CLUSTAL X (1.81) multiple sequence alignment input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 CAATATCAATAACTACCATTGTTTAC---TTTCCTTACCTATCATCATCC chr2D_1 CAATATCAATAATTACCATTGTTGTAGTATTTCCTTACTTATCATCAACC chr2A_2 -AATATCAATAATTACCATTGTTGTA----TTTCGTTCTTATCACCATCC SNPs ------------S----------SSS------------S----------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 ATTAATTAT---GTGTTATTTTCTTCCTTATTTTTCTAAGGTGTAGATTA chr2D_1 ATTAATTAC---GTATTATTTTCTTCCTTATTTGTCTAAGGTGTAGATTA chr2A_2 ATTAATTAAGTAGTATTATTTTCTTCCTTGTTTTTCTAAGGTGTAGATTA SNPs --------S-----S----------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TATGATCAGTATCAATAATT-ACCATTGTT---ACATTTCCTTATTATCA chr2D_1 TATGATCAGTATCAATAATT-ACCATTGTCATAATATTTCCTTGCTTACC chr2A_2 TATGATCAGTATCAATAATTTACCATTGTC---ATATTTCCTTACTTACC SNPs -----------------------------S----S---------S-SS-S forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 CCAGCCATTAATTTTGTATTA---TTTTTCCTTATTTGAACGAGGTGAAT chr2D_1 CTCAACCATAGATTAAGCAATATTTTCTTCCTTATATGTACTAGGTGAAG chr2A_2 CTCAACCATTGACTACACAATATTTTCTTCCTTATATGTAGTAGGTGGAG SNPs -SSSS-SS--SS--SSSSSSS-----S--------S--S--S-------S forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 ATTATATGATCAATATCAATAATTACCACGGTTATTTGCTTACG------ chr2D_1 ATTATATGATCAATATCAATAATTACCGCGGTTATTTGCTTACTCCTACT chr2A_2 ATTATATGATCAATATCAATAATTACCAAGGTTATTTGCTTACT------ SNPs -------------------------------------------S------ forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TACCCTCAAGGCCTCAACCATTGGTTACACAATATTATCTTCCTTATATG chr2D_1 TAC--------CCTCAACCATTGATTACACAATATTTTCTTCCTTATATG chr2A_2 TAC--------CCTCAACCATTGATTACACAATATTTTTTTCCTTATATG SNPs ---SSSSSSSS------------S------------S------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TACC---AGGTGAAGATTATATGATCAATATCATCAATTACCATTGTTAT chr2D_1 TACTAGTAGGTGAAGATTATATGATCACTATCATTAATTACCATTGTTAT chr2A_2 TACTGGT---TGAAGATTATATGATCAATATCACTAATTACCATTGTTAT SNPs ---S------------------------------S--------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TTACTTATTTAGCATCATCTACTAATTACATATTATTTTCTTCCATACTT chr2D_1 TTACTTACTTACCATCATCTAGTAATTACATAACATTTTCTTCCATATTA chr2A_2 TTACTTACCTACCACCATCTAGTAATTACATATTATTTTCTTCTATACTT SNPs -------S---S---------S---------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 GTACGTACTAGGTGAAGATTATA-TGATCAATGTCATTAATTATTAAAAA chr2D_1 GTACGTACCAGGTGAAGATTATA-TGATCAATGTCATTAATTATTAAAAT chr2A_2 GTACGTACTAGGTGAAGATTATACTGATCGATGTCATTAATTATTAAAAT SNPs -------------------------------------------------S forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TTGAAAAAAAGATCCTCATATAAAAATGCCAAAC--AAAAAATTGCAGGG chr2D_1 CTGAAAAAT--ATTCTCATATAAAAAATGGAAAACAAAAATTTTGCGGGA chr2A_2 TTGAAAAGT--ATCCTCATATAAAAATTGGCAAACAAAAAATTTGGGGCA SNPs --------SSS----------------SSS---S-------S----S--S forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 AAATCGTAAACAAGATTGACCATTGCTTCCTCCGTTCACAAATACTCCAT chr2D_1 AAATGGTAAGAAAAATTGACCACTATTCCCTCCGTTCACAAAATAAGAGG chr2A_2 AAATGGTAAACAAAATTGACTACTGCTCCCCAC-TTCACAAATATAAGAT SNPs ----S--------S--------S----S----------------SSSS-- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 CCGTTCCGATTTACTCGTCGTGGTTTTACTAAAACCATGACGAGTAAATC chr2D_1 TTCTAACT------------------------------------------ chr2A_2 -------------------------------------------------- SNPs SSS-SS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 GGAACGGATATTCTAACTTTTTC-TGAATTGAATGTATATAGACATATTT chr2D_1 -----------------TTTTTC-TGATTCGGATGTATATAGACATATTT chr2A_2 -------ATATTCTAACTTTTTCCTGAATCAGATGTATATAGACATATTT SNPs SSSSSSS----------------------S-S------------------ forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TAATGTGTTTATTCGCTCATTTTAGTCCGTGTGTAGATCATATTAAAATG chr2D_1 TAATATGTTTGTTCACTCATTTTAGCCCGTACGTAGACCATATTGAAATG chr2A_2 TAATATGTTTGCTTACTCATTTTAATCCGTTTGTAGATCATATTAAAATG SNPs ----S-----S---S---------------S------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TCCAAAAGATTTTATATTTATGAACGGAGGGAGTACATTGTTCTAAAG-- chr2D_1 TTCAAAACGTCTTATATTCATGAACGGATGAAGTACATCATTTCTAAAAA chr2A_2 TCCAAAAGATCTCATATTTGTGGACGGAGGAAGTACATCATTCTAG--AA SNPs ----------S-------------------S-------SS-------S-- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 -AAGTACAATAGAAATGATGCAAAGGCTGACCAAGGATTTCCTATATATA chr2D_1 AAAGTACAATAGAAATGATGCAAAGGCTGACCAAGGATTTCCTATATATA chr2A_2 AAAGTACAATAGAAATGATGCAAAGGCTGACCAAGGATTTCCTACATATA SNPs -------------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TTATCCTGAACTCACACCAACTGTCCAACATAATCTGAGGGTTTCAGTAG chr2D_1 ATATCCTGAACTCACACCAACTGTCCAACATAATCTGAGGGTTTCAGTAG chr2A_2 TTATCCTGAACTCACACCAACTGTCCAACATAATCCGAGGGTTTCAGTAG SNPs -------------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 ACCAACTAAAATCCAATAGTTTTATCGGCATCGGCATCGGCATCGTCTTT chr2D_1 ACCAACTAAAATCCAATAGTT-TATGGGCATCGGCATCGTCATCGTCTTT chr2A_2 ACCAACTAAAACCCAATAGTT-TATCGGCATGGGCATCGTCGTCGTCTTT SNPs ---------------------S-----------------S---------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TTTACAA-TTTTTGCGTGTGGGAAGCAGTGGGAAACTCCAGCACTCGTGC chr2D_1 TTTCCAA-TTTTGCGTGTGGCGAAGCAGTGGGAAGCTCCAGCACTCGTGC chr2A_2 TTTCCAATTTTTGCGTGTGGCGAAGCAGTGGGAAGCTCTAGCACTCGTGC SNPs ---S--------SSSSSSS-S-------------S--------------- forward_935 ---------------GTGTGGGAAGCAGTGGGAAA--------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 CATCGACCGCACTCCATTTACATCCTTTTTAAAACCGTGGGTGCGCGCTA chr2D_1 CATCGACCGCACTCCATTTATATACTTTTAGAAACCGTGGGTGCGTGCTA chr2A_2 CATCGACCGCACTCCATTCATACCCTTTTAAAAACCGTGGGTGCGCGCTA SNPs --------------------S--------S-------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 ------------------------------GCCGGAGACAACCACCAAAC chr2B_1_TraesCS2B01G145600 TAAATACCAAGGGTCTCCGTCCACCTCGCCGCCGGAGACAACCACCAAAC chr2D_1 TAAATACCAAGGGTCTCCGTCCAGCTCGCCGCCGGAGACAACCACCAAAC chr2A_2 TAAATACCAAGGGTCTCCGTCCACCTCGCCGCCGGAGACAACCACCAAAC SNPs -------------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 CCACGCATCCCC--------TCCCCTCCTCCTTCCACAGCGAGCGCGGCG chr2B_1_TraesCS2B01G145600 CCACGCATCCCC--------TCCCCTCCTCCTTCCACAGCGAGCGCGGCG chr2D_1 CCACGCG--------TCCCCTCCCCTCCTCTTTCCACAG----CGCGGCG chr2A_2 CCACGCATCCCCAGCTCCCCTCGCCTCCTCTTTCCACAG----CGCGGCG SNPs ------------------------------S--------SSSS------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 CCGATGGCCACGGCACACTGTTACCCGCCGCCG---CCGCCCATCGCCCA chr2B_1_TraesCS2B01G145600 CCGATGGCCACGGCACACTGTTACCCGCCGCCG---CCGCCCATCGCCCA chr2D_1 CCGATGGCCACGGCGCACTACTACCCGCCGCCGCCGCCGCCGATCGCCCA chr2A_2 CCGATGGCCACGGCACACTGCTACCCGCCGCCG---CCGCCCATCGCCCA SNPs --------------------S----------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 CGCGCTTCCAAGGCCGCACGCCGCCGACAGCGCCGTCGCCCTCCTCCCCG chr2B_1_TraesCS2B01G145600 CGCGCTTCCAAGGCCGCACGCCGCCGACAGCGCCGTCGCCCTCCTCCCCG chr2D_1 CCCGCTTCCAAGGCCGCACGCCGCCGACAACGCCG---------TCCCCG chr2A_2 CGCGCTTCCAAGGCCGCACGCCGCCGACGGCGCCGTTGCCCTCCTCCCCG SNPs ------------------------------------S------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 ACGACGGCGGCAGCGACAGCGAGAGCGTGGCGGAGTCGTCGTGCCCGCAC chr2B_1_TraesCS2B01G145600 ACGACGGCGGCAGCGACAGCGAGAGCGTGGCGGAGTCGTCGTGCCCGCAC chr2D_1 ACGACGGCGGCAGCGACAGCGAGAGCGTGGCGGAGTCGTCGTGCCCGCAC chr2A_2 ACGACGGCGGCAGCGACAGCGAGAGCGTGGCCGAGTCGTCGTGCCCGCAC SNPs -------------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 CCGC------GCCGGCCGACGGCGAGCGGGGACGAGGAGGAGGAGGAGGA chr2B_1_TraesCS2B01G145600 CCGC------GCCGGCCGACGGCGAGCGGGGACGAGGAGGAGGAGGAGGA chr2D_1 CAGCACCCGCGCCGGCCGACGGCCA---GGGACGAGGAGGAGGAGGAGGA chr2A_2 CCGCGCGTGCGCCGGCCGACGGCGAGCCGGGACGAGGAGGAGGAGGAGGA SNPs ---------------------------S---------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 GGACGGGTGCA---GCGGCAGCTGCGTGGAGGCGGACGAGTACTGGGGG- chr2B_1_TraesCS2B01G145600 GGACGGGTGCA---GCGGCAGCTGCGTGGAGGCGGACGAGTACTGGGGG- chr2D_1 ---CGGGTGCA---GCGGCAGCTGCGTGGAGGCGGACGAGTACTGGGGCT chr2A_2 ---CAACGACGGGTGCAGCAGCTGCGTGGAGGTGGACGAGTACTGGGGCT SNPs SSS---------------------------------------------S- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 --TACTAC---CAGCAGCAGCAGCATCCGCAGGAAGCCGACGAAGAGGAG chr2B_1_TraesCS2B01G145600 --TACTAC---CAGCAGCAGCAGCATCCGCAGGAAGCCGACGAAGAGGAG chr2D_1 ACTACTAC---CAGCAGCAGCAGCATCCGCAGGAAGCCGACGACGAGGAG chr2A_2 ACTACCAGCAGCAGCAACAGCAGCATCCGCAGGAAGCCGACGACGAGGAG SNPs -------------------------------------------S------ forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 GAGGTCAGCACGGCGAGCGTCTGGTGGAAGAAGAAACGGGCGGCGGCGGC chr2B_1_TraesCS2B01G145600 GAGGTCAGCACGGCGAGCGTCTGGTGGAAGAAGAAACGGGCGGCGGCGGC chr2D_1 GAGGTCAGCACGGCGAGCGTCTGGTGGAAGAAGAAACGGGCAGCGGCGGC chr2A_2 GAGGTCAGCACGTTGAGCGTCTGGTGGAAGAAGAAACGGGCGGCGGCGGC SNPs -------------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 GGCTGGTAGGGCCGGCGGCGCGTTCCCCTCGGCGGTGGGG---------- chr2B_1_TraesCS2B01G145600 GGCTGGTAGGGCCGGCGGCGCGTTCCCCTCGGCGGTGGGG---------- chr2D_1 GGCTGGTAGGGCCGGCGGCGTGTTCCCTTCGTCTTCGTCGGCTGCGGCCC chr2A_2 GGCTAGTAGGGCTGGCGGCGCGTTCCCCTCGGCGTTCCCCTCGGCGGTGG SNPs ----------------------------------S--SS----------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 --CGTGAGGGGGAGGAGAAGAAGGCGGAGGACCCGAAGCGGGCGGCGGCG chr2B_1_TraesCS2B01G145600 --CGTGAGGGGGAGGAGAAGAAGGCGGAGGACCCGAAGCGGGCGGCGGCG chr2D_1 GTCGTGAGGGGGAGGAGAAGAAGGCGGAGGACCCGAAGCGGGCGGCGGCG chr2A_2 GTGGTGAGGGGGAGGAGAAGAAGGCGGAGGACCCGAAGCGGGCGGCGGCG SNPs -------------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 CGGCAGGAGGAGGACCGCAAGTTCTGGGCGGACTGCCTCGCCACAGGGTA chr2B_1_TraesCS2B01G145600 CGGCAGGAGGAGGACCGCAAGTTCTGGGCGGACTGCCTCGCCACAGGGTA chr2D_1 CGGCAGGAGGAGGACCGCAAGTTCTGGGCGGACTGCCTCGCCACCGGGTA chr2A_2 CGGCAGGAGGAGGACCGCAAGTTCTGGGCCGACTGCCTCGCCACCGGGTA SNPs --------------------------------------------S----- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 CCCATGAACGGACCCCGGGGGAAGCCATAGCTCGGCATGCAAAGGCCATG chr2B_1_TraesCS2B01G145600 CCCATGAACGGACCCCGGGGGAAGCCATAGCTCGGCATGCAAAGGCCATG chr2D_1 CCCATG----------A----AAGCCATAGCTCAGCATGCAAAGGCCATG chr2A_2 CCCCTGAAACCCAGGAA----AAGCCATAGGTCGGCATGCAAAGGCCATG SNPs --------SSSSSSSSSSSSS----------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 GCAAA-AAGCCATGAGCGCCGCTAACCGAAACTGCAGCCCG---ACCCAA chr2B_1_TraesCS2B01G145600 GCAAA-AAGCCATGAGCGCCGCTAACCGAAACTGCAGCCCG---ACCCAA chr2D_1 GCAAA-AAGCCATGAGCGCCGCTAACCGAAACTGCAGCCCG---ACCCAA chr2A_2 GCAAAGAAGCCATGAGCGCCGCCAACCGAAACTGCAGCCGCTCAACCCAA SNPs -------------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 GCGTATGTCTA--------------------------------------- chr2B_1_TraesCS2B01G145600 GCGTATGTCTACCTTT------TTTTTTG---------TTTCTTTTCTTT chr2D_1 GCGTATGCCTACCTTTGTTTGTTTGTTTG---------TTTGTTTTCTTT chr2A_2 GCGTATGCCTACCTTTGTTTGTTTCTTTCCATTTTTCTTTTGATTTCCTT SNPs -------S----------------S----------------S-------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 GTACAGA------ATATTC-----AACTCCTCAACAAGTCATTGGGTGGC chr2D_1 GTACATACATAATATATTC-----AACTCCTCAACAAGTCATTGGGTGGC chr2A_2 GTACATA------ATATTCAACGGAACTCCTCAACAAGCCACTGGGTGGC SNPs -----S-------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 GTATTTTGACCCCCGC-AAGCTTTACAGAAAGAATTGATCTTCTCTTTAG chr2D_1 GTATTTTGACCCCCGT-AAGCTTTACAGAAAGAATCGATCTTCTTCTTCT chr2A_2 GTATTTTGACCCCCGTAAAGCTCTACAGAAAGACTCGATCTTCTTCTTCT SNPs ---------------S-------------------S--------SS--SS forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 -------------------------------------------------- chr2D_1 TTTCTTGTTTTTTTTAATAGTTTGGATTGCTTACCACATGTGTCAGGTGG chr2A_2 TTTCTTGTC----------------------------------------- SNPs -------------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 --------TTGTTGTTGAGGGTGAAA-----GGATTGAATTTCTGTGCAA chr2D_1 TTCTTTTCTTGTTGTTGAGGGCGAAA-----GAATTGAATCTCTGTGCAA chr2A_2 -------------GTTGCGGGTGAAAGAATTGAATTGAATCTCCGTGCAA SNPs --------------------------------S-------S--------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 ACCTAGTAA----------------------------------------- chr2D_1 ACTAGTACGTAGTAGAAAATAGAGAACTGCTATACAGACGACATTCACAG chr2A_2 ACTAGTACTAC--------------------------------------- SNPs --SSSSSSS----------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 -------------------------------------------------- chr2D_1 ACGATTTCAGCACGACACTCCATCTCACACCATTCATTCAAGACACCAAT chr2A_2 -------------------------------------------------- SNPs -------------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 -------------------------------------------------- chr2D_1 GTACAGAAAGTTGTTGGATTTGAAATCGGCTCAGGATCGTGCAAGCAAAT chr2A_2 -------------------------------------------------- SNPs -------------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 --------------------GTAGAAAACACTGTGCATTTTTGTTCCTTG chr2D_1 ATCGTCTGTGAAGTAGTTTCGTAGAAAATACAGTGCATTTTGCTTCCTTG chr2A_2 ---------------------TAGAAAATACATTTTTCTTTTCTTAGCTT SNPs ----------------------------S--S----------S------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TTT-TAGATGGGGGGTGGTCAATTAAAGCAGCGGTGGGACGCCAAAGCCA chr2D_1 TTG-TAGATGGGGGGTGGTCAATTAAAGCAGCGGTGGGACGC-------- chr2A_2 GGTCTAGATGGGGGGTGGTCAATTAAAGCAGCGGCGGGACGCCAGGGCCA SNPs --------------------------------------------SS---- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 GTGGCCAATGGCATTGCCGGCGGCCACCAACCGGTGGAGAGACATGGGAC chr2D_1 -------------------------ACCAACCGGTCGAGAGACATGG--- chr2A_2 G-------TGGCATTGCCGGCGGCCACCAACCGGTGGAGGGGCATGGGTG SNPs -SSSSSSS----------------------------------------SS forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 ATGGGTGCAGGAGAGGTGGCAGGCAAGGAGATCTC-------TCGTCCGC chr2D_1 ------------GAGGTGGCAGGCAAGGAGATCTC-------TCCGCCGC chr2A_2 C------CAGGAGAGGTGGCAGGCAAGGAGATCTCCTCCGCCTCCGCCGC SNPs SSSSSSS-------------------------------------SS---- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TTTAAATTCCCGCCCTTCCTCGTCAAACTCCCAATTGGACAGACAGAC-- chr2D_1 TTTAAATTCCCGTCCTTCCTCGTCAAACTCCCAATTGGACGGACAGACAG chr2A_2 TTTAAATCCCCGTCCTTCCTCGTCAAACTCCCAATT----GGACACACGC SNPs ------------S---------------------------S--------- forward_935 -------------------------------------------------- reverse_2313 ------------CCCTTCCTCGTCAAACTCCC------------------ input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 --GGTGGCCGATCACCGACGGAGCATCGCATTCCGTCCGTCCGTGCGTCC chr2D_1 ACGGTGGCCGATCACCGACGGAGCATCGCATTCCGTCCGTCCGTCCGTCC chr2A_2 ACGGCGGCCGATCACCGACGGGGCATGGCAT--------TCCGTCCGTCC SNPs --------------------------------------------S----- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TAGGCTCATGTTCATGTAGGTCCTAGCCCGG---ATCGCGGGGCCT---G chr2D_1 TAGGCTCATGTTCATGTAGGTCCTAGCCCGGGGGATCGCGGGGCCT---G chr2A_2 TAGGCTCATGCA---GTAGGTCCTAGCCCGG---ATCGCGGGGCCTCCGG SNPs -------------------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TGGAACGTGCGTCAGTTGCGCGCGCCAACGACCGGTGGCGAGTATGGTCC chr2D_1 TGGAACGTGCGTCAGTTGCGCGCGCCAACGACCGGCGGGGAATATGGTCC chr2A_2 TGGAACGTGCGCCGGTTGCGCGCGCCAACGACCGGCGGGGAATATGGTCC SNPs -----------------------------------S--S--S-------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 AAGCTCGGCCGCGTAACCA------------TGTGTGTTTATGATGGGTT chr2D_1 ACGCTCGGCCGCGTAACCA--------TGTGTGTGTGTTTATGATGGTTT chr2A_2 ACGCTCGGCCGCGTAACCATGTGTGTGTGTGTGTGTGTTTATGATGGGTT SNPs -S------------------------------------------------ forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TGGTGCGTAAAGCGGCCAGAGTTATTTAAAGGGGGCAAAGCCAAGCTGCG chr2D_1 TGGTGCGTAAAGCGGCCCGAGTTAAATAAAGGGGGCAAAGCCAAGCTGCG chr2A_2 TGGTGCGTAAAGCGGCCGGGGTTAAATAAGGGGGGCAAGGCCAAGCTGCT SNPs -----------------S------SS------------------------ forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 GTTGCTTGTCCAATGGAAAGATGGTTTTCCCTTTTAATTATGTTATAAAC chr2D_1 GTTGCTTGTCCAATGGAAAGATGGTTTTCCCTTTTAATTATGTTTAAAAA chr2A_2 GTTGCTTCTCCTTGAGAAAGATGG-------TTTCAGTTATGTTTAAAAG SNPs --------------------------------------------SS---S forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 CGGTGGCTTCT------------TTCTTTCTTTCTTTCCGAGCTACAGCT chr2D_1 AAA-CTGGCGGCTGTTGCTCAGCTTCTTTCTTTCTTTCCGAGCTACAGCT chr2A_2 AAAACTGGCGGCTGTTGCTCAGCTTCTTTCTTTCTTTCCGAGCTACAGCT SNPs SSSSSSSSSSS--------------------------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 AGTACTGTAGTTGGC-TTATACAAAGACAGCACGTGTGGCACGCCCTTGA chr2D_1 AGTACTGTGGTTGGCTTTATAGGAAGACAGCACGTGTGGCACGCCCCTGA chr2A_2 GGTACTGTAGTTGGCTTTATAGAAAGACAGCACGTGTGGCACGCAGCTGA SNPs ---------------------S------------------------S--- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 CCATGTTTTCCAGAATGCCTAGCACCG-AGGCATTGTCATAGGTGCCGGC chr2D_1 CCATGGTTTCCAGCATGTCTAGCACCT-AGGCATTGTCATAGGCGCCGGC chr2A_2 CCATGTTTTCTAGAAAGTCTAGCACCTAAGGCATTGTCATAGGTGCCGGC SNPs -----------------S--------S----------------------- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TTCCCAGGAAACTCGTCGCTTAAAAAACAGGCATATGAAGAGACGAAAAT chr2D_1 ATCC---------------------------------------------- chr2A_2 ATCCCACAAAACTCATCGATTAAGAAACATGCATG-----------AAAT SNPs S-----SS------S---S----S-----S----SSSSSSSSSSSS---- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 GAAGCGGAAACTTTCCGGTTTTTTCAGCAGGAAAATAGAAATGGAGAGGA chr2D_1 -------------------------------------------------- chr2A_2 GGAGCGGAAACTTTCTGTTGT-------AGAAAAACAGAAACGGAGAGAA SNPs -S-------------S-S-S-SSSSSSS--S----S-----S------S- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 AAAAAGGAAAATGAAAGCGCAATTCACAAAACAGAAACGGAAATGGATTT chr2D_1 -------------------------------------------------- chr2A_2 AAAACAGAAA-TGAAAGGGCAGTTCATAAAACAAAAACGAAAACAGAATT SNPs ----SS----S------S---S----S------S-----S---SS--S-- forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 -------------------------------------------------- chr2B_1_TraesCS2B01G145600 TTTTTGTGCGGAAACGGAACAGCCTTTTCTGGTGGAACGGACGCAGAAAC chr2D_1 -------------------------------------------------- chr2A_2 TTTT---------------------------------------------- SNPs ----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_935 -------------------------------------------------- reverse_2313 -------------------------------------------------- input_sequence_73208 ------ chr2B_1_TraesCS2B01G145600 GGAATT chr2D_1 ------ chr2A_2 ------ SNPs SSSSSS forward_935 ------ reverse_2313 ------