diff --git a/.ipynb_checkpoints/k3l_test-checkpoint.tsv b/.ipynb_checkpoints/k3l_test-checkpoint.tsv new file mode 100644 index 0000000..535bf37 --- /dev/null +++ b/.ipynb_checkpoints/k3l_test-checkpoint.tsv @@ -0,0 +1,94 @@ +name sub_window_name wt position iupac codon_sub iupac_aa add_synonymous_codon contains_missense_stop remove_missense_stop_codon primer homology_arm sub_window forward_primer forward_primer_tm forward_primer_gc forward_primer_len reverse_primer_name reverse_primer reverse_primer_tm reverse_primer_gc reverse_primer_len +window_1-1_GCG11HCG window_1-1 GCG 11 HCG GCG11HCG TPS 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATHCGggwgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT HCGggwgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GCG11GDG window_1-1 GCG 11 GDG GCG11GDG EGV 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATGDGggwgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT GDGggwgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GGT12HGT window_1-1 GGT 12 HGT GGT12HGT SRC 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwHGTgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwHGTgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GGT12GHT window_1-1 GGT 12 GHT GGT12GHT DAV 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwGHTgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwGHTgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GAT13HAT window_1-1 GAT 13 HAT GAT13HAT NHY 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwHATgtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwHATgtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GAT13GBT window_1-1 GAT 13 GBT GAT13GBT AGV 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwGBTgtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwGBTgtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GAT13GAA window_1-1 GAT 13 GAA GAT13GAA E 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwGAAgtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwGAAgtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GTA14WTA window_1-1 GTA 14 WTA GTA14WTA IL 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgayWTAatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgayWTAatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GTA14GVA window_1-1 GTA 14 GVA GTA14GVA EAG 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgayGVAatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgayGVAatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_ATA15KTA window_1-1 ATA 15 KTA ATA15KTA VL 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwKTAaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwKTAaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_ATA15AVA window_1-1 ATA 15 AVA ATA15AVA KTR 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwAVAaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwAVAaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_ATA15ATG window_1-1 ATA 15 ATG ATA15ATG M 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwATGaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwATGaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_AAG16SAG window_1-1 AAG 16 SAG AAG16SAG QE 0.0 1.0 1.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwSAGGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwatwSAG GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_AAG16ABG window_1-1 AAG 16 ABG AAG16ABG TRM 0.0 1.0 1.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwABGGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwatwABG GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_AAG16AAT window_1-1 AAG 16 AAT AAG16AAT N 0.0 1.0 1.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwAATGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwatwAAT GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-2_GGC17HGC window_1-2 GGC 17 HGC GGC17HGC SRC 0.0 0.0 0.0 ATGCGGGTGATGTAATAAAGHGCagrGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG HGCagr GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 +window_1-2_GGC17GHC window_1-2 GGC 17 GHC GGC17GHC DAV 0.0 0.0 0.0 ATGCGGGTGATGTAATAAAGGHCagrGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG GHCagr GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 +window_1-2_AGA18GGA window_1-2 AGA 18 GGA AGA18GGA G 0.0 1.0 1.0 ATGCGGGTGATGTAATAAAGggwGGAGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG ggwGGA GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 +window_1-2_AGA18AHA window_1-2 AGA 18 AHA AGA18AHA KTI 0.0 1.0 1.0 ATGCGGGTGATGTAATAAAGggwAHAGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG ggwAHA GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 +window_1-2_AGA18AGT window_1-2 AGA 18 AGT AGA18AGT S 0.0 1.0 1.0 ATGCGGGTGATGTAATAAAGggwAGTGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG ggwAGT GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 +window_2-1_AGT43KGT window_2-1 AGT 43 KGT AGT43KGT GC 1.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGKGTgtwaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG KGTgtwaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_AGT43AHT window_2-1 AGT 43 AHT AGT43AHT NTI 1.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGAHTgtwaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG AHTgtwaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_AGT43AGM window_2-1 AGT 43 AGM AGT43AGM RS 1.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGAGMgtwaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG AGMgtwaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_GTT44HTT window_2-1 GTT 44 HTT GTT44HTT ILF 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwHTTaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwHTTaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_GTT44GVT window_2-1 GTT 44 GVT GTT44GVT DAG 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwGVTaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwGVTaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_AAG45SAG window_2-1 AAG 45 SAG AAG45SAG QE 0.0 1.0 1.0 TTGAAGCTATCTTGGCAGAGtcwgtwSAGatgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwSAGatg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_AAG45ABG window_2-1 AAG 45 ABG AAG45ABG TRM 0.0 1.0 1.0 TTGAAGCTATCTTGGCAGAGtcwgtwABGatgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwABGatg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_AAG45AAT window_2-1 AAG 45 AAT AAG45AAT N 0.0 1.0 1.0 TTGAAGCTATCTTGGCAGAGtcwgtwAATatgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwAATatg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_ATG46KTG window_2-1 ATG 46 KTG ATG46KTG VL 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwaarKTGCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwaarKTG CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_ATG46AVG window_2-1 ATG 46 AVG ATG46AVG KTR 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwaarAVGCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwaarAVG CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_ATG46ATT window_2-1 ATG 46 ATT ATG46ATT I 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwaarATTCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwaarATT CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-2_CAT47DAT window_2-2 CAT 47 DAT CAT47DAT NDY 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGDATatggayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG DATatggayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_CAT47CBT window_2-2 CAT 47 CBT CAT47CBT PRL 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGCBTatggayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG CBTatggayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_CAT47CAA window_2-2 CAT 47 CAA CAT47CAA Q 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGCAAatggayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG CAAatggayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_ATG48KTG window_2-2 ATG 48 KTG ATG48KTG VL 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayKTGgayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayKTGgayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_ATG48AVG window_2-2 ATG 48 AVG ATG48AVG KTR 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayAVGgayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayAVGgayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_ATG48ATT window_2-2 ATG 48 ATT ATG48ATT I 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayATTgayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayATTgayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_GAT49HAT window_2-2 GAT 49 HAT GAT49HAT NHY 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatgHATagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatgHATagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_GAT49GBT window_2-2 GAT 49 GBT GAT49GBT AGV 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatgGBTagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatgGBTagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_GAT49GAA window_2-2 GAT 49 GAA GAT49GAA E 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatgGAAagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatgGAAagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_AGA50GGA window_2-2 AGA 50 GGA AGA50GGA G 0.0 1.0 1.0 TGGCAGAGAGTGTTAAGATGcayatggayGGAtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayGGAtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_AGA50AHA window_2-2 AGA 50 AHA AGA50AHA KTI 0.0 1.0 1.0 TGGCAGAGAGTGTTAAGATGcayatggayAHAtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayAHAtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_AGA50AGT window_2-2 AGA 50 AGT AGA50AGT S 0.0 1.0 1.0 TGGCAGAGAGTGTTAAGATGcayatggayAGTtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayAGTtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_TAT51VAT window_2-2 TAT 51 VAT TAT51VAT NHD 0.0 1.0 1.0 TGGCAGAGAGTGTTAAGATGcayatggayagrVATGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayagrVAT GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_TAT51TBT window_2-2 TAT 51 TBT TAT51TBT SCF 0.0 1.0 1.0 TGGCAGAGAGTGTTAAGATGcayatggayagrTBTGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayagrTBT GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_3-1_GAT71HAT window_3-1 GAT 71 HAT GAT71HAT NHY 0.0 0.0 0.0 AAGTTAAAGTGATTAGAGTTHATtayacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT HATtayacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_GAT71GBT window_3-1 GAT 71 GBT GAT71GBT AGV 0.0 0.0 0.0 AAGTTAAAGTGATTAGAGTTGBTtayacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT GBTtayacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_GAT71GAA window_3-1 GAT 71 GAA GAT71GAA E 0.0 0.0 0.0 AAGTTAAAGTGATTAGAGTTGAAtayacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT GAAtayacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_TAT72VAT window_3-1 TAT 72 VAT TAT72VAT NHD 0.0 1.0 1.0 AAGTTAAAGTGATTAGAGTTgayVATacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gayVATacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_TAT72TBT window_3-1 TAT 72 TBT TAT72TBT SCF 0.0 1.0 1.0 AAGTTAAAGTGATTAGAGTTgayTBTacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gayTBTacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_ACA73BCA window_3-1 ACA 73 BCA ACA73BCA PAS 0.0 0.0 0.0 AAGTTAAAGTGATTAGAGTTgaytayBCAaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayBCAaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_ACA73ADA window_3-1 ACA 73 ADA ACA73ADA KRI 0.0 0.0 0.0 AAGTTAAAGTGATTAGAGTTgaytayADAaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayADAaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_AAA74SAA window_3-1 AAA 74 SAA AAA74SAA QE 0.0 1.0 1.0 AAGTTAAAGTGATTAGAGTTgaytayacwSAAGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayacwSAA GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_AAA74ABA window_3-1 AAA 74 ABA AAA74ABA TRI 0.0 1.0 1.0 AAGTTAAAGTGATTAGAGTTgaytayacwABAGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayacwABA GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_AAA74AAT window_3-1 AAA 74 AAT AAA74AAT N 0.0 1.0 1.0 AAGTTAAAGTGATTAGAGTTgaytayacwAATGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayacwAAT GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-2_GGA75AGA window_3-2 GGA 75 AGA GGA75AGA R 0.0 1.0 1.0 TTAGAGTTGATTATACAAAAAGAtayatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA AGAtayatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GGA75GHA window_3-2 GGA 75 GHA GGA75GHA EAV 0.0 1.0 1.0 TTAGAGTTGATTATACAAAAGHAtayatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA GHAtayatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_TAT76VAT window_3-2 TAT 76 VAT TAT76VAT NHD 0.0 1.0 1.0 TTAGAGTTGATTATACAAAAggwVATatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwVATatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_TAT76TBT window_3-2 TAT 76 TBT TAT76TBT SCF 0.0 1.0 1.0 TTAGAGTTGATTATACAAAAggwTBTatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwTBTatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_ATA77KTA window_3-2 ATA 77 KTA ATA77KTA VL 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayKTAgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayKTAgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_ATA77AVA window_3-2 ATA 77 AVA ATA77AVA KTR 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayAVAgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayAVAgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_ATA77ATG window_3-2 ATA 77 ATG ATA77ATG M 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayATGgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayATGgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GAT78HAT window_3-2 GAT 78 HAT GAT78HAT NHY 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwHATgtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwHATgtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GAT78GBT window_3-2 GAT 78 GBT GAT78GBT AGV 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwGBTgtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwGBTgtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GAT78GAA window_3-2 GAT 78 GAA GAT78GAA E 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwGAAgtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwGAAgtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GTC79HTC window_3-2 GTC 79 HTC GTC79HTC ILF 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwgayHTCAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwgayHTC AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GTC79GVC window_3-2 GTC 79 GVC GTC79GVC DAG 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwgayGVCAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwgayGVC AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-3_AAT80BAT window_3-3 AAT 80 BAT AAT80BAT HDY 0.0 0.0 0.0 CAAAAGGATATATAGATGTCBATtayaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC BATtayaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AAT80ABT window_3-3 AAT 80 ABT AAT80ABT TSI 0.0 0.0 0.0 CAAAAGGATATATAGATGTCABTtayaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC ABTtayaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AAT80AAA window_3-3 AAT 80 AAA AAT80AAA K 0.0 0.0 0.0 CAAAAGGATATATAGATGTCAAAtayaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC AAAtayaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_TAC81VAC window_3-3 TAC 81 VAC TAC81VAC NHD 0.0 1.0 1.0 CAAAAGGATATATAGATGTCaayVACaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aayVACaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_TAC81TBC window_3-3 TAC 81 TBC TAC81TBC SCF 0.0 1.0 1.0 CAAAAGGATATATAGATGTCaayTBCaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aayTBCaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AAA82SAA window_3-3 AAA 82 SAA AAA82SAA QE 0.0 1.0 1.0 CAAAAGGATATATAGATGTCaaytaySAAagratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytaySAAagratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AAA82ABA window_3-3 AAA 82 ABA AAA82ABA TRI 0.0 1.0 1.0 CAAAAGGATATATAGATGTCaaytayABAagratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayABAagratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AAA82AAT window_3-3 AAA 82 AAT AAA82AAT N 0.0 1.0 1.0 CAAAAGGATATATAGATGTCaaytayAATagratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayAATagratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AGG83KGG window_3-3 AGG 83 KGG AGG83KGG GW 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaarKGGatgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaarKGGatgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AGG83AHG window_3-3 AGG 83 AHG AGG83AHG KTM 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaarAHGatgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaarAHGatgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AGG83AGT window_3-3 AGG 83 AGT AGG83AGT S 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaarAGTatgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaarAGTatgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_ATG84KTG window_3-3 ATG 84 KTG ATG84KTG VL 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragrKTGtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragrKTGtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_ATG84AVG window_3-3 ATG 84 AVG ATG84AVG KTR 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragrAVGtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragrAVGtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_ATG84ATT window_3-3 ATG 84 ATT ATG84ATT I 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragrATTtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragrATTtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_TGT85SGT window_3-3 TGT 85 SGT TGT85SGT RG 1.0 1.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragratgSGTAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragratgSGT AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_TGT85THT window_3-3 TGT 85 THT TGT85THT YSF 1.0 1.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragratgTHTAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragratgTHT AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_TGT85TGG window_3-3 TGT 85 TGG TGT85TGG W 1.0 1.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragratgTGGAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragratgTGG AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-4_AGA86GGA window_3-4 AGA 86 GGA AGA86GGA G 0.0 1.0 1.0 TCAATTACAAAAGGATGTGTGGAcaycarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT GGAcaycar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_AGA86AHA window_3-4 AGA 86 AHA AGA86AHA KTI 0.0 1.0 1.0 TCAATTACAAAAGGATGTGTAHAcaycarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT AHAcaycar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_AGA86AGT window_3-4 AGA 86 AGT AGA86AGT S 0.0 1.0 1.0 TCAATTACAAAAGGATGTGTAGTcaycarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT AGTcaycar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAT87DAT window_3-4 CAT 87 DAT CAT87DAT NDY 0.0 0.0 0.0 TCAATTACAAAAGGATGTGTagrDATcarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrDATcar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAT87CBT window_3-4 CAT 87 CBT CAT87CBT PRL 0.0 0.0 0.0 TCAATTACAAAAGGATGTGTagrCBTcarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrCBTcar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAT87CAA window_3-4 CAT 87 CAA CAT87CAA Q 0.0 0.0 0.0 TCAATTACAAAAGGATGTGTagrCAAcarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrCAAcar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAA88RAA window_3-4 CAA 88 RAA CAA88RAA KE 0.0 1.0 1.0 TCAATTACAAAAGGATGTGTagrcayRAATAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrcayRAA TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAA88CBA window_3-4 CAA 88 CBA CAA88CBA PRL 0.0 1.0 1.0 TCAATTACAAAAGGATGTGTagrcayCBATAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrcayCBA TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAA88CAT window_3-4 CAA 88 CAT CAA88CAT H 0.0 1.0 1.0 TCAATTACAAAAGGATGTGTagrcayCATTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrcayCAT TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 diff --git a/check_k3l_test.ipynb b/check_k3l_test.ipynb index 1313e4a..f67ab4a 100644 --- a/check_k3l_test.ipynb +++ b/check_k3l_test.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 197, + "execution_count": 1, "id": "fbb00f64-ecc8-412d-ae57-9a4036440f6a", "metadata": {}, "outputs": [], @@ -14,7 +14,7 @@ }, { "cell_type": "code", - "execution_count": 198, + "execution_count": 16, "id": "26ba439a-d6c4-4037-82a1-cd8c07350940", "metadata": {}, "outputs": [], @@ -27,7 +27,7 @@ }, { "cell_type": "code", - "execution_count": 199, + "execution_count": 17, "id": "63e6329d-bd91-4b54-8c8a-670fb45e183d", "metadata": {}, "outputs": [ @@ -54,14 +54,14 @@ " \n", " name\n", " sub_window_name\n", - " wt\n", + " wt_codon\n", " position\n", - " iupac\n", + " iupac_codon\n", " codon_sub\n", " iupac_aa\n", - " synonymous_codons\n", - " no_stop_codons\n", - " primer\n", + " add_synonymous_codon\n", + " contains_missense_stop\n", + " remove_missense_stop_codon\n", " ...\n", " sub_window\n", " forward_primer\n", @@ -87,7 +87,7 @@ " NHY\n", " 0.0\n", " 0.0\n", - " TTTGTTATTCGTTGCCCAATgcwggwHATgtwatwaarGGCAGAGT...\n", + " 0.0\n", " ...\n", " gcwggwHATgtwatwaar\n", " GGCAGAGTATACGAGAAGGATT\n", @@ -111,7 +111,7 @@ " AGV\n", " 0.0\n", " 0.0\n", - " TTTGTTATTCGTTGCCCAATgcwggwGBTgtwatwaarGGCAGAGT...\n", + " 0.0\n", " ...\n", " gcwggwGBTgtwatwaar\n", " GGCAGAGTATACGAGAAGGATT\n", @@ -135,7 +135,7 @@ " E\n", " 0.0\n", " 0.0\n", - " TTTGTTATTCGTTGCCCAATgcwggwGAAgtwatwaarGGCAGAGT...\n", + " 0.0\n", " ...\n", " gcwggwGAAgtwatwaar\n", " GGCAGAGTATACGAGAAGGATT\n", @@ -150,44 +150,44 @@ " \n", " \n", "\n", - "

3 rows × 21 columns

\n", + "

3 rows × 22 columns

\n", "" ], "text/plain": [ - " name sub_window_name wt position iupac codon_sub \\\n", - "4 window_1-1_GAT13HAT window_1-1 GAT 13 HAT GAT13HAT \n", - "5 window_1-1_GAT13GBT window_1-1 GAT 13 GBT GAT13GBT \n", - "6 window_1-1_GAT13GAA window_1-1 GAT 13 GAA GAT13GAA \n", + " name sub_window_name wt_codon position iupac_codon \\\n", + "4 window_1-1_GAT13HAT window_1-1 GAT 13 HAT \n", + "5 window_1-1_GAT13GBT window_1-1 GAT 13 GBT \n", + "6 window_1-1_GAT13GAA window_1-1 GAT 13 GAA \n", "\n", - " iupac_aa synonymous_codons no_stop_codons \\\n", - "4 NHY 0.0 0.0 \n", - "5 AGV 0.0 0.0 \n", - "6 E 0.0 0.0 \n", + " codon_sub iupac_aa add_synonymous_codon contains_missense_stop \\\n", + "4 GAT13HAT NHY 0.0 0.0 \n", + "5 GAT13GBT AGV 0.0 0.0 \n", + "6 GAT13GAA E 0.0 0.0 \n", "\n", - " primer ... sub_window \\\n", - "4 TTTGTTATTCGTTGCCCAATgcwggwHATgtwatwaarGGCAGAGT... ... gcwggwHATgtwatwaar \n", - "5 TTTGTTATTCGTTGCCCAATgcwggwGBTgtwatwaarGGCAGAGT... ... gcwggwGBTgtwatwaar \n", - "6 TTTGTTATTCGTTGCCCAATgcwggwGAAgtwatwaarGGCAGAGT... ... gcwggwGAAgtwatwaar \n", + " remove_missense_stop_codon ... sub_window \\\n", + "4 0.0 ... gcwggwHATgtwatwaar \n", + "5 0.0 ... gcwggwGBTgtwatwaar \n", + "6 0.0 ... gcwggwGAAgtwatwaar \n", "\n", - " forward_primer forward_primer_tm forward_primer_gc \\\n", - "4 GGCAGAGTATACGAGAAGGATT 51.3 45.5 \n", - "5 GGCAGAGTATACGAGAAGGATT 51.3 45.5 \n", - "6 GGCAGAGTATACGAGAAGGATT 51.3 45.5 \n", + " forward_primer forward_primer_tm forward_primer_gc \\\n", + "4 GGCAGAGTATACGAGAAGGATT 51.3 45.5 \n", + "5 GGCAGAGTATACGAGAAGGATT 51.3 45.5 \n", + "6 GGCAGAGTATACGAGAAGGATT 51.3 45.5 \n", "\n", " forward_primer_len reverse_primer_name reverse_primer \\\n", "4 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA \n", "5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA \n", "6 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA \n", "\n", - " reverse_primer_tm reverse_primer_gc reverse_primer_len \n", - "4 55.1 36.0 25 \n", - "5 55.1 36.0 25 \n", - "6 55.1 36.0 25 \n", + " reverse_primer_tm reverse_primer_gc reverse_primer_len \n", + "4 55.1 36.0 25 \n", + "5 55.1 36.0 25 \n", + "6 55.1 36.0 25 \n", "\n", - "[3 rows x 21 columns]" + "[3 rows x 22 columns]" ] }, - "execution_count": 199, + "execution_count": 17, "metadata": {}, "output_type": "execute_result" } @@ -198,14 +198,14 @@ }, { "cell_type": "code", - "execution_count": 200, + "execution_count": 18, "id": "1005e0a7-f88d-4d96-a82f-2af7975d45c8", "metadata": {}, "outputs": [], "source": [ "# gather iupac-encoded aa missense variants by position\n", "df1 = df.groupby('position')['iupac_aa'].apply(list).reset_index()\n", - "map_dict = dict(zip(df.position, df.wt))\n", + "map_dict = dict(zip(df.position, df.wt_codon))\n", "df1['wt_codon'] =df1.position.map(map_dict)\n", "df1.iupac_aa = df1.iupac_aa.str.join('').str.split('')\n", "df1.iupac_aa = df1.iupac_aa.apply(lambda x: set(x))\n", @@ -215,7 +215,7 @@ }, { "cell_type": "code", - "execution_count": 201, + "execution_count": 19, "id": "73d853dc-ab2d-4161-8977-103a95824fdc", "metadata": {}, "outputs": [], @@ -234,535 +234,54 @@ " else: \n", " continue\n", " return set(missense_aa)\n", - "df1['wt_missense'] = df1.wt_codon.apply(aa_missense_variants)\n", - "\n", - "# take sets and remove iupac_aa from wt_aa (reciprocal, may have synonymous in the iupac and stops in the wt)\n", - "#df1['difference'] = (df1.wt_aa - df1.iupac_aa)" + "df1['wt_missense'] = df1.wt_codon.apply(aa_missense_variants)" ] }, { "cell_type": "code", - "execution_count": 202, + "execution_count": 20, "id": "6583af6b-0349-4e05-ba94-d97f11346d4f", "metadata": {}, "outputs": [], "source": [ - "df1['diff_1'] = df1.wt_missense - df1.iupac_aa\n", - "df1['diff_2'] = df1.iupac_aa - df1.wt_missense\n", - "\n", + "# should just be stop codons removed\n", + "df1['missing_from_wt'] = df1.wt_missense - df1.iupac_aa\n", + "# should just be synonymous variants\n", + "df1['added_from_wt'] = df1.iupac_aa - df1.wt_missense\n", + "# should just be stops and wt/synonymous variants\n", "df1['sym_diff'] = df1.apply(lambda x: x['iupac_aa'].symmetric_difference(x['wt_missense']), axis=1)" ] }, { "cell_type": "code", - "execution_count": 203, + "execution_count": 36, "id": "afa9f8d5-429b-4756-9ed6-4b22ea0f4839", "metadata": {}, "outputs": [ { "data": { - "text/html": [ - "
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positioniupac_aawt_codonwt_aawt_missensediff_1diff_2sym_diff
011{S, G, P, V, E, T}GCGA{G, S, P, V, E, T}{}{}{}
112{S, C, D, R, V, A}GGTG{S, C, D, R, V, A}{}{}{}
213{G, N, V, A, E, Y, H}GATD{G, N, V, A, E, Y, H}{}{}{}
314{G, I, L, A, E}GTAV{G, I, L, A, E}{}{}{}
415{K, V, R, L, M, T}ATAI{K, V, R, L, M, T}{}{}{}
516{Q, N, K, R, *, E, M, T}AAGK{Q, N, R, *, E, M, T}{}{K}{K}
617{S, C, D, R, V, A}GGCG{S, C, D, R, V, A}{}{}{}
718{G, S, I, K, *, T}AGAR{G, S, I, K, *, T}{}{}{}
843{G, I, N, C, R, T}AGTS{G, I, N, C, R, T}{}{}{}
944{G, I, D, L, A, F}GTTV{G, I, D, L, A, F}{}{}{}
1045{Q, N, R, *, E, M, T}AAGK{Q, N, R, *, E, M, T}{}{}{}
1146{I, K, V, R, L, T}ATGM{I, K, V, R, L, T}{}{}{}
1247{Q, N, P, D, R, L, Y}CATH{Q, N, P, D, R, L, Y}{}{}{}
1348{I, K, V, R, L, T}ATGM{I, K, V, R, L, T}{}{}{}
1449{G, N, V, A, E, Y, H}GATD{G, N, V, A, E, Y, H}{}{}{}
1550{G, S, I, K, *, T}AGAR{G, S, I, K, *, T}{}{}{}
1651{S, N, C, D, *, F, H}TATY{S, N, C, D, *, F, H}{}{}{}
1771{G, N, V, A, E, Y, H}GATD{G, N, V, A, E, Y, H}{}{}{}
1872{S, N, C, D, F, H}TATY{S, N, C, D, *, F, H}{*}{}{*}
1973{S, I, K, P, R, A}ACAT{S, I, K, P, R, A}{}{}{}
2074{Q, I, N, R, *, E, T}AAAK{Q, I, N, R, *, E, T}{}{}{}
2175{G, V, R, *, A, E}GGAG{V, R, *, A, E}{}{G}{G}
2276{S, N, C, D, *, F, H}TATY{S, N, C, D, *, F, H}{}{}{}
2377{K, V, R, L, M, T}ATAI{K, V, R, L, M, T}{}{}{}
2478{G, N, V, A, E, Y, H}GATD{G, N, V, A, E, Y, H}{}{}{}
2579{G, I, D, L, A, F}GTCV{G, I, D, L, A, F}{}{}{}
2680{S, I, K, D, T, Y, H}AATN{S, I, K, D, T, Y, H}{}{}{}
2781{S, N, C, D, *, F, H}TACY{S, N, C, D, *, F, H}{}{}{}
2882{Q, I, N, R, *, E, T}AAAK{Q, I, N, R, *, E, T}{}{}{}
2983{G, W, S, K, R, M, T}AGGR{G, W, S, K, M, T}{}{R}{R}
3084{I, K, V, R, L, T}ATGM{I, K, V, R, L, T}{}{}{}
3185{G, S, W, R, *, F, Y}TGTC{S, G, W, R, *, F, Y}{}{}{}
3286{G, S, I, K, *, T}AGAR{G, S, I, K, *, T}{}{}{}
3387{Q, N, P, D, R, L, Y}CATH{Q, N, P, D, R, L, Y}{}{}{}
3488{K, P, R, *, L, E, H}CAAQ{K, P, R, *, L, E, H}{}{}{}
\n", - "
" - ], "text/plain": [ - " position iupac_aa wt_codon wt_aa wt_missense \\\n", - "0 11 {S, G, P, V, E, T} GCG A {G, S, P, V, E, T} \n", - "1 12 {S, C, D, R, V, A} GGT G {S, C, D, R, V, A} \n", - "2 13 {G, N, V, A, E, Y, H} GAT D {G, N, V, A, E, Y, H} \n", - "3 14 {G, I, L, A, E} GTA V {G, I, L, A, E} \n", - "4 15 {K, V, R, L, M, T} ATA I {K, V, R, L, M, T} \n", - "5 16 {Q, N, K, R, *, E, M, T} AAG K {Q, N, R, *, E, M, T} \n", - "6 17 {S, C, D, R, V, A} GGC G {S, C, D, R, V, A} \n", - "7 18 {G, S, I, K, *, T} AGA R {G, S, I, K, *, T} \n", - "8 43 {G, I, N, C, R, T} AGT S {G, I, N, C, R, T} \n", - "9 44 {G, I, D, L, A, F} GTT V {G, I, D, L, A, F} \n", - "10 45 {Q, N, R, *, E, M, T} AAG K {Q, N, R, *, E, M, T} \n", - "11 46 {I, K, V, R, L, T} ATG M {I, K, V, R, L, T} \n", - "12 47 {Q, N, P, D, R, L, Y} CAT H {Q, N, P, D, R, L, Y} \n", - "13 48 {I, K, V, R, L, T} ATG M {I, K, V, R, L, T} \n", - "14 49 {G, N, V, A, E, Y, H} GAT D {G, N, V, A, E, Y, H} \n", - "15 50 {G, S, I, K, *, T} AGA R {G, S, I, K, *, T} \n", - "16 51 {S, N, C, D, *, F, H} TAT Y {S, N, C, D, *, F, H} \n", - "17 71 {G, N, V, A, E, Y, H} GAT D {G, N, V, A, E, Y, H} \n", - "18 72 {S, N, C, D, F, H} TAT Y {S, N, C, D, *, F, H} \n", - "19 73 {S, I, K, P, R, A} ACA T {S, I, K, P, R, A} \n", - "20 74 {Q, I, N, R, *, E, T} AAA K {Q, I, N, R, *, E, T} \n", - "21 75 {G, V, R, *, A, E} GGA G {V, R, *, A, E} \n", - "22 76 {S, N, C, D, *, F, H} TAT Y {S, N, C, D, *, F, H} \n", - "23 77 {K, V, R, L, M, T} ATA I {K, V, R, L, M, T} \n", - "24 78 {G, N, V, A, E, Y, H} GAT D {G, N, V, A, E, Y, H} \n", - "25 79 {G, I, D, L, A, F} GTC V {G, I, D, L, A, F} \n", - "26 80 {S, I, K, D, T, Y, H} AAT N {S, I, K, D, T, Y, H} \n", - "27 81 {S, N, C, D, *, F, H} TAC Y {S, N, C, D, *, F, H} \n", - "28 82 {Q, I, N, R, *, E, T} AAA K {Q, I, N, R, *, E, T} \n", - "29 83 {G, W, S, K, R, M, T} AGG R {G, W, S, K, M, T} \n", - "30 84 {I, K, V, R, L, T} ATG M {I, K, V, R, L, T} \n", - "31 85 {G, S, W, R, *, F, Y} TGT C {S, G, W, R, *, F, Y} \n", - "32 86 {G, S, I, K, *, T} AGA R {G, S, I, K, *, T} \n", - "33 87 {Q, N, P, D, R, L, Y} CAT H {Q, N, P, D, R, L, Y} \n", - "34 88 {K, P, R, *, L, E, H} CAA Q {K, P, R, *, L, E, H} \n", - "\n", - " diff_1 diff_2 sym_diff \n", - "0 {} {} {} \n", - "1 {} {} {} \n", - "2 {} {} {} \n", - "3 {} {} {} \n", - "4 {} {} {} \n", - "5 {} {K} {K} \n", - "6 {} {} {} \n", - "7 {} {} {} \n", - "8 {} {} {} \n", - "9 {} {} {} \n", - "10 {} {} {} \n", - "11 {} {} {} \n", - "12 {} {} {} \n", - "13 {} {} {} \n", - "14 {} {} {} \n", - "15 {} {} {} \n", - "16 {} {} {} \n", - "17 {} {} {} \n", - "18 {*} {} {*} \n", - "19 {} {} {} \n", - "20 {} {} {} \n", - "21 {} {G} {G} \n", - "22 {} {} {} \n", - "23 {} {} {} \n", - "24 {} {} {} \n", - "25 {} {} {} \n", - "26 {} {} {} \n", - "27 {} {} {} \n", - "28 {} {} {} \n", - "29 {} {R} {R} \n", - "30 {} {} {} \n", - "31 {} {} {} \n", - "32 {} {} {} \n", - "33 {} {} {} \n", - "34 {} {} {} " + "0" ] }, - "execution_count": 203, + "execution_count": 36, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "df1" + "def check_sym_diff(row):\n", + " sym_set = row['sym_diff']\n", + " wt_aa = str(row['wt_aa'])\n", + " for i in sym_set:\n", + " if i not in [\"*\", wt_aa]:\n", + " return True\n", + " else:\n", + " return False\n", + " \n", + " \n", + "df1['check_sym'] = df1.apply(check_sym_diff, axis=1)\n", + "df1.check_sym.sum()" ] }, { diff --git a/k3l_test.fa b/k3l_test.fa index 1ac70b6..b892154 100644 --- a/k3l_test.fa +++ b/k3l_test.fa @@ -16,28 +16,30 @@ TTTGTTATTCGTTGCCCAATgcwggwGAAgtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAATgcwggwgayWTAatwaarGGCAGAGTATACGAGAAGGATT >window_1-1_GTA14GVA TTTGTTATTCGTTGCCCAATgcwggwgayGVAatwaarGGCAGAGTATACGAGAAGGATT +>window_1-1_GTA14GTT +TTTGTTATTCGTTGCCCAATgcwggwgayGTTatwaarGGCAGAGTATACGAGAAGGATT >window_1-1_ATA15KTA TTTGTTATTCGTTGCCCAATgcwggwgaygtwKTAaarGGCAGAGTATACGAGAAGGATT >window_1-1_ATA15AVA TTTGTTATTCGTTGCCCAATgcwggwgaygtwAVAaarGGCAGAGTATACGAGAAGGATT >window_1-1_ATA15ATG TTTGTTATTCGTTGCCCAATgcwggwgaygtwATGaarGGCAGAGTATACGAGAAGGATT ->window_1-1_AAG16BAG -TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwBAGGGCAGAGTATACGAGAAGGATT +>window_1-1_AAG16SAG +TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwSAGGGCAGAGTATACGAGAAGGATT >window_1-1_AAG16ABG TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwABGGGCAGAGTATACGAGAAGGATT ->window_1-1_AAG16AAW -TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwAAWGGCAGAGTATACGAGAAGGATT +>window_1-1_AAG16AAT +TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwAATGGCAGAGTATACGAGAAGGATT >window_1-2_GGC17HGC ATGCGGGTGATGTAATAAAGHGCagrGTATACGAGAAGGATTATGCTCTATAT >window_1-2_GGC17GHC ATGCGGGTGATGTAATAAAGGHCagrGTATACGAGAAGGATTATGCTCTATAT ->window_1-2_AGA18KGA -ATGCGGGTGATGTAATAAAGggwKGAGTATACGAGAAGGATTATGCTCTATAT +>window_1-2_AGA18GGA +ATGCGGGTGATGTAATAAAGggwGGAGTATACGAGAAGGATTATGCTCTATAT >window_1-2_AGA18AHA ATGCGGGTGATGTAATAAAGggwAHAGTATACGAGAAGGATTATGCTCTATAT ->window_1-2_AGA18AGT -ATGCGGGTGATGTAATAAAGggwAGTGTATACGAGAAGGATTATGCTCTATAT +>window_1-2_AGA18AGK +ATGCGGGTGATGTAATAAAGggwAGKGTATACGAGAAGGATTATGCTCTATAT >window_2-1_AGT43KGT TTGAAGCTATCTTGGCAGAGKGTgtwaaratgCATATGGATAGATATGTTGAATATAGGGA >window_2-1_AGT43AHT @@ -48,8 +50,8 @@ TTGAAGCTATCTTGGCAGAGAGAgtwaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAGtcwHTTaaratgCATATGGATAGATATGTTGAATATAGGGA >window_2-1_GTT44GVT TTGAAGCTATCTTGGCAGAGtcwGVTaaratgCATATGGATAGATATGTTGAATATAGGGA ->window_2-1_AAG45BAG -TTGAAGCTATCTTGGCAGAGtcwgtwBAGatgCATATGGATAGATATGTTGAATATAGGGA +>window_2-1_AAG45SAG +TTGAAGCTATCTTGGCAGAGtcwgtwSAGatgCATATGGATAGATATGTTGAATATAGGGA >window_2-1_AAG45ABG TTGAAGCTATCTTGGCAGAGtcwgtwABGatgCATATGGATAGATATGTTGAATATAGGGA >window_2-1_AAG45AAT @@ -64,8 +66,8 @@ TTGAAGCTATCTTGGCAGAGtcwgtwaarATTCATATGGATAGATATGTTGAATATAGGGA TGGCAGAGAGTGTTAAGATGDATatggayagrtayGTTGAATATAGGGATAAACTGGTAG >window_2-2_CAT47CBT TGGCAGAGAGTGTTAAGATGCBTatggayagrtayGTTGAATATAGGGATAAACTGGTAG ->window_2-2_CAT47CAA -TGGCAGAGAGTGTTAAGATGCAAatggayagrtayGTTGAATATAGGGATAAACTGGTAG +>window_2-2_CAT47CAM +TGGCAGAGAGTGTTAAGATGCAMatggayagrtayGTTGAATATAGGGATAAACTGGTAG >window_2-2_ATG48KTG TGGCAGAGAGTGTTAAGATGcayKTGgayagrtayGTTGAATATAGGGATAAACTGGTAG >window_2-2_ATG48AVG @@ -88,8 +90,6 @@ TGGCAGAGAGTGTTAAGATGcayatggayAGTtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATGcayatggayagrVATGTTGAATATAGGGATAAACTGGTAG >window_2-2_TAT51TBT TGGCAGAGAGTGTTAAGATGcayatggayagrTBTGTTGAATATAGGGATAAACTGGTAG ->window_2-2_TAT51TAA -TGGCAGAGAGTGTTAAGATGcayatggayagrTAAGTTGAATATAGGGATAAACTGGTAG >window_3-1_GAT71HAT AAGTTAAAGTGATTAGAGTTHATtayacwaarGGATATATAGATGTCAATTACAAAAGGATG >window_3-1_GAT71GBT @@ -104,24 +104,20 @@ AAGTTAAAGTGATTAGAGTTgayTBTacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTTgaytayBCAaarGGATATATAGATGTCAATTACAAAAGGATG >window_3-1_ACA73ADA AAGTTAAAGTGATTAGAGTTgaytayADAaarGGATATATAGATGTCAATTACAAAAGGATG ->window_3-1_AAA74BAA -AAGTTAAAGTGATTAGAGTTgaytayacwBAAGGATATATAGATGTCAATTACAAAAGGATG +>window_3-1_AAA74SAA +AAGTTAAAGTGATTAGAGTTgaytayacwSAAGGATATATAGATGTCAATTACAAAAGGATG >window_3-1_AAA74ABA AAGTTAAAGTGATTAGAGTTgaytayacwABAGGATATATAGATGTCAATTACAAAAGGATG >window_3-1_AAA74AAT AAGTTAAAGTGATTAGAGTTgaytayacwAATGGATATATAGATGTCAATTACAAAAGGATG ->window_3-2_GGA75WGA -TTAGAGTTGATTATACAAAAWGAtayatwgaygtwAATTACAAAAGGATGTGTAGACATC +>window_3-2_GGA75AGA +TTAGAGTTGATTATACAAAAAGAtayatwgaygtwAATTACAAAAGGATGTGTAGACATC >window_3-2_GGA75GHA TTAGAGTTGATTATACAAAAGHAtayatwgaygtwAATTACAAAAGGATGTGTAGACATC ->window_3-2_GGA75GGT -TTAGAGTTGATTATACAAAAGGTtayatwgaygtwAATTACAAAAGGATGTGTAGACATC >window_3-2_TAT76VAT TTAGAGTTGATTATACAAAAggwVATatwgaygtwAATTACAAAAGGATGTGTAGACATC >window_3-2_TAT76TBT TTAGAGTTGATTATACAAAAggwTBTatwgaygtwAATTACAAAAGGATGTGTAGACATC ->window_3-2_TAT76TAA -TTAGAGTTGATTATACAAAAggwTAAatwgaygtwAATTACAAAAGGATGTGTAGACATC >window_3-2_ATA77KTA TTAGAGTTGATTATACAAAAggwtayKTAgaygtwAATTACAAAAGGATGTGTAGACATC >window_3-2_ATA77AVA @@ -150,8 +146,8 @@ CAAAAGGATATATAGATGTCaayVACaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTCaayTBCaaragratgtgyAGACATCAATAGTAGCTGTCGA >window_3-3_TAC81TAA CAAAAGGATATATAGATGTCaayTAAaaragratgtgyAGACATCAATAGTAGCTGTCGA ->window_3-3_AAA82BAA -CAAAAGGATATATAGATGTCaaytayBAAagratgtgyAGACATCAATAGTAGCTGTCGA +>window_3-3_AAA82SAA +CAAAAGGATATATAGATGTCaaytaySAAagratgtgyAGACATCAATAGTAGCTGTCGA >window_3-3_AAA82ABA CAAAAGGATATATAGATGTCaaytayABAagratgtgyAGACATCAATAGTAGCTGTCGA >window_3-3_AAA82AAT @@ -160,8 +156,8 @@ CAAAAGGATATATAGATGTCaaytayAATagratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTCaaytayaarKGGatgtgyAGACATCAATAGTAGCTGTCGA >window_3-3_AGG83AHG CAAAAGGATATATAGATGTCaaytayaarAHGatgtgyAGACATCAATAGTAGCTGTCGA ->window_3-3_AGG83AGW -CAAAAGGATATATAGATGTCaaytayaarAGWatgtgyAGACATCAATAGTAGCTGTCGA +>window_3-3_AGG83AGT +CAAAAGGATATATAGATGTCaaytayaarAGTatgtgyAGACATCAATAGTAGCTGTCGA >window_3-3_ATG84KTG CAAAAGGATATATAGATGTCaaytayaaragrKTGtgyAGACATCAATAGTAGCTGTCGA >window_3-3_ATG84AVG @@ -172,10 +168,10 @@ CAAAAGGATATATAGATGTCaaytayaaragrATTtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTCaaytayaaragratgSGTAGACATCAATAGTAGCTGTCGA >window_3-3_TGT85THT CAAAAGGATATATAGATGTCaaytayaaragratgTHTAGACATCAATAGTAGCTGTCGA ->window_3-3_TGT85TGR -CAAAAGGATATATAGATGTCaaytayaaragratgTGRAGACATCAATAGTAGCTGTCGA ->window_3-4_AGA86KGA -TCAATTACAAAAGGATGTGTKGAcaycarTAGTAGCTGTCGAGTCGC +>window_3-3_TGT85TGG +CAAAAGGATATATAGATGTCaaytayaaragratgTGGAGACATCAATAGTAGCTGTCGA +>window_3-4_AGA86GGA +TCAATTACAAAAGGATGTGTGGAcaycarTAGTAGCTGTCGAGTCGC >window_3-4_AGA86AHA TCAATTACAAAAGGATGTGTAHAcaycarTAGTAGCTGTCGAGTCGC >window_3-4_AGA86AGT @@ -186,9 +182,9 @@ TCAATTACAAAAGGATGTGTagrDATcarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGTagrCBTcarTAGTAGCTGTCGAGTCGC >window_3-4_CAT87CAA TCAATTACAAAAGGATGTGTagrCAAcarTAGTAGCTGTCGAGTCGC ->window_3-4_CAA88DAA -TCAATTACAAAAGGATGTGTagrcayDAATAGTAGCTGTCGAGTCGC +>window_3-4_CAA88RAA +TCAATTACAAAAGGATGTGTagrcayRAATAGTAGCTGTCGAGTCGC >window_3-4_CAA88CBA TCAATTACAAAAGGATGTGTagrcayCBATAGTAGCTGTCGAGTCGC ->window_3-4_CAA88CAT -TCAATTACAAAAGGATGTGTagrcayCATTAGTAGCTGTCGAGTCGC +>window_3-4_CAA88CAK +TCAATTACAAAAGGATGTGTagrcayCAKTAGTAGCTGTCGAGTCGC diff --git a/k3l_test.tsv b/k3l_test.tsv index 0513709..57043b4 100644 --- a/k3l_test.tsv +++ b/k3l_test.tsv @@ -1,98 +1,96 @@ -name sub_window_name wt position iupac codon_sub iupac_aa synonymous_codons no_stop_codons primer homology_arm sub_window forward_primer forward_primer_tm forward_primer_gc forward_primer_len reverse_primer_name reverse_primer reverse_primer_tm reverse_primer_gc reverse_primer_len -window_1-1_GCG11HCG window_1-1 GCG 11 HCG GCG11HCG TPS 0.0 0.0 TTTGTTATTCGTTGCCCAATHCGggwgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT HCGggwgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_GCG11GDG window_1-1 GCG 11 GDG GCG11GDG EGV 0.0 0.0 TTTGTTATTCGTTGCCCAATGDGggwgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT GDGggwgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_GGT12HGT window_1-1 GGT 12 HGT GGT12HGT SRC 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwHGTgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwHGTgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_GGT12GHT window_1-1 GGT 12 GHT GGT12GHT DAV 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwGHTgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwGHTgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_GAT13HAT window_1-1 GAT 13 HAT GAT13HAT NHY 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwHATgtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwHATgtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_GAT13GBT window_1-1 GAT 13 GBT GAT13GBT AGV 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwGBTgtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwGBTgtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_GAT13GAA window_1-1 GAT 13 GAA GAT13GAA E 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwGAAgtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwGAAgtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_GTA14WTA window_1-1 GTA 14 WTA GTA14WTA IL 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgayWTAatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgayWTAatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_GTA14GVA window_1-1 GTA 14 GVA GTA14GVA EAG 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgayGVAatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgayGVAatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_ATA15KTA window_1-1 ATA 15 KTA ATA15KTA VL 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwKTAaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwKTAaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_ATA15AVA window_1-1 ATA 15 AVA ATA15AVA KTR 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwAVAaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwAVAaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_ATA15ATG window_1-1 ATA 15 ATG ATA15ATG M 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwATGaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwATGaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_AAG16BAG window_1-1 AAG 16 BAG AAG16BAG QE* 1.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwBAGGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwatwBAG GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_AAG16ABG window_1-1 AAG 16 ABG AAG16ABG TRM 1.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwABGGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwatwABG GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-1_AAG16AAW window_1-1 AAG 16 AAW AAG16AAW KN 1.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwAAWGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwatwAAW GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 -window_1-2_GGC17HGC window_1-2 GGC 17 HGC GGC17HGC SRC 0.0 0.0 ATGCGGGTGATGTAATAAAGHGCagrGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG HGCagr GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 -window_1-2_GGC17GHC window_1-2 GGC 17 GHC GGC17GHC DAV 0.0 0.0 ATGCGGGTGATGTAATAAAGGHCagrGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG GHCagr GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 -window_1-2_AGA18KGA window_1-2 AGA 18 KGA AGA18KGA G* 0.0 0.0 ATGCGGGTGATGTAATAAAGggwKGAGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG ggwKGA GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 -window_1-2_AGA18AHA window_1-2 AGA 18 AHA AGA18AHA KTI 0.0 0.0 ATGCGGGTGATGTAATAAAGggwAHAGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG ggwAHA GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 -window_1-2_AGA18AGT window_1-2 AGA 18 AGT AGA18AGT S 0.0 0.0 ATGCGGGTGATGTAATAAAGggwAGTGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG ggwAGT GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 -window_2-1_AGT43KGT window_2-1 AGT 43 KGT AGT43KGT GC 0.0 0.0 TTGAAGCTATCTTGGCAGAGKGTgtwaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG KGTgtwaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 -window_2-1_AGT43AHT window_2-1 AGT 43 AHT AGT43AHT NTI 0.0 0.0 TTGAAGCTATCTTGGCAGAGAHTgtwaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG AHTgtwaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 -window_2-1_AGT43AGA window_2-1 AGT 43 AGA AGT43AGA R 0.0 0.0 TTGAAGCTATCTTGGCAGAGAGAgtwaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG AGAgtwaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 -window_2-1_GTT44HTT window_2-1 GTT 44 HTT GTT44HTT ILF 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwHTTaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwHTTaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 -window_2-1_GTT44GVT window_2-1 GTT 44 GVT GTT44GVT DAG 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwGVTaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwGVTaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 -window_2-1_AAG45BAG window_2-1 AAG 45 BAG AAG45BAG QE* 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwBAGatgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwBAGatg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 -window_2-1_AAG45ABG window_2-1 AAG 45 ABG AAG45ABG TRM 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwABGatgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwABGatg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 -window_2-1_AAG45AAT window_2-1 AAG 45 AAT AAG45AAT N 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwAATatgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwAATatg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 -window_2-1_ATG46KTG window_2-1 ATG 46 KTG ATG46KTG VL 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwaarKTGCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwaarKTG CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 -window_2-1_ATG46AVG window_2-1 ATG 46 AVG ATG46AVG KTR 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwaarAVGCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwaarAVG CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 -window_2-1_ATG46ATT window_2-1 ATG 46 ATT ATG46ATT I 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwaarATTCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwaarATT CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 -window_2-2_CAT47DAT window_2-2 CAT 47 DAT CAT47DAT NDY 0.0 0.0 TGGCAGAGAGTGTTAAGATGDATatggayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG DATatggayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_CAT47CBT window_2-2 CAT 47 CBT CAT47CBT PRL 0.0 0.0 TGGCAGAGAGTGTTAAGATGCBTatggayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG CBTatggayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_CAT47CAA window_2-2 CAT 47 CAA CAT47CAA Q 0.0 0.0 TGGCAGAGAGTGTTAAGATGCAAatggayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG CAAatggayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_ATG48KTG window_2-2 ATG 48 KTG ATG48KTG VL 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayKTGgayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayKTGgayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_ATG48AVG window_2-2 ATG 48 AVG ATG48AVG KTR 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayAVGgayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayAVGgayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_ATG48ATT window_2-2 ATG 48 ATT ATG48ATT I 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayATTgayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayATTgayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_GAT49HAT window_2-2 GAT 49 HAT GAT49HAT NHY 0.0 1.0 TGGCAGAGAGTGTTAAGATGcayatgHATagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatgHATagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_GAT49GBT window_2-2 GAT 49 GBT GAT49GBT AGV 0.0 1.0 TGGCAGAGAGTGTTAAGATGcayatgGBTagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatgGBTagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_GAT49GAA window_2-2 GAT 49 GAA GAT49GAA E 0.0 1.0 TGGCAGAGAGTGTTAAGATGcayatgGAAagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatgGAAagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_AGA50KGA window_2-2 AGA 50 KGA AGA50KGA G* 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatggayKGAtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayKGAtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_AGA50AHA window_2-2 AGA 50 AHA AGA50AHA KTI 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatggayAHAtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayAHAtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_AGA50AGT window_2-2 AGA 50 AGT AGA50AGT S 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatggayAGTtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayAGTtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_TAT51VAT window_2-2 TAT 51 VAT TAT51VAT NHD 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatggayagrVATGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayagrVAT GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_TAT51TBT window_2-2 TAT 51 TBT TAT51TBT SCF 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatggayagrTBTGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayagrTBT GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_2-2_TAT51TAA window_2-2 TAT 51 TAA TAT51TAA * 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatggayagrTAAGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayagrTAA GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 -window_3-1_GAT71HAT window_3-1 GAT 71 HAT GAT71HAT NHY 0.0 0.0 AAGTTAAAGTGATTAGAGTTHATtayacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT HATtayacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 -window_3-1_GAT71GBT window_3-1 GAT 71 GBT GAT71GBT AGV 0.0 0.0 AAGTTAAAGTGATTAGAGTTGBTtayacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT GBTtayacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 -window_3-1_GAT71GAA window_3-1 GAT 71 GAA GAT71GAA E 0.0 0.0 AAGTTAAAGTGATTAGAGTTGAAtayacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT GAAtayacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 -window_3-1_TAT72VAT window_3-1 TAT 72 VAT TAT72VAT NHD 0.0 1.0 AAGTTAAAGTGATTAGAGTTgayVATacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gayVATacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 -window_3-1_TAT72TBT window_3-1 TAT 72 TBT TAT72TBT SCF 0.0 1.0 AAGTTAAAGTGATTAGAGTTgayTBTacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gayTBTacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 -window_3-1_ACA73BCA window_3-1 ACA 73 BCA ACA73BCA PAS 0.0 0.0 AAGTTAAAGTGATTAGAGTTgaytayBCAaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayBCAaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 -window_3-1_ACA73ADA window_3-1 ACA 73 ADA ACA73ADA KRI 0.0 0.0 AAGTTAAAGTGATTAGAGTTgaytayADAaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayADAaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 -window_3-1_AAA74BAA window_3-1 AAA 74 BAA AAA74BAA QE* 0.0 0.0 AAGTTAAAGTGATTAGAGTTgaytayacwBAAGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayacwBAA GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 -window_3-1_AAA74ABA window_3-1 AAA 74 ABA AAA74ABA TRI 0.0 0.0 AAGTTAAAGTGATTAGAGTTgaytayacwABAGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayacwABA GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 -window_3-1_AAA74AAT window_3-1 AAA 74 AAT AAA74AAT N 0.0 0.0 AAGTTAAAGTGATTAGAGTTgaytayacwAATGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayacwAAT GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 -window_3-2_GGA75WGA window_3-2 GGA 75 WGA GGA75WGA R* 1.0 0.0 TTAGAGTTGATTATACAAAAWGAtayatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA WGAtayatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_GGA75GHA window_3-2 GGA 75 GHA GGA75GHA EAV 1.0 0.0 TTAGAGTTGATTATACAAAAGHAtayatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA GHAtayatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_GGA75GGT window_3-2 GGA 75 GGT GGA75GGT G 1.0 0.0 TTAGAGTTGATTATACAAAAGGTtayatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA GGTtayatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_TAT76VAT window_3-2 TAT 76 VAT TAT76VAT NHD 0.0 0.0 TTAGAGTTGATTATACAAAAggwVATatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwVATatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_TAT76TBT window_3-2 TAT 76 TBT TAT76TBT SCF 0.0 0.0 TTAGAGTTGATTATACAAAAggwTBTatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwTBTatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_TAT76TAA window_3-2 TAT 76 TAA TAT76TAA * 0.0 0.0 TTAGAGTTGATTATACAAAAggwTAAatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwTAAatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_ATA77KTA window_3-2 ATA 77 KTA ATA77KTA VL 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayKTAgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayKTAgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_ATA77AVA window_3-2 ATA 77 AVA ATA77AVA KTR 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayAVAgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayAVAgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_ATA77ATG window_3-2 ATA 77 ATG ATA77ATG M 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayATGgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayATGgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_GAT78HAT window_3-2 GAT 78 HAT GAT78HAT NHY 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwHATgtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwHATgtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_GAT78GBT window_3-2 GAT 78 GBT GAT78GBT AGV 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwGBTgtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwGBTgtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_GAT78GAA window_3-2 GAT 78 GAA GAT78GAA E 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwGAAgtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwGAAgtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_GTC79HTC window_3-2 GTC 79 HTC GTC79HTC ILF 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwgayHTCAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwgayHTC AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-2_GTC79GVC window_3-2 GTC 79 GVC GTC79GVC DAG 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwgayGVCAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwgayGVC AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 -window_3-3_AAT80BAT window_3-3 AAT 80 BAT AAT80BAT HDY 0.0 0.0 CAAAAGGATATATAGATGTCBATtayaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC BATtayaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_AAT80ABT window_3-3 AAT 80 ABT AAT80ABT TSI 0.0 0.0 CAAAAGGATATATAGATGTCABTtayaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC ABTtayaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_AAT80AAA window_3-3 AAT 80 AAA AAT80AAA K 0.0 0.0 CAAAAGGATATATAGATGTCAAAtayaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC AAAtayaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_TAC81VAC window_3-3 TAC 81 VAC TAC81VAC NHD 0.0 0.0 CAAAAGGATATATAGATGTCaayVACaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aayVACaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_TAC81TBC window_3-3 TAC 81 TBC TAC81TBC SCF 0.0 0.0 CAAAAGGATATATAGATGTCaayTBCaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aayTBCaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_TAC81TAA window_3-3 TAC 81 TAA TAC81TAA * 0.0 0.0 CAAAAGGATATATAGATGTCaayTAAaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aayTAAaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_AAA82BAA window_3-3 AAA 82 BAA AAA82BAA QE* 0.0 0.0 CAAAAGGATATATAGATGTCaaytayBAAagratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayBAAagratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_AAA82ABA window_3-3 AAA 82 ABA AAA82ABA TRI 0.0 0.0 CAAAAGGATATATAGATGTCaaytayABAagratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayABAagratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_AAA82AAT window_3-3 AAA 82 AAT AAA82AAT N 0.0 0.0 CAAAAGGATATATAGATGTCaaytayAATagratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayAATagratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_AGG83KGG window_3-3 AGG 83 KGG AGG83KGG GW 1.0 0.0 CAAAAGGATATATAGATGTCaaytayaarKGGatgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaarKGGatgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_AGG83AHG window_3-3 AGG 83 AHG AGG83AHG KTM 1.0 0.0 CAAAAGGATATATAGATGTCaaytayaarAHGatgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaarAHGatgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_AGG83AGW window_3-3 AGG 83 AGW AGG83AGW RS 1.0 0.0 CAAAAGGATATATAGATGTCaaytayaarAGWatgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaarAGWatgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_ATG84KTG window_3-3 ATG 84 KTG ATG84KTG VL 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragrKTGtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragrKTGtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_ATG84AVG window_3-3 ATG 84 AVG ATG84AVG KTR 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragrAVGtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragrAVGtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_ATG84ATT window_3-3 ATG 84 ATT ATG84ATT I 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragrATTtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragrATTtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_TGT85SGT window_3-3 TGT 85 SGT TGT85SGT RG 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragratgSGTAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragratgSGT AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_TGT85THT window_3-3 TGT 85 THT TGT85THT YSF 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragratgTHTAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragratgTHT AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-3_TGT85TGR window_3-3 TGT 85 TGR TGT85TGR *W 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragratgTGRAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragratgTGR AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 -window_3-4_AGA86KGA window_3-4 AGA 86 KGA AGA86KGA G* 0.0 0.0 TCAATTACAAAAGGATGTGTKGAcaycarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT KGAcaycar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 -window_3-4_AGA86AHA window_3-4 AGA 86 AHA AGA86AHA KTI 0.0 0.0 TCAATTACAAAAGGATGTGTAHAcaycarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT AHAcaycar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 -window_3-4_AGA86AGT window_3-4 AGA 86 AGT AGA86AGT S 0.0 0.0 TCAATTACAAAAGGATGTGTAGTcaycarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT AGTcaycar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 -window_3-4_CAT87DAT window_3-4 CAT 87 DAT CAT87DAT NDY 0.0 0.0 TCAATTACAAAAGGATGTGTagrDATcarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrDATcar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 -window_3-4_CAT87CBT window_3-4 CAT 87 CBT CAT87CBT PRL 0.0 0.0 TCAATTACAAAAGGATGTGTagrCBTcarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrCBTcar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 -window_3-4_CAT87CAA window_3-4 CAT 87 CAA CAT87CAA Q 0.0 0.0 TCAATTACAAAAGGATGTGTagrCAAcarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrCAAcar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 -window_3-4_CAA88DAA window_3-4 CAA 88 DAA CAA88DAA KE* 0.0 0.0 TCAATTACAAAAGGATGTGTagrcayDAATAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrcayDAA TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 -window_3-4_CAA88CBA window_3-4 CAA 88 CBA CAA88CBA PRL 0.0 0.0 TCAATTACAAAAGGATGTGTagrcayCBATAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrcayCBA TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 -window_3-4_CAA88CAT window_3-4 CAA 88 CAT CAA88CAT H 0.0 0.0 TCAATTACAAAAGGATGTGTagrcayCATTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrcayCAT TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +name sub_window_name wt_codon position iupac_codon codon_sub iupac_aa add_synonymous_codon contains_missense_stop remove_missense_stop_codon primer homology_arm sub_window forward_primer forward_primer_tm forward_primer_gc forward_primer_len reverse_primer_name reverse_primer reverse_primer_tm reverse_primer_gc reverse_primer_len +window_1-1_GCG11HCG window_1-1 GCG 11 HCG GCG11HCG TPS 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATHCGggwgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT HCGggwgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GCG11GDG window_1-1 GCG 11 GDG GCG11GDG EGV 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATGDGggwgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT GDGggwgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GGT12HGT window_1-1 GGT 12 HGT GGT12HGT SRC 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwHGTgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwHGTgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GGT12GHT window_1-1 GGT 12 GHT GGT12GHT DAV 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwGHTgaygtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwGHTgaygtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GAT13HAT window_1-1 GAT 13 HAT GAT13HAT NHY 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwHATgtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwHATgtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GAT13GBT window_1-1 GAT 13 GBT GAT13GBT AGV 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwGBTgtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwGBTgtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GAT13GAA window_1-1 GAT 13 GAA GAT13GAA E 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwGAAgtwatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwGAAgtwatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GTA14WTA window_1-1 GTA 14 WTA GTA14WTA IL 1.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgayWTAatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgayWTAatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GTA14GVA window_1-1 GTA 14 GVA GTA14GVA EAG 1.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgayGVAatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgayGVAatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_GTA14GTT window_1-1 GTA 14 GTT GTA14GTT V 1.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgayGTTatwaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgayGTTatwaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_ATA15KTA window_1-1 ATA 15 KTA ATA15KTA VL 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwKTAaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwKTAaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_ATA15AVA window_1-1 ATA 15 AVA ATA15AVA KTR 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwAVAaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwAVAaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_ATA15ATG window_1-1 ATA 15 ATG ATA15ATG M 0.0 0.0 0.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwATGaarGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwATGaar GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_AAG16SAG window_1-1 AAG 16 SAG AAG16SAG QE 0.0 1.0 1.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwSAGGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwatwSAG GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_AAG16ABG window_1-1 AAG 16 ABG AAG16ABG TRM 0.0 1.0 1.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwABGGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwatwABG GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-1_AAG16AAT window_1-1 AAG 16 AAT AAG16AAT N 0.0 1.0 1.0 TTTGTTATTCGTTGCCCAATgcwggwgaygtwatwAATGGCAGAGTATACGAGAAGGATT TTTGTTATTCGTTGCCCAAT gcwggwgaygtwatwAAT GGCAGAGTATACGAGAAGGATT 51.3 45.5 22 rev_window_1-1 ATTGGGCAACGAATAACAAAATGCA 55.1 36.0 25 +window_1-2_GGC17HGC window_1-2 GGC 17 HGC GGC17HGC SRC 0.0 0.0 0.0 ATGCGGGTGATGTAATAAAGHGCagrGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG HGCagr GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 +window_1-2_GGC17GHC window_1-2 GGC 17 GHC GGC17GHC DAV 0.0 0.0 0.0 ATGCGGGTGATGTAATAAAGGHCagrGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG GHCagr GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 +window_1-2_AGA18GGA window_1-2 AGA 18 GGA AGA18GGA G 1.0 1.0 1.0 ATGCGGGTGATGTAATAAAGggwGGAGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG ggwGGA GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 +window_1-2_AGA18AHA window_1-2 AGA 18 AHA AGA18AHA KTI 1.0 1.0 1.0 ATGCGGGTGATGTAATAAAGggwAHAGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG ggwAHA GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 +window_1-2_AGA18AGK window_1-2 AGA 18 AGK AGA18AGK RS 1.0 1.0 1.0 ATGCGGGTGATGTAATAAAGggwAGKGTATACGAGAAGGATTATGCTCTATAT ATGCGGGTGATGTAATAAAG ggwAGK GTATACGAGAAGGATTATGCTCTATAT 50.1 33.3 27 rev_window_1-2 CTTTATTACATCACCCGCATTGGGC 56.8 48.0 25 +window_2-1_AGT43KGT window_2-1 AGT 43 KGT AGT43KGT GC 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGKGTgtwaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG KGTgtwaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_AGT43AHT window_2-1 AGT 43 AHT AGT43AHT NTI 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGAHTgtwaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG AHTgtwaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_AGT43AGA window_2-1 AGT 43 AGA AGT43AGA R 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGAGAgtwaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG AGAgtwaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_GTT44HTT window_2-1 GTT 44 HTT GTT44HTT ILF 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwHTTaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwHTTaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_GTT44GVT window_2-1 GTT 44 GVT GTT44GVT DAG 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwGVTaaratgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwGVTaaratg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_AAG45SAG window_2-1 AAG 45 SAG AAG45SAG QE 0.0 1.0 1.0 TTGAAGCTATCTTGGCAGAGtcwgtwSAGatgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwSAGatg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_AAG45ABG window_2-1 AAG 45 ABG AAG45ABG TRM 0.0 1.0 1.0 TTGAAGCTATCTTGGCAGAGtcwgtwABGatgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwABGatg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_AAG45AAT window_2-1 AAG 45 AAT AAG45AAT N 0.0 1.0 1.0 TTGAAGCTATCTTGGCAGAGtcwgtwAATatgCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwAATatg CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_ATG46KTG window_2-1 ATG 46 KTG ATG46KTG VL 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwaarKTGCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwaarKTG CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_ATG46AVG window_2-1 ATG 46 AVG ATG46AVG KTR 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwaarAVGCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwaarAVG CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-1_ATG46ATT window_2-1 ATG 46 ATT ATG46ATT I 0.0 0.0 0.0 TTGAAGCTATCTTGGCAGAGtcwgtwaarATTCATATGGATAGATATGTTGAATATAGGGA TTGAAGCTATCTTGGCAGAG tcwgtwaarATT CATATGGATAGATATGTTGAATATAGGGA 50.5 31.0 29 rev_window_2-1 CTCTGCCAAGATAGCTTCAAAGTGA 55.1 44.0 25 +window_2-2_CAT47DAT window_2-2 CAT 47 DAT CAT47DAT NDY 1.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGDATatggayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG DATatggayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_CAT47CBT window_2-2 CAT 47 CBT CAT47CBT PRL 1.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGCBTatggayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG CBTatggayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_CAT47CAM window_2-2 CAT 47 CAM CAT47CAM QH 1.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGCAMatggayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG CAMatggayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_ATG48KTG window_2-2 ATG 48 KTG ATG48KTG VL 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayKTGgayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayKTGgayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_ATG48AVG window_2-2 ATG 48 AVG ATG48AVG KTR 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayAVGgayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayAVGgayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_ATG48ATT window_2-2 ATG 48 ATT ATG48ATT I 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayATTgayagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayATTgayagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_GAT49HAT window_2-2 GAT 49 HAT GAT49HAT NHY 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatgHATagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatgHATagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_GAT49GBT window_2-2 GAT 49 GBT GAT49GBT AGV 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatgGBTagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatgGBTagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_GAT49GAA window_2-2 GAT 49 GAA GAT49GAA E 0.0 0.0 0.0 TGGCAGAGAGTGTTAAGATGcayatgGAAagrtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatgGAAagrtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_AGA50KGA window_2-2 AGA 50 KGA AGA50KGA G* 0.0 1.0 0.0 TGGCAGAGAGTGTTAAGATGcayatggayKGAtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayKGAtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_AGA50AHA window_2-2 AGA 50 AHA AGA50AHA KTI 0.0 1.0 0.0 TGGCAGAGAGTGTTAAGATGcayatggayAHAtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayAHAtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_AGA50AGT window_2-2 AGA 50 AGT AGA50AGT S 0.0 1.0 0.0 TGGCAGAGAGTGTTAAGATGcayatggayAGTtayGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayAGTtay GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_TAT51VAT window_2-2 TAT 51 VAT TAT51VAT NHD 0.0 1.0 1.0 TGGCAGAGAGTGTTAAGATGcayatggayagrVATGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayagrVAT GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_2-2_TAT51TBT window_2-2 TAT 51 TBT TAT51TBT SCF 0.0 1.0 1.0 TGGCAGAGAGTGTTAAGATGcayatggayagrTBTGTTGAATATAGGGATAAACTGGTAG TGGCAGAGAGTGTTAAGATG cayatggayagrTBT GTTGAATATAGGGATAAACTGGTAG 48.9 36.0 25 rev_window_2-2 CATCTTAACACTCTCTGCCAAGATAGC 55.7 44.4 27 +window_3-1_GAT71HAT window_3-1 GAT 71 HAT GAT71HAT NHY 0.0 0.0 0.0 AAGTTAAAGTGATTAGAGTTHATtayacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT HATtayacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_GAT71GBT window_3-1 GAT 71 GBT GAT71GBT AGV 0.0 0.0 0.0 AAGTTAAAGTGATTAGAGTTGBTtayacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT GBTtayacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_GAT71GAA window_3-1 GAT 71 GAA GAT71GAA E 0.0 0.0 0.0 AAGTTAAAGTGATTAGAGTTGAAtayacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT GAAtayacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_TAT72VAT window_3-1 TAT 72 VAT TAT72VAT NHD 0.0 1.0 1.0 AAGTTAAAGTGATTAGAGTTgayVATacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gayVATacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_TAT72TBT window_3-1 TAT 72 TBT TAT72TBT SCF 0.0 1.0 1.0 AAGTTAAAGTGATTAGAGTTgayTBTacwaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gayTBTacwaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_ACA73BCA window_3-1 ACA 73 BCA ACA73BCA PAS 0.0 0.0 0.0 AAGTTAAAGTGATTAGAGTTgaytayBCAaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayBCAaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_ACA73ADA window_3-1 ACA 73 ADA ACA73ADA KRI 0.0 0.0 0.0 AAGTTAAAGTGATTAGAGTTgaytayADAaarGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayADAaar GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_AAA74SAA window_3-1 AAA 74 SAA AAA74SAA QE 0.0 1.0 1.0 AAGTTAAAGTGATTAGAGTTgaytayacwSAAGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayacwSAA GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_AAA74ABA window_3-1 AAA 74 ABA AAA74ABA TRI 0.0 1.0 1.0 AAGTTAAAGTGATTAGAGTTgaytayacwABAGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayacwABA GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-1_AAA74AAT window_3-1 AAA 74 AAT AAA74AAT N 0.0 1.0 1.0 AAGTTAAAGTGATTAGAGTTgaytayacwAATGGATATATAGATGTCAATTACAAAAGGATG AAGTTAAAGTGATTAGAGTT gaytayacwAAT GGATATATAGATGTCAATTACAAAAGGATG 51.1 30.0 30 rev_window_3-1 AACTCTAATCACTTTAACTTTTACAGTTTTCCC 55.1 30.3 33 +window_3-2_GGA75AGA window_3-2 GGA 75 AGA GGA75AGA R 0.0 1.0 1.0 TTAGAGTTGATTATACAAAAAGAtayatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA AGAtayatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GGA75GHA window_3-2 GGA 75 GHA GGA75GHA EAV 0.0 1.0 1.0 TTAGAGTTGATTATACAAAAGHAtayatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA GHAtayatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_TAT76VAT window_3-2 TAT 76 VAT TAT76VAT NHD 0.0 1.0 1.0 TTAGAGTTGATTATACAAAAggwVATatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwVATatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_TAT76TBT window_3-2 TAT 76 TBT TAT76TBT SCF 0.0 1.0 1.0 TTAGAGTTGATTATACAAAAggwTBTatwgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwTBTatwgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_ATA77KTA window_3-2 ATA 77 KTA ATA77KTA VL 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayKTAgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayKTAgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_ATA77AVA window_3-2 ATA 77 AVA ATA77AVA KTR 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayAVAgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayAVAgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_ATA77ATG window_3-2 ATA 77 ATG ATA77ATG M 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayATGgaygtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayATGgaygtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GAT78HAT window_3-2 GAT 78 HAT GAT78HAT NHY 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwHATgtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwHATgtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GAT78GBT window_3-2 GAT 78 GBT GAT78GBT AGV 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwGBTgtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwGBTgtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GAT78GAA window_3-2 GAT 78 GAA GAT78GAA E 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwGAAgtwAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwGAAgtw AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GTC79HTC window_3-2 GTC 79 HTC GTC79HTC ILF 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwgayHTCAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwgayHTC AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-2_GTC79GVC window_3-2 GTC 79 GVC GTC79GVC DAG 0.0 0.0 0.0 TTAGAGTTGATTATACAAAAggwtayatwgayGVCAATTACAAAAGGATGTGTAGACATC TTAGAGTTGATTATACAAAA ggwtayatwgayGVC AATTACAAAAGGATGTGTAGACATC 49.7 32.0 25 rev_window_3-2 TTTTGTATAATCAACTCTAATCACTTTAACTTTTACAGT 55.2 23.1 39 +window_3-3_AAT80BAT window_3-3 AAT 80 BAT AAT80BAT HDY 0.0 0.0 0.0 CAAAAGGATATATAGATGTCBATtayaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC BATtayaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AAT80ABT window_3-3 AAT 80 ABT AAT80ABT TSI 0.0 0.0 0.0 CAAAAGGATATATAGATGTCABTtayaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC ABTtayaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AAT80AAA window_3-3 AAT 80 AAA AAT80AAA K 0.0 0.0 0.0 CAAAAGGATATATAGATGTCAAAtayaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC AAAtayaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_TAC81VAC window_3-3 TAC 81 VAC TAC81VAC NHD 0.0 1.0 0.0 CAAAAGGATATATAGATGTCaayVACaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aayVACaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_TAC81TBC window_3-3 TAC 81 TBC TAC81TBC SCF 0.0 1.0 0.0 CAAAAGGATATATAGATGTCaayTBCaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aayTBCaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_TAC81TAA window_3-3 TAC 81 TAA TAC81TAA * 0.0 1.0 0.0 CAAAAGGATATATAGATGTCaayTAAaaragratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aayTAAaaragratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AAA82SAA window_3-3 AAA 82 SAA AAA82SAA QE 0.0 1.0 1.0 CAAAAGGATATATAGATGTCaaytaySAAagratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytaySAAagratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AAA82ABA window_3-3 AAA 82 ABA AAA82ABA TRI 0.0 1.0 1.0 CAAAAGGATATATAGATGTCaaytayABAagratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayABAagratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AAA82AAT window_3-3 AAA 82 AAT AAA82AAT N 0.0 1.0 1.0 CAAAAGGATATATAGATGTCaaytayAATagratgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayAATagratgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AGG83KGG window_3-3 AGG 83 KGG AGG83KGG GW 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaarKGGatgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaarKGGatgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AGG83AHG window_3-3 AGG 83 AHG AGG83AHG KTM 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaarAHGatgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaarAHGatgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_AGG83AGT window_3-3 AGG 83 AGT AGG83AGT S 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaarAGTatgtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaarAGTatgtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_ATG84KTG window_3-3 ATG 84 KTG ATG84KTG VL 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragrKTGtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragrKTGtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_ATG84AVG window_3-3 ATG 84 AVG ATG84AVG KTR 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragrAVGtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragrAVGtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_ATG84ATT window_3-3 ATG 84 ATT ATG84ATT I 0.0 0.0 0.0 CAAAAGGATATATAGATGTCaaytayaaragrATTtgyAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragrATTtgy AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_TGT85SGT window_3-3 TGT 85 SGT TGT85SGT RG 0.0 1.0 1.0 CAAAAGGATATATAGATGTCaaytayaaragratgSGTAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragratgSGT AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_TGT85THT window_3-3 TGT 85 THT TGT85THT YSF 0.0 1.0 1.0 CAAAAGGATATATAGATGTCaaytayaaragratgTHTAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragratgTHT AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-3_TGT85TGG window_3-3 TGT 85 TGG TGT85TGG W 0.0 1.0 1.0 CAAAAGGATATATAGATGTCaaytayaaragratgTGGAGACATCAATAGTAGCTGTCGA CAAAAGGATATATAGATGTC aaytayaaragratgTGG AGACATCAATAGTAGCTGTCGA 50.6 40.9 22 rev_window_3-3 GACATCTATATATCCTTTTGTATAATCAACTCTAATCACT 55.5 27.5 40 +window_3-4_AGA86GGA window_3-4 AGA 86 GGA AGA86GGA G 0.0 1.0 1.0 TCAATTACAAAAGGATGTGTGGAcaycarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT GGAcaycar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_AGA86AHA window_3-4 AGA 86 AHA AGA86AHA KTI 0.0 1.0 1.0 TCAATTACAAAAGGATGTGTAHAcaycarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT AHAcaycar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_AGA86AGT window_3-4 AGA 86 AGT AGA86AGT S 0.0 1.0 1.0 TCAATTACAAAAGGATGTGTAGTcaycarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT AGTcaycar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAT87DAT window_3-4 CAT 87 DAT CAT87DAT NDY 0.0 0.0 0.0 TCAATTACAAAAGGATGTGTagrDATcarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrDATcar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAT87CBT window_3-4 CAT 87 CBT CAT87CBT PRL 0.0 0.0 0.0 TCAATTACAAAAGGATGTGTagrCBTcarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrCBTcar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAT87CAA window_3-4 CAT 87 CAA CAT87CAA Q 0.0 0.0 0.0 TCAATTACAAAAGGATGTGTagrCAAcarTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrCAAcar TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAA88RAA window_3-4 CAA 88 RAA CAA88RAA KE 1.0 1.0 1.0 TCAATTACAAAAGGATGTGTagrcayRAATAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrcayRAA TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAA88CBA window_3-4 CAA 88 CBA CAA88CBA PRL 1.0 1.0 1.0 TCAATTACAAAAGGATGTGTagrcayCBATAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrcayCBA TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 +window_3-4_CAA88CAK window_3-4 CAA 88 CAK CAA88CAK QH 1.0 1.0 1.0 TCAATTACAAAAGGATGTGTagrcayCAKTAGTAGCTGTCGAGTCGC TCAATTACAAAAGGATGTGT agrcayCAK TAGTAGCTGTCGAGTCGC 50.3 55.6 18 rev_window_3-4 ACACATCCTTTTGTAATTGACATCTATATATCCT 55.0 29.4 34 diff --git a/main.ipynb b/main.ipynb index 09e0254..ca2749c 100644 --- a/main.ipynb +++ b/main.ipynb @@ -31,6 +31,109 @@ "import main_package # my package" ] }, + { + "cell_type": "code", + "execution_count": 2, + "id": "2be52f4e-e187-4013-ae20-b084bd165f33", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "T\n", + "A\n", + "C\n" + ] + } + ], + "source": [ + "wt_codon = 'TAC'\n", + "for i in wt_codon:\n", + " print(i)" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "7710a011-9cd8-44af-a72b-c5baa1143228", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "False" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "a = ['a','b','c','b']\n", + "b = ''.join(set(a))\n", + "'d' in b" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0ac2170a-3ef5-42ca-a46c-3bc175f6d4c9", + "metadata": {}, + "outputs": [], + "source": [ + "Seq('TAC').translate(" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "4f23f732-0734-446c-97bc-a024db373185", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "True" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# need a function to check if wt codon has any stop codons\n", + "def unique_missense_variants(codon, codon_table='Standard'):\n", + " \"\"\"Return all unique AA variants for a given codon\n", + " INPUT: codon (str)\n", + " RETURN: unique AAs (str)\n", + " \"\"\"\n", + " aa = str(Seq(codon).translate(table=codon_table))\n", + " nucs = 'ACTG'\n", + " missense_aa_list = []\n", + " for i in range(len(codon)):\n", + " for n in nucs:\n", + " new_codon = codon[:i] + n + codon[i+1:]\n", + " new_aa = str(Seq(new_codon).translate(table=codon_table))\n", + " if new_aa == aa:\n", + " continue\n", + " else:\n", + " missense_aa_list.append(new_aa)\n", + " return ''.join(set(missense_aa_list))\n", + "\n", + "def contains_stop_missense_variant(codon, codon_table='Standard'):\n", + " \"\"\"Check if codon contains a stop missense variant\n", + " INPUT: codon (str)\n", + " RETURN: boolean (bool)\"\"\"\n", + " missense_aa = unique_missense_variants(codon, codon_table=codon_table)\n", + " return \"*\" in missense_aa\n", + "\n", + "codon = 'TAC'\n", + "contains_stop_missense_variant(codon)" + ] + }, { "cell_type": "code", "execution_count": 2, diff --git a/main_package/__pycache__/codon_table.cpython-39.pyc b/main_package/__pycache__/codon_table.cpython-39.pyc index bba7c0b..4ed8f1b 100644 Binary files a/main_package/__pycache__/codon_table.cpython-39.pyc and b/main_package/__pycache__/codon_table.cpython-39.pyc differ diff --git a/main_package/__pycache__/primer_design.cpython-39.pyc b/main_package/__pycache__/primer_design.cpython-39.pyc index 0b632f9..e6523d6 100644 Binary files a/main_package/__pycache__/primer_design.cpython-39.pyc and b/main_package/__pycache__/primer_design.cpython-39.pyc differ diff --git a/main_package/codon_table.py b/main_package/codon_table.py index 931fc96..072cbe6 100644 --- a/main_package/codon_table.py +++ b/main_package/codon_table.py @@ -8,6 +8,32 @@ iupac_dict = {'A':'A','C':'C','G':'G','T':'T','AC':'M','AG':'R','AT':'W','CG':'S','CT':'Y','GT':'K','ACG':'V','ACT':'H','AGT':'D','CGT':'B','ACGT':'N'} rev_iupac_dict = {value:key for key,value in iupac_dict.items()} +def unique_missense_variants(codon, codon_table='Standard'): + """Return all unique AA variants for a given codon + INPUT: codon (str) + RETURN: unique AAs (str) + """ + aa = str(Seq(codon).translate(table=codon_table)) + nucs = 'ACTG' + missense_aa_list = [] + for i in range(len(codon)): + for n in nucs: + new_codon = codon[:i] + n + codon[i+1:] + new_aa = str(Seq(new_codon).translate(table=codon_table)) + if new_aa == aa: + continue + else: + missense_aa_list.append(new_aa) + return ''.join(set(missense_aa_list)) + +def contains_stop_missense_variant(codon, codon_table='Standard'): + """Check if codon contains a stop missense variant + INPUT: codon (str) + RETURN: boolean (bool) + """ + missense_aa = unique_missense_variants(codon, codon_table=codon_table) + return "*" in missense_aa + def iupac_to_aa(iupac_codon): """Return string of AAs encoded by input iupac missense codon""" nuc_lists = [list(rev_iupac_dict[n]) for n in iupac_codon] diff --git a/main_package/primer_design.py b/main_package/primer_design.py index 5341531..d0b3fc6 100644 --- a/main_package/primer_design.py +++ b/main_package/primer_design.py @@ -1,4 +1,8 @@ #!/usr/bin/env python3 + +# functions to design DMS primers +# many functions require "args" input from script + from . import codon_table from Bio.Seq import Seq from Bio.SeqUtils import MeltingTemp as mt @@ -109,32 +113,41 @@ def codons_list(seq): # generate synonymous vector codon list (top 2 codons for yeast) synonymous_win = [yeast_synonymous_dict[i].lower() for i in vect_list] - # generate iupac missense codons list (with synonymous codons) + # generate list of iupac missense codons to use + # check to add synonymous variants and remove stop codons iupac_codons = [] - syn_bool_list = [] - no_stop_list = [] - for i, wt_codon in enumerate(wt_list): - syn_bool = rng.choice([True, False], p=[args.syn_snp_rate, 1-args.syn_snp_rate]) ### args.syn_snp_rate - syn_bool_list.append(syn_bool) - - no_stop_bool = rng.choice([True, False], p=[args.stop_rate, 1-args.stop_rate]) ### args.stop_rate - no_stop_list.append(no_stop_bool) - - # missense_dict, synonymous_dict, no_stop_dict, no_stop_syn_dict + add_synonymous_codon_list = [] + contains_stop_list = [] + remove_stop_list = [] + for wt_codon in wt_list: + # include synonymous variants (bool) + syn_bool = rng.choice([True, False], p=[args.syn_snp_rate, 1-args.syn_snp_rate]) + add_synonymous_codon_list.append(syn_bool) + + # check if codon contains stop missense variants + stop_bool = codon_table.contains_stop_missense_variant(wt_codon, args.codon_table) + contains_stop_list.append(stop_bool) + + # if codon contains stop variants + if stop_bool: + # remove stop variant (bool) + remove_stop_bool = rng.choice([True, False], p=[args.remove_stop_rate, 1-args.remove_stop_rate]) + else: + remove_stop_bool = False + remove_stop_list.append(remove_stop_bool) - # need a sub-step to check if codon contains stop codon - # need a function to check if the wt codon encodes a missense stop codon - if syn_bool and no_stop_bool: - # use no_stop_syn_dictionary + # assign iupac codons for wt_codon + if syn_bool and remove_stop_bool: + # use no_stop_syn_dictionary, add syn and remove stops iupac_codons.append(no_stop_syn_dict[wt_codon]) - elif syn_bool and not no_stop_bool: - # use synonymous_dictionary + elif syn_bool and not remove_stop_bool: + # use syn_dict, add syn and keep stops iupac_codons.append(synonymous_dict[wt_codon]) - elif no_stop_bool and not syn_bool: - # use no_stop_dict + elif not syn_bool and remove_stop_bool: + # use the no_stop_dict, no syn and remove stops iupac_codons.append(no_stop_dict[wt_codon]) else: - # use missense dict + # use missense_dict, no syn and keep stops iupac_codons.append(missense_dict[wt_codon]) # make full-length oligo (homology arm, sub-window, primer), generate dataframe @@ -153,8 +166,32 @@ def codons_list(seq): full_forward_primer = data_dict['homology_arm'] + sub_window + data_dict['forward_primer'] # add values to data_dict - dict_keys = ['name','codon_sub','wt','position','iupac', 'iupac_aa','sub_window', 'primer', 'synonymous_codons', 'no_stop_codons'] - dict_values = [forward_primer_name, codon_sub, wt_list[i], aa_position, iupac_codon, iupac_aa, sub_window, full_forward_primer, syn_bool_list[i], no_stop_list[i]] + dict_keys = [ + 'name', + 'codon_sub', + 'wt_codon', + 'position', + 'iupac_codon', + 'iupac_aa', + 'sub_window', + 'primer', + 'add_synonymous_codon', + 'contains_missense_stop', + 'remove_missense_stop_codon' + ] + dict_values = [ + forward_primer_name, + codon_sub, + wt_list[i], + aa_position, + iupac_codon, + iupac_aa, + sub_window, + full_forward_primer, + add_synonymous_codon_list[i], + contains_stop_list[i], + remove_stop_list[i] + ] for (key,value) in zip(dict_keys,dict_values): data_dict[key] = value diff --git a/script.py b/script.py index dff6d31..16bde76 100644 --- a/script.py +++ b/script.py @@ -22,7 +22,7 @@ parser.add_argument("--melt_temp", help="Melting temp of fwd primer", type=int, default=50) parser.add_argument("--rev_melt_temp", help="Melting temp of rev primer", type=int, default=55) parser.add_argument("--syn_snp_rate", help="Percentage of synonymous SNPs 0-1", type=float, default=.05) -parser.add_argument("--stop_rate", help="Percentage of stop codon SNPs to remove, default = 90% of stop SNPs", type=float, default=.90) +parser.add_argument("--remove_stop_rate", help="Percentage of stop codon SNPs to remove, default = 90% of stop SNPs", type=float, default=.90) parser.add_argument("--rng_seed", help="Set seed for repoducibly selecting synonymous codon sites", type=int, default=42) parser.add_argument("--out_dir", help='Local output directory e.g. "data"', type=str) args = parser.parse_args() @@ -59,7 +59,7 @@ seq_data['gene_end'] = gene_end seq_data['fasta_file'] = [] seq_data['df'] = pd.DataFrame() -seq_data['rng'] = np.random.RandomState(42) +seq_data['rng'] = np.random.RandomState(int(args.rng_seed)) # this needs to be fixed (user input? yaml?) targ_windows = ['window_1', 'window_2', 'window_3'] @@ -112,7 +112,7 @@ df['reverse_primer_gc'] = df['reverse_primer'].apply(GC).round(1) df['reverse_primer_len'] = df['reverse_primer'].str.len() -cols = ['name','sub_window_name','wt','position','iupac','codon_sub','iupac_aa','synonymous_codons','no_stop_codons','primer','homology_arm','sub_window','forward_primer','forward_primer_tm','forward_primer_gc','forward_primer_len','reverse_primer_name','reverse_primer','reverse_primer_tm','reverse_primer_gc','reverse_primer_len'] +cols = ['name','sub_window_name','wt_codon','position','iupac_codon','codon_sub','iupac_aa','add_synonymous_codon','contains_missense_stop','remove_missense_stop_codon','primer','homology_arm','sub_window','forward_primer','forward_primer_tm','forward_primer_gc','forward_primer_len','reverse_primer_name','reverse_primer','reverse_primer_tm','reverse_primer_gc','reverse_primer_len'] df = df[cols] # save dataframe as .tsv