": [ @@ -439,7 +439,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GAGCATAAAGCCTGACGAGA", "idt": {"name": "staple49", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A7"}, "domains": [ @@ -448,7 +448,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CTAAATCGGTTAAGGCTTGC", "idt": {"name": "staple50", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B7"}, "domains": [ @@ -457,7 +457,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TGTACCAAAAATTCAGTGAA", "idt": {"name": "staple51", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C7"}, "domains": [ @@ -466,7 +466,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ACATTATGACAAAGCTGCTC", "idt": {"name": "staple52", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D7"}, "domains": [ @@ -475,7 +475,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CCTGTAATACTCAACGTAAC", "idt": {"name": "staple53", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E7"}, "domains": [ @@ -484,7 +484,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TTTTGCGGGAATTACCCAAA", "idt": {"name": "staple54", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F7"}, "domains": [ @@ -493,7 +493,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GAAGCCTTTACCGGATATTC", "idt": {"name": "staple55", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G7"}, "domains": [ @@ -502,7 +502,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TTTCAACGCATTGACAAGAA", "idt": {"name": "staple56", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H7"}, "domains": [ @@ -511,7 +511,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AGGATAAAAAAAGAGTAATC", "idt": {"name": "staple57", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A8"}, "domains": [ @@ -520,7 +520,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TTTTTAGAACGACCTTCATC", "idt": {"name": "staple58", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B8"}, "domains": [ @@ -529,7 +529,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CCTCATATATTAGGCTGGCT", "idt": {"name": "staple59", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C8"}, "domains": [ @@ -538,7 +538,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TTTAAATGCAACCAGGCGCA", "idt": {"name": "staple60", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D8"}, "domains": [ @@ -547,7 +547,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "ATGCCTGAGTCGGTGTACAG", "idt": {"name": "staple61", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E8"}, "domains": [ @@ -556,7 +556,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AATGTGTAGGGACAGATGAA", "idt": {"name": "staple62", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F8"}, "domains": [ @@ -565,7 +565,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TAAAGATTCATTTGAAAGAG", "idt": {"name": "staple63", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G8"}, "domains": [ @@ -574,7 +574,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AAAGGGTGAGACTGACCAAC", "idt": {"name": "staple64", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H8"}, "domains": [ @@ -583,7 +583,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AAAGGCCGGAAGGGAACCGA", "idt": {"name": "staple65", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A9"}, "domains": [ @@ -592,7 +592,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GACAGTCAAAGTCAATCATA", "idt": {"name": "staple66", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B9"}, "domains": [ @@ -601,7 +601,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TCACCATCAAGGCGCAGACG", "idt": {"name": "staple67", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C9"}, "domains": [ @@ -610,7 +610,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TATGATATTCGCCGGAACGA", "idt": {"name": "staple68", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D9"}, "domains": [ @@ -619,7 +619,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AACCGTTCTAATGTTACTTA", "idt": {"name": "staple69", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E9"}, "domains": [ @@ -628,7 +628,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GCTGATAAATGACCTGCTCC", "idt": {"name": "staple70", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F9"}, "domains": [ @@ -637,7 +637,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TAATGCCGGACGAAATCCGC", "idt": {"name": "staple71", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G9"}, "domains": [ @@ -646,7 +646,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GAGGGTAGCTTAAATTGTGT", "idt": {"name": "staple72", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H9"}, "domains": [ @@ -655,7 +655,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ATTTTTGAGACATCGCCTGA", "idt": {"name": "staple73", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A10"}, "domains": [ @@ -664,7 +664,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GATCTACAAAAGATTTGTAT", "idt": {"name": "staple74", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B10"}, "domains": [ @@ -673,7 +673,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GGCTATCAGGAGTACAACGG", "idt": {"name": "staple75", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C10"}, "domains": [ @@ -682,7 +682,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TCATTGCCTGCGCGAAACAA", "idt": {"name": "staple76", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D10"}, "domains": [ @@ -691,7 +691,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AGAGTCTGGATTATACCAAG", "idt": {"name": "staple77", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E10"}, "domains": [ @@ -700,7 +700,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GCAAACAAGACCCCCAGCGA", "idt": {"name": "staple78", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F10"}, "domains": [ @@ -709,7 +709,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GAATCGATGATCATCTTTGA", "idt": {"name": "staple79", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G10"}, "domains": [ @@ -718,7 +718,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "ACGGTAATCGACTAAAACAC", "idt": {"name": "staple80", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H10"}, "domains": [ @@ -727,7 +727,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TAAAACTAGCAAAAGAATAC", "idt": {"name": "staple81", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A11"}, "domains": [ @@ -736,7 +736,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "ATGTCAATCACGAAAGAGGC", "idt": {"name": "staple82", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B11"}, "domains": [ @@ -745,7 +745,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TATGTACCCCCAACCTAAAA", "idt": {"name": "staple83", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C11"}, "domains": [ @@ -754,7 +754,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GGTTGATAATACGAAGGCAC", "idt": {"name": "staple84", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D11"}, "domains": [ @@ -763,7 +763,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CAGAAAAGCCTAATGCCACT", "idt": {"name": "staple85", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E11"}, "domains": [ @@ -772,7 +772,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CCAAAAACAGGTAAAATACG", "idt": {"name": "staple86", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F11"}, "domains": [ @@ -781,7 +781,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GAAGATTGTACATTAAACGG", "idt": {"name": "staple87", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G11"}, "domains": [ @@ -790,7 +790,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TAAGCAAATAAGGAAGTTTC", "idt": {"name": "staple88", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H11"}, "domains": [ @@ -799,7 +799,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TTTAAATTGTCTTTTTCATG", "idt": {"name": "staple89", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A12"}, "domains": [ @@ -808,7 +808,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AAACGTTAATGGACTAAAGA", "idt": {"name": "staple90", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B12"}, "domains": [ @@ -817,7 +817,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ATTTTGTTAAGAGGCTTTGA", "idt": {"name": "staple91", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C12"}, "domains": [ @@ -826,7 +826,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AATTCGCATTAACGGCTACA", "idt": {"name": "staple92", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D12"}, "domains": [ @@ -835,7 +835,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AAATTTTTGTCGAGGGTAGC", "idt": {"name": "staple93", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E12"}, "domains": [ @@ -844,7 +844,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TAAATCAGCTAGCATCGGAA", "idt": {"name": "staple94", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F12"}, "domains": [ @@ -853,7 +853,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CATTTTTTAAAGCGAAAGAC", "idt": {"name": "staple95", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G12"}, "domains": [ @@ -862,7 +862,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CCAATAGGAACACCCTCAGC", "idt": {"name": "staple96", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H12"}, "domains": [ @@ -871,7 +871,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CGCCATCAAAGCGGGATCGT", "idt": {"name": "staple97", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A1"}, "domains": [ @@ -880,7 +880,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AATAATTCGCGGCCGCTTTT", "idt": {"name": "staple98", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B1"}, "domains": [ @@ -889,7 +889,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GTCTGGCCTTGGGAGTTAAA", "idt": {"name": "staple99", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C1"}, "domains": [ @@ -898,7 +898,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CCTGTAGCCAGAGGCTTGCA", "idt": {"name": "staple100", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D1"}, "domains": [ @@ -907,7 +907,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GCTTTCATCATTCGGTCGCT", "idt": {"name": "staple101", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E1"}, "domains": [ @@ -916,7 +916,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "ACATTAAATGAACCGATATA", "idt": {"name": "staple102", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F1"}, "domains": [ @@ -925,7 +925,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TGAGCGAGTAGCCCACGCAT", "idt": {"name": "staple103", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G1"}, "domains": [ @@ -934,7 +934,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ACAACCCGTCAACAACCATC", "idt": {"name": "staple104", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H1"}, "domains": [ @@ -943,7 +943,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GGATTCTCCGCGACAATGAC", "idt": {"name": "staple105", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A2"}, "domains": [ @@ -952,7 +952,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TGGGAACAAAATAGTTGCGC", "idt": {"name": "staple106", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B2"}, "domains": [ @@ -961,7 +961,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CGGCGGATTGCTTGATACCG", "idt": {"name": "staple107", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C2"}, "domains": [ @@ -970,7 +970,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "ACCGTAATGGTCTTAAACAG", "idt": {"name": "staple108", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D2"}, "domains": [ @@ -979,7 +979,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GATAGGTCACGAGGTGAATT", "idt": {"name": "staple109", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E2"}, "domains": [ @@ -988,7 +988,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GTTGGTGTAGGCTTGCTTTC", "idt": {"name": "staple110", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F2"}, "domains": [ @@ -997,7 +997,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "ATGGGCGCATCGGTTTATCA", "idt": {"name": "staple111", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G2"}, "domains": [ @@ -1006,7 +1006,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CGTAACCGTGTTAATTGTAT", "idt": {"name": "staple112", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H2"}, "domains": [ @@ -1015,7 +1015,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CATCTGCCAGAAAGGAGCCT", "idt": {"name": "staple113", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A3"}, "domains": [ @@ -1024,7 +1024,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TTTGAGGGGAAAAGGCTCCA", "idt": {"name": "staple114", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B3"}, "domains": [ @@ -1033,7 +1033,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CGACGACAGTTCTCCAAAAA", "idt": {"name": "staple115", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C3"}, "domains": [ @@ -1042,7 +1042,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "ATCGGCCTCAACGTTGAAAA", "idt": {"name": "staple116", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D3"}, "domains": [ @@ -1051,7 +1051,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GGAAGATCGCTAATTTTTTC", "idt": {"name": "staple117", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E3"}, "domains": [ @@ -1060,7 +1060,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ACTCCAGCCATTGCGAATAA", "idt": {"name": "staple118", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F3"}, "domains": [ @@ -1069,7 +1069,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GCTTTCCGGCACTAAAGGAA", "idt": {"name": "staple119", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G3"}, "domains": [ @@ -1078,7 +1078,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "ACCGCTTCTGGAAAGGAACA", "idt": {"name": "staple120", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H3"}, "domains": [ @@ -1087,7 +1087,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GTGCCGGAAAAGTGAGAATA", "idt": {"name": "staple121", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A4"}, "domains": [ @@ -1096,7 +1096,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CCAGGCAAAGGTTTCAGCGG", "idt": {"name": "staple122", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B4"}, "domains": [ @@ -1105,7 +1105,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CGCCATTCGCACTTTCAACA", "idt": {"name": "staple123", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C4"}, "domains": [ @@ -1114,7 +1114,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CATTCAGGCTTTGCTAAACA", "idt": {"name": "staple124", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D4"}, "domains": [ @@ -1123,7 +1123,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GCGCAACTGTGTATGGGATT", "idt": {"name": "staple125", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E4"}, "domains": [ @@ -1132,7 +1132,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TGGGAAGGGCTGAATTTTCT", "idt": {"name": "staple126", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F4"}, "domains": [ @@ -1141,7 +1141,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GATCGGTGCGCGTTAGTAAA", "idt": {"name": "staple127", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G4"}, "domains": [ @@ -1150,7 +1150,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GGCCTCTTCGTCTTTCCAGA", "idt": {"name": "staple128", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H4"}, "domains": [ @@ -1159,7 +1159,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CTATTACGCCAGTTTTGTCG", "idt": {"name": "staple129", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A5"}, "domains": [ @@ -1168,7 +1168,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AGCTGGCGAAAACGATCTAA", "idt": {"name": "staple130", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B5"}, "domains": [ @@ -1177,7 +1177,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AGGGGGATGTTAGTTAGCGT", "idt": {"name": "staple131", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C5"}, "domains": [ @@ -1186,7 +1186,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GCTGCAAGGCACAGCCCTCA", "idt": {"name": "staple132", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D5"}, "domains": [ @@ -1195,7 +1195,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GATTAAGTTGCATTCCACAG", "idt": {"name": "staple133", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E5"}, "domains": [ @@ -1204,7 +1204,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GGTAACGCCAACGCCTGTAG", "idt": {"name": "staple134", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F5"}, "domains": [ @@ -1213,7 +1213,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GGGTTTTCCCACAAACTACA", "idt": {"name": "staple135", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G5"}, "domains": [ @@ -1222,7 +1222,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AGTCACGACGCGTCACCAGT", "idt": {"name": "staple136", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H5"}, "domains": [ @@ -1231,7 +1231,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TTGTAAAACGCACTGAGTTT", "idt": {"name": "staple137", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A6"}, "domains": [ @@ -1240,7 +1240,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ACGGCCAGTGTGTACCGTAA", "idt": {"name": "staple138", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B6"}, "domains": [ @@ -1249,7 +1249,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CCAAGCTTGCTAGGAACCCA", "idt": {"name": "staple139", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C6"}, "domains": [ @@ -1258,7 +1258,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "ATGCCTGCAGGCAAGCCCAA", "idt": {"name": "staple140", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D6"}, "domains": [ @@ -1267,7 +1267,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GTCGACTCTATTCAGGGATA", "idt": {"name": "staple141", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E6"}, "domains": [ @@ -1276,7 +1276,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GAGGATCCCCCACCCTCATT", "idt": {"name": "staple142", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F6"}, "domains": [ @@ -1285,7 +1285,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GGGTACCGAGTCAGAGCCAC", "idt": {"name": "staple143", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G6"}, "domains": [ @@ -1294,7 +1294,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CTCGAATTCGACCGCCACCC", "idt": {"name": "staple144", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H6"}, "domains": [ @@ -1303,7 +1303,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TAATCATGGTCACCCTCAGA", "idt": {"name": "staple145", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A7"}, "domains": [ @@ -1312,7 +1312,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CATAGCTGTTTCAGAACCGC", "idt": {"name": "staple146", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B7"}, "domains": [ @@ -1321,7 +1321,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TCCTGTGTGAACCGCCACCC", "idt": {"name": "staple147", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C7"}, "domains": [ @@ -1330,7 +1330,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AATTGTTATCGAGGTTTAGT", "idt": {"name": "staple148", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D7"}, "domains": [ @@ -1339,7 +1339,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CGCTCACAATCCGTACTCAG", "idt": {"name": "staple149", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E7"}, "domains": [ @@ -1348,7 +1348,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TCCACACAACAGGTGTATCA", "idt": {"name": "staple150", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F7"}, "domains": [ @@ -1357,7 +1357,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "ATACGAGCCGAGCCCGGAAT", "idt": {"name": "staple151", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G7"}, "domains": [ @@ -1366,7 +1366,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GAAGCATAAAATATAAGTAT", "idt": {"name": "staple152", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H7"}, "domains": [ @@ -1375,7 +1375,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GTGTAAAGCCGAGAGGGTTG", "idt": {"name": "staple153", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A8"}, "domains": [ @@ -1384,7 +1384,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TGGGGTGCCTAAGTGCCGTC", "idt": {"name": "staple154", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B8"}, "domains": [ @@ -1393,7 +1393,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AATGAGTGAGCCAGGCGGAT", "idt": {"name": "staple155", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C8"}, "domains": [ @@ -1402,7 +1402,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CTAACTCACATTGCTCAGTA", "idt": {"name": "staple156", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D8"}, "domains": [ @@ -1411,7 +1411,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TTAATTGCGTTAGCGGGGTT", "idt": {"name": "staple157", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E8"}, "domains": [ @@ -1420,7 +1420,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TGCGCTCACTGGATTAGGAT", "idt": {"name": "staple158", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F8"}, "domains": [ @@ -1429,7 +1429,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GCCCGCTTTCCTCAAGAGAA", "idt": {"name": "staple159", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G8"}, "domains": [ @@ -1438,7 +1438,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CAGTCGGGAAGCTGAGACTC", "idt": {"name": "staple160", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H8"}, "domains": [ @@ -1447,7 +1447,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ACCTGTCGTGGTATTAAGAG", "idt": {"name": "staple161", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A9"}, "domains": [ @@ -1456,7 +1456,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CCAGCTGCATAAACATGAAA", "idt": {"name": "staple162", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B9"}, "domains": [ @@ -1465,7 +1465,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TAATGAATCGTATTATTCTG", "idt": {"name": "staple163", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C9"}, "domains": [ @@ -1474,7 +1474,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GCCAACGCGCTTTCGGAACC", "idt": {"name": "staple164", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D9"}, "domains": [ @@ -1483,7 +1483,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GGGGAGAGGCCCCCTGCCTA", "idt": {"name": "staple165", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E9"}, "domains": [ @@ -1492,7 +1492,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GGTTTGCGTACAGTTAATGC", "idt": {"name": "staple166", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F9"}, "domains": [ @@ -1501,7 +1501,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TTGGGCGCCACCCGTATAAA", "idt": {"name": "staple167", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G9"}, "domains": [ @@ -1510,7 +1510,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GGGTGGTTTTAGTAACAGTG", "idt": {"name": "staple168", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H9"}, "domains": [ @@ -1519,7 +1519,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TCTTTTCACCCAGTGCCTTG", "idt": {"name": "staple169", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A10"}, "domains": [ @@ -1528,7 +1528,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AGTGAGACGGTTAACGGGGT", "idt": {"name": "staple170", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B10"}, "domains": [ @@ -1537,7 +1537,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GCAACAGCTGGTAATAAGTT", "idt": {"name": "staple171", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C10"}, "domains": [ @@ -1546,7 +1546,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "ATTGCCCTTCGAGTGTACTG", "idt": {"name": "staple172", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D10"}, "domains": [ @@ -1555,7 +1555,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "ACCGCCTGGCGATGATACAG", "idt": {"name": "staple173", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E10"}, "domains": [ @@ -1564,7 +1564,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CCTGAGAGAGCATGGCTTTT", "idt": {"name": "staple174", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F10"}, "domains": [ @@ -1573,7 +1573,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TTGCAGCAAGAAGCGTCATA", "idt": {"name": "staple175", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G10"}, "domains": [ @@ -1582,7 +1582,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CGGTCCACGCCCGTTCCAGT", "idt": {"name": "staple176", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H10"}, "domains": [ @@ -1591,7 +1591,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TGGTTTGCCCTCTGAATTTA", "idt": {"name": "staple177", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A11"}, "domains": [ @@ -1600,7 +1600,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CAGCAGGCGAAAGCGCAGTC", "idt": {"name": "staple178", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B11"}, "domains": [ @@ -1609,7 +1609,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AAATCCTGTTCCAGAATGGA", "idt": {"name": "staple179", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C11"}, "domains": [ @@ -1618,7 +1618,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TGATGGTGGTCTCATTAAAG", "idt": {"name": "staple180", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D11"}, "domains": [ @@ -1627,7 +1627,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TCCGAAATCGCAAATAAATC", "idt": {"name": "staple181", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E11"}, "domains": [ @@ -1636,7 +1636,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GCAAAATCCCTATTCACAAA", "idt": {"name": "staple182", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F11"}, "domains": [ @@ -1645,7 +1645,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TTATAAATCATTGGCCTTGA", "idt": {"name": "staple183", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G11"}, "domains": [ @@ -1654,7 +1654,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AAAGAATAGCGGTCAGACGA", "idt": {"name": "staple184", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H11"}, "domains": [ @@ -1663,7 +1663,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CCGAGATAGGGGTTGAGGCA", "idt": {"name": "staple185", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A12"}, "domains": [ @@ -1672,7 +1672,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GTTGAGTGTTATTGACAGGA", "idt": {"name": "staple186", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B12"}, "domains": [ @@ -1681,7 +1681,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GTTCCAGTTTCGCCGCCAGC", "idt": {"name": "staple187", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C12"}, "domains": [ @@ -1690,7 +1690,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GGAACAAGAGCCACCAGAGC", "idt": {"name": "staple188", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D12"}, "domains": [ @@ -1699,7 +1699,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TCCACTATTAACCAGAACCA", "idt": {"name": "staple189", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E12"}, "domains": [ @@ -1708,7 +1708,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AAGAACGTGGCAGAGCCGCC", "idt": {"name": "staple190", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F12"}, "domains": [ @@ -1717,7 +1717,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "ACTCCAACGTCCACCACCCT", "idt": {"name": "staple191", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G12"}, "domains": [ @@ -1726,7 +1726,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "CAAAGGGCGAACCCTCAGAG", "idt": {"name": "staple192", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H12"}, "domains": [ @@ -1735,7 +1735,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AAAACCGTCTCAGAACCGCC", "idt": {"name": "staple193", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "A1"}, "domains": [ @@ -1744,7 +1744,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "ATCAGGGCGACCGCCACCCT", "idt": {"name": "staple194", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "B1"}, "domains": [ @@ -1753,7 +1753,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TGGCCCACTATCCCTCAGAG", "idt": {"name": "staple195", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "C1"}, "domains": [ @@ -1762,7 +1762,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CGTGAACCATCGGAACCGCC", "idt": {"name": "staple196", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "D1"}, "domains": [ @@ -1771,7 +1771,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CACCCAAATCGAGCCACCAC", "idt": {"name": "staple197", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "E1"}, "domains": [ @@ -1780,7 +1780,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AAGTTTTTTGACCGGAACCA", "idt": {"name": "staple198", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "F1"}, "domains": [ @@ -1789,7 +1789,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GGGTCGAGGTAATCAAAATC", "idt": {"name": "staple199", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "G1"}, "domains": [ @@ -1798,7 +1798,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GCCGTAAAGCATCTTTTCAT", "idt": {"name": "staple200", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "H1"}, "domains": [ @@ -1807,7 +1807,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "ACTAAATCGGAGCGTTTGCC", "idt": {"name": "staple201", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "A2"}, "domains": [ @@ -1816,7 +1816,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AACCCTAAAGCCCCCTTATT", "idt": {"name": "staple202", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "B2"}, "domains": [ @@ -1825,7 +1825,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GGAGCCCCCGTCGGTCATAG", "idt": {"name": "staple203", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "C2"}, "domains": [ @@ -1834,7 +1834,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "ATTTAGAGCTATCGGCATTT", "idt": {"name": "staple204", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "D2"}, "domains": [ @@ -1843,7 +1843,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TGACGGGGAAGCGCGTTTTC", "idt": {"name": "staple205", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "E2"}, "domains": [ @@ -1852,7 +1852,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AGCCGGCGAATCAGACTGTA", "idt": {"name": "staple206", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "F2"}, "domains": [ @@ -1861,7 +1861,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CGTGGCGAGAGCCTTTAGCG", "idt": {"name": "staple207", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "G2"}, "domains": [ @@ -1870,7 +1870,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AAGGAAGGGAAATCAAGTTT", "idt": {"name": "staple208", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "H2"}, "domains": [ diff --git a/examples/output_designs/long_range_crossovers.dna b/examples/output_designs/long_range_crossovers.dna index 96f21359..e43e95df 100644 --- a/examples/output_designs/long_range_crossovers.dna +++ b/examples/output_designs/long_range_crossovers.dna @@ -21,168 +21,168 @@ ], "strands": [ { - "color": "#aaaa00", + "color": "#cc0000", "domains": [ {"helix": 0, "forward": false, "start": 0, "end": 16}, {"helix": 15, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#b8056c", + "color": "#f7931e", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, {"helix": 0, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#007200", + "color": "#f74308", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 48}, {"helix": 15, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#cc0000", + "color": "#57bb00", "domains": [ {"helix": 1, "forward": false, "start": 0, "end": 16}, {"helix": 14, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#f7931e", + "color": "#888888", "domains": [ {"helix": 14, "forward": true, "start": 16, "end": 32}, {"helix": 1, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#f74308", + "color": "#32b86c", "domains": [ {"helix": 1, "forward": false, "start": 32, "end": 48}, {"helix": 14, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#57bb00", + "color": "#333333", "domains": [ {"helix": 2, "forward": false, "start": 0, "end": 16}, {"helix": 13, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#888888", + "color": "#320096", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, {"helix": 2, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#32b86c", + "color": "#03b6a2", "domains": [ {"helix": 2, "forward": false, "start": 32, "end": 48}, {"helix": 13, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#333333", + "color": "#7300de", "domains": [ {"helix": 3, "forward": false, "start": 0, "end": 16}, {"helix": 12, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#320096", + "color": "#aaaa00", "domains": [ {"helix": 12, "forward": true, "start": 16, "end": 32}, {"helix": 3, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#03b6a2", + "color": "#b8056c", "domains": [ {"helix": 3, "forward": false, "start": 32, "end": 48}, {"helix": 12, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#7300de", + "color": "#007200", "domains": [ {"helix": 4, "forward": false, "start": 0, "end": 16}, {"helix": 11, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#aaaa00", + "color": "#cc0000", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, {"helix": 4, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#b8056c", + "color": "#f7931e", "domains": [ {"helix": 4, "forward": false, "start": 32, "end": 48}, {"helix": 11, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#007200", + "color": "#f74308", "domains": [ {"helix": 5, "forward": false, "start": 0, "end": 16}, {"helix": 10, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#cc0000", + "color": "#57bb00", "domains": [ {"helix": 10, "forward": true, "start": 16, "end": 32}, {"helix": 5, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#f7931e", + "color": "#888888", "domains": [ {"helix": 5, "forward": false, "start": 32, "end": 48}, {"helix": 10, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#f74308", + "color": "#32b86c", "domains": [ {"helix": 6, "forward": false, "start": 0, "end": 16}, {"helix": 9, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#57bb00", + "color": "#333333", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, {"helix": 6, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#888888", + "color": "#320096", "domains": [ {"helix": 6, "forward": false, "start": 32, "end": 48}, {"helix": 9, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#32b86c", + "color": "#03b6a2", "domains": [ {"helix": 7, "forward": false, "start": 0, "end": 16}, {"helix": 8, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#333333", + "color": "#7300de", "domains": [ {"helix": 8, "forward": true, "start": 16, "end": 32}, {"helix": 7, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#320096", + "color": "#aaaa00", "domains": [ {"helix": 7, "forward": false, "start": 32, "end": 48}, {"helix": 8, "forward": true, "start": 32, "end": 48} diff --git a/examples/output_designs/loopouts_all_types.dna b/examples/output_designs/loopouts_all_types.dna index c54f3f0d..788758b0 100644 --- a/examples/output_designs/loopouts_all_types.dna +++ b/examples/output_designs/loopouts_all_types.dna @@ -8,7 +8,7 @@ ], "strands": [ { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "ACGACGACTTTACGTCGTCGTTTTACGACGACGATTTACTTACGCACGACGATTTTTTTTTTACGTTGCAGGTCGTCGTGACGACGACTGTCGTCGT", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 8}, diff --git a/examples/output_designs/many_helices_modifications.dna b/examples/output_designs/many_helices_modifications.dna index 31eb5071..6c63322e 100644 --- a/examples/output_designs/many_helices_modifications.dna +++ b/examples/output_designs/many_helices_modifications.dna @@ -12,12 +12,6 @@ {"grid_position": [0, 7]} ], "modifications_in_design": { - "/5Biosg/": { - "display_text": "B", - "idt_text": "/5Biosg/", - "display_connector": false, - "location": "5'" - }, "/iBiodT/": { "display_text": "B", "idt_text": "/iBiodT/", @@ -25,6 +19,12 @@ "location": "internal", "allowed_bases": ["T"] }, + "/5Biosg/": { + "display_text": "B", + "idt_text": "/5Biosg/", + "display_connector": false, + "location": "5'" + }, "/3Cy3Sp/": { "display_text": "Cy3", "idt_text": "/3Cy3Sp/", @@ -40,7 +40,7 @@ }, "strands": [ { - "color": "#7300de", + "color": "#007200", "sequence": "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 16, "deletions": [11, 12]}, diff --git a/examples/output_designs/proposal.dna b/examples/output_designs/proposal.dna index c03a732a..f6bae9df 100644 --- a/examples/output_designs/proposal.dna +++ b/examples/output_designs/proposal.dna @@ -108,7 +108,7 @@ "is_scaffold": true }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AACAATATTACCGATAGTTGCGCCGACAATGA", "idt": {"name": "ST15[248]0[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -117,7 +117,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ACTTTGAAATCATAAGGGAACCGTATAAGTA", "idt": {"name": "ST2[231]1[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -126,7 +126,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TAGCCCGGACGTCGAGAGGGTTGAAACTGACCA", "idt": {"name": "ST1[248]2[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -135,7 +135,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CAACACTAAAGGAATTACGAGGCAATCAAAAT", "idt": {"name": "ST4[231]3[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -144,7 +144,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CACCGGAATGCCATCTTTTCATATAGTAAGAG", "idt": {"name": "ST3[248]4[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -153,7 +153,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TTAGAGCTAAGAGGTCATTTTTGCGGAATAC", "idt": {"name": "ST6[231]5[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -162,7 +162,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CCAAAAGAAGGAAACGCAATAATAACGGATGGC", "idt": {"name": "ST5[248]6[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -171,7 +171,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TAAATGCAAATTTTTAGAACCCTTTTTAGCG", "idt": {"name": "ST8[231]7[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -180,7 +180,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AACCTCCCGTAAGAACGCGAGGCGCATATATTT", "idt": {"name": "ST7[248]8[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -189,7 +189,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GCTTTCATTTCGCGTCTGGCCTTCCTGTTTAG", "idt": {"name": "ST10[231]9[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -198,7 +198,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TATCATATATTACTAGAAAAAGCCTGTAGCCA", "idt": {"name": "ST9[248]10[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -207,7 +207,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CTAGAGGAGCTTGCATGCCTGCATTACCTGA", "idt": {"name": "ST12[231]11[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -216,7 +216,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GCAAAAGAAGAATTATTCATTTCAAGGTCGACT", "idt": {"name": "ST11[248]12[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -225,7 +225,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TCCCTTATATGGTGGTTCCGAAAAATATCTT", "idt": {"name": "ST14[231]13[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -234,7 +234,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TAGGAGCACAGGAAGGTTATCTAATCGGCAAAA", "idt": {"name": "ST13[248]14[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -243,7 +243,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CAACAACCATCGGCCTTGCTGGTAATATCCAG", "idt": {"name": "ST0[231]15[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -252,7 +252,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GAGCTTGAAAGTTTCCATTAAACGAACCTAAA", "idt": {"name": "ST15[56]1[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -262,7 +262,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "ACGAAAGAGAGTAGTAAATTGGGCTGAATTAC", "idt": {"name": "ST1[56]3[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -272,7 +272,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CTTATGCGGCTTTAAACAGTTCAGTCTTTAC", "idt": {"name": "ST3[56]5[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -282,7 +282,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CCTGACTATCTGTTTAGCTATATTTAATTCTAC", "idt": {"name": "ST5[56]7[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -292,7 +292,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TAATAGTAGCCTGAGAGTCTGGAGAACTAGCA", "idt": {"name": "ST7[56]9[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -302,7 +302,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TGTCAATCGATCGCACTCCAGCCCAGGCAAA", "idt": {"name": "ST9[56]11[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -312,7 +312,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GCGCCATTCGCGCTCACTGCCCGCTTTAATGAA", "idt": {"name": "ST11[56]13[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -322,7 +322,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TCGGCCAACGGGTCGAGGTGCCGTCCGATTTA", "idt": {"name": "ST13[56]15[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -332,7 +332,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CATGAGGCGGGGAAAGCCGGCGCAAATCAAG", "idt": {"name": "ST0[71]14[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -342,7 +342,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CAGAACGGCAAAAGAATACACGACTTTTT", "idt": {"name": "ST2[71]0[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -352,7 +352,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CTCAAATATTTTAAGAACTGGCGAGAAACAC", "idt": {"name": "ST4[71]2[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -362,7 +362,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CAATAACTATAGTCAGAAGCATGAATCCCC", "idt": {"name": "ST6[71]4[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -372,7 +372,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GTCATTGTAGCATTAACATCCCAAATGGT", "idt": {"name": "ST8[71]6[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -382,7 +382,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TCAGGAAATATGTACCCCGGTTGGCTATCAG", "idt": {"name": "ST10[71]8[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -392,7 +392,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TTGCGTTGCCATTCAGGCTGCGTATCGGCC", "idt": {"name": "ST12[71]10[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -402,7 +402,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TTTTTTGGCGCGGGGAGAGGCCACATTAA", "idt": {"name": "ST14[71]12[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -412,7 +412,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GAGAAAGGGGCTTTGAGGACTAAATAAAACAC", "idt": {"name": "ST15[88]1[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -422,7 +422,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TCATCTTTGAAGGCTTGCCCTGACTCATTATA", "idt": {"name": "ST1[88]3[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -432,7 +432,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CCAGTCAGGTCATAAATATTCATAAGCGGAT", "idt": {"name": "ST3[88]5[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -442,7 +442,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TGCATCAAACATTAGATACATTTCGAATAAATC", "idt": {"name": "ST5[88]7[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -452,7 +452,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "ATACAGGCATGAGAGATCTACAAAGATAATCA", "idt": {"name": "ST7[88]9[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -462,7 +462,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GAAAAGCCGAGGGGACGACGACAGCAACTGT", "idt": {"name": "ST9[88]11[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -472,7 +472,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TGGGAAGGGAATGAGTGAGCTAACTGGTTTGCG", "idt": {"name": "ST11[88]13[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -482,7 +482,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "TATTGGGCGACGTGAACCATCACCAACGTGGC", "idt": {"name": "ST13[88]15[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -492,7 +492,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GCTACAGAAAGGGATTTTTATAATCAGGGCGAT", "idt": {"name": "ST0[103]14[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -502,7 +502,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CAGTGAATACCCCCAGCGATTATTAGCAACG", "idt": {"name": "ST2[103]0[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -512,7 +512,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GCGGAATCGACGTTGGGAAGAAAACTGCTCATT", "idt": {"name": "ST4[103]2[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -522,7 +522,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AGTTTGACAAGATTAAGAGGAAGTCCAATACT", "idt": {"name": "ST6[103]4[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -532,7 +532,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GCTATTTTAGGCAAAGAATTAGCGTAGATTT", "idt": {"name": "ST8[103]6[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -542,7 +542,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GCCAGTTTCCAAAAACAGGAAGATGAGAGGGTA", "idt": {"name": "ST10[103]8[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -552,7 +552,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GGGTGCCTCGATCGGTGCGGGCCCGTGCATCT", "idt": {"name": "ST12[103]10[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -562,7 +562,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GGCCCACTCCAGGGTGGTTTTTCAAAGCCTG", "idt": {"name": "ST14[103]12[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -572,7 +572,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GCCACCGAGCATCGGAACGAGGGACCAAGC", "idt": {"name": "ST15[120]1[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -582,7 +582,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GCGAAACAATCAACGTAACAAAGATCTACG", "idt": {"name": "ST1[120]3[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -592,7 +592,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TTAATAAATAGACTGGATAGCGCCCGAAA", "idt": {"name": "ST3[120]5[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -602,7 +602,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "GACTTCAAACAATTCTGCGAACGAAAAATTA", "idt": {"name": "ST5[120]7[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -612,7 +612,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AGCAATAAAATAAATTAATGCCGTGTATAA", "idt": {"name": "ST7[120]9[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -622,7 +622,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GCAAATATGGGCGCATCGTAACTCTTCGC", "idt": {"name": "ST9[120]11[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -632,7 +632,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TATTACGCCGGAAGCATAAAGTGTTTTTCAC", "idt": {"name": "ST11[120]13[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -642,7 +642,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CAGTGAGACGAAAAACCGTCTATCAGTGAG", "idt": {"name": "ST13[120]15[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -652,7 +652,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GAAAGACAGTAAAAGAGTCTGTCCCTCCAACGT", "idt": {"name": "ST0[135]14[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -662,7 +662,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TACCCAAAAGTACAACGGAGATTTCAGCAGC", "idt": {"name": "ST2[135]0[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -672,7 +672,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AAAATGTTACGAACTAACGGAACAGATATTCAT", "idt": {"name": "ST4[135]2[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -682,7 +682,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TTGATTCCTATCGCGTTTTAATTGGTAATAGT", "idt": {"name": "ST6[135]4[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -692,7 +692,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TCTAGCTGGCCTCAGAGCATAAATATAACAG", "idt": {"name": "ST8[135]6[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -702,7 +702,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GTGTAGATTTAAATTGTAAACGTTTTCAACCGT", "idt": {"name": "ST10[135]8[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -712,7 +712,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TACGAGCCAGCTGGCGAAAGGGGGTCACGTTG", "idt": {"name": "ST12[135]10[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -722,7 +722,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CAAAGGGCGGGCAACAGCTGATTACACAACA", "idt": {"name": "ST14[135]12[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -732,7 +732,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AATTAACCTGCGGGATCGTCACCCTGTATCAT", "idt": {"name": "ST15[152]1[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -742,7 +742,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CGCCTGATATCTTGACAAGAACCGACATTATT", "idt": {"name": "ST1[152]3[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -752,7 +752,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "ACAGGTAGAGTTTTGCCAGAGGGCGAGCTTC", "idt": {"name": "ST3[152]5[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -762,7 +762,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AAAGCGAACTGGAAGTTTCATTCCAGCTAAATC", "idt": {"name": "ST5[152]7[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -772,7 +772,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GGTTGTACCACCATCAATATGATAAATATTTT", "idt": {"name": "ST7[152]9[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -782,7 +782,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GTTAAAATACCGTAATGGGATAGGATGTGCT", "idt": {"name": "ST9[152]11[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -792,7 +792,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GCAAGGCGAATCCGCTCACAATTCCGCCCTTCA", "idt": {"name": "ST11[152]13[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -802,7 +802,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CCGCCTGGCATTAAAGAACGTGGAATCACGCA", "idt": {"name": "ST13[152]15[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -812,7 +812,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CCGCTTTGTTGTAGCAATACTTGGAACAAGA", "idt": {"name": "ST0[167]14[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -822,7 +822,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AGAGTAAAATTGTGTCGAAATGTTAAAGG", "idt": {"name": "ST2[167]0[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -832,7 +832,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "CAAAAGAAAAGATTCATCAGTTCCTTCATCA", "idt": {"name": "ST4[167]2[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -842,7 +842,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CGGTGTCCAGACCGGAAGCAAAGGCTTTTG", "idt": {"name": "ST6[167]4[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -852,7 +852,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TCAAATCAAAAACATTATGACCTAAAGTA", "idt": {"name": "ST8[167]6[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -862,7 +862,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CGGATTGTCGCATTAAATTTTTCGGAGACAG", "idt": {"name": "ST10[167]8[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -872,7 +872,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AATTGTTTTAAGTTGGGTAACAACAAACGG", "idt": {"name": "ST12[167]10[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -882,7 +882,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GTCCACTCCTGAGAGAGTTGCCTGTGTGA", "idt": {"name": "ST14[167]12[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -892,7 +892,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AGTAATAACTGAGGCTTGCAGGGACCGCGACC", "idt": {"name": "ST15[184]1[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -902,7 +902,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TGCTCCATGGCATAGGCTGGCTGAGAGATTTA", "idt": {"name": "ST1[184]3[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -912,7 +912,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GGAATACCAACCAAAATAGCGAGACTCCAAC", "idt": {"name": "ST3[184]5[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -922,7 +922,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AGGTCAGGATGTTTTAAATATGCAACCTGTAAT", "idt": {"name": "ST5[184]7[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -932,7 +932,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "ACTTTTGCGAAGGGTGAGAAAGGCGTTAAATC", "idt": {"name": "ST7[184]9[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -942,7 +942,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AGCTCATTCGGATTCTCCGTGGGGCCAGGGT", "idt": {"name": "ST9[184]11[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -952,7 +952,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TTTCCCAGTTGGTCATAGCTGTTTCAGCAAGCG", "idt": {"name": "ST11[184]13[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -962,7 +962,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GTCCACGCTGTGTTGTTCCAGTTTCTTTGATT", "idt": {"name": "ST13[184]15[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -972,7 +972,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TTCGGTCGCATCACTTGCCTGAGTGCCCGAGAT", "idt": {"name": "ST0[199]14[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -982,7 +982,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GACCAGGCTTACTTAGCCGGAACCCGATATA", "idt": {"name": "ST2[199]0[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -992,7 +992,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ACGATAAAACATTCAACTAATGCACGGTGTACA", "idt": {"name": "ST4[199]2[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1002,7 +1002,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GCTCAACATTAGAGAGTACCTTTTACCAGACG", "idt": {"name": "ST6[199]4[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1012,7 +1012,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AGATTCAAGGAGAAGCCTTTATTATGCTGTA", "idt": {"name": "ST8[199]6[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1022,7 +1022,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CAACCCGTTTTTAACCAATAGGAATGTAGGTAA", "idt": {"name": "ST10[199]8[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1032,7 +1032,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "CGTAATCACACGACGTTGTAAAAAGCGAGTAA", "idt": {"name": "ST12[199]10[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1042,7 +1042,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AGGGTTGAGGTTTGCCCCAGCAGCTCGAATT", "idt": {"name": "ST14[199]12[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1052,7 +1052,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CTCAAACTATCGCCCACGCATAAGAGGCGC", "idt": {"name": "ST15[216]1[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1062,7 +1062,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AGACGGTCAAGAGGACAGATGAAGATACAT", "idt": {"name": "ST1[216]3[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1072,7 +1072,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AACGCCAATCATAACCCTCGTTAATTGCT", "idt": {"name": "ST3[216]5[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1082,7 +1082,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CCTTTTGATTAATTGCTGAATATATCAACGC", "idt": {"name": "ST5[216]7[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1092,7 +1092,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "AAGGATAAAATGCCTGAGTAATGCGCCATC", "idt": {"name": "ST7[216]9[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1102,7 +1102,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AAAAATAACAACATTAAATGTGCGACGGC", "idt": {"name": "ST9[216]11[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1112,7 +1112,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CAGTGCCAATCCCCGGGTACCGAGGCGAAAA", "idt": {"name": "ST11[216]13[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1122,7 +1122,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TCCTGTTTGAAATCAAAAGAATAAGAAGAA", "idt": {"name": "ST13[216]15[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1132,7 +1132,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "AGCTTGATACCGCCAGCCATTGCAGTTGAAA", "idt": {"name": "ST0[263]14[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1142,7 +1142,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TAAGTGCATAGGTGTATCACCTCTTAAAC", "idt": {"name": "ST2[263]0[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1152,7 +1152,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TAGCGTTCCAGAGCCACCACCGCCAGGCGGA", "idt": {"name": "ST4[263]2[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1162,7 +1162,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AAACCGACTGGCATGATTAAGCCCCCTTAT", "idt": {"name": "ST6[263]4[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1172,7 +1172,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GGTATTCACTTGCGGGAGGTTCCAGAAGG", "idt": {"name": "ST8[263]6[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1182,7 +1182,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AATCATAGCGTTATACAAATTCGGCTTATCC", "idt": {"name": "ST10[263]8[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1192,7 +1192,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CAGAGGCGATGATGAAACAAAAAACACCGG", "idt": {"name": "ST12[263]10[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1202,7 +1202,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "GGAATTGTAACAACTAATAGAAAATCGCG", "idt": {"name": "ST14[263]12[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1212,7 +1212,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AAAACGCTGCTTTCGAGGTGAATTGTACTCAG", "idt": {"name": "ST15[280]1[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1222,7 +1222,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GAGGTTTAGGGGTTTTGCTCAGTAGAACCGCC", "idt": {"name": "ST1[280]3[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1232,7 +1232,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TCCCTCAGCATTTTCGGTCATAGACTCCTTA", "idt": {"name": "ST3[280]5[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1242,7 +1242,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TTACGCAGTTAGCCGAACAAAGTTATTGAAGCC", "idt": {"name": "ST5[280]7[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1252,7 +1252,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TTAAATCAAAAATCAGATATAGAATTACCAGT", "idt": {"name": "ST7[280]9[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1262,7 +1262,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ATAAAGCCGCGTTAAATAAGAATCATCAAGA", "idt": {"name": "ST9[280]11[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1272,7 +1272,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "AAACAAAATTGAATACCAAGTTACATTAGAGCC", "idt": {"name": "ST11[280]13[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1282,7 +1282,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "GTCAATAGACAGTTGGCAAATCAACAACAGGA", "idt": {"name": "ST13[280]15[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1292,7 +1292,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "ATCAGCTTCATGGAAATACCTACACTCAATCAA", "idt": {"name": "ST0[295]14[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1302,7 +1302,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GATTAGCGTACCGCCACCCTCAGATCGGTTT", "idt": {"name": "ST2[295]0[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1312,7 +1312,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TTCATCGGAGCCGCCACCCTCAGAAAGGATTAG", "idt": {"name": "ST4[295]2[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1322,7 +1322,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TAAGCAGAATGTTAGCAAACGTATAGCGCGTT", "idt": {"name": "ST6[295]4[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1332,7 +1332,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TAGCAAGCGATTAGTTGCTATTTAAGAAAAG", "idt": {"name": "ST8[295]6[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1342,7 +1342,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TAAATAAGAACGCTCAACAGTAGGCGCGCCCAA", "idt": {"name": "ST10[295]8[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1352,7 +1352,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GATTGCTTTAATTACATTTAACAACCGTGTGA", "idt": {"name": "ST12[295]10[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1362,7 +1362,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TATCTGGTTAATACATTTGAGGAATTCGCCT", "idt": {"name": "ST14[295]12[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1372,7 +1372,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GCTCAATCGGAGCCTTTAATTGTAACCGCC", "idt": {"name": "ST15[312]1[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1382,7 +1382,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "ACCCTCAGAAGACTCCTCAAGAGACCGCCA", "idt": {"name": "ST1[312]3[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1392,7 +1392,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CCCTCAGATTAGCGTCAGACTGGAAAATA", "idt": {"name": "ST3[312]5[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1402,7 +1402,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CATACATAAACCGAAGCCCTTTTTTGCACCC", "idt": {"name": "ST5[312]7[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1412,7 +1412,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AGCTACAATGTAGGAATCATTACGCTTAAT", "idt": {"name": "ST7[312]9[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1422,7 +1422,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TGAGAATCGGTTTGAAATACCGATTTCAT", "idt": {"name": "ST9[312]11[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1432,7 +1432,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TTGAATTACGAGAAACAATAACGGTTTAGAA", "idt": {"name": "ST11[312]13[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1442,7 +1442,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GTATTAGACTCAAATATCAAACCTTTTGAC", "idt": {"name": "ST13[312]15[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1452,7 +1452,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CTCCAAAAGTCTGAAATGGATTATCATCACCTT", "idt": {"name": "ST0[327]14[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1462,7 +1462,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AGAGGCTGACCGCCACCCTCAGAAAAAAAGG", "idt": {"name": "ST2[327]0[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1472,7 +1472,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "GTTTGCCTGCCACCACCCTCAGAGAAAGTATTA", "idt": {"name": "ST4[327]2[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1482,7 +1482,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GCTATCTTAGGTGGCAACATATACAGAATCAA", "idt": {"name": "ST6[327]4[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1492,7 +1492,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TTTTCATCTTTATCCTGAATCTTTAGCAATA", "idt": {"name": "ST8[327]6[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1502,7 +1502,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "AATTTAATGCCATATTTAACAACGCCGTTTTTA", "idt": {"name": "ST10[327]8[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1512,7 +1512,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TACATCGGCTTTTTTAATGGAAATCTGACCTA", "idt": {"name": "ST12[327]10[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1522,7 +1522,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GCTGAACCTTTACAAACAATTCGGTACCTTT", "idt": {"name": "ST14[327]12[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1532,7 +1532,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GCAGATTCCGTTGAAAATCTCCAAGCCACCAC", "idt": {"name": "ST15[344]1[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1542,7 +1542,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CCTCATTTTTTATTCTGAAACATGCCGCCACC", "idt": {"name": "ST1[344]3[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1552,7 +1552,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AGAACCACCGTAATCAGTAGCGAAAAGAAAC", "idt": {"name": "ST3[344]5[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1562,7 +1562,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "GCAAAGACAGCAAGAAACAATGAAAACCAACGC", "idt": {"name": "ST5[344]7[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1572,7 +1572,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TAACGAGCGTCGAGAACAAGCAAGCCAACATG", "idt": {"name": "ST7[344]9[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1582,7 +1582,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "TAATTTAGTAGTTAATTTCATCTCAGTACAT", "idt": {"name": "ST9[344]11[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1592,7 +1592,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "AAATCAATATGAATATACAGTAACAACAACTCG", "idt": {"name": "ST11[344]13[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1602,7 +1602,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "TATTAAATCATGAAAAATCTAAAGTTACATTG", "idt": {"name": "ST13[344]15[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1612,7 +1612,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TTTTTCAACCAGTCACACGACCTGAGAGCCA", "idt": {"name": "ST0[359]14[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1622,7 +1622,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "GAACCTACAGGGATAGCAAGCATAATAAT", "idt": {"name": "ST2[359]0[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1632,7 +1632,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GCAGCACCACCAGAGCCGCCGCCCTATTTCG", "idt": {"name": "ST4[359]2[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1642,7 +1642,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AATAAGACCACGGAATAAGTTCCATCGATA", "idt": {"name": "ST6[359]4[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1652,7 +1652,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GCACTCATCTTTCCAGAGCCTAGCCCAAT", "idt": {"name": "ST8[359]6[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1662,7 +1662,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "TATATTTGCAGAGGCATTTTCGCCAAGTACC", "idt": {"name": "ST10[359]8[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1672,7 +1672,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CGTCAGATATGTGAGTGAATATTTTTCAAA", "idt": {"name": "ST12[359]10[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1682,7 +1682,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GCAGCAACTTTGCCCGAACGTAGGTTTAA", "idt": {"name": "ST14[359]12[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1692,7 +1692,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AAGGGACAACTAAAGGAATTGCGACCAATAGG", "idt": {"name": "ST15[376]1[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1702,7 +1702,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AACCCATGTAGTTAATGCCCCCTGCAGCATTG", "idt": {"name": "ST1[376]3[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1712,7 +1712,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "ACAGGAGGACGTCACCAATGAAATATTTTGT", "idt": {"name": "ST3[376]5[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1722,7 +1722,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CACAATCAACACAAGAATTGAGTTAAATTTGCC", "idt": {"name": "ST5[376]7[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1732,7 +1732,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AGTTACAAAAGAACGGGTATTAAAAGCCAGTA", "idt": {"name": "ST7[376]9[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1742,7 +1742,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "ATAAGAGAAGAACGCGAGAAAACACCTTGCT", "idt": {"name": "ST9[376]11[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1752,7 +1752,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TCTGTAAATAATTGCGTAGATTTTCTATTAATT", "idt": {"name": "ST11[376]13[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1762,7 +1762,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TTAAAAGTTGCAACAGTGCCACGCAGTAATAA", "idt": {"name": "ST13[376]15[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1772,7 +1772,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AAGGAACATTCTGGCCAACAGAGACAGTATTAA", "idt": {"name": "ST0[391]14[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1782,7 +1782,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "GTATAAACACCGTAACACTGAGTAGAATAGA", "idt": {"name": "ST2[391]0[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1792,7 +1792,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GGCCGGAATTGAGGCAGGTCAGACACAGTGCCC", "idt": {"name": "ST4[391]2[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1802,7 +1802,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "AGATAACCTAGAAAATTCATATGCATTAGCAA", "idt": {"name": "ST6[391]4[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1812,7 +1812,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TCATTCCAATAAACAGCCATATTTATCAGAG", "idt": {"name": "ST8[391]6[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1822,7 +1822,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "CAAGACAAATATAAAGTACCGACACTTTCCTTA", "idt": {"name": "ST10[391]8[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1832,7 +1832,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "AATAAAGACGTCGCTATTAATTAATCCAATCG", "idt": {"name": "ST12[391]10[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1842,7 +1842,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CACCGCCTTGAGTAACATTATCAAAAACAGA", "idt": {"name": "ST14[391]12[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1852,7 +1852,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CTTCTGACAGTTTCAGCGGAGTGTTCGTCA", "idt": {"name": "ST15[408]1[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1862,7 +1862,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CCAGTACAACAGTGCCTTGAGTAGATTGGC", "idt": {"name": "ST1[408]3[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1872,7 +1872,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "CTTGATATAGTAGCACCATTACGTTTACC", "idt": {"name": "ST3[408]5[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1882,7 +1882,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AGCGCCAAAGTAATTGAGCGCTAAATTTATC", "idt": {"name": "ST5[408]7[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1892,7 +1892,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CCAATCCAACAATAATCGGCTGTAAAGGTA", "idt": {"name": "ST7[408]9[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1902,7 +1902,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AAGTAATTAAATGCTGATGCAAATTTTCC", "idt": {"name": "ST9[408]11[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1912,7 +1912,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CTTAGAATCAAATTATTTGCACGTTTTTGCG", "idt": {"name": "ST11[408]13[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1922,7 +1922,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GAACAAAGAAGAGGTGAGGCGGTTAGAACC", "idt": {"name": "ST13[408]15[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1932,7 +1932,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "CTTTCAACCTGAAAGCGTAAGAATCCAGCAGAA", "idt": {"name": "ST0[423]14[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1942,7 +1942,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "AACGGGGTACTACAACGCCTGTACTAAACAA", "idt": {"name": "ST2[423]0[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1952,7 +1952,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "AAATCACCTCACAAACAAATAAATATAAGTTTT", "idt": {"name": "ST4[423]2[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1962,7 +1962,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "GTCAGAGGGACAAAAGGGCGACAGAGCCAGCA", "idt": {"name": "ST6[423]4[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1972,7 +1972,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "AAACCAATATAAGAAACGATTTTTGAACAAA", "idt": {"name": "ST8[423]6[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1982,7 +1982,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CTATATGTCTGTCCAGACGACGACAGCATGTAG", "idt": {"name": "ST10[423]8[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1992,7 +1992,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CCATATCACTTGAAAACATAGCGGTTATATAA", "idt": {"name": "ST12[423]10[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2002,7 +2002,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "GATAAAACAACCACCAGAAGGAGAGAACCTA", "idt": {"name": "ST14[423]12[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2012,7 +2012,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "CAGACAATTCTGTATGGGATTTTGGCATTCCA", "idt": {"name": "ST15[440]1[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2022,7 +2022,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "CAGACAGCCAGGAGTGTACTGGTACCTCATTA", "idt": {"name": "ST1[440]3[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2032,7 +2032,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "AAGCCAGAAGCCATTTGGGAATTATTCAACCG", "idt": {"name": "ST3[440]5[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2042,7 +2042,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "ATTGAGGGAATTAACTGAACACCCTTGTTTAA", "idt": {"name": "ST5[440]7[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2052,7 +2052,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "CGTCAAAACCCATCCTAATTTACGAATAAACA", "idt": {"name": "ST7[440]9[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2062,7 +2062,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "ACATGTTCCTCCGGCTTAGGTTGGATAGCTTA", "idt": {"name": "ST9[440]11[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2072,7 +2072,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "GATTAAGAGAATAATGGAAGGGTTCGGAATTA", "idt": {"name": "ST11[440]13[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2082,7 +2082,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TCATCATAAATACCGAACGAACCAACGTGGCA", "idt": {"name": "ST13[440]15[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2092,7 +2092,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "TGAATTTATTTTTGAATGGCTAAACATCGC", "idt": {"name": "ST0[455]14[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2102,7 +2102,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "GATGATACCTCATAGTTAGCGTTTAGTAAA", "idt": {"name": "ST2[455]0[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2112,7 +2112,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "CGACTTGATGGAAAGCGCAGTCTGGCTTTT", "idt": {"name": "ST4[455]2[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2122,7 +2122,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "ACGGGAGAGGGAAGGTAAATATACCGTCAC", "idt": {"name": "ST6[455]4[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2132,7 +2132,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "ATAATATATGAAAATAGCAGCCCGCATTAG", "idt": {"name": "ST8[455]6[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2142,7 +2142,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "TTTTAACAGCTAATGCAGAACGCAAGAAAA", "idt": {"name": "ST10[455]8[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2152,7 +2152,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "TACTTCTCGCTGAGAAGAGTCAGACTACCT", "idt": {"name": "ST12[455]10[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2162,7 +2162,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "CATTAAATTCCTGATTATCAGATTGGATTA", "idt": {"name": "ST14[455]12[456]", "scale": "25nm", "purification": "STD"}, "domains": [ diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 2b27dd68..76216188 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1622,11 +1622,13 @@ class StrandBuilder: """ def __init__(self, design: DNADesign, helix: int, offset: int): - self.design = design - self.current_helix = helix - self.current_offset = offset - self.loopout_length = None - self.strand = None + self.design: DNADesign = design + self.current_helix: int = helix + self.current_offset: int = offset + self.loopout_length: Optional[int] = None + self.strand: Optional[Strand] = None + self.just_moved_to_helix: bool = True + self.last_domain: Optional[Domain] = None def cross(self, helix: int, offset: int = None) -> StrandBuilder: """ @@ -1637,6 +1639,7 @@ def cross(self, helix: int, offset: int = None) -> StrandBuilder: (i.e., a "vertical" crossover) :return: self """ + self.last_domain = None self.current_helix = helix if offset is not None: self.current_offset = offset @@ -1653,10 +1656,7 @@ def loopout(self, helix: int, length: int, offset: int = None) -> StrandBuilder: :return: self """ self.loopout_length = length - self.current_helix = helix - if offset is not None: - self.current_offset = offset - return self + return self.cross(helix, offset) def to(self, offset: int) -> StrandBuilder: """ @@ -1667,10 +1667,24 @@ def to(self, offset: int) -> StrandBuilder: and if :py:meth:`StrandBuilder.loopout` was last called on this :any:`StrandBuilder`, also a new :any:`Loopout`. + If two instances of :py:meth:`StrandBuilder.to` are chained together, this creates two domains + on the same helix. The two offsets must move in the same direction. In other words, if the starting + offset is ``s``, and we call ``.to(o1).to(o2)``, then either ``s < o1 < o2`` or ``o2 < o1 < s`` + must be true. + + To simply change the current offset after calling :py:meth:`StrandBuilder.to`, without creating + a new Domain, call :py:meth:`StrandBuilder.update_to`. + :param offset: new offset to extend to. If less than current offset, the new :any:`Domain` is reverse, otherwise it is forward. :return: self """ + if self.last_domain and ((self.last_domain.forward and offset < self.current_offset) or ( + not self.last_domain.forward and offset > self.current_offset)): + raise IllegalDNADesignError('offsets must be monotonic ' + '(strictly increasing or strictly decreasing) ' + 'when calling to() twice in a row') + if offset > self.current_offset: forward = True start = self.current_offset @@ -1683,6 +1697,7 @@ def to(self, offset: int) -> StrandBuilder: raise IllegalDNADesignError(f'offset {offset} cannot be equal to current offset') domain = Domain(helix=self.current_helix, forward=forward, start=start, end=end) + self.last_domain = domain if self.strand: if self.loopout_length is not None: self.design.append_domain(self.strand, Loopout(self.loopout_length)) @@ -1696,6 +1711,36 @@ def to(self, offset: int) -> StrandBuilder: return self + def update_to(self, offset: int) -> StrandBuilder: + """ + Like :py:meth:`StrandBuilder.to`, but changes the current offset after calling + :py:meth:`StrandBuilder.to`, without creating + a new Domain, call :py:meth:`StrandBuilder.update_to`. + + If :py:meth:`StrandBuilder.cross` or :py:meth:`StrandBuilder.loopout` was just called, + then :py:meth:`StrandBuilder.to` and :py:meth:`StrandBuilder.update_to` have the same effect. + + :param offset: new offset to extend to. If less than current offset, + the new :any:`Domain` is reverse, otherwise it is forward. + :return: self + """ + if not self.last_domain: + return self.to(offset) + + domain = self.last_domain + if (self.last_domain.forward and offset < self.current_offset) or ( + not self.last_domain.forward and offset > self.current_offset): + raise IllegalDNADesignError(f'when calling ') + + if domain.forward: + domain.set_end(offset) + else: + domain.set_start(offset) + + self.current_offset = offset + + return self + def as_scaffold(self) -> StrandBuilder: """ Makes Strand being built a scaffold. diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 9d2a97a0..86597c51 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -216,6 +216,83 @@ def test_strand__multiple_strands_overlap_error(self): design.strand(0, 2).to(8) + def test_strand__call_to_twice_legally(self): + design = self.design_6helix + sb = design.strand(0, 0) + sb.to(10) + sb.cross(1) + sb.to(5) + sb.to(0) + expected_strand = sc.Strand([ + sc.Domain(0, True, 0, 10), + sc.Domain(1, False, 5, 10), + sc.Domain(1, False, 0, 5), + ]) + self.assertEqual(1, len(design.strands)) + self.assertEqual(expected_strand, design.strands[0]) + self.assertEqual(1, len(design.helices[0].domains)) + self.assertEqual(2, len(design.helices[1].domains)) + self.assertEqual(0, len(design.helices[2].domains)) + self.assertEqual(0, len(design.helices[3].domains)) + self.assertEqual(0, len(design.helices[4].domains)) + self.assertEqual(0, len(design.helices[5].domains)) + + def test_strand__call_update_to_twice_legally(self): + design = self.design_6helix + sb = design.strand(0, 0) + sb.to(10) + sb.cross(1) + sb.update_to(5) + sb.update_to(0) + expected_strand = sc.Strand([ + sc.Domain(0, True, 0, 10), + sc.Domain(1, False, 0, 10), + ]) + self.assertEqual(1, len(design.strands)) + self.assertEqual(expected_strand, design.strands[0]) + self.assertEqual(1, len(design.helices[0].domains)) + self.assertEqual(1, len(design.helices[1].domains)) + self.assertEqual(0, len(design.helices[2].domains)) + self.assertEqual(0, len(design.helices[3].domains)) + self.assertEqual(0, len(design.helices[4].domains)) + self.assertEqual(0, len(design.helices[5].domains)) + + def test_strand__call_to_then_update_to_legally(self): + design = self.design_6helix + sb = design.strand(0, 0) + sb.to(10) + sb.cross(1) + sb.to(5) + sb.update_to(0) + expected_strand = sc.Strand([ + sc.Domain(0, True, 0, 10), + sc.Domain(1, False, 0, 10), + ]) + self.assertEqual(1, len(design.strands)) + self.assertEqual(expected_strand, design.strands[0]) + self.assertEqual(1, len(design.helices[0].domains)) + self.assertEqual(1, len(design.helices[1].domains)) + self.assertEqual(0, len(design.helices[2].domains)) + self.assertEqual(0, len(design.helices[3].domains)) + self.assertEqual(0, len(design.helices[4].domains)) + self.assertEqual(0, len(design.helices[5].domains)) + + def test_strand__call_to_twice_increase_decrease_forward(self): + design = self.design_6helix + sb = design.strand(0, 0) + sb.to(10) + with self.assertRaises(sc.IllegalDNADesignError): + sb.to(5) + + def test_strand__call_to_twice_decrease_increase_reverse(self): + design = self.design_6helix + sb = design.strand(0, 10) + sb.to(0) + with self.assertRaises(sc.IllegalDNADesignError): + sb.to(5) + + + class TestCreateHelix(unittest.TestCase): def test_helix_constructor_no_max_offset_with_major_ticks(self): diff --git a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna index e7744f8a..b5073768 100644 --- a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna +++ b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna @@ -59,7 +59,7 @@ "is_scaffold": true }, { - "color": "#333333", + "color": "#f7931e", "sequence": "GCCGCTTTTGCGGGATTTGCAGGGAGTTAAAG", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -67,7 +67,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "CAAGAGTAATCTTGACGCTGGCTGACCTTCAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -75,7 +75,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "TGCAAAAGAAGTTTTGAATAGCGAGAGGCTTT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -83,7 +83,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "ACGGTGTCTGGAAGTTAATATGCAACTAAAGT", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, @@ -91,7 +91,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "AGTCAAATCACCATCAGAGAAAGGCCGGAGAC", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, @@ -99,7 +99,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "GGCGGATTGACCGTAACTCCGTGGGAACAAAC", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, @@ -107,7 +107,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "AAATTGTTATCCGCTCAGCTGTTTCCTGTGTG", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, @@ -115,7 +115,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "GAGTCCACTATTAAAGTTCCAGTTTGGAACAA", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, @@ -123,7 +123,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "AACCCATGTACCGTAAGCAAGCCCAATAGG", "domains": [ {"helix": 0, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "AGCCAGAATGGAAAGATAAATCCTCATTAA", "domains": [ {"helix": 2, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -139,7 +139,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "ACTTGAGCCATTTGGTTATCACCGTCACCG", "domains": [ {"helix": 4, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -147,7 +147,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "AACCCACAAGAATTGTAATATCAGAGAGAT", "domains": [ {"helix": 6, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -155,7 +155,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "CATCGTAGGAATCATAGCCGTTTTTATTTT", "domains": [ {"helix": 8, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -163,7 +163,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "TAATTACTAGAAAAATAAACACCGGAATCA", "domains": [ {"helix": 10, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -171,7 +171,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "TTAATTACATTTAACATCAAGAAAACAAAA", "domains": [ {"helix": 12, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -179,7 +179,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "CTTTGCCCGAACGTTAACTCGTATTAAATC", "domains": [ {"helix": 14, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -187,14 +187,14 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "AGAATAGAAAGGAACAACTAAAGGAATTGCG", "domains": [ {"helix": 0, "forward": false, "start": 216, "end": 248, "deletions": [225]} ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "TACCAAGCCTCATCTTTGACCCCCTCAAGAG", "domains": [ {"helix": 2, "forward": false, "start": 208, "end": 216}, @@ -202,7 +202,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "AAGGATTAAGAGGCTGAGACTCCAGCGATTA", "domains": [ {"helix": 1, "forward": true, "start": 232, "end": 240}, @@ -210,7 +210,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "AATCTACGACCAGTCAGGACGTTGTTCATAA", "domains": [ {"helix": 4, "forward": false, "start": 208, "end": 216}, @@ -218,7 +218,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "TCAAAATCAGCGTTTGCCATCTTGGAAGAAA", "domains": [ {"helix": 3, "forward": true, "start": 232, "end": 240}, @@ -226,7 +226,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "GCCCGAAATTGCATCAAAAAGATTACGTAGA", "domains": [ {"helix": 6, "forward": false, "start": 208, "end": 216}, @@ -234,7 +234,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "AAATACATGCAGTATGTTAGCAAAAGAGGAA", "domains": [ {"helix": 5, "forward": true, "start": 232, "end": 240}, @@ -242,7 +242,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "CAAAATTACATACAGGCAAGGCAACCTAATT", "domains": [ {"helix": 8, "forward": false, "start": 208, "end": 216}, @@ -250,7 +250,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "TGCCAGTTAGCGTCTTTCCAGAGAGAATTAG", "domains": [ {"helix": 7, "forward": true, "start": 232, "end": 240}, @@ -258,7 +258,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "TTGTATAAAGAAAAGCCCCAAAAAACAATAA", "domains": [ {"helix": 10, "forward": false, "start": 208, "end": 216}, @@ -266,7 +266,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "ACAACATGTCTGTCCAGACGACGCAGGAAGA", "domains": [ {"helix": 9, "forward": true, "start": 232, "end": 240}, @@ -274,7 +274,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "CTCTTCGCTTGGGAAGGGCGATCGAGACTAC", "domains": [ {"helix": 12, "forward": false, "start": 208, "end": 216}, @@ -282,7 +282,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "CTTTTTAAAATCATAGGTCTGAGGTGCGGGC", "domains": [ {"helix": 11, "forward": true, "start": 232, "end": 240}, @@ -290,7 +290,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "CTTTTCACGTATTGGGCGCCAGGGAAACAGA", "domains": [ {"helix": 14, "forward": false, "start": 208, "end": 216}, @@ -298,7 +298,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "AATAAAGAAATTATTTGCACGTATGGTTTTT", "domains": [ {"helix": 13, "forward": true, "start": 232, "end": 240}, @@ -306,14 +306,14 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "GAACGTGGCGAGAAAGGAAGGGAATCACCTT", "domains": [ {"helix": 15, "forward": true, "start": 200, "end": 232, "deletions": [225]} ] }, { - "color": "#007200", + "color": "#320096", "sequence": "CCGATATATTCGGTCGCTGAGGCCGTCACC", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -321,7 +321,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "CTCAGCAGAGACCAGGCGCATAGAAGAACC", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -330,7 +330,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "GGATATTCGACGATAAAAACCAACCAGAGG", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -339,7 +339,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "GGGTAATAGCTCAACATGTTTTATCATTCC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 48}, @@ -348,7 +348,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "ATATAACAAAGATTCAAAAGGGTATATGAT", "domains": [ {"helix": 7, "forward": true, "start": 40, "end": 48}, @@ -357,7 +357,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "ATTCAACCACAACCCGTCGGATTTGGGATA", "domains": [ {"helix": 9, "forward": true, "start": 40, "end": 48}, @@ -366,7 +366,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "GGTCACGTCGTAATCATGGTCATACAATTC", "domains": [ {"helix": 11, "forward": true, "start": 40, "end": 48}, @@ -375,7 +375,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "CACACAACTAGGGTTGAGTGTTGAACGTGG", "domains": [ {"helix": 13, "forward": true, "start": 40, "end": 48}, @@ -384,7 +384,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "ACTCCAACGTCAAAGGGCGAAAAAAAAGAATA", "domains": [ {"helix": 15, "forward": true, "start": 40, "end": 64}, @@ -392,7 +392,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "CGGTGTACCGAAAGACAGCATCGGACGCATAA", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -401,7 +401,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "TACCAGACATTACCCAAATCAACGCAGATGAA", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -410,7 +410,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "ATGCTGTAGTAAAATGTTTAGACTCCCTCGTT", "domains": [ {"helix": 6, "forward": false, "start": 48, "end": 56}, @@ -419,7 +419,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "TGTAGGTAGTTGATTCCCAATTCTTGAATATA", "domains": [ {"helix": 8, "forward": false, "start": 48, "end": 56}, @@ -428,7 +428,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "AGCGAGTAGTTCTAGCTGATAAATGAGTAATG", "domains": [ {"helix": 10, "forward": false, "start": 48, "end": 56}, @@ -437,7 +437,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "CTCGAATTTGGTGTAGATGGGCGCTAAATGTG", "domains": [ {"helix": 12, "forward": false, "start": 48, "end": 56}, @@ -446,7 +446,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "GCCCGAGAATACGAGCCGGAAGCAGTACCGAG", "domains": [ {"helix": 14, "forward": false, "start": 48, "end": 56}, @@ -455,7 +455,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "GACAATGACAACAACCATCGCCCAACGAGGG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -463,7 +463,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "TAGCAACGCAACTTTGAAAGAGGATAACAAAG", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -472,7 +472,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "CTGCTCATAGCAACACTATCATAAGGATAGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -481,7 +481,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "TCCAATACCTTAGAGCTTAATTGCGCGAACGA", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 80}, @@ -490,7 +490,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "GTAGATTTTTTAAATGCAATGCCTTAATGCCG", "domains": [ {"helix": 7, "forward": true, "start": 72, "end": 80}, @@ -499,7 +499,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "GAGAGGGTCAGCTTTCATCAACATATCGTAAC", "domains": [ {"helix": 9, "forward": true, "start": 72, "end": 80}, @@ -508,7 +508,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "CGTGCATCTCTAGAGGATCCCCGGTAAAGTGT", "domains": [ {"helix": 11, "forward": true, "start": 72, "end": 80}, @@ -517,7 +517,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "AAAGCCTGAATCCCTTATAAATCACCGTCTAT", "domains": [ {"helix": 13, "forward": true, "start": 72, "end": 80}, @@ -526,7 +526,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "CAGGGCGATGGCCCACTACGTGATTCCGAAA", "domains": [ {"helix": 15, "forward": true, "start": 72, "end": 96, "deletions": [81]}, @@ -534,7 +534,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "AACTGACGCTACAGAGGCTTTGGTTGCGCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -543,7 +543,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "TAGTAAGTCAGTGAATAAGGCTGGGAACCG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -552,7 +552,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "CGGATGGTGCGGAATCGTCATAACGAGGCA", "domains": [ {"helix": 6, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -561,7 +561,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "CATATATAGTTTGACCATTAGACATTTTTG", "domains": [ {"helix": 8, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -570,7 +570,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "CTGTAGCAGCTATTTTTGAGAGAGAACCCT", "domains": [ {"helix": 10, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -579,7 +579,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "GGTCGACTGCCAGTTTGAGGGGTGGCCTTC", "domains": [ {"helix": 12, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -588,7 +588,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "TCGGCAAGGGTGCCTAATGAGTTGCCTGCA", "domains": [ {"helix": 14, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -597,7 +597,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "TTCTTAAACAGCTTGATACCGATAAGGACTAA", "domains": [ {"helix": 0, "forward": false, "start": 96, "end": 120}, @@ -605,7 +605,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "AGACTTTTAGACGGTCAATCATAATGCCCTGA", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -614,7 +614,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "CGAGAAACAACGCCAAAAGGAATTAATATTCA", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -623,7 +623,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "TTGAATCCCCTTTTGATAAGAGGTTACATTTC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 112}, @@ -632,7 +632,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "GCAAATGGAAGGATAAAAATTTTTATCTACAA", "domains": [ {"helix": 7, "forward": true, "start": 104, "end": 112}, @@ -641,7 +641,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "AGGCTATCAAAAATAATTCGCGTCACGACGAC", "domains": [ {"helix": 9, "forward": true, "start": 104, "end": 112}, @@ -650,7 +650,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "AGTATCGGCAGTGCCAAGCTTGCAGAGCTAAC", "domains": [ {"helix": 11, "forward": true, "start": 104, "end": 112}, @@ -659,7 +659,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "TCACATTATCCTGTTTGATGGTGGACCATCAC", "domains": [ {"helix": 13, "forward": true, "start": 104, "end": 112}, @@ -668,7 +668,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "CCAAATCAAGTTTTTTGGGGTCGACCCCAGCA", "domains": [ {"helix": 15, "forward": true, "start": 104, "end": 128}, @@ -676,7 +676,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "CGAGGCGCTCATGAGGAAGTTTCCAGGTGAAT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -685,7 +685,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "AGATACATACCAGAACGAGTAGTAAGCCGGAA", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -694,7 +694,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "TAATTGCTCCCTCAAATGCTTTAAACTAATGC", "domains": [ {"helix": 6, "forward": false, "start": 112, "end": 120}, @@ -703,7 +703,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "TTCAACGCTCAATAACCTGTTTAGAGTACCTT", "domains": [ {"helix": 8, "forward": false, "start": 112, "end": 120}, @@ -712,7 +712,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "ACGCCATCAGGTCATTGCCTGAGAGCCTTTAT", "domains": [ {"helix": 10, "forward": false, "start": 112, "end": 120}, @@ -721,7 +721,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "ACGACGGCCCTCAGGAAGATCGCACAATAGGA", "domains": [ {"helix": 12, "forward": false, "start": 112, "end": 120}, @@ -730,7 +730,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "GGCGAAAAATTGCGTTGCGCTCACGTTGTAAA", "domains": [ {"helix": 14, "forward": false, "start": 112, "end": 120}, @@ -739,7 +739,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "ATCGGTTTATCAGCTTGCTTTCGATTAAAC", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -747,7 +747,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "GGGTAAAATGCTCCATGTTACTTAATTGGG", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -756,7 +756,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "CTTGAGATGGAATACCACATTCAACAGTTC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -765,7 +765,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "AGAAAACGAGGTCAGGATTAGAGCTATATT", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 144}, @@ -774,7 +774,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "TTCATTTGACTTTTGCGGGAGAAGTCTGGA", "domains": [ {"helix": 7, "forward": true, "start": 136, "end": 144}, @@ -783,7 +783,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "GCAAACAAAGCTCATTTTTTAACCTCCAGC", "domains": [ {"helix": 9, "forward": true, "start": 136, "end": 144}, @@ -792,7 +792,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "CAGCTTTCTTTCCCAGTCACGACTGCCCGC", "domains": [ {"helix": 11, "forward": true, "start": 136, "end": 144}, @@ -801,7 +801,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "TTTCCAGTGTCCACGCTGGTTTGGGTGCCG", "domains": [ {"helix": 13, "forward": true, "start": 136, "end": 144}, @@ -810,7 +810,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "TAAAGCACTAAATCGGAACCCTAAAGAGTTGC", "domains": [ {"helix": 15, "forward": true, "start": 136, "end": 160}, @@ -818,7 +818,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "CCGCGACCTACGTAATGCCACTACTTAATTGT", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -827,7 +827,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "GAGATTTAGGTTTAATTTCAACTTGTCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, @@ -836,7 +836,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "ACTCCAACAGAATGACCATAAATCCATCAGTT", "domains": [ {"helix": 6, "forward": false, "start": 144, "end": 152}, @@ -845,7 +845,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "CCTGTAATGGGCGCGAGCTGAAAAGGAAGCAA", "domains": [ {"helix": 8, "forward": false, "start": 144, "end": 152}, @@ -854,7 +854,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "GTTAAATCGAGAATCGATGAACGGATTATGAC", "domains": [ {"helix": 10, "forward": false, "start": 144, "end": 152}, @@ -863,7 +863,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "GCCAGGGTCGGCACCGCTTCTGGTAAATTTTT", "domains": [ {"helix": 12, "forward": false, "start": 144, "end": 152}, @@ -872,7 +872,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "AGCAAGCGCGGGAAACCTGTCGTGTGGGTAAC", "domains": [ {"helix": 14, "forward": false, "start": 144, "end": 152}, @@ -881,7 +881,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "AAAAAAGGCTCCAAAAGGAGCCTGAAGGCAC", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 184, "deletions": [177]}, @@ -889,7 +889,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "CAACCTAATCGCCTGATAAATTGTTAATCATT", "domains": [ {"helix": 1, "forward": true, "start": 168, "end": 176}, @@ -898,7 +898,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "GTGAATTATACAGGTAGAAAGATTAAAAATCA", "domains": [ {"helix": 3, "forward": true, "start": 168, "end": 176}, @@ -907,7 +907,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "GGTCTTTACAAAGCGAACCAGACCGGTGGCAT", "domains": [ {"helix": 5, "forward": true, "start": 168, "end": 176}, @@ -916,7 +916,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "CAATTCTACGGTTGTACCAAAAACTAATCGTA", "domains": [ {"helix": 7, "forward": true, "start": 168, "end": 176}, @@ -925,7 +925,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "AAACTAGCTGTTAAAATTCGCATTGCCGGAAA", "domains": [ {"helix": 9, "forward": true, "start": 168, "end": 176}, @@ -934,7 +934,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "CCAGGCAATGCAAGGCGATTAAGTCCAGCTGC", "domains": [ {"helix": 11, "forward": true, "start": 168, "end": 176}, @@ -943,7 +943,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "ATTAATGAACCGCCTGGCCCTGAGAGGGAGCC", "domains": [ {"helix": 13, "forward": true, "start": 168, "end": 176}, @@ -952,7 +952,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "CCCGATTTAGAGCTTGACGGGGAAGCTGATT", "domains": [ {"helix": 15, "forward": true, "start": 168, "end": 192, "deletions": [177]}, @@ -960,7 +960,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "TGTATCAAACGAAAGAGGCAAAATCTCCAA", "domains": [ {"helix": 2, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -969,7 +969,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "ACATTATCCTTATGCGATTTTACGGAGATT", "domains": [ {"helix": 4, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -978,7 +978,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "CGAGCTTCCCTGACTATTATAGACGGAACA", "domains": [ {"helix": 6, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -987,7 +987,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "GCTAAATCTAATAGTAGTAGCATTTTAATT", "domains": [ {"helix": 8, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -996,7 +996,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "AATATTTATGTCAATCATATGTAGCATAAA", "domains": [ {"helix": 10, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1005,7 +1005,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "GATGTGCAGCGCCATTCGCCATTAAACGTT", "domains": [ {"helix": 12, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1014,7 +1014,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "GCCCTTCATCGGCCAACGCGCGGAAAGGGG", "domains": [ {"helix": 14, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1023,7 +1023,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "AATAATAATTTTTTCACGTTGAAAAGAATACA", "domains": [ {"helix": 0, "forward": false, "start": 192, "end": 216}, @@ -1031,7 +1031,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "CTAAAACAGCGAAACAAAGTACAAAGAACTGG", "domains": [ {"helix": 1, "forward": true, "start": 200, "end": 208}, @@ -1040,7 +1040,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "CTCATTATTTAATAAAACGAACTATCAGAAGC", "domains": [ {"helix": 3, "forward": true, "start": 200, "end": 208}, @@ -1049,7 +1049,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "AAAGCGGAGACTTCAAATATCGCGTTAACATC", "domains": [ {"helix": 5, "forward": true, "start": 200, "end": 208}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "CAATAAATAGCAATAAAGCCTCAGACCCCGGT", "domains": [ {"helix": 7, "forward": true, "start": 200, "end": 208}, @@ -1067,7 +1067,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "TGATAATCGCAAATATTTAAATTGTCAGGCTG", "domains": [ {"helix": 9, "forward": true, "start": 200, "end": 208}, @@ -1076,7 +1076,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "CGCAACTGTATTACGCCAGCTGGCGGGAGAGG", "domains": [ {"helix": 11, "forward": true, "start": 200, "end": 208}, @@ -1085,7 +1085,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "CGGTTTGCCAGTGAGACGGGCAACAAGCCGGC", "domains": [ {"helix": 13, "forward": true, "start": 200, "end": 208}, @@ -1094,7 +1094,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "GCTGAACCTCAAATATCAAACCCTGAACCTAC", "domains": [ {"helix": 15, "forward": true, "start": 232, "end": 256}, @@ -1102,7 +1102,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "AAGTATTAGGATTAGCGGGGTTTTGCGGAGTG", "domains": [ {"helix": 2, "forward": false, "start": 240, "end": 248}, @@ -1111,7 +1111,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "CCCTTATTACCGGAACCAGAGCCAAAACATGA", "domains": [ {"helix": 4, "forward": false, "start": 240, "end": 248}, @@ -1120,7 +1120,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "CTTATTACACATAAAGGTGGCAACTCATAGCC", "domains": [ {"helix": 6, "forward": false, "start": 240, "end": 248}, @@ -1129,7 +1129,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "CGCTAACGACAAAATAAACAGCCATAAGACTC", "domains": [ {"helix": 8, "forward": false, "start": 240, "end": 248}, @@ -1138,7 +1138,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "AAAGTAATTTCAGCTAATGCAGAACTTACCAA", "domains": [ {"helix": 10, "forward": false, "start": 240, "end": 248}, @@ -1147,7 +1147,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "TTTATCAACCTCCGGCTTAGGTTGCAAAAGGT", "domains": [ {"helix": 12, "forward": false, "start": 240, "end": 248}, @@ -1156,7 +1156,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "CATATCAAAATTGCGTAGATTTTCATAGTGAA", "domains": [ {"helix": 14, "forward": false, "start": 240, "end": 248}, @@ -1165,7 +1165,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "CTAAACAACTTTCAACAGTTTCAGCTCAGTA", "domains": [ {"helix": 0, "forward": false, "start": 256, "end": 280, "deletions": [273]}, @@ -1173,7 +1173,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "CCAGGCGGGGAACCTATTATTCTGCCACCGGA", "domains": [ {"helix": 1, "forward": true, "start": 264, "end": 272}, @@ -1182,7 +1182,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "ACCGCCTCTCATCGGCATTTTCGGATATAAAA", "domains": [ {"helix": 3, "forward": true, "start": 264, "end": 272}, @@ -1191,7 +1191,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "GAAACGCAAAAGAACTGGCATGATTATTATTT", "domains": [ {"helix": 5, "forward": true, "start": 264, "end": 272}, @@ -1200,7 +1200,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "ATCCCAATCAATTTTATCCTGAATCGCGCCTG", "domains": [ {"helix": 7, "forward": true, "start": 264, "end": 272}, @@ -1209,7 +1209,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "TTTATCAAGAATATAAAGTACCGAGGTTATAT", "domains": [ {"helix": 9, "forward": true, "start": 264, "end": 272}, @@ -1218,7 +1218,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "AACTATATACGCTGAGAAGAGTCAAGGTTTAA", "domains": [ {"helix": 11, "forward": true, "start": 264, "end": 272}, @@ -1227,7 +1227,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "CGTCAGATAATAATGGAAGGGTTACAATCAAT", "domains": [ {"helix": 13, "forward": true, "start": 264, "end": 272}, @@ -1236,7 +1236,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "ATCTGGTCAGTTGGCAAATCAACTGGATTAT", "domains": [ {"helix": 15, "forward": true, "start": 264, "end": 288, "deletions": [273]}, @@ -1244,7 +1244,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "CTATTTCATAAGTGCCGTCGAGGGATTTTG", "domains": [ {"helix": 2, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1253,7 +1253,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "CGCGTTTCCTCAGAGCCGCCACCCCCCTGC", "domains": [ {"helix": 4, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1262,7 +1262,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "ATACCCAAAGACACCACGGAATGACTGTAG", "domains": [ {"helix": 6, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1271,7 +1271,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "CCAGCTACCAAATAAGAAACGAATAACGGA", "domains": [ {"helix": 8, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1280,7 +1280,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "AATAAGACAATAGATAAGTCCTTTTTGCAC", "domains": [ {"helix": 10, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1289,7 +1289,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "GATTAAGGTAAATGCTGATGCAGAGCCAGT", "domains": [ {"helix": 12, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1298,7 +1298,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "ACTTCTGGAATATACAGTAACAATAGCTTA", "domains": [ {"helix": 14, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1307,7 +1307,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "GTTAGTAAATGAATTTTCTGTATGAGGGTTGA", "domains": [ {"helix": 0, "forward": false, "start": 288, "end": 312}, @@ -1315,7 +1315,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "TATAAGTAGTATAAACAGTTAATGCCTCAGAA", "domains": [ {"helix": 1, "forward": true, "start": 296, "end": 304}, @@ -1324,7 +1324,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "CCGCCACCTTTGCCTTTAGCGTCAAAGTTTAT", "domains": [ {"helix": 3, "forward": true, "start": 296, "end": 304}, @@ -1333,7 +1333,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "TTTGTCACCCGAGGAAACGCAATATTTTTTGT", "domains": [ {"helix": 5, "forward": true, "start": 296, "end": 304}, @@ -1342,7 +1342,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "TTAACGTCTCAAGATTAGTTGCTAGAACAAGA", "domains": [ {"helix": 7, "forward": true, "start": 296, "end": 304}, @@ -1351,7 +1351,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "AAAATAATAGGCAGAGGCATTTTCAATCCAAT", "domains": [ {"helix": 9, "forward": true, "start": 296, "end": 304}, @@ -1360,7 +1360,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "CGCAAGACCCTTGAAAACATAGCGGTACCTTT", "domains": [ {"helix": 11, "forward": true, "start": 296, "end": 304}, @@ -1369,7 +1369,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "TACATCGGTATAATCCTGATTGTTAGTTGAAA", "domains": [ {"helix": 13, "forward": true, "start": 296, "end": 304}, @@ -1378,7 +1378,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "GGAATTGAGGAAGGTTATCTAAAAGATGGCAA", "domains": [ {"helix": 15, "forward": true, "start": 296, "end": 320}, @@ -1386,7 +1386,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "CAGTGCCCTAGCCCGGAATAGGTGTTCCAGAC", "domains": [ {"helix": 2, "forward": false, "start": 304, "end": 312}, @@ -1395,7 +1395,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "GAATCAAGCTCAGAGCCACCACCCTTGAGTAA", "domains": [ {"helix": 4, "forward": false, "start": 304, "end": 312}, @@ -1404,7 +1404,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "GAAGGAAAAATCAATAGAAAATTCTAGCGACA", "domains": [ {"helix": 6, "forward": false, "start": 304, "end": 312}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "GCCTTAAAAAAAATGAAAATAGCAAGTTACCA", "domains": [ {"helix": 8, "forward": false, "start": 304, "end": 312}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "TGTAATTTATCCCATCCTAATTTAGTTTTGAA", "domains": [ {"helix": 10, "forward": false, "start": 304, "end": 312}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "CTTAGAATAAAGAACGCGAGAAAACGCCAACA", "domains": [ {"helix": 12, "forward": false, "start": 304, "end": 312}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "TTCATCAAGAGAAACAATAACGGAAATTTTCC", "domains": [ {"helix": 14, "forward": false, "start": 304, "end": 312}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "AACGATCTAAAGTTTTGTCGTCTTATCACC", "domains": [ {"helix": 0, "forward": false, "start": 320, "end": 344, "deletions": [321]}, @@ -1457,7 +1457,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "GTACTCAGAACGGGGTCAGTGCCTCAGAGC", "domains": [ {"helix": 1, "forward": true, "start": 328, "end": 336}, @@ -1466,7 +1466,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "CGCCACCACAGCACCGTAATCAGATATGGT", "domains": [ {"helix": 3, "forward": true, "start": 328, "end": 336}, @@ -1475,7 +1475,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "TTACCAGCCAGATAGCCGAACAAGCCTTTA", "domains": [ {"helix": 5, "forward": true, "start": 328, "end": 336}, @@ -1484,7 +1484,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "CAGAGAGACCCGACTTGCGGGAGCGAGCAT", "domains": [ {"helix": 7, "forward": true, "start": 328, "end": 336}, @@ -1493,7 +1493,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "GTAGAAACCGCCATATTTAACAACTTTTTC", "domains": [ {"helix": 9, "forward": true, "start": 328, "end": 336}, @@ -1502,7 +1502,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "AAATATATTCGTCGCTATTAATTTTCGCCT", "domains": [ {"helix": 11, "forward": true, "start": 328, "end": 336}, @@ -1511,7 +1511,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "GATTGCTTTCCTGATTATCAGATTATCTTT", "domains": [ {"helix": 13, "forward": true, "start": 328, "end": 336}, @@ -1520,7 +1520,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "AGGAGCACTAACAACTAATAGATTGGAATTAT", "domains": [ {"helix": 15, "forward": true, "start": 328, "end": 352}, @@ -1528,7 +1528,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "TAAGTTTTGAGGTTTAGTACCGCCGTTAGCGT", "domains": [ {"helix": 2, "forward": false, "start": 336, "end": 344}, @@ -1537,7 +1537,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "ATCGATAGGAACCACCACCAGAGCACTGGTAA", "domains": [ {"helix": 4, "forward": false, "start": 336, "end": 344}, @@ -1546,7 +1546,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "AAAGTAAGGCCAAAGACAAAAGGGATGAAACC", "domains": [ {"helix": 6, "forward": false, "start": 336, "end": 344}, @@ -1555,7 +1555,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "GCGAACCTATAACATAAAAACAGGTTTTAAGA", "domains": [ {"helix": 8, "forward": false, "start": 336, "end": 344}, @@ -1564,7 +1564,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "TTGAGAATCAATCAATAATCGGCTGCGTTTTA", "domains": [ {"helix": 10, "forward": false, "start": 336, "end": 344}, @@ -1573,7 +1573,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "TCTGTAAATTTAGTTAATTTCATCGGGCTTAA", "domains": [ {"helix": 12, "forward": false, "start": 336, "end": 344}, @@ -1582,7 +1582,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "CATCATATTGAATACCAAGTTACAACCTTGCT", "domains": [ {"helix": 14, "forward": false, "start": 336, "end": 344}, @@ -1591,7 +1591,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "GCATTCCACAGACAGCCCTCATAACCCTCAG", "domains": [ {"helix": 0, "forward": false, "start": 352, "end": 376, "deletions": [369]}, @@ -1599,7 +1599,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "AACCGCCAGATGATACAGGAGTGTCGCCGCCA", "domains": [ {"helix": 1, "forward": true, "start": 360, "end": 368}, @@ -1608,7 +1608,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "GCATTGACGCCGGAAACGTCACCACGACATTC", "domains": [ {"helix": 3, "forward": true, "start": 360, "end": 368}, @@ -1617,7 +1617,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "AACCGATTATCTTACCGAAGCCCTGAAGCGCA", "domains": [ {"helix": 5, "forward": true, "start": 360, "end": 368}, @@ -1626,7 +1626,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "TTAGACGGATTCTAAGAACGCGAGGTCTTTCC", "domains": [ {"helix": 7, "forward": true, "start": 360, "end": 368}, @@ -1635,7 +1635,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "TTATCATTCCAACGCTCAACAGTATTCTGACC", "domains": [ {"helix": 9, "forward": true, "start": 360, "end": 368}, @@ -1644,7 +1644,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "TAAATTTATATATGTGAGTGAATAAAATCGCG", "domains": [ {"helix": 11, "forward": true, "start": 360, "end": 368}, @@ -1653,7 +1653,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "CAGAGGCGAACCACCAGAAGGAGCAGAGCCGT", "domains": [ {"helix": 13, "forward": true, "start": 360, "end": 368}, @@ -1662,7 +1662,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "CAATAGATAATACATTTGAGGATTTTGCGGA", "domains": [ {"helix": 15, "forward": true, "start": 360, "end": 384, "deletions": [369]}, @@ -1670,7 +1670,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "GGCTTTTCCCTCAGAACCGCCACGCCTGTA", "domains": [ {"helix": 2, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1679,7 +1679,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "TAGCAAGAGGAGGTTGAGGCAGTCATACAT", "domains": [ {"helix": 4, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1688,7 +1688,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "AATAGCTGAGGGAGGGAAGGTAATTACCAT", "domains": [ {"helix": 6, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1697,7 +1697,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "ATCCGGTGAGAATTAACTGAACGAAATAGC", "domains": [ {"helix": 8, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1706,7 +1706,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "TATAAAGCCAAGAACGGGTATTGAAGGCTT", "domains": [ {"helix": 10, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1715,7 +1715,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "AAATCAAATGGTTTGAAATACCCTTACCAG", "domains": [ {"helix": 12, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1724,7 +1724,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "ACAAAGAAATTATTCATTTCAACAGTACAT", "domains": [ {"helix": 14, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1733,7 +1733,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "TTTCGTCACCAGTACAAACTACAACCCTCAGA", "domains": [ {"helix": 0, "forward": false, "start": 384, "end": 408}, @@ -1741,7 +1741,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "GCCACCACACCGTTCCAGTAAGCGGTCAGACG", "domains": [ {"helix": 1, "forward": true, "start": 392, "end": 400}, @@ -1750,7 +1750,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "ATTGGCCTAATCACCAGTAGCACCAATATTGA", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 400}, @@ -1759,7 +1759,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "CGGAAATTAAGAGCAAGAAACAATACCCTGAA", "domains": [ {"helix": 5, "forward": true, "start": 392, "end": 400}, @@ -1768,7 +1768,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "CAAAGTCAAAGCAAATCAGATATAAAACCAAG", "domains": [ {"helix": 7, "forward": true, "start": 392, "end": 400}, @@ -1777,7 +1777,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "TACCGCACATGCGTTATACAAATTGACCGTGT", "domains": [ {"helix": 9, "forward": true, "start": 392, "end": 400}, @@ -1786,7 +1786,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "GATAAATACCTTTTTTAATGGAAATTACCTGA", "domains": [ {"helix": 11, "forward": true, "start": 392, "end": 400}, @@ -1795,7 +1795,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "GCAAAAGATGAGTAACATTATCATTTAGAAGT", "domains": [ {"helix": 13, "forward": true, "start": 392, "end": 400}, @@ -1804,7 +1804,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "ATTAGACTTTACAAACAATTCGACATTAATTT", "domains": [ {"helix": 15, "forward": true, "start": 392, "end": 416}, @@ -1812,7 +1812,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "CTGAATTTCCTCATTTTCAGGGATACACTGAG", "domains": [ {"helix": 2, "forward": false, "start": 400, "end": 408}, @@ -1821,7 +1821,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "GCCAGCAATGATATTCACAAACAACGCAGTCT", "domains": [ {"helix": 4, "forward": false, "start": 400, "end": 408}, @@ -1830,7 +1830,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "CCAATAATATTCATTAAAGGTGAAGAATTAGA", "domains": [ {"helix": 6, "forward": false, "start": 400, "end": 408}, @@ -1839,7 +1839,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "CCAATAGCGAGGGTAATTGAGCGCAGTTAAGC", "domains": [ {"helix": 8, "forward": false, "start": 400, "end": 408}, @@ -1848,7 +1848,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "AGTATCATTCATCGAGAACAAGCATACCGCGC", "domains": [ {"helix": 10, "forward": false, "start": 400, "end": 408}, @@ -1857,7 +1857,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "TTGAATTAAGGCGTTAAATAAGAAGCCTGTTT", "domains": [ {"helix": 12, "forward": false, "start": 400, "end": 408}, @@ -1866,7 +1866,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "TAAAAGTTAGATGATGAAACAAACAATTTCAT", "domains": [ {"helix": 14, "forward": false, "start": 400, "end": 408}, diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna index 30a5f92e..b56366e6 100644 --- a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna @@ -17,7 +17,7 @@ "is_scaffold": true }, { - "color": "#333333", + "color": "#f7931e", "sequence": "GTTACGTTACGTTACGTTGTTACGTTACGTTAC", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, @@ -25,7 +25,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "ACGTTACGTTACGTTACCGTTACGTTACGTTACGTT", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, diff --git a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna index a3f34eb8..70dcc78b 100644 --- a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna +++ b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna @@ -29,7 +29,7 @@ "is_scaffold": true }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -37,7 +37,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -45,7 +45,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -53,7 +53,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 176}, @@ -61,7 +61,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", "domains": [ {"helix": 2, "forward": false, "start": 160, "end": 176}, @@ -69,7 +69,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", "domains": [ {"helix": 4, "forward": false, "start": 160, "end": 176}, @@ -77,14 +77,14 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", "domains": [ {"helix": 0, "forward": false, "start": 88, "end": 120} ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -92,7 +92,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -100,7 +100,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -108,7 +108,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -116,14 +116,14 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -140,7 +140,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -149,7 +149,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 64}, @@ -157,7 +157,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -166,7 +166,7 @@ ] }, { - "color": "#007200", + "color": "#320096", "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -175,7 +175,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "AATGAATCGGCCAACGCGCGGGGAGTTGCAG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -183,7 +183,7 @@ ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "CAAGCGGTCCTGTTTGATGGTGGTACGTGGAC", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -192,7 +192,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "TCCAACGTTGGCCCACTACGTGAAAGCCGGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -201,7 +201,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "AGTATCGGCCTCAGGAAGATCGCAGTGCGGGC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 128}, @@ -209,7 +209,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -218,7 +218,7 @@ ] }, { - "color": "#32b86c", + "color": "#cc0000", "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -227,7 +227,7 @@ ] }, { - "color": "#333333", + "color": "#f7931e", "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -235,7 +235,7 @@ ] }, { - "color": "#320096", + "color": "#f74308", "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -244,7 +244,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "sequence": "GCCAGGGTTGGGAAGGGCGATCGCTCCAGC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -253,7 +253,7 @@ ] }, { - "color": "#7300de", + "color": "#888888", "sequence": "CAGCTTTCCGGCACCGCTTCTGGTCAGGCTGC", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 160}, @@ -261,7 +261,7 @@ ] }, { - "color": "#aaaa00", + "color": "#32b86c", "sequence": "GTCGACTCACGAGCCGGAAGCATACTAACTCA", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -270,7 +270,7 @@ ] }, { - "color": "#b8056c", + "color": "#333333", "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, From 5b001fa694b8aa78e28a2b852a91b142df2a6742 Mon Sep 17 00:00:00 2001 From: David Doty Date: Wed, 24 Jun 2020 15:08:20 -0700 Subject: [PATCH 13/30] fixes #92 --- ...elix_origami_barrel_from_algoSST_paper.dna | 30 +- .../16_helix_origami_rectangle.dna | 416 ++++++++-------- .../16_helix_origami_rectangle_idt.dna | 416 ++++++++-------- .../16_helix_origami_rectangle_no_seq.dna | 416 ++++++++-------- ...elix_origami_rectangle_no_seq_no_twist.dna | 416 ++++++++-------- .../16_helix_origami_rectangle_no_twist.dna | 416 ++++++++-------- ...ami_rectangle_seed_tiles_grow_from_top.dna | 416 ++++++++-------- ..._origami_rectangle_shifted_seam_no_seq.dna | 416 ++++++++-------- .../1_staple_1_helix_origami.dna | 2 +- .../1_staple_1_helix_origami_mismatches.dna | 2 +- ...le_1_helix_origami_position_nondefault.dna | 2 +- .../1_staple_1_helix_origami_roll.dna | 2 +- ...elix_origami_rectangle_twist_corrected.dna | 240 +--------- ...x_2_strands_multiple_substrands_no_seq.dna | 4 +- .../2_staple_2_helix_modifications.dna | 52 +- .../2_staple_2_helix_origami_6bases_wide.dna | 4 +- .../2_staple_2_helix_origami_deletions.dna | 4 +- ...elix_origami_deletions_insertions_mods.dna | 4 +- ...etions_insertions_mods_chained_methods.dna | 4 +- ...ix_origami_deletions_insertions_no_seq.dna | 4 +- .../3_helix_deletions_insertions.dna | 20 +- examples/output_designs/4_helix_grid_none.dna | 2 +- ..._none_min_offset_position_x_nondefault.dna | 8 +- .../4_helix_min_offsets_nonzero.dna | 2 +- .../56_helix_origami_rectangle.dna | 448 +++++++++--------- .../64_helix_origami_rectangle.dna | 384 +++++++-------- .../6_helix_6_col_origami_rectangle.dna | 36 +- .../6_helix_bundle_honeycomb.dna | 174 +------ .../6_helix_origami_rectangle.dna | 60 +-- ...origami_rectangle_helices_out_of_order.dna | 60 +-- examples/output_designs/hairpin.dna | 2 +- .../output_designs/idt-plates-explicit.dna | 416 ++++++++-------- .../output_designs/long_range_crossovers.dna | 48 +- .../output_designs/loopouts_all_types.dna | 2 +- .../many_helices_modifications.dna | 26 +- examples/output_designs/proposal.dna | 416 ++++++++-------- scadnano/scadnano.py | 65 ++- ...st_16_helix_origami_rectangle_no_twist.dna | 414 ++++++++-------- ...e_2_helix_origami_deletions_insertions.dna | 4 +- .../test_6_helix_origami_rectangle.dna | 52 +- 40 files changed, 2785 insertions(+), 3120 deletions(-) diff --git a/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna b/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna index c06acb18..c9e4445d 100644 --- a/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna +++ b/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna @@ -143,7 +143,7 @@ "is_scaffold": true }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "TGTTAGTGAACAATATTACCGATAGTTGCGCCGACAATGA", "domains": [ {"helix": 18, "forward": false, "start": 248, "end": 256}, @@ -152,7 +152,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "ACTTTGAAATCATAAGGGAACCGTATAAGTA", "domains": [ {"helix": 4, "forward": false, "start": 224, "end": 232}, @@ -160,7 +160,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TAGCCCGGACGTCGAGAGGGTTGAAACTGACCA", "domains": [ {"helix": 3, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, @@ -168,7 +168,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "CAACACTAAAGGAATTACGAGGCAATCAAAAT", "domains": [ {"helix": 6, "forward": false, "start": 224, "end": 232}, @@ -176,7 +176,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CACCGGAATGCCATCTTTTCATATAGTAAGAG", "domains": [ {"helix": 5, "forward": true, "start": 248, "end": 256}, @@ -184,7 +184,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TTAGAGCTAAGAGGTCATTTTTGCGGAATAC", "domains": [ {"helix": 8, "forward": false, "start": 224, "end": 232}, @@ -192,7 +192,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CCAAAAGAAGGAAACGCAATAATAACGGATGGC", "domains": [ {"helix": 7, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, @@ -200,7 +200,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "TAAATGCAAATTTTTAGAACCCTTTTTAGCG", "domains": [ {"helix": 10, "forward": false, "start": 224, "end": 232}, @@ -208,7 +208,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "AACCTCCCGTAAGAACGCGAGGCGCATATATTT", "domains": [ {"helix": 9, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, @@ -216,7 +216,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GCTTTCATTTCGCGTCTGGCCTTCCTGTTTAG", "domains": [ {"helix": 12, "forward": false, "start": 224, "end": 232}, @@ -224,7 +224,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "TATCATATATTACTAGAAAAAGCCTGTAGCCA", "domains": [ {"helix": 11, "forward": true, "start": 248, "end": 256}, @@ -232,7 +232,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "CTAGAGGAGCTTGCATGCCTGCATTACCTGA", "domains": [ {"helix": 14, "forward": false, "start": 224, "end": 232}, @@ -240,7 +240,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GCAAAAGAAGAATTATTCATTTCAAGGTCGACT", "domains": [ {"helix": 13, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, @@ -248,7 +248,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "TCCCTTATATGGTGGTTCCGAAAAATATCTT", "domains": [ {"helix": 16, "forward": false, "start": 224, "end": 232}, @@ -256,7 +256,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "TAGGAGCACAGGAAGGTTATCTAATCGGCAAAA", "domains": [ {"helix": 15, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, diff --git a/examples/output_designs/16_helix_origami_rectangle.dna b/examples/output_designs/16_helix_origami_rectangle.dna index bdc835fa..8a58b0c8 100644 --- a/examples/output_designs/16_helix_origami_rectangle.dna +++ b/examples/output_designs/16_helix_origami_rectangle.dna @@ -59,7 +59,7 @@ "is_scaffold": true }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "ACAACCATCGCCCACGTGCGCCGACAATGACA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -67,7 +67,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GAGGACAGATGAACGGCTGACCAACTTTGAAA", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -75,7 +75,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TCGTTTACCAGACGACAACACTATCATAACCC", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -83,7 +83,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CTGTAGCTCAACATGTATTGCTGAATATAATG", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, @@ -91,7 +91,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "ATTCAAAAGGGTGAGATAATGTGTAGGTAAAG", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, @@ -99,7 +99,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GATTCTCCGTGGGAACGAGTAACAACCCGTCG", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, @@ -107,7 +107,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GTTTCCTGTGTGAAATAATCATGGTCATAGCT", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, @@ -115,7 +115,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "ACAAGAGTCCACTATTGTTGTTCCAGTTTGGA", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, @@ -123,7 +123,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "ACCGCCACCCTCAGAATACCGCCACCCTCAGA", "domains": [ {"helix": 0, "forward": false, "start": 416, "end": 432}, @@ -131,7 +131,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CCGCCGCCAGCATTGAAGAACCACCACCAGAG", "domains": [ {"helix": 2, "forward": false, "start": 416, "end": 432}, @@ -139,7 +139,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AGACAAAAGGGCGACAGGTTTACCAGCGCCAA", "domains": [ {"helix": 4, "forward": false, "start": 416, "end": 432}, @@ -147,7 +147,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AGAGAATAACATAAAAATAGCAGCCTTTACAG", "domains": [ {"helix": 6, "forward": false, "start": 416, "end": 432}, @@ -155,7 +155,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CGAGCATGTAGAAACCATCCCATCCTAATTTA", "domains": [ {"helix": 8, "forward": false, "start": 416, "end": 432}, @@ -163,7 +163,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CGCGAGAAAACTTTTTATCGCAAGACAAAGAA", "domains": [ {"helix": 10, "forward": false, "start": 416, "end": 432}, @@ -171,7 +171,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TCGGGAGAAACAATAAAACAGTACCTTTTACA", "domains": [ {"helix": 12, "forward": false, "start": 416, "end": 432}, @@ -179,7 +179,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TTGAAAGGAATTGAGGGTTGGCAAATCAACAG", "domains": [ {"helix": 14, "forward": false, "start": 416, "end": 432}, @@ -187,14 +187,14 @@ ] }, { - "color": "#7300de", + "color": "#32b86c", "sequence": "ACGTTAGTAAATGAATTTTCTGTATGGGATTT", "domains": [ {"helix": 0, "forward": false, "start": 216, "end": 248} ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "AAACGAAATGCCACTACGAAGGCAAAACAGTT", "domains": [ {"helix": 2, "forward": false, "start": 208, "end": 216}, @@ -202,7 +202,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "AATGCCCCGTAACAGTGCCCGTATCCAACCTA", "domains": [ {"helix": 1, "forward": true, "start": 232, "end": 240}, @@ -210,7 +210,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CGATTTTATTAATCATTGTGAATTATCAAGTT", "domains": [ {"helix": 4, "forward": false, "start": 208, "end": 216}, @@ -218,7 +218,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TGCCTTTAAATCAGTAGCGACAGAACCTTATG", "domains": [ {"helix": 3, "forward": true, "start": 232, "end": 240}, @@ -226,7 +226,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "TCAGAAGCAGGTCTTTACCCTGACAGTTACCA", "domains": [ {"helix": 6, "forward": false, "start": 208, "end": 216}, @@ -234,7 +234,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "GAAGGAAAGCAGATAGCCGAACAATATTATAG", "domains": [ {"helix": 5, "forward": true, "start": 232, "end": 240}, @@ -242,7 +242,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "CAATAAATACTAATAGTAGTAGCACTTGCGGG", "domains": [ {"helix": 8, "forward": false, "start": 208, "end": 216}, @@ -250,7 +250,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "AGGTTTTGTTAGCGAACCTCCCGATTAACATC", "domains": [ {"helix": 7, "forward": true, "start": 232, "end": 240}, @@ -258,7 +258,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "AGAAAAGCTCATATGTACCCCGGTAGAATCGC", "domains": [ {"helix": 10, "forward": false, "start": 208, "end": 216}, @@ -266,7 +266,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CATATTTACAGTAGGGCTTAATTGTGATAATC", "domains": [ {"helix": 9, "forward": true, "start": 232, "end": 240}, @@ -274,7 +274,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "GGCGATCGTCAGGCTGCGCAACTGCCTTGCTT", "domains": [ {"helix": 12, "forward": false, "start": 208, "end": 216}, @@ -282,7 +282,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "CTGTAAATATATGTGAGTGAATAATTGGGAAG", "domains": [ {"helix": 11, "forward": true, "start": 232, "end": 240}, @@ -290,7 +290,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "TGGTTTTTCGGTTTGCGTATTGGGAGAAGGAG", "domains": [ {"helix": 14, "forward": false, "start": 208, "end": 216}, @@ -298,7 +298,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CGGAATTAGAACAAAGAAACCACCCGCCAGGG", "domains": [ {"helix": 13, "forward": true, "start": 232, "end": 240}, @@ -306,14 +306,14 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GAACGTGGCGAGAAAGGAAGGGAACGAACTGA", "domains": [ {"helix": 15, "forward": true, "start": 200, "end": 232} ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CTTAAACAGCTTGATACCGATAGTCATAACCG", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56}, @@ -321,7 +321,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "ATATATTCTCATAAGGGAACCGAATGTACAGA", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -330,7 +330,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CCAGGCGCGAGGCATAGTAAGAGCGATAAAAA", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -339,7 +339,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CCAAAATAGATGGCTTAGAGCTTATTTAAATA", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 48}, @@ -348,7 +348,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TGCAACTAAAATGCAATGCCTGAGAAGGCCGG", "domains": [ {"helix": 7, "forward": true, "start": 40, "end": 48}, @@ -357,7 +357,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AGACAGTCAACATTAAATGTGAGCAAACGGCG", "domains": [ {"helix": 9, "forward": true, "start": 40, "end": 48}, @@ -366,7 +366,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GATTGACCCCGAGCTCGAATTCGTTGTTATCC", "domains": [ {"helix": 11, "forward": true, "start": 40, "end": 48}, @@ -375,7 +375,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "GCTCACAACGAGATAGGGTTGAGTAAAGAACG", "domains": [ {"helix": 13, "forward": true, "start": 40, "end": 48}, @@ -384,7 +384,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TGGACTCCAACGTCAAAGGGCGAAAATCAAAA", "domains": [ {"helix": 15, "forward": true, "start": 40, "end": 64}, @@ -392,7 +392,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ACGGTCAAGGTCGCTGAGGCTTGCGTGAATTT", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -401,7 +401,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GGAATTACATAGGCTGGCTGACCTAGGCGCAG", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -410,7 +410,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TTTTTGCGGCGAGAGGCTTTTGCACGCCAAAA", "domains": [ {"helix": 6, "forward": false, "start": 48, "end": 56}, @@ -419,7 +419,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TATATTTTAAGTACGGTGTCTGGAAGAGGTCA", "domains": [ {"helix": 8, "forward": false, "start": 48, "end": 56}, @@ -428,7 +428,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CTTTCATCAAATCACCATCAATATAACCCTCA", "domains": [ {"helix": 10, "forward": false, "start": 48, "end": 56}, @@ -437,7 +437,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CCCGGGTAGTAATGGGATAGGTCAGTAGCCAG", "domains": [ {"helix": 12, "forward": false, "start": 48, "end": 56}, @@ -446,7 +446,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GAATAGCCTTCCACACAACATACGAGAGGATC", "domains": [ {"helix": 14, "forward": false, "start": 48, "end": 56}, @@ -455,7 +455,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "TCGGTTTATCAGCTTGCTTTCGAGAGGGAGTT", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88}, @@ -463,7 +463,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AAAGGCCGTTACTTAGCCGGAACGTCATCAAG", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -472,7 +472,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AGTAATCTTAATGCAGATACATAAAAAGAAGT", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -481,7 +481,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "TTTGCCAGATTGCTCCTTTTGATAAGTTTCAT", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 80}, @@ -490,7 +490,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TCCATATAGGATAAAAATTTTTAGGATATTCA", "domains": [ {"helix": 7, "forward": true, "start": 72, "end": 80}, @@ -499,7 +499,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "ACCGTTCTCGCGTCTGGCCTTCCTCGTTGGTG", "domains": [ {"helix": 9, "forward": true, "start": 72, "end": 80}, @@ -508,7 +508,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TAGATGGGCCTGCAGGTCGACTCTAGCCGGAA", "domains": [ {"helix": 11, "forward": true, "start": 72, "end": 80}, @@ -517,7 +517,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GCATAAAGGGCAAAATCCCTTATAAAACCGTC", "domains": [ {"helix": 13, "forward": true, "start": 72, "end": 80}, @@ -526,7 +526,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TATCAGGGCGATGGCCCACTACGTTGGTGGTT", "domains": [ {"helix": 15, "forward": true, "start": 72, "end": 96}, @@ -534,7 +534,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GCTCCATGCTTTTGCGGGATCGTCTAATTGTA", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88}, @@ -543,7 +543,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CATTCAACTGACAAGAACCGGATACGCGACCT", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88}, @@ -552,7 +552,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TACCTTTAAGGGGGTAATAGTAAAGAATACCA", "domains": [ {"helix": 6, "forward": false, "start": 80, "end": 88}, @@ -561,7 +561,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CAACGCAAACAGTTGATTCCCAATTTAGAGAG", "domains": [ {"helix": 8, "forward": false, "start": 80, "end": 88}, @@ -570,7 +570,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AAATAATTAGCTGATAAATTAATGCTTTATTT", "domains": [ {"helix": 10, "forward": false, "start": 80, "end": 88}, @@ -579,7 +579,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "CTTGCATGCGCATCGTAACCGTGCGCCATCAA", "domains": [ {"helix": 12, "forward": false, "start": 80, "end": 88}, @@ -588,7 +588,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CCGAAATCTGTAAAGCCTGGGGTGGTGCCAAG", "domains": [ {"helix": 14, "forward": false, "start": 80, "end": 88}, @@ -597,7 +597,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "AAAAAAGGCTCCAAAAGGAGCCTTACCCTCAG", "domains": [ {"helix": 0, "forward": false, "start": 96, "end": 120}, @@ -605,7 +605,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CAGCGAAAAAATTGTGTCGAAATCTTCATTAC", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -614,7 +614,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CCAAATCAATCAGTTGAGATTTAGATGTTTAG", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -623,7 +623,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ACTGGATACTCCAACAGGTCAGGATCTGCGAA", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 112}, @@ -632,7 +632,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CGAGTAGACTTTTGCGGGAGAAGCCCGGAGAG", "domains": [ {"helix": 7, "forward": true, "start": 104, "end": 112}, @@ -641,7 +641,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "GGTAGCTATTTAACCAATAGGAACATCTGCCA", "domains": [ {"helix": 9, "forward": true, "start": 104, "end": 112}, @@ -650,7 +650,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GTTTGAGGTGTAAAACGACGGCCACCTAATGA", "domains": [ {"helix": 11, "forward": true, "start": 104, "end": 112}, @@ -659,7 +659,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GTGAGCTACGAAAATCCTGTTTGAGAACCATC", "domains": [ {"helix": 13, "forward": true, "start": 104, "end": 112}, @@ -668,7 +668,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "ACCCAAATCAAGTTTTTTGGGGTCGGTTTGCC", "domains": [ {"helix": 15, "forward": true, "start": 104, "end": 128}, @@ -676,7 +676,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CGCCTGATGACAGCATCGGAACGAATCTCCAA", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -685,7 +685,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AAAGATTCACGTAACAAAGCTGCTTGTATCAT", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -694,7 +694,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "GAAGCAAAGCGTCCAATACTGCGGACAGGTAG", "domains": [ {"helix": 6, "forward": false, "start": 112, "end": 120}, @@ -703,7 +703,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CTGTAATATTTAGTTTGACCATTACCAGACCG", "domains": [ {"helix": 8, "forward": false, "start": 112, "end": 120}, @@ -712,7 +712,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GCTCATTTTTTTTGAGAGATCTACTTATGACC", "domains": [ {"helix": 10, "forward": false, "start": 112, "end": 120}, @@ -721,7 +721,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CACGACGTGGACGACGACAGTATCTTAAATCA", "domains": [ {"helix": 12, "forward": false, "start": 112, "end": 120}, @@ -730,7 +730,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CCAGCAGGACTCACATTAATTGCGTTCCCAGT", "domains": [ {"helix": 14, "forward": false, "start": 112, "end": 120}, @@ -739,7 +739,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "AATAATAATTTTTTCACGTTGAAAGGGTAGCA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152}, @@ -747,7 +747,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "ACGGCTACAAGTACAACGGAGATTCATTCAGT", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -756,7 +756,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "GAATAAGGACGGAACAACATTATTAATCGTCA", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -765,7 +765,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TAAATATTCGAGCTTCAAAGCGAAGATACATT", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 144}, @@ -774,7 +774,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TCGCAAATGGTTGTACCAAAAACAAAAGGCTA", "domains": [ {"helix": 7, "forward": true, "start": 136, "end": 144}, @@ -783,7 +783,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TCAGGTCATCGCATTAAATTTTTGGGCCTCAG", "domains": [ {"helix": 9, "forward": true, "start": 136, "end": 144}, @@ -792,7 +792,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GAAGATCGGGGTAACGCCAGGGTTTTGCGCTC", "domains": [ {"helix": 11, "forward": true, "start": 136, "end": 144}, @@ -801,7 +801,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "ACTGCCCGGCAAGCGGTCCACGCTGAGGTGCC", "domains": [ {"helix": 13, "forward": true, "start": 136, "end": 144}, @@ -810,7 +810,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "GTAAAGCACTAAATCGGAACCCTACCCTGAGA", "domains": [ {"helix": 15, "forward": true, "start": 136, "end": 160}, @@ -818,7 +818,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GCGAAACAAGAGGCTTTGAGGACTGAATTGCG", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -827,7 +827,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "ACGAACTACTTGCCCTGACGAGAATACCAAGC", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, @@ -836,7 +836,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TTTTAATTCATTGAATCCCCCTCATTAATAAA", "domains": [ {"helix": 6, "forward": false, "start": 144, "end": 152}, @@ -845,7 +845,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GCTAAATCGGTCAATAACCTGTTTATATCGCG", "domains": [ {"helix": 8, "forward": false, "start": 144, "end": 152}, @@ -854,7 +854,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "GTTAAAATTTGCCTGAGAGTCTGGAGCATAAA", "domains": [ {"helix": 10, "forward": false, "start": 144, "end": 152}, @@ -863,7 +863,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "ATTAAGTTCACTCCAGCCAGCTTTAATATTTT", "domains": [ {"helix": 12, "forward": false, "start": 144, "end": 152}, @@ -872,7 +872,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "GAGTTGCACTTTCCAGTCGGGAAAGCAAGGCG", "domains": [ {"helix": 14, "forward": false, "start": 144, "end": 152}, @@ -881,7 +881,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GAGAATAGAAAGGAACAACTAAAGAAAGACTT", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 184}, @@ -889,7 +889,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TTTCATGATGACCCCCAGCGATTAACACCAGA", "domains": [ {"helix": 1, "forward": true, "start": 168, "end": 176}, @@ -898,7 +898,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "ACGAGTAGGGAAGAAAAATCTACGAATGCTTT", "domains": [ {"helix": 3, "forward": true, "start": 168, "end": 176}, @@ -907,7 +907,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AAACAGTTGCCCGAAAGACTTCAAAGCTATAT", "domains": [ {"helix": 5, "forward": true, "start": 168, "end": 176}, @@ -916,7 +916,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "TTTCATTTAGCAATAAAGCCTCAGAGCAAACA", "domains": [ {"helix": 7, "forward": true, "start": 168, "end": 176}, @@ -925,7 +925,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AGAGAATCTTAAATTGTAAACGTTCCGGCACC", "domains": [ {"helix": 9, "forward": true, "start": 168, "end": 176}, @@ -934,7 +934,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GCTTCTGGGAAAGGGGGATGTGCTCCTGTCGT", "domains": [ {"helix": 11, "forward": true, "start": 168, "end": 176}, @@ -943,7 +943,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GCCAGCTGGCCCTTCACCGCCTGGAAGGGAGC", "domains": [ {"helix": 13, "forward": true, "start": 168, "end": 176}, @@ -952,7 +952,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CCCCGATTTAGAGCTTGACGGGGACGGGCAAC", "domains": [ {"helix": 15, "forward": true, "start": 168, "end": 192}, @@ -960,7 +960,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CTCATCTTGGAAGTTTCCATTAAAAGCGGAGT", "domains": [ {"helix": 2, "forward": false, "start": 176, "end": 184}, @@ -969,7 +969,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "GGACGTTGTAAATTGGGCTTGAGACTAAAACA", "domains": [ {"helix": 4, "forward": false, "start": 176, "end": 184}, @@ -978,7 +978,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "AAGAGGAACAGAAAACGAGAATGAACCAGTCA", "domains": [ {"helix": 6, "forward": false, "start": 176, "end": 184}, @@ -987,7 +987,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "CAAAATTAGGGGCGCGAGCTGAAAAAAAGATT", "domains": [ {"helix": 8, "forward": false, "start": 176, "end": 184}, @@ -996,7 +996,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GCAAATATGATGAACGGTAATCGTAGAATTAG", "domains": [ {"helix": 10, "forward": false, "start": 176, "end": 184}, @@ -1005,7 +1005,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CAGCTGGCTGCCGGAAACCAGGCATTGTATAA", "domains": [ {"helix": 12, "forward": false, "start": 176, "end": 184}, @@ -1014,7 +1014,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "AGCTGATTCATTAATGAATCGGCCTATTACGC", "domains": [ {"helix": 14, "forward": false, "start": 176, "end": 184}, @@ -1023,7 +1023,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "TGCTAAACAACTTTCAACAGTTTCCGGGTAAA", "domains": [ {"helix": 0, "forward": false, "start": 192, "end": 216}, @@ -1031,7 +1031,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "ATACGTAAGAGGCAAAAGAATACATGGTTTAA", "domains": [ {"helix": 1, "forward": true, "start": 200, "end": 208}, @@ -1040,7 +1040,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TTTCAACTAGAACTGGCTCATTATCCATAAAT", "domains": [ {"helix": 3, "forward": true, "start": 200, "end": 208}, @@ -1049,7 +1049,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CAAAAATCAAAGCGGATTGCATCAAGGTGGCA", "domains": [ {"helix": 5, "forward": true, "start": 200, "end": 208}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "TCAATTCTCATACAGGCAAGGCAAAAAACTAG", "domains": [ {"helix": 7, "forward": true, "start": 200, "end": 208}, @@ -1067,7 +1067,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CATGTCAACCCAAAAACAGGAAGAAAGCGCCA", "domains": [ {"helix": 9, "forward": true, "start": 200, "end": 208}, @@ -1076,7 +1076,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TTCGCCATGTGCGGGCCTCTTCGCAACGCGCG", "domains": [ {"helix": 11, "forward": true, "start": 200, "end": 208}, @@ -1085,7 +1085,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "GGGAGAGGCTTTTCACCAGTGAGAAAGCCGGC", "domains": [ {"helix": 13, "forward": true, "start": 200, "end": 208}, @@ -1094,7 +1094,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "TAGCCCTAAAACATCGCCATTAAAACATTATC", "domains": [ {"helix": 15, "forward": true, "start": 232, "end": 256}, @@ -1102,7 +1102,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TGCCTTGACTGCCTATTTCGGAACCTTTCCAG", "domains": [ {"helix": 2, "forward": false, "start": 240, "end": 248}, @@ -1111,7 +1111,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AGCACCGTGCGTCAGACTGTAGCGGGGGTCAG", "domains": [ {"helix": 4, "forward": false, "start": 240, "end": 248}, @@ -1120,7 +1120,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "AAAAGTAACCGAGGAAACGCAATATCGATAGC", "domains": [ {"helix": 6, "forward": false, "start": 240, "end": 248}, @@ -1129,7 +1129,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GAGGCGTTAAGCCTTAAATCAAGATTTTTAAG", "domains": [ {"helix": 8, "forward": false, "start": 240, "end": 248}, @@ -1138,7 +1138,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "ACGCTCAAACAACGCCAACATGTAAAGAACGC", "domains": [ {"helix": 10, "forward": false, "start": 240, "end": 248}, @@ -1147,7 +1147,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AAATCAATCGTCGCTATTAATTAATAAAGCCA", "domains": [ {"helix": 12, "forward": false, "start": 240, "end": 248}, @@ -1156,7 +1156,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "ATTTTGCGTCATCATATTCCTGATCAGTACAT", "domains": [ {"helix": 14, "forward": false, "start": 240, "end": 248}, @@ -1165,7 +1165,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CGTAACGATCTAAAGTTTTGTCGTCTATTATT", "domains": [ {"helix": 0, "forward": false, "start": 256, "end": 280}, @@ -1173,7 +1173,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CTGAAACAGGTAATAAGTTTTAACCGTTTTCA", "domains": [ {"helix": 1, "forward": true, "start": 264, "end": 272}, @@ -1182,7 +1182,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TCGGCATTGTCACCAATGAAACCAATAACGGA", "domains": [ {"helix": 3, "forward": true, "start": 264, "end": 272}, @@ -1191,7 +1191,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "ATACCCAATATCTTACCGAAGCCCTTAGTTGC", "domains": [ {"helix": 5, "forward": true, "start": 264, "end": 272}, @@ -1200,7 +1200,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TATTTTGCGCTTATCCGGTATTCTATTTAGGC", "domains": [ {"helix": 7, "forward": true, "start": 264, "end": 272}, @@ -1209,7 +1209,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "AGAGGCATCAAATTCTTACCAGTATTTTCCCT", "domains": [ {"helix": 9, "forward": true, "start": 264, "end": 272}, @@ -1218,7 +1218,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TAGAATCCCCTTTTTTAATGGAAATATCAGAT", "domains": [ {"helix": 11, "forward": true, "start": 264, "end": 272}, @@ -1227,7 +1227,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GATGGCAATTTAAAAGTTTGAGTAAATACCGA", "domains": [ {"helix": 13, "forward": true, "start": 264, "end": 272}, @@ -1236,7 +1236,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "ACGAACCACCAGCAGAAGATAAAACCCGAACG", "domains": [ {"helix": 15, "forward": true, "start": 264, "end": 288}, @@ -1244,7 +1244,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "AGTGTACTTGAAAGTATTAAGAGGATAGTTAG", "domains": [ {"helix": 2, "forward": false, "start": 272, "end": 280}, @@ -1253,7 +1253,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CCGGAAACTTCGGTCATAGCCCCCGATACAGG", "domains": [ {"helix": 4, "forward": false, "start": 272, "end": 280}, @@ -1262,7 +1262,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GCAATAGCAAGAACTGGCATGATTTAGCAAGG", "domains": [ {"helix": 6, "forward": false, "start": 272, "end": 280}, @@ -1271,7 +1271,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TATAGAAGACCCAGCTACAATTTTATGAAATA", "domains": [ {"helix": 8, "forward": false, "start": 272, "end": 280}, @@ -1280,7 +1280,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GCGTTATATTTCGAGCCAGTAATAAAATCAGA", "domains": [ {"helix": 10, "forward": false, "start": 272, "end": 280}, @@ -1289,7 +1289,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "TTGAATTATTGAAAACATAGCGATTATCATAT", "domains": [ {"helix": 12, "forward": false, "start": 272, "end": 280}, @@ -1298,7 +1298,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TTATTAATTTCATCAATATAATCCAATTTCAT", "domains": [ {"helix": 14, "forward": false, "start": 272, "end": 280}, @@ -1307,7 +1307,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TGTAGCATTCCACAGACAGCCCTCCTGAGACT", "domains": [ {"helix": 0, "forward": false, "start": 288, "end": 312}, @@ -1315,7 +1315,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CCTCAAGAATACATGGCTTTTGATTTATTAGC", "domains": [ {"helix": 1, "forward": true, "start": 296, "end": 304}, @@ -1324,7 +1324,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GTTTGCCAGTAGCACCATTACCATAAGACTCC", "domains": [ {"helix": 3, "forward": true, "start": 296, "end": 304}, @@ -1333,7 +1333,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TTATTACGATAAGAGCAAGAAACAATCCTGAA", "domains": [ {"helix": 5, "forward": true, "start": 296, "end": 304}, @@ -1342,7 +1342,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TCTTACCAGCGCCCAATAGCAAGCAGAGAATA", "domains": [ {"helix": 7, "forward": true, "start": 296, "end": 304}, @@ -1351,7 +1351,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TAAAGTACGAAAAAGCCTGTTTAGAGCTTAGA", "domains": [ {"helix": 9, "forward": true, "start": 296, "end": 304}, @@ -1360,7 +1360,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TTAAGACGATTAATTACATTTAACTGATTGTT", "domains": [ {"helix": 11, "forward": true, "start": 296, "end": 304}, @@ -1369,7 +1369,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "TGGATTATCGTATTAAATCCTTTGCAGAGGTG", "domains": [ {"helix": 13, "forward": true, "start": 296, "end": 304}, @@ -1378,7 +1378,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AGGCGGTCAGTATTAACACCGCCTAAACAATT", "domains": [ {"helix": 15, "forward": true, "start": 296, "end": 320}, @@ -1386,7 +1386,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TAAGCGTCGAAGGATTAGGATTAGACAACGCC", "domains": [ {"helix": 2, "forward": false, "start": 304, "end": 312}, @@ -1395,7 +1395,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AATCACCATCTTTTCATAATCAAACGTTCCAG", "domains": [ {"helix": 4, "forward": false, "start": 304, "end": 312}, @@ -1404,7 +1404,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GCCCAATACAGTATGTTAGCAAACGCCAGCAA", "domains": [ {"helix": 6, "forward": false, "start": 304, "end": 312}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TCATTACCACGCTAACGAGCGTCTTGAGTTAA", "domains": [ {"helix": 8, "forward": false, "start": 304, "end": 312}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "AATTACTACGACAAAAGGTAAAGTCGTAGGAA", "domains": [ {"helix": 10, "forward": false, "start": 304, "end": 312}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "AAAACAAACTGAGAAGAGTCAATAGGAATCAT", "domains": [ {"helix": 12, "forward": false, "start": 304, "end": 312}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CGACAACTACTTCTGAATAATGGAACATCAAG", "domains": [ {"helix": 14, "forward": false, "start": 304, "end": 312}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TGAGTTTCGTCACCAGTACAAACTCGGGGTTT", "domains": [ {"helix": 0, "forward": false, "start": 320, "end": 344}, @@ -1457,7 +1457,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TGCTCAGTCAGTCTCTGAATTTACATCACCGG", "domains": [ {"helix": 1, "forward": true, "start": 328, "end": 336}, @@ -1466,7 +1466,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "AACCAGAGCCATTTGGGAATTAGAGTAGAAAA", "domains": [ {"helix": 3, "forward": true, "start": 328, "end": 336}, @@ -1475,7 +1475,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TACATACAGATAACCCACAAGAATTTCCAGAG", "domains": [ {"helix": 5, "forward": true, "start": 328, "end": 336}, @@ -1484,7 +1484,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CCTAATTTCCGTTTTTATTTTCATAATTCTGT", "domains": [ {"helix": 7, "forward": true, "start": 328, "end": 336}, @@ -1493,7 +1493,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CCAGACGAAATAAGAATAAACACCGTGAATTT", "domains": [ {"helix": 9, "forward": true, "start": 328, "end": 336}, @@ -1502,7 +1502,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "ATCAAAATGAAGATGATGAAACAAAGGGTTAG", "domains": [ {"helix": 11, "forward": true, "start": 328, "end": 336}, @@ -1511,7 +1511,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AACCTACCAAGTATTAGACTTTACGCAACAGT", "domains": [ {"helix": 13, "forward": true, "start": 328, "end": 336}, @@ -1520,7 +1520,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GCCACGCTGAGAGCCAGCAGCAAAACATTTGA", "domains": [ {"helix": 15, "forward": true, "start": 328, "end": 352}, @@ -1528,7 +1528,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "GGAAAGCGACCAGGCGGATAAGTGCGTAACAC", "domains": [ {"helix": 2, "forward": false, "start": 336, "end": 344}, @@ -1537,7 +1537,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GACTTGAGCCACCACCGGAACCGCGCCAGAAT", "domains": [ {"helix": 4, "forward": false, "start": 336, "end": 344}, @@ -1546,7 +1546,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ATCAGAGATAAAGGTGGCAACATACCGTCACC", "domains": [ {"helix": 6, "forward": false, "start": 336, "end": 344}, @@ -1555,7 +1555,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CAAGCAAGGCCAGTTACAAAATAAGCGCTAAT", "domains": [ {"helix": 8, "forward": false, "start": 336, "end": 344}, @@ -1564,7 +1564,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "AGGCGTTACGACAATAAACAACATATCGAGAA", "domains": [ {"helix": 10, "forward": false, "start": 336, "end": 344}, @@ -1573,7 +1573,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GAGCAAAACATAGGTCTGAGAGACGATAAATA", "domains": [ {"helix": 12, "forward": false, "start": 336, "end": 344}, @@ -1582,7 +1582,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GGATTTAGATATCAAAATTATTTGAATTACCT", "domains": [ {"helix": 14, "forward": false, "start": 336, "end": 344}, @@ -1591,7 +1591,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CAAGCCCAATAGGAACCCATGTACCCGTCGAG", "domains": [ {"helix": 0, "forward": false, "start": 352, "end": 376}, @@ -1599,7 +1599,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AGGGTTGAATAAATCCTCATTAAACTCCCTCA", "domains": [ {"helix": 1, "forward": true, "start": 360, "end": 368}, @@ -1608,7 +1608,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GAGCCGCCTAAAGGTGAATTATCATAAAAGAA", "domains": [ {"helix": 3, "forward": true, "start": 360, "end": 368}, @@ -1617,7 +1617,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "ACGCAAAGGTCAGAGGGTAATTGAACAGCCAT", "domains": [ {"helix": 5, "forward": true, "start": 360, "end": 368}, @@ -1626,7 +1626,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "ATTATTTAACCAAGTACCGCACTCGTTCAGCT", "domains": [ {"helix": 7, "forward": true, "start": 360, "end": 368}, @@ -1635,7 +1635,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "AATGCAGAGAAATACCGACCGTGTTACCTTTT", "domains": [ {"helix": 9, "forward": true, "start": 360, "end": 368}, @@ -1644,7 +1644,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TAACCTCCGCGAATTATTCATTTCCACGTAAA", "domains": [ {"helix": 11, "forward": true, "start": 360, "end": 368}, @@ -1653,7 +1653,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "ACAGAAATGCCGTCAATAGATAATTGAAAAAT", "domains": [ {"helix": 13, "forward": true, "start": 360, "end": 368}, @@ -1662,7 +1662,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CTAAAGCATCACCTTGCTGAACCTCAACTAAT", "domains": [ {"helix": 15, "forward": true, "start": 360, "end": 384}, @@ -1670,7 +1670,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "ACAAACAATATAAGTATAGCCCGGAGGGATAG", "domains": [ {"helix": 2, "forward": false, "start": 368, "end": 376}, @@ -1679,7 +1679,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TTATTCATACCCTCAGAACCGCCATGATATTC", "domains": [ {"helix": 4, "forward": false, "start": 368, "end": 376}, @@ -1688,7 +1688,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TGAACAAAACACCACGGAATAAGTGACGGAAA", "domains": [ {"helix": 6, "forward": false, "start": 368, "end": 376}, @@ -1697,7 +1697,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GGTATTAATCCCAATCCAAATAAGGAACACCC", "domains": [ {"helix": 8, "forward": false, "start": 368, "end": 376}, @@ -1706,7 +1706,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "AATGGTTTACGCGCCTGTTTATCACAAGAACG", "domains": [ {"helix": 10, "forward": false, "start": 368, "end": 376}, @@ -1715,7 +1715,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GCGCAGAGGGCTTAGGTTGGGTTACTAAATTT", "domains": [ {"helix": 12, "forward": false, "start": 368, "end": 376}, @@ -1724,7 +1724,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AGATTAGAAAAGAAATTGCGTAGAACAAAATC", "domains": [ {"helix": 14, "forward": false, "start": 368, "end": 376}, @@ -1733,7 +1733,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "CTCAGAGCCACCACCCTCATTTTCAATAGGTG", "domains": [ {"helix": 0, "forward": false, "start": 384, "end": 408}, @@ -1741,7 +1741,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "TATCACCGGTCAGACGATTGGCCTCCCTCAGA", "domains": [ {"helix": 1, "forward": true, "start": 392, "end": 400}, @@ -1750,7 +1750,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GCCACCACAGGGAAGGTAAATATTTTATTTTG", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 400}, @@ -1759,7 +1759,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TCACAATCGACGGGAGAATTAACTAAACGATT", "domains": [ {"helix": 5, "forward": true, "start": 392, "end": 400}, @@ -1768,7 +1768,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TTTTGTTTTCTTTCCTTATCATTCACAATAGA", "domains": [ {"helix": 7, "forward": true, "start": 392, "end": 400}, @@ -1777,7 +1777,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TAAGTCCTAATTTCATCTTCTGACTATAACTA", "domains": [ {"helix": 9, "forward": true, "start": 392, "end": 400}, @@ -1786,7 +1786,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "TATGTAAACTTTGAATACCAAGTTTTTTCAGG", "domains": [ {"helix": 11, "forward": true, "start": 392, "end": 400}, @@ -1795,7 +1795,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TTTAACGTTCTTTAGGAGCACTAACAAATATC", "domains": [ {"helix": 13, "forward": true, "start": 392, "end": 400}, @@ -1804,7 +1804,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AAACCCTCAATCAATATCTGGTCAAAGGTTAT", "domains": [ {"helix": 15, "forward": true, "start": 392, "end": 416}, @@ -1812,7 +1812,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TGAGGCAGTACTCAGGAGGTTTAGCCGCCACC", "domains": [ {"helix": 2, "forward": false, "start": 400, "end": 408}, @@ -1821,7 +1821,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "ATTGAGGGCCTCAGAGCCGCCACCCAGGAGGT", "domains": [ {"helix": 4, "forward": false, "start": 400, "end": 408}, @@ -1830,7 +1830,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GCGCATTAAATAGAAAATTCATATTTCAACCG", "domains": [ {"helix": 6, "forward": false, "start": 400, "end": 408}, @@ -1839,7 +1839,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "ATCGGCTGAACGTCAAAAATGAAAACAGGGAA", "domains": [ {"helix": 8, "forward": false, "start": 400, "end": 408}, @@ -1848,7 +1848,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TTTTAGTTGAACAAGAAAAATAATAATCAATA", "domains": [ {"helix": 10, "forward": false, "start": 400, "end": 408}, @@ -1857,7 +1857,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CCTGATTGTGCTGATGCAAATCCACAAATATA", "domains": [ {"helix": 12, "forward": false, "start": 400, "end": 408}, @@ -1866,7 +1866,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CTAAAATACAGATGAATATACAGTCGGATTCG", "domains": [ {"helix": 14, "forward": false, "start": 400, "end": 408}, diff --git a/examples/output_designs/16_helix_origami_rectangle_idt.dna b/examples/output_designs/16_helix_origami_rectangle_idt.dna index f1e11f96..d1b5569c 100644 --- a/examples/output_designs/16_helix_origami_rectangle_idt.dna +++ b/examples/output_designs/16_helix_origami_rectangle_idt.dna @@ -59,7 +59,7 @@ "is_scaffold": true }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "ACAACCATCGCCCACGTGCGCCGACAATGACA", "idt": {"name": "ST1[16]0[16]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -68,7 +68,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GAGGACAGATGAACGGCTGACCAACTTTGAAA", "idt": {"name": "ST3[16]2[16]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -77,7 +77,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TCGTTTACCAGACGACAACACTATCATAACCC", "idt": {"name": "ST5[16]4[16]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -86,7 +86,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CTGTAGCTCAACATGTATTGCTGAATATAATG", "idt": {"name": "ST7[16]6[16]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -95,7 +95,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "ATTCAAAAGGGTGAGATAATGTGTAGGTAAAG", "idt": {"name": "ST9[16]8[16]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -104,7 +104,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GATTCTCCGTGGGAACGAGTAACAACCCGTCG", "idt": {"name": "ST11[16]10[16]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -113,7 +113,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GTTTCCTGTGTGAAATAATCATGGTCATAGCT", "idt": {"name": "ST13[16]12[16]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -122,7 +122,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "ACAAGAGTCCACTATTGTTGTTCCAGTTTGGA", "idt": {"name": "ST15[16]14[16]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -131,7 +131,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "ACCGCCACCCTCAGAATACCGCCACCCTCAGA", "idt": {"name": "ST0[431]1[431]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -140,7 +140,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CCGCCGCCAGCATTGAAGAACCACCACCAGAG", "idt": {"name": "ST2[431]3[431]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -149,7 +149,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AGACAAAAGGGCGACAGGTTTACCAGCGCCAA", "idt": {"name": "ST4[431]5[431]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -158,7 +158,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AGAGAATAACATAAAAATAGCAGCCTTTACAG", "idt": {"name": "ST6[431]7[431]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -167,7 +167,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CGAGCATGTAGAAACCATCCCATCCTAATTTA", "idt": {"name": "ST8[431]9[431]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -176,7 +176,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CGCGAGAAAACTTTTTATCGCAAGACAAAGAA", "idt": {"name": "ST10[431]11[431]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -185,7 +185,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TCGGGAGAAACAATAAAACAGTACCTTTTACA", "idt": {"name": "ST12[431]13[431]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -194,7 +194,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TTGAAAGGAATTGAGGGTTGGCAAATCAACAG", "idt": {"name": "ST14[431]15[431]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -203,7 +203,7 @@ ] }, { - "color": "#7300de", + "color": "#32b86c", "sequence": "ACGTTAGTAAATGAATTTTCTGTATGGGATTT", "idt": {"name": "ST0[247]0[216]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -211,7 +211,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "AAACGAAATGCCACTACGAAGGCAAAACAGTT", "idt": {"name": "ST2[215]1[231]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -220,7 +220,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "AATGCCCCGTAACAGTGCCCGTATCCAACCTA", "idt": {"name": "ST1[232]2[216]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -229,7 +229,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CGATTTTATTAATCATTGTGAATTATCAAGTT", "idt": {"name": "ST4[215]3[231]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -238,7 +238,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TGCCTTTAAATCAGTAGCGACAGAACCTTATG", "idt": {"name": "ST3[232]4[216]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -247,7 +247,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "TCAGAAGCAGGTCTTTACCCTGACAGTTACCA", "idt": {"name": "ST6[215]5[231]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -256,7 +256,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "GAAGGAAAGCAGATAGCCGAACAATATTATAG", "idt": {"name": "ST5[232]6[216]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -265,7 +265,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "CAATAAATACTAATAGTAGTAGCACTTGCGGG", "idt": {"name": "ST8[215]7[231]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -274,7 +274,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "AGGTTTTGTTAGCGAACCTCCCGATTAACATC", "idt": {"name": "ST7[232]8[216]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -283,7 +283,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "AGAAAAGCTCATATGTACCCCGGTAGAATCGC", "idt": {"name": "ST10[215]9[231]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -292,7 +292,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CATATTTACAGTAGGGCTTAATTGTGATAATC", "idt": {"name": "ST9[232]10[216]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -301,7 +301,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "GGCGATCGTCAGGCTGCGCAACTGCCTTGCTT", "idt": {"name": "ST12[215]11[231]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -310,7 +310,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "CTGTAAATATATGTGAGTGAATAATTGGGAAG", "idt": {"name": "ST11[232]12[216]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -319,7 +319,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "TGGTTTTTCGGTTTGCGTATTGGGAGAAGGAG", "idt": {"name": "ST14[215]13[231]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -328,7 +328,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CGGAATTAGAACAAAGAAACCACCCGCCAGGG", "idt": {"name": "ST13[232]14[216]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -337,7 +337,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GAACGTGGCGAGAAAGGAAGGGAACGAACTGA", "idt": {"name": "ST15[200]15[231]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -345,7 +345,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CTTAAACAGCTTGATACCGATAGTCATAACCG", "idt": {"name": "ST0[55]1[39]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -354,7 +354,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "ATATATTCTCATAAGGGAACCGAATGTACAGA", "idt": {"name": "ST1[40]3[39]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -364,7 +364,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CCAGGCGCGAGGCATAGTAAGAGCGATAAAAA", "idt": {"name": "ST3[40]5[39]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -374,7 +374,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CCAAAATAGATGGCTTAGAGCTTATTTAAATA", "idt": {"name": "ST5[40]7[39]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -384,7 +384,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TGCAACTAAAATGCAATGCCTGAGAAGGCCGG", "idt": {"name": "ST7[40]9[39]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -394,7 +394,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AGACAGTCAACATTAAATGTGAGCAAACGGCG", "idt": {"name": "ST9[40]11[39]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -404,7 +404,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GATTGACCCCGAGCTCGAATTCGTTGTTATCC", "idt": {"name": "ST11[40]13[39]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -414,7 +414,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "GCTCACAACGAGATAGGGTTGAGTAAAGAACG", "idt": {"name": "ST13[40]15[39]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -424,7 +424,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TGGACTCCAACGTCAAAGGGCGAAAATCAAAA", "idt": {"name": "ST15[40]14[56]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -433,7 +433,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ACGGTCAAGGTCGCTGAGGCTTGCGTGAATTT", "idt": {"name": "ST2[55]0[56]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -443,7 +443,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GGAATTACATAGGCTGGCTGACCTAGGCGCAG", "idt": {"name": "ST4[55]2[56]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -453,7 +453,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TTTTTGCGGCGAGAGGCTTTTGCACGCCAAAA", "idt": {"name": "ST6[55]4[56]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -463,7 +463,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TATATTTTAAGTACGGTGTCTGGAAGAGGTCA", "idt": {"name": "ST8[55]6[56]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -473,7 +473,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CTTTCATCAAATCACCATCAATATAACCCTCA", "idt": {"name": "ST10[55]8[56]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -483,7 +483,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CCCGGGTAGTAATGGGATAGGTCAGTAGCCAG", "idt": {"name": "ST12[55]10[56]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -493,7 +493,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GAATAGCCTTCCACACAACATACGAGAGGATC", "idt": {"name": "ST14[55]12[56]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -503,7 +503,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "TCGGTTTATCAGCTTGCTTTCGAGAGGGAGTT", "idt": {"name": "ST0[87]1[71]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -512,7 +512,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AAAGGCCGTTACTTAGCCGGAACGTCATCAAG", "idt": {"name": "ST1[72]3[71]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -522,7 +522,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AGTAATCTTAATGCAGATACATAAAAAGAAGT", "idt": {"name": "ST3[72]5[71]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -532,7 +532,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "TTTGCCAGATTGCTCCTTTTGATAAGTTTCAT", "idt": {"name": "ST5[72]7[71]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -542,7 +542,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TCCATATAGGATAAAAATTTTTAGGATATTCA", "idt": {"name": "ST7[72]9[71]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -552,7 +552,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "ACCGTTCTCGCGTCTGGCCTTCCTCGTTGGTG", "idt": {"name": "ST9[72]11[71]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -562,7 +562,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TAGATGGGCCTGCAGGTCGACTCTAGCCGGAA", "idt": {"name": "ST11[72]13[71]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -572,7 +572,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GCATAAAGGGCAAAATCCCTTATAAAACCGTC", "idt": {"name": "ST13[72]15[71]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -582,7 +582,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TATCAGGGCGATGGCCCACTACGTTGGTGGTT", "idt": {"name": "ST15[72]14[88]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -591,7 +591,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GCTCCATGCTTTTGCGGGATCGTCTAATTGTA", "idt": {"name": "ST2[87]0[88]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -601,7 +601,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CATTCAACTGACAAGAACCGGATACGCGACCT", "idt": {"name": "ST4[87]2[88]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -611,7 +611,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TACCTTTAAGGGGGTAATAGTAAAGAATACCA", "idt": {"name": "ST6[87]4[88]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -621,7 +621,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CAACGCAAACAGTTGATTCCCAATTTAGAGAG", "idt": {"name": "ST8[87]6[88]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -631,7 +631,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AAATAATTAGCTGATAAATTAATGCTTTATTT", "idt": {"name": "ST10[87]8[88]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -641,7 +641,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "CTTGCATGCGCATCGTAACCGTGCGCCATCAA", "idt": {"name": "ST12[87]10[88]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -651,7 +651,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CCGAAATCTGTAAAGCCTGGGGTGGTGCCAAG", "idt": {"name": "ST14[87]12[88]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -661,7 +661,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "AAAAAAGGCTCCAAAAGGAGCCTTACCCTCAG", "idt": {"name": "ST0[119]1[103]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -670,7 +670,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CAGCGAAAAAATTGTGTCGAAATCTTCATTAC", "idt": {"name": "ST1[104]3[103]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -680,7 +680,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CCAAATCAATCAGTTGAGATTTAGATGTTTAG", "idt": {"name": "ST3[104]5[103]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -690,7 +690,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ACTGGATACTCCAACAGGTCAGGATCTGCGAA", "idt": {"name": "ST5[104]7[103]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -700,7 +700,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CGAGTAGACTTTTGCGGGAGAAGCCCGGAGAG", "idt": {"name": "ST7[104]9[103]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -710,7 +710,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "GGTAGCTATTTAACCAATAGGAACATCTGCCA", "idt": {"name": "ST9[104]11[103]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -720,7 +720,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GTTTGAGGTGTAAAACGACGGCCACCTAATGA", "idt": {"name": "ST11[104]13[103]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -730,7 +730,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GTGAGCTACGAAAATCCTGTTTGAGAACCATC", "idt": {"name": "ST13[104]15[103]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -740,7 +740,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "ACCCAAATCAAGTTTTTTGGGGTCGGTTTGCC", "idt": {"name": "ST15[104]14[120]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -749,7 +749,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CGCCTGATGACAGCATCGGAACGAATCTCCAA", "idt": {"name": "ST2[119]0[120]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -759,7 +759,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AAAGATTCACGTAACAAAGCTGCTTGTATCAT", "idt": {"name": "ST4[119]2[120]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -769,7 +769,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "GAAGCAAAGCGTCCAATACTGCGGACAGGTAG", "idt": {"name": "ST6[119]4[120]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -779,7 +779,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CTGTAATATTTAGTTTGACCATTACCAGACCG", "idt": {"name": "ST8[119]6[120]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -789,7 +789,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GCTCATTTTTTTTGAGAGATCTACTTATGACC", "idt": {"name": "ST10[119]8[120]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -799,7 +799,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CACGACGTGGACGACGACAGTATCTTAAATCA", "idt": {"name": "ST12[119]10[120]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -809,7 +809,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CCAGCAGGACTCACATTAATTGCGTTCCCAGT", "idt": {"name": "ST14[119]12[120]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -819,7 +819,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "AATAATAATTTTTTCACGTTGAAAGGGTAGCA", "idt": {"name": "ST0[151]1[135]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -828,7 +828,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "ACGGCTACAAGTACAACGGAGATTCATTCAGT", "idt": {"name": "ST1[136]3[135]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -838,7 +838,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "GAATAAGGACGGAACAACATTATTAATCGTCA", "idt": {"name": "ST3[136]5[135]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -848,7 +848,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TAAATATTCGAGCTTCAAAGCGAAGATACATT", "idt": {"name": "ST5[136]7[135]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -858,7 +858,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TCGCAAATGGTTGTACCAAAAACAAAAGGCTA", "idt": {"name": "ST7[136]9[135]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -868,7 +868,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TCAGGTCATCGCATTAAATTTTTGGGCCTCAG", "idt": {"name": "ST9[136]11[135]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -878,7 +878,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GAAGATCGGGGTAACGCCAGGGTTTTGCGCTC", "idt": {"name": "ST11[136]13[135]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -888,7 +888,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "ACTGCCCGGCAAGCGGTCCACGCTGAGGTGCC", "idt": {"name": "ST13[136]15[135]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -898,7 +898,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "GTAAAGCACTAAATCGGAACCCTACCCTGAGA", "idt": {"name": "ST15[136]14[152]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -907,7 +907,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GCGAAACAAGAGGCTTTGAGGACTGAATTGCG", "idt": {"name": "ST2[151]0[152]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -917,7 +917,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "ACGAACTACTTGCCCTGACGAGAATACCAAGC", "idt": {"name": "ST4[151]2[152]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -927,7 +927,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TTTTAATTCATTGAATCCCCCTCATTAATAAA", "idt": {"name": "ST6[151]4[152]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -937,7 +937,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GCTAAATCGGTCAATAACCTGTTTATATCGCG", "idt": {"name": "ST8[151]6[152]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -947,7 +947,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "GTTAAAATTTGCCTGAGAGTCTGGAGCATAAA", "idt": {"name": "ST10[151]8[152]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -957,7 +957,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "ATTAAGTTCACTCCAGCCAGCTTTAATATTTT", "idt": {"name": "ST12[151]10[152]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -967,7 +967,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "GAGTTGCACTTTCCAGTCGGGAAAGCAAGGCG", "idt": {"name": "ST14[151]12[152]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -977,7 +977,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GAGAATAGAAAGGAACAACTAAAGAAAGACTT", "idt": {"name": "ST0[183]1[167]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -986,7 +986,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TTTCATGATGACCCCCAGCGATTAACACCAGA", "idt": {"name": "ST1[168]3[167]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -996,7 +996,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "ACGAGTAGGGAAGAAAAATCTACGAATGCTTT", "idt": {"name": "ST3[168]5[167]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1006,7 +1006,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AAACAGTTGCCCGAAAGACTTCAAAGCTATAT", "idt": {"name": "ST5[168]7[167]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1016,7 +1016,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "TTTCATTTAGCAATAAAGCCTCAGAGCAAACA", "idt": {"name": "ST7[168]9[167]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1026,7 +1026,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AGAGAATCTTAAATTGTAAACGTTCCGGCACC", "idt": {"name": "ST9[168]11[167]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1036,7 +1036,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GCTTCTGGGAAAGGGGGATGTGCTCCTGTCGT", "idt": {"name": "ST11[168]13[167]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1046,7 +1046,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GCCAGCTGGCCCTTCACCGCCTGGAAGGGAGC", "idt": {"name": "ST13[168]15[167]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1056,7 +1056,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CCCCGATTTAGAGCTTGACGGGGACGGGCAAC", "idt": {"name": "ST15[168]14[184]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1065,7 +1065,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CTCATCTTGGAAGTTTCCATTAAAAGCGGAGT", "idt": {"name": "ST2[183]0[184]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1075,7 +1075,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "GGACGTTGTAAATTGGGCTTGAGACTAAAACA", "idt": {"name": "ST4[183]2[184]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1085,7 +1085,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "AAGAGGAACAGAAAACGAGAATGAACCAGTCA", "idt": {"name": "ST6[183]4[184]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1095,7 +1095,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "CAAAATTAGGGGCGCGAGCTGAAAAAAAGATT", "idt": {"name": "ST8[183]6[184]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1105,7 +1105,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GCAAATATGATGAACGGTAATCGTAGAATTAG", "idt": {"name": "ST10[183]8[184]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1115,7 +1115,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CAGCTGGCTGCCGGAAACCAGGCATTGTATAA", "idt": {"name": "ST12[183]10[184]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1125,7 +1125,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "AGCTGATTCATTAATGAATCGGCCTATTACGC", "idt": {"name": "ST14[183]12[184]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1135,7 +1135,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "TGCTAAACAACTTTCAACAGTTTCCGGGTAAA", "idt": {"name": "ST0[215]1[199]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1144,7 +1144,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "ATACGTAAGAGGCAAAAGAATACATGGTTTAA", "idt": {"name": "ST1[200]3[199]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1154,7 +1154,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TTTCAACTAGAACTGGCTCATTATCCATAAAT", "idt": {"name": "ST3[200]5[199]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1164,7 +1164,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CAAAAATCAAAGCGGATTGCATCAAGGTGGCA", "idt": {"name": "ST5[200]7[199]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1174,7 +1174,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "TCAATTCTCATACAGGCAAGGCAAAAAACTAG", "idt": {"name": "ST7[200]9[199]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1184,7 +1184,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CATGTCAACCCAAAAACAGGAAGAAAGCGCCA", "idt": {"name": "ST9[200]11[199]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1194,7 +1194,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TTCGCCATGTGCGGGCCTCTTCGCAACGCGCG", "idt": {"name": "ST11[200]13[199]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1204,7 +1204,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "GGGAGAGGCTTTTCACCAGTGAGAAAGCCGGC", "idt": {"name": "ST13[200]15[199]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1214,7 +1214,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "TAGCCCTAAAACATCGCCATTAAAACATTATC", "idt": {"name": "ST15[232]14[248]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1223,7 +1223,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TGCCTTGACTGCCTATTTCGGAACCTTTCCAG", "idt": {"name": "ST2[247]0[248]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1233,7 +1233,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AGCACCGTGCGTCAGACTGTAGCGGGGGTCAG", "idt": {"name": "ST4[247]2[248]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1243,7 +1243,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "AAAAGTAACCGAGGAAACGCAATATCGATAGC", "idt": {"name": "ST6[247]4[248]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1253,7 +1253,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GAGGCGTTAAGCCTTAAATCAAGATTTTTAAG", "idt": {"name": "ST8[247]6[248]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1263,7 +1263,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "ACGCTCAAACAACGCCAACATGTAAAGAACGC", "idt": {"name": "ST10[247]8[248]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1273,7 +1273,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AAATCAATCGTCGCTATTAATTAATAAAGCCA", "idt": {"name": "ST12[247]10[248]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1283,7 +1283,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "ATTTTGCGTCATCATATTCCTGATCAGTACAT", "idt": {"name": "ST14[247]12[248]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1293,7 +1293,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CGTAACGATCTAAAGTTTTGTCGTCTATTATT", "idt": {"name": "ST0[279]1[263]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1302,7 +1302,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CTGAAACAGGTAATAAGTTTTAACCGTTTTCA", "idt": {"name": "ST1[264]3[263]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1312,7 +1312,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TCGGCATTGTCACCAATGAAACCAATAACGGA", "idt": {"name": "ST3[264]5[263]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1322,7 +1322,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "ATACCCAATATCTTACCGAAGCCCTTAGTTGC", "idt": {"name": "ST5[264]7[263]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1332,7 +1332,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TATTTTGCGCTTATCCGGTATTCTATTTAGGC", "idt": {"name": "ST7[264]9[263]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1342,7 +1342,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "AGAGGCATCAAATTCTTACCAGTATTTTCCCT", "idt": {"name": "ST9[264]11[263]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1352,7 +1352,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TAGAATCCCCTTTTTTAATGGAAATATCAGAT", "idt": {"name": "ST11[264]13[263]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1362,7 +1362,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GATGGCAATTTAAAAGTTTGAGTAAATACCGA", "idt": {"name": "ST13[264]15[263]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1372,7 +1372,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "ACGAACCACCAGCAGAAGATAAAACCCGAACG", "idt": {"name": "ST15[264]14[280]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1381,7 +1381,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "AGTGTACTTGAAAGTATTAAGAGGATAGTTAG", "idt": {"name": "ST2[279]0[280]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1391,7 +1391,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CCGGAAACTTCGGTCATAGCCCCCGATACAGG", "idt": {"name": "ST4[279]2[280]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1401,7 +1401,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GCAATAGCAAGAACTGGCATGATTTAGCAAGG", "idt": {"name": "ST6[279]4[280]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1411,7 +1411,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TATAGAAGACCCAGCTACAATTTTATGAAATA", "idt": {"name": "ST8[279]6[280]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1421,7 +1421,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GCGTTATATTTCGAGCCAGTAATAAAATCAGA", "idt": {"name": "ST10[279]8[280]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1431,7 +1431,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "TTGAATTATTGAAAACATAGCGATTATCATAT", "idt": {"name": "ST12[279]10[280]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1441,7 +1441,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TTATTAATTTCATCAATATAATCCAATTTCAT", "idt": {"name": "ST14[279]12[280]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1451,7 +1451,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TGTAGCATTCCACAGACAGCCCTCCTGAGACT", "idt": {"name": "ST0[311]1[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1460,7 +1460,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CCTCAAGAATACATGGCTTTTGATTTATTAGC", "idt": {"name": "ST1[296]3[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1470,7 +1470,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GTTTGCCAGTAGCACCATTACCATAAGACTCC", "idt": {"name": "ST3[296]5[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1480,7 +1480,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TTATTACGATAAGAGCAAGAAACAATCCTGAA", "idt": {"name": "ST5[296]7[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1490,7 +1490,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TCTTACCAGCGCCCAATAGCAAGCAGAGAATA", "idt": {"name": "ST7[296]9[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1500,7 +1500,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TAAAGTACGAAAAAGCCTGTTTAGAGCTTAGA", "idt": {"name": "ST9[296]11[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1510,7 +1510,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TTAAGACGATTAATTACATTTAACTGATTGTT", "idt": {"name": "ST11[296]13[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1520,7 +1520,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "TGGATTATCGTATTAAATCCTTTGCAGAGGTG", "idt": {"name": "ST13[296]15[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1530,7 +1530,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AGGCGGTCAGTATTAACACCGCCTAAACAATT", "idt": {"name": "ST15[296]14[312]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1539,7 +1539,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TAAGCGTCGAAGGATTAGGATTAGACAACGCC", "idt": {"name": "ST2[311]0[312]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1549,7 +1549,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AATCACCATCTTTTCATAATCAAACGTTCCAG", "idt": {"name": "ST4[311]2[312]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1559,7 +1559,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GCCCAATACAGTATGTTAGCAAACGCCAGCAA", "idt": {"name": "ST6[311]4[312]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1569,7 +1569,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TCATTACCACGCTAACGAGCGTCTTGAGTTAA", "idt": {"name": "ST8[311]6[312]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1579,7 +1579,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "AATTACTACGACAAAAGGTAAAGTCGTAGGAA", "idt": {"name": "ST10[311]8[312]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1589,7 +1589,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "AAAACAAACTGAGAAGAGTCAATAGGAATCAT", "idt": {"name": "ST12[311]10[312]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1599,7 +1599,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CGACAACTACTTCTGAATAATGGAACATCAAG", "idt": {"name": "ST14[311]12[312]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1609,7 +1609,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TGAGTTTCGTCACCAGTACAAACTCGGGGTTT", "idt": {"name": "ST0[343]1[327]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1618,7 +1618,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TGCTCAGTCAGTCTCTGAATTTACATCACCGG", "idt": {"name": "ST1[328]3[327]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1628,7 +1628,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "AACCAGAGCCATTTGGGAATTAGAGTAGAAAA", "idt": {"name": "ST3[328]5[327]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1638,7 +1638,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TACATACAGATAACCCACAAGAATTTCCAGAG", "idt": {"name": "ST5[328]7[327]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1648,7 +1648,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CCTAATTTCCGTTTTTATTTTCATAATTCTGT", "idt": {"name": "ST7[328]9[327]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1658,7 +1658,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CCAGACGAAATAAGAATAAACACCGTGAATTT", "idt": {"name": "ST9[328]11[327]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1668,7 +1668,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "ATCAAAATGAAGATGATGAAACAAAGGGTTAG", "idt": {"name": "ST11[328]13[327]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1678,7 +1678,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AACCTACCAAGTATTAGACTTTACGCAACAGT", "idt": {"name": "ST13[328]15[327]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1688,7 +1688,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GCCACGCTGAGAGCCAGCAGCAAAACATTTGA", "idt": {"name": "ST15[328]14[344]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1697,7 +1697,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "GGAAAGCGACCAGGCGGATAAGTGCGTAACAC", "idt": {"name": "ST2[343]0[344]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1707,7 +1707,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GACTTGAGCCACCACCGGAACCGCGCCAGAAT", "idt": {"name": "ST4[343]2[344]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1717,7 +1717,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ATCAGAGATAAAGGTGGCAACATACCGTCACC", "idt": {"name": "ST6[343]4[344]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1727,7 +1727,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CAAGCAAGGCCAGTTACAAAATAAGCGCTAAT", "idt": {"name": "ST8[343]6[344]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1737,7 +1737,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "AGGCGTTACGACAATAAACAACATATCGAGAA", "idt": {"name": "ST10[343]8[344]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1747,7 +1747,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GAGCAAAACATAGGTCTGAGAGACGATAAATA", "idt": {"name": "ST12[343]10[344]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1757,7 +1757,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GGATTTAGATATCAAAATTATTTGAATTACCT", "idt": {"name": "ST14[343]12[344]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1767,7 +1767,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CAAGCCCAATAGGAACCCATGTACCCGTCGAG", "idt": {"name": "ST0[375]1[359]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1776,7 +1776,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AGGGTTGAATAAATCCTCATTAAACTCCCTCA", "idt": {"name": "ST1[360]3[359]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1786,7 +1786,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GAGCCGCCTAAAGGTGAATTATCATAAAAGAA", "idt": {"name": "ST3[360]5[359]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1796,7 +1796,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "ACGCAAAGGTCAGAGGGTAATTGAACAGCCAT", "idt": {"name": "ST5[360]7[359]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1806,7 +1806,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "ATTATTTAACCAAGTACCGCACTCGTTCAGCT", "idt": {"name": "ST7[360]9[359]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1816,7 +1816,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "AATGCAGAGAAATACCGACCGTGTTACCTTTT", "idt": {"name": "ST9[360]11[359]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1826,7 +1826,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TAACCTCCGCGAATTATTCATTTCCACGTAAA", "idt": {"name": "ST11[360]13[359]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1836,7 +1836,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "ACAGAAATGCCGTCAATAGATAATTGAAAAAT", "idt": {"name": "ST13[360]15[359]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1846,7 +1846,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CTAAAGCATCACCTTGCTGAACCTCAACTAAT", "idt": {"name": "ST15[360]14[376]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1855,7 +1855,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "ACAAACAATATAAGTATAGCCCGGAGGGATAG", "idt": {"name": "ST2[375]0[376]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1865,7 +1865,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TTATTCATACCCTCAGAACCGCCATGATATTC", "idt": {"name": "ST4[375]2[376]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1875,7 +1875,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TGAACAAAACACCACGGAATAAGTGACGGAAA", "idt": {"name": "ST6[375]4[376]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1885,7 +1885,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GGTATTAATCCCAATCCAAATAAGGAACACCC", "idt": {"name": "ST8[375]6[376]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1895,7 +1895,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "AATGGTTTACGCGCCTGTTTATCACAAGAACG", "idt": {"name": "ST10[375]8[376]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1905,7 +1905,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GCGCAGAGGGCTTAGGTTGGGTTACTAAATTT", "idt": {"name": "ST12[375]10[376]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1915,7 +1915,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AGATTAGAAAAGAAATTGCGTAGAACAAAATC", "idt": {"name": "ST14[375]12[376]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1925,7 +1925,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "CTCAGAGCCACCACCCTCATTTTCAATAGGTG", "idt": {"name": "ST0[407]1[391]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1934,7 +1934,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "TATCACCGGTCAGACGATTGGCCTCCCTCAGA", "idt": {"name": "ST1[392]3[391]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1944,7 +1944,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GCCACCACAGGGAAGGTAAATATTTTATTTTG", "idt": {"name": "ST3[392]5[391]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1954,7 +1954,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TCACAATCGACGGGAGAATTAACTAAACGATT", "idt": {"name": "ST5[392]7[391]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1964,7 +1964,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TTTTGTTTTCTTTCCTTATCATTCACAATAGA", "idt": {"name": "ST7[392]9[391]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1974,7 +1974,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TAAGTCCTAATTTCATCTTCTGACTATAACTA", "idt": {"name": "ST9[392]11[391]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1984,7 +1984,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "TATGTAAACTTTGAATACCAAGTTTTTTCAGG", "idt": {"name": "ST11[392]13[391]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1994,7 +1994,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TTTAACGTTCTTTAGGAGCACTAACAAATATC", "idt": {"name": "ST13[392]15[391]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2004,7 +2004,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AAACCCTCAATCAATATCTGGTCAAAGGTTAT", "idt": {"name": "ST15[392]14[408]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2013,7 +2013,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TGAGGCAGTACTCAGGAGGTTTAGCCGCCACC", "idt": {"name": "ST2[407]0[408]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2023,7 +2023,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "ATTGAGGGCCTCAGAGCCGCCACCCAGGAGGT", "idt": {"name": "ST4[407]2[408]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2033,7 +2033,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GCGCATTAAATAGAAAATTCATATTTCAACCG", "idt": {"name": "ST6[407]4[408]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2043,7 +2043,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "ATCGGCTGAACGTCAAAAATGAAAACAGGGAA", "idt": {"name": "ST8[407]6[408]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2053,7 +2053,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TTTTAGTTGAACAAGAAAAATAATAATCAATA", "idt": {"name": "ST10[407]8[408]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2063,7 +2063,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CCTGATTGTGCTGATGCAAATCCACAAATATA", "idt": {"name": "ST12[407]10[408]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2073,7 +2073,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CTAAAATACAGATGAATATACAGTCGGATTCG", "idt": {"name": "ST14[407]12[408]", "scale": "25nm", "purification": "STD"}, "domains": [ diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq.dna b/examples/output_designs/16_helix_origami_rectangle_no_seq.dna index 369f9431..e65aceb2 100644 --- a/examples/output_designs/16_helix_origami_rectangle_no_seq.dna +++ b/examples/output_designs/16_helix_origami_rectangle_no_seq.dna @@ -58,236 +58,236 @@ "is_scaffold": true }, { - "color": "#32b86c", + "color": "#f74308", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, {"helix": 0, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, {"helix": 2, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#320096", + "color": "#888888", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, {"helix": 4, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#03b6a2", + "color": "#32b86c", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, {"helix": 6, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#7300de", + "color": "#333333", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, {"helix": 8, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#aaaa00", + "color": "#320096", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, {"helix": 10, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#b8056c", + "color": "#03b6a2", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, {"helix": 12, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#007200", + "color": "#7300de", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, {"helix": 14, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#cc0000", + "color": "#aaaa00", "domains": [ {"helix": 0, "forward": false, "start": 416, "end": 432}, {"helix": 1, "forward": true, "start": 416, "end": 432} ] }, { - "color": "#f7931e", + "color": "#b8056c", "domains": [ {"helix": 2, "forward": false, "start": 416, "end": 432}, {"helix": 3, "forward": true, "start": 416, "end": 432} ] }, { - "color": "#f74308", + "color": "#007200", "domains": [ {"helix": 4, "forward": false, "start": 416, "end": 432}, {"helix": 5, "forward": true, "start": 416, "end": 432} ] }, { - "color": "#57bb00", + "color": "#cc0000", "domains": [ {"helix": 6, "forward": false, "start": 416, "end": 432}, {"helix": 7, "forward": true, "start": 416, "end": 432} ] }, { - "color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 8, "forward": false, "start": 416, "end": 432}, {"helix": 9, "forward": true, "start": 416, "end": 432} ] }, { - "color": "#32b86c", + "color": "#f74308", "domains": [ {"helix": 10, "forward": false, "start": 416, "end": 432}, {"helix": 11, "forward": true, "start": 416, "end": 432} ] }, { - "color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 12, "forward": false, "start": 416, "end": 432}, {"helix": 13, "forward": true, "start": 416, "end": 432} ] }, { - "color": "#320096", + "color": "#888888", "domains": [ {"helix": 14, "forward": false, "start": 416, "end": 432}, {"helix": 15, "forward": true, "start": 416, "end": 432} ] }, { - "color": "#7300de", + "color": "#32b86c", "domains": [ {"helix": 0, "forward": false, "start": 216, "end": 248} ] }, { - "color": "#03b6a2", + "color": "#333333", "domains": [ {"helix": 2, "forward": false, "start": 208, "end": 216}, {"helix": 1, "forward": true, "start": 208, "end": 232} ] }, { - "color": "#7300de", + "color": "#320096", "domains": [ {"helix": 1, "forward": true, "start": 232, "end": 240}, {"helix": 2, "forward": false, "start": 216, "end": 240} ] }, { - 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"color": "#cc0000", + "color": "#aaaa00", "domains": [ {"helix": 4, "forward": false, "start": 272, "end": 280}, {"helix": 3, "forward": true, "start": 272, "end": 288}, @@ -1122,7 +1122,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "domains": [ {"helix": 6, "forward": false, "start": 272, "end": 280}, {"helix": 5, "forward": true, "start": 272, "end": 288}, @@ -1130,7 +1130,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "domains": [ {"helix": 8, "forward": false, "start": 272, "end": 280}, {"helix": 7, "forward": true, "start": 272, "end": 288}, @@ -1138,7 +1138,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "domains": [ {"helix": 10, "forward": false, "start": 272, "end": 280}, {"helix": 9, "forward": true, "start": 272, "end": 288}, @@ -1146,7 +1146,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 12, "forward": false, "start": 272, "end": 280}, {"helix": 11, "forward": true, "start": 272, "end": 288}, @@ -1154,7 +1154,7 @@ ] }, { - 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"color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 6, "forward": false, "start": 304, "end": 312}, {"helix": 5, "forward": true, "start": 304, "end": 320}, @@ -1256,7 +1256,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "domains": [ {"helix": 8, "forward": false, "start": 304, "end": 312}, {"helix": 7, "forward": true, "start": 304, "end": 320}, @@ -1264,7 +1264,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 10, "forward": false, "start": 304, "end": 312}, {"helix": 9, "forward": true, "start": 304, "end": 320}, @@ -1272,7 +1272,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "domains": [ {"helix": 12, "forward": false, "start": 304, "end": 312}, {"helix": 11, "forward": true, "start": 304, "end": 320}, @@ -1280,7 +1280,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "domains": [ {"helix": 14, "forward": false, "start": 304, "end": 312}, {"helix": 13, "forward": true, "start": 304, "end": 320}, @@ -1288,14 +1288,14 @@ ] }, { - "color": "#7300de", + "color": "#333333", "domains": [ {"helix": 0, "forward": false, "start": 320, "end": 344}, {"helix": 1, "forward": true, "start": 320, "end": 328} ] }, { - "color": "#aaaa00", + "color": "#320096", "domains": [ {"helix": 1, "forward": true, "start": 328, "end": 336}, {"helix": 2, "forward": false, "start": 320, "end": 336}, @@ -1303,7 +1303,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "domains": [ {"helix": 3, "forward": true, "start": 328, "end": 336}, {"helix": 4, "forward": false, "start": 320, "end": 336}, @@ -1311,7 +1311,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "domains": [ {"helix": 5, "forward": true, "start": 328, "end": 336}, {"helix": 6, "forward": false, "start": 320, "end": 336}, @@ -1319,7 +1319,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "domains": [ {"helix": 7, "forward": true, "start": 328, "end": 336}, {"helix": 8, "forward": false, "start": 320, "end": 336}, @@ -1327,7 +1327,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "domains": [ {"helix": 9, "forward": true, "start": 328, "end": 336}, {"helix": 10, "forward": false, "start": 320, "end": 336}, @@ -1335,7 +1335,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "domains": [ {"helix": 11, "forward": true, "start": 328, "end": 336}, {"helix": 12, "forward": false, "start": 320, "end": 336}, @@ -1343,7 +1343,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "domains": [ {"helix": 13, "forward": true, "start": 328, "end": 336}, {"helix": 14, "forward": false, "start": 320, "end": 336}, @@ -1351,14 +1351,14 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 15, "forward": true, "start": 328, "end": 352}, {"helix": 14, "forward": false, "start": 344, "end": 352} ] }, { - "color": "#32b86c", + "color": "#f74308", "domains": [ {"helix": 2, "forward": false, "start": 336, "end": 344}, {"helix": 1, "forward": true, "start": 336, "end": 352}, @@ -1366,7 +1366,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 4, "forward": false, "start": 336, "end": 344}, {"helix": 3, "forward": true, "start": 336, "end": 352}, @@ -1374,7 +1374,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "domains": [ {"helix": 6, "forward": false, "start": 336, "end": 344}, {"helix": 5, "forward": true, "start": 336, "end": 352}, @@ -1382,7 +1382,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "domains": [ {"helix": 8, "forward": false, "start": 336, "end": 344}, {"helix": 7, "forward": true, "start": 336, "end": 352}, @@ -1390,7 +1390,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "domains": [ {"helix": 10, "forward": false, "start": 336, "end": 344}, {"helix": 9, "forward": true, "start": 336, "end": 352}, @@ -1398,7 +1398,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "domains": [ {"helix": 12, "forward": false, "start": 336, "end": 344}, {"helix": 11, "forward": true, "start": 336, "end": 352}, @@ -1406,7 +1406,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "domains": [ {"helix": 14, "forward": false, "start": 336, "end": 344}, {"helix": 13, "forward": true, "start": 336, "end": 352}, @@ -1414,14 +1414,14 @@ ] }, { - "color": "#007200", + "color": "#7300de", "domains": [ {"helix": 0, "forward": false, "start": 352, "end": 376}, {"helix": 1, "forward": true, "start": 352, "end": 360} ] }, { - "color": "#cc0000", + "color": "#aaaa00", "domains": [ {"helix": 1, "forward": true, "start": 360, "end": 368}, {"helix": 2, "forward": false, "start": 352, "end": 368}, @@ -1429,7 +1429,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "domains": [ {"helix": 3, "forward": true, "start": 360, "end": 368}, {"helix": 4, "forward": false, "start": 352, "end": 368}, @@ -1437,7 +1437,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "domains": [ {"helix": 5, "forward": true, "start": 360, "end": 368}, {"helix": 6, "forward": false, "start": 352, "end": 368}, @@ -1445,7 +1445,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "domains": [ {"helix": 7, "forward": true, "start": 360, "end": 368}, {"helix": 8, "forward": false, "start": 352, "end": 368}, @@ -1453,7 +1453,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 9, "forward": true, "start": 360, "end": 368}, {"helix": 10, "forward": false, "start": 352, "end": 368}, @@ -1461,7 +1461,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "domains": [ {"helix": 11, "forward": true, "start": 360, "end": 368}, {"helix": 12, "forward": false, "start": 352, "end": 368}, @@ -1469,7 +1469,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 13, "forward": true, "start": 360, "end": 368}, {"helix": 14, "forward": false, "start": 352, "end": 368}, @@ -1477,14 +1477,14 @@ ] }, { - "color": "#320096", + "color": "#888888", "domains": [ {"helix": 15, "forward": true, "start": 360, "end": 384}, {"helix": 14, "forward": false, "start": 376, "end": 384} ] }, { - "color": "#03b6a2", + "color": "#32b86c", "domains": [ {"helix": 2, "forward": false, "start": 368, "end": 376}, {"helix": 1, "forward": true, "start": 368, "end": 384}, @@ -1492,7 +1492,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "domains": [ {"helix": 4, "forward": false, "start": 368, "end": 376}, {"helix": 3, "forward": true, "start": 368, "end": 384}, @@ -1500,7 +1500,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "domains": [ {"helix": 6, "forward": false, "start": 368, "end": 376}, {"helix": 5, "forward": true, "start": 368, "end": 384}, @@ -1508,7 +1508,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "domains": [ {"helix": 8, "forward": false, "start": 368, "end": 376}, {"helix": 7, "forward": true, "start": 368, "end": 384}, @@ -1516,7 +1516,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "domains": [ {"helix": 10, "forward": false, "start": 368, "end": 376}, {"helix": 9, "forward": true, "start": 368, "end": 384}, @@ -1524,7 +1524,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "domains": [ {"helix": 12, "forward": false, "start": 368, "end": 376}, {"helix": 11, "forward": true, "start": 368, "end": 384}, @@ -1532,7 +1532,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "domains": [ {"helix": 14, "forward": false, "start": 368, "end": 376}, {"helix": 13, "forward": true, "start": 368, "end": 384}, @@ -1540,14 +1540,14 @@ ] }, { - "color": "#f74308", + "color": "#007200", "domains": [ {"helix": 0, "forward": false, "start": 384, "end": 408}, {"helix": 1, "forward": true, "start": 384, "end": 392} ] }, { - "color": "#57bb00", + "color": "#cc0000", "domains": [ {"helix": 1, "forward": true, "start": 392, "end": 400}, {"helix": 2, "forward": false, "start": 384, "end": 400}, @@ -1555,7 +1555,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 400}, {"helix": 4, "forward": false, "start": 384, "end": 400}, @@ -1563,7 +1563,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "domains": [ {"helix": 5, "forward": true, "start": 392, "end": 400}, {"helix": 6, "forward": false, "start": 384, "end": 400}, @@ -1571,7 +1571,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 7, "forward": true, "start": 392, "end": 400}, {"helix": 8, "forward": false, "start": 384, "end": 400}, @@ -1579,7 +1579,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "domains": [ {"helix": 9, "forward": true, "start": 392, "end": 400}, {"helix": 10, "forward": false, "start": 384, "end": 400}, @@ -1587,7 +1587,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "domains": [ {"helix": 11, "forward": true, "start": 392, "end": 400}, {"helix": 12, "forward": false, "start": 384, "end": 400}, @@ -1595,7 +1595,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "domains": [ {"helix": 13, "forward": true, "start": 392, "end": 400}, {"helix": 14, "forward": false, "start": 384, "end": 400}, @@ -1603,14 +1603,14 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "domains": [ {"helix": 15, "forward": true, "start": 392, "end": 416}, {"helix": 14, "forward": false, "start": 408, "end": 416} ] }, { - "color": "#b8056c", + "color": "#03b6a2", "domains": [ {"helix": 2, "forward": false, "start": 400, "end": 408}, {"helix": 1, "forward": true, "start": 400, "end": 416}, @@ -1618,7 +1618,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "domains": [ {"helix": 4, "forward": false, "start": 400, "end": 408}, {"helix": 3, "forward": true, "start": 400, "end": 416}, @@ -1626,7 +1626,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "domains": [ {"helix": 6, "forward": false, "start": 400, "end": 408}, {"helix": 5, "forward": true, "start": 400, "end": 416}, @@ -1634,7 +1634,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "domains": [ {"helix": 8, "forward": false, "start": 400, "end": 408}, {"helix": 7, "forward": true, "start": 400, "end": 416}, @@ -1642,7 +1642,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "domains": [ {"helix": 10, "forward": false, "start": 400, "end": 408}, {"helix": 9, "forward": true, "start": 400, "end": 416}, @@ -1650,7 +1650,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "domains": [ {"helix": 12, "forward": false, "start": 400, "end": 408}, {"helix": 11, "forward": true, "start": 400, "end": 416}, @@ -1658,7 +1658,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 14, "forward": false, "start": 400, "end": 408}, {"helix": 13, "forward": true, "start": 400, "end": 416}, diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna b/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna index af114c70..9aeca60e 100644 --- a/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna +++ b/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna @@ -58,236 +58,236 @@ "is_scaffold": true }, { - "color": "#32b86c", + "color": "#f74308", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, {"helix": 0, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, {"helix": 2, "forward": false, "start": 16, "end": 32} ] }, { - 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"color": "#57bb00", + "color": "#cc0000", "domains": [ {"helix": 7, "forward": true, "start": 360, "end": 368}, {"helix": 8, "forward": false, "start": 352, "end": 368}, @@ -1453,7 +1453,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 9, "forward": true, "start": 360, "end": 368}, {"helix": 10, "forward": false, "start": 352, "end": 368}, @@ -1461,7 +1461,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "domains": [ {"helix": 11, "forward": true, "start": 360, "end": 368}, {"helix": 12, "forward": false, "start": 352, "end": 368}, @@ -1469,7 +1469,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 13, "forward": true, "start": 360, "end": 368}, {"helix": 14, "forward": false, "start": 352, "end": 368}, @@ -1477,14 +1477,14 @@ ] }, { - "color": "#320096", + "color": "#888888", "domains": [ {"helix": 15, "forward": true, "start": 360, "end": 384}, {"helix": 14, "forward": false, "start": 376, "end": 384} ] }, { - "color": "#03b6a2", + "color": "#32b86c", "domains": [ {"helix": 2, "forward": false, "start": 368, "end": 376}, {"helix": 1, "forward": true, "start": 368, "end": 384}, @@ -1492,7 +1492,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "domains": [ {"helix": 4, "forward": false, "start": 368, "end": 376}, {"helix": 3, "forward": true, "start": 368, "end": 384}, @@ -1500,7 +1500,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "domains": [ {"helix": 6, "forward": false, "start": 368, "end": 376}, {"helix": 5, "forward": true, "start": 368, "end": 384}, @@ -1508,7 +1508,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "domains": [ {"helix": 8, "forward": false, "start": 368, "end": 376}, {"helix": 7, "forward": true, "start": 368, "end": 384}, @@ -1516,7 +1516,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "domains": [ {"helix": 10, "forward": false, "start": 368, "end": 376}, {"helix": 9, "forward": true, "start": 368, "end": 384}, @@ -1524,7 +1524,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "domains": [ {"helix": 12, "forward": false, "start": 368, "end": 376}, {"helix": 11, "forward": true, "start": 368, "end": 384}, @@ -1532,7 +1532,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "domains": [ {"helix": 14, "forward": false, "start": 368, "end": 376}, {"helix": 13, "forward": true, "start": 368, "end": 384}, @@ -1540,14 +1540,14 @@ ] }, { - "color": "#f74308", + "color": "#007200", "domains": [ {"helix": 0, "forward": false, "start": 384, "end": 408, "deletions": [385]}, {"helix": 1, "forward": true, "start": 384, "end": 392, "deletions": [385]} ] }, { - "color": "#57bb00", + "color": "#cc0000", "domains": [ {"helix": 1, "forward": true, "start": 392, "end": 400}, {"helix": 2, "forward": false, "start": 384, "end": 400, "deletions": [385]}, @@ -1555,7 +1555,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 400}, {"helix": 4, "forward": false, "start": 384, "end": 400, "deletions": [385]}, @@ -1563,7 +1563,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "domains": [ {"helix": 5, "forward": true, "start": 392, "end": 400}, {"helix": 6, "forward": false, "start": 384, "end": 400, "deletions": [385]}, @@ -1571,7 +1571,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 7, "forward": true, "start": 392, "end": 400}, {"helix": 8, "forward": false, "start": 384, "end": 400, "deletions": [385]}, @@ -1579,7 +1579,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "domains": [ {"helix": 9, "forward": true, "start": 392, "end": 400}, {"helix": 10, "forward": false, "start": 384, "end": 400, "deletions": [385]}, @@ -1587,7 +1587,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "domains": [ {"helix": 11, "forward": true, "start": 392, "end": 400}, {"helix": 12, "forward": false, "start": 384, "end": 400, "deletions": [385]}, @@ -1595,7 +1595,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "domains": [ {"helix": 13, "forward": true, "start": 392, "end": 400}, {"helix": 14, "forward": false, "start": 384, "end": 400, "deletions": [385]}, @@ -1603,14 +1603,14 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "domains": [ {"helix": 15, "forward": true, "start": 392, "end": 416}, {"helix": 14, "forward": false, "start": 408, "end": 416} ] }, { - "color": "#b8056c", + "color": "#03b6a2", "domains": [ {"helix": 2, "forward": false, "start": 400, "end": 408}, {"helix": 1, "forward": true, "start": 400, "end": 416}, @@ -1618,7 +1618,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "domains": [ {"helix": 4, "forward": false, "start": 400, "end": 408}, {"helix": 3, "forward": true, "start": 400, "end": 416}, @@ -1626,7 +1626,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "domains": [ {"helix": 6, "forward": false, "start": 400, "end": 408}, {"helix": 5, "forward": true, "start": 400, "end": 416}, @@ -1634,7 +1634,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "domains": [ {"helix": 8, "forward": false, "start": 400, "end": 408}, {"helix": 7, "forward": true, "start": 400, "end": 416}, @@ -1642,7 +1642,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "domains": [ {"helix": 10, "forward": false, "start": 400, "end": 408}, {"helix": 9, "forward": true, "start": 400, "end": 416}, @@ -1650,7 +1650,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "domains": [ {"helix": 12, "forward": false, "start": 400, "end": 408}, {"helix": 11, "forward": true, "start": 400, "end": 416}, @@ -1658,7 +1658,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 14, "forward": false, "start": 400, "end": 408}, {"helix": 13, "forward": true, "start": 400, "end": 416}, diff --git a/examples/output_designs/16_helix_origami_rectangle_no_twist.dna b/examples/output_designs/16_helix_origami_rectangle_no_twist.dna index 04374c03..907dfc40 100644 --- a/examples/output_designs/16_helix_origami_rectangle_no_twist.dna +++ b/examples/output_designs/16_helix_origami_rectangle_no_twist.dna @@ -59,7 +59,7 @@ "is_scaffold": true }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "GCCGCTTTTGCGGGATTTGCAGGGAGTTAAAG", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -67,7 +67,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CAAGAGTAATCTTGACGCTGGCTGACCTTCAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -75,7 +75,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TGCAAAAGAAGTTTTGAATAGCGAGAGGCTTT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -83,7 +83,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "ACGGTGTCTGGAAGTTAATATGCAACTAAAGT", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, @@ -91,7 +91,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "AGTCAAATCACCATCAGAGAAAGGCCGGAGAC", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, @@ -99,7 +99,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GGCGGATTGACCGTAACTCCGTGGGAACAAAC", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, @@ -107,7 +107,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "AAATTGTTATCCGCTCAGCTGTTTCCTGTGTG", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, @@ -115,7 +115,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GAGTCCACTATTAAAGTTCCAGTTTGGAACAA", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, @@ -123,7 +123,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AACCCATGTACCGTAAGCAAGCCCAATAGG", "domains": [ {"helix": 0, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AGCCAGAATGGAAAGATAAATCCTCATTAA", "domains": [ {"helix": 2, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -139,7 +139,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "ACTTGAGCCATTTGGTTATCACCGTCACCG", "domains": [ {"helix": 4, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -147,7 +147,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AACCCACAAGAATTGTAATATCAGAGAGAT", "domains": [ {"helix": 6, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -155,7 +155,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CATCGTAGGAATCATAGCCGTTTTTATTTT", "domains": [ {"helix": 8, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -163,7 +163,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TAATTACTAGAAAAATAAACACCGGAATCA", "domains": [ {"helix": 10, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -171,7 +171,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TTAATTACATTTAACATCAAGAAAACAAAA", "domains": [ {"helix": 12, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -179,7 +179,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CTTTGCCCGAACGTTAACTCGTATTAAATC", "domains": [ {"helix": 14, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -187,14 +187,14 @@ ] }, { - "color": "#7300de", + "color": "#32b86c", "sequence": "AGAATAGAAAGGAACAACTAAAGGAATTGCG", "domains": [ {"helix": 0, "forward": false, "start": 216, "end": 248, "deletions": [225]} ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "TACCAAGCCTCATCTTTGACCCCCTCAAGAG", "domains": [ {"helix": 2, "forward": false, "start": 208, "end": 216}, @@ -202,7 +202,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "AAGGATTAAGAGGCTGAGACTCCAGCGATTA", "domains": [ {"helix": 1, "forward": true, "start": 232, "end": 240}, @@ -210,7 +210,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "AATCTACGACCAGTCAGGACGTTGTTCATAA", "domains": [ {"helix": 4, "forward": false, "start": 208, "end": 216}, @@ -218,7 +218,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TCAAAATCAGCGTTTGCCATCTTGGAAGAAA", "domains": [ {"helix": 3, "forward": true, "start": 232, "end": 240}, @@ -226,7 +226,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GCCCGAAATTGCATCAAAAAGATTACGTAGA", "domains": [ {"helix": 6, "forward": false, "start": 208, "end": 216}, @@ -234,7 +234,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "AAATACATGCAGTATGTTAGCAAAAGAGGAA", "domains": [ {"helix": 5, "forward": true, "start": 232, "end": 240}, @@ -242,7 +242,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "CAAAATTACATACAGGCAAGGCAACCTAATT", "domains": [ {"helix": 8, "forward": false, "start": 208, "end": 216}, @@ -250,7 +250,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "TGCCAGTTAGCGTCTTTCCAGAGAGAATTAG", "domains": [ {"helix": 7, "forward": true, "start": 232, "end": 240}, @@ -258,7 +258,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "TTGTATAAAGAAAAGCCCCAAAAAACAATAA", "domains": [ {"helix": 10, "forward": false, "start": 208, "end": 216}, @@ -266,7 +266,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "ACAACATGTCTGTCCAGACGACGCAGGAAGA", "domains": [ {"helix": 9, "forward": true, "start": 232, "end": 240}, @@ -274,7 +274,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CTCTTCGCTTGGGAAGGGCGATCGAGACTAC", "domains": [ {"helix": 12, "forward": false, "start": 208, "end": 216}, @@ -282,7 +282,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "CTTTTTAAAATCATAGGTCTGAGGTGCGGGC", "domains": [ {"helix": 11, "forward": true, "start": 232, "end": 240}, @@ -290,7 +290,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "CTTTTCACGTATTGGGCGCCAGGGAAACAGA", "domains": [ {"helix": 14, "forward": false, "start": 208, "end": 216}, @@ -298,7 +298,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "AATAAAGAAATTATTTGCACGTATGGTTTTT", "domains": [ {"helix": 13, "forward": true, "start": 232, "end": 240}, @@ -306,14 +306,14 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GAACGTGGCGAGAAAGGAAGGGAATCACCTT", "domains": [ {"helix": 15, "forward": true, "start": 200, "end": 232, "deletions": [225]} ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CCGATATATTCGGTCGCTGAGGCCGTCACC", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -321,7 +321,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CTCAGCAGAGACCAGGCGCATAGAAGAACC", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -330,7 +330,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GGATATTCGACGATAAAAACCAACCAGAGG", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -339,7 +339,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GGGTAATAGCTCAACATGTTTTATCATTCC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 48}, @@ -348,7 +348,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "ATATAACAAAGATTCAAAAGGGTATATGAT", "domains": [ {"helix": 7, "forward": true, "start": 40, "end": 48}, @@ -357,7 +357,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "ATTCAACCACAACCCGTCGGATTTGGGATA", "domains": [ {"helix": 9, "forward": true, "start": 40, "end": 48}, @@ -366,7 +366,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GGTCACGTCGTAATCATGGTCATACAATTC", "domains": [ {"helix": 11, "forward": true, "start": 40, "end": 48}, @@ -375,7 +375,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CACACAACTAGGGTTGAGTGTTGAACGTGG", "domains": [ {"helix": 13, "forward": true, "start": 40, "end": 48}, @@ -384,7 +384,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "ACTCCAACGTCAAAGGGCGAAAAAAAAGAATA", "domains": [ {"helix": 15, "forward": true, "start": 40, "end": 64}, @@ -392,7 +392,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CGGTGTACCGAAAGACAGCATCGGACGCATAA", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -401,7 +401,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "TACCAGACATTACCCAAATCAACGCAGATGAA", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -410,7 +410,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "ATGCTGTAGTAAAATGTTTAGACTCCCTCGTT", "domains": [ {"helix": 6, "forward": false, "start": 48, "end": 56}, @@ -419,7 +419,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TGTAGGTAGTTGATTCCCAATTCTTGAATATA", "domains": [ {"helix": 8, "forward": false, "start": 48, "end": 56}, @@ -428,7 +428,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "AGCGAGTAGTTCTAGCTGATAAATGAGTAATG", "domains": [ {"helix": 10, "forward": false, "start": 48, "end": 56}, @@ -437,7 +437,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CTCGAATTTGGTGTAGATGGGCGCTAAATGTG", "domains": [ {"helix": 12, "forward": false, "start": 48, "end": 56}, @@ -446,7 +446,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GCCCGAGAATACGAGCCGGAAGCAGTACCGAG", "domains": [ {"helix": 14, "forward": false, "start": 48, "end": 56}, @@ -455,7 +455,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GACAATGACAACAACCATCGCCCAACGAGGG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -463,7 +463,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TAGCAACGCAACTTTGAAAGAGGATAACAAAG", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -472,7 +472,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CTGCTCATAGCAACACTATCATAAGGATAGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -481,7 +481,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "TCCAATACCTTAGAGCTTAATTGCGCGAACGA", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 80}, @@ -490,7 +490,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "GTAGATTTTTTAAATGCAATGCCTTAATGCCG", "domains": [ {"helix": 7, "forward": true, "start": 72, "end": 80}, @@ -499,7 +499,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GAGAGGGTCAGCTTTCATCAACATATCGTAAC", "domains": [ {"helix": 9, "forward": true, "start": 72, "end": 80}, @@ -508,7 +508,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CGTGCATCTCTAGAGGATCCCCGGTAAAGTGT", "domains": [ {"helix": 11, "forward": true, "start": 72, "end": 80}, @@ -517,7 +517,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "AAAGCCTGAATCCCTTATAAATCACCGTCTAT", "domains": [ {"helix": 13, "forward": true, "start": 72, "end": 80}, @@ -526,7 +526,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "CAGGGCGATGGCCCACTACGTGATTCCGAAA", "domains": [ {"helix": 15, "forward": true, "start": 72, "end": 96, "deletions": [81]}, @@ -534,7 +534,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AACTGACGCTACAGAGGCTTTGGTTGCGCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -543,7 +543,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TAGTAAGTCAGTGAATAAGGCTGGGAACCG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -552,7 +552,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CGGATGGTGCGGAATCGTCATAACGAGGCA", "domains": [ {"helix": 6, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -561,7 +561,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CATATATAGTTTGACCATTAGACATTTTTG", "domains": [ {"helix": 8, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -570,7 +570,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CTGTAGCAGCTATTTTTGAGAGAGAACCCT", "domains": [ {"helix": 10, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -579,7 +579,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "GGTCGACTGCCAGTTTGAGGGGTGGCCTTC", "domains": [ {"helix": 12, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -588,7 +588,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "TCGGCAAGGGTGCCTAATGAGTTGCCTGCA", "domains": [ {"helix": 14, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -597,7 +597,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "TTCTTAAACAGCTTGATACCGATAAGGACTAA", "domains": [ {"helix": 0, "forward": false, "start": 96, "end": 120}, @@ -605,7 +605,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "AGACTTTTAGACGGTCAATCATAATGCCCTGA", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -614,7 +614,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CGAGAAACAACGCCAAAAGGAATTAATATTCA", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -623,7 +623,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TTGAATCCCCTTTTGATAAGAGGTTACATTTC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 112}, @@ -632,7 +632,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GCAAATGGAAGGATAAAAATTTTTATCTACAA", "domains": [ {"helix": 7, "forward": true, "start": 104, "end": 112}, @@ -641,7 +641,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "AGGCTATCAAAAATAATTCGCGTCACGACGAC", "domains": [ {"helix": 9, "forward": true, "start": 104, "end": 112}, @@ -650,7 +650,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AGTATCGGCAGTGCCAAGCTTGCAGAGCTAAC", "domains": [ {"helix": 11, "forward": true, "start": 104, "end": 112}, @@ -659,7 +659,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TCACATTATCCTGTTTGATGGTGGACCATCAC", "domains": [ {"helix": 13, "forward": true, "start": 104, "end": 112}, @@ -668,7 +668,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CCAAATCAAGTTTTTTGGGGTCGACCCCAGCA", "domains": [ {"helix": 15, "forward": true, "start": 104, "end": 128}, @@ -676,7 +676,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CGAGGCGCTCATGAGGAAGTTTCCAGGTGAAT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -685,7 +685,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AGATACATACCAGAACGAGTAGTAAGCCGGAA", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -694,7 +694,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TAATTGCTCCCTCAAATGCTTTAAACTAATGC", "domains": [ {"helix": 6, "forward": false, "start": 112, "end": 120}, @@ -703,7 +703,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "TTCAACGCTCAATAACCTGTTTAGAGTACCTT", "domains": [ {"helix": 8, "forward": false, "start": 112, "end": 120}, @@ -712,7 +712,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "ACGCCATCAGGTCATTGCCTGAGAGCCTTTAT", "domains": [ {"helix": 10, "forward": false, "start": 112, "end": 120}, @@ -721,7 +721,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "ACGACGGCCCTCAGGAAGATCGCACAATAGGA", "domains": [ {"helix": 12, "forward": false, "start": 112, "end": 120}, @@ -730,7 +730,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GGCGAAAAATTGCGTTGCGCTCACGTTGTAAA", "domains": [ {"helix": 14, "forward": false, "start": 112, "end": 120}, @@ -739,7 +739,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ATCGGTTTATCAGCTTGCTTTCGATTAAAC", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -747,7 +747,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GGGTAAAATGCTCCATGTTACTTAATTGGG", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -756,7 +756,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "CTTGAGATGGAATACCACATTCAACAGTTC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -765,7 +765,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AGAAAACGAGGTCAGGATTAGAGCTATATT", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 144}, @@ -774,7 +774,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TTCATTTGACTTTTGCGGGAGAAGTCTGGA", "domains": [ {"helix": 7, "forward": true, "start": 136, "end": 144}, @@ -783,7 +783,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GCAAACAAAGCTCATTTTTTAACCTCCAGC", "domains": [ {"helix": 9, "forward": true, "start": 136, "end": 144}, @@ -792,7 +792,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CAGCTTTCTTTCCCAGTCACGACTGCCCGC", "domains": [ {"helix": 11, "forward": true, "start": 136, "end": 144}, @@ -801,7 +801,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "TTTCCAGTGTCCACGCTGGTTTGGGTGCCG", "domains": [ {"helix": 13, "forward": true, "start": 136, "end": 144}, @@ -810,7 +810,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TAAAGCACTAAATCGGAACCCTAAAGAGTTGC", "domains": [ {"helix": 15, "forward": true, "start": 136, "end": 160}, @@ -818,7 +818,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CCGCGACCTACGTAATGCCACTACTTAATTGT", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -827,7 +827,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GAGATTTAGGTTTAATTTCAACTTGTCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, @@ -836,7 +836,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "ACTCCAACAGAATGACCATAAATCCATCAGTT", "domains": [ {"helix": 6, "forward": false, "start": 144, "end": 152}, @@ -845,7 +845,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CCTGTAATGGGCGCGAGCTGAAAAGGAAGCAA", "domains": [ {"helix": 8, "forward": false, "start": 144, "end": 152}, @@ -854,7 +854,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "GTTAAATCGAGAATCGATGAACGGATTATGAC", "domains": [ {"helix": 10, "forward": false, "start": 144, "end": 152}, @@ -863,7 +863,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GCCAGGGTCGGCACCGCTTCTGGTAAATTTTT", "domains": [ {"helix": 12, "forward": false, "start": 144, "end": 152}, @@ -872,7 +872,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "AGCAAGCGCGGGAAACCTGTCGTGTGGGTAAC", "domains": [ {"helix": 14, "forward": false, "start": 144, "end": 152}, @@ -881,7 +881,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AAAAAAGGCTCCAAAAGGAGCCTGAAGGCAC", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 184, "deletions": [177]}, @@ -889,7 +889,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CAACCTAATCGCCTGATAAATTGTTAATCATT", "domains": [ {"helix": 1, "forward": true, "start": 168, "end": 176}, @@ -898,7 +898,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GTGAATTATACAGGTAGAAAGATTAAAAATCA", "domains": [ {"helix": 3, "forward": true, "start": 168, "end": 176}, @@ -907,7 +907,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GGTCTTTACAAAGCGAACCAGACCGGTGGCAT", "domains": [ {"helix": 5, "forward": true, "start": 168, "end": 176}, @@ -916,7 +916,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CAATTCTACGGTTGTACCAAAAACTAATCGTA", "domains": [ {"helix": 7, "forward": true, "start": 168, "end": 176}, @@ -925,7 +925,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AAACTAGCTGTTAAAATTCGCATTGCCGGAAA", "domains": [ {"helix": 9, "forward": true, "start": 168, "end": 176}, @@ -934,7 +934,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CCAGGCAATGCAAGGCGATTAAGTCCAGCTGC", "domains": [ {"helix": 11, "forward": true, "start": 168, "end": 176}, @@ -943,7 +943,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "ATTAATGAACCGCCTGGCCCTGAGAGGGAGCC", "domains": [ {"helix": 13, "forward": true, "start": 168, "end": 176}, @@ -952,7 +952,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CCCGATTTAGAGCTTGACGGGGAAGCTGATT", "domains": [ {"helix": 15, "forward": true, "start": 168, "end": 192, "deletions": [177]}, @@ -960,7 +960,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TGTATCAAACGAAAGAGGCAAAATCTCCAA", "domains": [ {"helix": 2, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -969,7 +969,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ACATTATCCTTATGCGATTTTACGGAGATT", "domains": [ {"helix": 4, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -978,7 +978,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CGAGCTTCCCTGACTATTATAGACGGAACA", "domains": [ {"helix": 6, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -987,7 +987,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "GCTAAATCTAATAGTAGTAGCATTTTAATT", "domains": [ {"helix": 8, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -996,7 +996,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AATATTTATGTCAATCATATGTAGCATAAA", "domains": [ {"helix": 10, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1005,7 +1005,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GATGTGCAGCGCCATTCGCCATTAAACGTT", "domains": [ {"helix": 12, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1014,7 +1014,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GCCCTTCATCGGCCAACGCGCGGAAAGGGG", "domains": [ {"helix": 14, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1023,7 +1023,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AATAATAATTTTTTCACGTTGAAAAGAATACA", "domains": [ {"helix": 0, "forward": false, "start": 192, "end": 216}, @@ -1031,7 +1031,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CTAAAACAGCGAAACAAAGTACAAAGAACTGG", "domains": [ {"helix": 1, "forward": true, "start": 200, "end": 208}, @@ -1040,7 +1040,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "CTCATTATTTAATAAAACGAACTATCAGAAGC", "domains": [ {"helix": 3, "forward": true, "start": 200, "end": 208}, @@ -1049,7 +1049,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AAAGCGGAGACTTCAAATATCGCGTTAACATC", "domains": [ {"helix": 5, "forward": true, "start": 200, "end": 208}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CAATAAATAGCAATAAAGCCTCAGACCCCGGT", "domains": [ {"helix": 7, "forward": true, "start": 200, "end": 208}, @@ -1067,7 +1067,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TGATAATCGCAAATATTTAAATTGTCAGGCTG", "domains": [ {"helix": 9, "forward": true, "start": 200, "end": 208}, @@ -1076,7 +1076,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CGCAACTGTATTACGCCAGCTGGCGGGAGAGG", "domains": [ {"helix": 11, "forward": true, "start": 200, "end": 208}, @@ -1085,7 +1085,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CGGTTTGCCAGTGAGACGGGCAACAAGCCGGC", "domains": [ {"helix": 13, "forward": true, "start": 200, "end": 208}, @@ -1094,7 +1094,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GCTGAACCTCAAATATCAAACCCTGAACCTAC", "domains": [ {"helix": 15, "forward": true, "start": 232, "end": 256}, @@ -1102,7 +1102,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "AAGTATTAGGATTAGCGGGGTTTTGCGGAGTG", "domains": [ {"helix": 2, "forward": false, "start": 240, "end": 248}, @@ -1111,7 +1111,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "CCCTTATTACCGGAACCAGAGCCAAAACATGA", "domains": [ {"helix": 4, "forward": false, "start": 240, "end": 248}, @@ -1120,7 +1120,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CTTATTACACATAAAGGTGGCAACTCATAGCC", "domains": [ {"helix": 6, "forward": false, "start": 240, "end": 248}, @@ -1129,7 +1129,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CGCTAACGACAAAATAAACAGCCATAAGACTC", "domains": [ {"helix": 8, "forward": false, "start": 240, "end": 248}, @@ -1138,7 +1138,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AAAGTAATTTCAGCTAATGCAGAACTTACCAA", "domains": [ {"helix": 10, "forward": false, "start": 240, "end": 248}, @@ -1147,7 +1147,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "TTTATCAACCTCCGGCTTAGGTTGCAAAAGGT", "domains": [ {"helix": 12, "forward": false, "start": 240, "end": 248}, @@ -1156,7 +1156,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "CATATCAAAATTGCGTAGATTTTCATAGTGAA", "domains": [ {"helix": 14, "forward": false, "start": 240, "end": 248}, @@ -1165,7 +1165,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CTAAACAACTTTCAACAGTTTCAGCTCAGTA", "domains": [ {"helix": 0, "forward": false, "start": 256, "end": 280, "deletions": [273]}, @@ -1173,7 +1173,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CCAGGCGGGGAACCTATTATTCTGCCACCGGA", "domains": [ {"helix": 1, "forward": true, "start": 264, "end": 272}, @@ -1182,7 +1182,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "ACCGCCTCTCATCGGCATTTTCGGATATAAAA", "domains": [ {"helix": 3, "forward": true, "start": 264, "end": 272}, @@ -1191,7 +1191,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GAAACGCAAAAGAACTGGCATGATTATTATTT", "domains": [ {"helix": 5, "forward": true, "start": 264, "end": 272}, @@ -1200,7 +1200,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ATCCCAATCAATTTTATCCTGAATCGCGCCTG", "domains": [ {"helix": 7, "forward": true, "start": 264, "end": 272}, @@ -1209,7 +1209,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "TTTATCAAGAATATAAAGTACCGAGGTTATAT", "domains": [ {"helix": 9, "forward": true, "start": 264, "end": 272}, @@ -1218,7 +1218,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "AACTATATACGCTGAGAAGAGTCAAGGTTTAA", "domains": [ {"helix": 11, "forward": true, "start": 264, "end": 272}, @@ -1227,7 +1227,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "CGTCAGATAATAATGGAAGGGTTACAATCAAT", "domains": [ {"helix": 13, "forward": true, "start": 264, "end": 272}, @@ -1236,7 +1236,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "ATCTGGTCAGTTGGCAAATCAACTGGATTAT", "domains": [ {"helix": 15, "forward": true, "start": 264, "end": 288, "deletions": [273]}, @@ -1244,7 +1244,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CTATTTCATAAGTGCCGTCGAGGGATTTTG", "domains": [ {"helix": 2, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1253,7 +1253,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CGCGTTTCCTCAGAGCCGCCACCCCCCTGC", "domains": [ {"helix": 4, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1262,7 +1262,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "ATACCCAAAGACACCACGGAATGACTGTAG", "domains": [ {"helix": 6, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1271,7 +1271,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "CCAGCTACCAAATAAGAAACGAATAACGGA", "domains": [ {"helix": 8, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1280,7 +1280,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AATAAGACAATAGATAAGTCCTTTTTGCAC", "domains": [ {"helix": 10, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1289,7 +1289,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GATTAAGGTAAATGCTGATGCAGAGCCAGT", "domains": [ {"helix": 12, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1298,7 +1298,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "ACTTCTGGAATATACAGTAACAATAGCTTA", "domains": [ {"helix": 14, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1307,7 +1307,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GTTAGTAAATGAATTTTCTGTATGAGGGTTGA", "domains": [ {"helix": 0, "forward": false, "start": 288, "end": 312}, @@ -1315,7 +1315,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TATAAGTAGTATAAACAGTTAATGCCTCAGAA", "domains": [ {"helix": 1, "forward": true, "start": 296, "end": 304}, @@ -1324,7 +1324,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CCGCCACCTTTGCCTTTAGCGTCAAAGTTTAT", "domains": [ {"helix": 3, "forward": true, "start": 296, "end": 304}, @@ -1333,7 +1333,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TTTGTCACCCGAGGAAACGCAATATTTTTTGT", "domains": [ {"helix": 5, "forward": true, "start": 296, "end": 304}, @@ -1342,7 +1342,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TTAACGTCTCAAGATTAGTTGCTAGAACAAGA", "domains": [ {"helix": 7, "forward": true, "start": 296, "end": 304}, @@ -1351,7 +1351,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "AAAATAATAGGCAGAGGCATTTTCAATCCAAT", "domains": [ {"helix": 9, "forward": true, "start": 296, "end": 304}, @@ -1360,7 +1360,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CGCAAGACCCTTGAAAACATAGCGGTACCTTT", "domains": [ {"helix": 11, "forward": true, "start": 296, "end": 304}, @@ -1369,7 +1369,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "TACATCGGTATAATCCTGATTGTTAGTTGAAA", "domains": [ {"helix": 13, "forward": true, "start": 296, "end": 304}, @@ -1378,7 +1378,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GGAATTGAGGAAGGTTATCTAAAAGATGGCAA", "domains": [ {"helix": 15, "forward": true, "start": 296, "end": 320}, @@ -1386,7 +1386,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "CAGTGCCCTAGCCCGGAATAGGTGTTCCAGAC", "domains": [ {"helix": 2, "forward": false, "start": 304, "end": 312}, @@ -1395,7 +1395,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GAATCAAGCTCAGAGCCACCACCCTTGAGTAA", "domains": [ {"helix": 4, "forward": false, "start": 304, "end": 312}, @@ -1404,7 +1404,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GAAGGAAAAATCAATAGAAAATTCTAGCGACA", "domains": [ {"helix": 6, "forward": false, "start": 304, "end": 312}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "GCCTTAAAAAAAATGAAAATAGCAAGTTACCA", "domains": [ {"helix": 8, "forward": false, "start": 304, "end": 312}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TGTAATTTATCCCATCCTAATTTAGTTTTGAA", "domains": [ {"helix": 10, "forward": false, "start": 304, "end": 312}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CTTAGAATAAAGAACGCGAGAAAACGCCAACA", "domains": [ {"helix": 12, "forward": false, "start": 304, "end": 312}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "TTCATCAAGAGAAACAATAACGGAAATTTTCC", "domains": [ {"helix": 14, "forward": false, "start": 304, "end": 312}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "AACGATCTAAAGTTTTGTCGTCTTATCACC", "domains": [ {"helix": 0, "forward": false, "start": 320, "end": 344, "deletions": [321]}, @@ -1457,7 +1457,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GTACTCAGAACGGGGTCAGTGCCTCAGAGC", "domains": [ {"helix": 1, "forward": true, "start": 328, "end": 336}, @@ -1466,7 +1466,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CGCCACCACAGCACCGTAATCAGATATGGT", "domains": [ {"helix": 3, "forward": true, "start": 328, "end": 336}, @@ -1475,7 +1475,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TTACCAGCCAGATAGCCGAACAAGCCTTTA", "domains": [ {"helix": 5, "forward": true, "start": 328, "end": 336}, @@ -1484,7 +1484,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CAGAGAGACCCGACTTGCGGGAGCGAGCAT", "domains": [ {"helix": 7, "forward": true, "start": 328, "end": 336}, @@ -1493,7 +1493,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GTAGAAACCGCCATATTTAACAACTTTTTC", "domains": [ {"helix": 9, "forward": true, "start": 328, "end": 336}, @@ -1502,7 +1502,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AAATATATTCGTCGCTATTAATTTTCGCCT", "domains": [ {"helix": 11, "forward": true, "start": 328, "end": 336}, @@ -1511,7 +1511,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GATTGCTTTCCTGATTATCAGATTATCTTT", "domains": [ {"helix": 13, "forward": true, "start": 328, "end": 336}, @@ -1520,7 +1520,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "AGGAGCACTAACAACTAATAGATTGGAATTAT", "domains": [ {"helix": 15, "forward": true, "start": 328, "end": 352}, @@ -1528,7 +1528,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TAAGTTTTGAGGTTTAGTACCGCCGTTAGCGT", "domains": [ {"helix": 2, "forward": false, "start": 336, "end": 344}, @@ -1537,7 +1537,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "ATCGATAGGAACCACCACCAGAGCACTGGTAA", "domains": [ {"helix": 4, "forward": false, "start": 336, "end": 344}, @@ -1546,7 +1546,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "AAAGTAAGGCCAAAGACAAAAGGGATGAAACC", "domains": [ {"helix": 6, "forward": false, "start": 336, "end": 344}, @@ -1555,7 +1555,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GCGAACCTATAACATAAAAACAGGTTTTAAGA", "domains": [ {"helix": 8, "forward": false, "start": 336, "end": 344}, @@ -1564,7 +1564,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TTGAGAATCAATCAATAATCGGCTGCGTTTTA", "domains": [ {"helix": 10, "forward": false, "start": 336, "end": 344}, @@ -1573,7 +1573,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TCTGTAAATTTAGTTAATTTCATCGGGCTTAA", "domains": [ {"helix": 12, "forward": false, "start": 336, "end": 344}, @@ -1582,7 +1582,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CATCATATTGAATACCAAGTTACAACCTTGCT", "domains": [ {"helix": 14, "forward": false, "start": 336, "end": 344}, @@ -1591,7 +1591,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GCATTCCACAGACAGCCCTCATAACCCTCAG", "domains": [ {"helix": 0, "forward": false, "start": 352, "end": 376, "deletions": [369]}, @@ -1599,7 +1599,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AACCGCCAGATGATACAGGAGTGTCGCCGCCA", "domains": [ {"helix": 1, "forward": true, "start": 360, "end": 368}, @@ -1608,7 +1608,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GCATTGACGCCGGAAACGTCACCACGACATTC", "domains": [ {"helix": 3, "forward": true, "start": 360, "end": 368}, @@ -1617,7 +1617,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AACCGATTATCTTACCGAAGCCCTGAAGCGCA", "domains": [ {"helix": 5, "forward": true, "start": 360, "end": 368}, @@ -1626,7 +1626,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "TTAGACGGATTCTAAGAACGCGAGGTCTTTCC", "domains": [ {"helix": 7, "forward": true, "start": 360, "end": 368}, @@ -1635,7 +1635,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "TTATCATTCCAACGCTCAACAGTATTCTGACC", "domains": [ {"helix": 9, "forward": true, "start": 360, "end": 368}, @@ -1644,7 +1644,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TAAATTTATATATGTGAGTGAATAAAATCGCG", "domains": [ {"helix": 11, "forward": true, "start": 360, "end": 368}, @@ -1653,7 +1653,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CAGAGGCGAACCACCAGAAGGAGCAGAGCCGT", "domains": [ {"helix": 13, "forward": true, "start": 360, "end": 368}, @@ -1662,7 +1662,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CAATAGATAATACATTTGAGGATTTTGCGGA", "domains": [ {"helix": 15, "forward": true, "start": 360, "end": 384, "deletions": [369]}, @@ -1670,7 +1670,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GGCTTTTCCCTCAGAACCGCCACGCCTGTA", "domains": [ {"helix": 2, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1679,7 +1679,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TAGCAAGAGGAGGTTGAGGCAGTCATACAT", "domains": [ {"helix": 4, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1688,7 +1688,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AATAGCTGAGGGAGGGAAGGTAATTACCAT", "domains": [ {"helix": 6, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1697,7 +1697,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "ATCCGGTGAGAATTAACTGAACGAAATAGC", "domains": [ {"helix": 8, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1706,7 +1706,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TATAAAGCCAAGAACGGGTATTGAAGGCTT", "domains": [ {"helix": 10, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1715,7 +1715,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AAATCAAATGGTTTGAAATACCCTTACCAG", "domains": [ {"helix": 12, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1724,7 +1724,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "ACAAAGAAATTATTCATTTCAACAGTACAT", "domains": [ {"helix": 14, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1733,7 +1733,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TTTCGTCACCAGTACAAACTACAACCCTCAGA", "domains": [ {"helix": 0, "forward": false, "start": 384, "end": 408}, @@ -1741,7 +1741,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GCCACCACACCGTTCCAGTAAGCGGTCAGACG", "domains": [ {"helix": 1, "forward": true, "start": 392, "end": 400}, @@ -1750,7 +1750,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "ATTGGCCTAATCACCAGTAGCACCAATATTGA", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 400}, @@ -1759,7 +1759,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CGGAAATTAAGAGCAAGAAACAATACCCTGAA", "domains": [ {"helix": 5, "forward": true, "start": 392, "end": 400}, @@ -1768,7 +1768,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CAAAGTCAAAGCAAATCAGATATAAAACCAAG", "domains": [ {"helix": 7, "forward": true, "start": 392, "end": 400}, @@ -1777,7 +1777,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TACCGCACATGCGTTATACAAATTGACCGTGT", "domains": [ {"helix": 9, "forward": true, "start": 392, "end": 400}, @@ -1786,7 +1786,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GATAAATACCTTTTTTAATGGAAATTACCTGA", "domains": [ {"helix": 11, "forward": true, "start": 392, "end": 400}, @@ -1795,7 +1795,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "GCAAAAGATGAGTAACATTATCATTTAGAAGT", "domains": [ {"helix": 13, "forward": true, "start": 392, "end": 400}, @@ -1804,7 +1804,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "ATTAGACTTTACAAACAATTCGACATTAATTT", "domains": [ {"helix": 15, "forward": true, "start": 392, "end": 416}, @@ -1812,7 +1812,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CTGAATTTCCTCATTTTCAGGGATACACTGAG", "domains": [ {"helix": 2, "forward": false, "start": 400, "end": 408}, @@ -1821,7 +1821,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GCCAGCAATGATATTCACAAACAACGCAGTCT", "domains": [ {"helix": 4, "forward": false, "start": 400, "end": 408}, @@ -1830,7 +1830,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CCAATAATATTCATTAAAGGTGAAGAATTAGA", "domains": [ {"helix": 6, "forward": false, "start": 400, "end": 408}, @@ -1839,7 +1839,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CCAATAGCGAGGGTAATTGAGCGCAGTTAAGC", "domains": [ {"helix": 8, "forward": false, "start": 400, "end": 408}, @@ -1848,7 +1848,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AGTATCATTCATCGAGAACAAGCATACCGCGC", "domains": [ {"helix": 10, "forward": false, "start": 400, "end": 408}, @@ -1857,7 +1857,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "TTGAATTAAGGCGTTAAATAAGAAGCCTGTTT", "domains": [ {"helix": 12, "forward": false, "start": 400, "end": 408}, @@ -1866,7 +1866,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "TAAAAGTTAGATGATGAAACAAACAATTTCAT", "domains": [ {"helix": 14, "forward": false, "start": 400, "end": 408}, diff --git a/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna b/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna index c2fb2406..4c71ecdd 100644 --- a/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna +++ b/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna @@ -143,14 +143,14 @@ "is_scaffold": true }, { - "color": "#333333", + "color": "#f74308", "sequence": "TCCAAAAGGAGCCTTTAATTGTATCGGTTTAT", "domains": [ {"helix": 2, "forward": false, "start": 232, "end": 264} ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "TACTTAGCCGAAATCCGCGACCTGCTCAAGAG", "domains": [ {"helix": 4, "forward": false, "start": 224, "end": 232}, @@ -158,7 +158,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "AAGGATTATAAGAGGCTGAGACTCCTCCATGT", "domains": [ {"helix": 3, "forward": true, "start": 248, "end": 256}, @@ -166,7 +166,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "AATGCAGAGATTTAGGAATACCACGCCTTTAG", "domains": [ {"helix": 6, "forward": false, "start": 224, "end": 232}, @@ -174,7 +174,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CGTCAGACCGACAGAATCAAGTTTATTCAACT", "domains": [ {"helix": 5, "forward": true, "start": 248, "end": 256}, @@ -182,7 +182,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "TTGCTCCTGTCAGGATTAGAGAGTCAATAGCT", "domains": [ {"helix": 8, "forward": false, "start": 224, "end": 232}, @@ -190,7 +190,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "ATCTTACCAGAAACAATGAAATAGACCTTTAA", "domains": [ {"helix": 7, "forward": true, "start": 248, "end": 256}, @@ -198,7 +198,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "GATAAAAAGAGAAGCCTTTATTTCAAGCAAGC", "domains": [ {"helix": 10, "forward": false, "start": 224, "end": 232}, @@ -206,7 +206,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "CGTTTTTACGCACTCATCGAGAACAACGCAAG", "domains": [ {"helix": 9, "forward": true, "start": 248, "end": 256}, @@ -214,7 +214,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "GCGTCTGGTAGGAACGCCATCAAATTTAGTTA", "domains": [ {"helix": 12, "forward": false, "start": 224, "end": 232}, @@ -222,7 +222,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "ATTTCATCACTTTTTCAAATATATAATAATTC", "domains": [ {"helix": 11, "forward": true, "start": 248, "end": 256}, @@ -230,7 +230,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "CTGCAGGTACGGCCAGTGCCAAGCTTAACGTC", "domains": [ {"helix": 14, "forward": false, "start": 224, "end": 232}, @@ -238,7 +238,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "AGATGAATGCGTAGATTTTCAGGTTTGCATGC", "domains": [ {"helix": 13, "forward": true, "start": 248, "end": 256}, @@ -246,7 +246,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "GCAAAATCTGTTTGATGGTGGTTCCCACGCTG", "domains": [ {"helix": 16, "forward": false, "start": 224, "end": 232}, @@ -254,7 +254,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "AGAGCCAGACCGCCTGCAACAGTGCGAAATCG", "domains": [ {"helix": 15, "forward": true, "start": 248, "end": 256}, @@ -262,14 +262,14 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "AGGAACGGTACGCCAGAATCCTGAGAAGTGTT", "domains": [ {"helix": 17, "forward": true, "start": 216, "end": 248} ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "ACAGCATCGGAACGAGGGTAGCAATTCATGAG", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 72}, @@ -277,7 +277,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "GAAGTTTCAGCTGCTCATTCAGTGCGAGTAGT", "domains": [ {"helix": 3, "forward": true, "start": 56, "end": 64}, @@ -286,7 +286,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AAATTGGGACTGCGGAATCGTCATAACAGTTC", "domains": [ {"helix": 5, "forward": true, "start": 56, "end": 64}, @@ -295,7 +295,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "AGAAAACGACCATTAGATACATTTTTCATTTG", "domains": [ {"helix": 7, "forward": true, "start": 56, "end": 64}, @@ -304,7 +304,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GGGCGCGAGATCTACAAAGGCTATGAGAATCG", "domains": [ {"helix": 9, "forward": true, "start": 56, "end": 64}, @@ -313,7 +313,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "ATGAACGGCAGTATCGGCCTCAGGCTTCTGGT", "domains": [ {"helix": 11, "forward": true, "start": 56, "end": 64}, @@ -322,7 +322,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GCCGGAAAAATTGCGTTGCGCTCACCAGCTGC", "domains": [ {"helix": 13, "forward": true, "start": 56, "end": 64}, @@ -331,7 +331,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "ATTAATGATGGGGTCGAGGTGCCGCCCGATTT", "domains": [ {"helix": 15, "forward": true, "start": 56, "end": 64}, @@ -340,7 +340,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AGAGCTTGACGGGGAAAGCCGGCGCCCAAATC", "domains": [ {"helix": 17, "forward": true, "start": 56, "end": 80}, @@ -348,7 +348,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CGTAACAACATTAAACGGGTAAAAAGCGAAAG", "domains": [ {"helix": 4, "forward": false, "start": 64, "end": 72}, @@ -357,7 +357,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CGTCCAATCTTGAGATGGTTTAATCAAATCAA", "domains": [ {"helix": 6, "forward": false, "start": 64, "end": 72}, @@ -366,7 +366,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "TTAGTTTGAGAATGACCATAAATCCTGGATAG", "domains": [ {"helix": 8, "forward": false, "start": 64, "end": 72}, @@ -375,7 +375,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TTTTGAGAGCTGAAAAGGTGGCATGAGTAGAT", "domains": [ {"helix": 10, "forward": false, "start": 64, "end": 72}, @@ -384,7 +384,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GACGACGATAATCGTAAAACTAGCGTAGCTAT", "domains": [ {"helix": 12, "forward": false, "start": 64, "end": 72}, @@ -393,7 +393,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "CTCACATTCCAGGCAAAGCGCCATTTTGAGGG", "domains": [ {"helix": 14, "forward": false, "start": 64, "end": 72}, @@ -402,7 +402,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AAGTTTTTATCGGCCAACGCGCGGTGAGCTAA", "domains": [ {"helix": 16, "forward": false, "start": 64, "end": 72}, @@ -411,7 +411,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TTTTGCGGGATCGTCACCCTCAGCTACGTAAT", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 104}, @@ -419,7 +419,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GCCACTACCCGGATATTCATTACCTTCAACTT", "domains": [ {"helix": 3, "forward": true, "start": 88, "end": 96}, @@ -428,7 +428,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "TAATCATTTAGTAAAATGTTTAGAAAAAATCA", "domains": [ {"helix": 5, "forward": true, "start": 88, "end": 96}, @@ -437,7 +437,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GGTCTTTATCCCAATTCTGCGAACCAATTCTA", "domains": [ {"helix": 7, "forward": true, "start": 88, "end": 96}, @@ -446,7 +446,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "CTAATAGTATTAATGCCGGAGAGGATGTCAAT", "domains": [ {"helix": 9, "forward": true, "start": 88, "end": 96}, @@ -455,7 +455,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CATATGTAACCGTGCATCTGCCAGTCGCCATT", "domains": [ {"helix": 11, "forward": true, "start": 88, "end": 96}, @@ -464,7 +464,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CAGGCTGCTGGGGTGCCTAATGAGGGAGAGGC", "domains": [ {"helix": 13, "forward": true, "start": 88, "end": 96}, @@ -473,7 +473,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "GGTTTGCGACTACGTGAACCATCAAACGTGGC", "domains": [ {"helix": 15, "forward": true, "start": 88, "end": 96}, @@ -482,7 +482,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GAGAAAGGAAGGGAATGCGCCGCTATCAGGGC", "domains": [ {"helix": 17, "forward": true, "start": 88, "end": 112}, @@ -490,7 +490,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "GACAAGAAGAAGGCACCAACCTAAAAGGCCGC", "domains": [ {"helix": 4, "forward": false, "start": 96, "end": 104}, @@ -499,7 +499,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GGGGGTAAGTGAATTACCTTATGCGTAATCTT", "domains": [ {"helix": 6, "forward": false, "start": 96, "end": 104}, @@ -508,7 +508,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "CAGTTGATCCCTGACTATTATAGTTTGCCAGA", "domains": [ {"helix": 8, "forward": false, "start": 96, "end": 104}, @@ -517,7 +517,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GCTGATAAAGTAGCATTAACATCCCCATATAA", "domains": [ {"helix": 10, "forward": false, "start": 96, "end": 104}, @@ -526,7 +526,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GCATCGTACCCCGGTTGATAATCACCGTTCTA", "domains": [ {"helix": 12, "forward": false, "start": 96, "end": 104}, @@ -535,7 +535,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GTAAAGCCGCAACTGTTGGGAAGGAGATGGGC", "domains": [ {"helix": 14, "forward": false, "start": 96, "end": 104}, @@ -544,7 +544,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GATGGCCCTATTGGGCGCCAGGGTCATAAAGT", "domains": [ {"helix": 16, "forward": false, "start": 96, "end": 104}, @@ -553,7 +553,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GTCGCTGAGGCTTGCAGGGAGTTAAACGAAAG", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 136}, @@ -561,7 +561,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AGGCAAAACTGACCTTCATCAAGAGATTTTAA", "domains": [ {"helix": 3, "forward": true, "start": 120, "end": 128}, @@ -570,7 +570,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GAACTGGCTTTTGCAAAAGAAGTTCAGAAGCA", "domains": [ {"helix": 5, "forward": true, "start": 120, "end": 128}, @@ -579,7 +579,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "AAGCGGATGTCTGGAAGTTTCATTAATAAATC", "domains": [ {"helix": 7, "forward": true, "start": 120, "end": 128}, @@ -588,7 +588,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "ATACAGGCTCAATATGATATTCAAGAAAAGCC", "domains": [ {"helix": 9, "forward": true, "start": 120, "end": 128}, @@ -597,7 +597,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CCAAAAACTAGGTCACGTTGGTGTGCGATCGG", "domains": [ {"helix": 11, "forward": true, "start": 120, "end": 128}, @@ -606,7 +606,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TGCGGGCCACATACGAGCCGGAAGGGTTTTTC", "domains": [ {"helix": 13, "forward": true, "start": 120, "end": 128}, @@ -615,7 +615,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "TTTTCACCGGGCGAAAAACCGTCTACAGGGCG", "domains": [ {"helix": 15, "forward": true, "start": 120, "end": 128}, @@ -624,7 +624,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "CGTACTATGGTTGCTTTGACGAGCGGACTCCA", "domains": [ {"helix": 17, "forward": true, "start": 120, "end": 144}, @@ -632,7 +632,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TAGGCTGGGAATACACTAAAACACTATATTCG", "domains": [ {"helix": 4, "forward": false, "start": 128, "end": 136}, @@ -641,7 +641,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CGAGAGGCTCATTATACCAGTCAGCAGGCGCA", "domains": [ {"helix": 6, "forward": false, "start": 128, "end": 136}, @@ -650,7 +650,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "AGTACGGTTGCATCAAAAAGATTACAAAATAG", "domains": [ {"helix": 8, "forward": false, "start": 128, "end": 136}, @@ -659,7 +659,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AATCACCAAAGGCAAAGAATTAGCGCAACTAA", "domains": [ {"helix": 10, "forward": false, "start": 128, "end": 136}, @@ -668,7 +668,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "TAATGGGAAGGAAGATTGTATAAGGACAGTCA", "domains": [ {"helix": 12, "forward": false, "start": 128, "end": 136}, @@ -677,7 +677,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TCCACACATCTTCGCTATTACGCCATTGACCG", "domains": [ {"helix": 14, "forward": false, "start": 128, "end": 136}, @@ -686,7 +686,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "ACGTCAAAAGTGAGACGGGCAACACTCACAAT", "domains": [ {"helix": 16, "forward": false, "start": 128, "end": 136}, @@ -695,7 +695,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CAACCATCGCCCACGCATAACCGATCATCTTT", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 168}, @@ -703,7 +703,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "GACCCCCATGAACGGTGTACAGACGACGTTGG", "domains": [ {"helix": 3, "forward": true, "start": 152, "end": 160}, @@ -712,7 +712,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GAAGAAAAAGACGACGATAAAAACAGAGGAAG", "domains": [ {"helix": 5, "forward": true, "start": 152, "end": 160}, @@ -721,7 +721,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CCCGAAAGAACATGTTTTAAATATAAAATTAA", "domains": [ {"helix": 7, "forward": true, "start": 152, "end": 160}, @@ -730,7 +730,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "GCAATAAAGGTGAGAAAGGCCGGACAAATATT", "domains": [ {"helix": 9, "forward": true, "start": 152, "end": 160}, @@ -739,7 +739,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TAAATTGTTGGGAACAAACGGCGGAGCTGGCG", "domains": [ {"helix": 11, "forward": true, "start": 152, "end": 160}, @@ -748,7 +748,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "AAAGGGGGGTGAAATTGTTATCCGGCTGATTG", "domains": [ {"helix": 13, "forward": true, "start": 152, "end": 160}, @@ -757,7 +757,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CCCTTCACCACTATTAAAGAACGTACGTATAA", "domains": [ {"helix": 15, "forward": true, "start": 152, "end": 160}, @@ -766,7 +766,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CGTGCTTTCCTCGTTAGAATCAGAGTTTGGAA", "domains": [ {"helix": 17, "forward": true, "start": 152, "end": 176}, @@ -774,7 +774,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AGGACAGAGCGATTATACCAAGCGAATGACAA", "domains": [ {"helix": 4, "forward": false, "start": 160, "end": 168}, @@ -783,7 +783,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CGTTTACCATCTACGTTAATAAAATTTGAAAG", "domains": [ {"helix": 6, "forward": false, "start": 160, "end": 168}, @@ -792,7 +792,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TGTAGCTCACTTCAAATATCGCGTATAACCCT", "domains": [ {"helix": 8, "forward": false, "start": 160, "end": 168}, @@ -801,7 +801,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "TTCAAAAGGCCTCAGAGCATAAAGTATAATGC", "domains": [ {"helix": 10, "forward": false, "start": 160, "end": 168}, @@ -810,7 +810,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "ATTCTCCGAAACGTTAATATTTTGGGTAAAGA", "domains": [ {"helix": 12, "forward": false, "start": 160, "end": 168}, @@ -819,7 +819,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TTTCCTGTATGTGCTGCAAGGCGACCCGTCGG", "domains": [ {"helix": 14, "forward": false, "start": 160, "end": 168}, @@ -828,7 +828,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CAAGAGTCCGCCTGGCCCTGAGAGCATAGCTG", "domains": [ {"helix": 16, "forward": false, "start": 160, "end": 168}, @@ -837,7 +837,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CTTGATACCGATAGTTGCGCCGACCGAAACAA", "domains": [ {"helix": 2, "forward": false, "start": 176, "end": 200}, @@ -845,7 +845,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "AGTACAACAACCGAACTGACCAACCGAACTAA", "domains": [ {"helix": 3, "forward": true, "start": 184, "end": 192}, @@ -854,7 +854,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "CGGAACAATAAGAGCAACACTATCTTTAATTC", "domains": [ {"helix": 5, "forward": true, "start": 184, "end": 192}, @@ -863,7 +863,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GAGCTTCAGAGCTTAATTGCTGAACTAAATCG", "domains": [ {"helix": 7, "forward": true, "start": 184, "end": 192}, @@ -872,7 +872,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GTTGTACCGCCTGAGTAATGTGTATTAAAATT", "domains": [ {"helix": 9, "forward": true, "start": 184, "end": 192}, @@ -881,7 +881,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CGCATTAATGTGAGCGAGTAACAATTAAGTTG", "domains": [ {"helix": 11, "forward": true, "start": 184, "end": 192}, @@ -890,7 +890,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GGTAACGCAATTCGTAATCATGGTAGTTGCAG", "domains": [ {"helix": 13, "forward": true, "start": 184, "end": 192}, @@ -899,7 +899,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CAAGCGGTGTTGAGTGTTGTTCCAGCGGGAGC", "domains": [ {"helix": 15, "forward": true, "start": 184, "end": 192}, @@ -908,7 +908,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TAAACAGGAGGCCGATTAAAGGGAAATAGCCC", "domains": [ {"helix": 17, "forward": true, "start": 184, "end": 208}, @@ -916,7 +916,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CATAAGGGGGAGATTTGTATCATCTTAAACAG", "domains": [ {"helix": 4, "forward": false, "start": 192, "end": 200}, @@ -925,7 +925,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "AGGCATAGCATTATTACAGGTAGACGGTCAAT", "domains": [ {"helix": 6, "forward": false, "start": 192, "end": 200}, @@ -934,7 +934,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "ATGGCTTAAAGCGAACCAGACCGGGAATTACG", "domains": [ {"helix": 8, "forward": false, "start": 192, "end": 200}, @@ -943,7 +943,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "AATGCAATAAAAACATTATGACCCTTTTGCGG", "domains": [ {"helix": 10, "forward": false, "start": 192, "end": 200}, @@ -952,7 +952,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ACATTAAAATTTTTGTTAAATCAGATATTTTA", "domains": [ {"helix": 12, "forward": false, "start": 192, "end": 200}, @@ -961,7 +961,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CGAGCTCGCAGGGTTTTCCCAGTCTTTCATCA", "domains": [ {"helix": 14, "forward": false, "start": 192, "end": 200}, @@ -970,7 +970,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "GAGATAGGCCACGCTGGTTTGCCCCCGGGTAC", "domains": [ {"helix": 16, "forward": false, "start": 192, "end": 200}, @@ -979,7 +979,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "CAGCTTGCTTTCGAGGTGAATTTCGCCTGATA", "domains": [ {"helix": 2, "forward": false, "start": 208, "end": 232}, @@ -987,7 +987,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "AATTGTGTCGGAACGAGGCGCAGAAAGATTCA", "domains": [ {"helix": 3, "forward": true, "start": 216, "end": 224}, @@ -996,7 +996,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TCAGTTGATACATAACGCCAAAAGAAGCAAAC", "domains": [ {"helix": 5, "forward": true, "start": 216, "end": 224}, @@ -1005,7 +1005,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "TCCAACAGTTTGATAAGAGGTCATTGTAATAC", "domains": [ {"helix": 7, "forward": true, "start": 216, "end": 224}, @@ -1014,7 +1014,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "TTTTGCGGTTTTTAGAACCCTCATCTCATTTT", "domains": [ {"helix": 9, "forward": true, "start": 216, "end": 224}, @@ -1023,7 +1023,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TTAACCAACCTTCCTGTAGCCAGCACGACGTT", "domains": [ {"helix": 11, "forward": true, "start": 216, "end": 224}, @@ -1032,7 +1032,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GTAAAACGCGACTCTAGAGGATCCCAGCAGGC", "domains": [ {"helix": 13, "forward": true, "start": 216, "end": 224}, @@ -1041,7 +1041,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "GAAAATCCCCTTATAAATCAAAAGTTTTAGAC", "domains": [ {"helix": 15, "forward": true, "start": 216, "end": 224}, @@ -1050,7 +1050,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TTTATAATCAGTGAGGCCACCGAGGGCGGTCA", "domains": [ {"helix": 17, "forward": true, "start": 248, "end": 272}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "GAAAGTATGGATTAGCGGGGTTTTAAAAAGGC", "domains": [ {"helix": 4, "forward": false, "start": 256, "end": 264}, @@ -1067,7 +1067,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ATCAGTAGTGTAGCGCGTTTTCATTGAAACAT", "domains": [ {"helix": 6, "forward": false, "start": 256, "end": 264}, @@ -1076,7 +1076,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "TAAGAGCAGAAGCCCTTTTTAAGAGCACCGTA", "domains": [ {"helix": 8, "forward": false, "start": 256, "end": 264}, @@ -1085,7 +1085,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "CCAAGTACTTTTCATCGTAGGAATCCCAATAA", "domains": [ {"helix": 10, "forward": false, "start": 256, "end": 264}, @@ -1094,7 +1094,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "GCGAGAAATTCTGACCTAAATTTAGTATTAAA", "domains": [ {"helix": 12, "forward": false, "start": 256, "end": 264}, @@ -1103,7 +1103,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "AAGAAATTATACAGTAACAGTACCCAAAGAAC", "domains": [ {"helix": 14, "forward": false, "start": 256, "end": 264}, @@ -1112,7 +1112,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GTATTAACCAGCAAATGAAAAATCCAGAAATA", "domains": [ {"helix": 16, "forward": false, "start": 256, "end": 264}, @@ -1121,7 +1121,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "TTTTTCACGTTGAAAATCTCCAAAGCTCAGTA", "domains": [ {"helix": 2, "forward": false, "start": 272, "end": 296}, @@ -1129,7 +1129,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CCAGGCGGTCGGAACCTATTATTCCGGCATTT", "domains": [ {"helix": 3, "forward": true, "start": 280, "end": 288}, @@ -1138,7 +1138,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "TCGGTCATGAAACCATCGATAGCAAAAGTAAG", "domains": [ {"helix": 5, "forward": true, "start": 280, "end": 288}, @@ -1147,7 +1147,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CAGATAGCCAAGAATTGAGTTAAGCATTACCG", "domains": [ {"helix": 7, "forward": true, "start": 280, "end": 288}, @@ -1156,7 +1156,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CGCCCAATATCATTCCAAGAACGGATGGTTTG", "domains": [ {"helix": 9, "forward": true, "start": 280, "end": 288}, @@ -1165,7 +1165,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "AAATACCGAAATCCAATCGCAAGATTTTACAT", "domains": [ {"helix": 11, "forward": true, "start": 280, "end": 288}, @@ -1174,7 +1174,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CGGGAGAATTATTTGCACGTAAAATAAAGCAT", "domains": [ {"helix": 13, "forward": true, "start": 280, "end": 288}, @@ -1183,7 +1183,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CACCTTGCGATAAAACAGAGGTGATAAAAGAG", "domains": [ {"helix": 15, "forward": true, "start": 280, "end": 288}, @@ -1192,7 +1192,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "TCTGTCCATCACGCAAATTAACCGCGAACCAC", "domains": [ {"helix": 17, "forward": true, "start": 280, "end": 304}, @@ -1200,7 +1200,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TGCCTATTATAAGTGCCGTCGAGAATAATAAT", "domains": [ {"helix": 4, "forward": false, "start": 288, "end": 296}, @@ -1209,7 +1209,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TCACCAATAGCCCCCTTATTAGCGATGCCCCC", "domains": [ {"helix": 6, "forward": false, "start": 288, "end": 296}, @@ -1218,7 +1218,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "ATAACCCACGAACAAAGTTACCAGCGGAAACG", "domains": [ {"helix": 8, "forward": false, "start": 288, "end": 296}, @@ -1227,7 +1227,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CTTTCCTTAGCAAGCAAATCAGATTCAGAGAG", "domains": [ {"helix": 10, "forward": false, "start": 288, "end": 296}, @@ -1236,7 +1236,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "GCTGATGCACCGTGTGATAAATAATCGGCTGT", "domains": [ {"helix": 12, "forward": false, "start": 288, "end": 296}, @@ -1245,7 +1245,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "TATCAAAAACAATAACGGATTCGCATGTAAAT", "domains": [ {"helix": 14, "forward": false, "start": 288, "end": 296}, @@ -1254,7 +1254,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "CAGCAGAATGAACCTCAAATATCAACCTACCA", "domains": [ {"helix": 16, "forward": false, "start": 288, "end": 296}, @@ -1263,7 +1263,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "AAGGAACAACTAAAGGAATTGCGAGGGTTGAT", "domains": [ {"helix": 2, "forward": false, "start": 304, "end": 328}, @@ -1271,7 +1271,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "ATAAGTATCCCGTATAAACAGTTATTTGCCAT", "domains": [ {"helix": 3, "forward": true, "start": 312, "end": 320}, @@ -1280,7 +1280,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CTTTTCATTTACCATTAGCAAGGCAAGGAAAC", "domains": [ {"helix": 5, "forward": true, "start": 312, "end": 320}, @@ -1289,7 +1289,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CGAGGAAATAATTGAGCGCTAATAATAGAAGG", "domains": [ {"helix": 7, "forward": true, "start": 312, "end": 320}, @@ -1298,7 +1298,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CTTATCCGAGAAACCAATCAATAAGGCGTTAA", "domains": [ {"helix": 9, "forward": true, "start": 312, "end": 320}, @@ -1307,7 +1307,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "ATAAGAATTGGGTTATATAACTATCTGATTGC", "domains": [ {"helix": 11, "forward": true, "start": 312, "end": 320}, @@ -1316,7 +1316,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TTTGAATATAATGGAAGGGTTAGAAACCCTCA", "domains": [ {"helix": 13, "forward": true, "start": 312, "end": 320}, @@ -1325,7 +1325,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "ATCAATATCATTAAAAATACCGAATTGTAGCA", "domains": [ {"helix": 15, "forward": true, "start": 312, "end": 320}, @@ -1334,7 +1334,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "ATACTTCTTTGATTAGTAATAACAAGCCCTAA", "domains": [ {"helix": 17, "forward": true, "start": 312, "end": 336}, @@ -1342,7 +1342,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TAACAGTGAGCCCGGAATAGGTGTAGAATAGA", "domains": [ {"helix": 4, "forward": false, "start": 320, "end": 328}, @@ -1351,7 +1351,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "TAGCACCAAATCAAAATCACCGGAGCCTTGAG", "domains": [ {"helix": 6, "forward": false, "start": 320, "end": 328}, @@ -1360,7 +1360,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "TCAGAGGGCGCAATAATAACGGAAATCACCAG", "domains": [ {"helix": 8, "forward": false, "start": 320, "end": 328}, @@ -1369,7 +1369,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "GAGCATGTGTATTCTAAGAACGCGGAACAAAG", "domains": [ {"helix": 10, "forward": false, "start": 320, "end": 328}, @@ -1378,7 +1378,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "GCTTAGGTAAACACCGGAATCATATAATTTAC", "domains": [ {"helix": 12, "forward": false, "start": 320, "end": 328}, @@ -1387,7 +1387,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CTTCTGAACCAAGTTACAAAATCGAACCTCCG", "domains": [ {"helix": 14, "forward": false, "start": 320, "end": 328}, @@ -1396,7 +1396,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "AACATCGCCTGGTCAGTTGGCAAAGGATTATA", "domains": [ {"helix": 16, "forward": false, "start": 320, "end": 328}, @@ -1405,7 +1405,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "ACTTTCAACAGTTTCAGCGGAGTGATCACCGT", "domains": [ {"helix": 2, "forward": false, "start": 336, "end": 360}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ACTCAGGATTTTAACGGGGTCAGTACCAGAGC", "domains": [ {"helix": 3, "forward": true, "start": 344, "end": 352}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CACCACCGAATTAGAGCCAGCAAATACCCAAA", "domains": [ {"helix": 5, "forward": true, "start": 344, "end": 352}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "AGAACTGGATTAACTGAACACCCTAGGCGTTT", "domains": [ {"helix": 7, "forward": true, "start": 344, "end": 352}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TAGCGAACAAATAATATCCCATCCATTACTAG", "domains": [ {"helix": 9, "forward": true, "start": 344, "end": 352}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "AAAAAGCCGAGAGACTACCTTTTTCGCAGAGG", "domains": [ {"helix": 11, "forward": true, "start": 344, "end": 352}, @@ -1458,7 +1458,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CGAATTATATAATCCTGATTGTTTTCAACAGT", "domains": [ {"helix": 13, "forward": true, "start": 344, "end": 352}, @@ -1467,7 +1467,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "TGAAAGGATAATGCGCGAACTGATTCACTTGC", "domains": [ {"helix": 15, "forward": true, "start": 344, "end": 352}, @@ -1476,7 +1476,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CTGAGTAGAAGAACTCAAACTATCAATGGCTA", "domains": [ {"helix": 17, "forward": true, "start": 344, "end": 368}, @@ -1484,7 +1484,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "GTAATAAGGGTTTAGTACCGCCACGCTAAACA", "domains": [ {"helix": 4, "forward": false, "start": 352, "end": 360}, @@ -1493,7 +1493,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CATTTGGGGAACCGCCTCCCTCAGGTGTACTG", "domains": [ {"helix": 6, "forward": false, "start": 352, "end": 360}, @@ -1502,7 +1502,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "ACGGGAGACATGATTAAGACTCCTACTTGAGC", "domains": [ {"helix": 8, "forward": false, "start": 352, "end": 360}, @@ -1511,7 +1511,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "AACAAGAACTCCCGACTTGCGGGACGCATTAG", "domains": [ {"helix": 10, "forward": false, "start": 352, "end": 360}, @@ -1520,7 +1520,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "ATAGGTCTTGTTTAGTATCATATGAAGTCCTG", "domains": [ {"helix": 12, "forward": false, "start": 352, "end": 360}, @@ -1529,7 +1529,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "TCATCAATTCATTTCAATTACCTGTCAAAATC", "domains": [ {"helix": 14, "forward": false, "start": 352, "end": 360}, @@ -1538,7 +1538,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "TTAGTCTTATTGAGGAAGGTTATCATGGCAAT", "domains": [ {"helix": 16, "forward": false, "start": 352, "end": 360}, @@ -1547,7 +1547,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "AATGAATTTTCTGTATGGGATTTTCCTCAGAA", "domains": [ {"helix": 2, "forward": false, "start": 368, "end": 392}, @@ -1555,7 +1555,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "CCGCCACCTTTTGATGATACAGGAAGCCGCCA", "domains": [ {"helix": 3, "forward": true, "start": 376, "end": 384}, @@ -1564,7 +1564,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CCCTCAGAATTATCACCGTCACCGTATTACGC", "domains": [ {"helix": 5, "forward": true, "start": 376, "end": 384}, @@ -1573,7 +1573,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "AGTATGTTCATAAAAACAGGGAAGGGTTTTGA", "domains": [ {"helix": 7, "forward": true, "start": 376, "end": 384}, @@ -1582,7 +1582,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AGCCTTAATTTATCAACAATAGATCGTTATAC", "domains": [ {"helix": 9, "forward": true, "start": 376, "end": 384}, @@ -1591,7 +1591,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "AAATTCTTGTCAATAGTGAATTTAAGCAAAAG", "domains": [ {"helix": 11, "forward": true, "start": 376, "end": 384}, @@ -1600,7 +1600,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AAGATGATTCCTGATTATCAGATGTAAAATAT", "domains": [ {"helix": 13, "forward": true, "start": 376, "end": 384}, @@ -1609,7 +1609,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CTTTAGGAACAGACAATATTTTTGGGCCTTGC", "domains": [ {"helix": 15, "forward": true, "start": 376, "end": 384}, @@ -1618,7 +1618,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "TGGTAATATCCAGAACAATATTACCGTAAGAA", "domains": [ {"helix": 17, "forward": true, "start": 376, "end": 400}, @@ -1626,7 +1626,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TACATGGCCTCAGAACCGCCACCCCGTTAGTA", "domains": [ {"helix": 4, "forward": false, "start": 384, "end": 392}, @@ -1635,7 +1635,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "AAAGGTGAACCGCCACCCTCAGAGAAGCGTCA", "domains": [ {"helix": 6, "forward": false, "start": 384, "end": 392}, @@ -1644,7 +1644,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "GAGAATAAAGCAAACGTAGAAAATTATTCATT", "domains": [ {"helix": 8, "forward": false, "start": 384, "end": 392}, @@ -1653,7 +1653,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CGCGCCTGATCAAGATTAGTTGCTTTTACAGA", "domains": [ {"helix": 10, "forward": false, "start": 384, "end": 392}, @@ -1662,7 +1662,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "TGAGAAGAACCAGTATAAAGCCAAATGCAGAA", "domains": [ {"helix": 12, "forward": false, "start": 384, "end": 392}, @@ -1671,7 +1671,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "CATCATATGAAACAAACATCAAGATAAGACGC", "domains": [ {"helix": 14, "forward": false, "start": 384, "end": 392}, @@ -1680,7 +1680,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TACGTGGCGCACTAACAACTAATAGGAATTAT", "domains": [ {"helix": 16, "forward": false, "start": 384, "end": 392}, @@ -1689,7 +1689,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "CTAAAGTTTTGTCGTCTTTCCAGATCAGAGCC", "domains": [ {"helix": 2, "forward": false, "start": 400, "end": 424}, @@ -1697,7 +1697,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "ACCACCCTAATTTACCGTTCCAGTCCACCACC", "domains": [ {"helix": 3, "forward": true, "start": 408, "end": 416}, @@ -1706,7 +1706,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "CTCAGAGCAAATATTGACGGAAATACATACAT", "domains": [ {"helix": 5, "forward": true, "start": 408, "end": 416}, @@ -1715,7 +1715,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "AAAGGTGGAATGAAAATAGCAGCCATTTTGCA", "domains": [ {"helix": 7, "forward": true, "start": 408, "end": 416}, @@ -1724,7 +1724,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "CCCAGCTAACAACATGTTCAGCTACGCTCAAC", "domains": [ {"helix": 9, "forward": true, "start": 408, "end": 416}, @@ -1733,7 +1733,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "AGTAGGGCTAGCGATAGCTTAGATAAACAAAA", "domains": [ {"helix": 11, "forward": true, "start": 408, "end": 416}, @@ -1742,7 +1742,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "TTAATTACAACCACCAGAAGGAGCGATTAGAG", "domains": [ {"helix": 13, "forward": true, "start": 408, "end": 416}, @@ -1751,7 +1751,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CCGTCAATCCTTCTGACCTGAAAGCGCCAGCC", "domains": [ {"helix": 15, "forward": true, "start": 408, "end": 416}, @@ -1760,7 +1760,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "ATTGCAACAGGAAAAACGCTCATGCCAACAGA", "domains": [ {"helix": 17, "forward": true, "start": 408, "end": 432}, @@ -1768,7 +1768,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "AGTCTCTGCATTTTCAGGGATAGCGTAACGAT", "domains": [ {"helix": 4, "forward": false, "start": 416, "end": 424}, @@ -1777,7 +1777,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "GGGAAGGTCGCCACCAGAACCACCGAAAGCGC", "domains": [ {"helix": 6, "forward": false, "start": 416, "end": 424}, @@ -1786,7 +1786,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "ACGTCAAACAACATATAAAAGAAATTGAGGGA", "domains": [ {"helix": 8, "forward": false, "start": 416, "end": 424}, @@ -1795,7 +1795,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "GACAATAACAATTTTATCCTGAATTTTGTTTA", "domains": [ {"helix": 10, "forward": false, "start": 416, "end": 424}, @@ -1804,7 +1804,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "TGAAAACATTAATTGAGAATCGCCCAGACGAC", "domains": [ {"helix": 12, "forward": false, "start": 416, "end": 424}, @@ -1813,7 +1813,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "AACAAAGAATTTAACAATTTCATTAGAATCCT", "domains": [ {"helix": 14, "forward": false, "start": 416, "end": 424}, @@ -1822,7 +1822,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GATAGAACAGATAATACATTTGAGTTTTGCGG", "domains": [ {"helix": 16, "forward": false, "start": 416, "end": 424}, @@ -1831,7 +1831,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "CCACAGACAGCCCTCATAGTTAGCAAGCCCAA", "domains": [ {"helix": 2, "forward": false, "start": 432, "end": 456}, @@ -1839,7 +1839,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "TAGGAACCCATTAAAGCCAGAATGACCAGAGC", "domains": [ {"helix": 3, "forward": true, "start": 440, "end": 448}, @@ -1848,7 +1848,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CGCCGCCAGGCGACATTCAACCGACGCAAAGA", "domains": [ {"helix": 5, "forward": true, "start": 440, "end": 448}, @@ -1857,7 +1857,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "sequence": "CACCACGGAAATAAGAAACGATTTCTTACCAA", "domains": [ {"helix": 7, "forward": true, "start": 440, "end": 448}, @@ -1866,7 +1866,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "sequence": "CGCTAACGGTAAAGTAATTCTGTCATATTTAA", "domains": [ {"helix": 9, "forward": true, "start": 440, "end": 448}, @@ -1875,7 +1875,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "sequence": "CAACGCCATAATTAATTTTCCCTTTGAATTAC", "domains": [ {"helix": 11, "forward": true, "start": 440, "end": 448}, @@ -1884,7 +1884,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "sequence": "CTTTTTTATTGAGTAACATTATCAGATTTAGA", "domains": [ {"helix": 13, "forward": true, "start": 440, "end": 448}, @@ -1893,7 +1893,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "sequence": "AGTATTAGAAAAGGGACATTCTGGGAAATACC", "domains": [ {"helix": 15, "forward": true, "start": 440, "end": 448}, @@ -1902,7 +1902,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "sequence": "TACATTTTGACGCTCAATCGTCTGTCACACGA", "domains": [ {"helix": 17, "forward": true, "start": 440, "end": 464}, @@ -1910,7 +1910,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "TAAATCCTCATGTACCGTAACACTGTAGCATT", "domains": [ {"helix": 4, "forward": false, "start": 448, "end": 456}, @@ -1919,7 +1919,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "sequence": "GACAAAAGGCATTGACAGGAGGTTCAAACAAA", "domains": [ {"helix": 6, "forward": false, "start": 448, "end": 456}, @@ -1928,7 +1928,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "sequence": "CCCAATCCAATAAGTTTATTTTGTGCGCCAAA", "domains": [ {"helix": 8, "forward": false, "start": 448, "end": 456}, @@ -1937,7 +1937,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "sequence": "GACAAAAGAGCGTCTTTCCAGAGCTTATTTAT", "domains": [ {"helix": 10, "forward": false, "start": 448, "end": 456}, @@ -1946,7 +1946,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "sequence": "GTCGCTATACATGTAATTTAGGCAAAAGTACC", "domains": [ {"helix": 12, "forward": false, "start": 448, "end": 456}, @@ -1955,7 +1955,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "sequence": "TTAAAAGTATGGAAACAGTACATATGTAAATC", "domains": [ {"helix": 14, "forward": false, "start": 448, "end": 456}, @@ -1964,7 +1964,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "sequence": "CCAGTAATACTTTACAAACAATTCTATTAATT", "domains": [ {"helix": 16, "forward": false, "start": 448, "end": 456}, diff --git a/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna b/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna index a25df6b1..f9ff0b84 100644 --- a/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna +++ b/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna @@ -58,236 +58,236 @@ "is_scaffold": true }, { - "color": "#32b86c", + "color": "#f74308", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, {"helix": 0, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, {"helix": 2, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#320096", + "color": "#888888", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, {"helix": 4, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#03b6a2", + "color": "#32b86c", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, {"helix": 6, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#7300de", + "color": "#333333", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, {"helix": 8, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#aaaa00", + "color": "#320096", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, {"helix": 10, "forward": false, "start": 16, "end": 32} ] }, { - 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"color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 13, "forward": true, "start": 360, "end": 368}, {"helix": 14, "forward": false, "start": 352, "end": 368}, @@ -1477,14 +1477,14 @@ ] }, { - "color": "#320096", + "color": "#888888", "domains": [ {"helix": 15, "forward": true, "start": 360, "end": 384}, {"helix": 14, "forward": false, "start": 376, "end": 384} ] }, { - "color": "#03b6a2", + "color": "#32b86c", "domains": [ {"helix": 2, "forward": false, "start": 368, "end": 376}, {"helix": 1, "forward": true, "start": 368, "end": 384}, @@ -1492,7 +1492,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "domains": [ {"helix": 4, "forward": false, "start": 368, "end": 376}, {"helix": 3, "forward": true, "start": 368, "end": 384}, @@ -1500,7 +1500,7 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "domains": [ {"helix": 6, "forward": false, "start": 368, "end": 376}, {"helix": 5, "forward": true, "start": 368, "end": 384}, @@ -1508,7 +1508,7 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "domains": [ {"helix": 8, "forward": false, "start": 368, "end": 376}, {"helix": 7, "forward": true, "start": 368, "end": 384}, @@ -1516,7 +1516,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "domains": [ {"helix": 10, "forward": false, "start": 368, "end": 376}, {"helix": 9, "forward": true, "start": 368, "end": 384}, @@ -1524,7 +1524,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "domains": [ {"helix": 12, "forward": false, "start": 368, "end": 376}, {"helix": 11, "forward": true, "start": 368, "end": 384}, @@ -1532,7 +1532,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "domains": [ {"helix": 14, "forward": false, "start": 368, "end": 376}, {"helix": 13, "forward": true, "start": 368, "end": 384}, @@ -1540,14 +1540,14 @@ ] }, { - "color": "#f74308", + "color": "#007200", "domains": [ {"helix": 0, "forward": false, "start": 384, "end": 408}, {"helix": 1, "forward": true, "start": 384, "end": 392} ] }, { - "color": "#57bb00", + "color": "#cc0000", "domains": [ {"helix": 1, "forward": true, "start": 392, "end": 400}, {"helix": 2, "forward": false, "start": 384, "end": 400}, @@ -1555,7 +1555,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 400}, {"helix": 4, "forward": false, "start": 384, "end": 400}, @@ -1563,7 +1563,7 @@ ] }, { - "color": "#32b86c", + "color": "#f74308", "domains": [ {"helix": 5, "forward": true, "start": 392, "end": 400}, {"helix": 6, "forward": false, "start": 384, "end": 400}, @@ -1571,7 +1571,7 @@ ] }, { - "color": "#333333", + "color": "#57bb00", "domains": [ {"helix": 7, "forward": true, "start": 392, "end": 400}, {"helix": 8, "forward": false, "start": 384, "end": 400}, @@ -1579,7 +1579,7 @@ ] }, { - "color": "#320096", + "color": "#888888", "domains": [ {"helix": 9, "forward": true, "start": 392, "end": 400}, {"helix": 10, "forward": false, "start": 384, "end": 400}, @@ -1587,7 +1587,7 @@ ] }, { - "color": "#03b6a2", + "color": "#32b86c", "domains": [ {"helix": 11, "forward": true, "start": 392, "end": 400}, {"helix": 12, "forward": false, "start": 384, "end": 400}, @@ -1595,7 +1595,7 @@ ] }, { - "color": "#7300de", + "color": "#333333", "domains": [ {"helix": 13, "forward": true, "start": 392, "end": 400}, {"helix": 14, "forward": false, "start": 384, "end": 400}, @@ -1603,14 +1603,14 @@ ] }, { - "color": "#aaaa00", + "color": "#320096", "domains": [ {"helix": 15, "forward": true, "start": 392, "end": 416}, {"helix": 14, "forward": false, "start": 408, "end": 416} ] }, { - "color": "#b8056c", + "color": "#03b6a2", "domains": [ {"helix": 2, "forward": false, "start": 400, "end": 408}, {"helix": 1, "forward": true, "start": 400, "end": 416}, @@ -1618,7 +1618,7 @@ ] }, { - "color": "#007200", + "color": "#7300de", "domains": [ {"helix": 4, "forward": false, "start": 400, "end": 408}, {"helix": 3, "forward": true, "start": 400, "end": 416}, @@ -1626,7 +1626,7 @@ ] }, { - "color": "#cc0000", + "color": "#aaaa00", "domains": [ {"helix": 6, "forward": false, "start": 400, "end": 408}, {"helix": 5, "forward": true, "start": 400, "end": 416}, @@ -1634,7 +1634,7 @@ ] }, { - "color": "#f7931e", + "color": "#b8056c", "domains": [ {"helix": 8, "forward": false, "start": 400, "end": 408}, {"helix": 7, "forward": true, "start": 400, "end": 416}, @@ -1642,7 +1642,7 @@ ] }, { - "color": "#f74308", + "color": "#007200", "domains": [ {"helix": 10, "forward": false, "start": 400, "end": 408}, {"helix": 9, "forward": true, "start": 400, "end": 416}, @@ -1650,7 +1650,7 @@ ] }, { - "color": "#57bb00", + "color": "#cc0000", "domains": [ {"helix": 12, "forward": false, "start": 400, "end": 408}, {"helix": 11, "forward": true, "start": 400, "end": 416}, @@ -1658,7 +1658,7 @@ ] }, { - "color": "#888888", + "color": "#f7931e", "domains": [ {"helix": 14, "forward": false, "start": 400, "end": 408}, {"helix": 13, "forward": true, "start": 400, "end": 416}, diff --git a/examples/output_designs/1_staple_1_helix_origami.dna b/examples/output_designs/1_staple_1_helix_origami.dna index 5c06a41e..c940a532 100644 --- a/examples/output_designs/1_staple_1_helix_origami.dna +++ b/examples/output_designs/1_staple_1_helix_origami.dna @@ -9,7 +9,7 @@ ], "strands": [ { - "color": "#32b86c", + "color": "#f74308", "sequence": "?AGTTAGTT", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 9} diff --git a/examples/output_designs/1_staple_1_helix_origami_mismatches.dna b/examples/output_designs/1_staple_1_helix_origami_mismatches.dna index b0c3a6c1..d79aeea3 100644 --- a/examples/output_designs/1_staple_1_helix_origami_mismatches.dna +++ b/examples/output_designs/1_staple_1_helix_origami_mismatches.dna @@ -6,7 +6,7 @@ ], "strands": [ { - "color": "#aaaa00", + "color": "#f74308", "sequence": "ATTCTCTTGCTTTTTTCA", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 10, "insertions": [[2, 4], [8, 4]]} diff --git a/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna b/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna index 5c0ba069..3a814be1 100644 --- a/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna +++ b/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna @@ -10,7 +10,7 @@ ], "strands": [ { - "color": "#b8056c", + "color": "#f74308", "sequence": "?AGTTAGTT", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 9} diff --git a/examples/output_designs/1_staple_1_helix_origami_roll.dna b/examples/output_designs/1_staple_1_helix_origami_roll.dna index 3c186cb5..e41f6827 100644 --- a/examples/output_designs/1_staple_1_helix_origami_roll.dna +++ b/examples/output_designs/1_staple_1_helix_origami_roll.dna @@ -6,7 +6,7 @@ ], "strands": [ { - "color": "#007200", + "color": "#f74308", "sequence": "?AGTTAGTT", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 9} diff --git a/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna b/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna index 04a8d593..c9211bb4 100644 --- a/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna +++ b/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna @@ -83,7 +83,6 @@ "is_scaffold": true }, { - "color": "#aaaa00", "sequence": "CATAGTTAGCGTAACGATCTAAAGTTTTGTCG", "idt": {"name": "ST0[159]0[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -91,7 +90,6 @@ ] }, { - "color": "#b8056c", "sequence": "GGAAGGGAGACCAGTAATAAAAGGGACATTC", "idt": {"name": "ST23[144]23[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -99,7 +97,7 @@ ] }, { - "color": "#7300de", + "color": "#f7931e", "sequence": "TTCACGTTGAAAATCTTGCGAATAATAATTTT", "idt": {"name": "ST1[8]0[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -108,7 +106,6 @@ ] }, { - "color": "#f7931e", "sequence": "GCCTTTAAAGTGAGAATAGAAAGGAACAACTA", "idt": {"name": "ST1[48]0[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -117,7 +114,6 @@ ] }, { - "color": "#f74308", "sequence": "TTCGAGGTTTTGCTAAACAACTTTCAACAGT", "idt": {"name": "ST1[80]0[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -126,7 +122,6 @@ ] }, { - "color": "#57bb00", "sequence": "GATAGTTGAGACGTTAGTAAATGAATTTTCTG", "idt": {"name": "ST1[112]0[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -135,7 +130,6 @@ ] }, { - "color": "#32b86c", "sequence": "GTTTTGCTTGTAGCATTCCACAGACAGCCCT", "idt": {"name": "ST1[176]0[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -144,7 +138,6 @@ ] }, { - "color": "#333333", "sequence": "CGAGAGGGTGAGTTTCGTCACCAGTACAAACT", "idt": {"name": "ST1[208]0[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -153,7 +146,6 @@ ] }, { - "color": "#320096", "sequence": "AGGTGTATAAGCCCAATAGGAACCCATGTACC", "idt": {"name": "ST1[240]0[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -162,7 +154,6 @@ ] }, { - "color": "#03b6a2", "sequence": "CCGCCACCCAGAGCCACCACCCTCATTTTCA", "idt": {"name": "ST1[272]0[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -171,7 +162,7 @@ ] }, { - "color": "#03b6a2", + "color": "#cc0000", "sequence": "TCAGAACCGCCACCCTCTCAGAACCGCCACCC", "idt": {"name": "ST0[295]1[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -180,7 +171,6 @@ ] }, { - "color": "#333333", "sequence": "AAGGAATCCAAAAAAAAGGCTCCAGAGGCT", "idt": {"name": "ST0[31]2[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -190,7 +180,6 @@ ] }, { - "color": "#320096", "sequence": "TTCAGCGGTTGTATCGGTTTATCAAGACAGCA", "idt": {"name": "ST0[63]2[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -200,7 +189,6 @@ ] }, { - "color": "#03b6a2", "sequence": "TATGGGATGAATTTCTTAAACAGCCTTTTGCG", "idt": {"name": "ST0[95]2[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -210,7 +198,6 @@ ] }, { - "color": "#7300de", "sequence": "TCTTTCCCGCCGACAATGACAAGTCGCTGA", "idt": {"name": "ST0[127]2[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -220,7 +207,6 @@ ] }, { - "color": "#cc0000", "sequence": "ACTCCTCAATAACCGATATATTCGCAACCATC", "idt": {"name": "ST2[159]1[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -229,7 +215,6 @@ ] }, { - "color": "#888888", "sequence": "GCCCACGCAGAGAAGGATTAGGATAGGCTGAG", "idt": {"name": "ST1[144]2[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -238,7 +223,6 @@ ] }, { - "color": "#b8056c", "sequence": "ACAACGCCCAGTACCAGGCGGATAACCTATTA", "idt": {"name": "ST0[191]2[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -248,7 +232,6 @@ ] }, { - "color": "#007200", "sequence": "GTAACACTTGATATAAGTATAGTAAACAGT", "idt": {"name": "ST0[223]2[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -258,7 +241,6 @@ ] }, { - "color": "#cc0000", "sequence": "GGGATAGCCACCGTACTCAGGAGGCGGGGTCA", "idt": {"name": "ST0[255]2[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -268,7 +250,7 @@ ] }, { - "color": "#b8056c", + "color": "#57bb00", "sequence": "GAGGAAGTTTCCATTACTAAAGACTTTTTCAT", "idt": {"name": "ST3[8]2[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -277,7 +259,6 @@ ] }, { - "color": "#888888", "sequence": "CTACGAAGAGGGTAGCAACGGCTACAAAAGGA", "idt": {"name": "ST3[48]1[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -287,7 +268,6 @@ ] }, { - "color": "#32b86c", "sequence": "CAAAAGAAACCCTCAGCAGCGAAGCTTGCT", "idt": {"name": "ST3[80]1[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -297,7 +277,6 @@ ] }, { - "color": "#333333", "sequence": "CCCCAGCGAGGGAGTTAAAGGCCGTTGATACC", "idt": {"name": "ST3[112]1[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -307,7 +286,6 @@ ] }, { - "color": "#03b6a2", "sequence": "AGGCAGGTCATGAAAGTATTAAGTAGCGGG", "idt": {"name": "ST3[176]1[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -317,7 +295,6 @@ ] }, { - "color": "#7300de", "sequence": "AAACAAATCCCTGCCTATTTCGGAAGTGCCGT", "idt": {"name": "ST3[208]1[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -327,7 +304,6 @@ ] }, { - "color": "#aaaa00", "sequence": "GAAAGCGCAGTAACAGTGCCCGTACCCGGAAT", "idt": {"name": "ST3[240]1[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -337,7 +313,6 @@ ] }, { - "color": "#b8056c", "sequence": "TAAGCGTCGGTAATAAGTTTTAATTTAGTA", "idt": {"name": "ST3[272]1[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -347,7 +322,7 @@ ] }, { - "color": "#aaaa00", + "color": "#f74308", "sequence": "GATACAGGAGTGTACTATACATGGCTTTTGAT", "idt": {"name": "ST2[295]3[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -356,7 +331,6 @@ ] }, { - "color": "#7300de", "sequence": "TTGAGGAAACGGGTAAAATACGTTTGAAAG", "idt": {"name": "ST2[31]4[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -366,7 +340,6 @@ ] }, { - "color": "#aaaa00", "sequence": "TCGGAACGGCACCAACCTAAAACGCGGTCAAT", "idt": {"name": "ST2[63]4[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -376,7 +349,6 @@ ] }, { - "color": "#b8056c", "sequence": "GGATCGTCTACACTAAAACACTCATCCATGTT", "idt": {"name": "ST2[95]4[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -386,7 +358,6 @@ ] }, { - "color": "#007200", "sequence": "GGCTTGCATTATACCAAGCGCGCTGATAAA", "idt": {"name": "ST2[127]4[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -396,7 +367,6 @@ ] }, { - "color": "#57bb00", "sequence": "CAGAGCCGAGATTTGTATCATCGCAAACAAAG", "idt": {"name": "ST4[159]3[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -405,7 +375,6 @@ ] }, { - "color": "#320096", "sequence": "TACAACGGCCGCCAGCATTGACAGACCACCAC", "idt": {"name": "ST3[144]4[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -414,7 +383,6 @@ ] }, { - "color": "#f7931e", "sequence": "TTCTGAAACAGACGATTGGCCTTGCAGAGCCA", "idt": {"name": "ST2[191]4[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -424,7 +392,6 @@ ] }, { - "color": "#f74308", "sequence": "TAATGCCAAATCCTCATTAAAGTCAGAGCC", "idt": {"name": "ST2[223]4[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -434,7 +401,6 @@ ] }, { - "color": "#57bb00", "sequence": "GTGCCTTGAGTCTCTGAATTTACCCGGAACCA", "idt": {"name": "ST2[255]4[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -444,7 +410,7 @@ ] }, { - "color": "#cc0000", + "color": "#32b86c", "sequence": "CCAGGCGCATAGGCTGATGAACGGTGTACAGA", "idt": {"name": "ST5[8]4[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -453,7 +419,6 @@ ] }, { - "color": "#320096", "sequence": "TTGACAAGAACCGAACTGACCAACTAATGCCA", "idt": {"name": "ST5[48]3[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -463,7 +428,6 @@ ] }, { - "color": "#03b6a2", "sequence": "CAACGTAAGGAACGAGGCGCAGAAAAGAGG", "idt": {"name": "ST5[80]3[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -473,7 +437,6 @@ ] }, { - "color": "#7300de", "sequence": "GGCTTGCCGAAATCCGCGACCTGCTCTTTGAC", "idt": {"name": "ST5[112]3[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -483,7 +446,6 @@ ] }, { - "color": "#b8056c", "sequence": "GTCACCAAAGAGCCGCCACCAGAGAGGTTG", "idt": {"name": "ST5[176]3[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -493,7 +455,6 @@ ] }, { - "color": "#007200", "sequence": "AATCAGTATCAGAACCGCCACCCTATATTCAC", "idt": {"name": "ST5[208]3[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -503,7 +464,6 @@ ] }, { - "color": "#cc0000", "sequence": "AGCGTCAGACCGGAACCGCCTCCCCCAGAATG", "idt": {"name": "ST5[240]3[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -513,7 +473,6 @@ ] }, { - "color": "#f7931e", "sequence": "TTTTCGGTCATAATCAAAATCACGTTCCAG", "idt": {"name": "ST5[272]3[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -523,7 +482,7 @@ ] }, { - "color": "#007200", + "color": "#888888", "sequence": "GCGTTTGCCATCTTTTCATAGCCCCCTTATTA", "idt": {"name": "ST4[295]5[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -532,7 +491,6 @@ ] }, { - "color": "#007200", "sequence": "AGGACAGGCTGACCTTCATCAAATAAAACG", "idt": {"name": "ST4[31]6[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -542,7 +500,6 @@ ] }, { - "color": "#cc0000", "sequence": "CATAAGGGAACCGGATATTCATTAAGTCAGGA", "idt": {"name": "ST4[63]6[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -552,7 +509,6 @@ ] }, { - "color": "#f7931e", "sequence": "ACTTAGCCCAAAGCTGCTCATTCATATGCGAT", "idt": {"name": "ST4[95]6[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -562,7 +518,6 @@ ] }, { - "color": "#f74308", "sequence": "TTGTGTCCTGACGAGAAACACCTAATTTCA", "idt": {"name": "ST4[127]6[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -572,7 +527,6 @@ ] }, { - "color": "#333333", "sequence": "TAGCACCATGGGCTTGAGATGGTTAGAACGAG", "idt": {"name": "ST6[159]5[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -581,7 +535,6 @@ ] }, { - "color": "#aaaa00", "sequence": "TAGTAAATTTACCATTAGCAAGGCATCACCAG", "idt": {"name": "ST5[144]6[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -590,7 +543,6 @@ ] }, { - "color": "#888888", "sequence": "CCACCCTCTGAAACCATCGATAGCCTTGAGCC", "idt": {"name": "ST4[191]6[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -600,7 +552,6 @@ ] }, { - "color": "#32b86c", "sequence": "GCCACCCGCGACAGAATCAAGTTTCATTAA", "idt": {"name": "ST4[223]6[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -610,7 +561,6 @@ ] }, { - "color": "#333333", "sequence": "GAGCCACCACTGTAGCGCGTTTTCGAGGGAGG", "idt": {"name": "ST4[255]6[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -620,7 +570,7 @@ ] }, { - "color": "#f74308", + "color": "#320096", "sequence": "AGGTAGAAAGATTCATGGAACAACATTATTAC", "idt": {"name": "ST7[8]6[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -629,7 +579,6 @@ ] }, { - "color": "#aaaa00", "sequence": "ATTCAACTAGAAAAATCTACGTTAGAGTAATC", "idt": {"name": "ST7[48]5[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -639,7 +588,6 @@ ] }, { - "color": "#b8056c", "sequence": "GGAATTACCTGGCTCATTATACCCCCAAAT", "idt": {"name": "ST7[80]5[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -649,7 +597,6 @@ ] }, { - "color": "#007200", "sequence": "CATAACCCTCATTGTGAATTACCTGTGAATAA", "idt": {"name": "ST7[112]5[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -659,7 +606,6 @@ ] }, { - "color": "#f7931e", "sequence": "GTTAGCAAATTAGAGCCAGCAAACGGAAAC", "idt": {"name": "ST7[176]5[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -669,7 +615,6 @@ ] }, { - "color": "#f74308", "sequence": "TGGCAACATTATCACCGTCACCGAAGCACCGT", "idt": {"name": "ST7[208]5[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -679,7 +624,6 @@ ] }, { - "color": "#57bb00", "sequence": "ACGGAATAATATTGACGGAAATTATTGCCTTT", "idt": {"name": "ST7[240]5[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -689,7 +633,6 @@ ] }, { - "color": "#888888", "sequence": "GAAAATTCGACATTCAACCGATTATCGGCA", "idt": {"name": "ST7[272]5[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -699,7 +642,7 @@ ] }, { - "color": "#f7931e", + "color": "#333333", "sequence": "CCAAAGACAAAAGGGCATATGGTTTACCAGCG", "idt": {"name": "ST6[295]7[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -708,7 +651,6 @@ ] }, { - "color": "#f74308", "sequence": "AACTAACCAGTTGAGATTTAGGTCAAATGC", "idt": {"name": "ST6[31]8[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -718,7 +660,6 @@ ] }, { - "color": "#57bb00", "sequence": "CGTTGGGAAATGCAGATACATAACCGGAATCG", "idt": {"name": "ST6[63]8[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -728,7 +669,6 @@ ] }, { - "color": "#888888", "sequence": "TTTAAGAAGAGGCATAGTAAGAGCAAATGTTT", "idt": {"name": "ST6[95]8[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -738,7 +678,6 @@ ] }, { - "color": "#32b86c", "sequence": "ACTTTAATCGTTTACCAGACGAAAAAGAAG", "idt": {"name": "ST6[127]8[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -748,7 +687,6 @@ ] }, { - "color": "#7300de", "sequence": "GGCATGATAGCGAGAGGCTTTTGCCGATAAAA", "idt": {"name": "ST8[159]7[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -757,7 +695,6 @@ ] }, { - "color": "#cc0000", "sequence": "ACCAAAATTAAGACTCCTTATTACAAAGAACT", "idt": {"name": "ST7[144]8[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -766,7 +703,6 @@ ] }, { - "color": "#320096", "sequence": "ATTTGGGAACGTAGAAAATACATACCGAGGAA", "idt": {"name": "ST6[191]8[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -776,7 +712,6 @@ ] }, { - "color": "#03b6a2", "sequence": "AGGTGAATATAAAAGAAACGCACAGATAGC", "idt": {"name": "ST6[223]8[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -786,7 +721,6 @@ ] }, { - "color": "#7300de", "sequence": "GAAGGTAAAGTTTATTTTGTCACAATCTTACC", "idt": {"name": "ST6[255]8[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -796,7 +730,7 @@ ] }, { - "color": "#888888", + "color": "#7300de", "sequence": "ATGACCATAAATCAAAAGTTCAGAAAACGAGA", "idt": {"name": "ST9[8]8[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -805,7 +739,6 @@ ] }, { - "color": "#cc0000", "sequence": "TATAGTCAATTCATTGAATCCCCCAATACCAC", "idt": {"name": "ST9[48]7[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -815,7 +748,6 @@ ] }, { - "color": "#f7931e", "sequence": "AAGATTAATAGCGTCCAATACTGGCCAAAA", "idt": {"name": "ST9[80]7[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -825,7 +757,6 @@ ] }, { - "color": "#f74308", "sequence": "ATCGCGTTAGAGGGGGTAATAGTAAACACTAT", "idt": {"name": "ST9[112]7[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -835,7 +766,6 @@ ] }, { - "color": "#888888", "sequence": "AAAAACAGATAACGGAATACCCAGCAGTAT", "idt": {"name": "ST9[176]7[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -845,7 +775,6 @@ ] }, { - "color": "#32b86c", "sequence": "AACTGAACAGTTACCAGAAGGAAACATAAAGG", "idt": {"name": "ST9[208]7[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -855,7 +784,6 @@ ] }, { - "color": "#333333", "sequence": "ATTGAGCGTTTTAAGAAAAGTAAGAAGACACC", "idt": {"name": "ST9[240]7[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -865,7 +793,6 @@ ] }, { - "color": "#320096", "sequence": "AAGAATTGGAAATAGCAATAGCTATCAATA", "idt": {"name": "ST9[272]7[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -875,7 +802,7 @@ ] }, { - "color": "#57bb00", + "color": "#03b6a2", "sequence": "AAGAGCAAGAAACAATAGTTAAGCCCAATAAT", "idt": {"name": "ST8[295]9[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -884,7 +811,6 @@ ] }, { - "color": "#32b86c", "sequence": "TTTAAACAATCAGGTCTTTACCTCAACATG", "idt": {"name": "ST8[31]10[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -894,7 +820,6 @@ ] }, { - "color": "#333333", "sequence": "TCATAAATGAAGCAAAGCGGATTGTAGAGCTT", "idt": {"name": "ST8[63]10[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -904,7 +829,6 @@ ] }, { - "color": "#320096", "sequence": "AGACTGGAGAGGAAGCCCGAAAGATTTTGATA", "idt": {"name": "ST8[95]10[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -914,7 +838,6 @@ ] }, { - "color": "#03b6a2", "sequence": "TTTTGCCTTAATTCGAGCTTCAGTCAGGAT", "idt": {"name": "ST8[127]10[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -924,7 +847,6 @@ ] }, { - "color": "#007200", "sequence": "AAAATAGCAAGCAAACTCCAACAGAAGCGAAC", "idt": {"name": "ST10[159]9[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -933,7 +855,6 @@ ] }, { - "color": "#57bb00", "sequence": "CAGACCGGAGCCTTTACAGAGAGACAAAAATG", "idt": {"name": "ST9[144]10[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -942,7 +863,6 @@ ] }, { - "color": "#aaaa00", "sequence": "ACGCAATAGGAAGCGCATTAGACGTCCAAATA", "idt": {"name": "ST8[191]10[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -952,7 +872,6 @@ ] }, { - "color": "#b8056c", "sequence": "CGAACAAACCCTGAACAAAGTCACAAAATA", "idt": {"name": "ST8[223]10[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -962,7 +881,6 @@ ] }, { - "color": "#007200", "sequence": "GAAGCCCTCTAATATCAGAGAGATCGAGCGTC", "idt": {"name": "ST8[255]10[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -972,7 +890,7 @@ ] }, { - "color": "#333333", + "color": "#b8056c", "sequence": "GGTGTCTGGAAGTTTCTATGCAACTAAAGTAC", "idt": {"name": "ST11[8]10[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -981,7 +899,6 @@ ] }, { - "color": "#57bb00", "sequence": "AATTCTGCAATATAATGCTGTAGCCTGACTAT", "idt": {"name": "ST11[48]9[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -991,7 +908,6 @@ ] }, { - "color": "#888888", "sequence": "ATTAGATATTTTTGCGGATGGCTCATCAAA", "idt": {"name": "ST11[80]9[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1001,7 +917,6 @@ ] }, { - "color": "#32b86c", "sequence": "GTTTAGCTTACCTTTAATTGCTCCCTTCAAAT", "idt": {"name": "ST11[112]9[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1011,7 +926,6 @@ ] }, { - "color": "#320096", "sequence": "ATCAGATATTTTTTGTTTAACGTATAACAT", "idt": {"name": "ST11[176]9[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1021,7 +935,6 @@ ] }, { - "color": "#03b6a2", "sequence": "GAACGCGAATATTATTTATCCCAAGGAGAATT", "idt": {"name": "ST11[208]9[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1031,7 +944,6 @@ ] }, { - "color": "#7300de", "sequence": "TTGCGGGAGCCTAATTTGCCAGTTAGAGGGTA", "idt": {"name": "ST11[240]9[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1041,7 +953,6 @@ ] }, { - "color": "#aaaa00", "sequence": "TTAGTTGCTCTTACCAACGCTAAAACCCAC", "idt": {"name": "ST11[272]9[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1051,7 +962,7 @@ ] }, { - "color": "#32b86c", + "color": "#aaaa00", "sequence": "ACAATTTTATCCTGAATATTTTGCACCCAGCT", "idt": {"name": "ST10[295]11[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1060,7 +971,6 @@ ] }, { - "color": "#03b6a2", "sequence": "TTTTAAAATTCCATATAACAGTGTTGTACC", "idt": {"name": "ST10[31]12[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1070,7 +980,6 @@ ] }, { - "color": "#7300de", "sequence": "AATTGCTGGAACGAGTAGATTTAGGCAATAAA", "idt": {"name": "ST10[63]12[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1080,7 +989,6 @@ ] }, { - "color": "#aaaa00", "sequence": "AGAGGTCACATTTCGCAAATGGTCTACAGGCA", "idt": {"name": "ST10[95]12[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1090,7 +998,6 @@ ] }, { - "color": "#b8056c", "sequence": "TAGAGAGATATTTTCATTTGGGAATAGTAG", "idt": {"name": "ST10[127]12[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1100,7 +1007,6 @@ ] }, { - "color": "#f74308", "sequence": "AGGAATCATGGCATCAATTCTACTGCGCGAGC", "idt": {"name": "ST12[159]11[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1109,7 +1015,6 @@ ] }, { - "color": "#333333", "sequence": "TGAAAAGGTTACCGCGCCCAATAGTTCATCGT", "idt": {"name": "ST11[144]12[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1118,7 +1023,6 @@ ] }, { - "color": "#cc0000", "sequence": "AGAAACGATAGAAGGCTTATCCGGACTCATCG", "idt": {"name": "ST10[191]12[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1128,7 +1032,6 @@ ] }, { - "color": "#f7931e", "sequence": "AACAGCCGGCGTTTTAGCGAACTTCCAAGA", "idt": {"name": "ST10[223]12[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1138,7 +1041,6 @@ ] }, { - "color": "#f74308", "sequence": "TTTCCAGAGGTTTTGAAGCCTTAAACCAATCA", "idt": {"name": "ST10[255]12[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1148,7 +1050,7 @@ ] }, { - "color": "#03b6a2", + "color": "#cc0000", "sequence": "CTTTTGCGGGAGAAGCTTATGACCCTGTAATA", "idt": {"name": "ST13[8]12[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1157,7 +1059,6 @@ ] }, { - "color": "#333333", "sequence": "AATTTTTAGCATAAAGCTAAATCGTGATTCCC", "idt": {"name": "ST13[48]11[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1167,7 +1068,6 @@ ] }, { - "color": "#320096", "sequence": "AATGCCTGAATTAGCAAAATTAATTTGACC", "idt": {"name": "ST13[80]11[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1177,7 +1077,6 @@ ] }, { - "color": "#03b6a2", "sequence": "AAGGGTGAAACATCCAATAAATCAAATAACCT", "idt": {"name": "ST13[112]11[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1187,7 +1086,6 @@ ] }, { - "color": "#aaaa00", "sequence": "TAAAGTACCAAGCCGTTTTTATTCAAGCAA", "idt": {"name": "ST13[176]11[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1197,7 +1095,6 @@ ] }, { - "color": "#b8056c", "sequence": "CCAGACGATTAAACCAAGTACCGCTATTCTAA", "idt": {"name": "ST13[208]11[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1207,7 +1104,6 @@ ] }, { - "color": "#007200", "sequence": "TAATGCAGCTGTCTTTCCTTATCACTCCCGAC", "idt": {"name": "ST13[240]11[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1217,7 +1113,6 @@ ] }, { - "color": "#cc0000", "sequence": "GATAAGTCTACGAGCATGTAGAAATCAAGA", "idt": {"name": "ST13[272]11[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1227,7 +1122,7 @@ ] }, { - "color": "#320096", + "color": "#007200", "sequence": "ATATCCCATCCTAATTCTGAACAAGAAAAATA", "idt": {"name": "ST12[295]13[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1236,7 +1131,6 @@ ] }, { - "color": "#b8056c", "sequence": "AAAAACACTTTATTTCAACGCAGAATCGAT", "idt": {"name": "ST12[31]14[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1246,7 +1140,6 @@ ] }, { - "color": "#007200", "sequence": "GCCTCAGAGAACCCTCATATATTTGGTCATTG", "idt": {"name": "ST12[63]14[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1256,7 +1149,6 @@ ] }, { - "color": "#cc0000", "sequence": "AGGCAAAGAGTAATGTGTAGGTAAGCTATTTT", "idt": {"name": "ST12[95]14[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1266,7 +1158,6 @@ ] }, { - "color": "#f7931e", "sequence": "TAGCATTGAAAGGCCGGAGACATCTAGCTG", "idt": {"name": "ST12[127]14[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1276,7 +1167,6 @@ ] }, { - "color": "#32b86c", "sequence": "GAGGCATTTATGATATTCAACCGTGTCAAATC", "idt": {"name": "ST14[159]13[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1285,7 +1175,6 @@ ] }, { - "color": "#7300de", "sequence": "ACCATCAATTCGAGCCAGTAATAATTTAGGCA", "idt": {"name": "ST13[144]14[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1294,7 +1183,6 @@ ] }, { - "color": "#57bb00", "sequence": "AGAACAAGCGACAAAAGGTAAAGTAATCGCCA", "idt": {"name": "ST12[191]14[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1304,7 +1192,6 @@ ] }, { - "color": "#888888", "sequence": "ACGGGTACGACAATAAACAACAAGCCAACG", "idt": {"name": "ST12[223]14[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1314,7 +1201,6 @@ ] }, { - "color": "#32b86c", "sequence": "ATAATCGGAACGCGCCTGTTTATCCATATGCG", "idt": {"name": "ST12[255]14[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1324,7 +1210,7 @@ ] }, { - "color": "#aaaa00", + "color": "#f74308", "sequence": "TGTCAATCATATGTACAATCGTAAAACTAGCA", "idt": {"name": "ST15[8]14[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1333,7 +1219,6 @@ ] }, { - "color": "#7300de", "sequence": "CCAAAAACTCTGGAGCAAACAAGAAGGATAAA", "idt": {"name": "ST15[48]13[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1343,7 +1228,6 @@ ] }, { - "color": "#aaaa00", "sequence": "TTAAATTGCTACAAAGGCTATCATAAATGC", "idt": {"name": "ST15[80]13[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1353,7 +1237,6 @@ ] }, { - "color": "#b8056c", "sequence": "TCGCATTAAATGCCGGAGAGGGTAAGATTCAA", "idt": {"name": "ST15[112]13[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1363,7 +1246,6 @@ ] }, { - "color": "#cc0000", "sequence": "AACGCGAGAACGCCAACATGTAAGAGAATA", "idt": {"name": "ST15[176]13[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1373,7 +1255,6 @@ ] }, { - "color": "#f7931e", "sequence": "TTAATTTCGTAGGGCTTAATTGAGAATTCTGT", "idt": {"name": "ST15[208]13[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1383,7 +1264,6 @@ ] }, { - "color": "#f74308", "sequence": "TTTGAAATATTCTTACCAGTATAATGTTCAGC", "idt": {"name": "ST15[240]13[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1393,7 +1273,6 @@ ] }, { - "color": "#57bb00", "sequence": "GTTAAATAAAGCCTGTTTAGTATAACAATA", "idt": {"name": "ST15[272]13[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1403,7 +1282,7 @@ ] }, { - "color": "#7300de", + "color": "#f7931e", "sequence": "TCATAATTACTAGAAAAGAATAAACACCGGAA", "idt": {"name": "ST14[295]15[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1412,7 +1291,6 @@ ] }, { - "color": "#f7931e", "sequence": "GAACGGTCCCGGTTGATAATCAGCGGATTG", "idt": {"name": "ST14[31]16[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1422,7 +1300,6 @@ ] }, { - "color": "#f74308", "sequence": "CCTGAGAGAGGAAGATTGTATAAGACAACCCG", "idt": {"name": "ST14[63]16[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1432,7 +1309,6 @@ ] }, { - "color": "#57bb00", "sequence": "TGAGAGATTAAACGTTAATATTTTAGCTTTCA", "idt": {"name": "ST14[95]16[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1442,7 +1318,6 @@ ] }, { - "color": "#888888", "sequence": "ATAAATTAATTTTTGTTAAATCAAAATAAT", "idt": {"name": "ST14[127]16[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1452,7 +1327,6 @@ ] }, { - "color": "#03b6a2", "sequence": "ATGCTGATAATAGGAACGCCATCAAGCTCATT", "idt": {"name": "ST16[159]15[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1461,7 +1335,6 @@ ] }, { - "color": "#007200", "sequence": "TTTTAACCGCAAATCCAATCGCAAATATGTAA", "idt": {"name": "ST15[144]16[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1470,7 +1343,6 @@ ] }, { - "color": "#333333", "sequence": "TATTTAACAAAACTTTTTCAAATATAACCTCC", "idt": {"name": "ST14[191]16[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1480,7 +1352,6 @@ ] }, { - "color": "#320096", "sequence": "CTCAACAATCTTCTGACCTAAATCAAAATC", "idt": {"name": "ST14[223]16[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1490,7 +1361,6 @@ ] }, { - "color": "#03b6a2", "sequence": "TTATACAAACCGACCGTGTGATAATAAGACGC", "idt": {"name": "ST14[255]16[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1500,7 +1370,7 @@ ] }, { - "color": "#007200", + "color": "#888888", "sequence": "GGTGTAGATGGGCGCATGGGATAGGTCACGTT", "idt": {"name": "ST17[8]16[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1509,7 +1379,6 @@ ] }, { - "color": "#007200", "sequence": "TGAGGGGATCCGTGGGAACAAACGGAAAAGCC", "idt": {"name": "ST17[48]15[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1519,7 +1388,6 @@ ] }, { - "color": "#cc0000", "sequence": "AGATCGCAAAATGTGAGCGAGTACAAATAT", "idt": {"name": "ST17[80]15[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1529,7 +1397,6 @@ ] }, { - "color": "#f7931e", "sequence": "TTCTGGTGTGGCCTTCCTGTAGCCGTTAAAAT", "idt": {"name": "ST17[112]15[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1539,7 +1406,6 @@ ] }, { - "color": "#57bb00", "sequence": "ATTACATTTTGGGTTATATAACTGACAAAG", "idt": {"name": "ST17[176]15[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1549,7 +1415,6 @@ ] }, { - "color": "#888888", "sequence": "TTTTAATGTGAGAGACTACCTTTTTATTTTAG", "idt": {"name": "ST17[208]15[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1559,7 +1424,6 @@ ] }, { - "color": "#32b86c", "sequence": "TGTGAGTGGTCAATAGTGAATTTATTTAATGG", "idt": {"name": "ST17[240]15[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1569,7 +1433,6 @@ ] }, { - "color": "#333333", "sequence": "TCGCTATTAGCGATAGCTTAGATATAAGGC", "idt": {"name": "ST17[272]15[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1579,7 +1442,7 @@ ] }, { - "color": "#b8056c", + "color": "#57bb00", "sequence": "GAATCCTTGAAAACATAATTAATTTTCCCTTA", "idt": {"name": "ST16[295]17[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1588,7 +1451,6 @@ ] }, { - "color": "#888888", "sequence": "ACCGTAATCGTAACCGTGCATCTTTCCCAG", "idt": {"name": "ST16[31]18[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1598,7 +1460,6 @@ ] }, { - "color": "#32b86c", "sequence": "TCGGATTCCGACGACAGTATCGGCTGCAAGGC", "idt": {"name": "ST16[63]18[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1608,7 +1469,6 @@ ] }, { - "color": "#333333", "sequence": "TCAACATTCTCCAGCCAGCTTTCCTATTACGC", "idt": {"name": "ST16[95]18[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1618,7 +1478,6 @@ ] }, { - "color": "#320096", "sequence": "TCGCGTCCCGGAAACCAGGCAATGGGAAGG", "idt": {"name": "ST16[127]18[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1628,7 +1487,6 @@ ] }, { - "color": "#b8056c", "sequence": "TGATGAAACAGGCTGCGCAACTGTAGCGCCAT", "idt": {"name": "ST18[159]17[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1637,7 +1495,6 @@ ] }, { - "color": "#f74308", "sequence": "TCGCCATTCAAACATCAAGAAAACAAAGAAGA", "idt": {"name": "ST17[144]18[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1646,7 +1503,6 @@ ] }, { - "color": "#7300de", "sequence": "GGCTTAGGTAACAATTTCATTTGAAGGCGAAT", "idt": {"name": "ST16[191]18[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1656,7 +1512,6 @@ ] }, { - "color": "#aaaa00", "sequence": "ATAGGTCGAAACAGTACATAAAGCTTTGAA", "idt": {"name": "ST16[223]18[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1666,7 +1521,6 @@ ] }, { - "color": "#b8056c", "sequence": "TGAGAAGAAATAACCTTGCTTCTGATCGGGAG", "idt": {"name": "ST16[255]18[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1676,7 +1530,7 @@ ] }, { - "color": "#f7931e", + "color": "#333333", "sequence": "CAGTGCCAAGCTTGCAGTTGTAAAACGACGGC", "idt": {"name": "ST19[8]18[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1685,7 +1539,6 @@ ] }, { - "color": "#f74308", "sequence": "ATCCCCGGTGGGTAACGCCAGGGTTGCCAGTT", "idt": {"name": "ST19[48]17[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1695,7 +1548,6 @@ ] }, { - "color": "#57bb00", "sequence": "ATGGTCATGAAAGGGGGATGTGCCTCAGGA", "idt": {"name": "ST19[80]17[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1705,7 +1557,6 @@ ] }, { - "color": "#888888", "sequence": "ATCCGCTCGTGCGGGCCTCTTCGCGGCACCGC", "idt": {"name": "ST19[112]17[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1715,7 +1566,6 @@ ] }, { - "color": "#333333", "sequence": "TAATCCTGTCAATTACCTGAGCAAAAATTA", "idt": {"name": "ST19[176]17[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1725,7 +1575,6 @@ ] }, { - "color": "#320096", "sequence": "AATGGAAGTTACAAAATCGCGCAGATTACCTT", "idt": {"name": "ST19[208]17[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1735,7 +1584,6 @@ ] }, { - "color": "#03b6a2", "sequence": "TTATTTGCACGGATTCGCCTGATTTCAATATA", "idt": {"name": "ST19[240]17[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1745,7 +1593,6 @@ ] }, { - "color": "#7300de", "sequence": "TGCGTAGAAACAGTACCTTTTACTAAATCG", "idt": {"name": "ST19[272]17[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1755,7 +1602,7 @@ ] }, { - "color": "#cc0000", + "color": "#32b86c", "sequence": "CAGATGAATATACAGTTTTTCAGGTTTAACGT", "idt": {"name": "ST18[295]19[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1764,7 +1611,6 @@ ] }, { - "color": "#320096", "sequence": "TCACGACTGCCTGCAGGTCGACATCGGCCA", "idt": {"name": "ST18[31]20[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1774,7 +1620,6 @@ ] }, { - "color": "#03b6a2", "sequence": "GATTAAGTGTACCGAGCTCGAATTCGGGAAAC", "idt": {"name": "ST18[63]20[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1784,7 +1629,6 @@ ] }, { - "color": "#7300de", "sequence": "CAGCTGGCAGCTGTTTCCTGTGTGATTGCGTT", "idt": {"name": "ST18[95]20[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1794,7 +1638,6 @@ ] }, { - "color": "#aaaa00", "sequence": "GCGATCGACAATTCCACACAACGGGTGCCT", "idt": {"name": "ST18[127]20[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1804,7 +1647,6 @@ ] }, { - "color": "#f7931e", "sequence": "CTGATTATTAAAGTGTAAAGCCTGATACGAGC", "idt": {"name": "ST20[159]19[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1813,7 +1655,6 @@ ] }, { - "color": "#32b86c", "sequence": "CGGAAGCACAGATGATGGCAATTCTCATATTC", "idt": {"name": "ST19[144]20[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1822,7 +1663,6 @@ ] }, { - "color": "#007200", "sequence": "TATTCATTATTGTTTGGATTATACAAAGAAAC", "idt": {"name": "ST18[191]20[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1832,7 +1672,6 @@ ] }, { - "color": "#cc0000", "sequence": "TACCAAGGGTTAGAACCTACCAAAGTTTGA", "idt": {"name": "ST18[223]20[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1842,7 +1681,6 @@ ] }, { - "color": "#f7931e", "sequence": "AAACAATAACGTAAAACAGAAATATAAATCCT", "idt": {"name": "ST18[255]20[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1852,7 +1690,7 @@ ] }, { - "color": "#57bb00", + "color": "#03b6a2", "sequence": "GTATTGGGCGCCAGGGGGGAGAGGCGGTTTGC", "idt": {"name": "ST21[8]20[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1861,7 +1699,6 @@ ] }, { - "color": "#32b86c", "sequence": "ACGGGCAACCAGCTGCATTAATGATCTAGAGG", "idt": {"name": "ST21[48]19[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1871,7 +1708,6 @@ ] }, { - "color": "#333333", "sequence": "GGCCCTGATGCCCGCTTTCCAGTCGTAATC", "idt": {"name": "ST21[80]19[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1881,7 +1717,6 @@ ] }, { - "color": "#320096", "sequence": "CTGGTTTGGAGCTAACTCACATTAAAATTGTT", "idt": {"name": "ST21[112]19[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1891,7 +1726,6 @@ ] }, { - "color": "#7300de", "sequence": "GTTGGCAAGGAGCGGAATTATCAATCAATA", "idt": {"name": "ST21[176]19[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1901,7 +1735,6 @@ ] }, { - "color": "#aaaa00", "sequence": "AAGGTTATTATCATTTTGCGGAACTTCTGAAT", "idt": {"name": "ST21[208]19[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1911,7 +1744,6 @@ ] }, { - "color": "#b8056c", "sequence": "ACAACTAAACGTTATTAATTTTAATATCAAAA", "idt": {"name": "ST21[240]19[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1921,7 +1753,6 @@ ] }, { - "color": "#007200", "sequence": "ATACATTTTTCGACAACTCGTATAAGAAAT", "idt": {"name": "ST21[272]19[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1931,7 +1762,7 @@ ] }, { - "color": "#f74308", + "color": "#320096", "sequence": "TAGACTTTACAAACAAGAGGATTTAGAAGTAT", "idt": {"name": "ST20[295]21[295]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1940,7 +1771,6 @@ ] }, { - "color": "#aaaa00", "sequence": "ACGCGCGTGGTTTTTCTTTTCAGTCAAAGG", "idt": {"name": "ST20[31]22[32]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1950,7 +1780,6 @@ ] }, { - "color": "#b8056c", "sequence": "CTGTCGTGCAGCTGATTGCCCTTCAGAGTCCA", "idt": {"name": "ST20[63]22[64]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1960,7 +1789,6 @@ ] }, { - "color": "#007200", "sequence": "GCGCTCACGAGAGTTGCAGCAAGCATAGGGTT", "idt": {"name": "ST20[95]22[96]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1970,7 +1798,6 @@ ] }, { - "color": "#cc0000", "sequence": "AATGAGTCCCCAGCAGGCGAAAAATCCCTT", "idt": {"name": "ST20[127]22[128]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1980,7 +1807,6 @@ ] }, { - "color": "#888888", "sequence": "AAATATCAGTTCCGAAATCGGCAAATCCTGTT", "idt": {"name": "ST22[159]21[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1989,7 +1815,6 @@ ] }, { - "color": "#03b6a2", "sequence": "TGATGGTGAACCCTCAATCAATATTGAACCTC", "idt": {"name": "ST21[144]22[160]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1998,7 +1823,6 @@ ] }, { - "color": "#f74308", "sequence": "CACCAGAAATCAACAGTTGAAAGGAGCAAATG", "idt": {"name": "ST20[191]22[192]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2008,7 +1832,6 @@ ] }, { - "color": "#57bb00", "sequence": "GTAACATCTAAAATATCTTTAGCGCCTGCA", "idt": {"name": "ST20[223]22[224]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2018,7 +1841,6 @@ ] }, { - "color": "#888888", "sequence": "TTGCCCGATAGATTAGAGCCGTCATAAAACAG", "idt": {"name": "ST20[255]22[256]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2028,7 +1850,7 @@ ] }, { - "color": "#32b86c", + "color": "#aaaa00", "sequence": "ATGGCCCACTACGTGAACCGTCTATCAGGGCG", "idt": {"name": "ST23[8]22[8]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2037,7 +1859,6 @@ ] }, { - "color": "#cc0000", "sequence": "GCGAAAAACCATCACCCAAATCAAGTTTTT", "idt": {"name": "ST22[31]23[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2046,7 +1867,6 @@ ] }, { - "color": "#03b6a2", "sequence": "TGGGGTCGGAACGTGGACTCCAACCCAGTGAG", "idt": {"name": "ST23[48]21[47]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2056,7 +1876,6 @@ ] }, { - "color": "#f7931e", "sequence": "CTATTAAAAGGTGCCGTAAAGCACTAAATCG", "idt": {"name": "ST22[63]23[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2065,7 +1884,6 @@ ] }, { - "color": "#7300de", "sequence": "GAACCCTATTCCAGTTTGGAACAACCGCCT", "idt": {"name": "ST23[80]21[79]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2075,7 +1893,6 @@ ] }, { - "color": "#f74308", "sequence": "GAGTGTTGAAGGGAGCCCCCGATTTAGAGCTT", "idt": {"name": "ST22[95]23[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2084,7 +1901,6 @@ ] }, { - "color": "#aaaa00", "sequence": "GACGGGGAAAAAGAATAGCCCGAGGGTCCACG", "idt": {"name": "ST23[112]21[111]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2094,7 +1910,6 @@ ] }, { - "color": "#57bb00", "sequence": "ATAAATCAAGCCGGCGAACGTGGCGAGAAA", "idt": {"name": "ST22[127]23[143]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2103,7 +1918,6 @@ ] }, { - "color": "#007200", "sequence": "TGGCCAACAAAGCATCACCTTGCCTGGTCA", "idt": {"name": "ST23[176]21[175]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2113,7 +1927,6 @@ ] }, { - "color": "#32b86c", "sequence": "AAAAATCTAGAGATAGAACCCTTCTGACCTGA", "idt": {"name": "ST22[191]23[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2122,7 +1935,6 @@ ] }, { - "color": "#cc0000", "sequence": "AAGCGTAACACGCTGAGAGCCAGCAATTGAGG", "idt": {"name": "ST23[208]21[207]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2132,7 +1944,6 @@ ] }, { - "color": "#333333", "sequence": "ACAGTGCGAATACGTGGCACAGACAATATT", "idt": {"name": "ST22[223]23[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2141,7 +1952,6 @@ ] }, { - "color": "#f7931e", "sequence": "TTTGAATGCGGTCAGTATTAACACGAGCACTA", "idt": {"name": "ST23[240]21[239]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2151,7 +1961,6 @@ ] }, { - "color": "#320096", "sequence": "AGGTGAGGGCTATTAGTCTTTAATGCGCGAA", "idt": {"name": "ST22[255]23[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2160,7 +1969,6 @@ ] }, { - "color": "#f74308", "sequence": "CTGATAGCACCACCAGCAGAAGAATAGATA", "idt": {"name": "ST23[272]21[271]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2170,7 +1978,7 @@ ] }, { - "color": "#888888", + "color": "#7300de", "sequence": "TAAAAATACCGAACGACCTAAAACATCGCCAT", "idt": {"name": "ST22[295]23[295]", "scale": "25nm", "purification": "STD"}, "domains": [ diff --git a/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna b/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna index e5d9d70f..ca6f8090 100644 --- a/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna +++ b/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna @@ -7,7 +7,7 @@ ], "strands": [ { - "color": "#320096", + "color": "#f74308", "domains": [ {"helix": 0, "forward": false, "start": 0, "end": 4}, {"helix": 1, "forward": true, "start": 0, "end": 8}, @@ -15,7 +15,7 @@ ] }, { - "color": "#03b6a2", + "color": "#57bb00", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 8} ] diff --git a/examples/output_designs/2_staple_2_helix_modifications.dna b/examples/output_designs/2_staple_2_helix_modifications.dna index 72a00094..c7ea1288 100644 --- a/examples/output_designs/2_staple_2_helix_modifications.dna +++ b/examples/output_designs/2_staple_2_helix_modifications.dna @@ -6,23 +6,17 @@ {"grid_position": [0, 1]} ], "modifications_in_design": { - "/iCy5/": { - "display_text": "Cy5", - "idt_text": "/iCy5/", - "display_connector": false, - "location": "internal" - }, - "/5Cy5/": { - "display_text": "Cy5", - "idt_text": "/5Cy5/", + "/3Cy3Sp/": { + "display_text": "Cy3", + "idt_text": "/3Cy3Sp/", "display_connector": false, - "location": "5'" + "location": "3'" }, - "/iCy3/": { - "display_text": "Cy3", - "idt_text": "/iCy3/", + "/3Bio/": { + "display_text": "B", + "idt_text": "/3Bio/", "display_connector": false, - "location": "internal" + "location": "3'" }, "/iBiodT/": { "display_text": "B", @@ -31,23 +25,29 @@ "location": "internal", "allowed_bases": ["T"] }, - "/5Biosg/": { - "display_text": "B", - "idt_text": "/5Biosg/", + "/iCy3/": { + "display_text": "Cy3", + "idt_text": "/iCy3/", + "display_connector": false, + "location": "internal" + }, + "/5Cy5/": { + "display_text": "Cy5", + "idt_text": "/5Cy5/", "display_connector": false, "location": "5'" }, - "/3Cy3Sp/": { - "display_text": "Cy3", - "idt_text": "/3Cy3Sp/", + "/iCy5/": { + "display_text": "Cy5", + "idt_text": "/iCy5/", "display_connector": false, - "location": "3'" + "location": "internal" }, - "/3Bio/": { + "/5Biosg/": { "display_text": "B", - "idt_text": "/3Bio/", + "idt_text": "/5Biosg/", "display_connector": false, - "location": "3'" + "location": "5'" } }, "strands": [ @@ -61,7 +61,7 @@ ] }, { - "color": "#7300de", + "color": "#f74308", "sequence": "AGTTAGTTAGTTAGTTTTAGTTAGTTAGTT", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[2, 1]]}, @@ -72,7 +72,7 @@ "internal_modifications": {"9": "/iCy3/", "10": "/iBiodT/", "11": "/iCy3/", "12": "/iCy5/", "4": "/iCy3/", "26": "/iCy5/"} }, { - "color": "#aaaa00", + "color": "#57bb00", "sequence": "TTAGTTAGTTAGTTAGTAGTTAGTTAGTTAG", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[29, 1]]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna b/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna index 46798974..b04218ba 100644 --- a/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna +++ b/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna @@ -7,7 +7,7 @@ ], "strands": [ { - "color": "#b8056c", + "color": "#f74308", "sequence": "TTTG", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 3, "deletions": [1]}, @@ -15,7 +15,7 @@ ] }, { - "color": "#007200", + "color": "#57bb00", "sequence": "GAAC", "domains": [ {"helix": 0, "forward": false, "start": 3, "end": 6, "deletions": [4]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions.dna b/examples/output_designs/2_staple_2_helix_origami_deletions.dna index c438c557..d4a07656 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions.dna @@ -7,7 +7,7 @@ ], "strands": [ { - "color": "#cc0000", + "color": "#f74308", "sequence": "GTTAGTTAGTTAGTTTAGTTAGTTAGTTA", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12]}, @@ -15,7 +15,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "AGTTAGTTAGTTAGTGTTAGTTAGTTAGTT", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna index dcaee9aa..a186cda3 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna @@ -26,7 +26,7 @@ "is_scaffold": true }, { - "color": "#888888", + "color": "#f74308", "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", "domains": [ {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, @@ -34,7 +34,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", "domains": [ {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna index e07fb076..f3267f9d 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna @@ -15,7 +15,7 @@ }, "strands": [ { - "color": "#333333", + "color": "#f74308", "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", "domains": [ {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, @@ -23,7 +23,7 @@ ] }, { - "color": "#320096", + "color": "#57bb00", "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", "domains": [ {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna index 42ad6256..efb1f765 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna @@ -17,14 +17,14 @@ "is_scaffold": true }, { - "color": "#7300de", + "color": "#f74308", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, {"helix": 0, "forward": false, "start": 0, "end": 16, "deletions": [11, 12], "insertions": [[6, 1]]} ] }, { - "color": "#aaaa00", + "color": "#57bb00", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, {"helix": 1, "forward": true, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} diff --git a/examples/output_designs/3_helix_deletions_insertions.dna b/examples/output_designs/3_helix_deletions_insertions.dna index ad5ae76e..f065f31b 100644 --- a/examples/output_designs/3_helix_deletions_insertions.dna +++ b/examples/output_designs/3_helix_deletions_insertions.dna @@ -19,7 +19,7 @@ "is_scaffold": true }, { - "color": "#b8056c", + "color": "#f74308", "sequence": "TTAGTTAGTTAGTTAGTTTAGTTAGTTAGTTAG", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, @@ -27,7 +27,7 @@ ] }, { - "color": "#007200", + "color": "#57bb00", "sequence": "TTAGTTAGTTAGTTAGTAGTTAGTTAGTTAGTTAGT", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, @@ -35,53 +35,53 @@ ] }, { - "color": "#cc0000", + "color": "#888888", "sequence": "AACTAACTAACTAACT", "domains": [ {"helix": 1, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#f7931e", + "color": "#32b86c", "sequence": "GGTAGGTAGGTAGGTA", "domains": [ {"helix": 1, "forward": true, "start": 48, "end": 64} ] }, { - "color": "#f74308", + "color": "#333333", "domains": [ {"helix": 2, "forward": false, "start": 32, "end": 48} ] }, { - "color": "#57bb00", + "color": "#320096", "domains": [ {"helix": 2, "forward": true, "start": 16, "end": 32} ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "AGTTAGTTAGTTAGTT", "domains": [ {"helix": 1, "forward": false, "start": 32, "end": 48} ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TACCTACCTACCTACC", "domains": [ {"helix": 1, "forward": false, "start": 48, "end": 64} ] }, { - "color": "#320096", + "color": "#aaaa00", "domains": [ {"helix": 2, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#888888", + "color": "#b8056c", "domains": [ {"helix": 2, "forward": true, "start": 0, "end": 16} ] diff --git a/examples/output_designs/4_helix_grid_none.dna b/examples/output_designs/4_helix_grid_none.dna index 18fb7f05..6e420fe7 100644 --- a/examples/output_designs/4_helix_grid_none.dna +++ b/examples/output_designs/4_helix_grid_none.dna @@ -20,7 +20,7 @@ ], "strands": [ { - "color": "#03b6a2", + "color": "#f74308", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 10} ] diff --git a/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna b/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna index 27b1c0f6..9400da45 100644 --- a/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna +++ b/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna @@ -23,25 +23,25 @@ ], "strands": [ { - "color": "#7300de", + "color": "#f74308", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#aaaa00", + "color": "#57bb00", "domains": [ {"helix": 1, "forward": true, "start": 8, "end": 16} ] }, { - "color": "#b8056c", + "color": "#888888", "domains": [ {"helix": 2, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#007200", + "color": "#32b86c", "domains": [ {"helix": 3, "forward": true, "start": 8, "end": 16} ] diff --git a/examples/output_designs/4_helix_min_offsets_nonzero.dna b/examples/output_designs/4_helix_min_offsets_nonzero.dna index 1addab18..f21827d9 100644 --- a/examples/output_designs/4_helix_min_offsets_nonzero.dna +++ b/examples/output_designs/4_helix_min_offsets_nonzero.dna @@ -9,7 +9,7 @@ ], "strands": [ { - "color": "#cc0000", + "color": "#f74308", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 29} ] diff --git a/examples/output_designs/56_helix_origami_rectangle.dna b/examples/output_designs/56_helix_origami_rectangle.dna index 205358d8..aeaa2cda 100644 --- a/examples/output_designs/56_helix_origami_rectangle.dna +++ b/examples/output_designs/56_helix_origami_rectangle.dna @@ -179,7 +179,7 @@ "is_scaffold": true }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "AATAGAAAATTCATATTTATTTTGTCACAATC", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -187,7 +187,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GTAGCACCATTACCATGCCAGCAAAATCACCA", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -195,7 +195,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TCTTTTCATAATCAAATTATTAGCGTTTGCCA", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -203,7 +203,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GTCAGACGATTGGCCTCAGGAGGTTGAGGCAG", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, @@ -211,7 +211,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "GTAACAGTGCCCGTATGGGGTCAGTGCCTTGA", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, @@ -219,7 +219,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TATAAGTATAGCCCGGCCGTCGAGAGGGTTGA", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, @@ -227,7 +227,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "GTCACCAGTACAAACTCGTAACACTGAGTTTC", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, @@ -235,7 +235,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "AAAGGAACAACTAAAGAGCGGAGTGAGAATAG", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, @@ -243,7 +243,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "ACAACCATCGCCCACGTGCGCCGACAATGACA", "domains": [ {"helix": 17, "forward": true, "start": 16, "end": 32}, @@ -251,7 +251,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GGAAGTTTCCATTAAAAAAGACTTTTTCATGA", "domains": [ {"helix": 19, "forward": true, "start": 16, "end": 32}, @@ -259,7 +259,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "AAATTGTGTCGAAATCTGTATCATCGCCTGAT", "domains": [ {"helix": 21, "forward": true, "start": 16, "end": 32}, @@ -267,7 +267,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "TGACAAGAACCGGATATCATCAAGAGTAATCT", "domains": [ {"helix": 23, "forward": true, "start": 16, "end": 32}, @@ -275,7 +275,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AGAACTGGCTCATTATACCTTATGCGATTTTA", "domains": [ {"helix": 25, "forward": true, "start": 16, "end": 32}, @@ -283,7 +283,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "GAGGCATAGTAAGAGCCGCCAAAAGGAATTAC", "domains": [ {"helix": 27, "forward": true, "start": 16, "end": 32}, @@ -291,7 +291,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CATTGAATCCCCCTCAAATCGTCATAAATATT", "domains": [ {"helix": 29, "forward": true, "start": 16, "end": 32}, @@ -299,7 +299,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CGAGCTTCAAAGCGAAATATCGCGTTTTAATT", "domains": [ {"helix": 31, "forward": true, "start": 16, "end": 32}, @@ -307,7 +307,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "AAGTACGGTGTCTGGATTTAAATATGCAACTA", "domains": [ {"helix": 33, "forward": true, "start": 16, "end": 32}, @@ -315,7 +315,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "ACTAATAGTAGTAGCAAGGTGGCATCAATTCT", "domains": [ {"helix": 35, "forward": true, "start": 16, "end": 32}, @@ -323,7 +323,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "GGATAAAAATTTTTAGCTTTATTTCAACGCAA", "domains": [ {"helix": 37, "forward": true, "start": 16, "end": 32}, @@ -331,7 +331,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "TTTTTGAGAGATCTACCCGGAGAGGGTAGCTA", "domains": [ {"helix": 39, "forward": true, "start": 16, "end": 32}, @@ -339,7 +339,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "TTAAATTGTAAACGTTTTGTATAAGCAAATAT", "domains": [ {"helix": 41, "forward": true, "start": 16, "end": 32}, @@ -347,7 +347,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "GATTCTCCGTGGGAACGAGTAACAACCCGTCG", "domains": [ {"helix": 43, "forward": true, "start": 16, "end": 32}, @@ -355,7 +355,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "TGCCGGAAACCAGGCACCGGCACCGCTTCTGG", "domains": [ {"helix": 45, "forward": true, "start": 16, "end": 32}, @@ -363,7 +363,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "TGTAAAACGACGGCCATTCCCAGTCACGACGT", "domains": [ {"helix": 47, "forward": true, "start": 16, "end": 32}, @@ -371,7 +371,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "TGTAAAGCCTGGGGTGAGCCGGAAGCATAAAG", "domains": [ {"helix": 49, "forward": true, "start": 16, "end": 32}, @@ -379,7 +379,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "CTTTTCACCAGTGAGACGCCAGGGTGGTTTTT", "domains": [ {"helix": 51, "forward": true, "start": 16, "end": 32}, @@ -387,7 +387,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CGAGATAGGGTTGAGTAATCAAAAGAATAGCC", "domains": [ {"helix": 53, "forward": true, "start": 16, "end": 32}, @@ -395,7 +395,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CTAAATCGGAACCCTAGAGGTGCCGTAAAGCA", "domains": [ {"helix": 55, "forward": true, "start": 16, "end": 32}, @@ -403,7 +403,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "AAGAACTGGCATGATTATAACGGAATACCCAA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 144}, @@ -411,7 +411,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "TATCTTACCGAAGCCCATGAAATAGCAATAGC", "domains": [ {"helix": 2, "forward": false, "start": 128, "end": 144}, @@ -419,7 +419,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "GTCAGAGGGTAATTGAGAACACCCTGAACAAA", "domains": [ {"helix": 4, "forward": false, "start": 128, "end": 144}, @@ -427,7 +427,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AACGTCAAAAATGAAAAAACGATTTTTTGTTT", "domains": [ {"helix": 6, "forward": false, "start": 128, "end": 144}, @@ -435,7 +435,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "ACGCTAACGAGCGTCTATCCTGAATCTTACCA", "domains": [ {"helix": 8, "forward": false, "start": 128, "end": 144}, @@ -443,7 +443,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "TTAGCGAACCTCCCGAAAGAACGCGAGGCGTT", "domains": [ {"helix": 10, "forward": false, "start": 128, "end": 144}, @@ -451,7 +451,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CCGTTTTTATTTTCATATCGAGAACAAGCAAG", "domains": [ {"helix": 12, "forward": false, "start": 128, "end": 144}, @@ -459,7 +459,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CGAGCATGTAGAAACCATCCCATCCTAATTTA", "domains": [ {"helix": 14, "forward": false, "start": 128, "end": 144}, @@ -467,7 +467,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CGACAATAAACAACATAATTCTGTCCAGACGA", "domains": [ {"helix": 16, "forward": false, "start": 128, "end": 144}, @@ -475,7 +475,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "ACAACGCCAACATGTAAGAATCGCCATATTTA", "domains": [ {"helix": 18, "forward": false, "start": 128, "end": 144}, @@ -483,7 +483,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GAAAAAGCCTGTTTAGGGAATCATAATTACTA", "domains": [ {"helix": 20, "forward": false, "start": 128, "end": 144}, @@ -491,7 +491,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "AATTTCATCTTCTGACCAAATATATTTTAGTT", "domains": [ {"helix": 22, "forward": false, "start": 128, "end": 144}, @@ -499,7 +499,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GGCTTAGGTTGGGTTATACCTTTTTAACCTCC", "domains": [ {"helix": 24, "forward": false, "start": 128, "end": 144}, @@ -507,7 +507,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TTGAAAACATAGCGATTTTTCCCTTAGAATCC", "domains": [ {"helix": 26, "forward": false, "start": 128, "end": 144}, @@ -515,7 +515,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "CCTTTTTTAATGGAAAAATTTCATTTGAATTA", "domains": [ {"helix": 28, "forward": false, "start": 128, "end": 144}, @@ -523,7 +523,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "GCGAATTATTCATTTCACAAAATCGCGCAGAG", "domains": [ {"helix": 30, "forward": false, "start": 128, "end": 144}, @@ -531,7 +531,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "CAGATGAATATACAGTTTTTCAGGTTTAACGT", "domains": [ {"helix": 32, "forward": false, "start": 128, "end": 144}, @@ -539,7 +539,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "ACTTCTGAATAATGGATGATTGTTTGGATTAT", "domains": [ {"helix": 34, "forward": false, "start": 128, "end": 144}, @@ -547,7 +547,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GAACAAAGAAACCACCACATTATCATTTTGCG", "domains": [ {"helix": 36, "forward": false, "start": 128, "end": 144}, @@ -555,7 +555,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "AAGTATTAGACTTTACACATTTGAGGATTTAG", "domains": [ {"helix": 38, "forward": false, "start": 128, "end": 144}, @@ -563,7 +563,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "TTGAAAGGAATTGAGGGTTGGCAAATCAACAG", "domains": [ {"helix": 40, "forward": false, "start": 128, "end": 144}, @@ -571,7 +571,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "GAGAGCCAGCAGCAAAGCAACAGTGCCACGCT", "domains": [ {"helix": 42, "forward": false, "start": 128, "end": 144}, @@ -579,7 +579,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AAACATCGCCATTAAACGAACTGATAGCCCTA", "domains": [ {"helix": 44, "forward": false, "start": 128, "end": 144}, @@ -587,7 +587,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AGATAGAACCCTTCTGACATTCTGGCCAACAG", "domains": [ {"helix": 46, "forward": false, "start": 128, "end": 144}, @@ -595,7 +595,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CTACATTTTGACGCTCACGCTCATGGAAATAC", "domains": [ {"helix": 48, "forward": false, "start": 128, "end": 144}, @@ -603,7 +603,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CCTGAGTAGAAGAACTGTAATAACATCACTTG", "domains": [ {"helix": 50, "forward": false, "start": 128, "end": 144}, @@ -611,7 +611,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TTTTATAATCAGTGAGGAATCCTGAGAAGTGT", "domains": [ {"helix": 52, "forward": false, "start": 128, "end": 144}, @@ -619,7 +619,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "ACGTGCTTTCCTCGTTTTGACGAGCACGTATA", "domains": [ {"helix": 54, "forward": false, "start": 128, "end": 144}, @@ -627,14 +627,14 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "TTATTACGCAGTATGTTAGCAAACGTAGAAAA", "domains": [ {"helix": 0, "forward": false, "start": 88, "end": 120} ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TTATTCATAGGGAAGGTAAATATTAGTTACCA", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88}, @@ -642,7 +642,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "GAAGGAAAGCAGATAGCCGAACAAGACGGAAA", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -650,7 +650,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "TGCCTTTAAATCAGTAGCGACAGATGAGTTAA", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88}, @@ -658,7 +658,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "GCCCAATAGATAACCCACAAGAATATCAAGTT", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -666,7 +666,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GCCACCACACCCTCAGAACCGCCAACAGGGAA", "domains": [ {"helix": 6, "forward": false, "start": 80, "end": 88}, @@ -674,7 +674,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "GCGCATTAAGAGAATAACATAAAACCCTCAGA", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 112}, @@ -682,7 +682,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "TAAGCGTCCAGTCTCTGAATTTACACAGCCAT", "domains": [ {"helix": 8, "forward": false, "start": 80, "end": 88}, @@ -690,7 +690,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "ATTATTTAGCCAGTTACAAAATAACGTTCCAG", "domains": [ {"helix": 7, "forward": true, "start": 104, "end": 112}, @@ -698,7 +698,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "CCTCAAGATGAAAGTATTAAGAGGTTAGTTGC", "domains": [ {"helix": 10, "forward": false, "start": 80, "end": 88}, @@ -706,7 +706,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "TATTTTGCAAGCCTTAAATCAAGACTGAGACT", "domains": [ {"helix": 9, "forward": true, "start": 104, "end": 112}, @@ -714,7 +714,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CTCAGAGCACCGCCACCCTCAGAAAAATCAGA", "domains": [ {"helix": 12, "forward": false, "start": 80, "end": 88}, @@ -722,7 +722,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "TATAGAAGGCGCCCAATAGCAAGCCCGCCACC", "domains": [ {"helix": 11, "forward": true, "start": 104, "end": 112}, @@ -730,7 +730,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "ACGTTAGTTCTAAAGTTTTGTCGTCAAGAACG", "domains": [ {"helix": 14, "forward": false, "start": 80, "end": 88}, @@ -738,7 +738,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "GGTATTAATCTTTCCTTATCATTCCTTTCCAG", "domains": [ {"helix": 13, "forward": true, "start": 104, "end": 112}, @@ -746,7 +746,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "TCGGTTTACTCCAAAAGGAGCCTTACAATAGA", "domains": [ {"helix": 16, "forward": false, "start": 80, "end": 88}, @@ -754,7 +754,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "TAAGTCCTACGCGCCTGTTTATCATAATTGTA", "domains": [ {"helix": 15, "forward": true, "start": 104, "end": 112}, @@ -762,7 +762,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "CAGCGAAACTTTTGCGGGATCGTCAGAGAATA", "domains": [ {"helix": 18, "forward": false, "start": 80, "end": 88}, @@ -770,7 +770,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "TAAAGTACTTTCGAGCCAGTAATAACCCTCAG", "domains": [ {"helix": 17, "forward": true, "start": 104, "end": 112}, @@ -778,7 +778,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "CTCATCTTGAGGCAAAAGAATACATAAAGCCA", "domains": [ {"helix": 20, "forward": false, "start": 80, "end": 88}, @@ -786,7 +786,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "ACGCTCAACAAATTCTTACCAGTACTAAAACA", "domains": [ {"helix": 19, "forward": true, "start": 104, "end": 112}, @@ -794,7 +794,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "CTTTGAAATCATAAGGGAACCGAAGATAAATA", "domains": [ {"helix": 22, "forward": false, "start": 80, "end": 88}, @@ -802,7 +802,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "AGGCGTTAGAAATACCGACCGTGTCTGACCAA", "domains": [ {"helix": 21, "forward": true, "start": 104, "end": 112}, @@ -810,7 +810,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "ACGAGTAGCTTGCCCTGACGAGAAATCGCAAG", "domains": [ {"helix": 24, "forward": false, "start": 80, "end": 88}, @@ -818,7 +818,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "ACAAAGAATGCTGATGCAAATCCAACACCAGA", "domains": [ {"helix": 23, "forward": true, "start": 104, "end": 112}, @@ -826,7 +826,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "AAAGATTCACGGAACAACATTATTGTGAATTT", "domains": [ {"helix": 26, "forward": false, "start": 80, "end": 88}, @@ -834,7 +834,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "ATCAAAATCTGAGAAGAGTCAATAACAGGTAG", "domains": [ {"helix": 25, "forward": true, "start": 104, "end": 112}, @@ -842,7 +842,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TTTGCCAGGCGAGAGGCTTTTGCACCTTGCTT", "domains": [ {"helix": 28, "forward": false, "start": 80, "end": 88}, @@ -850,7 +850,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "CTGTAAATATATGTGAGTGAATAAAAAGAAGT", "domains": [ {"helix": 27, "forward": true, "start": 104, "end": 112}, @@ -858,7 +858,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "TCAGAAGCAGGTCTTTACCCTGACACATCAAG", "domains": [ {"helix": 30, "forward": false, "start": 80, "end": 88}, @@ -866,7 +866,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "AAAACAAAGAAGATGATGAAACAATATTATAG", "domains": [ {"helix": 29, "forward": true, "start": 104, "end": 112}, @@ -874,7 +874,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "TTTTTGCGATTGCTCCTTTTGATACGGATTCG", "domains": [ {"helix": 32, "forward": false, "start": 80, "end": 88}, @@ -882,7 +882,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "CCTGATTGTCGGGAGAAACAATAAAGAGGTCA", "domains": [ {"helix": 31, "forward": true, "start": 104, "end": 112}, @@ -890,7 +890,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "TCGCAAATTTTAGTTTGACCATTACACGTAAA", "domains": [ {"helix": 34, "forward": false, "start": 80, "end": 88}, @@ -898,7 +898,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "ACAGAAATATATCAAAATTATTTGGATACATT", "domains": [ {"helix": 33, "forward": true, "start": 104, "end": 112}, @@ -906,7 +906,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "GCTAAATCAGCAATAAAGCCTCAGTATCAGAT", "domains": [ {"helix": 36, "forward": false, "start": 80, "end": 88}, @@ -914,7 +914,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "GATGGCAATCATCATATTCCTGATAGCATAAA", "domains": [ {"helix": 35, "forward": true, "start": 104, "end": 112}, @@ -922,7 +922,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "AGACAGTCATTCAAAAGGGTGAGACCCGAACG", "domains": [ {"helix": 38, "forward": false, "start": 80, "end": 88}, @@ -930,7 +930,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "TTATTAATCGTATTAAATCCTTTGAAGGCCGG", "domains": [ {"helix": 37, "forward": true, "start": 104, "end": 112}, @@ -938,7 +938,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "CATGTCAAGATGAACGGTAATCGTCAACTAAT", "domains": [ {"helix": 40, "forward": false, "start": 80, "end": 88}, @@ -946,7 +946,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "AGATTAGATCTTTAGGAGCACTAAAAAACTAG", "domains": [ {"helix": 39, "forward": true, "start": 104, "end": 112}, @@ -954,7 +954,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "AAATAATTTTTAACCAATAGGAACCAAATATC", "domains": [ {"helix": 42, "forward": false, "start": 80, "end": 88}, @@ -962,7 +962,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "AAACCCTCTCACCTTGCTGAACCTGCCATCAA", "domains": [ {"helix": 41, "forward": true, "start": 104, "end": 112}, @@ -970,7 +970,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "GTTTGAGGCGCATCGTAACCGTGCCAGAGGTG", "domains": [ {"helix": 44, "forward": false, "start": 80, "end": 88}, @@ -978,7 +978,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "AGGCGGTCCCAGCAGAAGATAAAAATCTGCCA", "domains": [ {"helix": 43, "forward": true, "start": 104, "end": 112}, @@ -986,7 +986,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "CAGCTGGCGTGCGGGCCTCTTCGCATATTTTT", "domains": [ {"helix": 46, "forward": false, "start": 80, "end": 88}, @@ -994,7 +994,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "GAATGGCTATACGTGGCACAGACATATTACGC", "domains": [ {"helix": 45, "forward": true, "start": 104, "end": 112}, @@ -1002,7 +1002,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "TCATAGCTCCGAGCTCGAATTCGTATTCACCA", "domains": [ {"helix": 48, "forward": false, "start": 80, "end": 88}, @@ -1010,7 +1010,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "GTCACACGTTATTTACATTGGCAGAATCATGG", "domains": [ {"helix": 47, "forward": true, "start": 104, "end": 112}, @@ -1018,7 +1018,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "GCCAGCTGCTTTCCAGTCGGGAAACAATATTA", "domains": [ {"helix": 50, "forward": false, "start": 80, "end": 88}, @@ -1026,7 +1026,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CCGCCAGCCTGGTAATATCCAGAACCTGTCGT", "domains": [ {"helix": 49, "forward": true, "start": 104, "end": 112}, @@ -1034,7 +1034,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "CCAGCAGGGCAAGCGGTCCACGCTAATTAACC", "domains": [ {"helix": 52, "forward": false, "start": 80, "end": 88}, @@ -1042,7 +1042,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GTTGTAGCGTCTGTCCATCACGCAGGTTTGCC", "domains": [ {"helix": 51, "forward": true, "start": 104, "end": 112}, @@ -1050,7 +1050,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TATCAGGGAACGTCAAAGGGCGAATTAAAGGG", "domains": [ {"helix": 54, "forward": false, "start": 80, "end": 88}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "ATTTTAGACTAAACAGGAGGCCGAAAACCGTC", "domains": [ {"helix": 53, "forward": true, "start": 104, "end": 112}, @@ -1066,14 +1066,14 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GAACGTGGCGAGAAAGGAAGGGAATGCGCCGC", "domains": [ {"helix": 55, "forward": true, "start": 72, "end": 104} ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "ACGCAAAGACACCACGGAATAAGTGGTTTACC", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56}, @@ -1081,7 +1081,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "AGCGCCAACCATTTGGGAATTAGATAGCAAGG", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -1090,7 +1090,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CCGGAAACTTCGGTCATAGCCCCCATCACCGG", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -1099,7 +1099,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AACCAGAGCCGCCGCCAGCATTGATGATATTC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 48}, @@ -1108,7 +1108,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "ACAAACAAGGTAATAAGTTTTAACAAACAGTT", "domains": [ {"helix": 7, "forward": true, "start": 40, "end": 48}, @@ -1117,7 +1117,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "AATGCCCCACCAGGCGGATAAGTGAATAGGTG", "domains": [ {"helix": 9, "forward": true, "start": 40, "end": 48}, @@ -1126,7 +1126,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "TATCACCGATAGGAACCCATGTACACAACGCC", "domains": [ {"helix": 11, "forward": true, "start": 40, "end": 48}, @@ -1135,7 +1135,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TGTAGCATAACTTTCAACAGTTTCGAATTGCG", "domains": [ {"helix": 13, "forward": true, "start": 40, "end": 48}, @@ -1144,7 +1144,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "AATAATAAGCTTGATACCGATAGTCATAACCG", "domains": [ {"helix": 15, "forward": true, "start": 40, "end": 48}, @@ -1153,7 +1153,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "ATATATTCAGAGGCTTTGAGGACTCGGGTAAA", "domains": [ {"helix": 17, "forward": true, "start": 40, "end": 48}, @@ -1162,7 +1162,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "ATACGTAAAAGTACAACGGAGATTCGCGACCT", "domains": [ {"helix": 19, "forward": true, "start": 40, "end": 48}, @@ -1171,7 +1171,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "GCTCCATGATAGGCTGGCTGACCTTTCATTAC", "domains": [ {"helix": 21, "forward": true, "start": 40, "end": 48}, @@ -1180,7 +1180,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CCAAATCATTAATCATTGTGAATTACCAGTCA", "domains": [ {"helix": 23, "forward": true, "start": 40, "end": 48}, @@ -1189,7 +1189,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "GGACGTTGTAATGCAGATACATAAAACACTAT", "domains": [ {"helix": 25, "forward": true, "start": 40, "end": 48}, @@ -1198,7 +1198,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CATAACCCGCGTCCAATACTGCGGAATGCTTT", "domains": [ {"helix": 27, "forward": true, "start": 40, "end": 48}, @@ -1207,7 +1207,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "AAACAGTTGCCCGAAAGACTTCAACCAGACCG", "domains": [ {"helix": 29, "forward": true, "start": 40, "end": 48}, @@ -1216,7 +1216,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GAAGCAAACTGTAGCTCAACATGTAGTTTCAT", "domains": [ {"helix": 31, "forward": true, "start": 40, "end": 48}, @@ -1225,7 +1225,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "TCCATATAGGGGCGCGAGCTGAAATTAACATC", "domains": [ {"helix": 33, "forward": true, "start": 40, "end": 48}, @@ -1234,7 +1234,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CAATAAATCTTTTGCGGGAGAAGCAACCCTCA", "domains": [ {"helix": 35, "forward": true, "start": 40, "end": 48}, @@ -1243,7 +1243,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "TATATTTTAGCTGATAAATTAATGAAAGGCTA", "domains": [ {"helix": 37, "forward": true, "start": 40, "end": 48}, @@ -1252,7 +1252,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TCAGGTCACCCAAAAACAGGAAGAAATATTTT", "domains": [ {"helix": 39, "forward": true, "start": 40, "end": 48}, @@ -1261,7 +1261,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GTTAAAATAACATTAAATGTGAGCAAACGGCG", "domains": [ {"helix": 41, "forward": true, "start": 40, "end": 48}, @@ -1270,7 +1270,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "GATTGACCCACTCCAGCCAGCTTTAAGCGCCA", "domains": [ {"helix": 43, "forward": true, "start": 40, "end": 48}, @@ -1279,7 +1279,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TTCGCCATGGGTAACGCCAGGGTTGTGCCAAG", "domains": [ {"helix": 45, "forward": true, "start": 40, "end": 48}, @@ -1288,7 +1288,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CTTGCATGTTCCACACAACATACGCCTAATGA", "domains": [ {"helix": 47, "forward": true, "start": 40, "end": 48}, @@ -1297,7 +1297,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GTGAGCTACGGTTTGCGTATTGGGCGGGCAAC", "domains": [ {"helix": 49, "forward": true, "start": 40, "end": 48}, @@ -1306,7 +1306,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "AGCTGATTGGCAAAATCCCTTATAGTTGTTCC", "domains": [ {"helix": 51, "forward": true, "start": 40, "end": 48}, @@ -1315,7 +1315,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "AGTTTGGACAAGTTTTTTGGGGTCAAGGGAGC", "domains": [ {"helix": 53, "forward": true, "start": 40, "end": 48}, @@ -1324,7 +1324,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CCCCGATTTAGAGCTTGACGGGGAGAACCATC", "domains": [ {"helix": 55, "forward": true, "start": 40, "end": 64}, @@ -1332,7 +1332,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GACTTGAGAGACAAAAGGGCGACATAAAAGAA", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -1341,7 +1341,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "TCGGCATTGTCACCAATGAAACCACCGTCACC", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -1350,7 +1350,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CACCAGAGCCACCACCGGAACCGCCGTTTTCA", "domains": [ {"helix": 6, "forward": false, "start": 48, "end": 56}, @@ -1359,7 +1359,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "AGTGTACTATAAATCCTCATTAAAAGAACCAC", "domains": [ {"helix": 8, "forward": false, "start": 48, "end": 56}, @@ -1368,7 +1368,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TGCTCAGTCTGCCTATTTCGGAACGATACAGG", "domains": [ {"helix": 10, "forward": false, "start": 48, "end": 56}, @@ -1377,7 +1377,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "CAAGCCCATACTCAGGAGGTTTAGCGGGGTTT", "domains": [ {"helix": 12, "forward": false, "start": 48, "end": 56}, @@ -1386,7 +1386,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "TGCTAAACTCCACAGACAGCCCTCAGGGATAG", "domains": [ {"helix": 14, "forward": false, "start": 48, "end": 56}, @@ -1395,7 +1395,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "CTTAAACATTTTTTCACGTTGAAATGGGATTT", "domains": [ {"helix": 16, "forward": false, "start": 48, "end": 56}, @@ -1404,7 +1404,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "ACGGCTACGGTCGCTGAGGCTTGCGTGAATTT", "domains": [ {"helix": 18, "forward": false, "start": 48, "end": 56}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GCGAAACATGCCACTACGAAGGCAGGGTAGCA", "domains": [ {"helix": 20, "forward": false, "start": 48, "end": 56}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CCAGGCGCTTACTTAGCCGGAACGTACCAAGC", "domains": [ {"helix": 22, "forward": false, "start": 48, "end": 56}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "TTTCAACTACGTAACAAAGCTGCTTGTACAGA", "domains": [ {"helix": 24, "forward": false, "start": 48, "end": 56}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CATTCAACGGAAGAAAAATCTACGTGGTTTAA", "domains": [ {"helix": 26, "forward": false, "start": 48, "end": 56}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "ACTGGATATCGTTTACCAGACGACGAATACCA", "domains": [ {"helix": 28, "forward": false, "start": 48, "end": 56}, @@ -1458,7 +1458,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AAGAGGAACAGAAAACGAGAATGAATGTTTAG", "domains": [ {"helix": 30, "forward": false, "start": 48, "end": 56}, @@ -1467,7 +1467,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "ATATAATGCTCCAACAGGTCAGGAAAAAGATT", "domains": [ {"helix": 32, "forward": false, "start": 48, "end": 56}, @@ -1476,7 +1476,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "TTTCATTTACAGTTGATTCCCAATATTGCTGA", "domains": [ {"helix": 34, "forward": false, "start": 48, "end": 56}, @@ -1485,7 +1485,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CTGTAATACATACAGGCAAGGCAAAGCTATAT", "domains": [ {"helix": 36, "forward": false, "start": 48, "end": 56}, @@ -1494,7 +1494,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "ACCGTTCTAAATGCAATGCCTGAGTTATGACC", "domains": [ {"helix": 38, "forward": false, "start": 48, "end": 56}, @@ -1503,7 +1503,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AGAAAAGCTTGCCTGAGAGTCTGGGATATTCA", "domains": [ {"helix": 40, "forward": false, "start": 48, "end": 56}, @@ -1512,7 +1512,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "CTTTCATCTCGCATTAAATTTTTGTGATAATC", "domains": [ {"helix": 42, "forward": false, "start": 48, "end": 56}, @@ -1521,7 +1521,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "GAAGATCGGTAATGGGATAGGTCAGTAGCCAG", "domains": [ {"helix": 44, "forward": false, "start": 48, "end": 56}, @@ -1530,7 +1530,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "ATTAAGTTTCAGGCTGCGCAACTGGGCCTCAG", "domains": [ {"helix": 46, "forward": false, "start": 48, "end": 56}, @@ -1539,7 +1539,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "GCTCACAACCTGCAGGTCGACTCTGCAAGGCG", "domains": [ {"helix": 48, "forward": false, "start": 48, "end": 56}, @@ -1548,7 +1548,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GGGAGAGGACTCACATTAATTGCGTGTTATCC", "domains": [ {"helix": 50, "forward": false, "start": 48, "end": 56}, @@ -1557,7 +1557,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CCGAAATCGCCCTTCACCGCCTGGAACGCGCG", "domains": [ {"helix": 52, "forward": false, "start": 48, "end": 56}, @@ -1566,7 +1566,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "ACCCAAATACAAGAGTCCACTATTTGGTGGTT", "domains": [ {"helix": 54, "forward": false, "start": 48, "end": 56}, @@ -1575,7 +1575,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "TACATACATAAAGGTGGCAACATATTCAACCG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88}, @@ -1583,7 +1583,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "ATTGAGGGTAAAGGTGAATTATCATCGATAGC", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -1592,7 +1592,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "AGCACCGTGCGTCAGACTGTAGCGCTCCCTCA", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -1601,7 +1601,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "GAGCCGCCCCTCAGAGCCGCCACCGCCAGAAT", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 80}, @@ -1610,7 +1610,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GGAAAGCGATACATGGCTTTTGATCTATTATT", "domains": [ {"helix": 7, "forward": true, "start": 72, "end": 80}, @@ -1619,7 +1619,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CTGAAACAGAAGGATTAGGATTAGTACCGCCA", "domains": [ {"helix": 9, "forward": true, "start": 72, "end": 80}, @@ -1628,7 +1628,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "CCCTCAGACACCACCCTCATTTTCATAGTTAG", "domains": [ {"helix": 11, "forward": true, "start": 72, "end": 80}, @@ -1637,7 +1637,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CGTAACGAAAATGAATTTTCTGTAATCTCCAA", "domains": [ {"helix": 13, "forward": true, "start": 72, "end": 80}, @@ -1646,7 +1646,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "AAAAAAGGTCAGCTTGCTTTCGAGAGGGAGTT", "domains": [ {"helix": 15, "forward": true, "start": 72, "end": 80}, @@ -1655,7 +1655,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "AAAGGCCGGACAGCATCGGAACGACCAACCTA", "domains": [ {"helix": 17, "forward": true, "start": 72, "end": 80}, @@ -1664,7 +1664,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "AAACGAAATGACCCCCAGCGATTAAGGCGCAG", "domains": [ {"helix": 19, "forward": true, "start": 72, "end": 80}, @@ -1673,7 +1673,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "ACGGTCAAGAGGACAGATGAACGGCATTCAGT", "domains": [ {"helix": 21, "forward": true, "start": 72, "end": 80}, @@ -1682,7 +1682,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GAATAAGGTAAATTGGGCTTGAGATTAATAAA", "domains": [ {"helix": 23, "forward": true, "start": 72, "end": 80}, @@ -1691,7 +1691,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "ACGAACTAATCAGTTGAGATTTAGGATAAAAA", "domains": [ {"helix": 25, "forward": true, "start": 72, "end": 80}, @@ -1700,7 +1700,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CCAAAATAAGGGGGTAATAGTAAACCATAAAT", "domains": [ {"helix": 27, "forward": true, "start": 72, "end": 80}, @@ -1709,7 +1709,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CAAAAATCAAAGCGGATTGCATCATTAGAGAG", "domains": [ {"helix": 29, "forward": true, "start": 72, "end": 80}, @@ -1718,7 +1718,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TACCTTTAGATGGCTTAGAGCTTATCTGCGAA", "domains": [ {"helix": 31, "forward": true, "start": 72, "end": 80}, @@ -1727,7 +1727,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "CGAGTAGAGGTCAATAACCTGTTTAGAATTAG", "domains": [ {"helix": 33, "forward": true, "start": 72, "end": 80}, @@ -1736,7 +1736,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CAAAATTAGGTTGTACCAAAAACATAATGTGT", "domains": [ {"helix": 35, "forward": true, "start": 72, "end": 80}, @@ -1745,7 +1745,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AGGTAAAGAAATCACCATCAATATAGCAAACA", "domains": [ {"helix": 37, "forward": true, "start": 72, "end": 80}, @@ -1754,7 +1754,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "AGAGAATCTCATATGTACCCCGGTTTAAATCA", "domains": [ {"helix": 39, "forward": true, "start": 72, "end": 80}, @@ -1763,7 +1763,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GCTCATTTCGCGTCTGGCCTTCCTCGTTGGTG", "domains": [ {"helix": 41, "forward": true, "start": 72, "end": 80}, @@ -1772,7 +1772,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "TAGATGGGGGACGACGACAGTATCTTGGGAAG", "domains": [ {"helix": 43, "forward": true, "start": 72, "end": 80}, @@ -1781,7 +1781,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GGCGATCGGAAAGGGGGATGTGCTAGAGGATC", "domains": [ {"helix": 45, "forward": true, "start": 72, "end": 80}, @@ -1790,7 +1790,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CCCGGGTAGTTTCCTGTGTGAAATTTGCGCTC", "domains": [ {"helix": 47, "forward": true, "start": 72, "end": 80}, @@ -1799,7 +1799,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "ACTGCCCGCATTAATGAATCGGCCCCCTGAGA", "domains": [ {"helix": 49, "forward": true, "start": 72, "end": 80}, @@ -1808,7 +1808,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GAGTTGCACGAAAATCCTGTTTGAAAAGAACG", "domains": [ {"helix": 51, "forward": true, "start": 72, "end": 80}, @@ -1817,7 +1817,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "TGGACTCCCGATGGCCCACTACGTAAGCCGGC", "domains": [ {"helix": 53, "forward": true, "start": 72, "end": 80}, @@ -1826,7 +1826,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "TACAGGGCGCGTACTATGGTTGCTAGAATCAG", "domains": [ {"helix": 55, "forward": true, "start": 104, "end": 128}, @@ -1834,7 +1834,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "AAAAGTAACCGAGGAAACGCAATAAAGACTCC", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -1843,7 +1843,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "ATCAGAGAATAAGAGCAAGAAACATTTTTAAG", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -1852,7 +1852,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CTTTACAGGACGGGAGAATTAACTGCGCTAAT", "domains": [ {"helix": 6, "forward": false, "start": 112, "end": 120}, @@ -1861,7 +1861,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "CCTAATTTTCCCAATCCAAATAAGATAGCAGC", "domains": [ {"helix": 8, "forward": false, "start": 112, "end": 120}, @@ -1870,7 +1870,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "AGGTTTTGACCCAGCTACAATTTTTTCCAGAG", "domains": [ {"helix": 10, "forward": false, "start": 112, "end": 120}, @@ -1879,7 +1879,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "TCATTACCGCTTATCCGGTATTCTCTTGCGGG", "domains": [ {"helix": 12, "forward": false, "start": 112, "end": 120}, @@ -1888,7 +1888,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "ATCGGCTGACCAAGTACCGCACTCCGTAGGAA", "domains": [ {"helix": 14, "forward": false, "start": 112, "end": 120}, @@ -1897,7 +1897,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "AATGCAGAGAACAAGAAAAATAATAATCAATA", "domains": [ {"helix": 16, "forward": false, "start": 112, "end": 120}, @@ -1906,7 +1906,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "AGAGGCATCGACAAAAGGTAAAGTGTTCAGCT", "domains": [ {"helix": 18, "forward": false, "start": 112, "end": 120}, @@ -1915,7 +1915,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GCGTTATACAGTAGGGCTTAATTGATTTAGGC", "domains": [ {"helix": 20, "forward": false, "start": 112, "end": 120}, @@ -1924,7 +1924,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AATGGTTTAATAAGAATAAACACCTATCATAT", "domains": [ {"helix": 22, "forward": false, "start": 112, "end": 120}, @@ -1933,7 +1933,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "TATGTAAACGCGAGAAAACTTTTTCTAAATTT", "domains": [ {"helix": 24, "forward": false, "start": 112, "end": 120}, @@ -1942,7 +1942,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "TTAAGACGCATAGGTCTGAGAGACTATAACTA", "domains": [ {"helix": 26, "forward": false, "start": 112, "end": 120}, @@ -1951,7 +1951,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "AAATCAATCGTCGCTATTAATTAAAGCTTAGA", "domains": [ {"helix": 28, "forward": false, "start": 112, "end": 120}, @@ -1960,7 +1960,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GAGCAAAAATTAATTACATTTAACCAGTACAT", "domains": [ {"helix": 30, "forward": false, "start": 112, "end": 120}, @@ -1969,7 +1969,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CTTTTACACTTTGAATACCAAGTTAATTACCT", "domains": [ {"helix": 32, "forward": false, "start": 112, "end": 120}, @@ -1978,7 +1978,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AACCTACCAAAGAAATTGCGTAGAAACAGTAC", "domains": [ {"helix": 34, "forward": false, "start": 112, "end": 120}, @@ -1987,7 +1987,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CGGAATTATTCATCAATATAATCCAGGGTTAG", "domains": [ {"helix": 36, "forward": false, "start": 112, "end": 120}, @@ -1996,7 +1996,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CGACAACTTTTAAAAGTTTGAGTAAGAAGGAG", "domains": [ {"helix": 38, "forward": false, "start": 112, "end": 120}, @@ -2005,7 +2005,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CTAAAATAGCCGTCAATAGATAATAAACAATT", "domains": [ {"helix": 40, "forward": false, "start": 112, "end": 120}, @@ -2014,7 +2014,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CTAAAGCAAATCAATATCTGGTCAAAGGTTAT", "domains": [ {"helix": 42, "forward": false, "start": 112, "end": 120}, @@ -2023,7 +2023,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "ACGAACCAAGTATTAACACCGCCTTGAAAAAT", "domains": [ {"helix": 44, "forward": false, "start": 112, "end": 120}, @@ -2032,7 +2032,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GCGTAAGAATTAGTCTTTAATGCGAATACCGA", "domains": [ {"helix": 46, "forward": false, "start": 112, "end": 120}, @@ -2041,7 +2041,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GAAATGGAACCAGTAATAAAAGGGACCTGAAA", "domains": [ {"helix": 48, "forward": false, "start": 112, "end": 120}, @@ -2050,7 +2050,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CGGCCTTGCATTGCAACAGGAAAAAATCGTCT", "domains": [ {"helix": 50, "forward": false, "start": 112, "end": 120}, @@ -2059,7 +2059,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GTAAAAGAAATACTTCTTTGATTACAAACTAT", "domains": [ {"helix": 52, "forward": false, "start": 112, "end": 120}, @@ -2068,7 +2068,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "AGCGGGAGCAGGAACGGTACGCCAGCCACCGA", "domains": [ {"helix": 54, "forward": false, "start": 112, "end": 120}, diff --git a/examples/output_designs/64_helix_origami_rectangle.dna b/examples/output_designs/64_helix_origami_rectangle.dna index 76ce6387..ba774cef 100644 --- a/examples/output_designs/64_helix_origami_rectangle.dna +++ b/examples/output_designs/64_helix_origami_rectangle.dna @@ -203,7 +203,7 @@ "is_scaffold": true }, { - "color": "#888888", + "color": "#f74308", "sequence": "GACAGCATCGGAACGAACCCTCAGCAGCGAAA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -211,7 +211,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "TGCCACTACGAAGGCACGGGTAAAATACGTAA", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -219,7 +219,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "AAGTACAACGGAGATTTACCAAGCGCGAAACA", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -227,7 +227,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "TCATAAGGGAACCGAAAGGCGCAGACGGTCAA", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, @@ -235,7 +235,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "TGACAAGAACCGGATATCATCAAGAGTAATCT", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, @@ -243,7 +243,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "TAAATTGGGCTTGAGAACACCAGAACGAGTAG", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, @@ -251,7 +251,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "GGAAGAAAAATCTACGACCAGTCAGGACGTTG", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, @@ -259,7 +259,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TAATGCAGATACATAAGAATACCACATTCAAC", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, @@ -267,7 +267,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GCGAGAGGCTTTTGCAGATAAAAACCAAAATA", "domains": [ {"helix": 17, "forward": true, "start": 16, "end": 32}, @@ -275,7 +275,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "CATTGAATCCCCCTCAAATCGTCATAAATATT", "domains": [ {"helix": 19, "forward": true, "start": 16, "end": 32}, @@ -283,7 +283,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "AAAGCGGATTGCATCATATTATAGTCAGAAGC", "domains": [ {"helix": 21, "forward": true, "start": 16, "end": 32}, @@ -291,7 +291,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "CTCCAACAGGTCAGGACCAGACCGGAAGCAAA", "domains": [ {"helix": 23, "forward": true, "start": 16, "end": 32}, @@ -299,7 +299,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "CTGTAGCTCAACATGTATTGCTGAATATAATG", "domains": [ {"helix": 25, "forward": true, "start": 16, "end": 32}, @@ -307,7 +307,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "TTTAGTTTGACCATTATCTGCGAACGAGTAGA", "domains": [ {"helix": 27, "forward": true, "start": 16, "end": 32}, @@ -315,7 +315,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "ACTAATAGTAGTAGCAAGGTGGCATCAATTCT", "domains": [ {"helix": 29, "forward": true, "start": 16, "end": 32}, @@ -323,7 +323,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "GGTTGTACCAAAAACAAGCATAAAGCTAAATC", "domains": [ {"helix": 31, "forward": true, "start": 16, "end": 32}, @@ -331,7 +331,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "AAATGCAATGCCTGAGAACCCTCATATATTTT", "domains": [ {"helix": 33, "forward": true, "start": 16, "end": 32}, @@ -339,7 +339,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "AGCTGATAAATTAATGGATATTCAACCGTTCT", "domains": [ {"helix": 35, "forward": true, "start": 16, "end": 32}, @@ -347,7 +347,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "GATGAACGGTAATCGTAGCAAACAAGAGAATC", "domains": [ {"helix": 37, "forward": true, "start": 16, "end": 32}, @@ -355,7 +355,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "TTAAATTGTAAACGTTTTGTATAAGCAAATAT", "domains": [ {"helix": 39, "forward": true, "start": 16, "end": 32}, @@ -363,7 +363,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CGCGTCTGGCCTTCCTGCCATCAAAAATAATT", "domains": [ {"helix": 41, "forward": true, "start": 16, "end": 32}, @@ -371,7 +371,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GTAATGGGATAGGTCAAAACGGCGGATTGACC", "domains": [ {"helix": 43, "forward": true, "start": 16, "end": 32}, @@ -379,7 +379,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "CACTCCAGCCAGCTTTGGCCTCAGGAAGATCG", "domains": [ {"helix": 45, "forward": true, "start": 16, "end": 32}, @@ -387,7 +387,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "GTGCGGGCCTCTTCGCTTGGGAAGGGCGATCG", "domains": [ {"helix": 47, "forward": true, "start": 16, "end": 32}, @@ -395,7 +395,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "TGTAAAACGACGGCCATTCCCAGTCACGACGT", "domains": [ {"helix": 49, "forward": true, "start": 16, "end": 32}, @@ -403,7 +403,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "GTTTCCTGTGTGAAATAATCATGGTCATAGCT", "domains": [ {"helix": 51, "forward": true, "start": 16, "end": 32}, @@ -411,7 +411,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "ACTCACATTAATTGCGCCTAATGAGTGAGCTA", "domains": [ {"helix": 53, "forward": true, "start": 16, "end": 32}, @@ -419,7 +419,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CGGTTTGCGTATTGGGAACGCGCGGGGAGAGG", "domains": [ {"helix": 55, "forward": true, "start": 16, "end": 32}, @@ -427,7 +427,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "GCAAGCGGTCCACGCTCCCTGAGAGAGTTGCA", "domains": [ {"helix": 57, "forward": true, "start": 16, "end": 32}, @@ -435,7 +435,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "CGAGATAGGGTTGAGTAATCAAAAGAATAGCC", "domains": [ {"helix": 59, "forward": true, "start": 16, "end": 32}, @@ -443,7 +443,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CGATGGCCCACTACGTAAACCGTCTATCAGGG", "domains": [ {"helix": 61, "forward": true, "start": 16, "end": 32}, @@ -451,7 +451,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "TAGAGCTTGACGGGGAAAGGGAGCCCCCGATT", "domains": [ {"helix": 63, "forward": true, "start": 16, "end": 32}, @@ -459,7 +459,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "ACAACCATCGCCCACGTGCGCCGACAATGACA", "domains": [ {"helix": 0, "forward": false, "start": 96, "end": 112}, @@ -467,7 +467,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CTCCAAAAGGAGCCTTATCTCCAAAAAAAAGG", "domains": [ {"helix": 2, "forward": false, "start": 96, "end": 112}, @@ -475,7 +475,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "AACTTTCAACAGTTTCTGGGATTTTGCTAAAC", "domains": [ {"helix": 4, "forward": false, "start": 96, "end": 112}, @@ -483,7 +483,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "TCCACAGACAGCCCTCACAACGCCTGTAGCAT", "domains": [ {"helix": 6, "forward": false, "start": 96, "end": 112}, @@ -491,7 +491,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "CACCACCCTCATTTTCCCGCCACCCTCAGAGC", "domains": [ {"helix": 8, "forward": false, "start": 96, "end": 112}, @@ -499,7 +499,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "TATAAGTATAGCCCGGCCGTCGAGAGGGTTGA", "domains": [ {"helix": 10, "forward": false, "start": 96, "end": 112}, @@ -507,7 +507,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "TGAAAGTATTAAGAGGCTATTATTCTGAAACA", "domains": [ {"helix": 12, "forward": false, "start": 96, "end": 112}, @@ -515,7 +515,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "GGTAATAAGTTTTAACGATACAGGAGTGTACT", "domains": [ {"helix": 14, "forward": false, "start": 96, "end": 112}, @@ -523,7 +523,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "ATAAATCCTCATTAAATGATATTCACAAACAA", "domains": [ {"helix": 16, "forward": false, "start": 96, "end": 112}, @@ -531,7 +531,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "CCTCAGAGCCGCCACCCCCTCAGAGCCACCAC", "domains": [ {"helix": 18, "forward": false, "start": 96, "end": 112}, @@ -539,7 +539,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "TCTTTTCATAATCAAATTATTAGCGTTTGCCA", "domains": [ {"helix": 20, "forward": false, "start": 96, "end": 112}, @@ -547,7 +547,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "AATCAGTAGCGACAGATCGATAGCAGCACCGT", "domains": [ {"helix": 22, "forward": false, "start": 96, "end": 112}, @@ -555,7 +555,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "CCATTTGGGAATTAGACCGTCACCGACTTGAG", "domains": [ {"helix": 24, "forward": false, "start": 96, "end": 112}, @@ -563,7 +563,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "AGACAAAAGGGCGACAGGTTTACCAGCGCCAA", "domains": [ {"helix": 26, "forward": false, "start": 96, "end": 112}, @@ -571,7 +571,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TAAAGGTGGCAACATAGTAGAAAATACATACA", "domains": [ {"helix": 28, "forward": false, "start": 96, "end": 112}, @@ -579,7 +579,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "CCGAGGAAACGCAATAAGTTACCAGAAGGAAA", "domains": [ {"helix": 30, "forward": false, "start": 96, "end": 112}, @@ -587,7 +587,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "ATAAGAGCAAGAAACATGAGTTAAGCCCAATA", "domains": [ {"helix": 32, "forward": false, "start": 96, "end": 112}, @@ -595,7 +595,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "GACGGGAGAATTAACTACAGGGAAGCGCATTA", "domains": [ {"helix": 34, "forward": false, "start": 96, "end": 112}, @@ -603,7 +603,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "TCCCAATCCAAATAAGACAGCCATATTATTTA", "domains": [ {"helix": 36, "forward": false, "start": 96, "end": 112}, @@ -611,7 +611,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "ACCCAGCTACAATTTTTTAGTTGCTATTTTGC", "domains": [ {"helix": 38, "forward": false, "start": 96, "end": 112}, @@ -619,7 +619,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "GCTTATCCGGTATTCTAAATCAGATATAGAAG", "domains": [ {"helix": 40, "forward": false, "start": 96, "end": 112}, @@ -627,7 +627,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "ACCAAGTACCGCACTCCAAGAACGGGTATTAA", "domains": [ {"helix": 42, "forward": false, "start": 96, "end": 112}, @@ -635,7 +635,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "GAACAAGAAAAATAATACAATAGATAAGTCCT", "domains": [ {"helix": 44, "forward": false, "start": 96, "end": 112}, @@ -643,7 +643,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "CGACAAAAGGTAAAGTAGAGAATATAAAGTAC", "domains": [ {"helix": 46, "forward": false, "start": 96, "end": 112}, @@ -651,7 +651,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CAGTAGGGCTTAATTGTAAAGCCAACGCTCAA", "domains": [ {"helix": 48, "forward": false, "start": 96, "end": 112}, @@ -659,7 +659,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "AATAAGAATAAACACCGATAAATAAGGCGTTA", "domains": [ {"helix": 50, "forward": false, "start": 96, "end": 112}, @@ -667,7 +667,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CGCGAGAAAACTTTTTATCGCAAGACAAAGAA", "domains": [ {"helix": 52, "forward": false, "start": 96, "end": 112}, @@ -675,7 +675,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CATAGGTCTGAGAGACGTGAATTTATCAAAAT", "domains": [ {"helix": 54, "forward": false, "start": 96, "end": 112}, @@ -683,7 +683,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "CGTCGCTATTAATTAACCTTGCTTCTGTAAAT", "domains": [ {"helix": 56, "forward": false, "start": 96, "end": 112}, @@ -691,7 +691,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "ATTAATTACATTTAACACATCAAGAAAACAAA", "domains": [ {"helix": 58, "forward": false, "start": 96, "end": 112}, @@ -699,7 +699,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "CTTTGAATACCAAGTTCGGATTCGCCTGATTG", "domains": [ {"helix": 60, "forward": false, "start": 96, "end": 112}, @@ -707,7 +707,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "AAAGAAATTGCGTAGACACGTAAAACAGAAAT", "domains": [ {"helix": 62, "forward": false, "start": 96, "end": 112}, @@ -715,14 +715,14 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "ATATATTCGGTCGCTGAGGCTTGCAGGGAGTT", "domains": [ {"helix": 0, "forward": false, "start": 56, "end": 88} ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "TTTCATGAAGAGGCTTTGAGGACTGTGAATTT", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -730,7 +730,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "CTTAAACATCAGCTTGCTTTCGAGAAAGACTT", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -738,7 +738,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "CTCATCTTGAGGCAAAAGAATACAGAATTGCG", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -746,7 +746,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "AATAATAAAAAGGAACAACTAAAGCTAAAACA", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -754,7 +754,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "GCTCCATGAAATTGTGTCGAAATCCTTTCCAG", "domains": [ {"helix": 6, "forward": false, "start": 48, "end": 56}, @@ -762,7 +762,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "ACGTTAGTTCTAAAGTTTTGTCGTCGCGACCT", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 80}, @@ -770,7 +770,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "CCAGGCGCGAGGACAGATGAACGGCGTAACAC", "domains": [ {"helix": 8, "forward": false, "start": 48, "end": 56}, @@ -778,7 +778,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "TGAGTTTCATAGGAACCCATGTACTGTACAGA", "domains": [ {"helix": 7, "forward": true, "start": 72, "end": 80}, @@ -786,7 +786,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "GAATAAGGACGTAACAAAGCTGCTTACCGCCA", "domains": [ {"helix": 10, "forward": false, "start": 48, "end": 56}, @@ -794,7 +794,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "CCCTCAGATACTCAGGAGGTTTAGCATTCAGT", "domains": [ {"helix": 9, "forward": true, "start": 72, "end": 80}, @@ -802,7 +802,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "CGATTTTATTAATCATTGTGAATTCGGGGTTT", "domains": [ {"helix": 12, "forward": false, "start": 48, "end": 56}, @@ -810,7 +810,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "TGCTCAGTGAAGGATTAGGATTAGACCTTATG", "domains": [ {"helix": 11, "forward": true, "start": 72, "end": 80}, @@ -818,7 +818,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "AAAGATTCACGGAACAACATTATTAAACAGTT", "domains": [ {"helix": 14, "forward": false, "start": 48, "end": 56}, @@ -826,7 +826,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "AATGCCCCGTAACAGTGCCCGTATACAGGTAG", "domains": [ {"helix": 13, "forward": true, "start": 72, "end": 80}, @@ -834,7 +834,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "CATAACCCGAGGCATAGTAAGAGCCGTTCCAG", "domains": [ {"helix": 16, "forward": false, "start": 48, "end": 56}, @@ -842,7 +842,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "TAAGCGTCCAGTCTCTGAATTTACAACACTAT", "domains": [ {"helix": 15, "forward": true, "start": 72, "end": 80}, @@ -850,7 +850,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "ACTGGATAAGGGGGTAATAGTAAACAGGAGGT", "domains": [ {"helix": 18, "forward": false, "start": 48, "end": 56}, @@ -858,7 +858,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "TGAGGCAGCCGCCGCCAGCATTGAATGTTTAG", "domains": [ {"helix": 17, "forward": true, "start": 72, "end": 80}, @@ -866,7 +866,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "CAAAAATCCAGAAAACGAGAATGACTCCCTCA", "domains": [ {"helix": 20, "forward": false, "start": 48, "end": 56}, @@ -874,7 +874,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "GAGCCGCCCCACCACCGGAACCGCCCATAAAT", "domains": [ {"helix": 19, "forward": true, "start": 72, "end": 80}, @@ -882,7 +882,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "TTTTAATTGCCCGAAAGACTTCAACGTTTTCA", "domains": [ {"helix": 22, "forward": false, "start": 48, "end": 56}, @@ -890,7 +890,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "TCGGCATTGCGTCAGACTGTAGCGATATCGCG", "domains": [ {"helix": 21, "forward": true, "start": 72, "end": 80}, @@ -898,7 +898,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "TTTTTGCGATTGCTCCTTTTGATATAGCAAGG", "domains": [ {"helix": 24, "forward": false, "start": 48, "end": 56}, @@ -906,7 +906,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "CCGGAAACGTAGCACCATTACCATAGAGGTCA", "domains": [ {"helix": 23, "forward": true, "start": 72, "end": 80}, @@ -914,7 +914,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "TCCATATAAAGTACGGTGTCTGGAGACGGAAA", "domains": [ {"helix": 26, "forward": false, "start": 48, "end": 56}, @@ -922,7 +922,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "TTATTCATAGGGAAGGTAAATATTAGTTTCAT", "domains": [ {"helix": 25, "forward": true, "start": 72, "end": 80}, @@ -930,7 +930,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "TTTCATTTGGTCAATAACCTGTTTTTATTTTG", "domains": [ {"helix": 28, "forward": false, "start": 48, "end": 56}, @@ -938,7 +938,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "TCACAATCACACCACGGAATAAGTAGCTATAT", "domains": [ {"helix": 27, "forward": true, "start": 72, "end": 80}, @@ -946,7 +946,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "CAAAATTACATACAGGCAAGGCAAAAGACTCC", "domains": [ {"helix": 30, "forward": false, "start": 48, "end": 56}, @@ -954,7 +954,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "TTATTACGAAGAACTGGCATGATTAGAATTAG", "domains": [ {"helix": 29, "forward": true, "start": 72, "end": 80}, @@ -962,7 +962,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "CAACGCAACTTTTGCGGGAGAAGCTTTTTAAG", "domains": [ {"helix": 32, "forward": false, "start": 48, "end": 56}, @@ -970,7 +970,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "AAAAGTAATATCTTACCGAAGCCCCTTTATTT", "domains": [ {"helix": 31, "forward": true, "start": 72, "end": 80}, @@ -978,7 +978,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "AGACAGTCATTCAAAAGGGTGAGAGCGCTAAT", "domains": [ {"helix": 34, "forward": false, "start": 48, "end": 56}, @@ -986,7 +986,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "ATCAGAGAGTCAGAGGGTAATTGAAAGGCCGG", "domains": [ {"helix": 33, "forward": true, "start": 72, "end": 80}, @@ -994,7 +994,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "TCAGGTCATTTTTGAGAGATCTACATAGCAGC", "domains": [ {"helix": 36, "forward": false, "start": 48, "end": 56}, @@ -1002,7 +1002,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "CTTTACAGAACGTCAAAAATGAAAAAAGGCTA", "domains": [ {"helix": 35, "forward": true, "start": 72, "end": 80}, @@ -1010,7 +1010,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "AGAAAAGCTCATATGTACCCCGGTTTCCAGAG", "domains": [ {"helix": 38, "forward": false, "start": 48, "end": 56}, @@ -1018,7 +1018,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "CCTAATTTACGCTAACGAGCGTCTTGATAATC", "domains": [ {"helix": 37, "forward": true, "start": 72, "end": 80}, @@ -1026,7 +1026,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "GCTCATTTTCGCATTAAATTTTTGCTTGCGGG", "domains": [ {"helix": 40, "forward": false, "start": 48, "end": 56}, @@ -1034,7 +1034,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "AGGTTTTGTTAGCGAACCTCCCGATTAAATCA", "domains": [ {"helix": 39, "forward": true, "start": 72, "end": 80}, @@ -1042,7 +1042,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "ACCCGTCGAACATTAAATGTGAGCCGTAGGAA", "domains": [ {"helix": 42, "forward": false, "start": 48, "end": 56}, @@ -1050,7 +1050,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "TCATTACCCCGTTTTTATTTTCATGAGTAACA", "domains": [ {"helix": 41, "forward": true, "start": 72, "end": 80}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "GTTTGAGGCGCATCGTAACCGTGCAATCAATA", "domains": [ {"helix": 44, "forward": false, "start": 48, "end": 56}, @@ -1066,7 +1066,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "ATCGGCTGCGAGCATGTAGAAACCATCTGCCA", "domains": [ {"helix": 43, "forward": true, "start": 72, "end": 80}, @@ -1074,7 +1074,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "TTCGCCATTGCCGGAAACCAGGCAGTTCAGCT", "domains": [ {"helix": 46, "forward": false, "start": 48, "end": 56}, @@ -1082,7 +1082,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "AATGCAGACGACAATAAACAACATAAGCGCCA", "domains": [ {"helix": 45, "forward": true, "start": 72, "end": 80}, @@ -1090,7 +1090,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "ATTAAGTTGAAAGGGGGATGTGCTATTTAGGC", "domains": [ {"helix": 48, "forward": false, "start": 48, "end": 56}, @@ -1098,7 +1098,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "AGAGGCATACAACGCCAACATGTAGCAAGGCG", "domains": [ {"helix": 47, "forward": true, "start": 72, "end": 80}, @@ -1106,7 +1106,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "CCCGGGTACCTGCAGGTCGACTCTTATCATAT", "domains": [ {"helix": 50, "forward": false, "start": 48, "end": 56}, @@ -1114,7 +1114,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "GCGTTATAGAAAAAGCCTGTTTAGAGAGGATC", "domains": [ {"helix": 49, "forward": true, "start": 72, "end": 80}, @@ -1122,7 +1122,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "GCATAAAGTTCCACACAACATACGCTAAATTT", "domains": [ {"helix": 52, "forward": false, "start": 48, "end": 56}, @@ -1130,7 +1130,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "AATGGTTTAATTTCATCTTCTGACAGCCGGAA", "domains": [ {"helix": 51, "forward": true, "start": 72, "end": 80}, @@ -1138,7 +1138,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "GCCAGCTGCTTTCCAGTCGGGAAATATAACTA", "domains": [ {"helix": 54, "forward": false, "start": 48, "end": 56}, @@ -1146,7 +1146,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "TATGTAAAGGCTTAGGTTGGGTTACCTGTCGT", "domains": [ {"helix": 53, "forward": true, "start": 72, "end": 80}, @@ -1154,7 +1154,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "AGCTGATTCTTTTCACCAGTGAGAAGCTTAGA", "domains": [ {"helix": 56, "forward": false, "start": 48, "end": 56}, @@ -1162,7 +1162,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "TTAAGACGTTGAAAACATAGCGATCGGGCAAC", "domains": [ {"helix": 55, "forward": true, "start": 72, "end": 80}, @@ -1170,7 +1170,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "CCGAAATCCGAAAATCCTGTTTGACAGTACAT", "domains": [ {"helix": 58, "forward": false, "start": 48, "end": 56}, @@ -1178,7 +1178,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "AAATCAATCCTTTTTTAATGGAAATGGTGGTT", "domains": [ {"helix": 57, "forward": true, "start": 72, "end": 80}, @@ -1186,7 +1186,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "TGGACTCCACAAGAGTCCACTATTAATTACCT", "domains": [ {"helix": 60, "forward": false, "start": 48, "end": 56}, @@ -1194,7 +1194,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "GAGCAAAAGCGAATTATTCATTTCAAAGAACG", "domains": [ {"helix": 59, "forward": true, "start": 72, "end": 80}, @@ -1202,7 +1202,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "GTAAAGCACAAGTTTTTTGGGGTCAACAGTAC", "domains": [ {"helix": 62, "forward": false, "start": 48, "end": 56}, @@ -1210,7 +1210,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "CTTTTACACAGATGAATATACAGTGAGGTGCC", "domains": [ {"helix": 61, "forward": true, "start": 72, "end": 80}, @@ -1218,14 +1218,14 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "GAACGTGGCGAGAAAGGAAGGGAAAGGGTTAG", "domains": [ {"helix": 63, "forward": true, "start": 40, "end": 72} ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "AAAGGCCGCTTTTGCGGGATCGTCGGGTAGCA", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56}, @@ -1233,7 +1233,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "ACGGCTACGGAAGTTTCCATTAAACCAACCTA", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -1242,7 +1242,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "AAACGAAATGACCCCCAGCGATTATGTATCAT", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -1251,7 +1251,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CGCCTGATTTACTTAGCCGGAACGCTGACCAA", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 48}, @@ -1260,7 +1260,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "CTTTGAAAATAGGCTGGCTGACCTTTCATTAC", "domains": [ {"helix": 7, "forward": true, "start": 40, "end": 48}, @@ -1269,7 +1269,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "CCAAATCACTTGCCCTGACGAGAATGGTTTAA", "domains": [ {"helix": 9, "forward": true, "start": 40, "end": 48}, @@ -1278,7 +1278,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "TTTCAACTAGAACTGGCTCATTATTTAATAAA", "domains": [ {"helix": 11, "forward": true, "start": 40, "end": 48}, @@ -1287,7 +1287,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "ACGAACTAATCAGTTGAGATTTAGCGCCAAAA", "domains": [ {"helix": 13, "forward": true, "start": 40, "end": 48}, @@ -1296,7 +1296,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "GGAATTACTCGTTTACCAGACGACAAAGAAGT", "domains": [ {"helix": 15, "forward": true, "start": 40, "end": 48}, @@ -1305,7 +1305,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TTTGCCAGGCGTCCAATACTGCGGAATGCTTT", "domains": [ {"helix": 17, "forward": true, "start": 40, "end": 48}, @@ -1314,7 +1314,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "AAACAGTTAGGTCTTTACCCTGACAAAAGATT", "domains": [ {"helix": 19, "forward": true, "start": 40, "end": 48}, @@ -1323,7 +1323,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "AAGAGGAACGAGCTTCAAAGCGAATTAGAGAG", "domains": [ {"helix": 21, "forward": true, "start": 40, "end": 48}, @@ -1332,7 +1332,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "TACCTTTAGATGGCTTAGAGCTTATTTAAATA", "domains": [ {"helix": 23, "forward": true, "start": 40, "end": 48}, @@ -1341,7 +1341,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "TGCAACTAACAGTTGATTCCCAATGATACATT", "domains": [ {"helix": 25, "forward": true, "start": 40, "end": 48}, @@ -1350,7 +1350,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "TCGCAAATGGGGCGCGAGCTGAAATTAACATC", "domains": [ {"helix": 27, "forward": true, "start": 40, "end": 48}, @@ -1359,7 +1359,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CAATAAATAGCAATAAAGCCTCAGTTATGACC", "domains": [ {"helix": 29, "forward": true, "start": 40, "end": 48}, @@ -1368,7 +1368,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CTGTAATAGGATAAAAATTTTTAGTAATGTGT", "domains": [ {"helix": 31, "forward": true, "start": 40, "end": 48}, @@ -1377,7 +1377,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "AGGTAAAGAAATCACCATCAATATCCGGAGAG", "domains": [ {"helix": 33, "forward": true, "start": 40, "end": 48}, @@ -1386,7 +1386,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "GGTAGCTATTGCCTGAGAGTCTGGAAAACTAG", "domains": [ {"helix": 35, "forward": true, "start": 40, "end": 48}, @@ -1395,7 +1395,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CATGTCAACCCAAAAACAGGAAGAAATATTTT", "domains": [ {"helix": 37, "forward": true, "start": 40, "end": 48}, @@ -1404,7 +1404,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "GTTAAAATTTTAACCAATAGGAACGTAGCCAG", "domains": [ {"helix": 39, "forward": true, "start": 40, "end": 48}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CTTTCATCGATTCTCCGTGGGAACCGTTGGTG", "domains": [ {"helix": 41, "forward": true, "start": 40, "end": 48}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TAGATGGGGGACGACGACAGTATCCCGGCACC", "domains": [ {"helix": 43, "forward": true, "start": 40, "end": 48}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GCTTCTGGTCAGGCTGCGCAACTGTATTACGC", "domains": [ {"helix": 45, "forward": true, "start": 40, "end": 48}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "CAGCTGGCGGGTAACGCCAGGGTTGTGCCAAG", "domains": [ {"helix": 47, "forward": true, "start": 40, "end": 48}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "CTTGCATGCCGAGCTCGAATTCGTTGTTATCC", "domains": [ {"helix": 49, "forward": true, "start": 40, "end": 48}, @@ -1458,7 +1458,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "GCTCACAATGTAAAGCCTGGGGTGTTGCGCTC", "domains": [ {"helix": 51, "forward": true, "start": 40, "end": 48}, @@ -1467,7 +1467,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "ACTGCCCGCATTAATGAATCGGCCCGCCAGGG", "domains": [ {"helix": 53, "forward": true, "start": 40, "end": 48}, @@ -1476,7 +1476,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "TGGTTTTTGCCCTTCACCGCCTGGGGTTTGCC", "domains": [ {"helix": 55, "forward": true, "start": 40, "end": 48}, @@ -1485,7 +1485,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CCAGCAGGGGCAAAATCCCTTATAGTTGTTCC", "domains": [ {"helix": 57, "forward": true, "start": 40, "end": 48}, @@ -1494,7 +1494,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "AGTTTGGAAACGTCAAAGGGCGAAGAACCATC", "domains": [ {"helix": 59, "forward": true, "start": 40, "end": 48}, @@ -1503,7 +1503,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "ACCCAAATCTAAATCGGAACCCTAAAGCCGGC", "domains": [ {"helix": 61, "forward": true, "start": 40, "end": 48}, @@ -1512,7 +1512,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "AACCTACCATATCAAAATTATTTGTTTTCAGG", "domains": [ {"helix": 63, "forward": true, "start": 72, "end": 96}, @@ -1520,7 +1520,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "TCGGTTTAGCTTGATACCGATAGTCATAACCG", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88}, @@ -1529,7 +1529,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "GAGAATAGTTTTTTCACGTTGAAATAATTGTA", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88}, @@ -1538,7 +1538,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "CGTAACGAAAATGAATTTTCTGTAAGCGGAGT", "domains": [ {"helix": 6, "forward": false, "start": 80, "end": 88}, @@ -1547,7 +1547,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "CAAGCCCAGTCACCAGTACAAACTATAGTTAG", "domains": [ {"helix": 8, "forward": false, "start": 80, "end": 88}, @@ -1556,7 +1556,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "TATCACCGACCGCCACCCTCAGAAAGGGATAG", "domains": [ {"helix": 10, "forward": false, "start": 80, "end": 88}, @@ -1565,7 +1565,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "CCTCAAGAACCAGGCGGATAAGTGAATAGGTG", "domains": [ {"helix": 12, "forward": false, "start": 80, "end": 88}, @@ -1574,7 +1574,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "TGCCTTGACTGCCTATTTCGGAACCTGAGACT", "domains": [ {"helix": 14, "forward": false, "start": 80, "end": 88}, @@ -1583,7 +1583,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "GGAAAGCGATACATGGCTTTTGATGGGGTCAG", "domains": [ {"helix": 16, "forward": false, "start": 80, "end": 88}, @@ -1592,7 +1592,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CACCAGAGGTCAGACGATTGGCCTGCCAGAAT", "domains": [ {"helix": 18, "forward": false, "start": 80, "end": 88}, @@ -1601,7 +1601,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "AACCAGAGACCCTCAGAACCGCCAAGAACCAC", "domains": [ {"helix": 20, "forward": false, "start": 80, "end": 88}, @@ -1610,7 +1610,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "TGCCTTTATTCGGTCATAGCCCCCATCACCGG", "domains": [ {"helix": 22, "forward": false, "start": 80, "end": 88}, @@ -1619,7 +1619,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "AATCACCAGTCACCAATGAAACCAATCAAGTT", "domains": [ {"helix": 24, "forward": false, "start": 80, "end": 88}, @@ -1628,7 +1628,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "ATTGAGGGTAAAGGTGAATTATCAGCCAGCAA", "domains": [ {"helix": 26, "forward": false, "start": 80, "end": 88}, @@ -1637,7 +1637,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "ACGCAAAGAATAGAAAATTCATATTTCAACCG", "domains": [ {"helix": 28, "forward": false, "start": 80, "end": 88}, @@ -1646,7 +1646,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "ATACCCAACAGTATGTTAGCAAACTAAAAGAA", "domains": [ {"helix": 30, "forward": false, "start": 80, "end": 88}, @@ -1655,7 +1655,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "GCAATAGCGCAGATAGCCGAACAAATAACGGA", "domains": [ {"helix": 32, "forward": false, "start": 80, "end": 88}, @@ -1664,7 +1664,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "TGAACAAAGATAACCCACAAGAATATGAAATA", "domains": [ {"helix": 34, "forward": false, "start": 80, "end": 88}, @@ -1673,7 +1673,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "TTTTGTTTAGAGAATAACATAAAAGAACACCC", "domains": [ {"helix": 36, "forward": false, "start": 80, "end": 88}, @@ -1682,7 +1682,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "TCTTACCAGCCAGTTACAAAATAAAAACGATT", "domains": [ {"helix": 38, "forward": false, "start": 80, "end": 88}, @@ -1691,7 +1691,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "GAGGCGTTAAGCCTTAAATCAAGAATCCTGAA", "domains": [ {"helix": 40, "forward": false, "start": 80, "end": 88}, @@ -1700,7 +1700,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "CAAGCAAGGCGCCCAATAGCAAGCAAGAACGC", "domains": [ {"helix": 42, "forward": false, "start": 80, "end": 88}, @@ -1709,7 +1709,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CTAATTTATCTTTCCTTATCATTCATCGAGAA", "domains": [ {"helix": 44, "forward": false, "start": 80, "end": 88}, @@ -1718,7 +1718,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CCAGACGAACGCGCCTGTTTATCAATCCCATC", "domains": [ {"helix": 46, "forward": false, "start": 80, "end": 88}, @@ -1727,7 +1727,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "CATATTTATTTCGAGCCAGTAATAAATTCTGT", "domains": [ {"helix": 48, "forward": false, "start": 80, "end": 88}, @@ -1736,7 +1736,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "AATTACTACAAATTCTTACCAGTAAGAATCGC", "domains": [ {"helix": 50, "forward": false, "start": 80, "end": 88}, @@ -1745,7 +1745,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "TTTTAGTTGAAATACCGACCGTGTGGAATCAT", "domains": [ {"helix": 52, "forward": false, "start": 80, "end": 88}, @@ -1754,7 +1754,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "TAACCTCCTGCTGATGCAAATCCACAAATATA", "domains": [ {"helix": 54, "forward": false, "start": 80, "end": 88}, @@ -1763,7 +1763,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "TAGAATCCCTGAGAAGAGTCAATATACCTTTT", "domains": [ {"helix": 56, "forward": false, "start": 80, "end": 88}, @@ -1772,7 +1772,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TTGAATTAATATGTGAGTGAATAATTTTCCCT", "domains": [ {"helix": 58, "forward": false, "start": 80, "end": 88}, @@ -1781,7 +1781,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "GCGCAGAGGAAGATGATGAAACAAAATTTCAT", "domains": [ {"helix": 60, "forward": false, "start": 80, "end": 88}, @@ -1790,7 +1790,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "TTTAACGTTCGGGAGAAACAATAAACAAAATC", "domains": [ {"helix": 62, "forward": false, "start": 80, "end": 88}, diff --git a/examples/output_designs/6_helix_6_col_origami_rectangle.dna b/examples/output_designs/6_helix_6_col_origami_rectangle.dna index b7753e3b..d6aacd04 100644 --- a/examples/output_designs/6_helix_6_col_origami_rectangle.dna +++ b/examples/output_designs/6_helix_6_col_origami_rectangle.dna @@ -29,7 +29,7 @@ "is_scaffold": true }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CGAGATAGGGTTGAGTAATCAAAAGAATAGCC", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16}, @@ -37,7 +37,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CGATGGCCCACTACGTAAACCGTCTATCAGGG", "domains": [ {"helix": 3, "forward": true, "start": 0, "end": 16}, @@ -45,7 +45,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TAGAGCTTGACGGGGAAAGGGAGCCCCCGATT", "domains": [ {"helix": 5, "forward": true, "start": 0, "end": 16}, @@ -53,7 +53,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GCAAGCGGTCCACGCTCCCTGAGAGAGTTGCA", "domains": [ {"helix": 0, "forward": false, "start": 80, "end": 96}, @@ -61,7 +61,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CGGTTTGCGTATTGGGAACGCGCGGGGAGAGG", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 96}, @@ -69,7 +69,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "ACTCACATTAATTGCGCCTAATGAGTGAGCTA", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 96}, @@ -77,14 +77,14 @@ ] }, { - "color": "#b8056c", + "color": "#03b6a2", "sequence": "CCAGCAGGCGAAAATCCTGTTTGATGGTGGTT", "domains": [ {"helix": 0, "forward": false, "start": 40, "end": 72} ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "TGGACTCCACAAGAGTCCACTATTCGGGCAAC", "domains": [ {"helix": 2, "forward": false, "start": 32, "end": 40}, @@ -92,7 +92,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "AGCTGATTCTTTTCACCAGTGAGAAAAGAACG", "domains": [ {"helix": 1, "forward": true, "start": 56, "end": 64}, @@ -100,7 +100,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GTAAAGCACAAGTTTTTTGGGGTCCCTGTCGT", "domains": [ {"helix": 4, "forward": false, "start": 32, "end": 40}, @@ -108,7 +108,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "GCCAGCTGCTTTCCAGTCGGGAAAGAGGTGCC", "domains": [ {"helix": 3, "forward": true, "start": 56, "end": 64}, @@ -116,14 +116,14 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GAACGTGGCGAGAAAGGAAGGGAAAGCCGGAA", "domains": [ {"helix": 5, "forward": true, "start": 24, "end": 56} ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "CCGAAATCGGCAAAATCCCTTATAGTTGTTCC", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 40}, @@ -131,7 +131,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "AGTTTGGAAACGTCAAAGGGCGAAGAACCATC", "domains": [ {"helix": 1, "forward": true, "start": 24, "end": 32}, @@ -140,7 +140,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "ACCCAAATCTAAATCGGAACCCTAAAGCCGGC", "domains": [ {"helix": 3, "forward": true, "start": 24, "end": 32}, @@ -149,7 +149,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "GCATAAAGTGTAAAGCCTGGGGTGTTGCGCTC", "domains": [ {"helix": 5, "forward": true, "start": 56, "end": 80}, @@ -157,7 +157,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "TGGTTTTTGCCCTTCACCGCCTGGGGTTTGCC", "domains": [ {"helix": 2, "forward": false, "start": 64, "end": 72}, @@ -166,7 +166,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "ACTGCCCGCATTAATGAATCGGCCCGCCAGGG", "domains": [ {"helix": 4, "forward": false, "start": 64, "end": 72}, diff --git a/examples/output_designs/6_helix_bundle_honeycomb.dna b/examples/output_designs/6_helix_bundle_honeycomb.dna index 62de1502..9592fa96 100644 --- a/examples/output_designs/6_helix_bundle_honeycomb.dna +++ b/examples/output_designs/6_helix_bundle_honeycomb.dna @@ -11,7 +11,6 @@ ], "strands": [ { - "color": "#320096", "sequence": "CATTTCTCCGAAGAGACGCATTTCACATGTGGGCCTTGAATC", "domains": [ {"helix": 3, "forward": true, "start": 56, "end": 70}, @@ -20,7 +19,6 @@ ] }, { - "color": "#57bb00", "sequence": "ACGCTCGCCCTGCTCAATGTCCCGCCAAGAATTGTCAACCTT", "domains": [ {"helix": 2, "forward": false, "start": 70, "end": 84}, @@ -29,7 +27,6 @@ ] }, { - "color": "#cc0000", "sequence": "ATCTCTGACCTCCTAGTCGGGAAACCTGGCACGAATATAGTT", "domains": [ {"helix": 4, "forward": false, "start": 56, "end": 70}, @@ -38,7 +35,6 @@ ] }, { - "color": "#007200", "sequence": "GGGAGTGACTCTATCAACTCGTCGGTGGTCGTGCCAGCTGCA", "domains": [ {"helix": 1, "forward": true, "start": 70, "end": 84}, @@ -47,7 +43,6 @@ ] }, { - "color": "#7300de", "sequence": "TGTGAATTCATGGGGATGTTCTTCTAAGGGAGGAGAAGCCAG", "domains": [ {"helix": 3, "forward": true, "start": 98, "end": 112}, @@ -56,7 +51,6 @@ ] }, { - "color": "#32b86c", "sequence": "GCTGCAAGGCGATGCCTCTTCGCTATTAAAGGGCGATCGGTG", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 126}, @@ -65,7 +59,6 @@ ] }, { - "color": "#f74308", "sequence": "CGCGCACGACTTAAAACGCGCGGGGAGACCAAGCTTTCTCCC", "domains": [ {"helix": 4, "forward": false, "start": 98, "end": 112}, @@ -74,7 +67,6 @@ ] }, { - "color": "#f7931e", "sequence": "GGTTAAGTTGGGTAAACGACGGCCAGTGGGCGGTTTGCGTAT", "domains": [ {"helix": 1, "forward": true, "start": 112, "end": 126}, @@ -83,7 +75,6 @@ ] }, { - "color": "#b8056c", "sequence": "AAAGCGCCATTCCGTGGTGCCGGAAACCCCTTTCCGGCACCG", "domains": [ {"helix": 3, "forward": true, "start": 140, "end": 154}, @@ -92,7 +83,6 @@ ] }, { - "color": "#320096", "sequence": "ATGGGCGCATCGTCGCGGATTGACCGTATCTCCGTGGGAACA", "domains": [ {"helix": 2, "forward": false, "start": 154, "end": 168}, @@ -101,7 +91,6 @@ ] }, { - "color": "#888888", "sequence": "AAGCCATTCAGGCTGTTTTTCTTTTCACACTCCAGCCAGCAG", "domains": [ {"helix": 4, "forward": false, "start": 140, "end": 154}, @@ -110,7 +99,6 @@ ] }, { - "color": "#57bb00", "sequence": "CTTAACCGTGCATCCTCAGGAAGATCGCCAGTGAGACGGGCA", "domains": [ {"helix": 1, "forward": true, "start": 154, "end": 168}, @@ -119,7 +107,6 @@ ] }, { - "color": "#cc0000", "sequence": "ATCAACATTAAACCTTCCTGTAGCCAGCGATAATTCGCGTCT", "domains": [ {"helix": 3, "forward": true, "start": 182, "end": 196}, @@ -128,7 +115,6 @@ ] }, { - "color": "#7300de", "sequence": "AAACGTTAATATCCAAAAACAGGAAGATGATAATCAGAAAAG", "domains": [ {"helix": 2, "forward": false, "start": 196, "end": 210}, @@ -137,7 +123,6 @@ ] }, { - "color": "#333333", "sequence": "CCTGTGAGCGAGTATTCACCGCCTGGCCCGCCATCAAAAACG", "domains": [ {"helix": 4, "forward": false, "start": 182, "end": 196}, @@ -146,7 +131,6 @@ ] }, { - "color": "#32b86c", "sequence": "GGTTTGTTAAAATTTTAACCAATAGGAACTGAGAGAGTTGCA", "domains": [ {"helix": 1, "forward": true, "start": 196, "end": 210}, @@ -155,7 +139,6 @@ ] }, { - "color": "#f74308", "sequence": "ATCGTAAAACTAAAGAGAATCGATGAACGTAGTCTGGAGCAA", "domains": [ {"helix": 3, "forward": true, "start": 224, "end": 238}, @@ -164,7 +147,6 @@ ] }, { - "color": "#b8056c", "sequence": "AACCGTTCTAGCAAAGGCCGGAGACAGTGATTCAAAAGGGTG", "domains": [ {"helix": 2, "forward": false, "start": 238, "end": 252}, @@ -173,7 +155,6 @@ ] }, { - "color": "#03b6a2", "sequence": "AGGCATGTCAATCACTGGTTTGCCCCAGTCATTGCCTGAGTA", "domains": [ {"helix": 4, "forward": false, "start": 224, "end": 238}, @@ -182,7 +163,6 @@ ] }, { - "color": "#320096", "sequence": "ACTGATAAATTAATCAAAGGCTATCAGGCAGGCGAAAATCCT", "domains": [ {"helix": 1, "forward": true, "start": 238, "end": 252}, @@ -191,7 +171,6 @@ ] }, { - "color": "#888888", "sequence": "ATATTTTAAATGAAAATTTTTAGAACCCCTTCAACGCAAGGA", "domains": [ {"helix": 3, "forward": true, "start": 266, "end": 280}, @@ -200,7 +179,6 @@ ] }, { - "color": "#cc0000", "sequence": "TAAAGCCTCAGAAATCATACAGGCAAGGGCATTAACATCCAA", "domains": [ {"helix": 2, "forward": false, "start": 280, "end": 294}, @@ -209,7 +187,6 @@ ] }, { - "color": "#aaaa00", "sequence": "TACAATGCCTGAGTCCGAAATCGGCAAAGAAGCCTTTATTAT", "domains": [ {"helix": 4, "forward": false, "start": 266, "end": 280}, @@ -218,7 +195,6 @@ ] }, { - "color": "#7300de", "sequence": "TAGCATAAAGCTAAATACTTTTGCGGGAATCCCTTATAAATC", "domains": [ {"helix": 1, "forward": true, "start": 280, "end": 294}, @@ -227,7 +203,6 @@ ] }, { - "color": "#333333", "sequence": "GAGCTGAAAAGGCATATTTTCATTTGGGAAATAACCTGTTTA", "domains": [ {"helix": 3, "forward": true, "start": 308, "end": 322}, @@ -236,7 +211,6 @@ ] }, { - "color": "#f74308", "sequence": "TTCATTCCATATTATGTTTTAAATATGCTAATGCTGTAGCTC", "domains": [ {"helix": 2, "forward": false, "start": 322, "end": 336}, @@ -245,7 +219,6 @@ ] }, { - "color": "#007200", "sequence": "AATGGCATCAATTCAGATAGGGTTGAGTCGCAAATGGTCAAC", "domains": [ {"helix": 4, "forward": false, "start": 308, "end": 322}, @@ -254,7 +227,6 @@ ] }, { - "color": "#b8056c", "sequence": "GCAACAGTTGATTCCATTAGATACATTTGTTGTTCCAGTTTG", "domains": [ {"helix": 1, "forward": true, "start": 322, "end": 336}, @@ -263,7 +235,6 @@ ] }, { - "color": "#03b6a2", "sequence": "TCATTTTTGCGGCAGCTCCTTTTGATAAGAGAGAGTACCTTT", "domains": [ {"helix": 3, "forward": true, "start": 350, "end": 364}, @@ -272,7 +243,6 @@ ] }, { - "color": "#888888", "sequence": "CCCGAAAGACTTTTGAAGCAAAGCGGATCCCTGACTATTATA", "domains": [ {"helix": 2, "forward": false, "start": 364, "end": 378}, @@ -281,7 +251,6 @@ ] }, { - "color": "#f7931e", "sequence": "GTATGGCTTAGAGCTATTAAAGAACGTGAGGTCAGGATTAGT", "domains": [ {"helix": 4, "forward": false, "start": 350, "end": 364}, @@ -290,7 +259,6 @@ ] }, { - "color": "#cc0000", "sequence": "AACAAATATCGCGTAAGCAAACTCCAACGACTCCAACGTCAA", "domains": [ {"helix": 1, "forward": true, "start": 364, "end": 378}, @@ -299,7 +267,6 @@ ] }, { - "color": "#aaaa00", "sequence": "AAAACGAGAATGCCATGCTTTAAACAGTCAATTGAATCCCCC", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 406}, @@ -308,7 +275,6 @@ ] }, { - "color": "#333333", "sequence": "AAAAGAAGTTTTAAAGACGACGATAAAATCATAACCCTCGTT", "domains": [ {"helix": 2, "forward": false, "start": 406, "end": 420}, @@ -317,7 +283,6 @@ ] }, { - "color": "#57bb00", "sequence": "TAACCATAAATCAATCTATCAGGGCGATTCATAAATATTCAA", "domains": [ {"helix": 4, "forward": false, "start": 392, "end": 406}, @@ -326,7 +291,6 @@ ] }, { - "color": "#f74308", "sequence": "TCGCCAGAGGGGGTATACTGCGGAATCGGGCCCACTACGTGA", "domains": [ {"helix": 1, "forward": true, "start": 406, "end": 420}, @@ -335,7 +299,6 @@ ] }, { - "color": "#007200", "sequence": "GCCAAAAGGAATATCTAATGCAGATACATAGGAATACCACAT", "domains": [ {"helix": 3, "forward": true, "start": 434, "end": 448}, @@ -344,7 +307,6 @@ ] }, { - "color": "#03b6a2", "sequence": "TTGGGAAGAAAAAAGCGATTTTAAGAACCATTGTGAATTACC", "domains": [ {"helix": 2, "forward": false, "start": 448, "end": 462}, @@ -353,7 +315,6 @@ ] }, { - "color": "#32b86c", "sequence": "TTTACGAGGCATAGCAAGTTTTTTGGGGAGTTGAGATTTAGA", "domains": [ {"helix": 4, "forward": false, "start": 434, "end": 448}, @@ -362,7 +323,6 @@ ] }, { - "color": "#888888", "sequence": "TCATCTACGTTAATTAGAAAGATTCATCTCGAGGTGCCGTAA", "domains": [ {"helix": 1, "forward": true, "start": 448, "end": 462}, @@ -371,7 +331,6 @@ ] }, { - "color": "#f7931e", "sequence": "GTAAATTGGGCTGAGAAACACCAGAACGGAAGGCTTGCCCTG", "domains": [ {"helix": 3, "forward": true, "start": 476, "end": 490}, @@ -380,7 +339,6 @@ ] }, { - "color": "#aaaa00", "sequence": "GACCTTCATCAAGACAGATGAACGGTGTACCAACTTTGAAAG", "domains": [ {"helix": 2, "forward": false, "start": 490, "end": 504}, @@ -389,7 +347,6 @@ ] }, { - "color": "#320096", "sequence": "AGTGAGATGGTTTAACCCTAAAGGGAGCATTCAGTGAATAAC", "domains": [ {"helix": 4, "forward": false, "start": 476, "end": 490}, @@ -398,7 +355,6 @@ ] }, { - "color": "#333333", "sequence": "ACGAGTAATCTTGATAACAAAGCTGCTCCCCCGATTTAGAGC", "domains": [ {"helix": 1, "forward": true, "start": 490, "end": 504}, @@ -407,7 +363,6 @@ ] }, { - "color": "#57bb00", "sequence": "ACGAGGCGCAGACACCATGTTACTTAGCTCAAATCCGCGACC", "domains": [ {"helix": 3, "forward": true, "start": 518, "end": 532}, @@ -416,7 +371,6 @@ ] }, { - "color": "#007200", "sequence": "TCATCTTTGACCCTACCTAAAACGAAAGGCCACTACGAAGGC", "domains": [ {"helix": 2, "forward": false, "start": 532, "end": 546}, @@ -425,7 +379,6 @@ ] }, { - "color": "#7300de", "sequence": "ACCGGTCAATCATACGGCGAACGTGGCGTAAATTGTGTCGAT", "domains": [ {"helix": 4, "forward": false, "start": 518, "end": 532}, @@ -434,7 +387,6 @@ ] }, { - "color": "#03b6a2", "sequence": "TGCCCAGCGATTATGTATCATCGCCTGAAGAAAGGAAGGGAA", "domains": [ {"helix": 1, "forward": true, "start": 532, "end": 546}, @@ -443,7 +395,6 @@ ] }, { - "color": "#32b86c", "sequence": "CATGAGGAAGTTAAGAGGACTAAAGACTAACGGCTACAGAGG", "domains": [ {"helix": 3, "forward": true, "start": 560, "end": 574}, @@ -452,7 +403,6 @@ ] }, { - "color": "#f7931e", "sequence": "GAGGCTTGCAGGTTCAACCATCGCCCACTTGCGCCGACAATG", "domains": [ {"helix": 2, "forward": false, "start": 574, "end": 588}, @@ -461,7 +411,6 @@ ] }, { - "color": "#b8056c", "sequence": "ACTCCATTAAACGGCGGGCGCTAGGGCGCGAGGGTAGCAAAG", "domains": [ {"helix": 4, "forward": false, "start": 560, "end": 574}, @@ -470,7 +419,6 @@ ] }, { - "color": "#aaaa00", "sequence": "CTGAGTTAAAGGCCAGACAGCATCGGAACTGGCAAGTGTAGC", "domains": [ {"helix": 1, "forward": true, "start": 574, "end": 588}, @@ -479,7 +427,6 @@ ] }, { - "color": "#320096", "sequence": "TTTCGAGGTGAAGTATCGGTTTATCAGCGTAGGAGCCTTTAA", "domains": [ {"helix": 3, "forward": true, "start": 602, "end": 616}, @@ -488,7 +435,6 @@ ] }, { - "color": "#57bb00", "sequence": "AGTGAGAATAGAGTATGGGATTTTGCTAAGTAAATGAATTTT", "domains": [ {"helix": 2, "forward": false, "start": 616, "end": 630}, @@ -497,7 +443,6 @@ ] }, { - "color": "#cc0000", "sequence": "CTTTTCTTAAACAGTAACCACCACACCCAAAGGCTCCAAACA", "domains": [ {"helix": 4, "forward": false, "start": 602, "end": 616}, @@ -506,7 +451,6 @@ ] }, { - "color": "#007200", "sequence": "TTAAGGAACAACTAAAAATCTCCAAAAAGCCGCGCTTAATGC", "domains": [ {"helix": 1, "forward": true, "start": 616, "end": 630}, @@ -515,7 +459,6 @@ ] }, { - "color": "#7300de", "sequence": "GCGTAACGATCTTCAGACAGCCCTCATAAAGCCTGTAGCATT", "domains": [ {"helix": 3, "forward": true, "start": 644, "end": 658}, @@ -524,7 +467,6 @@ ] }, { - "color": "#32b86c", "sequence": "CACCCTCATTTTACAGAACCGCCACCCTTTTAGTACCGCCAC", "domains": [ {"helix": 2, "forward": false, "start": 658, "end": 672}, @@ -533,7 +475,6 @@ ] }, { - "color": "#f74308", "sequence": "CCAAAGTTTTGTCGCGTACTATGGTTGCACAAACTACAACTA", "domains": [ {"helix": 4, "forward": false, "start": 644, "end": 658}, @@ -542,7 +483,6 @@ ] }, { - "color": "#f7931e", "sequence": "CCCAGGGATAGCAAGTTTCGTCACCAGTTTTGACGAGCACGT", "domains": [ {"helix": 1, "forward": true, "start": 658, "end": 672}, @@ -551,7 +491,6 @@ ] }, { - "color": "#b8056c", "sequence": "GTATAGCCCGGACCTCGAGAGGGTTGATCAAGGCGGATAAGT", "domains": [ {"helix": 3, "forward": true, "start": 686, "end": 700}, @@ -560,7 +499,6 @@ ] }, { - "color": "#320096", "sequence": "TATTATTCTGAACGCGTATAAACAGTTAGCCTTGAGTAACAG", "domains": [ {"helix": 2, "forward": false, "start": 700, "end": 714}, @@ -569,7 +507,6 @@ ] }, { - "color": "#888888", "sequence": "TGATAGGTGTATCATCGTTAGAATCAGATTGCTCAGTACCTG", "domains": [ {"helix": 4, "forward": false, "start": 686, "end": 700}, @@ -578,7 +515,6 @@ ] }, { - "color": "#57bb00", "sequence": "GCACATGAAAGTATGGATTAGCGGGGTTGCGGGAGCTAAACA", "domains": [ {"helix": 1, "forward": true, "start": 700, "end": 714}, @@ -587,7 +523,6 @@ ] }, { - "color": "#cc0000", "sequence": "ACAGGAGTGTACCCTACATGGCTTTTGATCGTTCCAGTAAGC", "domains": [ {"helix": 3, "forward": true, "start": 728, "end": 742}, @@ -596,7 +531,6 @@ ] }, { - "color": "#7300de", "sequence": "GGTCAGACGATTCAACCAGAGCCGCCGCGCCGCCACCAGAAC", "domains": [ {"helix": 2, "forward": false, "start": 742, "end": 756}, @@ -605,7 +539,6 @@ ] }, { - "color": "#333333", "sequence": "CATGGTAATAAGTTGGGATTTTAGACAGTCTGAATTTACCCT", "domains": [ {"helix": 4, "forward": false, "start": 728, "end": 742}, @@ -614,7 +547,6 @@ ] }, { - "color": "#32b86c", "sequence": "GTGGCCTTGATATTTGGAAAGCGCAGTCGAACGGTACGCCAG", "domains": [ {"helix": 1, "forward": true, "start": 742, "end": 756}, @@ -623,7 +555,6 @@ ] }, { - "color": "#f74308", "sequence": "CCCTCAGAACCGGTCCTCCCTCAGAGCCTCGCCACCACCGGA", "domains": [ {"helix": 3, "forward": true, "start": 770, "end": 784}, @@ -632,7 +563,6 @@ ] }, { - "color": "#b8056c", "sequence": "GCGCGTTTTCATCGAGCGACAGAATCAAAGCAGCACCGTAAT", "domains": [ {"helix": 2, "forward": false, "start": 784, "end": 798}, @@ -641,7 +571,6 @@ ] }, { - "color": "#03b6a2", "sequence": "CACCACCCTCAGAGTTTTTATAATCAGTACCGGAACCAGACT", "domains": [ {"helix": 4, "forward": false, "start": 770, "end": 784}, @@ -650,7 +579,6 @@ ] }, { - "color": "#320096", "sequence": "ACCGGCATTTTCGGTCATAATCAAAATCGAGGCCACCGAGTA", "domains": [ {"helix": 1, "forward": true, "start": 784, "end": 798}, @@ -659,7 +587,6 @@ ] }, { - "color": "#888888", "sequence": "TTAGCAAGGCCGTTCCAGTAGCACCATTTTAGAGCCAGCAAA", "domains": [ {"helix": 3, "forward": true, "start": 812, "end": 826}, @@ -668,7 +595,6 @@ ] }, { - "color": "#cc0000", "sequence": "GAGGGAGGGAAGCAACCAGCGCCAAAGAAGAAAATTCATATG", "domains": [ {"helix": 2, "forward": false, "start": 826, "end": 840}, @@ -677,7 +603,6 @@ ] }, { - "color": "#aaaa00", "sequence": "GTGAAACGTCACCATCACGCAAATTAACCATTTGGGAATTAG", "domains": [ {"helix": 4, "forward": false, "start": 812, "end": 826}, @@ -686,7 +611,6 @@ ] }, { - "color": "#7300de", "sequence": "ATGTAAATATTGACTCACCGACTTGAGCCGTTGTAGCAATAC", "domains": [ {"helix": 1, "forward": true, "start": 826, "end": 840}, @@ -695,7 +619,6 @@ ] }, { - "color": "#333333", "sequence": "AAGACACCACGGCAACATATAAAAGAAAAAATACATAAAGGT", "domains": [ {"helix": 3, "forward": true, "start": 854, "end": 868}, @@ -704,7 +627,6 @@ ] }, { - "color": "#f74308", "sequence": "CGCAATAATAACCAGATAGCCGAACAAATTTTAAGAAAAGTA", "domains": [ {"helix": 2, "forward": false, "start": 868, "end": 882}, @@ -713,7 +635,6 @@ ] }, { - "color": "#007200", "sequence": "AGAATAAGTTTATTATAACATCACTTGCCGTAGAAAATACAG", "domains": [ {"helix": 4, "forward": false, "start": 854, "end": 868}, @@ -722,7 +643,6 @@ ] }, { - "color": "#b8056c", "sequence": "GGGGAATACCCAAAAGTATGTTAGCAAACTGAGTAGAAGAAC", "domains": [ {"helix": 1, "forward": true, "start": 868, "end": 882}, @@ -731,7 +651,6 @@ ] }, { - "color": "#03b6a2", "sequence": "AAACAATGAAATAACCCAATAATAAGAGTACAAGAATTGAGT", "domains": [ {"helix": 3, "forward": true, "start": 896, "end": 910}, @@ -740,7 +659,6 @@ ] }, { - "color": "#888888", "sequence": "AGCGCATTAGACAGTAGCAGCCTTTACATAACGTCAAAAATG", "domains": [ {"helix": 2, "forward": false, "start": 910, "end": 924}, @@ -749,7 +667,6 @@ ] }, { - "color": "#f7931e", "sequence": "AAAGCAATAGCTATTTGCTGGTAATATCAGAGATAACCCAAG", "domains": [ {"helix": 4, "forward": false, "start": 896, "end": 910}, @@ -758,7 +675,6 @@ ] }, { - "color": "#cc0000", "sequence": "TAGGGAGAATTAACAGCGCTAATATCAGCAGAACAATATTAC", "domains": [ {"helix": 1, "forward": true, "start": 910, "end": 924}, @@ -767,7 +683,6 @@ ] }, { - "color": "#aaaa00", "sequence": "TTATTTATCCCAGTACAAAATAAACAGCAAGCCTAATTTGCC", "domains": [ {"helix": 3, "forward": true, "start": 938, "end": 952}, @@ -776,7 +691,6 @@ ] }, { - "color": "#333333", "sequence": "TTAAATCAAGATTTTTTAGCGAACCTCCTCTAAGAACGCGAG", "domains": [ {"helix": 2, "forward": false, "start": 952, "end": 966}, @@ -785,7 +699,6 @@ ] }, { - "color": "#57bb00", "sequence": "GCATCCAAATAAGAACAGGAAAAACGCTCGTCTTTCCAGAAG", "domains": [ {"helix": 4, "forward": false, "start": 938, "end": 952}, @@ -794,7 +707,6 @@ ] }, { - "color": "#f74308", "sequence": "AGTAGTTGCTATTTCCAACGCTAACGAGCATGGAAATACCTA", "domains": [ {"helix": 1, "forward": true, "start": 952, "end": 966}, @@ -803,7 +715,6 @@ ] }, { - "color": "#007200", "sequence": "ATAGCAAGCAAAATGAATCATTACCGCGATTTTATTTTCATC", "domains": [ {"helix": 3, "forward": true, "start": 980, "end": 994}, @@ -812,7 +723,6 @@ ] }, { - "color": "#03b6a2", "sequence": "CAATAATCGGCTAGAATATCCCATCCTAGTCCTGAACAAGAA", "domains": [ {"helix": 2, "forward": false, "start": 994, "end": 1008}, @@ -821,7 +731,6 @@ ] }, { - "color": "#32b86c", "sequence": "AATCAGATATAGAAATCGTCTGAAATGGAAGCAAGCCGTTTT", "domains": [ {"helix": 4, "forward": false, "start": 980, "end": 994}, @@ -830,7 +739,6 @@ ] }, { - "color": "#888888", "sequence": "GTGTCTTTCCTTATCACTCATCGAGAACATTATTTACATTGG", "domains": [ {"helix": 1, "forward": true, "start": 994, "end": 1008}, @@ -839,7 +747,6 @@ ] }, { - "color": "#f7931e", "sequence": "GCTAATGCAGAACGCAATAAACAACATGGTTCTGTCCAGACG", "domains": [ {"helix": 3, "forward": true, "start": 1022, "end": 1036}, @@ -848,7 +755,6 @@ ] }, { - "color": "#aaaa00", "sequence": "CAACGCCAACATGACTCAACAGTAGGGCACCAGTATAAAGCC", "domains": [ {"helix": 2, "forward": false, "start": 1036, "end": 1050}, @@ -857,7 +763,6 @@ ] }, { - "color": "#320096", "sequence": "AACGCGCCTGTTTAACACGACCAGTAATAGGTAAAGTAATAT", "domains": [ {"helix": 4, "forward": false, "start": 1022, "end": 1036}, @@ -866,7 +771,6 @@ ] }, { - "color": "#333333", "sequence": "ACGTAATTTAGGCAAAAGTACCGACAAAAAAAGGGACATTCT", "domains": [ {"helix": 1, "forward": true, "start": 1036, "end": 1050}, @@ -875,7 +779,6 @@ ] }, { - "color": "#57bb00", "sequence": "AAAGCCTGTTTAGCGAATCATAATTACTCCATAAGAATAAAC", "domains": [ {"helix": 3, "forward": true, "start": 1064, "end": 1078}, @@ -884,7 +787,6 @@ ] }, { - "color": "#007200", "sequence": "TCAAATATATTTCGAAATCCAATCGCAAATATGTAAATGCTG", "domains": [ {"helix": 2, "forward": false, "start": 1078, "end": 1092}, @@ -893,7 +795,6 @@ ] }, { - "color": "#7300de", "sequence": "ATGTATCATATGCGGAACCCTTCTGACCATAAGGCGTTAAAG", "domains": [ {"helix": 4, "forward": false, "start": 1064, "end": 1078}, @@ -902,7 +803,6 @@ ] }, { - "color": "#03b6a2", "sequence": "ACTAGTTAATTTCACGACCGTGTGATAATGAAAGCGTAAGAA", "domains": [ {"helix": 1, "forward": true, "start": 1078, "end": 1092}, @@ -911,7 +811,6 @@ ] }, { - "color": "#32b86c", "sequence": "ACCTTTTTAACCCATCATAGGTCTGAGATTAGTGAATTTATC", "domains": [ {"helix": 3, "forward": true, "start": 1106, "end": 1120}, @@ -920,7 +819,6 @@ ] }, { - "color": "#f7931e", "sequence": "AATCGTCGCTATAATAAATCAATATATGTTTAATGGAAACAG", "domains": [ {"helix": 2, "forward": false, "start": 1120, "end": 1134}, @@ -929,7 +827,6 @@ ] }, { - "color": "#b8056c", "sequence": "TATCCGGCTTAGGTAATATTTTTGAATGAGAAGAGTCAATTA", "domains": [ {"helix": 4, "forward": false, "start": 1106, "end": 1120}, @@ -938,7 +835,6 @@ ] }, { - "color": "#aaaa00", "sequence": "AATAATTAATTTTCAGATTAAGACGCTGGCTATTAGTCTTTA", "domains": [ {"helix": 1, "forward": true, "start": 1120, "end": 1134}, @@ -947,7 +843,6 @@ ] }, { - "color": "#320096", "sequence": "AATTAATTACATATCAAACATCAAGAAAAAAAAGAAGATGAT", "domains": [ {"helix": 3, "forward": true, "start": 1148, "end": 1162}, @@ -956,7 +851,6 @@ ] }, { - "color": "#57bb00", "sequence": "AATAACGGATTCAAGAATATACAGTAACTCAGGTTTAACGTC", "domains": [ {"helix": 2, "forward": false, "start": 1162, "end": 1176}, @@ -965,7 +859,6 @@ ] }, { - "color": "#cc0000", "sequence": "AGTTAACAATTTCAAGCCCTAAAACATCATTACCTGAGCAAA", "domains": [ {"helix": 4, "forward": false, "start": 1148, "end": 1162}, @@ -974,7 +867,6 @@ ] }, { - "color": "#007200", "sequence": "GAGCCTGATTGCTTAATTATTCATTTCAGCCATTAAAAATAC", "domains": [ {"helix": 1, "forward": true, "start": 1162, "end": 1176}, @@ -983,7 +875,6 @@ ] }, { - "color": "#7300de", "sequence": "TTGCACGTAAAACACTACCATATCAAAACAATGGAAGGGTTA", "domains": [ {"helix": 3, "forward": true, "start": 1190, "end": 1204}, @@ -992,7 +883,6 @@ ] }, { - "color": "#32b86c", "sequence": "GGAATTATCATCACTTATCATTTTGCGGTTAAAAGTTTGAGT", "domains": [ {"helix": 2, "forward": false, "start": 1204, "end": 1218}, @@ -1001,7 +891,6 @@ ] }, { - "color": "#f74308", "sequence": "AACAGAAATAAAGAGCAGAAGATAAAACTACTTCTGAATAAA", "domains": [ {"helix": 4, "forward": false, "start": 1190, "end": 1204}, @@ -1010,7 +899,6 @@ ] }, { - "color": "#f7931e", "sequence": "GAATATTCCTGATTGATTGTTTGGATTAAGAGGTGAGGCGGT", "domains": [ {"helix": 1, "forward": true, "start": 1204, "end": 1218}, @@ -1019,7 +907,6 @@ ] }, { - "color": "#888888", "sequence": "TTAATGACTGTAAGGATACCGACAGTGCTGTCTAATCTATTT", "domains": [ {"helix": 5, "forward": true, "start": 84, "end": 91}, @@ -1029,7 +916,6 @@ ] }, { - "color": "#03b6a2", "sequence": "CTGCCATATCGGCCGTGTCCTTAGTGCTAATAACCCCGCTGT", "domains": [ {"helix": 0, "forward": false, "start": 91, "end": 98}, @@ -1039,7 +925,6 @@ ] }, { - "color": "#333333", "sequence": "TGGGCGCGTTGTAAACGCCAGGGTTTTCAGAAAGGGGGATGT", "domains": [ {"helix": 5, "forward": true, "start": 126, "end": 133}, @@ -1049,7 +934,6 @@ ] }, { - "color": "#aaaa00", "sequence": "TCACGACCAGGGTGGCGCAACTGTTGGGCGCCAGCTGGCGGC", "domains": [ {"helix": 0, "forward": false, "start": 133, "end": 140}, @@ -1059,7 +943,6 @@ ] }, { - "color": "#03b6a2", "sequence": "ACAGCTGTATCGGCTGCCAGTTTGAGGGTTACGTTGGTGTAG", "domains": [ {"helix": 5, "forward": true, "start": 168, "end": 175}, @@ -1069,7 +952,6 @@ ] }, { - "color": "#007200", "sequence": "ACGACAGATTGCCCACAACCCGTCGGATATGGGATAGGTCTC", "domains": [ {"helix": 0, "forward": false, "start": 175, "end": 182}, @@ -1079,7 +961,6 @@ ] }, { - "color": "#aaaa00", "sequence": "GCAAGCGTCATTTTCGCATTAAATTTTTGGTATTTAAATTGT", "domains": [ {"helix": 5, "forward": true, "start": 210, "end": 217}, @@ -1089,7 +970,6 @@ ] }, { - "color": "#f7931e", "sequence": "AATCAGCGTCCACGTATGTACCCCGGTTTGTATAAGCAAATA", "domains": [ {"helix": 0, "forward": false, "start": 217, "end": 224}, @@ -1099,7 +979,6 @@ ] }, { - "color": "#007200", "sequence": "GTTTGATAGATCTAGCCGGAGAGGGTAGTCAATATGATATTC", "domains": [ {"helix": 5, "forward": true, "start": 252, "end": 259}, @@ -1109,7 +988,6 @@ ] }, { - "color": "#57bb00", "sequence": "TTTTGAGGGTGGTTAATGTGTAGGTAAACAAATCACCATCAT", "domains": [ {"helix": 0, "forward": false, "start": 259, "end": 266}, @@ -1119,7 +997,6 @@ ] }, { - "color": "#f7931e", "sequence": "AAAAGAACCCTGTAATCGGTTGTACCAAGCAAAATTAAGCAA", "domains": [ {"helix": 5, "forward": true, "start": 294, "end": 301}, @@ -1129,7 +1006,6 @@ ] }, { - "color": "#32b86c", "sequence": "ATTATGATAGCCCGTACTAATAGTAGTACAAAGAATTAGCGC", "domains": [ {"helix": 0, "forward": false, "start": 301, "end": 308}, @@ -1139,7 +1015,6 @@ ] }, { - "color": "#57bb00", "sequence": "GAACAAGGTTTGACCCAATTCTGCGAACGAGTGTCTGGAAGT", "domains": [ {"helix": 5, "forward": true, "start": 336, "end": 343}, @@ -1149,7 +1024,6 @@ ] }, { - "color": "#320096", "sequence": "AGATTTAAGTCCACTTAATTGCTGAATAAACTAAAGTACGGG", "domains": [ {"helix": 0, "forward": false, "start": 343, "end": 350}, @@ -1159,7 +1033,6 @@ ] }, { - "color": "#32b86c", "sequence": "AGGGCGAAGACCGGTTTAATTCGAGCTTTCATTAAGAGGAAG", "domains": [ {"helix": 5, "forward": true, "start": 378, "end": 385}, @@ -1169,7 +1042,6 @@ ] }, { - "color": "#7300de", "sequence": "GCGAACCAAAACCGAAATCAGGTCTTTATGCATCAAAAAGAG", "domains": [ {"helix": 0, "forward": false, "start": 385, "end": 392}, @@ -1179,7 +1051,6 @@ ] }, { - "color": "#320096", "sequence": "ACCATCAGCGTCCAAATAGTAAAATGTTTAAGAGGCTTTTGC", "domains": [ {"helix": 5, "forward": true, "start": 420, "end": 427}, @@ -1189,7 +1060,6 @@ ] }, { - "color": "#b8056c", "sequence": "CTGGATACCCAAATTAAGAGCAACACTAACCAAAATAGCGAC", "domains": [ {"helix": 0, "forward": false, "start": 427, "end": 434}, @@ -1199,7 +1069,6 @@ ] }, { - "color": "#7300de", "sequence": "AGCACTATTACAGGAAAACGAACTAACGAGCCAGTCAGGACG", "domains": [ {"helix": 5, "forward": true, "start": 462, "end": 469}, @@ -1209,7 +1078,6 @@ ] }, { - "color": "#cc0000", "sequence": "AACATTAAATCGGAATTTCAACTTTAATTGGCTCATTATATA", "domains": [ {"helix": 0, "forward": false, "start": 469, "end": 476}, @@ -1219,7 +1087,6 @@ ] }, { - "color": "#b8056c", "sequence": "TTGACGGATCAACGCAAGAACCGGATATCGCATAGGCTGGCT", "domains": [ {"helix": 5, "forward": true, "start": 504, "end": 511}, @@ -1229,7 +1096,6 @@ ] }, { - "color": "#f74308", "sequence": "TACCCAAGGAAAGCAGGGAACCGAACTGACAGACCAGGCGGA", "domains": [ {"helix": 0, "forward": false, "start": 511, "end": 518}, @@ -1239,7 +1105,6 @@ ] }, { - "color": "#cc0000", "sequence": "GAAAGCGGAGATTTACCAAGCGCGAAACTTACACTAAAACAC", "domains": [ {"helix": 5, "forward": true, "start": 546, "end": 553}, @@ -1249,7 +1114,6 @@ ] }, { - "color": "#888888", "sequence": "TACAACGAAAGGAGGTAAAATACGTAATAGGCAAAAGAATTT", "domains": [ {"helix": 0, "forward": false, "start": 553, "end": 560}, @@ -1259,7 +1123,6 @@ ] }, { - "color": "#f74308", "sequence": "GGTCACGCAGCGAAGCTTTTGCGGGATCTTTATTCGGTCGCT", "domains": [ {"helix": 5, "forward": true, "start": 588, "end": 595}, @@ -1269,7 +1132,6 @@ ] }, { - "color": "#333333", "sequence": "CCCTCAGCTGCGCGCTTGATACCGATAGGCATAACCGATAGC", "domains": [ {"helix": 0, "forward": false, "start": 595, "end": 602}, @@ -1279,7 +1141,6 @@ ] }, { - "color": "#888888", "sequence": "GCCGCTACACGTTGAAGGAATTGCGAATGTCAGTTTCAGCGG", "domains": [ {"helix": 5, "forward": true, "start": 630, "end": 637}, @@ -1289,7 +1150,6 @@ ] }, { - "color": "#03b6a2", "sequence": "ATTTTTTCAGGGCGTCTTTCCAGACGTTAACAACTTTCAATA", "domains": [ {"helix": 0, "forward": false, "start": 637, "end": 644}, @@ -1299,7 +1159,6 @@ ] }, { - "color": "#333333", "sequence": "ATAACGTACACTGAGCCCAATAGGAACCATCCTCAGAGCCAC", "domains": [ {"helix": 5, "forward": true, "start": 672, "end": 679}, @@ -1309,7 +1168,6 @@ ] }, { - "color": "#aaaa00", "sequence": "TACCGTAGCTTTCCCCGTACTCAGGAGGCAGAACCGCCACAA", "domains": [ {"helix": 0, "forward": false, "start": 679, "end": 686}, @@ -1319,7 +1177,6 @@ ] }, { - "color": "#03b6a2", "sequence": "GGAGGCCAGGATTATAAGAGGCTGAGACTGTATTTCGGAACC", "domains": [ {"helix": 5, "forward": true, "start": 714, "end": 721}, @@ -1329,7 +1186,6 @@ ] }, { - "color": "#007200", "sequence": "CAAGAGAGATTAAATTAACGGGGTCAGTATGCCCCCTGCCAT", "domains": [ {"helix": 0, "forward": false, "start": 721, "end": 728}, @@ -1339,7 +1195,6 @@ ] }, { - "color": "#aaaa00", "sequence": "AATCCTGGCCAGAACACAAACAAATAAAGCGAGGTTGAGGCA", "domains": [ {"helix": 5, "forward": true, "start": 756, "end": 763}, @@ -1349,7 +1204,6 @@ ] }, { - "color": "#f7931e", "sequence": "CATTAAAAGAAGTGCCACCACCCTCAGACAGCATTGACAGCA", "domains": [ {"helix": 0, "forward": false, "start": 763, "end": 770}, @@ -1359,7 +1213,6 @@ ] }, { - "color": "#007200", "sequence": "AAAGAGTCATCTTTTCATAGCCCCCTTAACCGTCAGACTGTA", "domains": [ {"helix": 5, "forward": true, "start": 798, "end": 805}, @@ -1369,7 +1222,6 @@ ] }, { - "color": "#57bb00", "sequence": "CGTTTGCCTGTCCAATGAAACCATCGATGTTTGCCTTTAGCA", "domains": [ {"helix": 0, "forward": false, "start": 805, "end": 812}, @@ -1379,7 +1231,6 @@ ] }, { - "color": "#f7931e", "sequence": "TTCTTTGATCACCGGGAAATTATTCATTCGATTCAACCGATT", "domains": [ {"helix": 5, "forward": true, "start": 840, "end": 847}, @@ -1389,7 +1240,6 @@ ] }, { - "color": "#32b86c", "sequence": "GTGAATTATTAGTATTGTCACAATCAATCAAAAGGGCGACCA", "domains": [ {"helix": 0, "forward": false, "start": 847, "end": 854}, @@ -1399,7 +1249,6 @@ ] }, { - "color": "#57bb00", "sequence": "TCAAACTATTACGCAGAACTGGCATGATCAAAACCGAGGAAA", "domains": [ {"helix": 5, "forward": true, "start": 882, "end": 889}, @@ -1409,7 +1258,6 @@ ] }, { - "color": "#320096", "sequence": "ACTCCTTATCGGCCCTTACCGAAGCCCTGTTACCAGAAGGAG", "domains": [ {"helix": 0, "forward": false, "start": 889, "end": 896}, @@ -1419,7 +1267,6 @@ ] }, { - "color": "#32b86c", "sequence": "CGCCAGCGTAATTGTGAACACCCTGAACCATAAAAACAGGGA", "domains": [ {"helix": 5, "forward": true, "start": 924, "end": 931}, @@ -1429,7 +1276,6 @@ ] }, { - "color": "#7300de", "sequence": "TCAGAGGCATTGCAAACGATTTTTTGTTGAGAGAATAACATA", "domains": [ {"helix": 0, "forward": false, "start": 931, "end": 938}, @@ -1439,7 +1285,6 @@ ] }, { - "color": "#320096", "sequence": "CATTTTGAATCTTATGCACCCAGCTACACCGGTTTTGAAGCC", "domains": [ {"helix": 5, "forward": true, "start": 966, "end": 973}, @@ -1449,7 +1294,6 @@ ] }, { - "color": "#b8056c", "sequence": "TATCCTGACGCTCAGGCTTATCCGGTATCGACTTGCGGGACA", "domains": [ {"helix": 0, "forward": false, "start": 973, "end": 980}, @@ -1459,7 +1303,6 @@ ] }, { - "color": "#7300de", "sequence": "CAGATTCAGTACCGCATTCCAAGAACGGTTGTAGAAACCAAT", "domains": [ {"helix": 5, "forward": true, "start": 1008, "end": 1015}, @@ -1469,7 +1312,6 @@ ] }, { - "color": "#cc0000", "sequence": "TAAACCAACCAGTCTCAACAATAGATAAATTTACGAGCATCA", "domains": [ {"helix": 0, "forward": false, "start": 1015, "end": 1022}, @@ -1479,7 +1321,6 @@ ] }, { - "color": "#b8056c", "sequence": "GGCCAACAGAATATGAGGCATTTTCGAGAGCGCCATATTTAA", "domains": [ {"helix": 5, "forward": true, "start": 1050, "end": 1057}, @@ -1489,7 +1330,6 @@ ] }, { - "color": "#f74308", "sequence": "TAATAAGAGAGATATTATACAAATTCTTTTAATTGAGAATAA", "domains": [ {"helix": 0, "forward": false, "start": 1057, "end": 1064}, @@ -1499,7 +1339,6 @@ ] }, { - "color": "#cc0000", "sequence": "TACGTGGGAAATACTCTTCTGACCTAAAGAGAGAAAACTTTT", "domains": [ {"helix": 5, "forward": true, "start": 1092, "end": 1099}, @@ -1509,7 +1348,6 @@ ] }, { - "color": "#888888", "sequence": "ATGGTTTCACAGACTGGGTTATATAACTGACAAAGAACGCCT", "domains": [ {"helix": 0, "forward": false, "start": 1099, "end": 1106}, @@ -1519,7 +1357,6 @@ ] }, { - "color": "#f74308", "sequence": "ATGCGCGATAGCTTCCTTAGAATCCTTGACCTTGCTTCTGTA", "domains": [ {"helix": 5, "forward": true, "start": 1134, "end": 1141}, @@ -1529,7 +1366,6 @@ ] }, { - "color": "#333333", "sequence": "CATAGCGAACTGATTTTGAATTACCTTTTGAGTGAATAACAA", "domains": [ {"helix": 0, "forward": false, "start": 1141, "end": 1148}, @@ -1539,7 +1375,6 @@ ] }, { - "color": "#888888", "sequence": "CGAACGAAGAGGCGTGAATACCAAGTTATTATCGGGAGAAAC", "domains": [ {"helix": 5, "forward": true, "start": 1176, "end": 1183}, @@ -1549,7 +1384,6 @@ ] }, { - "color": "#03b6a2", "sequence": "ATCGCGCACCACCAAATTGCGTAGATTTAGTACCTTTTACAT", "domains": [ {"helix": 0, "forward": false, "start": 1183, "end": 1190}, @@ -1559,7 +1393,6 @@ ] }, { - "color": "#333333", "sequence": "CAGTATTTAATCCTATCAGATGATGGCATCACCAGAAGGAGC", "domains": [ {"helix": 5, "forward": true, "start": 1218, "end": 1225}, @@ -1569,7 +1402,6 @@ ] }, { - "color": "#aaaa00", "sequence": "ATCAATAAACACCGGAACGTTATTAATTAACAAAGAAACCGA", "domains": [ {"helix": 0, "forward": false, "start": 1225, "end": 1232}, @@ -1579,7 +1411,7 @@ ] }, { - "color": "#888888", + "color": "#cc0000", "sequence": "ACTGCCCGAAATTGTCATGGTCATAGCTAAACGGAGGATCCC", "domains": [ {"helix": 5, "forward": true, "start": 42, "end": 49}, @@ -1589,7 +1421,6 @@ ] }, { - "color": "#333333", "sequence": "CCTGTGTGCTTTCCGGTTGGTGTAATGAACCTCGATAAAGAT", "domains": [ {"helix": 0, "forward": false, "start": 49, "end": 56}, @@ -1599,7 +1430,7 @@ ] }, { - "color": "#57bb00", + "color": "#007200", "sequence": "CTAATCCTTTGCCCCCTGCAACAGTGCCAATACATTTGAGTC", "domains": [ {"helix": 4, "forward": false, "start": 1232, "end": 1246}, @@ -1608,7 +1439,6 @@ ] }, { - "color": "#b8056c", "sequence": "CAACTCGTATTACAACTTTACAAACAATATGATTTAGAAGTA", "domains": [ {"helix": 3, "forward": true, "start": 1232, "end": 1246}, diff --git a/examples/output_designs/6_helix_origami_rectangle.dna b/examples/output_designs/6_helix_origami_rectangle.dna index 07553463..c33f6377 100644 --- a/examples/output_designs/6_helix_origami_rectangle.dna +++ b/examples/output_designs/6_helix_origami_rectangle.dna @@ -29,7 +29,7 @@ "is_scaffold": true }, { - "color": "#888888", + "color": "#f74308", "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -37,7 +37,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -45,7 +45,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -53,7 +53,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 176}, @@ -61,7 +61,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", "domains": [ {"helix": 2, "forward": false, "start": 160, "end": 176}, @@ -69,7 +69,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", "domains": [ {"helix": 4, "forward": false, "start": 160, "end": 176}, @@ -77,14 +77,14 @@ ] }, { - "color": "#f7931e", + "color": "#03b6a2", "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", "domains": [ {"helix": 0, "forward": false, "start": 88, "end": 120} ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -92,7 +92,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -100,7 +100,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -108,7 +108,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -116,14 +116,14 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -140,7 +140,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -149,7 +149,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 64}, @@ -157,7 +157,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -166,7 +166,7 @@ ] }, { - "color": "#03b6a2", + "color": "#333333", "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -175,7 +175,7 @@ ] }, { - "color": "#7300de", + "color": "#320096", "sequence": "AATGAATCGGCCAACGCGCGGGGAGTTGCAG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -183,7 +183,7 @@ ] }, { - "color": "#aaaa00", + "color": "#03b6a2", "sequence": "CAAGCGGTCCTGTTTGATGGTGGTACGTGGAC", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -192,7 +192,7 @@ ] }, { - "color": "#b8056c", + "color": "#7300de", "sequence": "TCCAACGTTGGCCCACTACGTGAAAGCCGGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -201,7 +201,7 @@ ] }, { - "color": "#007200", + "color": "#aaaa00", "sequence": "AGTATCGGCCTCAGGAAGATCGCAGTGCGGGC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 128}, @@ -209,7 +209,7 @@ ] }, { - "color": "#cc0000", + "color": "#b8056c", "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -218,7 +218,7 @@ ] }, { - "color": "#f7931e", + "color": "#007200", "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -227,7 +227,7 @@ ] }, { - "color": "#f74308", + "color": "#cc0000", "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -235,7 +235,7 @@ ] }, { - "color": "#57bb00", + "color": "#f7931e", "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -244,7 +244,7 @@ ] }, { - "color": "#888888", + "color": "#f74308", "sequence": "GCCAGGGTTGGGAAGGGCGATCGCTCCAGC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -253,7 +253,7 @@ ] }, { - "color": "#32b86c", + "color": "#57bb00", "sequence": "CAGCTTTCCGGCACCGCTTCTGGTCAGGCTGC", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 160}, @@ -261,7 +261,7 @@ ] }, { - "color": "#333333", + "color": "#888888", "sequence": "GTCGACTCACGAGCCGGAAGCATACTAACTCA", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -270,7 +270,7 @@ ] }, { - "color": "#320096", + "color": "#32b86c", "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, diff --git a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna index c4630e16..a9cb37d5 100644 --- a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna +++ b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna @@ -30,7 +30,7 @@ "is_scaffold": true }, { - "color": "#03b6a2", + "color": "#f74308", "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -38,7 +38,7 @@ ] }, { - "color": "#7300de", + "color": "#57bb00", "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -46,7 +46,7 @@ ] }, { - "color": "#aaaa00", + "color": "#888888", "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -54,7 +54,7 @@ ] }, { - "color": "#b8056c", + "color": "#32b86c", "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 176}, @@ -62,7 +62,7 @@ ] }, { - "color": "#007200", + "color": "#333333", "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", "domains": [ {"helix": 2, "forward": false, "start": 160, "end": 176}, @@ -70,7 +70,7 @@ ] }, { - "color": "#cc0000", + "color": "#320096", "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", "domains": [ {"helix": 4, "forward": false, "start": 160, "end": 176}, @@ -78,14 +78,14 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", "domains": [ {"helix": 0, "forward": false, "start": 88, "end": 120} ] }, { - "color": "#f7931e", + "color": "#7300de", "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -93,7 +93,7 @@ ] }, { - "color": "#f74308", + "color": "#aaaa00", "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -101,7 +101,7 @@ ] }, { - "color": "#57bb00", + "color": "#b8056c", "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -109,7 +109,7 @@ ] }, { - "color": "#888888", + "color": "#007200", "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -117,14 +117,14 @@ ] }, { - "color": "#333333", + "color": "#cc0000", "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} ] }, { - "color": "#320096", + "color": "#f7931e", "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -132,7 +132,7 @@ ] }, { - "color": "#03b6a2", + "color": "#f74308", "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -141,7 +141,7 @@ ] }, { - "color": "#7300de", + "color": "#57bb00", "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -150,7 +150,7 @@ ] }, { - "color": "#aaaa00", + "color": "#888888", "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 64}, @@ -158,7 +158,7 @@ ] }, { - "color": "#b8056c", + "color": "#32b86c", "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -167,7 +167,7 @@ ] }, { - "color": "#007200", + "color": "#333333", "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -176,7 +176,7 @@ ] }, { - "color": "#cc0000", + "color": "#320096", "sequence": "AATGAATCGGCCAACGCGCGGGGAGTTGCAG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -184,7 +184,7 @@ ] }, { - "color": "#f7931e", + "color": "#03b6a2", "sequence": "CAAGCGGTCCTGTTTGATGGTGGTACGTGGAC", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -193,7 +193,7 @@ ] }, { - "color": "#f74308", + "color": "#7300de", "sequence": "TCCAACGTTGGCCCACTACGTGAAAGCCGGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -202,7 +202,7 @@ ] }, { - "color": "#57bb00", + "color": "#aaaa00", "sequence": "AGTATCGGCCTCAGGAAGATCGCAGTGCGGGC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 128}, @@ -210,7 +210,7 @@ ] }, { - "color": "#888888", + "color": "#b8056c", "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -219,7 +219,7 @@ ] }, { - "color": "#32b86c", + "color": "#007200", "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -228,7 +228,7 @@ ] }, { - "color": "#333333", + "color": "#cc0000", "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -236,7 +236,7 @@ ] }, { - "color": "#320096", + "color": "#f7931e", "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -245,7 +245,7 @@ ] }, { - "color": "#03b6a2", + "color": "#f74308", "sequence": "GCCAGGGTTGGGAAGGGCGATCGCTCCAGC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -254,7 +254,7 @@ ] }, { - "color": "#7300de", + "color": "#57bb00", "sequence": "CAGCTTTCCGGCACCGCTTCTGGTCAGGCTGC", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 160}, @@ -262,7 +262,7 @@ ] }, { - "color": "#aaaa00", + "color": "#888888", "sequence": "GTCGACTCACGAGCCGGAAGCATACTAACTCA", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -271,7 +271,7 @@ ] }, { - "color": "#b8056c", + "color": "#32b86c", "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, diff --git a/examples/output_designs/hairpin.dna b/examples/output_designs/hairpin.dna index 629c9951..16306317 100644 --- a/examples/output_designs/hairpin.dna +++ b/examples/output_designs/hairpin.dna @@ -6,7 +6,7 @@ ], "strands": [ { - "color": "#007200", + "color": "#f74308", "sequence": "AAAAACCCCCTGCATGGGGGTTTTT", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 10}, diff --git a/examples/output_designs/idt-plates-explicit.dna b/examples/output_designs/idt-plates-explicit.dna index 27024292..cef66c11 100644 --- a/examples/output_designs/idt-plates-explicit.dna +++ b/examples/output_designs/idt-plates-explicit.dna @@ -7,7 +7,7 @@ ], "strands": [ { - "color": "#cc0000", + "color": "#f74308", "sequence": "CTATTATAGTTTTACCCTGA", "idt": {"name": "staple1", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A1"}, "domains": [ @@ -16,7 +16,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "CAGAAGCAAAAAATCAGGTC", "idt": {"name": "staple2", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B1"}, "domains": [ @@ -25,7 +25,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "GCGGATTGCACATAAATCAA", "idt": {"name": "staple3", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C1"}, "domains": [ @@ -34,7 +34,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "TCAAAAAGATCGAGAATGAC", "idt": {"name": "staple4", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D1"}, "domains": [ @@ -43,7 +43,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "TAAGAGGAAGGTTCAGAAAA", "idt": {"name": "staple5", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E1"}, "domains": [ @@ -52,7 +52,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "CCCGAAAGACGCTTTAAACA", "idt": {"name": "staple6", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F1"}, "domains": [ @@ -61,7 +61,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "TTCAAATATCCCCCTCAAAT", "idt": {"name": "staple7", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G1"}, "domains": [ @@ -70,7 +70,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "GCGTTTTAATTCATTGAATC", "idt": {"name": "staple8", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H1"}, "domains": [ @@ -79,7 +79,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "TCGAGCTTCATCATAAATAT", "idt": {"name": "staple9", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A2"}, "domains": [ @@ -88,7 +88,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "AAGCGAACCATGCGGAATCG", "idt": {"name": "staple10", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B2"}, "domains": [ @@ -97,7 +97,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "GACCGGAAGCCGTCCAATAC", "idt": {"name": "staple11", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C2"}, "domains": [ @@ -106,7 +106,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "AAACTCCAACGACTGGATAG", "idt": {"name": "staple12", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D2"}, "domains": [ @@ -115,7 +115,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "AGGTCAGGATAAAATGTTTA", "idt": {"name": "staple13", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E2"}, "domains": [ @@ -124,7 +124,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "TAGAGAGTACGGGTAATAGT", "idt": {"name": "staple14", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F2"}, "domains": [ @@ -133,7 +133,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "CTTTAATTGCTTGCCAGAGG", "idt": {"name": "staple15", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G2"}, "domains": [ @@ -142,7 +142,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "TCCTTTTGATAAAAGAAGTT", "idt": {"name": "staple16", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H2"}, "domains": [ @@ -151,7 +151,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "AAGAGGTCATAGGCTTTTGC", "idt": {"name": "staple17", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A3"}, "domains": [ @@ -160,7 +160,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "TTTTGCGGATAAATAGCGAG", "idt": {"name": "staple18", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B3"}, "domains": [ @@ -169,7 +169,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "GGCTTAGAGCATAAAAACCA", "idt": {"name": "staple19", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C3"}, "domains": [ @@ -178,7 +178,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "TTAATTGCTGCCAGACGACG", "idt": {"name": "staple20", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D3"}, "domains": [ @@ -187,7 +187,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "AATATAATGCCCCTCGTTTA", "idt": {"name": "staple21", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E3"}, "domains": [ @@ -196,7 +196,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "TGTAGCTCAAACTATCATAA", "idt": {"name": "staple22", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F3"}, "domains": [ @@ -205,7 +205,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "CATGTTTTAATAAGAGCAAC", "idt": {"name": "staple23", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G3"}, "domains": [ @@ -214,7 +214,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "ATATGCAACTCGAGGCATAG", "idt": {"name": "staple24", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H3"}, "domains": [ @@ -223,7 +223,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "AAAGTACGGTAAAGGAATTA", "idt": {"name": "staple25", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A4"}, "domains": [ @@ -232,7 +232,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "GTCTGGAAGTCATAACGCCA", "idt": {"name": "staple26", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B4"}, "domains": [ @@ -241,7 +241,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "TTCATTCCATAATGCAGATA", "idt": {"name": "staple27", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C4"}, "domains": [ @@ -250,7 +250,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "ATAACAGTTGACATTCAACT", "idt": {"name": "staple28", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D4"}, "domains": [ @@ -259,7 +259,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "ATTCCCAATTTAGGAATACC", "idt": {"name": "staple29", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E4"}, "domains": [ @@ -268,7 +268,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "CTGCGAACGAAGTTGAGATT", "idt": {"name": "staple30", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F4"}, "domains": [ @@ -277,7 +277,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GTAGATTTAGAAGATTCATC", "idt": {"name": "staple31", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G4"}, "domains": [ @@ -286,7 +286,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TTTGACCATTTACAGGTAGA", "idt": {"name": "staple32", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H4"}, "domains": [ @@ -295,7 +295,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "AGATACATTTACAACATTAT", "idt": {"name": "staple33", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A5"}, "domains": [ @@ -304,7 +304,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "CGCAAATGGTAACTAACGGA", "idt": {"name": "staple34", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B5"}, "domains": [ @@ -313,7 +313,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "CAATAACCTGTAATAAAACG", "idt": {"name": "staple35", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C5"}, "domains": [ @@ -322,7 +322,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "TTTAGCTATAAAATCTACGT", "idt": {"name": "staple36", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D5"}, "domains": [ @@ -331,7 +331,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TTTTCATTTGTTGGGAAGAA", "idt": {"name": "staple37", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E5"}, "domains": [ @@ -340,7 +340,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "GGGCGCGAGCAGTCAGGACG", "idt": {"name": "staple38", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F5"}, "domains": [ @@ -349,7 +349,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "TGAAAAGGTGTCATTATACC", "idt": {"name": "staple39", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G5"}, "domains": [ @@ -358,7 +358,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "GCATCAATTCAAGAACTGGC", "idt": {"name": "staple40", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H5"}, "domains": [ @@ -367,7 +367,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "TACTAATAGTATGCGATTTT", "idt": {"name": "staple41", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A6"}, "domains": [ @@ -376,7 +376,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "AGTAGCATTAGAATTACCTT", "idt": {"name": "staple42", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B6"}, "domains": [ @@ -385,7 +385,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "ACATCCAATATAATCATTGT", "idt": {"name": "staple43", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C6"}, "domains": [ @@ -394,7 +394,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "AATCATACAGATTTCAACTT", "idt": {"name": "staple44", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D6"}, "domains": [ @@ -403,7 +403,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "GCAAGGCAAAAGATGGTTTA", "idt": {"name": "staple45", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E6"}, "domains": [ @@ -412,7 +412,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "GAATTAGCAAATTGGGCTTG", "idt": {"name": "staple46", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F6"}, "domains": [ @@ -421,7 +421,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "AATTAAGCAACGAGTAGTAA", "idt": {"name": "staple47", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G6"}, "domains": [ @@ -430,7 +430,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "TAAAGCCTCAAACACCAGAA", "idt": {"name": "staple48", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H6"}, "domains": [ @@ -439,7 +439,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GAGCATAAAGCCTGACGAGA", "idt": {"name": "staple49", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A7"}, "domains": [ @@ -448,7 +448,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "CTAAATCGGTTAAGGCTTGC", "idt": {"name": "staple50", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B7"}, "domains": [ @@ -457,7 +457,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "TGTACCAAAAATTCAGTGAA", "idt": {"name": "staple51", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C7"}, "domains": [ @@ -466,7 +466,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "ACATTATGACAAAGCTGCTC", "idt": {"name": "staple52", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D7"}, "domains": [ @@ -475,7 +475,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "CCTGTAATACTCAACGTAAC", "idt": {"name": "staple53", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E7"}, "domains": [ @@ -484,7 +484,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "TTTTGCGGGAATTACCCAAA", "idt": {"name": "staple54", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F7"}, "domains": [ @@ -493,7 +493,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "GAAGCCTTTACCGGATATTC", "idt": {"name": "staple55", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G7"}, "domains": [ @@ -502,7 +502,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "TTTCAACGCATTGACAAGAA", "idt": {"name": "staple56", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H7"}, "domains": [ @@ -511,7 +511,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "AGGATAAAAAAAGAGTAATC", "idt": {"name": "staple57", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A8"}, "domains": [ @@ -520,7 +520,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TTTTTAGAACGACCTTCATC", "idt": {"name": "staple58", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B8"}, "domains": [ @@ -529,7 +529,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "CCTCATATATTAGGCTGGCT", "idt": {"name": "staple59", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C8"}, "domains": [ @@ -538,7 +538,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "TTTAAATGCAACCAGGCGCA", "idt": {"name": "staple60", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D8"}, "domains": [ @@ -547,7 +547,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "ATGCCTGAGTCGGTGTACAG", "idt": {"name": "staple61", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E8"}, "domains": [ @@ -556,7 +556,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "AATGTGTAGGGACAGATGAA", "idt": {"name": "staple62", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F8"}, "domains": [ @@ -565,7 +565,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TAAAGATTCATTTGAAAGAG", "idt": {"name": "staple63", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G8"}, "domains": [ @@ -574,7 +574,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "AAAGGGTGAGACTGACCAAC", "idt": {"name": "staple64", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H8"}, "domains": [ @@ -583,7 +583,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "AAAGGCCGGAAGGGAACCGA", "idt": {"name": "staple65", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A9"}, "domains": [ @@ -592,7 +592,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "GACAGTCAAAGTCAATCATA", "idt": {"name": "staple66", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B9"}, "domains": [ @@ -601,7 +601,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "TCACCATCAAGGCGCAGACG", "idt": {"name": "staple67", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C9"}, "domains": [ @@ -610,7 +610,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "TATGATATTCGCCGGAACGA", "idt": {"name": "staple68", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D9"}, "domains": [ @@ -619,7 +619,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "AACCGTTCTAATGTTACTTA", "idt": {"name": "staple69", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E9"}, "domains": [ @@ -628,7 +628,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GCTGATAAATGACCTGCTCC", "idt": {"name": "staple70", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F9"}, "domains": [ @@ -637,7 +637,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TAATGCCGGACGAAATCCGC", "idt": {"name": "staple71", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G9"}, "domains": [ @@ -646,7 +646,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "GAGGGTAGCTTAAATTGTGT", "idt": {"name": "staple72", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H9"}, "domains": [ @@ -655,7 +655,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "ATTTTTGAGACATCGCCTGA", "idt": {"name": "staple73", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A10"}, "domains": [ @@ -664,7 +664,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "GATCTACAAAAGATTTGTAT", "idt": {"name": "staple74", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B10"}, "domains": [ @@ -673,7 +673,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GGCTATCAGGAGTACAACGG", "idt": {"name": "staple75", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C10"}, "domains": [ @@ -682,7 +682,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TCATTGCCTGCGCGAAACAA", "idt": {"name": "staple76", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D10"}, "domains": [ @@ -691,7 +691,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "AGAGTCTGGATTATACCAAG", "idt": {"name": "staple77", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E10"}, "domains": [ @@ -700,7 +700,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "GCAAACAAGACCCCCAGCGA", "idt": {"name": "staple78", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F10"}, "domains": [ @@ -709,7 +709,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "GAATCGATGATCATCTTTGA", "idt": {"name": "staple79", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G10"}, "domains": [ @@ -718,7 +718,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "ACGGTAATCGACTAAAACAC", "idt": {"name": "staple80", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H10"}, "domains": [ @@ -727,7 +727,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "TAAAACTAGCAAAAGAATAC", "idt": {"name": "staple81", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A11"}, "domains": [ @@ -736,7 +736,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "ATGTCAATCACGAAAGAGGC", "idt": {"name": "staple82", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B11"}, "domains": [ @@ -745,7 +745,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "TATGTACCCCCAACCTAAAA", "idt": {"name": "staple83", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C11"}, "domains": [ @@ -754,7 +754,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "GGTTGATAATACGAAGGCAC", "idt": {"name": "staple84", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D11"}, "domains": [ @@ -763,7 +763,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "CAGAAAAGCCTAATGCCACT", "idt": {"name": "staple85", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E11"}, "domains": [ @@ -772,7 +772,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "CCAAAAACAGGTAAAATACG", "idt": {"name": "staple86", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F11"}, "domains": [ @@ -781,7 +781,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "GAAGATTGTACATTAAACGG", "idt": {"name": "staple87", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G11"}, "domains": [ @@ -790,7 +790,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "TAAGCAAATAAGGAAGTTTC", "idt": {"name": "staple88", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H11"}, "domains": [ @@ -799,7 +799,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TTTAAATTGTCTTTTTCATG", "idt": {"name": "staple89", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A12"}, "domains": [ @@ -808,7 +808,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "AAACGTTAATGGACTAAAGA", "idt": {"name": "staple90", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B12"}, "domains": [ @@ -817,7 +817,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "ATTTTGTTAAGAGGCTTTGA", "idt": {"name": "staple91", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C12"}, "domains": [ @@ -826,7 +826,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "AATTCGCATTAACGGCTACA", "idt": {"name": "staple92", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D12"}, "domains": [ @@ -835,7 +835,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "AAATTTTTGTCGAGGGTAGC", "idt": {"name": "staple93", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E12"}, "domains": [ @@ -844,7 +844,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "TAAATCAGCTAGCATCGGAA", "idt": {"name": "staple94", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F12"}, "domains": [ @@ -853,7 +853,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "CATTTTTTAAAGCGAAAGAC", "idt": {"name": "staple95", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G12"}, "domains": [ @@ -862,7 +862,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "CCAATAGGAACACCCTCAGC", "idt": {"name": "staple96", "scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H12"}, "domains": [ @@ -871,7 +871,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "CGCCATCAAAGCGGGATCGT", "idt": {"name": "staple97", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A1"}, "domains": [ @@ -880,7 +880,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "AATAATTCGCGGCCGCTTTT", "idt": {"name": "staple98", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B1"}, "domains": [ @@ -889,7 +889,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "GTCTGGCCTTGGGAGTTAAA", "idt": {"name": "staple99", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C1"}, "domains": [ @@ -898,7 +898,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "CCTGTAGCCAGAGGCTTGCA", "idt": {"name": "staple100", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D1"}, "domains": [ @@ -907,7 +907,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GCTTTCATCATTCGGTCGCT", "idt": {"name": "staple101", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E1"}, "domains": [ @@ -916,7 +916,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "ACATTAAATGAACCGATATA", "idt": {"name": "staple102", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F1"}, "domains": [ @@ -925,7 +925,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "TGAGCGAGTAGCCCACGCAT", "idt": {"name": "staple103", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G1"}, "domains": [ @@ -934,7 +934,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "ACAACCCGTCAACAACCATC", "idt": {"name": "staple104", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H1"}, "domains": [ @@ -943,7 +943,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "GGATTCTCCGCGACAATGAC", "idt": {"name": "staple105", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A2"}, "domains": [ @@ -952,7 +952,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "TGGGAACAAAATAGTTGCGC", "idt": {"name": "staple106", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B2"}, "domains": [ @@ -961,7 +961,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CGGCGGATTGCTTGATACCG", "idt": {"name": "staple107", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C2"}, "domains": [ @@ -970,7 +970,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "ACCGTAATGGTCTTAAACAG", "idt": {"name": "staple108", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D2"}, "domains": [ @@ -979,7 +979,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GATAGGTCACGAGGTGAATT", "idt": {"name": "staple109", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E2"}, "domains": [ @@ -988,7 +988,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "GTTGGTGTAGGCTTGCTTTC", "idt": {"name": "staple110", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F2"}, "domains": [ @@ -997,7 +997,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "ATGGGCGCATCGGTTTATCA", "idt": {"name": "staple111", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G2"}, "domains": [ @@ -1006,7 +1006,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "CGTAACCGTGTTAATTGTAT", "idt": {"name": "staple112", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H2"}, "domains": [ @@ -1015,7 +1015,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "CATCTGCCAGAAAGGAGCCT", "idt": {"name": "staple113", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A3"}, "domains": [ @@ -1024,7 +1024,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "TTTGAGGGGAAAAGGCTCCA", "idt": {"name": "staple114", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B3"}, "domains": [ @@ -1033,7 +1033,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "CGACGACAGTTCTCCAAAAA", "idt": {"name": "staple115", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C3"}, "domains": [ @@ -1042,7 +1042,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "ATCGGCCTCAACGTTGAAAA", "idt": {"name": "staple116", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D3"}, "domains": [ @@ -1051,7 +1051,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "GGAAGATCGCTAATTTTTTC", "idt": {"name": "staple117", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E3"}, "domains": [ @@ -1060,7 +1060,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "ACTCCAGCCATTGCGAATAA", "idt": {"name": "staple118", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F3"}, "domains": [ @@ -1069,7 +1069,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "GCTTTCCGGCACTAAAGGAA", "idt": {"name": "staple119", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G3"}, "domains": [ @@ -1078,7 +1078,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "ACCGCTTCTGGAAAGGAACA", "idt": {"name": "staple120", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H3"}, "domains": [ @@ -1087,7 +1087,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "GTGCCGGAAAAGTGAGAATA", "idt": {"name": "staple121", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A4"}, "domains": [ @@ -1096,7 +1096,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "CCAGGCAAAGGTTTCAGCGG", "idt": {"name": "staple122", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B4"}, "domains": [ @@ -1105,7 +1105,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "CGCCATTCGCACTTTCAACA", "idt": {"name": "staple123", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C4"}, "domains": [ @@ -1114,7 +1114,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "CATTCAGGCTTTGCTAAACA", "idt": {"name": "staple124", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D4"}, "domains": [ @@ -1123,7 +1123,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "GCGCAACTGTGTATGGGATT", "idt": {"name": "staple125", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E4"}, "domains": [ @@ -1132,7 +1132,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "TGGGAAGGGCTGAATTTTCT", "idt": {"name": "staple126", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F4"}, "domains": [ @@ -1141,7 +1141,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GATCGGTGCGCGTTAGTAAA", "idt": {"name": "staple127", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G4"}, "domains": [ @@ -1150,7 +1150,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "GGCCTCTTCGTCTTTCCAGA", "idt": {"name": "staple128", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H4"}, "domains": [ @@ -1159,7 +1159,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "CTATTACGCCAGTTTTGTCG", "idt": {"name": "staple129", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A5"}, "domains": [ @@ -1168,7 +1168,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "AGCTGGCGAAAACGATCTAA", "idt": {"name": "staple130", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B5"}, "domains": [ @@ -1177,7 +1177,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "AGGGGGATGTTAGTTAGCGT", "idt": {"name": "staple131", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C5"}, "domains": [ @@ -1186,7 +1186,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "GCTGCAAGGCACAGCCCTCA", "idt": {"name": "staple132", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D5"}, "domains": [ @@ -1195,7 +1195,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "GATTAAGTTGCATTCCACAG", "idt": {"name": "staple133", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E5"}, "domains": [ @@ -1204,7 +1204,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "GGTAACGCCAACGCCTGTAG", "idt": {"name": "staple134", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F5"}, "domains": [ @@ -1213,7 +1213,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GGGTTTTCCCACAAACTACA", "idt": {"name": "staple135", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G5"}, "domains": [ @@ -1222,7 +1222,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "AGTCACGACGCGTCACCAGT", "idt": {"name": "staple136", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H5"}, "domains": [ @@ -1231,7 +1231,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "TTGTAAAACGCACTGAGTTT", "idt": {"name": "staple137", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A6"}, "domains": [ @@ -1240,7 +1240,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "ACGGCCAGTGTGTACCGTAA", "idt": {"name": "staple138", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B6"}, "domains": [ @@ -1249,7 +1249,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "CCAAGCTTGCTAGGAACCCA", "idt": {"name": "staple139", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C6"}, "domains": [ @@ -1258,7 +1258,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "ATGCCTGCAGGCAAGCCCAA", "idt": {"name": "staple140", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D6"}, "domains": [ @@ -1267,7 +1267,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "GTCGACTCTATTCAGGGATA", "idt": {"name": "staple141", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E6"}, "domains": [ @@ -1276,7 +1276,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "GAGGATCCCCCACCCTCATT", "idt": {"name": "staple142", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F6"}, "domains": [ @@ -1285,7 +1285,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "GGGTACCGAGTCAGAGCCAC", "idt": {"name": "staple143", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G6"}, "domains": [ @@ -1294,7 +1294,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "CTCGAATTCGACCGCCACCC", "idt": {"name": "staple144", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H6"}, "domains": [ @@ -1303,7 +1303,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "TAATCATGGTCACCCTCAGA", "idt": {"name": "staple145", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A7"}, "domains": [ @@ -1312,7 +1312,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CATAGCTGTTTCAGAACCGC", "idt": {"name": "staple146", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B7"}, "domains": [ @@ -1321,7 +1321,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "TCCTGTGTGAACCGCCACCC", "idt": {"name": "staple147", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C7"}, "domains": [ @@ -1330,7 +1330,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "AATTGTTATCGAGGTTTAGT", "idt": {"name": "staple148", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D7"}, "domains": [ @@ -1339,7 +1339,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "CGCTCACAATCCGTACTCAG", "idt": {"name": "staple149", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E7"}, "domains": [ @@ -1348,7 +1348,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "TCCACACAACAGGTGTATCA", "idt": {"name": "staple150", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F7"}, "domains": [ @@ -1357,7 +1357,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "ATACGAGCCGAGCCCGGAAT", "idt": {"name": "staple151", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G7"}, "domains": [ @@ -1366,7 +1366,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "GAAGCATAAAATATAAGTAT", "idt": {"name": "staple152", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H7"}, "domains": [ @@ -1375,7 +1375,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GTGTAAAGCCGAGAGGGTTG", "idt": {"name": "staple153", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A8"}, "domains": [ @@ -1384,7 +1384,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TGGGGTGCCTAAGTGCCGTC", "idt": {"name": "staple154", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B8"}, "domains": [ @@ -1393,7 +1393,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "AATGAGTGAGCCAGGCGGAT", "idt": {"name": "staple155", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C8"}, "domains": [ @@ -1402,7 +1402,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "CTAACTCACATTGCTCAGTA", "idt": {"name": "staple156", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D8"}, "domains": [ @@ -1411,7 +1411,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "TTAATTGCGTTAGCGGGGTT", "idt": {"name": "staple157", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E8"}, "domains": [ @@ -1420,7 +1420,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "TGCGCTCACTGGATTAGGAT", "idt": {"name": "staple158", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F8"}, "domains": [ @@ -1429,7 +1429,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "GCCCGCTTTCCTCAAGAGAA", "idt": {"name": "staple159", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G8"}, "domains": [ @@ -1438,7 +1438,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "CAGTCGGGAAGCTGAGACTC", "idt": {"name": "staple160", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H8"}, "domains": [ @@ -1447,7 +1447,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "ACCTGTCGTGGTATTAAGAG", "idt": {"name": "staple161", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A9"}, "domains": [ @@ -1456,7 +1456,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "CCAGCTGCATAAACATGAAA", "idt": {"name": "staple162", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B9"}, "domains": [ @@ -1465,7 +1465,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "TAATGAATCGTATTATTCTG", "idt": {"name": "staple163", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C9"}, "domains": [ @@ -1474,7 +1474,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "GCCAACGCGCTTTCGGAACC", "idt": {"name": "staple164", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D9"}, "domains": [ @@ -1483,7 +1483,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "GGGGAGAGGCCCCCTGCCTA", "idt": {"name": "staple165", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E9"}, "domains": [ @@ -1492,7 +1492,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GGTTTGCGTACAGTTAATGC", "idt": {"name": "staple166", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F9"}, "domains": [ @@ -1501,7 +1501,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TTGGGCGCCACCCGTATAAA", "idt": {"name": "staple167", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G9"}, "domains": [ @@ -1510,7 +1510,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "GGGTGGTTTTAGTAACAGTG", "idt": {"name": "staple168", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H9"}, "domains": [ @@ -1519,7 +1519,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "TCTTTTCACCCAGTGCCTTG", "idt": {"name": "staple169", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A10"}, "domains": [ @@ -1528,7 +1528,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "AGTGAGACGGTTAACGGGGT", "idt": {"name": "staple170", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B10"}, "domains": [ @@ -1537,7 +1537,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "GCAACAGCTGGTAATAAGTT", "idt": {"name": "staple171", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C10"}, "domains": [ @@ -1546,7 +1546,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "ATTGCCCTTCGAGTGTACTG", "idt": {"name": "staple172", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D10"}, "domains": [ @@ -1555,7 +1555,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "ACCGCCTGGCGATGATACAG", "idt": {"name": "staple173", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E10"}, "domains": [ @@ -1564,7 +1564,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "CCTGAGAGAGCATGGCTTTT", "idt": {"name": "staple174", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F10"}, "domains": [ @@ -1573,7 +1573,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TTGCAGCAAGAAGCGTCATA", "idt": {"name": "staple175", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G10"}, "domains": [ @@ -1582,7 +1582,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "CGGTCCACGCCCGTTCCAGT", "idt": {"name": "staple176", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H10"}, "domains": [ @@ -1591,7 +1591,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "TGGTTTGCCCTCTGAATTTA", "idt": {"name": "staple177", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A11"}, "domains": [ @@ -1600,7 +1600,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "CAGCAGGCGAAAGCGCAGTC", "idt": {"name": "staple178", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B11"}, "domains": [ @@ -1609,7 +1609,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "AAATCCTGTTCCAGAATGGA", "idt": {"name": "staple179", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C11"}, "domains": [ @@ -1618,7 +1618,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TGATGGTGGTCTCATTAAAG", "idt": {"name": "staple180", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D11"}, "domains": [ @@ -1627,7 +1627,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "TCCGAAATCGCAAATAAATC", "idt": {"name": "staple181", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E11"}, "domains": [ @@ -1636,7 +1636,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "GCAAAATCCCTATTCACAAA", "idt": {"name": "staple182", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F11"}, "domains": [ @@ -1645,7 +1645,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "TTATAAATCATTGGCCTTGA", "idt": {"name": "staple183", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G11"}, "domains": [ @@ -1654,7 +1654,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "AAAGAATAGCGGTCAGACGA", "idt": {"name": "staple184", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H11"}, "domains": [ @@ -1663,7 +1663,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CCGAGATAGGGGTTGAGGCA", "idt": {"name": "staple185", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A12"}, "domains": [ @@ -1672,7 +1672,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "GTTGAGTGTTATTGACAGGA", "idt": {"name": "staple186", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B12"}, "domains": [ @@ -1681,7 +1681,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GTTCCAGTTTCGCCGCCAGC", "idt": {"name": "staple187", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C12"}, "domains": [ @@ -1690,7 +1690,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "GGAACAAGAGCCACCAGAGC", "idt": {"name": "staple188", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D12"}, "domains": [ @@ -1699,7 +1699,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "TCCACTATTAACCAGAACCA", "idt": {"name": "staple189", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E12"}, "domains": [ @@ -1708,7 +1708,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "AAGAACGTGGCAGAGCCGCC", "idt": {"name": "staple190", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F12"}, "domains": [ @@ -1717,7 +1717,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "ACTCCAACGTCCACCACCCT", "idt": {"name": "staple191", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G12"}, "domains": [ @@ -1726,7 +1726,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "CAAAGGGCGAACCCTCAGAG", "idt": {"name": "staple192", "scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H12"}, "domains": [ @@ -1735,7 +1735,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "AAAACCGTCTCAGAACCGCC", "idt": {"name": "staple193", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "A1"}, "domains": [ @@ -1744,7 +1744,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "ATCAGGGCGACCGCCACCCT", "idt": {"name": "staple194", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "B1"}, "domains": [ @@ -1753,7 +1753,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "TGGCCCACTATCCCTCAGAG", "idt": {"name": "staple195", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "C1"}, "domains": [ @@ -1762,7 +1762,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "CGTGAACCATCGGAACCGCC", "idt": {"name": "staple196", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "D1"}, "domains": [ @@ -1771,7 +1771,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "CACCCAAATCGAGCCACCAC", "idt": {"name": "staple197", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "E1"}, "domains": [ @@ -1780,7 +1780,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "AAGTTTTTTGACCGGAACCA", "idt": {"name": "staple198", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "F1"}, "domains": [ @@ -1789,7 +1789,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "GGGTCGAGGTAATCAAAATC", "idt": {"name": "staple199", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "G1"}, "domains": [ @@ -1798,7 +1798,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GCCGTAAAGCATCTTTTCAT", "idt": {"name": "staple200", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "H1"}, "domains": [ @@ -1807,7 +1807,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "ACTAAATCGGAGCGTTTGCC", "idt": {"name": "staple201", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "A2"}, "domains": [ @@ -1816,7 +1816,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "AACCCTAAAGCCCCCTTATT", "idt": {"name": "staple202", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "B2"}, "domains": [ @@ -1825,7 +1825,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "GGAGCCCCCGTCGGTCATAG", "idt": {"name": "staple203", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "C2"}, "domains": [ @@ -1834,7 +1834,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "ATTTAGAGCTATCGGCATTT", "idt": {"name": "staple204", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "D2"}, "domains": [ @@ -1843,7 +1843,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "TGACGGGGAAGCGCGTTTTC", "idt": {"name": "staple205", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "E2"}, "domains": [ @@ -1852,7 +1852,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "AGCCGGCGAATCAGACTGTA", "idt": {"name": "staple206", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "F2"}, "domains": [ @@ -1861,7 +1861,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "CGTGGCGAGAGCCTTTAGCG", "idt": {"name": "staple207", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "G2"}, "domains": [ @@ -1870,7 +1870,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "AAGGAAGGGAAATCAAGTTT", "idt": {"name": "staple208", "scale": "25nm", "purification": "STD", "plate": "plate3", "well": "H2"}, "domains": [ diff --git a/examples/output_designs/long_range_crossovers.dna b/examples/output_designs/long_range_crossovers.dna index e43e95df..dd9abbee 100644 --- a/examples/output_designs/long_range_crossovers.dna +++ b/examples/output_designs/long_range_crossovers.dna @@ -21,168 +21,168 @@ ], "strands": [ { - "color": "#cc0000", + "color": "#f74308", "domains": [ {"helix": 0, "forward": false, "start": 0, "end": 16}, {"helix": 15, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#f7931e", + "color": "#57bb00", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, {"helix": 0, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#f74308", + "color": "#888888", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 48}, {"helix": 15, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#57bb00", + "color": "#32b86c", "domains": [ {"helix": 1, "forward": false, "start": 0, "end": 16}, {"helix": 14, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#888888", + "color": "#333333", "domains": [ {"helix": 14, "forward": true, "start": 16, "end": 32}, {"helix": 1, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#32b86c", + "color": "#320096", "domains": [ {"helix": 1, "forward": false, "start": 32, "end": 48}, {"helix": 14, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#333333", + "color": "#03b6a2", "domains": [ {"helix": 2, "forward": false, "start": 0, "end": 16}, {"helix": 13, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#320096", + "color": "#7300de", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, {"helix": 2, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "domains": [ {"helix": 2, "forward": false, "start": 32, "end": 48}, {"helix": 13, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#7300de", + "color": "#b8056c", "domains": [ {"helix": 3, "forward": false, "start": 0, "end": 16}, {"helix": 12, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#aaaa00", + "color": "#007200", "domains": [ {"helix": 12, "forward": true, "start": 16, "end": 32}, {"helix": 3, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#b8056c", + "color": "#cc0000", "domains": [ {"helix": 3, "forward": false, "start": 32, "end": 48}, {"helix": 12, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#007200", + "color": "#f7931e", "domains": [ {"helix": 4, "forward": false, "start": 0, "end": 16}, {"helix": 11, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#cc0000", + "color": "#f74308", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, {"helix": 4, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#f7931e", + "color": "#57bb00", "domains": [ {"helix": 4, "forward": false, "start": 32, "end": 48}, {"helix": 11, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#f74308", + "color": "#888888", "domains": [ {"helix": 5, "forward": false, "start": 0, "end": 16}, {"helix": 10, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#57bb00", + "color": "#32b86c", "domains": [ {"helix": 10, "forward": true, "start": 16, "end": 32}, {"helix": 5, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#888888", + "color": "#333333", "domains": [ {"helix": 5, "forward": false, "start": 32, "end": 48}, {"helix": 10, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#32b86c", + "color": "#320096", "domains": [ {"helix": 6, "forward": false, "start": 0, "end": 16}, {"helix": 9, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#333333", + "color": "#03b6a2", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, {"helix": 6, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#320096", + "color": "#7300de", "domains": [ {"helix": 6, "forward": false, "start": 32, "end": 48}, {"helix": 9, "forward": true, "start": 32, "end": 48} ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "domains": [ {"helix": 7, "forward": false, "start": 0, "end": 16}, {"helix": 8, "forward": true, "start": 0, "end": 16} ] }, { - "color": "#7300de", + "color": "#b8056c", "domains": [ {"helix": 8, "forward": true, "start": 16, "end": 32}, {"helix": 7, "forward": false, "start": 16, "end": 32} ] }, { - "color": "#aaaa00", + "color": "#007200", "domains": [ {"helix": 7, "forward": false, "start": 32, "end": 48}, {"helix": 8, "forward": true, "start": 32, "end": 48} diff --git a/examples/output_designs/loopouts_all_types.dna b/examples/output_designs/loopouts_all_types.dna index 788758b0..f2d7c0ac 100644 --- a/examples/output_designs/loopouts_all_types.dna +++ b/examples/output_designs/loopouts_all_types.dna @@ -8,7 +8,7 @@ ], "strands": [ { - "color": "#b8056c", + "color": "#f74308", "sequence": "ACGACGACTTTACGTCGTCGTTTTACGACGACGATTTACTTACGCACGACGATTTTTTTTTTACGTTGCAGGTCGTCGTGACGACGACTGTCGTCGT", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 8}, diff --git a/examples/output_designs/many_helices_modifications.dna b/examples/output_designs/many_helices_modifications.dna index 6c63322e..c8f09903 100644 --- a/examples/output_designs/many_helices_modifications.dna +++ b/examples/output_designs/many_helices_modifications.dna @@ -12,6 +12,18 @@ {"grid_position": [0, 7]} ], "modifications_in_design": { + "/3Cy3Sp/": { + "display_text": "Cy3", + "idt_text": "/3Cy3Sp/", + "display_connector": false, + "location": "3'" + }, + "/iCy3/": { + "display_text": "Cy3", + "idt_text": "/iCy3/", + "display_connector": false, + "location": "internal" + }, "/iBiodT/": { "display_text": "B", "idt_text": "/iBiodT/", @@ -24,23 +36,11 @@ "idt_text": "/5Biosg/", "display_connector": false, "location": "5'" - }, - "/3Cy3Sp/": { - "display_text": "Cy3", - "idt_text": "/3Cy3Sp/", - "display_connector": false, - "location": "3'" - }, - "/iCy3/": { - "display_text": "Cy3", - "idt_text": "/iCy3/", - "display_connector": false, - "location": "internal" } }, "strands": [ { - "color": "#007200", + "color": "#f74308", "sequence": "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT", "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 16, "deletions": [11, 12]}, diff --git a/examples/output_designs/proposal.dna b/examples/output_designs/proposal.dna index f6bae9df..e47a19ee 100644 --- a/examples/output_designs/proposal.dna +++ b/examples/output_designs/proposal.dna @@ -108,7 +108,7 @@ "is_scaffold": true }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "AACAATATTACCGATAGTTGCGCCGACAATGA", "idt": {"name": "ST15[248]0[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -117,7 +117,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "ACTTTGAAATCATAAGGGAACCGTATAAGTA", "idt": {"name": "ST2[231]1[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -126,7 +126,7 @@ ] }, { - "color": "#f7931e", + "color": "#888888", "sequence": "TAGCCCGGACGTCGAGAGGGTTGAAACTGACCA", "idt": {"name": "ST1[248]2[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -135,7 +135,7 @@ ] }, { - "color": "#f74308", + "color": "#32b86c", "sequence": "CAACACTAAAGGAATTACGAGGCAATCAAAAT", "idt": {"name": "ST4[231]3[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -144,7 +144,7 @@ ] }, { - "color": "#57bb00", + "color": "#333333", "sequence": "CACCGGAATGCCATCTTTTCATATAGTAAGAG", "idt": {"name": "ST3[248]4[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -153,7 +153,7 @@ ] }, { - "color": "#888888", + "color": "#320096", "sequence": "TTAGAGCTAAGAGGTCATTTTTGCGGAATAC", "idt": {"name": "ST6[231]5[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -162,7 +162,7 @@ ] }, { - "color": "#32b86c", + "color": "#03b6a2", "sequence": "CCAAAAGAAGGAAACGCAATAATAACGGATGGC", "idt": {"name": "ST5[248]6[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -171,7 +171,7 @@ ] }, { - "color": "#333333", + "color": "#7300de", "sequence": "TAAATGCAAATTTTTAGAACCCTTTTTAGCG", "idt": {"name": "ST8[231]7[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -180,7 +180,7 @@ ] }, { - "color": "#320096", + "color": "#aaaa00", "sequence": "AACCTCCCGTAAGAACGCGAGGCGCATATATTT", "idt": {"name": "ST7[248]8[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -189,7 +189,7 @@ ] }, { - "color": "#03b6a2", + "color": "#b8056c", "sequence": "GCTTTCATTTCGCGTCTGGCCTTCCTGTTTAG", "idt": {"name": "ST10[231]9[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -198,7 +198,7 @@ ] }, { - "color": "#7300de", + "color": "#007200", "sequence": "TATCATATATTACTAGAAAAAGCCTGTAGCCA", "idt": {"name": "ST9[248]10[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -207,7 +207,7 @@ ] }, { - "color": "#aaaa00", + "color": "#cc0000", "sequence": "CTAGAGGAGCTTGCATGCCTGCATTACCTGA", "idt": {"name": "ST12[231]11[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -216,7 +216,7 @@ ] }, { - "color": "#b8056c", + "color": "#f7931e", "sequence": "GCAAAAGAAGAATTATTCATTTCAAGGTCGACT", "idt": {"name": "ST11[248]12[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -225,7 +225,7 @@ ] }, { - "color": "#007200", + "color": "#f74308", "sequence": "TCCCTTATATGGTGGTTCCGAAAAATATCTT", "idt": {"name": "ST14[231]13[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -234,7 +234,7 @@ ] }, { - "color": "#cc0000", + "color": "#57bb00", "sequence": "TAGGAGCACAGGAAGGTTATCTAATCGGCAAAA", "idt": {"name": "ST13[248]14[232]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -243,7 +243,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CAACAACCATCGGCCTTGCTGGTAATATCCAG", "idt": {"name": "ST0[231]15[247]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -252,7 +252,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "GAGCTTGAAAGTTTCCATTAAACGAACCTAAA", "idt": {"name": "ST15[56]1[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -262,7 +262,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "ACGAAAGAGAGTAGTAAATTGGGCTGAATTAC", "idt": {"name": "ST1[56]3[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -272,7 +272,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "CTTATGCGGCTTTAAACAGTTCAGTCTTTAC", "idt": {"name": "ST3[56]5[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -282,7 +282,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "CCTGACTATCTGTTTAGCTATATTTAATTCTAC", "idt": {"name": "ST5[56]7[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -292,7 +292,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "TAATAGTAGCCTGAGAGTCTGGAGAACTAGCA", "idt": {"name": "ST7[56]9[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -302,7 +302,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "TGTCAATCGATCGCACTCCAGCCCAGGCAAA", "idt": {"name": "ST9[56]11[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -312,7 +312,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GCGCCATTCGCGCTCACTGCCCGCTTTAATGAA", "idt": {"name": "ST11[56]13[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -322,7 +322,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TCGGCCAACGGGTCGAGGTGCCGTCCGATTTA", "idt": {"name": "ST13[56]15[55]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -332,7 +332,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "CATGAGGCGGGGAAAGCCGGCGCAAATCAAG", "idt": {"name": "ST0[71]14[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -342,7 +342,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "CAGAACGGCAAAAGAATACACGACTTTTT", "idt": {"name": "ST2[71]0[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -352,7 +352,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "CTCAAATATTTTAAGAACTGGCGAGAAACAC", "idt": {"name": "ST4[71]2[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -362,7 +362,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "CAATAACTATAGTCAGAAGCATGAATCCCC", "idt": {"name": "ST6[71]4[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -372,7 +372,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "GTCATTGTAGCATTAACATCCCAAATGGT", "idt": {"name": "ST8[71]6[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -382,7 +382,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "TCAGGAAATATGTACCCCGGTTGGCTATCAG", "idt": {"name": "ST10[71]8[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -392,7 +392,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "TTGCGTTGCCATTCAGGCTGCGTATCGGCC", "idt": {"name": "ST12[71]10[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -402,7 +402,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TTTTTTGGCGCGGGGAGAGGCCACATTAA", "idt": {"name": "ST14[71]12[72]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -412,7 +412,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "GAGAAAGGGGCTTTGAGGACTAAATAAAACAC", "idt": {"name": "ST15[88]1[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -422,7 +422,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "TCATCTTTGAAGGCTTGCCCTGACTCATTATA", "idt": {"name": "ST1[88]3[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -432,7 +432,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "CCAGTCAGGTCATAAATATTCATAAGCGGAT", "idt": {"name": "ST3[88]5[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -442,7 +442,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "TGCATCAAACATTAGATACATTTCGAATAAATC", "idt": {"name": "ST5[88]7[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -452,7 +452,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "ATACAGGCATGAGAGATCTACAAAGATAATCA", "idt": {"name": "ST7[88]9[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -462,7 +462,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "GAAAAGCCGAGGGGACGACGACAGCAACTGT", "idt": {"name": "ST9[88]11[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -472,7 +472,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "TGGGAAGGGAATGAGTGAGCTAACTGGTTTGCG", "idt": {"name": "ST11[88]13[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -482,7 +482,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "TATTGGGCGACGTGAACCATCACCAACGTGGC", "idt": {"name": "ST13[88]15[87]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -492,7 +492,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "GCTACAGAAAGGGATTTTTATAATCAGGGCGAT", "idt": {"name": "ST0[103]14[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -502,7 +502,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CAGTGAATACCCCCAGCGATTATTAGCAACG", "idt": {"name": "ST2[103]0[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -512,7 +512,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "GCGGAATCGACGTTGGGAAGAAAACTGCTCATT", "idt": {"name": "ST4[103]2[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -522,7 +522,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "AGTTTGACAAGATTAAGAGGAAGTCCAATACT", "idt": {"name": "ST6[103]4[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -532,7 +532,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "GCTATTTTAGGCAAAGAATTAGCGTAGATTT", "idt": {"name": "ST8[103]6[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -542,7 +542,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "GCCAGTTTCCAAAAACAGGAAGATGAGAGGGTA", "idt": {"name": "ST10[103]8[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -552,7 +552,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "GGGTGCCTCGATCGGTGCGGGCCCGTGCATCT", "idt": {"name": "ST12[103]10[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -562,7 +562,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "GGCCCACTCCAGGGTGGTTTTTCAAAGCCTG", "idt": {"name": "ST14[103]12[104]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -572,7 +572,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GCCACCGAGCATCGGAACGAGGGACCAAGC", "idt": {"name": "ST15[120]1[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -582,7 +582,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "GCGAAACAATCAACGTAACAAAGATCTACG", "idt": {"name": "ST1[120]3[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -592,7 +592,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "TTAATAAATAGACTGGATAGCGCCCGAAA", "idt": {"name": "ST3[120]5[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -602,7 +602,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "GACTTCAAACAATTCTGCGAACGAAAAATTA", "idt": {"name": "ST5[120]7[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -612,7 +612,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "AGCAATAAAATAAATTAATGCCGTGTATAA", "idt": {"name": "ST7[120]9[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -622,7 +622,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "GCAAATATGGGCGCATCGTAACTCTTCGC", "idt": {"name": "ST9[120]11[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -632,7 +632,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "TATTACGCCGGAAGCATAAAGTGTTTTTCAC", "idt": {"name": "ST11[120]13[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -642,7 +642,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "CAGTGAGACGAAAAACCGTCTATCAGTGAG", "idt": {"name": "ST13[120]15[119]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -652,7 +652,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GAAAGACAGTAAAAGAGTCTGTCCCTCCAACGT", "idt": {"name": "ST0[135]14[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -662,7 +662,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TACCCAAAAGTACAACGGAGATTTCAGCAGC", "idt": {"name": "ST2[135]0[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -672,7 +672,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "AAAATGTTACGAACTAACGGAACAGATATTCAT", "idt": {"name": "ST4[135]2[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -682,7 +682,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "TTGATTCCTATCGCGTTTTAATTGGTAATAGT", "idt": {"name": "ST6[135]4[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -692,7 +692,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "TCTAGCTGGCCTCAGAGCATAAATATAACAG", "idt": {"name": "ST8[135]6[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -702,7 +702,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GTGTAGATTTAAATTGTAAACGTTTTCAACCGT", "idt": {"name": "ST10[135]8[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -712,7 +712,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TACGAGCCAGCTGGCGAAAGGGGGTCACGTTG", "idt": {"name": "ST12[135]10[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -722,7 +722,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "CAAAGGGCGGGCAACAGCTGATTACACAACA", "idt": {"name": "ST14[135]12[136]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -732,7 +732,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "AATTAACCTGCGGGATCGTCACCCTGTATCAT", "idt": {"name": "ST15[152]1[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -742,7 +742,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "CGCCTGATATCTTGACAAGAACCGACATTATT", "idt": {"name": "ST1[152]3[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -752,7 +752,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "ACAGGTAGAGTTTTGCCAGAGGGCGAGCTTC", "idt": {"name": "ST3[152]5[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -762,7 +762,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "AAAGCGAACTGGAAGTTTCATTCCAGCTAAATC", "idt": {"name": "ST5[152]7[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -772,7 +772,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "GGTTGTACCACCATCAATATGATAAATATTTT", "idt": {"name": "ST7[152]9[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -782,7 +782,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GTTAAAATACCGTAATGGGATAGGATGTGCT", "idt": {"name": "ST9[152]11[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -792,7 +792,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "GCAAGGCGAATCCGCTCACAATTCCGCCCTTCA", "idt": {"name": "ST11[152]13[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -802,7 +802,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "CCGCCTGGCATTAAAGAACGTGGAATCACGCA", "idt": {"name": "ST13[152]15[151]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -812,7 +812,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "CCGCTTTGTTGTAGCAATACTTGGAACAAGA", "idt": {"name": "ST0[167]14[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -822,7 +822,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "AGAGTAAAATTGTGTCGAAATGTTAAAGG", "idt": {"name": "ST2[167]0[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -832,7 +832,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "CAAAAGAAAAGATTCATCAGTTCCTTCATCA", "idt": {"name": "ST4[167]2[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -842,7 +842,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "CGGTGTCCAGACCGGAAGCAAAGGCTTTTG", "idt": {"name": "ST6[167]4[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -852,7 +852,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "TCAAATCAAAAACATTATGACCTAAAGTA", "idt": {"name": "ST8[167]6[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -862,7 +862,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "CGGATTGTCGCATTAAATTTTTCGGAGACAG", "idt": {"name": "ST10[167]8[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -872,7 +872,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "AATTGTTTTAAGTTGGGTAACAACAAACGG", "idt": {"name": "ST12[167]10[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -882,7 +882,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "GTCCACTCCTGAGAGAGTTGCCTGTGTGA", "idt": {"name": "ST14[167]12[168]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -892,7 +892,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "AGTAATAACTGAGGCTTGCAGGGACCGCGACC", "idt": {"name": "ST15[184]1[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -902,7 +902,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "TGCTCCATGGCATAGGCTGGCTGAGAGATTTA", "idt": {"name": "ST1[184]3[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -912,7 +912,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GGAATACCAACCAAAATAGCGAGACTCCAAC", "idt": {"name": "ST3[184]5[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -922,7 +922,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "AGGTCAGGATGTTTTAAATATGCAACCTGTAAT", "idt": {"name": "ST5[184]7[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -932,7 +932,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "ACTTTTGCGAAGGGTGAGAAAGGCGTTAAATC", "idt": {"name": "ST7[184]9[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -942,7 +942,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "AGCTCATTCGGATTCTCCGTGGGGCCAGGGT", "idt": {"name": "ST9[184]11[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -952,7 +952,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "TTTCCCAGTTGGTCATAGCTGTTTCAGCAAGCG", "idt": {"name": "ST11[184]13[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -962,7 +962,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GTCCACGCTGTGTTGTTCCAGTTTCTTTGATT", "idt": {"name": "ST13[184]15[183]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -972,7 +972,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TTCGGTCGCATCACTTGCCTGAGTGCCCGAGAT", "idt": {"name": "ST0[199]14[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -982,7 +982,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "GACCAGGCTTACTTAGCCGGAACCCGATATA", "idt": {"name": "ST2[199]0[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -992,7 +992,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "ACGATAAAACATTCAACTAATGCACGGTGTACA", "idt": {"name": "ST4[199]2[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1002,7 +1002,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "GCTCAACATTAGAGAGTACCTTTTACCAGACG", "idt": {"name": "ST6[199]4[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1012,7 +1012,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "AGATTCAAGGAGAAGCCTTTATTATGCTGTA", "idt": {"name": "ST8[199]6[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1022,7 +1022,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CAACCCGTTTTTAACCAATAGGAATGTAGGTAA", "idt": {"name": "ST10[199]8[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1032,7 +1032,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "CGTAATCACACGACGTTGTAAAAAGCGAGTAA", "idt": {"name": "ST12[199]10[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1042,7 +1042,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "AGGGTTGAGGTTTGCCCCAGCAGCTCGAATT", "idt": {"name": "ST14[199]12[200]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1052,7 +1052,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "CTCAAACTATCGCCCACGCATAAGAGGCGC", "idt": {"name": "ST15[216]1[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1062,7 +1062,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "AGACGGTCAAGAGGACAGATGAAGATACAT", "idt": {"name": "ST1[216]3[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1072,7 +1072,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "AACGCCAATCATAACCCTCGTTAATTGCT", "idt": {"name": "ST3[216]5[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1082,7 +1082,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "CCTTTTGATTAATTGCTGAATATATCAACGC", "idt": {"name": "ST5[216]7[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1092,7 +1092,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "AAGGATAAAATGCCTGAGTAATGCGCCATC", "idt": {"name": "ST7[216]9[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1102,7 +1102,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "AAAAATAACAACATTAAATGTGCGACGGC", "idt": {"name": "ST9[216]11[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1112,7 +1112,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "CAGTGCCAATCCCCGGGTACCGAGGCGAAAA", "idt": {"name": "ST11[216]13[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1122,7 +1122,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "TCCTGTTTGAAATCAAAAGAATAAGAAGAA", "idt": {"name": "ST13[216]15[215]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1132,7 +1132,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "AGCTTGATACCGCCAGCCATTGCAGTTGAAA", "idt": {"name": "ST0[263]14[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1142,7 +1142,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "TAAGTGCATAGGTGTATCACCTCTTAAAC", "idt": {"name": "ST2[263]0[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1152,7 +1152,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "TAGCGTTCCAGAGCCACCACCGCCAGGCGGA", "idt": {"name": "ST4[263]2[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1162,7 +1162,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "AAACCGACTGGCATGATTAAGCCCCCTTAT", "idt": {"name": "ST6[263]4[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1172,7 +1172,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GGTATTCACTTGCGGGAGGTTCCAGAAGG", "idt": {"name": "ST8[263]6[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1182,7 +1182,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "AATCATAGCGTTATACAAATTCGGCTTATCC", "idt": {"name": "ST10[263]8[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1192,7 +1192,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "CAGAGGCGATGATGAAACAAAAAACACCGG", "idt": {"name": "ST12[263]10[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1202,7 +1202,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "GGAATTGTAACAACTAATAGAAAATCGCG", "idt": {"name": "ST14[263]12[264]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1212,7 +1212,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "AAAACGCTGCTTTCGAGGTGAATTGTACTCAG", "idt": {"name": "ST15[280]1[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1222,7 +1222,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GAGGTTTAGGGGTTTTGCTCAGTAGAACCGCC", "idt": {"name": "ST1[280]3[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1232,7 +1232,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TCCCTCAGCATTTTCGGTCATAGACTCCTTA", "idt": {"name": "ST3[280]5[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1242,7 +1242,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "TTACGCAGTTAGCCGAACAAAGTTATTGAAGCC", "idt": {"name": "ST5[280]7[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1252,7 +1252,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "TTAAATCAAAAATCAGATATAGAATTACCAGT", "idt": {"name": "ST7[280]9[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1262,7 +1262,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "ATAAAGCCGCGTTAAATAAGAATCATCAAGA", "idt": {"name": "ST9[280]11[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1272,7 +1272,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "AAACAAAATTGAATACCAAGTTACATTAGAGCC", "idt": {"name": "ST11[280]13[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1282,7 +1282,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "GTCAATAGACAGTTGGCAAATCAACAACAGGA", "idt": {"name": "ST13[280]15[279]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1292,7 +1292,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "ATCAGCTTCATGGAAATACCTACACTCAATCAA", "idt": {"name": "ST0[295]14[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1302,7 +1302,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GATTAGCGTACCGCCACCCTCAGATCGGTTT", "idt": {"name": "ST2[295]0[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1312,7 +1312,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TTCATCGGAGCCGCCACCCTCAGAAAGGATTAG", "idt": {"name": "ST4[295]2[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1322,7 +1322,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "TAAGCAGAATGTTAGCAAACGTATAGCGCGTT", "idt": {"name": "ST6[295]4[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1332,7 +1332,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "TAGCAAGCGATTAGTTGCTATTTAAGAAAAG", "idt": {"name": "ST8[295]6[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1342,7 +1342,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "TAAATAAGAACGCTCAACAGTAGGCGCGCCCAA", "idt": {"name": "ST10[295]8[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1352,7 +1352,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GATTGCTTTAATTACATTTAACAACCGTGTGA", "idt": {"name": "ST12[295]10[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1362,7 +1362,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TATCTGGTTAATACATTTGAGGAATTCGCCT", "idt": {"name": "ST14[295]12[296]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1372,7 +1372,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "GCTCAATCGGAGCCTTTAATTGTAACCGCC", "idt": {"name": "ST15[312]1[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1382,7 +1382,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "ACCCTCAGAAGACTCCTCAAGAGACCGCCA", "idt": {"name": "ST1[312]3[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1392,7 +1392,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "CCCTCAGATTAGCGTCAGACTGGAAAATA", "idt": {"name": "ST3[312]5[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1402,7 +1402,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "CATACATAAACCGAAGCCCTTTTTTGCACCC", "idt": {"name": "ST5[312]7[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1412,7 +1412,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "AGCTACAATGTAGGAATCATTACGCTTAAT", "idt": {"name": "ST7[312]9[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1422,7 +1422,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "TGAGAATCGGTTTGAAATACCGATTTCAT", "idt": {"name": "ST9[312]11[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1432,7 +1432,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "TTGAATTACGAGAAACAATAACGGTTTAGAA", "idt": {"name": "ST11[312]13[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1442,7 +1442,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "GTATTAGACTCAAATATCAAACCTTTTGAC", "idt": {"name": "ST13[312]15[311]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1452,7 +1452,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "CTCCAAAAGTCTGAAATGGATTATCATCACCTT", "idt": {"name": "ST0[327]14[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1462,7 +1462,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "AGAGGCTGACCGCCACCCTCAGAAAAAAAGG", "idt": {"name": "ST2[327]0[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1472,7 +1472,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "GTTTGCCTGCCACCACCCTCAGAGAAAGTATTA", "idt": {"name": "ST4[327]2[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1482,7 +1482,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GCTATCTTAGGTGGCAACATATACAGAATCAA", "idt": {"name": "ST6[327]4[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1492,7 +1492,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TTTTCATCTTTATCCTGAATCTTTAGCAATA", "idt": {"name": "ST8[327]6[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1502,7 +1502,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "AATTTAATGCCATATTTAACAACGCCGTTTTTA", "idt": {"name": "ST10[327]8[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1512,7 +1512,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "TACATCGGCTTTTTTAATGGAAATCTGACCTA", "idt": {"name": "ST12[327]10[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1522,7 +1522,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "GCTGAACCTTTACAAACAATTCGGTACCTTT", "idt": {"name": "ST14[327]12[328]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1532,7 +1532,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "GCAGATTCCGTTGAAAATCTCCAAGCCACCAC", "idt": {"name": "ST15[344]1[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1542,7 +1542,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CCTCATTTTTTATTCTGAAACATGCCGCCACC", "idt": {"name": "ST1[344]3[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1552,7 +1552,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "AGAACCACCGTAATCAGTAGCGAAAAGAAAC", "idt": {"name": "ST3[344]5[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1562,7 +1562,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "GCAAAGACAGCAAGAAACAATGAAAACCAACGC", "idt": {"name": "ST5[344]7[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1572,7 +1572,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TAACGAGCGTCGAGAACAAGCAAGCCAACATG", "idt": {"name": "ST7[344]9[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1582,7 +1582,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "TAATTTAGTAGTTAATTTCATCTCAGTACAT", "idt": {"name": "ST9[344]11[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1592,7 +1592,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "AAATCAATATGAATATACAGTAACAACAACTCG", "idt": {"name": "ST11[344]13[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1602,7 +1602,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "TATTAAATCATGAAAAATCTAAAGTTACATTG", "idt": {"name": "ST13[344]15[343]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1612,7 +1612,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "TTTTTCAACCAGTCACACGACCTGAGAGCCA", "idt": {"name": "ST0[359]14[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1622,7 +1622,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "GAACCTACAGGGATAGCAAGCATAATAAT", "idt": {"name": "ST2[359]0[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1632,7 +1632,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "GCAGCACCACCAGAGCCGCCGCCCTATTTCG", "idt": {"name": "ST4[359]2[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1642,7 +1642,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "AATAAGACCACGGAATAAGTTCCATCGATA", "idt": {"name": "ST6[359]4[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1652,7 +1652,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "GCACTCATCTTTCCAGAGCCTAGCCCAAT", "idt": {"name": "ST8[359]6[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1662,7 +1662,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "TATATTTGCAGAGGCATTTTCGCCAAGTACC", "idt": {"name": "ST10[359]8[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1672,7 +1672,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CGTCAGATATGTGAGTGAATATTTTTCAAA", "idt": {"name": "ST12[359]10[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1682,7 +1682,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "GCAGCAACTTTGCCCGAACGTAGGTTTAA", "idt": {"name": "ST14[359]12[360]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1692,7 +1692,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "AAGGGACAACTAAAGGAATTGCGACCAATAGG", "idt": {"name": "ST15[376]1[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1702,7 +1702,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "AACCCATGTAGTTAATGCCCCCTGCAGCATTG", "idt": {"name": "ST1[376]3[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1712,7 +1712,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "ACAGGAGGACGTCACCAATGAAATATTTTGT", "idt": {"name": "ST3[376]5[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1722,7 +1722,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "CACAATCAACACAAGAATTGAGTTAAATTTGCC", "idt": {"name": "ST5[376]7[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1732,7 +1732,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "AGTTACAAAAGAACGGGTATTAAAAGCCAGTA", "idt": {"name": "ST7[376]9[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1742,7 +1742,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "ATAAGAGAAGAACGCGAGAAAACACCTTGCT", "idt": {"name": "ST9[376]11[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1752,7 +1752,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TCTGTAAATAATTGCGTAGATTTTCTATTAATT", "idt": {"name": "ST11[376]13[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1762,7 +1762,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "TTAAAAGTTGCAACAGTGCCACGCAGTAATAA", "idt": {"name": "ST13[376]15[375]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1772,7 +1772,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "AAGGAACATTCTGGCCAACAGAGACAGTATTAA", "idt": {"name": "ST0[391]14[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1782,7 +1782,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "GTATAAACACCGTAACACTGAGTAGAATAGA", "idt": {"name": "ST2[391]0[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1792,7 +1792,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "GGCCGGAATTGAGGCAGGTCAGACACAGTGCCC", "idt": {"name": "ST4[391]2[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1802,7 +1802,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "AGATAACCTAGAAAATTCATATGCATTAGCAA", "idt": {"name": "ST6[391]4[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1812,7 +1812,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "TCATTCCAATAAACAGCCATATTTATCAGAG", "idt": {"name": "ST8[391]6[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1822,7 +1822,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "CAAGACAAATATAAAGTACCGACACTTTCCTTA", "idt": {"name": "ST10[391]8[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1832,7 +1832,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "AATAAAGACGTCGCTATTAATTAATCCAATCG", "idt": {"name": "ST12[391]10[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1842,7 +1842,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "CACCGCCTTGAGTAACATTATCAAAAACAGA", "idt": {"name": "ST14[391]12[392]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1852,7 +1852,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "CTTCTGACAGTTTCAGCGGAGTGTTCGTCA", "idt": {"name": "ST15[408]1[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1862,7 +1862,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "CCAGTACAACAGTGCCTTGAGTAGATTGGC", "idt": {"name": "ST1[408]3[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1872,7 +1872,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "CTTGATATAGTAGCACCATTACGTTTACC", "idt": {"name": "ST3[408]5[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1882,7 +1882,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "AGCGCCAAAGTAATTGAGCGCTAAATTTATC", "idt": {"name": "ST5[408]7[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1892,7 +1892,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "CCAATCCAACAATAATCGGCTGTAAAGGTA", "idt": {"name": "ST7[408]9[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1902,7 +1902,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "AAGTAATTAAATGCTGATGCAAATTTTCC", "idt": {"name": "ST9[408]11[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1912,7 +1912,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "CTTAGAATCAAATTATTTGCACGTTTTTGCG", "idt": {"name": "ST11[408]13[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1922,7 +1922,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "GAACAAAGAAGAGGTGAGGCGGTTAGAACC", "idt": {"name": "ST13[408]15[407]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1932,7 +1932,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CTTTCAACCTGAAAGCGTAAGAATCCAGCAGAA", "idt": {"name": "ST0[423]14[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1942,7 +1942,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "AACGGGGTACTACAACGCCTGTACTAAACAA", "idt": {"name": "ST2[423]0[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1952,7 +1952,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "AAATCACCTCACAAACAAATAAATATAAGTTTT", "idt": {"name": "ST4[423]2[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1962,7 +1962,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "GTCAGAGGGACAAAAGGGCGACAGAGCCAGCA", "idt": {"name": "ST6[423]4[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1972,7 +1972,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "AAACCAATATAAGAAACGATTTTTGAACAAA", "idt": {"name": "ST8[423]6[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1982,7 +1982,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "CTATATGTCTGTCCAGACGACGACAGCATGTAG", "idt": {"name": "ST10[423]8[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -1992,7 +1992,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "CCATATCACTTGAAAACATAGCGGTTATATAA", "idt": {"name": "ST12[423]10[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2002,7 +2002,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "GATAAAACAACCACCAGAAGGAGAGAACCTA", "idt": {"name": "ST14[423]12[424]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2012,7 +2012,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "CAGACAATTCTGTATGGGATTTTGGCATTCCA", "idt": {"name": "ST15[440]1[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2022,7 +2022,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "CAGACAGCCAGGAGTGTACTGGTACCTCATTA", "idt": {"name": "ST1[440]3[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2032,7 +2032,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "AAGCCAGAAGCCATTTGGGAATTATTCAACCG", "idt": {"name": "ST3[440]5[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2042,7 +2042,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "ATTGAGGGAATTAACTGAACACCCTTGTTTAA", "idt": {"name": "ST5[440]7[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2052,7 +2052,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "CGTCAAAACCCATCCTAATTTACGAATAAACA", "idt": {"name": "ST7[440]9[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2062,7 +2062,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "ACATGTTCCTCCGGCTTAGGTTGGATAGCTTA", "idt": {"name": "ST9[440]11[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2072,7 +2072,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "GATTAAGAGAATAATGGAAGGGTTCGGAATTA", "idt": {"name": "ST11[440]13[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2082,7 +2082,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "TCATCATAAATACCGAACGAACCAACGTGGCA", "idt": {"name": "ST13[440]15[439]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2092,7 +2092,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "TGAATTTATTTTTGAATGGCTAAACATCGC", "idt": {"name": "ST0[455]14[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2102,7 +2102,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "GATGATACCTCATAGTTAGCGTTTAGTAAA", "idt": {"name": "ST2[455]0[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2112,7 +2112,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "CGACTTGATGGAAAGCGCAGTCTGGCTTTT", "idt": {"name": "ST4[455]2[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2122,7 +2122,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "ACGGGAGAGGGAAGGTAAATATACCGTCAC", "idt": {"name": "ST6[455]4[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2132,7 +2132,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "ATAATATATGAAAATAGCAGCCCGCATTAG", "idt": {"name": "ST8[455]6[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2142,7 +2142,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "TTTTAACAGCTAATGCAGAACGCAAGAAAA", "idt": {"name": "ST10[455]8[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2152,7 +2152,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "TACTTCTCGCTGAGAAGAGTCAGACTACCT", "idt": {"name": "ST12[455]10[456]", "scale": "25nm", "purification": "STD"}, "domains": [ @@ -2162,7 +2162,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "CATTAAATTCCTGATTATCAGATTGGATTA", "idt": {"name": "ST14[455]12[456]", "scale": "25nm", "purification": "STD"}, "domains": [ diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 76216188..00c4693d 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -215,10 +215,27 @@ def __iter__(self): return self def __next__(self): - color = self._colors[self._current_color_idx] + color = self.current_color() self._current_color_idx = (self._current_color_idx + 1) % len(self._colors) return color + def current_color(self): + return self._colors[self._current_color_idx] + + def __hash__(self): + return hash(self.current_color()) + + def __eq__(self, other): + if not isinstance(other, ColorCycler): + return False + return self._current_color_idx == other._current_color_idx + + def __str__(self): + repr(self) + + def __repr__(self): + return f'ColorCycler({self.current_color()})' + @property def colors(self): """The colors that are cycled through when calling ``next()`` on some :any:`ColorCycler`.""" @@ -236,8 +253,6 @@ def colors(self, newcolors): default_strand_color = Color(0, 0, 0) """Default color for non-scaffold strand(s).""" -color_cycler = ColorCycler() - # # END Colors @@ -1848,12 +1863,6 @@ class Strand(_JSONSerializable): a color is assigned by cycling through a list of defaults given by :meth:`ColorCycler.colors`""" - automatically_assign_color: bool = field(repr=False, default=True) - """If `automatically_assign_color` = ``False`` and `color` = ``None``, do not automatically - assign a :any:`Color` to this :any:`Strand`. - In this case color will be set to its default of ``None`` and will not be - written to the JSON with :py:meth:`DNADesign.write_scadnano_file` or :py:meth:`DNADesign.to_json`.""" - idt: Optional[IDTFields] = None """Fields used when ordering strands from the synthesis company IDT (Integrated DNA Technologies, Coralville, IA). If present (i.e., not equal to :const:`None`) @@ -1922,15 +1931,6 @@ def to_json_serializable(self, suppress_indent: bool = True): return dct def __post_init__(self): - # if color not specified, pick one by cycling through list of staple colors, - # unless caller specified not to - global color_cycler - if self.color is None and self.automatically_assign_color: - if self.is_scaffold: - self.color = default_scaffold_color - else: - self.color = next(color_cycler) - self._helix_idx_domain_map = defaultdict(list) for domain in self.domains: @@ -2549,6 +2549,14 @@ class DNADesign(_JSONSerializable): Optional field. If not specified, it will be set to the identity permutation [0, ..., len(helices)-1]. """ + automatically_assign_color: bool = field(repr=False, default=True) + """If `automatically_assign_color` = ``False``, then for any :any:`Strand` such that + `Strand.color` = ``None``, do not automatically assign a :any:`Color` to it. + In this case color will be set to its default of ``None`` and will not be + written to the JSON with :py:meth:`DNADesign.write_scadnano_file` or :py:meth:`DNADesign.to_json`.""" + + color_cycler: ColorCycler = field(default_factory=lambda: ColorCycler(), init=False) + def __init__(self, *, helices: Optional[Union[List[Helix], Dict[int, Helix]]] = None, strands: List[Strand] = None, @@ -2560,6 +2568,7 @@ def __init__(self, *, self.grid = grid self.major_tick_distance = major_tick_distance self.helices_view_order = helices_view_order + self.color_cycler = ColorCycler() if self.strands is None: self.strands = [] @@ -2591,6 +2600,22 @@ def __post_init__(self): self._set_and_check_helices_view_order() + if self.automatically_assign_color: + self._assign_colors_to_strands() + + def _assign_colors_to_strands(self): + # if color not specified, pick one by cycling through list of staple colors, + # unless caller specified not to + for strand in self.strands: + self._assign_color_to_strand(strand) + + def _assign_color_to_strand(self, strand: Strand): + if strand.color is None and self.automatically_assign_color: + if strand.is_scaffold: + strand.color = default_scaffold_color + else: + strand.color = next(self.color_cycler) + @staticmethod def from_scadnano_file(filename: str) -> DNADesign: """ @@ -3468,6 +3493,8 @@ def add_strand(self, strand: Strand): if domain.is_domain(): self.helices[domain.helix].domains.append(domain) self._check_strands_overlap_legally(domain_to_check=domain) + if self.automatically_assign_color: + self._assign_color_to_strand(strand) def remove_strand(self, strand: Strand): """Remove `strand` from this design.""" @@ -4002,7 +4029,7 @@ def add_nick(self, helix: int, offset: int, forward: bool): strand_after = Strand(domains=[domain_to_add_after] + domains_after, dna_sequence=dna_sequence_after_whole, - automatically_assign_color=True, use_default_idt=idt_present) + use_default_idt=idt_present) self.helices[helix].domains.remove(domain_to_remove) self.helices[helix].domains.extend([domain_to_add_before, domain_to_add_after]) diff --git a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna index b5073768..907dfc40 100644 --- a/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna +++ b/tests_inputs/cadnano_v2_export/test_16_helix_origami_rectangle_no_twist.dna @@ -59,7 +59,7 @@ "is_scaffold": true }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "GCCGCTTTTGCGGGATTTGCAGGGAGTTAAAG", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -67,7 +67,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CAAGAGTAATCTTGACGCTGGCTGACCTTCAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -75,7 +75,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TGCAAAAGAAGTTTTGAATAGCGAGAGGCTTT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -83,7 +83,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "ACGGTGTCTGGAAGTTAATATGCAACTAAAGT", "domains": [ {"helix": 7, "forward": true, "start": 16, "end": 32}, @@ -91,7 +91,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AGTCAAATCACCATCAGAGAAAGGCCGGAGAC", "domains": [ {"helix": 9, "forward": true, "start": 16, "end": 32}, @@ -99,7 +99,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "GGCGGATTGACCGTAACTCCGTGGGAACAAAC", "domains": [ {"helix": 11, "forward": true, "start": 16, "end": 32}, @@ -107,7 +107,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "AAATTGTTATCCGCTCAGCTGTTTCCTGTGTG", "domains": [ {"helix": 13, "forward": true, "start": 16, "end": 32}, @@ -115,7 +115,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GAGTCCACTATTAAAGTTCCAGTTTGGAACAA", "domains": [ {"helix": 15, "forward": true, "start": 16, "end": 32}, @@ -123,7 +123,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "AACCCATGTACCGTAAGCAAGCCCAATAGG", "domains": [ {"helix": 0, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "AGCCAGAATGGAAAGATAAATCCTCATTAA", "domains": [ {"helix": 2, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -139,7 +139,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "ACTTGAGCCATTTGGTTATCACCGTCACCG", "domains": [ {"helix": 4, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -147,7 +147,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AACCCACAAGAATTGTAATATCAGAGAGAT", "domains": [ {"helix": 6, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -155,7 +155,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "CATCGTAGGAATCATAGCCGTTTTTATTTT", "domains": [ {"helix": 8, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -163,7 +163,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "TAATTACTAGAAAAATAAACACCGGAATCA", "domains": [ {"helix": 10, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -171,7 +171,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "TTAATTACATTTAACATCAAGAAAACAAAA", "domains": [ {"helix": 12, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -179,7 +179,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CTTTGCCCGAACGTTAACTCGTATTAAATC", "domains": [ {"helix": 14, "forward": false, "start": 416, "end": 432, "deletions": [417]}, @@ -194,7 +194,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "TACCAAGCCTCATCTTTGACCCCCTCAAGAG", "domains": [ {"helix": 2, "forward": false, "start": 208, "end": 216}, @@ -202,7 +202,7 @@ ] }, { - "color": "#32b86c", + "color": "#320096", "sequence": "AAGGATTAAGAGGCTGAGACTCCAGCGATTA", "domains": [ {"helix": 1, "forward": true, "start": 232, "end": 240}, @@ -210,7 +210,7 @@ ] }, { - "color": "#333333", + "color": "#03b6a2", "sequence": "AATCTACGACCAGTCAGGACGTTGTTCATAA", "domains": [ {"helix": 4, "forward": false, "start": 208, "end": 216}, @@ -218,7 +218,7 @@ ] }, { - "color": "#320096", + "color": "#7300de", "sequence": "TCAAAATCAGCGTTTGCCATCTTGGAAGAAA", "domains": [ {"helix": 3, "forward": true, "start": 232, "end": 240}, @@ -226,7 +226,7 @@ ] }, { - "color": "#03b6a2", + "color": "#aaaa00", "sequence": "GCCCGAAATTGCATCAAAAAGATTACGTAGA", "domains": [ {"helix": 6, "forward": false, "start": 208, "end": 216}, @@ -234,7 +234,7 @@ ] }, { - "color": "#7300de", + "color": "#b8056c", "sequence": "AAATACATGCAGTATGTTAGCAAAAGAGGAA", "domains": [ {"helix": 5, "forward": true, "start": 232, "end": 240}, @@ -242,7 +242,7 @@ ] }, { - "color": "#aaaa00", + "color": "#007200", "sequence": "CAAAATTACATACAGGCAAGGCAACCTAATT", "domains": [ {"helix": 8, "forward": false, "start": 208, "end": 216}, @@ -250,7 +250,7 @@ ] }, { - "color": "#b8056c", + "color": "#cc0000", "sequence": "TGCCAGTTAGCGTCTTTCCAGAGAGAATTAG", "domains": [ {"helix": 7, "forward": true, "start": 232, "end": 240}, @@ -258,7 +258,7 @@ ] }, { - "color": "#007200", + "color": "#f7931e", "sequence": "TTGTATAAAGAAAAGCCCCAAAAAACAATAA", "domains": [ {"helix": 10, "forward": false, "start": 208, "end": 216}, @@ -266,7 +266,7 @@ ] }, { - "color": "#cc0000", + "color": "#f74308", "sequence": "ACAACATGTCTGTCCAGACGACGCAGGAAGA", "domains": [ {"helix": 9, "forward": true, "start": 232, "end": 240}, @@ -274,7 +274,7 @@ ] }, { - "color": "#f7931e", + "color": "#57bb00", "sequence": "CTCTTCGCTTGGGAAGGGCGATCGAGACTAC", "domains": [ {"helix": 12, "forward": false, "start": 208, "end": 216}, @@ -282,7 +282,7 @@ ] }, { - "color": "#f74308", + "color": "#888888", "sequence": "CTTTTTAAAATCATAGGTCTGAGGTGCGGGC", "domains": [ {"helix": 11, "forward": true, "start": 232, "end": 240}, @@ -290,7 +290,7 @@ ] }, { - "color": "#57bb00", + "color": "#32b86c", "sequence": "CTTTTCACGTATTGGGCGCCAGGGAAACAGA", "domains": [ {"helix": 14, "forward": false, "start": 208, "end": 216}, @@ -298,7 +298,7 @@ ] }, { - "color": "#888888", + "color": "#333333", "sequence": "AATAAAGAAATTATTTGCACGTATGGTTTTT", "domains": [ {"helix": 13, "forward": true, "start": 232, "end": 240}, @@ -306,14 +306,14 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "GAACGTGGCGAGAAAGGAAGGGAATCACCTT", "domains": [ {"helix": 15, "forward": true, "start": 200, "end": 232, "deletions": [225]} ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CCGATATATTCGGTCGCTGAGGCCGTCACC", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -321,7 +321,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CTCAGCAGAGACCAGGCGCATAGAAGAACC", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -330,7 +330,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "GGATATTCGACGATAAAAACCAACCAGAGG", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -339,7 +339,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GGGTAATAGCTCAACATGTTTTATCATTCC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 48}, @@ -348,7 +348,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "ATATAACAAAGATTCAAAAGGGTATATGAT", "domains": [ {"helix": 7, "forward": true, "start": 40, "end": 48}, @@ -357,7 +357,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "ATTCAACCACAACCCGTCGGATTTGGGATA", "domains": [ {"helix": 9, "forward": true, "start": 40, "end": 48}, @@ -366,7 +366,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GGTCACGTCGTAATCATGGTCATACAATTC", "domains": [ {"helix": 11, "forward": true, "start": 40, "end": 48}, @@ -375,7 +375,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CACACAACTAGGGTTGAGTGTTGAACGTGG", "domains": [ {"helix": 13, "forward": true, "start": 40, "end": 48}, @@ -384,7 +384,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "ACTCCAACGTCAAAGGGCGAAAAAAAAGAATA", "domains": [ {"helix": 15, "forward": true, "start": 40, "end": 64}, @@ -392,7 +392,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CGGTGTACCGAAAGACAGCATCGGACGCATAA", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -401,7 +401,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "TACCAGACATTACCCAAATCAACGCAGATGAA", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -410,7 +410,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "ATGCTGTAGTAAAATGTTTAGACTCCCTCGTT", "domains": [ {"helix": 6, "forward": false, "start": 48, "end": 56}, @@ -419,7 +419,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TGTAGGTAGTTGATTCCCAATTCTTGAATATA", "domains": [ {"helix": 8, "forward": false, "start": 48, "end": 56}, @@ -428,7 +428,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "AGCGAGTAGTTCTAGCTGATAAATGAGTAATG", "domains": [ {"helix": 10, "forward": false, "start": 48, "end": 56}, @@ -437,7 +437,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CTCGAATTTGGTGTAGATGGGCGCTAAATGTG", "domains": [ {"helix": 12, "forward": false, "start": 48, "end": 56}, @@ -446,7 +446,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "GCCCGAGAATACGAGCCGGAAGCAGTACCGAG", "domains": [ {"helix": 14, "forward": false, "start": 48, "end": 56}, @@ -455,7 +455,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GACAATGACAACAACCATCGCCCAACGAGGG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -463,7 +463,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "TAGCAACGCAACTTTGAAAGAGGATAACAAAG", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -472,7 +472,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "CTGCTCATAGCAACACTATCATAAGGATAGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -481,7 +481,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "TCCAATACCTTAGAGCTTAATTGCGCGAACGA", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 80}, @@ -490,7 +490,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "GTAGATTTTTTAAATGCAATGCCTTAATGCCG", "domains": [ {"helix": 7, "forward": true, "start": 72, "end": 80}, @@ -499,7 +499,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GAGAGGGTCAGCTTTCATCAACATATCGTAAC", "domains": [ {"helix": 9, "forward": true, "start": 72, "end": 80}, @@ -508,7 +508,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CGTGCATCTCTAGAGGATCCCCGGTAAAGTGT", "domains": [ {"helix": 11, "forward": true, "start": 72, "end": 80}, @@ -517,7 +517,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "AAAGCCTGAATCCCTTATAAATCACCGTCTAT", "domains": [ {"helix": 13, "forward": true, "start": 72, "end": 80}, @@ -526,7 +526,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CAGGGCGATGGCCCACTACGTGATTCCGAAA", "domains": [ {"helix": 15, "forward": true, "start": 72, "end": 96, "deletions": [81]}, @@ -534,7 +534,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AACTGACGCTACAGAGGCTTTGGTTGCGCC", "domains": [ {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -543,7 +543,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "TAGTAAGTCAGTGAATAAGGCTGGGAACCG", "domains": [ {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -552,7 +552,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CGGATGGTGCGGAATCGTCATAACGAGGCA", "domains": [ {"helix": 6, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -561,7 +561,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CATATATAGTTTGACCATTAGACATTTTTG", "domains": [ {"helix": 8, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -570,7 +570,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CTGTAGCAGCTATTTTTGAGAGAGAACCCT", "domains": [ {"helix": 10, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -579,7 +579,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "GGTCGACTGCCAGTTTGAGGGGTGGCCTTC", "domains": [ {"helix": 12, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -588,7 +588,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "TCGGCAAGGGTGCCTAATGAGTTGCCTGCA", "domains": [ {"helix": 14, "forward": false, "start": 80, "end": 88, "deletions": [81]}, @@ -597,7 +597,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "TTCTTAAACAGCTTGATACCGATAAGGACTAA", "domains": [ {"helix": 0, "forward": false, "start": 96, "end": 120}, @@ -605,7 +605,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "AGACTTTTAGACGGTCAATCATAATGCCCTGA", "domains": [ {"helix": 1, "forward": true, "start": 104, "end": 112}, @@ -614,7 +614,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CGAGAAACAACGCCAAAAGGAATTAATATTCA", "domains": [ {"helix": 3, "forward": true, "start": 104, "end": 112}, @@ -623,7 +623,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TTGAATCCCCTTTTGATAAGAGGTTACATTTC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 112}, @@ -632,7 +632,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GCAAATGGAAGGATAAAAATTTTTATCTACAA", "domains": [ {"helix": 7, "forward": true, "start": 104, "end": 112}, @@ -641,7 +641,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AGGCTATCAAAAATAATTCGCGTCACGACGAC", "domains": [ {"helix": 9, "forward": true, "start": 104, "end": 112}, @@ -650,7 +650,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AGTATCGGCAGTGCCAAGCTTGCAGAGCTAAC", "domains": [ {"helix": 11, "forward": true, "start": 104, "end": 112}, @@ -659,7 +659,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "TCACATTATCCTGTTTGATGGTGGACCATCAC", "domains": [ {"helix": 13, "forward": true, "start": 104, "end": 112}, @@ -668,7 +668,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CCAAATCAAGTTTTTTGGGGTCGACCCCAGCA", "domains": [ {"helix": 15, "forward": true, "start": 104, "end": 128}, @@ -676,7 +676,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CGAGGCGCTCATGAGGAAGTTTCCAGGTGAAT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -685,7 +685,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "AGATACATACCAGAACGAGTAGTAAGCCGGAA", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -694,7 +694,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "TAATTGCTCCCTCAAATGCTTTAAACTAATGC", "domains": [ {"helix": 6, "forward": false, "start": 112, "end": 120}, @@ -703,7 +703,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "TTCAACGCTCAATAACCTGTTTAGAGTACCTT", "domains": [ {"helix": 8, "forward": false, "start": 112, "end": 120}, @@ -712,7 +712,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "ACGCCATCAGGTCATTGCCTGAGAGCCTTTAT", "domains": [ {"helix": 10, "forward": false, "start": 112, "end": 120}, @@ -721,7 +721,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "ACGACGGCCCTCAGGAAGATCGCACAATAGGA", "domains": [ {"helix": 12, "forward": false, "start": 112, "end": 120}, @@ -730,7 +730,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GGCGAAAAATTGCGTTGCGCTCACGTTGTAAA", "domains": [ {"helix": 14, "forward": false, "start": 112, "end": 120}, @@ -739,7 +739,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "ATCGGTTTATCAGCTTGCTTTCGATTAAAC", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -747,7 +747,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GGGTAAAATGCTCCATGTTACTTAATTGGG", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -756,7 +756,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "CTTGAGATGGAATACCACATTCAACAGTTC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -765,7 +765,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AGAAAACGAGGTCAGGATTAGAGCTATATT", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 144}, @@ -774,7 +774,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "TTCATTTGACTTTTGCGGGAGAAGTCTGGA", "domains": [ {"helix": 7, "forward": true, "start": 136, "end": 144}, @@ -783,7 +783,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GCAAACAAAGCTCATTTTTTAACCTCCAGC", "domains": [ {"helix": 9, "forward": true, "start": 136, "end": 144}, @@ -792,7 +792,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CAGCTTTCTTTCCCAGTCACGACTGCCCGC", "domains": [ {"helix": 11, "forward": true, "start": 136, "end": 144}, @@ -801,7 +801,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "TTTCCAGTGTCCACGCTGGTTTGGGTGCCG", "domains": [ {"helix": 13, "forward": true, "start": 136, "end": 144}, @@ -810,7 +810,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "TAAAGCACTAAATCGGAACCCTAAAGAGTTGC", "domains": [ {"helix": 15, "forward": true, "start": 136, "end": 160}, @@ -818,7 +818,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "CCGCGACCTACGTAATGCCACTACTTAATTGT", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -827,7 +827,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GAGATTTAGGTTTAATTTCAACTTGTCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, @@ -836,7 +836,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "ACTCCAACAGAATGACCATAAATCCATCAGTT", "domains": [ {"helix": 6, "forward": false, "start": 144, "end": 152}, @@ -845,7 +845,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CCTGTAATGGGCGCGAGCTGAAAAGGAAGCAA", "domains": [ {"helix": 8, "forward": false, "start": 144, "end": 152}, @@ -854,7 +854,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "GTTAAATCGAGAATCGATGAACGGATTATGAC", "domains": [ {"helix": 10, "forward": false, "start": 144, "end": 152}, @@ -863,7 +863,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GCCAGGGTCGGCACCGCTTCTGGTAAATTTTT", "domains": [ {"helix": 12, "forward": false, "start": 144, "end": 152}, @@ -872,7 +872,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AGCAAGCGCGGGAAACCTGTCGTGTGGGTAAC", "domains": [ {"helix": 14, "forward": false, "start": 144, "end": 152}, @@ -881,7 +881,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AAAAAAGGCTCCAAAAGGAGCCTGAAGGCAC", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 184, "deletions": [177]}, @@ -889,7 +889,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CAACCTAATCGCCTGATAAATTGTTAATCATT", "domains": [ {"helix": 1, "forward": true, "start": 168, "end": 176}, @@ -898,7 +898,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GTGAATTATACAGGTAGAAAGATTAAAAATCA", "domains": [ {"helix": 3, "forward": true, "start": 168, "end": 176}, @@ -907,7 +907,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "GGTCTTTACAAAGCGAACCAGACCGGTGGCAT", "domains": [ {"helix": 5, "forward": true, "start": 168, "end": 176}, @@ -916,7 +916,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CAATTCTACGGTTGTACCAAAAACTAATCGTA", "domains": [ {"helix": 7, "forward": true, "start": 168, "end": 176}, @@ -925,7 +925,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "AAACTAGCTGTTAAAATTCGCATTGCCGGAAA", "domains": [ {"helix": 9, "forward": true, "start": 168, "end": 176}, @@ -934,7 +934,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "CCAGGCAATGCAAGGCGATTAAGTCCAGCTGC", "domains": [ {"helix": 11, "forward": true, "start": 168, "end": 176}, @@ -943,7 +943,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "ATTAATGAACCGCCTGGCCCTGAGAGGGAGCC", "domains": [ {"helix": 13, "forward": true, "start": 168, "end": 176}, @@ -952,7 +952,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CCCGATTTAGAGCTTGACGGGGAAGCTGATT", "domains": [ {"helix": 15, "forward": true, "start": 168, "end": 192, "deletions": [177]}, @@ -960,7 +960,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "TGTATCAAACGAAAGAGGCAAAATCTCCAA", "domains": [ {"helix": 2, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -969,7 +969,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "ACATTATCCTTATGCGATTTTACGGAGATT", "domains": [ {"helix": 4, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -978,7 +978,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "CGAGCTTCCCTGACTATTATAGACGGAACA", "domains": [ {"helix": 6, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -987,7 +987,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "GCTAAATCTAATAGTAGTAGCATTTTAATT", "domains": [ {"helix": 8, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -996,7 +996,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AATATTTATGTCAATCATATGTAGCATAAA", "domains": [ {"helix": 10, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1005,7 +1005,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "GATGTGCAGCGCCATTCGCCATTAAACGTT", "domains": [ {"helix": 12, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1014,7 +1014,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GCCCTTCATCGGCCAACGCGCGGAAAGGGG", "domains": [ {"helix": 14, "forward": false, "start": 176, "end": 184, "deletions": [177]}, @@ -1023,7 +1023,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "AATAATAATTTTTTCACGTTGAAAAGAATACA", "domains": [ {"helix": 0, "forward": false, "start": 192, "end": 216}, @@ -1031,7 +1031,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CTAAAACAGCGAAACAAAGTACAAAGAACTGG", "domains": [ {"helix": 1, "forward": true, "start": 200, "end": 208}, @@ -1040,7 +1040,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CTCATTATTTAATAAAACGAACTATCAGAAGC", "domains": [ {"helix": 3, "forward": true, "start": 200, "end": 208}, @@ -1049,7 +1049,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AAAGCGGAGACTTCAAATATCGCGTTAACATC", "domains": [ {"helix": 5, "forward": true, "start": 200, "end": 208}, @@ -1058,7 +1058,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "CAATAAATAGCAATAAAGCCTCAGACCCCGGT", "domains": [ {"helix": 7, "forward": true, "start": 200, "end": 208}, @@ -1067,7 +1067,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "TGATAATCGCAAATATTTAAATTGTCAGGCTG", "domains": [ {"helix": 9, "forward": true, "start": 200, "end": 208}, @@ -1076,7 +1076,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CGCAACTGTATTACGCCAGCTGGCGGGAGAGG", "domains": [ {"helix": 11, "forward": true, "start": 200, "end": 208}, @@ -1085,7 +1085,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CGGTTTGCCAGTGAGACGGGCAACAAGCCGGC", "domains": [ {"helix": 13, "forward": true, "start": 200, "end": 208}, @@ -1094,7 +1094,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GCTGAACCTCAAATATCAAACCCTGAACCTAC", "domains": [ {"helix": 15, "forward": true, "start": 232, "end": 256}, @@ -1102,7 +1102,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AAGTATTAGGATTAGCGGGGTTTTGCGGAGTG", "domains": [ {"helix": 2, "forward": false, "start": 240, "end": 248}, @@ -1111,7 +1111,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "CCCTTATTACCGGAACCAGAGCCAAAACATGA", "domains": [ {"helix": 4, "forward": false, "start": 240, "end": 248}, @@ -1120,7 +1120,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CTTATTACACATAAAGGTGGCAACTCATAGCC", "domains": [ {"helix": 6, "forward": false, "start": 240, "end": 248}, @@ -1129,7 +1129,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CGCTAACGACAAAATAAACAGCCATAAGACTC", "domains": [ {"helix": 8, "forward": false, "start": 240, "end": 248}, @@ -1138,7 +1138,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "AAAGTAATTTCAGCTAATGCAGAACTTACCAA", "domains": [ {"helix": 10, "forward": false, "start": 240, "end": 248}, @@ -1147,7 +1147,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "TTTATCAACCTCCGGCTTAGGTTGCAAAAGGT", "domains": [ {"helix": 12, "forward": false, "start": 240, "end": 248}, @@ -1156,7 +1156,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CATATCAAAATTGCGTAGATTTTCATAGTGAA", "domains": [ {"helix": 14, "forward": false, "start": 240, "end": 248}, @@ -1165,7 +1165,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "CTAAACAACTTTCAACAGTTTCAGCTCAGTA", "domains": [ {"helix": 0, "forward": false, "start": 256, "end": 280, "deletions": [273]}, @@ -1173,7 +1173,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "CCAGGCGGGGAACCTATTATTCTGCCACCGGA", "domains": [ {"helix": 1, "forward": true, "start": 264, "end": 272}, @@ -1182,7 +1182,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "ACCGCCTCTCATCGGCATTTTCGGATATAAAA", "domains": [ {"helix": 3, "forward": true, "start": 264, "end": 272}, @@ -1191,7 +1191,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GAAACGCAAAAGAACTGGCATGATTATTATTT", "domains": [ {"helix": 5, "forward": true, "start": 264, "end": 272}, @@ -1200,7 +1200,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "ATCCCAATCAATTTTATCCTGAATCGCGCCTG", "domains": [ {"helix": 7, "forward": true, "start": 264, "end": 272}, @@ -1209,7 +1209,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "TTTATCAAGAATATAAAGTACCGAGGTTATAT", "domains": [ {"helix": 9, "forward": true, "start": 264, "end": 272}, @@ -1218,7 +1218,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AACTATATACGCTGAGAAGAGTCAAGGTTTAA", "domains": [ {"helix": 11, "forward": true, "start": 264, "end": 272}, @@ -1227,7 +1227,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "CGTCAGATAATAATGGAAGGGTTACAATCAAT", "domains": [ {"helix": 13, "forward": true, "start": 264, "end": 272}, @@ -1236,7 +1236,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "ATCTGGTCAGTTGGCAAATCAACTGGATTAT", "domains": [ {"helix": 15, "forward": true, "start": 264, "end": 288, "deletions": [273]}, @@ -1244,7 +1244,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CTATTTCATAAGTGCCGTCGAGGGATTTTG", "domains": [ {"helix": 2, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1253,7 +1253,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CGCGTTTCCTCAGAGCCGCCACCCCCCTGC", "domains": [ {"helix": 4, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1262,7 +1262,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "ATACCCAAAGACACCACGGAATGACTGTAG", "domains": [ {"helix": 6, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1271,7 +1271,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CCAGCTACCAAATAAGAAACGAATAACGGA", "domains": [ {"helix": 8, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1280,7 +1280,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "AATAAGACAATAGATAAGTCCTTTTTGCAC", "domains": [ {"helix": 10, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1289,7 +1289,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GATTAAGGTAAATGCTGATGCAGAGCCAGT", "domains": [ {"helix": 12, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1298,7 +1298,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "ACTTCTGGAATATACAGTAACAATAGCTTA", "domains": [ {"helix": 14, "forward": false, "start": 272, "end": 280, "deletions": [273]}, @@ -1307,7 +1307,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "GTTAGTAAATGAATTTTCTGTATGAGGGTTGA", "domains": [ {"helix": 0, "forward": false, "start": 288, "end": 312}, @@ -1315,7 +1315,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TATAAGTAGTATAAACAGTTAATGCCTCAGAA", "domains": [ {"helix": 1, "forward": true, "start": 296, "end": 304}, @@ -1324,7 +1324,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "CCGCCACCTTTGCCTTTAGCGTCAAAGTTTAT", "domains": [ {"helix": 3, "forward": true, "start": 296, "end": 304}, @@ -1333,7 +1333,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "TTTGTCACCCGAGGAAACGCAATATTTTTTGT", "domains": [ {"helix": 5, "forward": true, "start": 296, "end": 304}, @@ -1342,7 +1342,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TTAACGTCTCAAGATTAGTTGCTAGAACAAGA", "domains": [ {"helix": 7, "forward": true, "start": 296, "end": 304}, @@ -1351,7 +1351,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "AAAATAATAGGCAGAGGCATTTTCAATCCAAT", "domains": [ {"helix": 9, "forward": true, "start": 296, "end": 304}, @@ -1360,7 +1360,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "CGCAAGACCCTTGAAAACATAGCGGTACCTTT", "domains": [ {"helix": 11, "forward": true, "start": 296, "end": 304}, @@ -1369,7 +1369,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "TACATCGGTATAATCCTGATTGTTAGTTGAAA", "domains": [ {"helix": 13, "forward": true, "start": 296, "end": 304}, @@ -1378,7 +1378,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GGAATTGAGGAAGGTTATCTAAAAGATGGCAA", "domains": [ {"helix": 15, "forward": true, "start": 296, "end": 320}, @@ -1386,7 +1386,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "CAGTGCCCTAGCCCGGAATAGGTGTTCCAGAC", "domains": [ {"helix": 2, "forward": false, "start": 304, "end": 312}, @@ -1395,7 +1395,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GAATCAAGCTCAGAGCCACCACCCTTGAGTAA", "domains": [ {"helix": 4, "forward": false, "start": 304, "end": 312}, @@ -1404,7 +1404,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "GAAGGAAAAATCAATAGAAAATTCTAGCGACA", "domains": [ {"helix": 6, "forward": false, "start": 304, "end": 312}, @@ -1413,7 +1413,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "GCCTTAAAAAAAATGAAAATAGCAAGTTACCA", "domains": [ {"helix": 8, "forward": false, "start": 304, "end": 312}, @@ -1422,7 +1422,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "TGTAATTTATCCCATCCTAATTTAGTTTTGAA", "domains": [ {"helix": 10, "forward": false, "start": 304, "end": 312}, @@ -1431,7 +1431,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CTTAGAATAAAGAACGCGAGAAAACGCCAACA", "domains": [ {"helix": 12, "forward": false, "start": 304, "end": 312}, @@ -1440,7 +1440,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "TTCATCAAGAGAAACAATAACGGAAATTTTCC", "domains": [ {"helix": 14, "forward": false, "start": 304, "end": 312}, @@ -1449,7 +1449,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "AACGATCTAAAGTTTTGTCGTCTTATCACC", "domains": [ {"helix": 0, "forward": false, "start": 320, "end": 344, "deletions": [321]}, @@ -1457,7 +1457,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "GTACTCAGAACGGGGTCAGTGCCTCAGAGC", "domains": [ {"helix": 1, "forward": true, "start": 328, "end": 336}, @@ -1466,7 +1466,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CGCCACCACAGCACCGTAATCAGATATGGT", "domains": [ {"helix": 3, "forward": true, "start": 328, "end": 336}, @@ -1475,7 +1475,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "TTACCAGCCAGATAGCCGAACAAGCCTTTA", "domains": [ {"helix": 5, "forward": true, "start": 328, "end": 336}, @@ -1484,7 +1484,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CAGAGAGACCCGACTTGCGGGAGCGAGCAT", "domains": [ {"helix": 7, "forward": true, "start": 328, "end": 336}, @@ -1493,7 +1493,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GTAGAAACCGCCATATTTAACAACTTTTTC", "domains": [ {"helix": 9, "forward": true, "start": 328, "end": 336}, @@ -1502,7 +1502,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "AAATATATTCGTCGCTATTAATTTTCGCCT", "domains": [ {"helix": 11, "forward": true, "start": 328, "end": 336}, @@ -1511,7 +1511,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GATTGCTTTCCTGATTATCAGATTATCTTT", "domains": [ {"helix": 13, "forward": true, "start": 328, "end": 336}, @@ -1520,7 +1520,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "AGGAGCACTAACAACTAATAGATTGGAATTAT", "domains": [ {"helix": 15, "forward": true, "start": 328, "end": 352}, @@ -1528,7 +1528,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "TAAGTTTTGAGGTTTAGTACCGCCGTTAGCGT", "domains": [ {"helix": 2, "forward": false, "start": 336, "end": 344}, @@ -1537,7 +1537,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "ATCGATAGGAACCACCACCAGAGCACTGGTAA", "domains": [ {"helix": 4, "forward": false, "start": 336, "end": 344}, @@ -1546,7 +1546,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "AAAGTAAGGCCAAAGACAAAAGGGATGAAACC", "domains": [ {"helix": 6, "forward": false, "start": 336, "end": 344}, @@ -1555,7 +1555,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GCGAACCTATAACATAAAAACAGGTTTTAAGA", "domains": [ {"helix": 8, "forward": false, "start": 336, "end": 344}, @@ -1564,7 +1564,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "TTGAGAATCAATCAATAATCGGCTGCGTTTTA", "domains": [ {"helix": 10, "forward": false, "start": 336, "end": 344}, @@ -1573,7 +1573,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "TCTGTAAATTTAGTTAATTTCATCGGGCTTAA", "domains": [ {"helix": 12, "forward": false, "start": 336, "end": 344}, @@ -1582,7 +1582,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CATCATATTGAATACCAAGTTACAACCTTGCT", "domains": [ {"helix": 14, "forward": false, "start": 336, "end": 344}, @@ -1591,7 +1591,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GCATTCCACAGACAGCCCTCATAACCCTCAG", "domains": [ {"helix": 0, "forward": false, "start": 352, "end": 376, "deletions": [369]}, @@ -1599,7 +1599,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "AACCGCCAGATGATACAGGAGTGTCGCCGCCA", "domains": [ {"helix": 1, "forward": true, "start": 360, "end": 368}, @@ -1608,7 +1608,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "GCATTGACGCCGGAAACGTCACCACGACATTC", "domains": [ {"helix": 3, "forward": true, "start": 360, "end": 368}, @@ -1617,7 +1617,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "AACCGATTATCTTACCGAAGCCCTGAAGCGCA", "domains": [ {"helix": 5, "forward": true, "start": 360, "end": 368}, @@ -1626,7 +1626,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "TTAGACGGATTCTAAGAACGCGAGGTCTTTCC", "domains": [ {"helix": 7, "forward": true, "start": 360, "end": 368}, @@ -1635,7 +1635,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "TTATCATTCCAACGCTCAACAGTATTCTGACC", "domains": [ {"helix": 9, "forward": true, "start": 360, "end": 368}, @@ -1644,7 +1644,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "TAAATTTATATATGTGAGTGAATAAAATCGCG", "domains": [ {"helix": 11, "forward": true, "start": 360, "end": 368}, @@ -1653,7 +1653,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CAGAGGCGAACCACCAGAAGGAGCAGAGCCGT", "domains": [ {"helix": 13, "forward": true, "start": 360, "end": 368}, @@ -1662,7 +1662,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "CAATAGATAATACATTTGAGGATTTTGCGGA", "domains": [ {"helix": 15, "forward": true, "start": 360, "end": 384, "deletions": [369]}, @@ -1670,7 +1670,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GGCTTTTCCCTCAGAACCGCCACGCCTGTA", "domains": [ {"helix": 2, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1679,7 +1679,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "TAGCAAGAGGAGGTTGAGGCAGTCATACAT", "domains": [ {"helix": 4, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1688,7 +1688,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "AATAGCTGAGGGAGGGAAGGTAATTACCAT", "domains": [ {"helix": 6, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1697,7 +1697,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "ATCCGGTGAGAATTAACTGAACGAAATAGC", "domains": [ {"helix": 8, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1706,7 +1706,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "TATAAAGCCAAGAACGGGTATTGAAGGCTT", "domains": [ {"helix": 10, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1715,7 +1715,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "AAATCAAATGGTTTGAAATACCCTTACCAG", "domains": [ {"helix": 12, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1724,7 +1724,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "ACAAAGAAATTATTCATTTCAACAGTACAT", "domains": [ {"helix": 14, "forward": false, "start": 368, "end": 376, "deletions": [369]}, @@ -1733,7 +1733,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "TTTCGTCACCAGTACAAACTACAACCCTCAGA", "domains": [ {"helix": 0, "forward": false, "start": 384, "end": 408}, @@ -1741,7 +1741,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "GCCACCACACCGTTCCAGTAAGCGGTCAGACG", "domains": [ {"helix": 1, "forward": true, "start": 392, "end": 400}, @@ -1750,7 +1750,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "ATTGGCCTAATCACCAGTAGCACCAATATTGA", "domains": [ {"helix": 3, "forward": true, "start": 392, "end": 400}, @@ -1759,7 +1759,7 @@ ] }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "CGGAAATTAAGAGCAAGAAACAATACCCTGAA", "domains": [ {"helix": 5, "forward": true, "start": 392, "end": 400}, @@ -1768,7 +1768,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "CAAAGTCAAAGCAAATCAGATATAAAACCAAG", "domains": [ {"helix": 7, "forward": true, "start": 392, "end": 400}, @@ -1777,7 +1777,7 @@ ] }, { - "color": "#57bb00", + "color": "#888888", "sequence": "TACCGCACATGCGTTATACAAATTGACCGTGT", "domains": [ {"helix": 9, "forward": true, "start": 392, "end": 400}, @@ -1786,7 +1786,7 @@ ] }, { - "color": "#888888", + "color": "#32b86c", "sequence": "GATAAATACCTTTTTTAATGGAAATTACCTGA", "domains": [ {"helix": 11, "forward": true, "start": 392, "end": 400}, @@ -1795,7 +1795,7 @@ ] }, { - "color": "#32b86c", + "color": "#333333", "sequence": "GCAAAAGATGAGTAACATTATCATTTAGAAGT", "domains": [ {"helix": 13, "forward": true, "start": 392, "end": 400}, @@ -1804,7 +1804,7 @@ ] }, { - "color": "#333333", + "color": "#320096", "sequence": "ATTAGACTTTACAAACAATTCGACATTAATTT", "domains": [ {"helix": 15, "forward": true, "start": 392, "end": 416}, @@ -1812,7 +1812,7 @@ ] }, { - "color": "#320096", + "color": "#03b6a2", "sequence": "CTGAATTTCCTCATTTTCAGGGATACACTGAG", "domains": [ {"helix": 2, "forward": false, "start": 400, "end": 408}, @@ -1821,7 +1821,7 @@ ] }, { - "color": "#03b6a2", + "color": "#7300de", "sequence": "GCCAGCAATGATATTCACAAACAACGCAGTCT", "domains": [ {"helix": 4, "forward": false, "start": 400, "end": 408}, @@ -1830,7 +1830,7 @@ ] }, { - "color": "#7300de", + "color": "#aaaa00", "sequence": "CCAATAATATTCATTAAAGGTGAAGAATTAGA", "domains": [ {"helix": 6, "forward": false, "start": 400, "end": 408}, @@ -1839,7 +1839,7 @@ ] }, { - "color": "#aaaa00", + "color": "#b8056c", "sequence": "CCAATAGCGAGGGTAATTGAGCGCAGTTAAGC", "domains": [ {"helix": 8, "forward": false, "start": 400, "end": 408}, @@ -1848,7 +1848,7 @@ ] }, { - "color": "#b8056c", + "color": "#007200", "sequence": "AGTATCATTCATCGAGAACAAGCATACCGCGC", "domains": [ {"helix": 10, "forward": false, "start": 400, "end": 408}, @@ -1857,7 +1857,7 @@ ] }, { - "color": "#007200", + "color": "#cc0000", "sequence": "TTGAATTAAGGCGTTAAATAAGAAGCCTGTTT", "domains": [ {"helix": 12, "forward": false, "start": 400, "end": 408}, @@ -1866,7 +1866,7 @@ ] }, { - "color": "#cc0000", + "color": "#f7931e", "sequence": "TAAAAGTTAGATGATGAAACAAACAATTTCAT", "domains": [ {"helix": 14, "forward": false, "start": 400, "end": 408}, diff --git a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna index b56366e6..fd5d8dd2 100644 --- a/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna +++ b/tests_inputs/cadnano_v2_export/test_2_stape_2_helix_origami_deletions_insertions.dna @@ -17,7 +17,7 @@ "is_scaffold": true }, { - "color": "#f7931e", + "color": "#f74308", "sequence": "GTTACGTTACGTTACGTTGTTACGTTACGTTAC", "domains": [ {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, @@ -25,7 +25,7 @@ ] }, { - "color": "#f74308", + "color": "#57bb00", "sequence": "ACGTTACGTTACGTTACCGTTACGTTACGTTACGTT", "domains": [ {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, diff --git a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna index 70dcc78b..c33f6377 100644 --- a/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna +++ b/tests_inputs/cadnano_v2_export/test_6_helix_origami_rectangle.dna @@ -29,7 +29,7 @@ "is_scaffold": true }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", "domains": [ {"helix": 1, "forward": true, "start": 16, "end": 32}, @@ -37,7 +37,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", "domains": [ {"helix": 3, "forward": true, "start": 16, "end": 32}, @@ -45,7 +45,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", "domains": [ {"helix": 5, "forward": true, "start": 16, "end": 32}, @@ -53,7 +53,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", "domains": [ {"helix": 0, "forward": false, "start": 160, "end": 176}, @@ -61,7 +61,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", "domains": [ {"helix": 2, "forward": false, "start": 160, "end": 176}, @@ -69,7 +69,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", "domains": [ {"helix": 4, "forward": false, "start": 160, "end": 176}, @@ -77,7 +77,7 @@ ] }, { - "color": "#cc0000", + "color": "#03b6a2", "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", "domains": [ {"helix": 0, "forward": false, "start": 88, "end": 120} @@ -116,14 +116,14 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", "domains": [ {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", "domains": [ {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, @@ -131,7 +131,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", "domains": [ {"helix": 1, "forward": true, "start": 40, "end": 48}, @@ -140,7 +140,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", "domains": [ {"helix": 3, "forward": true, "start": 40, "end": 48}, @@ -149,7 +149,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", "domains": [ {"helix": 5, "forward": true, "start": 40, "end": 64}, @@ -157,7 +157,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", "domains": [ {"helix": 2, "forward": false, "start": 48, "end": 56}, @@ -166,7 +166,7 @@ ] }, { - "color": "#320096", + "color": "#333333", "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", "domains": [ {"helix": 4, "forward": false, "start": 48, "end": 56}, @@ -175,7 +175,7 @@ ] }, { - "color": "#03b6a2", + "color": "#320096", "sequence": "AATGAATCGGCCAACGCGCGGGGAGTTGCAG", "domains": [ {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, @@ -183,7 +183,7 @@ ] }, { - "color": "#7300de", + "color": "#03b6a2", "sequence": "CAAGCGGTCCTGTTTGATGGTGGTACGTGGAC", "domains": [ {"helix": 1, "forward": true, "start": 72, "end": 80}, @@ -192,7 +192,7 @@ ] }, { - "color": "#aaaa00", + "color": "#7300de", "sequence": "TCCAACGTTGGCCCACTACGTGAAAGCCGGCG", "domains": [ {"helix": 3, "forward": true, "start": 72, "end": 80}, @@ -201,7 +201,7 @@ ] }, { - "color": "#b8056c", + "color": "#aaaa00", "sequence": "AGTATCGGCCTCAGGAAGATCGCAGTGCGGGC", "domains": [ {"helix": 5, "forward": true, "start": 104, "end": 128}, @@ -209,7 +209,7 @@ ] }, { - "color": "#007200", + "color": "#b8056c", "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", "domains": [ {"helix": 2, "forward": false, "start": 112, "end": 120}, @@ -218,7 +218,7 @@ ] }, { - "color": "#cc0000", + "color": "#007200", "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", "domains": [ {"helix": 4, "forward": false, "start": 112, "end": 120}, @@ -227,7 +227,7 @@ ] }, { - "color": "#f7931e", + "color": "#cc0000", "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", "domains": [ {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, @@ -235,7 +235,7 @@ ] }, { - "color": "#f74308", + "color": "#f7931e", "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", "domains": [ {"helix": 1, "forward": true, "start": 136, "end": 144}, @@ -244,7 +244,7 @@ ] }, { - "color": "#57bb00", + "color": "#f74308", "sequence": "GCCAGGGTTGGGAAGGGCGATCGCTCCAGC", "domains": [ {"helix": 3, "forward": true, "start": 136, "end": 144}, @@ -253,7 +253,7 @@ ] }, { - "color": "#888888", + "color": "#57bb00", "sequence": "CAGCTTTCCGGCACCGCTTCTGGTCAGGCTGC", "domains": [ {"helix": 5, "forward": true, "start": 136, "end": 160}, @@ -261,7 +261,7 @@ ] }, { - "color": "#32b86c", + "color": "#888888", "sequence": "GTCGACTCACGAGCCGGAAGCATACTAACTCA", "domains": [ {"helix": 2, "forward": false, "start": 144, "end": 152}, @@ -270,7 +270,7 @@ ] }, { - "color": "#333333", + "color": "#32b86c", "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", "domains": [ {"helix": 4, "forward": false, "start": 144, "end": 152}, From 700c95a6d0c58f8b7b6b49de8191e2723b22d77b Mon Sep 17 00:00:00 2001 From: David Doty Date: Wed, 24 Jun 2020 15:24:54 -0700 Subject: [PATCH 14/30] added Kelly colors, but not using them yet --- .../2_staple_2_helix_modifications.dna | 38 +++++++++---------- .../many_helices_modifications.dna | 16 ++++---- scadnano/scadnano.py | 11 ++++++ 3 files changed, 38 insertions(+), 27 deletions(-) diff --git a/examples/output_designs/2_staple_2_helix_modifications.dna b/examples/output_designs/2_staple_2_helix_modifications.dna index c7ea1288..2366cdff 100644 --- a/examples/output_designs/2_staple_2_helix_modifications.dna +++ b/examples/output_designs/2_staple_2_helix_modifications.dna @@ -6,17 +6,11 @@ {"grid_position": [0, 1]} ], "modifications_in_design": { - "/3Cy3Sp/": { - "display_text": "Cy3", - "idt_text": "/3Cy3Sp/", - "display_connector": false, - "location": "3'" - }, - "/3Bio/": { + "/5Biosg/": { "display_text": "B", - "idt_text": "/3Bio/", + "idt_text": "/5Biosg/", "display_connector": false, - "location": "3'" + "location": "5'" }, "/iBiodT/": { "display_text": "B", @@ -25,11 +19,11 @@ "location": "internal", "allowed_bases": ["T"] }, - "/iCy3/": { - "display_text": "Cy3", - "idt_text": "/iCy3/", + "/3Bio/": { + "display_text": "B", + "idt_text": "/3Bio/", "display_connector": false, - "location": "internal" + "location": "3'" }, "/5Cy5/": { "display_text": "Cy5", @@ -37,17 +31,23 @@ "display_connector": false, "location": "5'" }, + "/3Cy3Sp/": { + "display_text": "Cy3", + "idt_text": "/3Cy3Sp/", + "display_connector": false, + "location": "3'" + }, + "/iCy3/": { + "display_text": "Cy3", + "idt_text": "/iCy3/", + "display_connector": false, + "location": "internal" + }, "/iCy5/": { "display_text": "Cy5", "idt_text": "/iCy5/", "display_connector": false, "location": "internal" - }, - "/5Biosg/": { - "display_text": "B", - "idt_text": "/5Biosg/", - "display_connector": false, - "location": "5'" } }, "strands": [ diff --git a/examples/output_designs/many_helices_modifications.dna b/examples/output_designs/many_helices_modifications.dna index c8f09903..85b1b019 100644 --- a/examples/output_designs/many_helices_modifications.dna +++ b/examples/output_designs/many_helices_modifications.dna @@ -12,11 +12,11 @@ {"grid_position": [0, 7]} ], "modifications_in_design": { - "/3Cy3Sp/": { - "display_text": "Cy3", - "idt_text": "/3Cy3Sp/", + "/5Biosg/": { + "display_text": "B", + "idt_text": "/5Biosg/", "display_connector": false, - "location": "3'" + "location": "5'" }, "/iCy3/": { "display_text": "Cy3", @@ -31,11 +31,11 @@ "location": "internal", "allowed_bases": ["T"] }, - "/5Biosg/": { - "display_text": "B", - "idt_text": "/5Biosg/", + "/3Cy3Sp/": { + "display_text": "Cy3", + "idt_text": "/3Cy3Sp/", "display_connector": false, - "location": "5'" + "location": "3'" } }, "strands": [ diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 00c4693d..61277c44 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -174,6 +174,13 @@ def from_cadnano_v2_int_hex(cls, hex_int): return Color(hex_string=hex_str[2:]) +# https://medium.com/@rjurney/kellys-22-colours-of-maximum-contrast-58edb70c90d1 +_kelly_colors = [#'F2F3F4', #almost white so it's no good + '222222', 'F3C300', '875692', 'F38400', 'A1CAF1', 'BE0032', 'C2B280', '848482', + '008856', 'E68FAC', '0067A5', 'F99379', '604E97', 'F6A600', 'B3446C', 'DCD300', '882D17', + '8DB600', '654522', 'E25822', '2B3D26'] + + class ColorCycler: """ Calling ``next(color_cycler)`` on a ColorCycler named ``color_cycler`` @@ -201,10 +208,14 @@ class ColorCycler: Color(136, 136, 136)] """List of colors to cycle through.""" + # _colors = [Color(hex_string=kelly_color) for kelly_color in _kelly_colors] + # """List of colors to cycle through.""" + def __init__(self): self._current_color_idx = 0 # random order order = [3, 11, 0, 12, 8, 1, 10, 6, 5, 9, 4, 7, 2] + #order = range(len(self._colors)) colors_shuffled = [None] * len(self._colors) for i, color in zip(order, self._colors): colors_shuffled[i] = color From 033529f6b1c93a5bd9ad2e48af4ad5bb853999d3 Mon Sep 17 00:00:00 2001 From: David Doty Date: Wed, 24 Jun 2020 16:36:41 -0700 Subject: [PATCH 15/30] closes #84 --- ...igami_deletions_insertions_new_geometry.py | 45 +++++++++ ...gami_deletions_insertions_new_geometry.dna | 42 +++++++++ scadnano/scadnano.py | 91 +++++++++++++++++-- tests/scadnano_tests.py | 27 +++++- 4 files changed, 197 insertions(+), 8 deletions(-) create mode 100644 examples/2_staple_2_helix_origami_deletions_insertions_new_geometry.py create mode 100644 examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.dna diff --git a/examples/2_staple_2_helix_origami_deletions_insertions_new_geometry.py b/examples/2_staple_2_helix_origami_deletions_insertions_new_geometry.py new file mode 100644 index 00000000..30e3ca26 --- /dev/null +++ b/examples/2_staple_2_helix_origami_deletions_insertions_new_geometry.py @@ -0,0 +1,45 @@ +import scadnano as sc + + +def main(): + # helices + helices = [sc.Helix(max_offset=48), sc.Helix(max_offset=48)] + + # left staple + stap_left_ss1 = sc.Domain(helix=1, forward=True, start=8, end=24) + stap_left_ss0 = sc.Domain(helix=0, forward=False, start=8, end=24) + stap_left = sc.Strand(domains=[stap_left_ss1, stap_left_ss0]) + + # right staple + stap_right_ss0 = sc.Domain(helix=0, forward=False, start=24, end=40) + stap_right_ss1 = sc.Domain(helix=1, forward=True, start=24, end=40) + stap_right = sc.Strand(domains=[stap_right_ss0, stap_right_ss1]) + + # scaffold + scaf_ss1_left = sc.Domain(helix=1, forward=False, start=8, end=24) + scaf_ss0 = sc.Domain(helix=0, forward=True, start=8, end=40) + loopout = sc.Loopout(length=3) + scaf_ss1_right = sc.Domain(helix=1, forward=False, start=24, end=40) + scaf = sc.Strand(domains=[scaf_ss1_left, scaf_ss0, loopout, scaf_ss1_right], is_scaffold=True) + + # geometry + geometry = sc.Geometry(z_step=0.2, helix_radius=1.2, inter_helix_gap=1.0) + + # whole design + design = sc.DNADesign(helices=helices, strands=[scaf, stap_left, stap_right], grid=sc.square, + geometry=geometry) + + # deletions and insertions added to design are added to both strands on a helix + design.add_deletion(helix=1, offset=20) + design.add_insertion(helix=0, offset=14, length=1) + design.add_insertion(helix=0, offset=26, length=2) + + # also assigns complement to strands other than scaf bound to it + design.assign_dna(scaf, 'AACGT' * 18) + + return design + + +if __name__ == '__main__': + design = main() + design.write_scadnano_file(directory='output_designs') diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.dna new file mode 100644 index 00000000..f051a64a --- /dev/null +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.dna @@ -0,0 +1,42 @@ +{ + "version": "0.9.1", + "grid": "square", + "geometry": { + "z_step": 0.2, + "helix_radius": 1.2, + "inter_helix_gap": 1.0 + }, + "helices": [ + {"max_offset": 48, "grid_position": [0, 0]}, + {"max_offset": 48, "grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", + "domains": [ + {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, + {"loopout": 3}, + {"helix": 1, "forward": false, "start": 24, "end": 40} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", + "domains": [ + {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} + ] + }, + { + "color": "#57bb00", + "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", + "domains": [ + {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, + {"helix": 1, "forward": true, "start": 24, "end": 40} + ] + } + ] +} \ No newline at end of file diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 61277c44..28c02031 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -175,10 +175,10 @@ def from_cadnano_v2_int_hex(cls, hex_int): # https://medium.com/@rjurney/kellys-22-colours-of-maximum-contrast-58edb70c90d1 -_kelly_colors = [#'F2F3F4', #almost white so it's no good - '222222', 'F3C300', '875692', 'F38400', 'A1CAF1', 'BE0032', 'C2B280', '848482', - '008856', 'E68FAC', '0067A5', 'F99379', '604E97', 'F6A600', 'B3446C', 'DCD300', '882D17', - '8DB600', '654522', 'E25822', '2B3D26'] +_kelly_colors = [ # 'F2F3F4', #almost white so it's no good + '222222', 'F3C300', '875692', 'F38400', 'A1CAF1', 'BE0032', 'C2B280', '848482', + '008856', 'E68FAC', '0067A5', 'F99379', '604E97', 'F6A600', 'B3446C', 'DCD300', '882D17', + '8DB600', '654522', 'E25822', '2B3D26'] class ColorCycler: @@ -215,7 +215,7 @@ def __init__(self): self._current_color_idx = 0 # random order order = [3, 11, 0, 12, 8, 1, 10, 6, 5, 9, 4, 7, 2] - #order = range(len(self._colors)) + # order = range(len(self._colors)) colors_shuffled = [None] * len(self._colors) for i, color in zip(order, self._colors): colors_shuffled[i] = color @@ -690,6 +690,14 @@ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249): helices_view_order_key = 'helices_view_order' is_origami_key = 'is_origami' design_modifications_key = 'modifications_in_design' +geometry_key = 'geometry' + +# Geometry keys +z_step_key = 'z_step' +helix_radius_key = 'helix_radius' +bases_per_turn_key = 'bases_per_turn' +minor_groove_angle_key = 'minor_groove_angle' +inter_helix_gap_key = 'inter_helix_gap' # Helix keys idx_on_helix_key = 'idx' @@ -2517,6 +2525,64 @@ def optional_field(default_value, json_map: dict, main_key: str, *legacy_keys: s return default_value +@dataclass +class Geometry(_JSONSerializable): + """Parameters controlling some geometric visualization/physical aspects of Design.""" + + z_step: float = 0.332 + """What is this?""" + + helix_radius: float = 1.0 + """Redius of a DNA helix in nanometers.""" + + bases_per_turn: float = 10.5 + """Number of DNA base pairs in in full turn of DNA.""" + + minor_groove_angle: float = 150.0 + """Minor groove angle in degrees.""" + + inter_helix_gap: float = 0.5 + """Gap between helices in nanometers (due to electrostatic repulsion; needed to display to scale).""" + + def is_default(self): + return self == _default_geometry + + @staticmethod + def from_json(json_map: dict) -> Geometry: + geometry = Geometry() + geometry.z_step = optional_field(_default_geometry.z_step, json_map, z_step_key) + geometry.helix_radius = optional_field(_default_geometry.helix_radius, json_map, helix_radius_key) + geometry.bases_per_turn = optional_field(_default_geometry.bases_per_turn, json_map, + bases_per_turn_key) + geometry.minor_groove_angle = optional_field(_default_geometry.minor_groove_angle, json_map, + minor_groove_angle_key) + geometry.inter_helix_gap = optional_field(_default_geometry.inter_helix_gap, json_map, + inter_helix_gap_key) + return geometry + + @staticmethod + def keys() -> List[str]: + return [z_step_key, helix_radius_key, bases_per_turn_key, minor_groove_angle_key, inter_helix_gap_key] + + def values(self) -> List[float]: + return [self.z_step, self.helix_radius, self.bases_per_turn, self.minor_groove_angle, + self.inter_helix_gap] + + @staticmethod + def default_values() -> List[float]: + return _default_geometry.values() + + def to_json_serializable(self, suppress_indent: bool = True): + dct = OrderedDict() + for name, val, val_default in zip(Geometry.keys(), self.values(), Geometry.default_values()): + if val != val_default: + dct[name] = val + return dct + + +_default_geometry = Geometry() + + @dataclass class DNADesign(_JSONSerializable): """Object representing the entire design of the DNA structure.""" @@ -2560,6 +2626,9 @@ class DNADesign(_JSONSerializable): Optional field. If not specified, it will be set to the identity permutation [0, ..., len(helices)-1]. """ + geometry: Geometry = field(default_factory=lambda: Geometry()) + """Controls some geometric/physical aspects of this :any:`DNADesign`.""" + automatically_assign_color: bool = field(repr=False, default=True) """If `automatically_assign_color` = ``False``, then for any :any:`Strand` such that `Strand.color` = ``None``, do not automatically assign a :any:`Color` to it. @@ -2573,13 +2642,15 @@ def __init__(self, *, strands: List[Strand] = None, grid: Grid = Grid.none, major_tick_distance: int = -1, - helices_view_order: List[int] = None): + helices_view_order: List[int] = None, + geometry: Geometry = None): self.helices = helices self.strands = strands self.grid = grid self.major_tick_distance = major_tick_distance self.helices_view_order = helices_view_order self.color_cycler = ColorCycler() + self.geometry = Geometry() if geometry is None else geometry if self.strands is None: self.strands = [] @@ -2723,12 +2794,17 @@ def from_scadnano_json_map(json_map: dict) -> DNADesign: all_mods[mod_key] = mod DNADesign.assign_modifications_to_strands(strands, strand_jsons, all_mods) + geometry = None + if geometry_key in json_map: + geometry = Geometry.from_json(json_map[geometry_key]) + return DNADesign( helices=helices, strands=strands, grid=grid, major_tick_distance=major_tick_distance, helices_view_order=helices_view_order, + geometry=geometry, ) def to_json_serializable(self, suppress_indent: bool = True): @@ -2736,6 +2812,9 @@ def to_json_serializable(self, suppress_indent: bool = True): dct[version_key] = __version__ dct[grid_key] = str(self.grid)[5:] # remove prefix 'Grid.' + if not self.geometry.is_default(): + dct[geometry_key] = self.geometry.to_json_serializable(suppress_indent) + if self.major_tick_distance >= 0 and ( self.major_tick_distance != default_major_tick_distance(self.grid)): dct[major_tick_distance_key] = self.major_tick_distance diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 86597c51..39d19c12 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -215,7 +215,6 @@ def test_strand__multiple_strands_overlap_error(self): with self.assertRaises(sc.IllegalDNADesignError): design.strand(0, 2).to(8) - def test_strand__call_to_twice_legally(self): design = self.design_6helix sb = design.strand(0, 0) @@ -292,7 +291,6 @@ def test_strand__call_to_twice_decrease_increase_reverse(self): sb.to(5) - class TestCreateHelix(unittest.TestCase): def test_helix_constructor_no_max_offset_with_major_ticks(self): @@ -2166,6 +2164,31 @@ def test_set_helix_idx(self): class TestJSON(unittest.TestCase): + def test_nondefault_geometry(self): + geometry_expected = sc.Geometry(z_step=10.0, helix_radius=4.0, bases_per_turn=11.0, minor_groove_angle=10.0, + inter_helix_gap=5.0) + design = sc.DNADesign(helices=[], strands=[], geometry=geometry_expected) + json_str = design.to_json() + design_from_json = sc.DNADesign.from_scadnano_json_str(json_str) + geometry_actual = design_from_json.geometry + self.assertAlmostEqual(geometry_expected.z_step, geometry_actual.z_step) + self.assertAlmostEqual(geometry_expected.helix_radius, geometry_actual.helix_radius) + self.assertAlmostEqual(geometry_expected.bases_per_turn, geometry_actual.bases_per_turn) + self.assertAlmostEqual(geometry_expected.minor_groove_angle, geometry_actual.minor_groove_angle) + self.assertAlmostEqual(geometry_expected.inter_helix_gap, geometry_actual.inter_helix_gap) + + def test_nondefault_geometry_some_default(self): + geometry_expected = sc.Geometry(z_step=10.0, minor_groove_angle=10.0, inter_helix_gap=5.0) + design = sc.DNADesign(helices=[], strands=[], geometry=geometry_expected) + json_str = design.to_json() + design_from_json = sc.DNADesign.from_scadnano_json_str(json_str) + geometry_actual = design_from_json.geometry + self.assertAlmostEqual(geometry_expected.z_step, geometry_actual.z_step) + self.assertAlmostEqual(geometry_expected.helix_radius, geometry_actual.helix_radius) + self.assertAlmostEqual(geometry_expected.bases_per_turn, geometry_actual.bases_per_turn) + self.assertAlmostEqual(geometry_expected.minor_groove_angle, geometry_actual.minor_groove_angle) + self.assertAlmostEqual(geometry_expected.inter_helix_gap, geometry_actual.inter_helix_gap) + def test_lack_of_NoIndent_on_helix_if_position_or_major_ticks_present(self): helices = [sc.Helix(position=sc.Position3D(0, 0, 0))] strands = [] From 2849caadf8392b8faf4036d6b2916393380092ba Mon Sep 17 00:00:00 2001 From: David Doty Date: Wed, 24 Jun 2020 17:19:14 -0700 Subject: [PATCH 16/30] closes #90 --- .../2_staple_2_helix_modifications.dna | 46 +++++++++---------- .../many_helices_modifications.dna | 14 +++--- scadnano/scadnano.py | 33 +++++++++---- 3 files changed, 54 insertions(+), 39 deletions(-) diff --git a/examples/output_designs/2_staple_2_helix_modifications.dna b/examples/output_designs/2_staple_2_helix_modifications.dna index 2366cdff..e528033e 100644 --- a/examples/output_designs/2_staple_2_helix_modifications.dna +++ b/examples/output_designs/2_staple_2_helix_modifications.dna @@ -6,48 +6,48 @@ {"grid_position": [0, 1]} ], "modifications_in_design": { - "/5Biosg/": { - "display_text": "B", - "idt_text": "/5Biosg/", - "display_connector": false, - "location": "5'" - }, - "/iBiodT/": { - "display_text": "B", - "idt_text": "/iBiodT/", - "display_connector": false, - "location": "internal", - "allowed_bases": ["T"] - }, "/3Bio/": { "display_text": "B", "idt_text": "/3Bio/", "display_connector": false, "location": "3'" }, + "/iCy3/": { + "display_text": "Cy3", + "idt_text": "/iCy3/", + "display_connector": false, + "location": "internal" + }, "/5Cy5/": { "display_text": "Cy5", "idt_text": "/5Cy5/", "display_connector": false, "location": "5'" }, - "/3Cy3Sp/": { - "display_text": "Cy3", - "idt_text": "/3Cy3Sp/", - "display_connector": false, - "location": "3'" - }, - "/iCy3/": { - "display_text": "Cy3", - "idt_text": "/iCy3/", + "/5Biosg/": { + "display_text": "B", + "idt_text": "/5Biosg/", "display_connector": false, - "location": "internal" + "location": "5'" }, "/iCy5/": { "display_text": "Cy5", "idt_text": "/iCy5/", "display_connector": false, "location": "internal" + }, + "/iBiodT/": { + "display_text": "B", + "idt_text": "/iBiodT/", + "display_connector": false, + "location": "internal", + "allowed_bases": ["T"] + }, + "/3Cy3Sp/": { + "display_text": "Cy3", + "idt_text": "/3Cy3Sp/", + "display_connector": false, + "location": "3'" } }, "strands": [ diff --git a/examples/output_designs/many_helices_modifications.dna b/examples/output_designs/many_helices_modifications.dna index 85b1b019..82c5ffda 100644 --- a/examples/output_designs/many_helices_modifications.dna +++ b/examples/output_designs/many_helices_modifications.dna @@ -12,11 +12,12 @@ {"grid_position": [0, 7]} ], "modifications_in_design": { - "/5Biosg/": { + "/iBiodT/": { "display_text": "B", - "idt_text": "/5Biosg/", + "idt_text": "/iBiodT/", "display_connector": false, - "location": "5'" + "location": "internal", + "allowed_bases": ["T"] }, "/iCy3/": { "display_text": "Cy3", @@ -24,12 +25,11 @@ "display_connector": false, "location": "internal" }, - "/iBiodT/": { + "/5Biosg/": { "display_text": "B", - "idt_text": "/iBiodT/", + "idt_text": "/5Biosg/", "display_connector": false, - "location": "internal", - "allowed_bases": ["T"] + "location": "5'" }, "/3Cy3Sp/": { "display_text": "Cy3", diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 28c02031..14d95d9f 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -2221,7 +2221,7 @@ def insert_domain(self, order, domain): if self.use_default_idt: self.set_default_idt() - def remove_domain(self, domain): + def remove_domain(self, domain: Union[Domain, Loopout]): # Only intended to be called by DNADesign.remove_domain self.domains.remove(domain) domain._parent_strand = None @@ -2230,13 +2230,13 @@ def remove_domain(self, domain): if self.use_default_idt: self.set_default_idt() - def contains_loopouts(self): + def contains_loopouts(self) -> bool: for domain in self.domains: if domain.is_loopout(): return True return False - def first_bound_domain(self): + def first_bound_domain(self) -> Domain: """First :any:`Domain` (i.e., not a :any:`Loopout`) on this :any:`Strand`. Currently the first and last strand must not be :any:`Loopout`'s, so this should return the same @@ -2246,7 +2246,7 @@ def first_bound_domain(self): if domain.is_domain(): return domain - def last_bound_domain(self): + def last_bound_domain(self) -> Domain: """Last :any:`Domain` (i.e., not a :any:`Loopout`) on this :any:`Strand`. Currently the first and last strand must not be :any:`Loopout`'s, so this should return the same @@ -2533,7 +2533,7 @@ class Geometry(_JSONSerializable): """What is this?""" helix_radius: float = 1.0 - """Redius of a DNA helix in nanometers.""" + """Radius of a DNA helix in nanometers.""" bases_per_turn: float = 10.5 """Number of DNA base pairs in in full turn of DNA.""" @@ -3848,7 +3848,8 @@ def _idt_strands(self, warn_duplicate_name: bool, warn_on_non_idt_strands: bool, f"does not have a field idt, so will not be part of IDT output.") return added_strands - def write_idt_bulk_input_file(self, directory: str = '.', filename: str = None, delimiter: str = ',', + def write_idt_bulk_input_file(self, directory: str = '.', filename: str = None, extension: str = None, + delimiter: str = ',', warn_duplicate_name: bool = True, warn_on_non_idt_strands: bool = True, export_non_modified_strand_version: bool = False): """Write ``.idt`` text file encoding the strands of this :any:`DNADesign` with the field @@ -3858,6 +3859,8 @@ def write_idt_bulk_input_file(self, directory: str = '.', filename: str = None, unless `filename` is explicitly specified. For instance, if the script is named ``my_origami.py``, then the sequences will be written to ``my_origami.idt``. + If `filename` is not specified but `extension` is, then that extension is used instead of ``idt``. + At least one of `filename` or `extension` must be ``None``. `directory` specifies a directory in which to place the file, either absolute or relative to the current working directory. Default is the current working directory. @@ -3877,7 +3880,9 @@ def write_idt_bulk_input_file(self, directory: str = '.', filename: str = None, """ contents = self.to_idt_bulk_input_format(delimiter, warn_duplicate_name, warn_on_non_idt_strands, export_non_modified_strand_version) - _write_file_same_name_as_running_python_script(contents, 'idt', directory, filename) + if extension is None: + extension = 'idt' + _write_file_same_name_as_running_python_script(contents, extension, directory, filename) def write_idt_plate_excel_file(self, directory: str = '.', filename: str = None, warn_duplicate_name: bool = False, warn_on_non_idt_strands: bool = False, @@ -4007,7 +4012,7 @@ def _write_plates_default(self, directory: str, filename: str, idt_strands: List workbook.save(filename_plate) - def write_scadnano_file(self, directory: str = '.', filename=None): + def write_scadnano_file(self, directory: str = '.', filename: str = None, extension: str = None): """Write ``.dna`` file representing this :any:`DNADesign`, suitable for reading by scadnano, with the output file having the same name as the running script but with ``.py`` changed to ``.dna``, unless `filename` is explicitly specified. @@ -4018,9 +4023,19 @@ def write_scadnano_file(self, directory: str = '.', filename=None): the current working directory. Default is the current working directory. The string written is that returned by :meth:`DNADesign.to_json`. + + :param directory: directory in which to put file (default: current) + :param filename: filename (default: name of script with .py replaced by .dna). + Mutually exclusive with `extension` + :param extension: extension for filename (default: .dna) + Mutually exclusive with `filename` """ contents = self.to_json() - _write_file_same_name_as_running_python_script(contents, 'dna', directory, filename) + if filename is not None and extension is not None: + raise ValueError('at least one of filename or extension must be None') + if extension is None: + extension = 'dna' + _write_file_same_name_as_running_python_script(contents, extension, directory, filename) def export_cadnano_v2(self, directory: str = '.', filename=None): """Write ``.json`` file representing this :any:`DNADesign`, suitable for reading by cadnano v2, From 6c67b5a8d5470cf1588fcc65dbfd95c3b64e702c Mon Sep 17 00:00:00 2001 From: David Doty Date: Wed, 24 Jun 2020 18:09:47 -0700 Subject: [PATCH 17/30] closes #86 --- ...lix_origami_deletions_insertions_labels.py | 44 +++++++++ .../2_staple_2_helix_modifications.dna | 42 ++++---- ...ix_origami_deletions_insertions_labels.dna | 40 ++++++++ .../many_helices_modifications.dna | 26 ++--- scadnano/scadnano.py | 99 +++++++++++++------ tests/scadnano_tests.py | 37 +++++++ 6 files changed, 223 insertions(+), 65 deletions(-) create mode 100644 examples/2_staple_2_helix_origami_deletions_insertions_labels.py create mode 100644 examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.dna diff --git a/examples/2_staple_2_helix_origami_deletions_insertions_labels.py b/examples/2_staple_2_helix_origami_deletions_insertions_labels.py new file mode 100644 index 00000000..ae1b913c --- /dev/null +++ b/examples/2_staple_2_helix_origami_deletions_insertions_labels.py @@ -0,0 +1,44 @@ +import scadnano as sc + + +def main(): + # helices + helices = [sc.Helix(max_offset=48), sc.Helix(max_offset=48)] + + # left staple + stap_left_ss1 = sc.Domain(helix=1, forward=True, start=8, end=24) + stap_left_ss0 = sc.Domain(helix=0, forward=False, start=8, end=24) + stap_left = sc.Strand(domains=[stap_left_ss1, stap_left_ss0], + label='left staple') + + # right staple + stap_right_ss0 = sc.Domain(helix=0, forward=False, start=24, end=40) + stap_right_ss1 = sc.Domain(helix=1, forward=True, start=24, end=40) + stap_right = sc.Strand(domains=[stap_right_ss0, stap_right_ss1], + label='right staple') + + # scaffold + scaf_ss1_left = sc.Domain(helix=1, forward=False, start=8, end=24) + scaf_ss0 = sc.Domain(helix=0, forward=True, start=8, end=40) + loopout = sc.Loopout(length=3) + scaf_ss1_right = sc.Domain(helix=1, forward=False, start=24, end=40) + scaf = sc.Strand(domains=[scaf_ss1_left, scaf_ss0, loopout, scaf_ss1_right], is_scaffold=True, + label='scaffold label') + + # whole design + design = sc.DNADesign(helices=helices, strands=[scaf, stap_left, stap_right], grid=sc.square) + + # deletions and insertions added to design are added to both strands on a helix + design.add_deletion(helix=1, offset=20) + design.add_insertion(helix=0, offset=14, length=1) + design.add_insertion(helix=0, offset=26, length=2) + + # also assigns complement to strands other than scaf bound to it + design.assign_dna(scaf, 'AACGT' * 18) + + return design + + +if __name__ == '__main__': + design = main() + design.write_scadnano_file(directory='output_designs') diff --git a/examples/output_designs/2_staple_2_helix_modifications.dna b/examples/output_designs/2_staple_2_helix_modifications.dna index e528033e..9ebc58a5 100644 --- a/examples/output_designs/2_staple_2_helix_modifications.dna +++ b/examples/output_designs/2_staple_2_helix_modifications.dna @@ -6,15 +6,9 @@ {"grid_position": [0, 1]} ], "modifications_in_design": { - "/3Bio/": { - "display_text": "B", - "idt_text": "/3Bio/", - "display_connector": false, - "location": "3'" - }, - "/iCy3/": { - "display_text": "Cy3", - "idt_text": "/iCy3/", + "/iCy5/": { + "display_text": "Cy5", + "idt_text": "/iCy5/", "display_connector": false, "location": "internal" }, @@ -24,18 +18,6 @@ "display_connector": false, "location": "5'" }, - "/5Biosg/": { - "display_text": "B", - "idt_text": "/5Biosg/", - "display_connector": false, - "location": "5'" - }, - "/iCy5/": { - "display_text": "Cy5", - "idt_text": "/iCy5/", - "display_connector": false, - "location": "internal" - }, "/iBiodT/": { "display_text": "B", "idt_text": "/iBiodT/", @@ -48,6 +30,24 @@ "idt_text": "/3Cy3Sp/", "display_connector": false, "location": "3'" + }, + "/5Biosg/": { + "display_text": "B", + "idt_text": "/5Biosg/", + "display_connector": false, + "location": "5'" + }, + "/iCy3/": { + "display_text": "Cy3", + "idt_text": "/iCy3/", + "display_connector": false, + "location": "internal" + }, + "/3Bio/": { + "display_text": "B", + "idt_text": "/3Bio/", + "display_connector": false, + "location": "3'" } }, "strands": [ diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.dna new file mode 100644 index 00000000..2dd4b33b --- /dev/null +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.dna @@ -0,0 +1,40 @@ +{ + "version": "0.9.1", + "grid": "square", + "helices": [ + {"max_offset": 48, "grid_position": [0, 0]}, + {"max_offset": 48, "grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", + "domains": [ + {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, + {"loopout": 3}, + {"helix": 1, "forward": false, "start": 24, "end": 40} + ], + "is_scaffold": true, + "label": "scaffold label" + }, + { + "color": "#f74308", + "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", + "domains": [ + {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} + ], + "label": "left staple" + }, + { + "color": "#57bb00", + "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", + "domains": [ + {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, + {"helix": 1, "forward": true, "start": 24, "end": 40} + ], + "label": "right staple" + } + ] +} \ No newline at end of file diff --git a/examples/output_designs/many_helices_modifications.dna b/examples/output_designs/many_helices_modifications.dna index 82c5ffda..1ca606cb 100644 --- a/examples/output_designs/many_helices_modifications.dna +++ b/examples/output_designs/many_helices_modifications.dna @@ -12,18 +12,11 @@ {"grid_position": [0, 7]} ], "modifications_in_design": { - "/iBiodT/": { - "display_text": "B", - "idt_text": "/iBiodT/", - "display_connector": false, - "location": "internal", - "allowed_bases": ["T"] - }, - "/iCy3/": { + "/3Cy3Sp/": { "display_text": "Cy3", - "idt_text": "/iCy3/", + "idt_text": "/3Cy3Sp/", "display_connector": false, - "location": "internal" + "location": "3'" }, "/5Biosg/": { "display_text": "B", @@ -31,11 +24,18 @@ "display_connector": false, "location": "5'" }, - "/3Cy3Sp/": { + "/iCy3/": { "display_text": "Cy3", - "idt_text": "/3Cy3Sp/", + "idt_text": "/iCy3/", "display_connector": false, - "location": "3'" + "location": "internal" + }, + "/iBiodT/": { + "display_text": "B", + "idt_text": "/iBiodT/", + "display_connector": false, + "location": "internal", + "allowed_bases": ["T"] } }, "strands": [ diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 14d95d9f..beb2dd14 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -50,11 +50,14 @@ import itertools import re from dataclasses import dataclass, field, InitVar, replace -from typing import Tuple, List, Set, Dict, Union, Optional, FrozenSet, Type +from typing import Tuple, List, Set, Dict, Union, Optional, FrozenSet, Type, TypeVar, Generic from collections import defaultdict, OrderedDict, Counter import sys import os.path +StrandLabel = TypeVar('StrandLabel') +DomainLabel = TypeVar('DomainLabel') + def _pairwise(iterable): """s -> (s0,s1), (s1,s2), (s2, s3), ...""" @@ -192,7 +195,7 @@ class ColorCycler: # These are copied from cadnano: # https://github.com/sdouglas/cadnano2/blob/master/views/styles.py#L97 - _colors = [Color(50, 184, 108), + _colors: List[Color] = [Color(50, 184, 108), Color(204, 0, 0), Color(247, 67, 8), Color(247, 147, 30), @@ -216,10 +219,10 @@ def __init__(self): # random order order = [3, 11, 0, 12, 8, 1, 10, 6, 5, 9, 4, 7, 2] # order = range(len(self._colors)) - colors_shuffled = [None] * len(self._colors) + colors_shuffled: List[Color] = [None] * len(self._colors) for i, color in zip(order, self._colors): colors_shuffled[i] = color - self._colors = colors_shuffled + self._colors: List[Color] = colors_shuffled def __iter__(self): # need to make ColorCycler an iterator @@ -230,7 +233,7 @@ def __next__(self): self._current_color_idx = (self._current_color_idx + 1) % len(self._colors) return color - def current_color(self): + def current_color(self) -> Color: return self._colors[self._current_color_idx] def __hash__(self): @@ -727,6 +730,7 @@ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249): modification_5p_key = '5prime_modification' modification_3p_key = '3prime_modification' modifications_int_key = 'internal_modifications' +strand_label_key = 'label' # Domain keys helix_idx_key = 'helix' @@ -736,6 +740,7 @@ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249): end_key = 'end' deletions_key = 'deletions' insertions_key = 'insertions' +domain_label_key = 'label' # Loopout keys loopout_key = 'loopout' @@ -1126,7 +1131,7 @@ def _is_close(x1: float, x2: float): @dataclass -class Domain(_JSONSerializable): +class Domain(_JSONSerializable, Generic[DomainLabel]): """ A maximal portion of a :any:`Strand` that is continguous on a single :any:`Helix`. A :any:`Strand` contains a list of :any:`Domain`'s (and also potentially :any:`Loopout`'s). @@ -1173,6 +1178,15 @@ class Domain(_JSONSerializable): This is the number of *extra* bases in addition to the base already at this position. The total number of bases at this offset is num_insertions+1.""" + label: DomainLabel = None + """Generic "label" object to associate to this :any:`Domain`. + + Useful for associating extra information with the :any:`Domain` that will be serialized, for example, + for DNA sequence design. It must be an object (e.g., a dict or primitive type such as str or int) + that is naturally JSON serializable. (Calling ``json.dumps`` on the object should succeed without + having to specify a custom encoder.) + """ + # not serialized; for efficiency _parent_strand: Strand = field(init=False, repr=False, compare=False, default=None) @@ -1210,6 +1224,8 @@ def to_json_serializable(self, suppress_indent: bool = True): dct[deletions_key] = self.deletions if len(self.insertions) > 0: dct[insertions_key] = self.insertions + if self.label is not None: + dct[domain_label_key] = self.label return NoIndent(dct) if suppress_indent else dct @staticmethod @@ -1389,7 +1405,7 @@ def _between_5p_and_offset(self, offset_to_test: int, offset_edge: int) -> bool: # The type hint 'Domain' must be in quotes since Domain is not yet defined. # This is a "forward reference": https://www.python.org/dev/peps/pep-0484/#forward-references - def overlaps(self, other: Domain) -> bool: + def overlaps(self, other: Domain[DomainLabel]) -> bool: r"""Indicates if this :any:`Domain`'s set of offsets (the set :math:`\{x \in \mathbb{N} \mid` ``self.start`` @@ -1403,7 +1419,7 @@ def overlaps(self, other: Domain) -> bool: self.forward == (not other.forward) and self.compute_overlap(other)[0] >= 0) - def overlaps_illegally(self, other: Domain): + def overlaps_illegally(self, other: Domain[DomainLabel]): r"""Indicates if this :any:`Domain`'s set of offsets (the set :math:`\{x \in \mathbb{N} \mid` ``self.start`` @@ -1417,7 +1433,7 @@ def overlaps_illegally(self, other: Domain): self.forward == other.forward and self.compute_overlap(other)[0] >= 0) - def compute_overlap(self, other: Domain) -> Tuple[int, int]: + def compute_overlap(self, other: Domain[DomainLabel]) -> Tuple[int, int]: """Return [left,right) offset indicating overlap between this Domain and `other`. Return ``(-1,-1)`` if they do not overlap (different helices, or non-overlapping regions @@ -1440,6 +1456,7 @@ def from_json(json_map): end = mandatory_field(Domain, json_map, end_key) deletions = json_map.get(deletions_key, []) insertions = list(map(tuple, json_map.get(insertions_key, []))) + label = json_map.get(domain_label_key) return Domain( helix=helix, forward=forward, @@ -1447,6 +1464,7 @@ def from_json(json_map): end=end, deletions=deletions, insertions=insertions, + label=label, ) @@ -1662,7 +1680,7 @@ def __init__(self, design: DNADesign, helix: int, offset: int): self.loopout_length: Optional[int] = None self.strand: Optional[Strand] = None self.just_moved_to_helix: bool = True - self.last_domain: Optional[Domain] = None + self.last_domain: Optional[Domain[DomainLabel]] = None def cross(self, helix: int, offset: int = None) -> StrandBuilder: """ @@ -1829,7 +1847,7 @@ def with_color(self, color: Color) -> StrandBuilder: @dataclass -class Strand(_JSONSerializable): +class Strand(_JSONSerializable, Generic[StrandLabel, DomainLabel]): """ Represents a single strand of DNA. @@ -1866,7 +1884,7 @@ class Strand(_JSONSerializable): uses for the scaffold. """ - domains: List[Union[Domain, Loopout]] + domains: List[Union[Domain[DomainLabel], Loopout]] """:any:`Domain`'s (or :any:`Loopout`'s) composing this Strand. Each :any:`Domain` is contiguous on a single :any:`Helix` and could be either single-stranded or double-stranded, @@ -1921,8 +1939,17 @@ class Strand(_JSONSerializable): So for an internal modified base on a sequence of length n, the allowed offsets are 0,...,n-1, and for an internal modification that goes between bases, the allowed offsets are 0,...,n-2.""" + label: StrandLabel = None + """Generic "label" object to associate to this :any:`Strand`. + + Useful for associating extra information with the Strand that will be serialized, for example, + for DNA sequence design. It must be an object (e.g., a dict or primitive type such as str or int) + that is naturally JSON serializable. (Calling ``json.dumps`` on the object should succeed without + having to specify a custom encoder.) + """ + # not serialized; efficient way to see a list of all domains on a given helix - _helix_idx_domain_map: Dict[int, List[Domain]] = field( + _helix_idx_domain_map: Dict[int, List[Domain[DomainLabel]]] = field( init=False, repr=False, compare=False, default=None) def to_json_serializable(self, suppress_indent: bool = True): @@ -1947,6 +1974,9 @@ def to_json_serializable(self, suppress_indent: bool = True): mods_dict[f"{offset}"] = mod.id dct[modifications_int_key] = NoIndent(mods_dict) if suppress_indent else mods_dict + if self.label is not None: + dct[strand_label_key] = self.label + return dct def __post_init__(self): @@ -1989,14 +2019,16 @@ def set_scaffold(self, is_scaf: bool = True): if is_scaf: self.color = default_scaffold_color + def set_label(self, label: StrandLabel): + """Sets label of this :any:`Strand`.""" + self.label = label + def set_color(self, color: Color): """Sets color of this :any:`Strand`.""" self.color = color def set_default_idt(self, use_default_idt: bool = True, skip_scaffold: bool = True): - """Sets idt field to be the default given the Domain data of this :any:`Strand`. - - """ + """Sets idt field to be the default given the Domain data of this :any:`Strand`.""" if skip_scaffold and self.is_scaffold: return self.use_default_idt = use_default_idt @@ -2048,11 +2080,11 @@ def remove_modification_internal(self, idx: int): if idx in self.modifications_int: del self.modifications_int[idx] - def first_domain(self) -> Union[Domain, Loopout]: + def first_domain(self) -> Union[Domain[DomainLabel], Loopout]: """First domain (of type either :any:`Domain` or :any:`Loopout`) on this :any:`Strand`.""" return self.domains[0] - def last_domain(self) -> Union[Domain, Loopout]: + def last_domain(self) -> Union[Domain[DomainLabel], Loopout]: """Last domain (of type either :any:`Domain` or :any:`Loopout`) on this :any:`Strand`.""" return self.domains[-1] @@ -2086,7 +2118,7 @@ def dna_length(self) -> int: acc += domain.dna_length() return acc - def bound_domains(self) -> List[Domain]: + def bound_domains(self) -> List[Domain[DomainLabel]]: """:any:`Domain`'s of this :any:`Strand` that are not :any:`Loopout`'s.""" return [domain for domain in self.domains if domain.is_domain()] @@ -2221,7 +2253,7 @@ def insert_domain(self, order, domain): if self.use_default_idt: self.set_default_idt() - def remove_domain(self, domain: Union[Domain, Loopout]): + def remove_domain(self, domain: Union[Domain[DomainLabel], Loopout]): # Only intended to be called by DNADesign.remove_domain self.domains.remove(domain) domain._parent_strand = None @@ -2236,7 +2268,7 @@ def contains_loopouts(self) -> bool: return True return False - def first_bound_domain(self) -> Domain: + def first_bound_domain(self) -> Domain[DomainLabel]: """First :any:`Domain` (i.e., not a :any:`Loopout`) on this :any:`Strand`. Currently the first and last strand must not be :any:`Loopout`'s, so this should return the same @@ -2246,7 +2278,7 @@ def first_bound_domain(self) -> Domain: if domain.is_domain(): return domain - def last_bound_domain(self) -> Domain: + def last_bound_domain(self) -> Domain[DomainLabel]: """Last :any:`Domain` (i.e., not a :any:`Loopout`) on this :any:`Strand`. Currently the first and last strand must not be :any:`Loopout`'s, so this should return the same @@ -2301,12 +2333,15 @@ def decimal_int_to_hex(d: int) -> str: color_str = decimal_int_to_hex(color_str) color = Color(hex_string=color_str) + label = json_map.get(strand_label_key) + return Strand( domains=domains, dna_sequence=dna_sequence, color=color, idt=idt, is_scaffold=is_scaffold, + label=label, ) def _ensure_modifications_legal(self, check_offsets_legal=False): @@ -3429,11 +3464,11 @@ def _check_helix_offsets(self): f'helix.max_offset = {helix.max_offset}' raise IllegalDNADesignError(err_msg) - def _check_strands_overlap_legally(self, domain_to_check: Domain = None): + def _check_strands_overlap_legally(self, domain_to_check: Domain[DomainLabel] = None): """If `Domain_to_check` is None, check all. Otherwise only check pairs where one is domain_to_check.""" - def err_msg(d1: Domain, d2: Domain, h_idx: int) -> str: + def err_msg(d1: Domain[DomainLabel], d2: Domain[DomainLabel], h_idx: int) -> str: return f"two domains overlap on helix {h_idx}: " \ f"\n{d1}\n and\n{d2}\n but have the same direction" @@ -3454,7 +3489,7 @@ def err_msg(d1: Domain, d2: Domain, h_idx: int) -> str: offsets_data.append((domain.end, False, domain)) offsets_data.sort(key=lambda offset_data: offset_data[0]) - current_domains: List[Domain] = [] + current_domains: List[Domain[DomainLabel]] = [] for offset, is_start, domain in offsets_data: if is_start: if len(current_domains) >= 2: @@ -3561,7 +3596,7 @@ def domain_at(self, helix: int, offset: int, forward: bool): return domain return None - def domains_at(self, helix: int, offset: int) -> List[Domain]: + def domains_at(self, helix: int, offset: int) -> List[Domain[DomainLabel]]: """Return list of :any:`Domain`'s that overlap `offset` on helix with idx `helix`. If constructed properly, this list should have 0, 1, or 2 elements.""" @@ -3593,7 +3628,7 @@ def remove_strand(self, strand: Strand): if domain.is_domain(): self.helices[domain.helix].domains.remove(domain) - def append_domain(self, strand: Strand, domain: Union[Domain, Loopout]): + def append_domain(self, strand: Strand, domain: Union[Domain[DomainLabel], Loopout]): """ Same as :any:`DNADesign.insert_domain`, but inserts at end. @@ -3602,7 +3637,7 @@ def append_domain(self, strand: Strand, domain: Union[Domain, Loopout]): """ self.insert_domain(strand, len(strand.domains), domain) - def insert_domain(self, strand: Strand, order: int, domain: Union[Domain, Loopout]): + def insert_domain(self, strand: Strand, order: int, domain: Union[Domain[DomainLabel], Loopout]): """Insert `Domain` into `strand` at index given by `order`. Uses same indexing as Python lists, e.g., ``design.insert_domain(strand, domain, 0)`` inserts ``domain`` as the new first :any:`Domain`.""" @@ -3619,7 +3654,7 @@ def insert_domain(self, strand: Strand, order: int, domain: Union[Domain, Loopou self.helices[domain.helix].domains.append(domain) self._check_strands_overlap_legally(domain_to_check=domain) - def remove_domain(self, strand: Strand, domain: Union[Domain, Loopout]): + def remove_domain(self, strand: Strand, domain: Union[Domain[DomainLabel], Loopout]): """Remove `Domain` from `strand`.""" assert strand in self.strands strand.remove_domain(domain) @@ -3684,13 +3719,13 @@ def add_insertion(self, helix: int, offset: int, length: int): if domain.contains_offset(offset): domain.insertions.append((offset, length)) - def set_start(self, domain: Domain, start: int): + def set_start(self, domain: Domain[DomainLabel], start: int): """Sets ``Domain.start`` to `start`.""" assert domain in (domain for strand in self.strands for domain in strand.domains) domain.set_start(start) self._check_strands_overlap_legally(domain) - def set_end(self, domain: Domain, end: int): + def set_end(self, domain: Domain[DomainLabel], end: int): """Sets ``Domain.end`` to `end`.""" assert domain in (domain for strand in self.strands for domain in strand.domains) domain.set_end(end) @@ -4018,6 +4053,8 @@ def write_scadnano_file(self, directory: str = '.', filename: str = None, extens unless `filename` is explicitly specified. For instance, if the script is named ``my_origami.py``, then the design will be written to ``my_origami.dna``. + If `extension` is specified (but `filename` is not), then the design will be written to + ``my_origami.`` `directory` specifies a directory in which to place the file, either absolute or relative to the current working directory. Default is the current working directory. diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 39d19c12..a448c9e7 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -2164,6 +2164,43 @@ def test_set_helix_idx(self): class TestJSON(unittest.TestCase): + def test_strand_labels(self): + helices = [sc.Helix(max_offset=100), sc.Helix(max_offset=100)] + strand0_expected = sc.Strand([sc.Domain(0, True, 0, 10)], label={ + 'name': 'strand 0', + 'num_domains': 1, + }) + strand1_expected = sc.Strand([sc.Domain(0, False, 0, 10), sc.Domain(1, True, 0, 10)], label={ + 'name': 'strand 1', + 'num_domains': 2, + }) + strands = [strand0_expected, strand1_expected] + design = sc.DNADesign(helices=helices, strands=strands, grid=sc.square) + json_str = design.to_json() + design_from_json = sc.DNADesign.from_scadnano_json_str(json_str) + strand0 = design_from_json.strands[0] + strand1 = design_from_json.strands[1] + self.assertDictEqual(strand0_expected.label, strand0.label) + self.assertDictEqual(strand1_expected.label, strand1.label) + + def test_domain_labels(self): + helices = [sc.Helix(max_offset=100), sc.Helix(max_offset=100)] + dom00_expected = sc.Domain(0, True, 0, 10, label='domain 00') + dom10_expected = sc.Domain(0, False, 0, 10) + dom11_expected = sc.Domain(1, True, 0, 10, label='domain 11') + strand0 = sc.Strand([dom00_expected]) + strand1 = sc.Strand([dom10_expected, dom11_expected]) + strands = [strand0, strand1] + design = sc.DNADesign(helices=helices, strands=strands, grid=sc.square) + json_str = design.to_json() + design_from_json = sc.DNADesign.from_scadnano_json_str(json_str) + dom00 = design_from_json.strands[0].domains[0] + dom10 = design_from_json.strands[1].domains[0] + dom11 = design_from_json.strands[1].domains[1] + self.assertEqual(dom00_expected.label, dom00.label) + self.assertIsNone(dom10.label) + self.assertEqual(dom11_expected.label, dom11.label) + def test_nondefault_geometry(self): geometry_expected = sc.Geometry(z_step=10.0, helix_radius=4.0, bases_per_turn=11.0, minor_groove_angle=10.0, inter_helix_gap=5.0) From 04620971315dbba6b95c28738179f77a71f4ad88 Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 25 Jun 2020 15:40:58 -0700 Subject: [PATCH 18/30] closes #88 --- scadnano/scadnano.py | 230 ++++++++++++++++++++++----- tests/scadnano_tests.py | 342 ++++++++++++++++++++++++++++++++++++---- 2 files changed, 505 insertions(+), 67 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index beb2dd14..a4301dd9 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -49,6 +49,7 @@ import enum import itertools import re +import copy from dataclasses import dataclass, field, InitVar, replace from typing import Tuple, List, Set, Dict, Union, Optional, FrozenSet, Type, TypeVar, Generic from collections import defaultdict, OrderedDict, Counter @@ -196,19 +197,19 @@ class ColorCycler: # These are copied from cadnano: # https://github.com/sdouglas/cadnano2/blob/master/views/styles.py#L97 _colors: List[Color] = [Color(50, 184, 108), - Color(204, 0, 0), - Color(247, 67, 8), - Color(247, 147, 30), - Color(170, 170, 0), - Color(87, 187, 0), - Color(0, 114, 0), - Color(3, 182, 162), - # Color(23, 0, 222), # don't like this because it looks too much like scaffold - Color(50, 0, 150), # this one is better contrast with scaffold - Color(184, 5, 108), - Color(51, 51, 51), - Color(115, 0, 222), - Color(136, 136, 136)] + Color(204, 0, 0), + Color(247, 67, 8), + Color(247, 147, 30), + Color(170, 170, 0), + Color(87, 187, 0), + Color(0, 114, 0), + Color(3, 182, 162), + # Color(23, 0, 222), # don't like this because it looks too much like scaffold + Color(50, 0, 150), # this one is better contrast with scaffold + Color(184, 5, 108), + Color(51, 51, 51), + Color(115, 0, 222), + Color(136, 136, 136)] """List of colors to cycle through.""" # _colors = [Color(hex_string=kelly_color) for kelly_color in _kelly_colors] @@ -1845,6 +1846,44 @@ def with_color(self, color: Color) -> StrandBuilder: self.strand.set_color(color) return self + def with_sequence(self, sequence: str, assign_complement: bool = True) -> StrandBuilder: + """ + Assigns `sequence` as DNA sequence of the :any:`Strand` being built. + This should be done after the :any:`Strand`'s structure is done being built, e.g., + + .. code-block:: Python + + design.strand(0, 0).to(10).cross(1).to(5).with_modification_5p(mod.biotin_5p).as_scaffold() + + :param sequence: the DNA sequence to assign + :param assign_complement: whether to automatically assign the complement to existing :any:`Strand`'s + bound to this :any:`Strand`. This has the same meaning as the parameter `assign_complement` in + :py:meth:`DNADesign.assign_dna`. + :return: self + """ + self.design.assign_dna(strand=self.strand, sequence=sequence, assign_complement=assign_complement) + return self + + def with_domain_sequence(self, sequence: str, assign_complement: bool = True) -> StrandBuilder: + """ + Assigns `sequence` as DNA sequence of the :any:`Strand` being built. + This should be done after the :any:`Strand`'s structure is done being built, e.g., + + .. code-block:: Python + + design.strand(0, 0).to(10).cross(1).to(5).with_modification_5p(mod.biotin_5p).as_scaffold() + + :param sequence: the DNA sequence to assign + :param assign_complement: whether to automatically assign the complement to existing :any:`Strand`'s + bound to this :any:`Strand`. This has the same meaning as the parameter `assign_complement` in + :py:meth:`DNADesign.assign_dna`. + :return: self + """ + last_domain = self.strand.domains[-1] + self.design.assign_dna(strand=self.strand, sequence=sequence, domain=last_domain, + assign_complement=assign_complement) + return self + @dataclass class Strand(_JSONSerializable, Generic[StrandLabel, DomainLabel]): @@ -2253,8 +2292,26 @@ def insert_domain(self, order, domain): if self.use_default_idt: self.set_default_idt() + # add wildcard symbols to DNA sequence to maintain its length + if self.dna_sequence is not None: + start_idx = self.dna_index_start_domain(domain) + end_idx = start_idx + domain.dna_length() + prefix = self.dna_sequence[:start_idx] + suffix = self.dna_sequence[start_idx:] + new_wildcards = DNA_base_wildcard * (end_idx - start_idx) + self.dna_sequence = prefix + new_wildcards + suffix + def remove_domain(self, domain: Union[Domain[DomainLabel], Loopout]): # Only intended to be called by DNADesign.remove_domain + + # remove relevant portion of DNA sequence to maintain its length + if self.dna_sequence is not None: + start_idx = self.dna_index_start_domain(domain) + end_idx = start_idx + domain.dna_length() + prefix = self.dna_sequence[:start_idx] + suffix = self.dna_sequence[end_idx:] + self.dna_sequence = prefix + suffix + self.domains.remove(domain) domain._parent_strand = None if domain.is_domain(): @@ -2262,6 +2319,22 @@ def remove_domain(self, domain: Union[Domain[DomainLabel], Loopout]): if self.use_default_idt: self.set_default_idt() + def dna_index_start_domain(self, domain: Domain[DomainLabel]): + """ + Returns index in DNA sequence of domain, e.g., if there are five domains + + 012 3 45 678 9 + AAA-C-GG-TTT-ACGT + + Then their indices, respectively in order, are 0, 3, 4, 6, 9. + + :param domain: :any: to find the start DNA index of + :return: index (within DNA sequence string) of substring of DNA starting with given :any:`Domain` + """ + domain_order = self.domains.index(domain) + idx = sum(self.domains[i].dna_length() for i in range(domain_order)) + return idx + def contains_loopouts(self) -> bool: for domain in self.domains: if domain.is_loopout(): @@ -2396,6 +2469,44 @@ def unmodified_version(self): return strand_nomods +def _pad_and_remove_whitespace_and_uppercase(sequence: str, strand: Strand, start: int = 0): + sequence = _remove_whitespace_and_uppercase(sequence) + padded_sequence = _pad_dna(sequence, strand.dna_length(), start) + return padded_sequence + + +def _remove_whitespace_and_uppercase(sequence): + sequence = re.sub(r'\s*', '', sequence) + sequence = sequence.upper() + return sequence + + +def _pad_dna(sequence: str, length: int, start: int = 0) -> str: + """Return `sequence` modified to have length `length`. + + If len(sequence) < length, pad with :py:data:`DNA_base_wildcard`. + + If len(sequence) > length, remove extra symbols, from 0 up to `start`, and at the end. + + :param sequence: sequence to pad + :param length: final length of padded sequence + :param start: index at which to start padding. If not specified, defaults to 0 + :return: padded sequence + """ + if start < 0: + raise ValueError(f'cannot pad DNA with negative start, but start = {start}') + elif start >= length: + raise ValueError(f'cannot pad DNA with start >= length, but start = {start} and ' + f'length = {length}') + if len(sequence) > length: + sequence = sequence[start:start + length] + elif len(sequence) < length: + prefix = DNA_base_wildcard * start + suffix = DNA_base_wildcard * (length - len(sequence) - start) + sequence = prefix + sequence + suffix + return sequence + + def _string_merge_wildcard(s1: str, s2: str, wildcard: str) -> str: """Takes a "union" of two equal-length strings `s1` and `s2`. Whenever one has a symbol `wildcard` and the other does not, the result has the non-wildcard symbol. @@ -2675,10 +2786,35 @@ class DNADesign(_JSONSerializable): def __init__(self, *, helices: Optional[Union[List[Helix], Dict[int, Helix]]] = None, strands: List[Strand] = None, + helix_template: Optional[Helix] = None, + num_helices: Optional[int] = None, grid: Grid = Grid.none, major_tick_distance: int = -1, helices_view_order: List[int] = None, geometry: Geometry = None): + """ + :param helices: List of :any:`Helix`'s; if missing, set based on either `helix_template` and + `num_helices`, or based on `strands`. + Mutually exlusive with `helix_template` and `num_helices` + :param strands: List of :any:`Strand`'s. If missing, will be empty. + :param helix_template: If specified, `num_helices` must be specified. + That many helices will be created, + modeled after this Helix. This Helix will not be any of them, so modifications to it will not + affect the :any:`DNADesign` after it is created. The ``idx`` field of `helix_template` will be + ignored, and the ``idx`` fields of the created helices will be 0 through `num_helices` - 1. + Mutually exclusive with `helices`. + :param num_helices: Number of :any:`Helix`'s to create, each of which is copied from `helix_template`. + If specified, `helix_template` must be specified + Mutually exclusive with `helices`. + :param grid: :any:`Grid` to use. + :param major_tick_distance: regularly spaced major ticks between all helices. + :any:`Helix.major_tick_distance` overrides this value for any :any:`Helix` in which it is + specified. + :param helices_view_order: order in which to view helices from top to bottom in web interface + main view + :param geometry: geometric physical parameters for visualization. + If not specified, a default set of parameters from the literature are used. + """ self.helices = helices self.strands = strands self.grid = grid @@ -2693,8 +2829,20 @@ def __init__(self, *, if self.major_tick_distance < 0 or self.major_tick_distance is None: self.major_tick_distance = default_major_tick_distance(self.grid) + if (self.helices is not None and (helix_template is not None or num_helices is not None)): + raise IllegalDNADesignError('helices is mutually exclusive with helix_template and num_helices; ' + 'you must specified the first, or the latter two') + + if (helix_template is not None and num_helices is None) or ( + helix_template is None and num_helices is not None): + raise IllegalDNADesignError('helix type must be specified if and only if num_helices is') + if self.helices is None: - if len(self.strands) > 0: + if helix_template is not None and num_helices is not None: + self.helices = {idx: copy.deepcopy(helix_template) for idx in range(num_helices)} + for idx, helix in self.helices.items(): + replace(helix, idx=idx) + elif len(self.strands) > 0: max_helix_idx = max( domain.helix for strand in self.strands for domain in strand.bound_domains()) self.helices = {idx: Helix(idx=idx) for idx in range(max_helix_idx + 1)} @@ -3747,7 +3895,8 @@ def move_strands_on_helices(self, delta: int): domain.helix += delta self._check_strands_reference_helices_legally() - def assign_dna(self, strand: Strand, sequence: str): + def assign_dna(self, strand: Strand, sequence: str, assign_complement: bool = True, + domain: Union[Domain, Loopout] = None): """ Assigns `sequence` as DNA sequence of `strand`. @@ -3763,8 +3912,30 @@ def assign_dna(self, strand: Strand, sequence: str): All whitespace in `sequence` is removed, and lowercase bases 'a', 'c', 'g', 't' are converted to uppercase. + + :param strand: :any:`Strand` to assign DNA sequence to + :param sequence: string of DNA bases to assign + :param assign_complement: whether to assign the complement DNA sequence to any :any:`Strand` that + is bound to this one (default True) + :param domain: :any:`Domain` on `strand` to assign. If ``None``, then the whole :any:`Strand` is + given a DNA sequence. Otherwise, only `domain` is assigned, and the rest of the :any:`Domain`'s + on `strand` are left alone (either keeping their DNA sequence, or being assigned + :py:const:`DNA_case_wildcard` if no DNA sequence was previously assigned.) + If `domain` is specified, then ``len(sequence)`` must be least than or equal to the number + of bases on `domain`. (i.e., ``domain.dna_length()``) """ - padded_sequence = _pad_and_remove_whitespace(sequence, strand) + start = 0 + if domain is not None: + pos = strand.domains.index(domain) + start = sum(prev_dom.dna_length() for prev_dom in strand.domains[:pos]) + if domain.dna_length() < len(sequence): + raise IllegalDNADesignError(f'cannot assign sequence {sequence} to strand domain ' + f'\n{domain}\n' + f'The number of bases on the domain is {domain.dna_length()} ' + f'but the length of the sequence is {len(sequence)}. The ' + f'length of the sequence must be at most the numebr of bases ' + f'on the domain.') + padded_sequence = _pad_and_remove_whitespace_and_uppercase(sequence, strand, start) if strand is None: raise IllegalDNADesignError('strand cannot be None to assign DNA to it') if strand not in self.strands: @@ -3789,6 +3960,9 @@ def assign_dna(self, strand: Strand, sequence: str): strand.set_dna_sequence(merged_sequence) + if not assign_complement: + return + for other_strand in self.strands: # note that possibly strand==other_strand; it might bind to itself at some point and we want to # allow a partial assignment to one domain to automatically assign the complement to the @@ -4478,30 +4652,6 @@ def _create_directory_and_set_filename(directory, filename): return relative_filename -def _remove_whitespace_and_uppercase(sequence): - sequence = re.sub(r'\s*', '', sequence) - sequence = sequence.upper() - return sequence - - -def _pad_and_remove_whitespace(sequence, strand): - sequence = _remove_whitespace_and_uppercase(sequence) - padded_sequence = _pad_dna(sequence, strand.dna_length()) - return padded_sequence - - -def _pad_dna(sequence: str, length: int) -> str: - """Return `sequence` modified to have length `length`. - - If len(sequence) < length, pad with :py:data:`DNA_base_wildcard`. - If len(sequence) > length, remove extra symbols.""" - if len(sequence) > length: - sequence = sequence[:length] - elif len(sequence) < length: - sequence += DNA_base_wildcard * (length - len(sequence)) - return sequence - - @dataclass class Crossover: """ diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index a448c9e7..e862633f 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -2738,6 +2738,78 @@ def test_strand_references_nonexistent_helix(self): with self.assertRaises(sc.IllegalDNADesignError): sc.DNADesign(grid=sc.square, helices=[h1, h2], strands=strands) +class TestInsertRemoveDomains(unittest.TestCase): + + def setUp(self) -> None: + self.design = sc.DNADesign(helix_template=sc.Helix(max_offset=100), num_helices=4, strands=[]) + self.design.strand(0, 0).to(3).cross(1).to(0).cross(2).to(3).with_sequence('ACA TCT GTG') + self.strand = self.design.strands[0] + + def test_3_helix_before_design(self): + expected_strand_before = sc.Strand([ + sc.Domain(0, True, 0, 3), + sc.Domain(1, False, 0, 3), + sc.Domain(2, True, 0, 3), + ], dna_sequence='ACA TCT GTG'.replace(' ', '')) + self.assertEqual(expected_strand_before, self.strand) + + def test_insert_domain_with_sequence(self): + design = sc.DNADesign(helix_template=sc.Helix(max_offset=100), num_helices=4, strands=[]) + design.strand(0, 0).to(3).cross(1).to(0).cross(3).to(3).with_sequence('ACA TCT GTG') + strand = design.strands[0] + + expected_strand_before = sc.Strand([ + sc.Domain(0, True, 0, 3), + sc.Domain(1, False, 0, 3), + sc.Domain(3, True, 0, 3), + ]) #, dna_sequence='ACA TCT GTG'.replace(' ', '')) + self.assertEqual(expected_strand_before, design.strands[0]) + + domain = sc.Domain(2, True, 0, 3) + design.insert_domain(strand, 2, domain) + expected_strand = sc.Strand([ + sc.Domain(0, True, 0, 3), + sc.Domain(1, False, 0, 3), + sc.Domain(2, True, 0, 3), + sc.Domain(3, True, 0, 3), + ], dna_sequence='ACA TCT ??? GTG'.replace(' ', '')) + self.assertEqual(expected_strand, design.strands[0]) + + def test_append_domain_with_sequence(self): + domain = sc.Domain(3, False, 0, 3) + self.design.append_domain(self.strand, domain) + expected_strand = sc.Strand([ + sc.Domain(0, True, 0, 3), + sc.Domain(1, False, 0, 3), + sc.Domain(2, True, 0, 3), + sc.Domain(3, False, 0, 3), + ], dna_sequence='ACA TCT GTG ???'.replace(' ','')) + self.assertEqual(expected_strand, self.strand) + + def test_remove_first_domain_with_sequence(self): + self.design.remove_domain(self.strand, self.strand.domains[0]) + expected_strand = sc.Strand([ + sc.Domain(1, False, 0, 3), + sc.Domain(2, True, 0, 3), + ], dna_sequence=' TCT GTG'.replace(' ', '')) + self.assertEqual(expected_strand, self.strand) + + def test_remove_middle_domain_with_sequence(self): + self.design.remove_domain(self.strand, self.strand.domains[1]) + expected_strand = sc.Strand([ + sc.Domain(0, True, 0, 3), + sc.Domain(2, True, 0, 3), + ], dna_sequence='ACA GTG'.replace(' ', '')) + self.assertEqual(expected_strand, self.strand) + + def test_remove_last_domain_with_sequence(self): + self.design.remove_domain(self.strand, self.strand.domains[2]) + expected_strand = sc.Strand([ + sc.Domain(0, True, 0, 3), + sc.Domain(1, False, 0, 3), + ], dna_sequence='ACA TCT GTG'.replace(' ', '')) + self.assertEqual(expected_strand, self.strand) + class TestAddStrand(unittest.TestCase): @@ -3346,43 +3418,259 @@ def test_assign_dna__wildcards_simple(self): design.assign_dna(strand_top2, 'GGA') self.assertEqual('AGGTCCGAA', strand_bot.dna_sequence) + +class TestAssignDNAToDomains(unittest.TestCase): + + def setUp(self) -> None: + """ + 012 345 678 901 234 567 890 + +---------------+ + | | + | +-----|-------+ +-+ + | | | | | | + -ACG> +TTC> -GGA+ -AAC+ -TGC> +TTG+ +GCA> + +TTC> -GGA+ -AAC+ -TGC> +TTG> - +TTC> -GGA+ -AAC+ -TGC> +TTG+ +GCA> + +TTC> -GGA+ -AAC+ -TGC> +TTG+ +GCA> + +???> -???+ -AAC+ -???> +???+ +???> + +TTC> -???+ -AAC+ -???> +???+ +???> + +TTC> -???+ -AAC+ -TGC> +???+ +???> + +TTC> -???+ -AAC+ -TGC> +???+ +???> + +TTC> -???+ -AAC+ -TGC> +TTG+ +???> + +TTC> -???+ -AAC+ -TGC> +TTG+ +GCA> + +TTC> -GGA+ -AAC+ -TGC> +TTG+ +GCA> + +TTC> -GGA+ -AAC+ -TGC> +TTG+ +GCA> + + -TGC> + +TTC> -AAC+ -TGC> + +TTC> -GGA+ -AAC+ -TGC> +TTG+ +GCA> + Date: Thu, 25 Jun 2020 17:25:48 -0700 Subject: [PATCH 19/30] updated docstrings --- scadnano/scadnano.py | 48 ++++++++++++++++++++++++++++++++++---------- 1 file changed, 37 insertions(+), 11 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index a4301dd9..e83272ff 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -390,13 +390,26 @@ class M13Variant(enum.Enum): """Variants of M13mp18 viral genome. "Standard" variant is p7249. Other variants are longer.""" p7249 = "p7249" - """"Standard" variant of M13mp18; 7249 bases long.""" + """"Standard" variant of M13mp18; 7249 bases long, available from, for example + + https://www.neb.com/products/n4040-m13mp18-single-stranded-dna + + http://www.bayoubiolabs.com/biochemicat/vectors/pUCM13/ + + https://www.tilibit.com/collections/scaffold-dna/products/single-stranded-scaffold-dna-type-p7249 + """ p7560 = "p7560" - """Variant of M13mp18 that is 7560 bases long.""" + """Variant of M13mp18 that is 7560 bases long. Available from, for example + + https://www.tilibit.com/collections/scaffold-dna/products/single-stranded-scaffold-dna-type-p7560 + """ p8064 = "p8064" - """Variant of M13mp18 that is 8064 bases long.""" + """Variant of M13mp18 that is 8064 bases long. Available from, for example + + https://www.tilibit.com/collections/scaffold-dna/products/single-stranded-scaffold-dna-type-p8064 + """ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249): @@ -1853,9 +1866,9 @@ def with_sequence(self, sequence: str, assign_complement: bool = True) -> Strand .. code-block:: Python - design.strand(0, 0).to(10).cross(1).to(5).with_modification_5p(mod.biotin_5p).as_scaffold() + design.strand(0, 0).to(10).cross(1).to(5).with_sequence('AAAAAAAAAACGCGC') - :param sequence: the DNA sequence to assign + :param sequence: the DNA sequence to assign to the :any:`Strand` :param assign_complement: whether to automatically assign the complement to existing :any:`Strand`'s bound to this :any:`Strand`. This has the same meaning as the parameter `assign_complement` in :py:meth:`DNADesign.assign_dna`. @@ -1866,14 +1879,22 @@ def with_sequence(self, sequence: str, assign_complement: bool = True) -> Strand def with_domain_sequence(self, sequence: str, assign_complement: bool = True) -> StrandBuilder: """ - Assigns `sequence` as DNA sequence of the :any:`Strand` being built. - This should be done after the :any:`Strand`'s structure is done being built, e.g., + Assigns `sequence` as DNA sequence of the most recently created :any:`Domain` in + the :any:`Strand` being built. This should be called immediately after a :any:`Domain` is created + via a call to + :py:meth:`StrandBuilder.to`, + :py:meth:`StrandBuilder.update_to`, + or + :py:meth:`StrandBuilder.loopout`, e.g., .. code-block:: Python - design.strand(0, 0).to(10).cross(1).to(5).with_modification_5p(mod.biotin_5p).as_scaffold() + design.strand(0, 5).to(8).with_domain_sequence('AAA')\ + .cross(1).to(5).with_domain_sequence('TTT')\ + .loopout(2, 4).with_domain_sequence('CCCC')\ + .to(10).with_domain_sequence('GGGGG') - :param sequence: the DNA sequence to assign + :param sequence: the DNA sequence to assign to the :any:`Domain` :param assign_complement: whether to automatically assign the complement to existing :any:`Strand`'s bound to this :any:`Strand`. This has the same meaning as the parameter `assign_complement` in :py:meth:`DNADesign.assign_dna`. @@ -3310,7 +3331,7 @@ def strand(self, helix: int, offset: int) -> StrandBuilder: sc.Domain(2, True, 5, 15), ])) - It returns an each call to + Each call to :py:meth:`DNADesign.strand`, :py:meth:`DNADesign.cross`, :py:meth:`DNADesign.loopout`, @@ -3318,9 +3339,14 @@ def strand(self, helix: int, offset: int) -> StrandBuilder: returns a :any:`StrandBuilder` object. Each call to - :py:meth:`DNADesign.to` + :py:meth:`DNADesign.to`, + :py:meth:`DNADesign.update_to`, + or + :py:meth:`DNADesign.loopout` modifies the :any:`DNADesign` by replacing the Strand with an updated version. + See the documentation for :any:`StrandBuilder` for the methods available to call in this way. + :param helix: starting :any:`Helix` :param offset: starting offset on `helix` :return: :any:`StrandBuilder` object representing the partially completed :any:`Strand` From b6bc81003d3a7b4e632ae78c9f9364dbb56874f5 Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 25 Jun 2020 17:36:48 -0700 Subject: [PATCH 20/30] cleaned up docstrings --- scadnano/scadnano.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index e83272ff..15893e54 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1739,7 +1739,7 @@ def to(self, offset: int) -> StrandBuilder: must be true. To simply change the current offset after calling :py:meth:`StrandBuilder.to`, without creating - a new Domain, call :py:meth:`StrandBuilder.update_to`. + a new Domain, call :py:meth:`StrandBuilder.update_to` instead. :param offset: new offset to extend to. If less than current offset, the new :any:`Domain` is reverse, otherwise it is forward. @@ -1779,14 +1779,15 @@ def to(self, offset: int) -> StrandBuilder: def update_to(self, offset: int) -> StrandBuilder: """ - Like :py:meth:`StrandBuilder.to`, but changes the current offset after calling - :py:meth:`StrandBuilder.to`, without creating - a new Domain, call :py:meth:`StrandBuilder.update_to`. + Like :py:meth:`StrandBuilder.to`, but changes the current offset without creating + a new :any:`Domain`. So unlike :py:meth:`StrandBuilder.to`, several consecutive calls to + :py:meth:`StrandBuilder.update_to` are equivalent to only making the final call. If :py:meth:`StrandBuilder.cross` or :py:meth:`StrandBuilder.loopout` was just called, then :py:meth:`StrandBuilder.to` and :py:meth:`StrandBuilder.update_to` have the same effect. - :param offset: new offset to extend to. If less than current offset, + :param offset: new offset to extend to. If less than offset of the last call to + :py:meth:`StrandBuilder.cross` or :py:meth:`StrandBuilder.loopout`, the new :any:`Domain` is reverse, otherwise it is forward. :return: self """ From 8c66ac07ee50793ae544128efe8bead318497ea3 Mon Sep 17 00:00:00 2001 From: David Doty Date: Fri, 26 Jun 2020 12:27:01 -0700 Subject: [PATCH 21/30] removed note about web interface in tutorial since none of the menus are shown --- tutorial/tutorial.md | 5 ----- 1 file changed, 5 deletions(-) diff --git a/tutorial/tutorial.md b/tutorial/tutorial.md index 92153e58..f84e4185 100644 --- a/tutorial/tutorial.md +++ b/tutorial/tutorial.md @@ -17,11 +17,6 @@ First, follow the [installation instructions](../README.md#installation) to inst -## Note about web interface - -The web interface for scadnano is somewhat in flux. As a result, some of the screenshots in this tutorial, and some of the names of menu items, have changed since this tutorial was released. The functionality is all still there, but you may have to search around a bit in the menu to find it. Once the interface has stabilized a bit more, this tutorial will be updated to contain screenshots from the latest version of scadnano. - - ## Viewing completed design The design will look like this when we are done: From 30a60db9f02dda6d04c42648032328193b6632bb Mon Sep 17 00:00:00 2001 From: David Doty Date: Fri, 26 Jun 2020 12:37:50 -0700 Subject: [PATCH 22/30] moved Python code from web interface README to here --- README.md | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 82 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index b1e0259f..307be0cb 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,87 @@ Early versions of this project didn't have well-defined versions. However, we wi Please report issues in the web interface at the [scadnano web interface GitHub repository](https://github.com/UC-Davis-molecular-computing/scadnano/issues), and report issues in the Python scripting library at the [scadnano Python package GitHub repository](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/issues). +## Example + +Consider the following design: + +![](https://github.com/UC-Davis-molecular-computing/scadnano/blob/master/doc-images/screenshot-initial.png) + +The following Python script produces this design. + +```python +import scadnano as sc +import modifications as mod + + +def main(): + # helices + helices = [sc.Helix(max_offset=48), sc.Helix(max_offset=48)] + + # left staple + stap_left_domain1 = sc.Domain(helix=1, forward=True, start=8, end=24) + stap_left_domain0 = sc.Domain(helix=0, forward=False, start=8, end=24) + stap_left = sc.Strand(domains=[stap_left_domain1, stap_left_domain0]) + + # right staple + stap_right_domain0 = sc.Domain(helix=0, forward=False, start=24, end=40) + stap_right_domain1 = sc.Domain(helix=1, forward=True, start=24, end=40) + stap_right = sc.Strand(domains=[stap_right_domain0, stap_right_domain1]) + stap_right.set_modification_5p(mod.biotin_5p) + + # scaffold + scaf_domain1_left = sc.Domain(helix=1, forward=False, start=8, end=24) + scaf_domain0 = sc.Domain(helix=0, forward=True, start=8, end=40) + loopout = sc.Loopout(length=3) + scaf_domain1_right = sc.Domain(helix=1, forward=False, start=24, end=40) + scaf = sc.Strand(domains=[scaf_domain1_left, scaf_domain0, loopout, scaf_domain1_right], is_scaffold=True) + + # whole design + design = sc.DNADesign(helices=helices, strands=[scaf, stap_left, stap_right], grid=sc.square) + + # deletions and insertions added to design are added to both strands on a helix + design.add_deletion(helix=1, offset=20) + design.add_insertion(helix=0, offset=14, length=1) + design.add_insertion(helix=0, offset=26, length=2) + + # also assigns complement to strands other than scaf bound to it + design.assign_dna(scaf, 'AACGT' * 18) + + return design + + +if __name__ == '__main__': + design = main() + design.write_scadnano_file(directory='output_designs') +``` + +Running the code above produces the `.dna` JSON file shown in the [web interface README](https://github.com/UC-Davis-molecular-computing/scadnano/blob/master/README.md#terminology). + + +## abbreviated syntax with chained methods +Instead of explicitly creating variables and objects representing each domain in each strand, there is a shorter syntax using chained method calls. Instead of the above, create only the helices first, then create the DNADesign. Then strands can be added using a shorter syntax, to describe how to draw the strand starting at the 5' end and moving to the 3' end. + +```python +# helices +helices = [sc.Helix(max_offset=48), sc.Helix(max_offset=48)] + +# whole design +design = sc.DNADesign(helices=helices, strands=[], grid=sc.square) + +# left staple +design.strand(1, 8).to(24).cross(0).to(8) + +# right staple +design.strand(0, 40).to(24).cross(1).to(40).with_modification_5p(mod.biotin_5p) + +# scaffold +design.strand(1, 24).to(8).cross(0).to(40).loopout(1, 3).to(24).as_scaffold() +``` + +The code for adding insertions, deletions, and assigning DNA would be the same as in the original script. + + + ## Installation The scadnano Python package requires Python version 3.7 or later. If you do not have that version (or later) of Python installed, follow [this link](https://www.python.org/downloads/) to install it. @@ -55,7 +136,7 @@ Once Python is installed, there are two ways you can install the scadnano Python * *optional*: [origami_rectangle.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/origami_rectangle.py); This can help create origami rectangles, but it is not necessary to use scadnano. * *optional*: [_version.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/_version.py) This ensures that the current version number is written into any `.dna` files written by the library; otherwise it may be out of date. (Which should not matter for the most part.) - Unfortunately, the scadnano package uses the Python package [xlwt](https://pypi.org/project/xlwt/) to write Excel files, so in order to call the method [`DNADesign.write_idt_plate_excel_file()`](https://scadnano-python-package.readthedocs.io/#scadnano.scadnano.DNADesign.write_idt_plate_excel_file) to export an Excel file with DNA sequences, xlwt must be installed. To install, type `pip install xlwt` at the command line. + The scadnano package uses the Python package [xlwt](https://pypi.org/project/xlwt/) to write Excel files, so in order to call the method [`DNADesign.write_idt_plate_excel_file()`](https://scadnano-python-package.readthedocs.io/#scadnano.scadnano.DNADesign.write_idt_plate_excel_file) to export an Excel file with DNA sequences, xlwt must be installed. To install, type `pip install xlwt` at the command line. From c8b3a2198c183210002da31166f60a79e867c6f3 Mon Sep 17 00:00:00 2001 From: David Doty Date: Fri, 26 Jun 2020 12:40:39 -0700 Subject: [PATCH 23/30] minor --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 307be0cb..e65cf585 100644 --- a/README.md +++ b/README.md @@ -78,7 +78,7 @@ if __name__ == '__main__': design.write_scadnano_file(directory='output_designs') ``` -Running the code above produces the `.dna` JSON file shown in the [web interface README](https://github.com/UC-Davis-molecular-computing/scadnano/blob/master/README.md#terminology). +Running the code above produces the `.dna` JSON file shown in the [web interface README](https://github.com/UC-Davis-molecular-computing/scadnano/blob/master/README.md#terminology). That section explains many of the terms used in the code (domain, helix, loopout, insertion, etc.). ## abbreviated syntax with chained methods From af0919995292ce80a15766855dea7443ff6d322b Mon Sep 17 00:00:00 2001 From: David Doty Date: Fri, 26 Jun 2020 12:44:10 -0700 Subject: [PATCH 24/30] reordered sections --- README.md | 85 ++++++++++++++++++++++++++++++++----------------------- 1 file changed, 50 insertions(+), 35 deletions(-) diff --git a/README.md b/README.md index e65cf585..7bd59a97 100644 --- a/README.md +++ b/README.md @@ -20,10 +20,58 @@ This module is used to write Python scripts outputting `.dna` files readable by Early versions of this project didn't have well-defined versions. However, we will try to announce breaking changes (and possibly new features) under the [GitHub releases page](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/releases). The version numbers in this Python library repo and the [web interface repo](https://github.com/UC-Davis-molecular-computing/scadnano/releases) won't always advance at the same time. However, when a breaking change is made, this will increment the minor or major version numbers in both libraries (version numbers are major.minor.patch, i.e., version 0.9.2 has minor version number 9). + + + + ## Reporting issues Please report issues in the web interface at the [scadnano web interface GitHub repository](https://github.com/UC-Davis-molecular-computing/scadnano/issues), and report issues in the Python scripting library at the [scadnano Python package GitHub repository](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/issues). + + + + + +## Installation + +The scadnano Python package requires Python version 3.7 or later. If you do not have that version (or later) of Python installed, follow [this link](https://www.python.org/downloads/) to install it. + +Once Python is installed, there are two ways you can install the scadnano Python package: + + +1. pip + + Use [pip](https://pypi.org/project/pip/) to install the package by executing the following at the command line: + ```console + pip install scadnano + ``` + + If your Python installation does not already have pip installed, you may have to install it. + Executing [this Python script](https://bootstrap.pypa.io/get-pip.py) should work; + see also + https://docs.python.org/3/installing/index.html + or + https://www.liquidweb.com/kb/install-pip-windows/. + +2. download + + As a simple alternative, you can download and place the following files (located in the [scadnano/](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/tree/master/scadnano) subfolder) + in your PYTHONPATH (e.g., in the same directory as the scripts you are running): + + * *required*: [scadnano.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/scadnano.py) + * *optional*: [modifications.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/modifications.py); This contains some common DNA modifications such as biotin and Cy3. + * *optional*: [origami_rectangle.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/origami_rectangle.py); This can help create origami rectangles, but it is not necessary to use scadnano. + * *optional*: [_version.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/_version.py) This ensures that the current version number is written into any `.dna` files written by the library; otherwise it may be out of date. (Which should not matter for the most part.) + + The scadnano package uses the Python package [xlwt](https://pypi.org/project/xlwt/) to write Excel files, so in order to call the method [`DNADesign.write_idt_plate_excel_file()`](https://scadnano-python-package.readthedocs.io/#scadnano.scadnano.DNADesign.write_idt_plate_excel_file) to export an Excel file with DNA sequences, xlwt must be installed. To install, type `pip install xlwt` at the command line. + + + + + + + ## Example Consider the following design: @@ -101,42 +149,9 @@ design.strand(0, 40).to(24).cross(1).to(40).with_modification_5p(mod.biotin_5p) design.strand(1, 24).to(8).cross(0).to(40).loopout(1, 3).to(24).as_scaffold() ``` -The code for adding insertions, deletions, and assigning DNA would be the same as in the original script. - - - -## Installation - -The scadnano Python package requires Python version 3.7 or later. If you do not have that version (or later) of Python installed, follow [this link](https://www.python.org/downloads/) to install it. - -Once Python is installed, there are two ways you can install the scadnano Python package: - - -1. pip - - Use [pip](https://pypi.org/project/pip/) to install the package by executing the following at the command line: - ```console - pip install scadnano - ``` - - If your Python installation does not already have pip installed, you may have to install it. - Executing [this Python script](https://bootstrap.pypa.io/get-pip.py) should work; - see also - https://docs.python.org/3/installing/index.html - or - https://www.liquidweb.com/kb/install-pip-windows/. - -2. download +Documentation is available in the [API docs](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.DNADesign.strand). - As a simple alternative, you can download and place the following files (located in the [scadnano/](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/tree/master/scadnano) subfolder) - in your PYTHONPATH (e.g., in the same directory as the scripts you are running): - - * *required*: [scadnano.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/scadnano.py) - * *optional*: [modifications.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/modifications.py); This contains some common DNA modifications such as biotin and Cy3. - * *optional*: [origami_rectangle.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/origami_rectangle.py); This can help create origami rectangles, but it is not necessary to use scadnano. - * *optional*: [_version.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/_version.py) This ensures that the current version number is written into any `.dna` files written by the library; otherwise it may be out of date. (Which should not matter for the most part.) - - The scadnano package uses the Python package [xlwt](https://pypi.org/project/xlwt/) to write Excel files, so in order to call the method [`DNADesign.write_idt_plate_excel_file()`](https://scadnano-python-package.readthedocs.io/#scadnano.scadnano.DNADesign.write_idt_plate_excel_file) to export an Excel file with DNA sequences, xlwt must be installed. To install, type `pip install xlwt` at the command line. +The code for adding insertions, deletions, and assigning DNA would be the same as in the original script. From 056ad5664cea3210082804501c8a7b23cca6814a Mon Sep 17 00:00:00 2001 From: David Doty Date: Fri, 26 Jun 2020 12:45:13 -0700 Subject: [PATCH 25/30] changed section title --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7bd59a97..4b351d18 100644 --- a/README.md +++ b/README.md @@ -174,7 +174,7 @@ A [tutorial](https://github.com/UC-Davis-molecular-computing/scadnano-python-pac -## Examples +## Other examples Several example scripts are located in the [examples/](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/tree/master/examples) subfolder. From 9f9a013dd1f6203ccd17ae3bee4869acae771ee7 Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 28 Jun 2020 09:45:55 -0700 Subject: [PATCH 26/30] changed name of z_step to rise_per_base_pair. --- scadnano/scadnano.py | 17 ++++++++++------- tests/scadnano_tests.py | 4 ++-- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 15893e54..1e0c19bf 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -710,7 +710,8 @@ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249): geometry_key = 'geometry' # Geometry keys -z_step_key = 'z_step' +rise_per_base_pair_key = 'rise_per_base_pair' +legacy_rise_per_base_pair_keys = ['z_step'] helix_radius_key = 'helix_radius' bases_per_turn_key = 'bases_per_turn' minor_groove_angle_key = 'minor_groove_angle' @@ -2697,14 +2698,14 @@ def optional_field(default_value, json_map: dict, main_key: str, *legacy_keys: s class Geometry(_JSONSerializable): """Parameters controlling some geometric visualization/physical aspects of Design.""" - z_step: float = 0.332 - """What is this?""" + rise_per_base_pair: float = 0.332 + """The distance in nanometers between two adjacent base pairs along the length of a DNA double helix.""" helix_radius: float = 1.0 """Radius of a DNA helix in nanometers.""" bases_per_turn: float = 10.5 - """Number of DNA base pairs in in full turn of DNA.""" + """Number of DNA base pairs in a full turn of DNA.""" minor_groove_angle: float = 150.0 """Minor groove angle in degrees.""" @@ -2718,7 +2719,8 @@ def is_default(self): @staticmethod def from_json(json_map: dict) -> Geometry: geometry = Geometry() - geometry.z_step = optional_field(_default_geometry.z_step, json_map, z_step_key) + geometry.rise_per_base_pair = optional_field(_default_geometry.rise_per_base_pair, json_map, + rise_per_base_pair_key, *legacy_rise_per_base_pair_keys) geometry.helix_radius = optional_field(_default_geometry.helix_radius, json_map, helix_radius_key) geometry.bases_per_turn = optional_field(_default_geometry.bases_per_turn, json_map, bases_per_turn_key) @@ -2730,10 +2732,11 @@ def from_json(json_map: dict) -> Geometry: @staticmethod def keys() -> List[str]: - return [z_step_key, helix_radius_key, bases_per_turn_key, minor_groove_angle_key, inter_helix_gap_key] + return [rise_per_base_pair_key, helix_radius_key, bases_per_turn_key, minor_groove_angle_key, + inter_helix_gap_key] def values(self) -> List[float]: - return [self.z_step, self.helix_radius, self.bases_per_turn, self.minor_groove_angle, + return [self.rise_per_base_pair, self.helix_radius, self.bases_per_turn, self.minor_groove_angle, self.inter_helix_gap] @staticmethod diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index e862633f..4b7c352a 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -2208,7 +2208,7 @@ def test_nondefault_geometry(self): json_str = design.to_json() design_from_json = sc.DNADesign.from_scadnano_json_str(json_str) geometry_actual = design_from_json.geometry - self.assertAlmostEqual(geometry_expected.z_step, geometry_actual.z_step) + self.assertAlmostEqual(geometry_expected.rise_per_base_pair, geometry_actual.rise_per_base_pair) self.assertAlmostEqual(geometry_expected.helix_radius, geometry_actual.helix_radius) self.assertAlmostEqual(geometry_expected.bases_per_turn, geometry_actual.bases_per_turn) self.assertAlmostEqual(geometry_expected.minor_groove_angle, geometry_actual.minor_groove_angle) @@ -2220,7 +2220,7 @@ def test_nondefault_geometry_some_default(self): json_str = design.to_json() design_from_json = sc.DNADesign.from_scadnano_json_str(json_str) geometry_actual = design_from_json.geometry - self.assertAlmostEqual(geometry_expected.z_step, geometry_actual.z_step) + self.assertAlmostEqual(geometry_expected.rise_per_base_pair, geometry_actual.rise_per_base_pair) self.assertAlmostEqual(geometry_expected.helix_radius, geometry_actual.helix_radius) self.assertAlmostEqual(geometry_expected.bases_per_turn, geometry_actual.bases_per_turn) self.assertAlmostEqual(geometry_expected.minor_groove_angle, geometry_actual.minor_groove_angle) From 1dc94795840bbc3c9f14169ffa7783b1affbd09a Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 28 Jun 2020 09:46:08 -0700 Subject: [PATCH 27/30] modified example with many DNA modifications to have every combination of modifications on forward and reverse strands, on both helices, to help with testing "invert y axis" view option in web interface. --- examples/2_staple_2_helix_modifications.py | 5 +++ .../2_staple_2_helix_modifications.dna | 31 ++++++++++--------- 2 files changed, 22 insertions(+), 14 deletions(-) diff --git a/examples/2_staple_2_helix_modifications.py b/examples/2_staple_2_helix_modifications.py index 2c43cbb3..8e43d80e 100644 --- a/examples/2_staple_2_helix_modifications.py +++ b/examples/2_staple_2_helix_modifications.py @@ -40,6 +40,11 @@ def main(): stap_right.set_modification_internal(5, mod.cy3_int) stap_right.set_modification_3p(mod.biotin_3p) + scaf.set_modification_5p(mod.biotin_5p) + scaf.set_modification_3p(mod.cy3_3p) + scaf.set_modification_internal(5, mod.cy5_int) + scaf.set_modification_internal(32, mod.cy3_int) + return design diff --git a/examples/output_designs/2_staple_2_helix_modifications.dna b/examples/output_designs/2_staple_2_helix_modifications.dna index 9ebc58a5..2b0f047b 100644 --- a/examples/output_designs/2_staple_2_helix_modifications.dna +++ b/examples/output_designs/2_staple_2_helix_modifications.dna @@ -6,18 +6,18 @@ {"grid_position": [0, 1]} ], "modifications_in_design": { - "/iCy5/": { - "display_text": "Cy5", - "idt_text": "/iCy5/", - "display_connector": false, - "location": "internal" - }, "/5Cy5/": { "display_text": "Cy5", "idt_text": "/5Cy5/", "display_connector": false, "location": "5'" }, + "/3Bio/": { + "display_text": "B", + "idt_text": "/3Bio/", + "display_connector": false, + "location": "3'" + }, "/iBiodT/": { "display_text": "B", "idt_text": "/iBiodT/", @@ -25,11 +25,11 @@ "location": "internal", "allowed_bases": ["T"] }, - "/3Cy3Sp/": { - "display_text": "Cy3", - "idt_text": "/3Cy3Sp/", + "/iCy5/": { + "display_text": "Cy5", + "idt_text": "/iCy5/", "display_connector": false, - "location": "3'" + "location": "internal" }, "/5Biosg/": { "display_text": "B", @@ -43,9 +43,9 @@ "display_connector": false, "location": "internal" }, - "/3Bio/": { - "display_text": "B", - "idt_text": "/3Bio/", + "/3Cy3Sp/": { + "display_text": "Cy3", + "idt_text": "/3Cy3Sp/", "display_connector": false, "location": "3'" } @@ -58,7 +58,10 @@ {"helix": 1, "forward": false, "start": 0, "end": 16, "deletions": [12], "insertions": [[2, 1]]}, {"helix": 0, "forward": true, "start": 0, "end": 32, "deletions": [11, 12, 24], "insertions": [[29, 1]]}, {"helix": 1, "forward": false, "start": 16, "end": 32, "deletions": [24]} - ] + ], + "5prime_modification": "/5Biosg/", + "3prime_modification": "/3Cy3Sp/", + "internal_modifications": {"5": "/iCy5/", "32": "/iCy3/"} }, { "color": "#f74308", From 3d4f93b653f753e1ff1c107b3224ded077a045f4 Mon Sep 17 00:00:00 2001 From: Benjamin Lee Date: Sun, 28 Jun 2020 10:01:35 -0700 Subject: [PATCH 28/30] Create release.yml --- .github/workflows/release.yml | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 .github/workflows/release.yml diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 00000000..fb75ffa0 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,25 @@ +name: "release" + +on: + push: + branches: + - "master" + +jobs: + release: + name: "Release" + runs-on: "ubuntu-latest" + + steps: + # ... + - name: "Build & test" + run: | + echo "done!" + - uses: "marvinpinto/action-automatic-releases@latest" + with: + repo_token: "${{ secrets.GITHUB_TOKEN }}" + automatic_release_tag: "latest" + prerelease: false + title: "Development Build [TODO: Replace label and number with version number]" + files: | + LICENSE.txt From 574268776ca5af9af48e8b69cf92b06ab30693ea Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 28 Jun 2020 10:04:06 -0700 Subject: [PATCH 29/30] changed name of z_step to rise_per_base_pair in unit tests --- tests/scadnano_tests.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 4b7c352a..cde5bcfe 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -2202,7 +2202,7 @@ def test_domain_labels(self): self.assertEqual(dom11_expected.label, dom11.label) def test_nondefault_geometry(self): - geometry_expected = sc.Geometry(z_step=10.0, helix_radius=4.0, bases_per_turn=11.0, minor_groove_angle=10.0, + geometry_expected = sc.Geometry(rise_per_base_pair=10.0, helix_radius=4.0, bases_per_turn=11.0, minor_groove_angle=10.0, inter_helix_gap=5.0) design = sc.DNADesign(helices=[], strands=[], geometry=geometry_expected) json_str = design.to_json() @@ -2215,7 +2215,7 @@ def test_nondefault_geometry(self): self.assertAlmostEqual(geometry_expected.inter_helix_gap, geometry_actual.inter_helix_gap) def test_nondefault_geometry_some_default(self): - geometry_expected = sc.Geometry(z_step=10.0, minor_groove_angle=10.0, inter_helix_gap=5.0) + geometry_expected = sc.Geometry(rise_per_base_pair=10.0, minor_groove_angle=10.0, inter_helix_gap=5.0) design = sc.DNADesign(helices=[], strands=[], geometry=geometry_expected) json_str = design.to_json() design_from_json = sc.DNADesign.from_scadnano_json_str(json_str) From 293b6d2940967612e7486863407faac33bf71f58 Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 28 Jun 2020 11:00:46 -0700 Subject: [PATCH 30/30] bumped version --- scadnano/_version.py | 2 +- scadnano/scadnano.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/scadnano/_version.py b/scadnano/_version.py index 924a0724..f78ca9a8 100644 --- a/scadnano/_version.py +++ b/scadnano/_version.py @@ -2,4 +2,4 @@ # taken from https://stackoverflow.com/questions/17583443/what-is-the-correct-way-to-share-package-version-with-setup-py-and-the-package/17626524#17626524 # The following line *must* be the last in the module, exactly as formatted: -__version__ = "0.9.1" +__version__ = "0.9.2" diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 1e0c19bf..fc136faf 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -331,7 +331,7 @@ class Grid(str, enum.Enum): from ._version import __version__ except ImportError: # this is so scadnano.py file works without _version.py being present, in case user downloads it - __version__ = "0.9.1" + __version__ = "0.9.2" default_idt_scale = "25nm" default_idt_purification = "STD"