added bool check for stops and add syn

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