CLUSTAL X (1.81) multiple sequence alignment input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 TAGTTGTGATTGGGCATGCGATCCCGCGTTGGTGTGACCCCGCGCGCTGT chr7D_1 TAGTTGTGATTGGGCATGCGATCCAGCGCTGGTGTGACCCGGCGCGCTGT chr7A_1 TAGTTGTGATTGGGCATGCGATCCAGCGCTGGTGTGACCCGGCGCGCTGT chr7A_383 -------------------------------------------------- SNPs ------------------------S---S-----------S--------- forward_25 ------TGATTGGGCATGCGATCCC------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 ATGGATCAAACTATATTTGAATTTTAAATTGACCTTGACTGACGGCATTG chr7D_1 ATGGATTAGACTACATTTGAATTTTAAATTGACCTTGACTGACGGCATTG chr7A_1 ATGGATCAAACTATATTTAAATTTTAAATTGACCTTGACTGATGGCATTG chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 GATGGCCGGCTCCGCATCCTTGTCCGCGGACGGATGCTGGAGAAAATTTG chr7D_1 GATGGCCGGCTCTGCATCCTTGTT--CGGAGGAATGCCGGAGAAAATTTG chr7A_1 GATGGCCGGCTCCGCATCCTTATT--CGGAGGAATGTCGGAGAAAATCTG chr7A_383 -------------------------------------------------- SNPs -----------------------SSS----S-S----S------------ forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 CTTGTTGTTGTCTAAGATGCCATAAGAGATTTTTTTAGCCATAGGAGTG- chr7D_1 CGCGTTGCTGTCGAAGATGCCATAACAGATTTTTTTTAGCCATAATAGGG chr7A_1 CGTGTTGCTGTCGAAGATGCCATAAGATATTTTTTTAGCCATAGGAGTG- chr7A_383 -------------------------------------------------- SNPs -S-----S----S------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 ----TTGCAGTAAATATATTTTTCAG------------------------ chr7D_1 GTGTTTGCAGTAAATATATTTTTTAG------------------------ chr7A_1 ----TCGCAGTAAATATTTTTTTAATCTAGGACGCCGCTAACTGCCACAC chr7A_383 -------------------------------------------------- SNPs -----------------------S-------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 GTGTAGCAGGAAGGGAGACGCACCACACGTCTCTAATGCAAACAAATTGC chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 CACGTCATTGCATGCATGCATGTAGGAATCTTTTTGGATTTTCAGTTTTT chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 AAAATGTTTTATCTCTTAAACAAAAAATCCGATTGAAGATCCGTTTTCAC chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 CATTAAATCCCTCACGATGAGATCTTCGAAACTAGATCCCATGTTGATAT chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 GTTTTGATGAAAAAAAAATTGGATTAAAAGTTGCCATGTCTATTGCATAT chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 GAATTGCCATGATGTTTACACTAAAGTTGCCATGATATTTTTCAGCTATT chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 TTCTTCTACATTAGAAGTAAATTTTGACATTTATAAAACGGGAAATTAAG chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 AAACTAGACTTGCCATGAACCATAAACTAAAATTGCCATGATACATGCAC chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 GTAAAATTGCCATGGTTCATACAAAAAATAATTTTCATGGTCAAAGTACT chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 GGAGTTGCCATCATCAAAATACTAAAATTGCCATGATCTACAAACTAAAA chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 TTGCCACATGGCAACTTTAGTTTAAGCCGTATGGCAACAGCAGTGTAAAC chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 ATCATGGCAACTTCTGGGCAAAAAAAAAATTTCGTCGAAACACATCAACA chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 TGGGGTCTAGTTTTGAAGATCTCGTCGAGACGGATTTAATGGTGAAAGCG chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 GATTTTTAGTTCGCCTTTTTATTTAGGAGATACAACATTTTTAAGCCGAA chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 AATCAATTTTTTTTACTGATGTCATCTATTCATACATGGCAAAATGAATG chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 GTGATGGAGCCGTGTGGGCGACGTGCAAACGCCCACACGTGTGGGTGTTA chr7A_383 -------------------------------------------------- SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------TCTAAGTTGTATGGGAATATCTTTTTGTGAGATATTC chr7D_1 -------------TCTAAGTAGTAAGGGAGTATCTTTTTGTGAGATATTC chr7A_1 ACATTTTCGTTAATCTAAGTAGTAAGGGAATATCTTTTTGTGAGATATTC chr7A_383 -------------------------------------------------- SNPs --------------------S---S------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 TTTTGATGATTTTTCGGCAACCCACGCGGTTGGGCTCCCTCTCGCAACCA chr7D_1 TTTTGATGGTTTTTCGGCGGCCCACGCGGTCGGGCTCCCTCTCGCAACCA chr7A_1 TTTTGATGATTTTTCGGCGGCCCAAGCGGCTGGGCTCCTCCCGCAACCAA chr7A_383 -------------------------------------------------- SNPs ------------------SS------------------------------ forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 AAATAGAAACTCAGCCGCCGC-----CGCCGCCCTTTTCTCTTCTTCTCC chr7D_1 AAATAGAAACTCAGCCGCCGCCGCGGCGCCGCCCCTTTCTCTTCTTCTCC chr7A_1 AAATAGAAACTCAGCCGCCGCCGCGGCGCCGCCCCTTTCTCTTCTTCTCC chr7A_383 -------------------------------------------------- SNPs ----------------------------------S--------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 CTCCCTCCCTGAGCGCAACCGTCCACCCAAATCCCCCGCTCGCCAGGACG chr7D_1 CTC-------------------CCACCCAAATCCCCCGCTCGCCACGACG chr7A_1 C----TCCCTGAGCGCAACCGCCCACCCAAATCCCCCGCTCGCCACGAGG chr7A_383 -----------------------------AATCCCCCGCTCGCCAGGAGG SNPs ---SS----------------S---------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 AACCGTCGCCTG---CGATGACGCGCCGAAGCCGGGAACGGCGCGCGGCC chr7D_1 AACCGCCGCCTG---CGATGACGCGCCGAAGCCGGGAACGCCGCGCGGCC chr7A_1 AACCGCCGCCTG---CGATGACGCGCCGAAGCCGGGAACGCCGCGCGGCC chr7A_383 AATCGCCGCCGCCTCCGATGACGCGCCAAAGCCGGGAACGGCGCGCGGTC SNPs -----S-------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 GCCGGCGACGGAGACC------------------CAGCTGGCCCCCCGCA chr7D_1 GCCGGCGACGGAGACC------------------CCGCCGGCCCCCCGCA chr7A_1 GCCGGCGACGGAGACC------------------CCGCCGGCCCCCCGCA chr7A_383 GCCTGCGAGGGAGGCCAGGCGGCAGCGCGCGCCGCCGCCTCGCCCCCGCA SNPs -----------------------------------S--S----------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 TTACGACCCCGACGAGGAGCGCCGCCTCGCCGAGGAGGTGCTATACCTCC chr7D_1 TTACGCCCCCGACGAGGAGCGCCGCCTCGCCGAGGAGGTGCTCTACCTCC chr7A_1 TTACGCCCCCGACGAGGAGCGCCGCCTCGCCGAGGAGGTGCTCTACCTCC chr7A_383 CTACGACGCGGACGAGGAGCGCCGCTT---CGAGGAGGTGGTCTACCTCC SNPs ------------------------------------------S------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 ACTCCCTCTGGCGCAGCGGCCCGCCCGCCCCCGCCCCCGCCGGGCCTCCC chr7D_1 ACTCCCTCTGGCGCAGGGGCCCGCCCGCCCCCGCCCCCGCCGGGCCTCCC chr7A_1 ACTCCCTCTGGCGCAGCGGCCCGCCCGCCCCCG------CCGGTCCTCCC chr7A_383 ACTCCCTCTGCCGCAGCGGCCCGT------CCGCCCCCGCCGGGGATCCC SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 GCGCAACCCGCCGGAGGCTCCCGCACCACCCGCCCCGCTCGCG------- chr7D_1 GCGCCACCCGCCGGAGGCTCCCGCGCCA---------GCGCCGGAGGCT- chr7A_1 GCGCGACCCGCCGGGGGCTCCCGCGCCACCCGCGCCAGCGCCGGAGGCTC chr7A_383 GCGCCACCCGCCGGAGTCTCCCGCGCCACCCGCGCCCGCGCCG------- SNPs ----S-------------------S--------S--SSSSS--------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 ----CCCGCTCGCGCCCGCCCCAAACAGCGGAAGCGCCGCAGGATCGAGC chr7D_1 --------------CCCGCCCCAACCAGCGGAAGCGCCGCAGGACCGAGC chr7A_1 CCGCCCCGCCCGCGCCCGCCCCAACCAGCGGAAGCGCCGCAGGACCGAGC chr7A_383 -----------------------ACCAGCGGAAGCGACGCAGGATCGAGC SNPs ---------S--------------S------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 GCCCCGCCGCGGAGCCCGAGGGACCCGGCGCCGACTGGCCCCTCGCGCCC chr7D_1 GCACCGCCGCGGAGCCCGAGGAACCCGGCGCCGACTGGCCCCTCGCGCCC chr7A_1 GCCCCGCCGCGGATTCCGAGGAGCCCGGCGCCGACTGGCCCCTCGCGCCC chr7A_383 GCGCCGCCGAGGCCGAATACGG---CGGCCCCGACTGGTCCCTCGCGCCC SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 TCCCCGCCCGCCTCCCCATCCCCCGCCTCCTGGCCCGACGCCA------- chr7D_1 TCCCCGCCCGCCTCCCCATCCCCCGCCTCCTGGCCCGACGCCGCCCCCTC chr7A_1 TCCCCGCCCGCCTCCCCATCCCCCGCCTCCTGGCCCGACGCCGCCCCCTC chr7A_383 GCCCCCACGGCCCCCT---------CCTCCTGGCCCAACTCCACTCCCGT SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 --CCCCCGCGCCCAGGCCACCGCC---GCAGCAGCCTTCCCCCGCCTCGC chr7D_1 CTCCCCCGCTCCCAGGCCGCCGCCGCAGCAGCAACCTTCCCCCGCCTCGC chr7A_1 CTCCCCCGCGCCCAGGCCGCAGCCGCAGCAGCAGCCTTCCCCCGCCTCGC chr7A_383 CTCCCCCGCGCCCAG------GCCGCAGCAGCAGCCTTCCACCGCCTCTC SNPs ------------------S------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 TCGCGCAGCGGGACGCCCTCCGCGCCGCGGAGGAGTTCTTCTCCGGGCGC chr7D_1 TCGCGCAGCGGGACGCCCTCCGCGCCGCCGAGGAGTTCTTCTCCGCGCGC chr7A_1 TCGCGCAGCGGGACGCGCTCCGCGCCGCCGAGGAGTTCTTCTCCGCGCGC chr7A_383 TCGCGCAGCGGGACGCCCTCCGCGCCGCCGAGGAGTTCTTCTCCAGGCGC SNPs ----------------------------S--------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 GGCGCCTCGGGCGAG---------------TCGGAGGGCTCCGAGTCGGA chr7D_1 GGCTCCTCGGGCGAGGACGGCGACGGCGAGTCCGAGGGGTCCGAGTCGGA chr7A_1 GGCGCCGAT---------GGCGACGACGAGTCAGAGGGGTCCGAGTCGGA chr7A_383 GGCGCCTCGGGCGAGGACTGCAACGAGGTT---GAGGGGCCCGAGTCGGA SNPs --------------------------------S-----S----------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 GGACGGCGGGGACGCGGCGGCGGAGTTCTTCCTGGGGCTGTTCGAGCGGG chr7D_1 GGACGGCGGGGACGCGGCGGCGGGGTTCTTCCTCGGGCTGTTCGAGCGGG chr7A_1 GGACGGCGGCGACGCGGCGGCCGAGTTCTTCCTGGGGCTGTTCGAGCGGG chr7A_383 AGACAGCTGGGACGAGGTGGCGGGGTTCTTCCTCGGGCTCTTCGAGCGGG SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 ACGCCGCGCTGCGGGGGTACTACGAGCGGAGCCACGAGGAGGGGGAGTTC chr7D_1 ACGCCGCGCTGCGGGGGTACTACGAGCGGTGCCACGAGGAGGGGGAGTTC chr7A_1 ACGCCGGGCTGCGGGGGTACTACGAGCGGAGCCACGAGGAGGGGGAGTTC chr7A_383 ACGCCGCGCTGCGGGGCTACTACGAGCGGAGCCACAGGGAGGGGGAGTTC SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 ------ATGGGGTGCGTGGGGAGGAAGGGGAAGGGCAGGAGCCAGGCCAG chr7B_1_TraesCS7B01G008000 CGGTGCATGGGGTGCGTGGGGAGGAAGGGGAAGGGCAGGAGCCAGGCCAG chr7D_1 CGGTGCATGGGGTGCGTGGGGAGGAAGAGGAAGGGCAGGGGCCAGGCCAG chr7A_1 CGGTGCATGGGGTGCGTGGGGAGGAAGAGGAAGGGCAGGGGCCAGGCCAG chr7A_383 GTGTGCATGGCGTGCGTGGGGAGGAATGTGAAGAA---GGGCCGGGCCAG SNPs ---------------------------------------S---------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 GAGGTTCCGGGACTGCAAAAGCCTCGTGCACCACGCGCGCGACGCCACGC chr7B_1_TraesCS7B01G008000 GAGGTTCCGGGACTGCAAAAGCCTCGTGCACCACGCGCGCGACGCCACGC chr7D_1 GAGGTTCCGGGACTGCAAAAGCCTCGTGCACCACGCGCGCGACGCCACGC chr7A_1 GAGGTTCCGGGACTGCGTCAGCCTCGTGCACCACGCGCGCGACGCCACGC chr7A_383 GCGGTTCCGGGACTGCATCAGCCTCGTGCGGCACGCACACGCCGCCACAC SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 GCTGCGGGAGGCCGCTGGCGCACCGCGCGCTCGCCGCCGCCGTCTGCCGC chr7B_1_TraesCS7B01G008000 GCTGCGGGAGGCCGCTGGCGCACCGCGCGCTCGCCGCCGCCGTCTGCCGC chr7D_1 GCTGCGGGAGGCCGCTGGCGCACCGCGCGCTCGCCGCCGCCGTCTGCCGC chr7A_1 GCTGCGGCAGGCCGCTTGCGCACCGCGCGCTCGCCGCCGCCGTCTGCCGT chr7A_383 GCGTCGGGAGGCCGCAGGCGCACCGCGCGCTCGCCGCCGCAGTCTGCCGC SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 GTGCTCGGCTGGGACGTCAAGCGGCTGCCCAGCATCGTCATCGACCCCCG chr7B_1_TraesCS7B01G008000 GTGCTCGGCTGGGACGTCAAGCGGCTGCCCAGCATCGTCATCGACCCCCG chr7D_1 GTTCTCGGCTGGGACGTCAAGCGGCTGCCCAGCATCGTCATCGACCCCTG chr7A_1 GTGCTCGGCTGGGACGTCAAGCGGCTGCCCAGCATCGTCATCGACCCCTG chr7A_383 GTCCTCGGCTGGGACGTCAAGCGGCTGCCAGGCATCGTCATCGACCCCCG SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 CGGCACGCTCGGCCAGGCCCTCCTCGCCAGGGAGGGCGAGGGCGAGAGCG chr7B_1_TraesCS7B01G008000 CGGCACGCTCGGCCAGGCCCTCCTCGCCAGGGAGGGCGAGGGCGAGAGCG chr7D_1 CGGCACGCTCGGCCAGGCGCTGCTCGCCAGGGAGGGGGCGAG-------- chr7A_1 CGGCACGCTCGGCCAGGCGCTGCTCGCCAGGGAGGGGGCGAG-------- chr7A_383 CCGCAGGCTGGGCCAGGCGCTCCTTGCCAGGGAGGGCGCAAG-------- SNPs ------------------S-------------------S-S-SSSSSSSS forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 ACGCCGCTGCTATTG------CTCACGAAGCAAAGGTTTCTCATCCCATT chr7B_1_TraesCS7B01G008000 ACGCCGCTGCTATTG------CTCACGAAGCAAAGGTTTCTCATCCCATT chr7D_1 -TGCCGCCGCTTCCACCGCC---CAGGAGGCAAAGG-TTCTCAGCCCATT chr7A_1 -TGCCGCCGCTTCCACCGCC---CAGGAGGCAAAGG-TTCTCAGCCCATT chr7A_383 -CGCCGCTGCGGCCGCCGCCACTCACGAGGCAAAGGTTTCTCAGCCCATT SNPs S----------SSS--------------S--------------S------ forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 CGTTGCTGCAGGTCGCTGACTGACGAGACTGTGTGCTAGTGCTTCGGCTG chr7B_1_TraesCS7B01G008000 CGTTGCTGCAGGTCGCTGACTGACGAGACTGTGTGCTAGTGCTTCGGCTG chr7D_1 CGTTGCCGCAGGTCGCTCACTGATGAGACTTTGTGCTGTAACTTAATTTG chr7A_1 CGTTGCTGCAGGTCGCTCACTGACGAGACTTTGTGCTGTAACTTAATTTG chr7A_383 TGTTTCTGCAGGTCGCTCACTGACGATACTGTCCTCGT--ACTTGGTCTG SNPs -----------------S-------------------SSSS---S-S--- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 ATTTTATTGTTGATTGCAGGACAATGTTGATGCTGGGGAGAATGGCCACA chr7B_1_TraesCS7B01G008000 ATTTTATTGTTGATTGCAGGACAATGTTGATGCTGGGGAGAATGGCCACA chr7D_1 ATTTAATTGTTGATTGCAGGAGAATGTTGATAGTGTGGACAATGATGGCA chr7A_1 ATTTAATTGTTGATCGCAGGAGAATGTTGATAGTGTGCACAATGATGGCG chr7A_383 ATTTAATTGTTTGTCGCAGGACAATGCTGATGCTGGGCAGAATGGTCACA SNPs ----S----------------------------------------S---- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 AGGATGCAGCGAAGGTGTGCACCTTGTTACGGTTAAATGGTGTTTGTTGA chr7B_1_TraesCS7B01G008000 AGGATGCAGCGAAGGTGTGCACCTTGTTACGGTTAAATGGTGTTTGTTGA chr7D_1 TGGATGCAGTGAAGGTGTGCGCCTTGTTACGTTAAAATGGTGGTTATTGA chr7A_1 TGGATGCAGTGAAGGTGTGCGCCTTGTTACGTTAAAATGGTGGTTATTGG chr7A_383 AGGATGCAGCGAAGGTGTGTACCTTGTTACATTAAAATGGTGGTTGTTGA SNPs -------------------------------S-S--------S------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 TGGTTGGTGAGATTGCTGGTCAATTAATCTGGTTTGGTTATTGATTTCAG chr7B_1_TraesCS7B01G008000 TGGTTGGTGAGATTGCTGGTCAATTAATCTGGTTTGGTTATTGATTTCAG chr7D_1 TGGTTGGCGAGATTGCTAGTCAGTTAATCTGGTTTCGTTATTGATTTCAG chr7A_1 TGGTTGGTGAGATTGCTGGTCAGCTGATCTGGTTTTGTTATTGATTTCAG chr7A_383 TGGTTGGTGACATTGCTGGTCAGTTAATCTGGTTTAGTTATTGATTTCAG SNPs ----------------------S------------S-------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 GAGGATGTTGGTCTGGAGAAGAATGGCTCCTTGAATGATGAAAGGAAGGT chr7B_1_TraesCS7B01G008000 GAGGATGTTGGTCTGGAGAAGAATGGCTCCTTGAATGATGAAAGGAAGGT chr7D_1 GAGGATGTTGGTTTGGACAAGAACGGCTCCTTGAATGATGACAGGAAGGT chr7A_1 GAGGATGTTGGTTCGGAGAAGAAGGGCTCCTTGAATGATGACAGGAAGGT chr7A_383 GAGGATGTTGGTTTGGAGAAGATGGGCTCCTTGAATGATGACAGGAAGGT SNPs ------------S----------S-----------------S-------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 AACAATGGTGTGCAAAGTTGTGGAGTGTTTGTTGATCACTGATGAGATCA chr7B_1_TraesCS7B01G008000 AACAATGGTGTGCAAAGTTGTGGAGTGTTTGTTGATCACTGATGAGATCA chr7D_1 AACGCTGGCGTGCAAAGTTG--------------ATCACTGACGAGATCA chr7A_1 AACGCTGGCGTGCAAAGTTG--------------ATCACTGACGAGATCA chr7A_383 AATGATGGCGTGCAAAGTTGTCGAGTGTTTATTCATCACTGACGAGATCA SNPs ---S----S------------S--------S--S--------S------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 CGAGGCTGCTGTTTGTTGTTCTGATTTGGTTGTTGATTGCAGGAGGATGT chr7B_1_TraesCS7B01G008000 CGAGGCTGCTGTTTGTTGTTCTGATTTGGTTGTTGATTGCAGGAGGATGT chr7D_1 CGAGACTACTGGTTGTTATTCTGATTTAGTTGTTGATTGCAGGAGGATGT chr7A_1 CGATACTACTGCTTGTTATTCTGATTTGGTTGTTGATTGCAGGAGGATGT chr7A_383 CGAGAATACTGTTTGTTATTCTAATTTGGTTGTTGATTG-AGGAGGATGT SNPs ----S--S---------S-------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 TGATAGTATAATGAATGAGGGCCCCTTGAGTGATGGGGATGCGGTGAAGG chr7B_1_TraesCS7B01G008000 TGATAGTATAATGAATGAGGGCCCCTTGAGTGATGGGGATGCGGTGAAGG chr7D_1 TGATAGTAGAATGAATGAGGCCGCA------------------------- chr7A_1 TGATAGTAGAATGAATGAGGCCGCA------------------------- chr7A_383 TGATAGTATGATGAATGACCGCCCC------------------------- SNPs -------------------------SSSSSSSSSSSSSSSSSSSSSSSSS forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 ----------------------------------GGGGATGCGGTGAAGG reverse_4204 -------------------------------------------------- input_sequence_52486 TTATGATCTAATTGGTGGTTAAATGATTACAGATTGATGATGAAATTGCT chr7B_1_TraesCS7B01G008000 TTATGATCTAATTGGTGGTTAAATGATTACAGATTGATGATGAAATTGCT chr7D_1 -------------------------------------------------- chr7A_1 -------------------------------------------------- chr7A_383 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 TTAT---------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 GCTGGATTATGATCTAATTTGGTTGTGACTTTCAGGAGGATGTTGATAGT chr7B_1_TraesCS7B01G008000 GCTGGATTATGATCTAATTTGGTTGTGACTTTCAGGAGGATGTTGATAGT chr7D_1 -------------------------------------------------- chr7A_1 -------------------------------------------------- chr7A_383 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 ATAATGAATGACGGCCCCTTGAGTGATGGGGATGCAACAAAGGTCTGGAA chr7B_1_TraesCS7B01G008000 ATAATGAATGACGGCCCCTTGAGTGATGGGGATGCAACAAAGGTCTGGAA chr7D_1 ------------------TTAAGTGATGGGGATGGAGCAAAGGTCTGCAA chr7A_1 ------------------TTAAGTGATGGGGATGGAGCAAAGGTCTGCAA chr7A_383 ------------------TTGAGTGATGGGGATGCGGCAATGGTCTGGAA SNPs SSSSSSSSSSSSSSSSSS------------------S------------- forward_25 -------------------------------------------------- reverse_2704 ---ATGAATGACGGCCCCTTGAG--------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 CATGT----TAAATGATTACAGATTGATGATGAAATTGTTGCTTGGTTAT chr7B_1_TraesCS7B01G008000 CATGT----TAAATGATTACAGATTGATGATGAAATTGTTGCTTGGTTAT chr7D_1 CATACAACATAAATGATTACTGATCGATCATGAGATTGTTGCTTGGTTAT chr7A_1 CATACAACATAAATGATTACTGATCGATCATGAGATTGTTGCTTGGTTAT chr7A_383 CGTTT----TAAATGATTACTGATTGATGATGAAATTGTTGCTTGGTTAT SNPs ---S----------------S----------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 GATCTACAATTTGGTAGTGACTTTCAGGAAGATGTTGATAAAGGGAAGAT chr7B_1_TraesCS7B01G008000 GATCTACAATTTGGTAGTGACTTTCAGGAAGATGTTGATAAAGGGAAGAT chr7D_1 GTTCTG--ATTTGGTTGTGACTTTCAGGACGGTGTTGATACAGGGAAGAT chr7A_1 GTTCTG--ATTTGGTTGTGACTTTCAGGACGGTGTTGATACAGGGAAGAT chr7A_383 GATCTA--ATTTGGTTGTGGCTTTCAGGAGGATGTTGATAAAGGGAAGAT SNPs ------SS-------S-------------S-------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 TGACCCTCCAAGTAATAACAATGATGAAGAGGTTCATGAGCAAGGGAATG chr7B_1_TraesCS7B01G008000 TGACCCTCCAAGTAATAACAATGATGAAGAGGTTCATGAGCAAGGGAATG chr7D_1 TGGCTCTCCAAGTAATGACAATGATGGAGAGGTTCATGGGCAAGACAATG chr7A_1 TGGCCCTCCAAGTAATAACAATGATGGAGAGGTTCATGTGCAAGGGAGTG chr7A_383 CTGCCCTCCAAGTAATAACAATGATGGAGAGGTTCATGAGCAAGGGAATA SNPs --S-----------------------S----------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 GTACAGGAACTGCTGAAAAGGTCTGTATTGATGATAATTAGCC--ATATA chr7B_1_TraesCS7B01G008000 GTACAGGAACTGCTGAAAAGGTCTGTATTGATGATAATTAGCC--ATATA chr7D_1 ATACAAGAACTGTTGAAAAGGTCTGTATCAGTGATAATTAGCCATATATA chr7A_1 GTGCAGGAACTGCTGAAAAGGTCTGTATCGATGATAATTAGCC--ATATA chr7A_383 GTAGAGGAATTGCTGAAAAGGTCTGTATCAATGATAATTAGCC--ATATA SNPs ----------------------------S--------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 AAGGTTAAAACTCCAATATGATGTACAATAGTATTT-------------- chr7B_1_TraesCS7B01G008000 AAGGTTAAAACTCCAATATGATGTACAATAGTATTT-------------- chr7D_1 AAGGTTAAAACTCCAATATGATGTACAGCAGTATTT-------------- chr7A_1 AAGGTTAAAACTCCAATATGATGTACAATAGTATTT-------------- chr7A_383 AAGGCTAAAACTCCAGTATGATAAAATTGATGGTTTAGGGGTAATTCTTG SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 -------------------------------------------------- chr7A_383 TATCTGCGGTATTATATACTTGGAATTAAAGGCAGTAACTTCACTATCTT SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 -------------------------------------------------- chr7A_383 ATGCACGGTGATACAAATGATATAGACCCACTGAGCTCCAAAGATATGAA SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 -------------------------------------------------- chr7A_383 CGATACAGACCCACTGAACTCCAAAGACACACCTAAGGAGCTATGTAAAG SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 -------------------------------------------------- chr7A_383 CTGTCCAGGAGGTCAGTACTGATATTGGCTTCTCATACTTATAGTAAGAC SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 -------------------------------------------------- chr7A_383 TGAGAACAGGAATATTTATTTAATGGCATCTTTGACAAGACTATTATTAA SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 -------------------------------------------------- chr7A_383 TCTACACATGTAATTACATTTGATTGCAAAGCTAGCTAGAGACTGCAGCT SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 --------------------------------------------TCATGA chr7B_1_TraesCS7B01G008000 --------------------------------------------TCATGA chr7D_1 --------------------------------------------TTATGA chr7A_1 --------------------------------------------TCATGA chr7A_383 GCACTAATTTTAAGCCAAGAGAAATGAGAAACCTTCTTGCAAGCTTATTC SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 TTTTGGTTGTTCAGTATTTT------------------------------ chr7B_1_TraesCS7B01G008000 TTTTGGTTGTTCAGTATTTT------------------------------ chr7D_1 TTTTGGTTGTTCAGTATTTT------------------------------ chr7A_1 TTTTGGTTGTTCAGTATTTT------------------------------ chr7A_383 TTTTGTTCTATTAGTGTTTTAGAGGTAAGATGTGCTTATTTTGCTCATGT SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 -------------------------------------------------- chr7A_383 AAATACGAACAAAACTATCTGTATGAAACAGTCCAACTGGTGCAGAGATT SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -----------------------CTTATCACATGCAGTTTAATGCTTTCT chr7B_1_TraesCS7B01G008000 -----------------------CTTATCACATGCAGTTTAATGCTTTCT chr7D_1 -----------------------CTTATAACATGCGGTTTAATGCTTTCT chr7A_1 -----------------------CTTATCACATGCGGTCTACTGCTTTCT chr7A_383 TGCATGCCAGTTCCTCTTACAAACTGATCACATGTGGTTTAGTTCTTTCT SNPs -----------------------------------S-------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 TACACTATCTGACGTAACTGTTGTTTGGCATGCAGGAAGGTGCTATTGGC chr7B_1_TraesCS7B01G008000 TACACTATCTGACGTAACTGTTGTTTGGCATGCAGGAAGGTGCTATTGGC chr7D_1 TACACAATCTGACATAACTGTTGTTTGGCATGCAGGAAGGTGCTATTGGC chr7A_1 TACACTATCTGACATAACTGTTGTTTGGCATGCAGGAAGGTGCTATTGGC chr7A_383 TGCACA-----------------------ATGCAGGAAGGTGATATTGGC SNPs -------------S------------------------------------ forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 ACTAAACAGGAGCATCCTAAGAGTACAGATGATATGAGGGGCACTTGTGA chr7B_1_TraesCS7B01G008000 ACTAAACAGGAGCATCCTAAGAGTACAGATGATATGAGGGGCACTTGTGA chr7D_1 AATAAACAGGAGCATCCTAAGAGTGCAGATGCTATGGGGGGCACTTGTGA chr7A_1 ACTAAACAGGAGCATCCTAAGAGTGCAGATGATATGAGGGGCACTTGTAA chr7A_383 AATAAACAGGAGCATGGTAAGAGTGCAGATGATATGGGGGGCACTTGTAA SNPs ------------------------S------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 TGTCAGACTAGAAAACAATTCATCGAAG---GTGCGTCTCTAACCTTCAC chr7B_1_TraesCS7B01G008000 TGTCAGACTAGAAAACAATTCATCGAAG---GTGCGTCTCTAACCTTCAC chr7D_1 TGTCAGACCAGAAAACAATTCATCAAAG---GTGCGTCTCTAACCTTCAC chr7A_1 TGTCAGACTAGAAAACAATTCATCAAAG---GTGCATCTCTAACCTTCAC chr7A_383 TGTCAGACTAGAAAACAATTCATCAAAGATGGTGTGTCTGTAACCTTCCC SNPs ------------------------S------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 ATTTGCATAACGTGATTGTTTTCTTCTGCTTATTGTAATTTTGGCATGCA chr7B_1_TraesCS7B01G008000 ATTTGCATAACGTGATTGTTTTCTTCTGCTTATTGTAATTTTGGCATGCA chr7D_1 ATTTGCTTAACGTGATTGTTTTCTTCTGCTTATTGTAATTTTGGCATGCA chr7A_1 ATTTGCATAATGTGATTGTTTTTTATTGCTTATTGTTATTTTGGCACGCA chr7A_383 ATTTTCATAACATGATTGTTTTCTTCTGCTTATTGTAACTTTGGCATGCA SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 GGAAGAAGCTGCTACAGAGAATAAGGAGGAGCATACTGAC-GTGTTGTTG chr7B_1_TraesCS7B01G008000 GGAAGAAGCTGCTACAGAGAATAAGGAGGAGCATACTGAC-GTGTTGTTG chr7D_1 GGAAGAAGCTGCTACAGAGAATAAGGAGGAGCATACTGACGGTGTTGTTG chr7A_1 GGAAGAAGCTGCTACAGAGAATAAGGAGGAGCATACTGACGGTGTTGTTG chr7A_383 GGAAGAAGCTGCTACAGAGAATAAGGAGGAGCATACTGAAGGTGTTGTTG SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 ACTCCGGAGATGATATTGGTAACTTGGGAAACAATTTAA----------- chr7B_1_TraesCS7B01G008000 ACTCCGGAGATGATATTGGTAACTTGGGAAACAATTTAATGGACTCATCA chr7D_1 ACTCCGGAGATGATATTGGTAACTTGGGAGACAATTTAGTGGACTCATCA chr7A_1 ACTCTCGAGATGATATTGGTAACTTGGGAAACAATTTAATGGACTCATCA chr7A_383 ACTTCGGAGATGATATTGGTAACTTGGGAAGGAATTTAATGGACTCATCA SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 AAGGTATTGTCTCTCTCTCT----TAACTCGTGGCATATTATCATGCTTG chr7D_1 AAGGTATTGTCTCTCTCT------TAACTCGTCGCATACCAGCATGCTTG chr7A_1 AAGGTATTGTCTCTCTCTCTCTCTTAACTCGTCGCATATCAGCATGCTTG chr7A_383 AAGGTATTGCCTCTCTCTCT----TAACTCGTCGCATATCAGTATGCTTG SNPs --------------------------------S------S-S-------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 AAATAAATCTGTTTTAAACTCCATGTACTGTGTGCAATCACTACCTTAGC chr7D_1 AAATCAATCTGTTTTAAACTTGATGTATTGTGTGCAATCACTACCTTAGG chr7A_1 AAATCAATCTGTTTT-AACTTGATGTGTTGTGTGCAATCACTACCTTAGG chr7A_383 AAATCAATCTGTTTTAAACTTGATGTGTTGTGTGCAATCACTACCTTAGA SNPs ----S---------------SS-----S---------------------S forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 TGTACTCGTGCACTCATGACATCTGGACATCACGAAAGGAGATTCTAGAT chr7D_1 TGTACTCGTGCACTCATGACATCTGGACATCACGAAAGGAGATTCTAGAT chr7A_1 TGTACTCGTGCACTCATGACATCTGGACATCGCGATAGGAGATTCTAGAT chr7A_383 TGTACTCGTGCAATCATGACATCTGGACATCGCGAAAGGAGATTCTAGAT SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 TGACAAGCCACTCACTGAACGTGTTGTCGTCCACCTGCCCATCCTACCCT chr7D_1 TGACAAGCCACTCACTGAACGTGTTATCGTCCACCTGCCCATCCTACCCT chr7A_1 TGACAAGCCACTCACTGAACGTGTTATCCTCCACCTGCCCATCCTAGCCT chr7A_383 TGACAAGCCACTCACTGAACGTGTTATCCTCCACCTGCCCATCCTACCCT SNPs -------------------------S------------------------ forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 CGCCAGTTTACAGCGCTCTCATCCAACCAAAAACGTTAACCCATGACTGG chr7D_1 CGCCAGTTTACAGCCCTCTCATCCAACCAAAAACCTTAACCCATGACTGA chr7A_1 CGCCAGTTTACAGCCCTCTCACCCAACCAAAAACCTTAACCCATGACTGG chr7A_383 CGCCAGTTTACAGCCCTCTCATCTAACCAAAAACCTTAACCCATGACTGG SNPs --------------S-------------------S--------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 GCAGGGCCAACGATGAACACCCGTAATGCCACAACAATAACAACGGGCCA chr7D_1 GCAGGGCCAACGATGAACGGGCATAATGCCACAACAATAACGACGGCCCA chr7A_1 GCAGGGCCAACGATGAACGGGCGTAATGCCACAACAATAATGGCGGCCCA chr7A_383 GCAGGGCCAACGATGAACGACTGTAATGCCACAGCAATAACGATGGACCA SNPs ------------------SS---------------------S----S--- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 TTTCTGCCTGCCAACCC-AAGCCTTGCCCGCAACCGTCTTTGGCCATCCA chr7D_1 TTTCTGCCTGCCAACTCAAAGCCTTGTCCGCAACTGTCTTTGGCCATCCA chr7A_1 TTTCTGCCTGCCAACCC-AAGCCTTGCCTGCAACTGTCTTTGGCCATCCA chr7A_383 TTTCTGCCTGATCAGGCCACC----------------------------- SNPs ----------------------------------S--------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 ACCTCCGCTCCCATGTCTCCTGCCTCCCTGACCAACCTCACCGGATCAGG chr7D_1 ACCTCCGCTCCCATGTCTCCTGCCTCCCTAACAAACCTC----------- chr7A_1 ACCTCTGCTCCCATGTCTCCTGCCTCCCTGACCAACCTTACCGGATCAG- chr7A_383 --------------------------------------C----------- SNPs -------------------------------------------------S forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 CCACCCTGACCCTCTCACAGACTGATCCGGTCACATGACTCGTGCCACCG chr7D_1 ------TGACCCTCTCGCAGCCTGATCTGGTCACATGGCTCGTGCCACCG chr7A_1 -------GACCTTGTCCCATCCTGATCCGGTCACATGACTCGTGCCACCG chr7A_383 ------TGACCCTCTCACAGCCTGACCCGGTCACATGACTCATGCCACCG SNPs SSSSSS--------------S----------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 ---CCCTGACCCTCTCACAGACT--------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 ATGGGGCCATCATCATGGGTAGTTTGGTACTCCCACCGACTTCACAGCTT chr7D_1 ATGGGGCCATCATCATGGGTAGTTGGGTACTCCCACCGACTTCACAGCTT chr7A_1 ATGGGGCCATCATCATGGGTAGTTGG-TACTCCCACCGACTTCACAGCTT chr7A_383 ATGGGGCCATCATCATGTGTAGTTGGGTACTCCCACTGACTTCACAGCTT SNPs ------------------------S------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 GCACAATGTTGTCAGATCTGCTGCATCTGCATTTCAAGGATTACACACA- chr7D_1 GCACAATGTTGTCAGATCTGCTGCATCTGCATTTTAAGGATTACACGCA- chr7A_1 GCACAATGTTGTCAGATCTGCTGCATCTGCATTTCAAAGATTACATGCA- chr7A_383 GCACAATGTTGTCAGATCTGCTGCATCTGCATTTCAAGGATTACACGCAA SNPs ----------------------------------------------S--- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 --------------------ATCCCACCATTCATTTTGGCATTACCAGAC chr7D_1 --------------------ATCCCACGATTCATTTTGGCATTACCCGAC chr7A_1 --------------------TTACCA---------------------GAC chr7A_383 TCTCACCATTCATTTTGGCATTACCA---------------------GAC SNPs ---------------------------S------------------S--- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 CTCATGTATATTTTTGTTATGCTAAATTGGGACATTATATTGCTGAGACA chr7D_1 CTCATGTATATCTTTCTTATGCATTTTTGGGACATTATATTGCCAAGACA chr7A_1 GTCATGTATATTTTTGTTATGCATTTTTGGGACACTTTTTAGGTA----- chr7A_383 CTCATGTAATTTTTTGTTATGCATTTTTGGGATATTATATGGCCGAGACA SNPs ----------------------SSSS------------------------ forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 CTGTTTAGGTAATAGAAGC-AACACTCTTCCGTCGTCCTTC---AAAAGA chr7D_1 CTGTTTAGATAATGGAAGCAAACACTGTTCCGGCCTCCT---TCAAAAGA chr7A_1 ----------AATGGAAGCAAACACTGTTCCGACCTCCTTCATCAAAAGA chr7A_383 CTGTTTAGGTAATGGAAGCAAACACTCTTCCGGCCTCCTTCATCAAAAGA SNPs -------------S------------------S-S--------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 TACACATGTTTGGTGCATTATCTTATATTTTTCTGGTTTTGCATTTTTGT chr7D_1 TACACATGTTTGGTGCATTATTTTATATTTTTCTG-TTTTGCATTTTTGT chr7A_1 TACACATGTTTGGTGCATTATCTTATATTTTTCTA-TTTTGTATTTTTGT chr7A_383 TACACATGTTTGGTGCATTATCTTATATTATTCTG-TTTTTGTTTTTTGT SNPs -----------------------------------S-------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 ACTGGTT-GTAATC------------------------------------ chr7D_1 ACTGGTTTGTAATT------------------------------------ chr7A_1 ACTGGTTGGTAATA------------------------------------ chr7A_383 ACTGGTTTGTAATACTCCCGCTGTCCCAAAATAAGTGTCCCAACTTTGTA SNPs -------------S------------------------------------ forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr7A_1 -------------------------------------------------- chr7A_383 CTAACTTCAGTACAAAGTTGTACTAGAGTTGAGACACTTATTTTCGGACG SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 ---------GGATATTTTGTTGAAAAAGTAGTATGTCAAACAGTATATTT chr7D_1 ---------GTATATTTTGTTGAAAAAGTAGTATGTCAAACAATATATTT chr7A_1 ---------GTATAGTTTGTTGAAAAAGTAGCATGTCAAACATTATATTT chr7A_383 GAGGGAGTAGTATATTTTGTTGAAAAAGTAGCATGTCAAGCAATATATTT SNPs ----------S-------------------------------S------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 GTGGGTTGCACTGGTGTACATAGATATTTTTTCTAATGCATTTTTGTGAT chr7D_1 GTGGGTTGCATTGGCGTACATAGATATTTTT-CTAATGCAGTTTTGTGAT chr7A_1 GTGGGTTGCATTGGCGTACATAGATATTTTTTCTAATGCATTTTTGTGAT chr7A_383 GTGGGTTACATTGGCGTACATAGATATCTTTCCTAATGCATTTTTGTGCT SNPs ----------S---S----------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 AGGCAAACATATTTGTCATACAT-TTTTTTATTCATTCAAATTATAAAAT chr7D_1 AGGCAAACATATTTGTCATACATTTTTTTT---CATTCAACTTATAAAAT chr7A_1 AGGCAAACATATTTGTCATACATTTTTTTTATTCATTCAAATTATAAAAT chr7A_383 AGGCAAACATATTTGTCATACA-TTTTTTTATCCATTCAAATTATAAAAT SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 TGGATGTGAGGAAGTGAGTCTCAGCCCAATTTGTGGAGGAATGACGTGAA chr7D_1 TGGATGTGAGGAAGTGAGTCTCAGCCAAATTTGTGGAGGGTTGACGTGAA chr7A_1 TGGATGTGAGGAAGTGAGTCTCAGCCAAATGTGTGGAGGGTTGACGTGAA chr7A_383 TGGATGTTGGGAAGTGAGTCTCAGCCAAATTTGTGGAGAGTTGACGTGAA SNPs --------------------------S------------SS--------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 -------------------------------------------------- chr7B_1_TraesCS7B01G008000 GACATACTAAGTGGCATGATATTTGATGTCCACCAGTCCTGATTTGGATT chr7D_1 GACATACTAAGTGGCATGATATTTGATGTCCACCAGTCCTGATTTGGATT chr7A_1 GACATACTAAGTGGCATGATATTTGATGTCCACCAGTCCTGATTTGGATT chr7A_383 GACATACTAAGTGTCATGATATTTGATGTCCACCAGTCCTGATTTGGATT SNPs -------------------------------------------------- forward_25 -------------------------------------------------- reverse_2704 -------------------------------------------------- forward_2604 -------------------------------------------------- reverse_4204 -------------------------------------------------- input_sequence_52486 ---------------- chr7B_1_TraesCS7B01G008000 CTCAACCACACGTTCT chr7D_1 CTCGACCACACGTTCT chr7A_1 CTCAACCACATGTTCT chr7A_383 CTCGACCACACGTTCT SNPs ---------------- forward_25 ---------------- reverse_2704 ---------------- forward_2604 ---------------- reverse_4204 ----------------