CLUSTAL X (1.81) multiple sequence alignment input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 GCCACCTTAGTAACCTAATCTAATACTAGCCGAA---------------- chr4A_1 GCCACCTTAGTAACCTAATCTAATACTAGCCG------------------ chrUn_30 ATGAGACCTACGATCCACATGTGACACAAATAGAACTCCACAAGCACTCT chr7A_30 ATGAGACCTACGATCCACATGTGACACAAATAGAACTCCACAAGCACTCT chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --------------------------------S----------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 CCTAAAATTAGTTGACTTAACATTGCCTATTTTGGGATTTCTATTCTCTC chr7A_30 CCTAAAATTAGTTGACTTAACATTGCCTATTTTGGGATTTCTATTCTCTC chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 CCTGCAAAATGTCTCCACTTCTTATCTCTACTACTCATCCTTGATCTTTA chr7A_30 CCTGCAAAATGTCTCCACTTCTTATCTCTACTACTCATCCTTGATCTTTA chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 ATTATATAGAACTAGAGATAGTTGTCTCCTTGTAGGGAGCACCTTATTTA chr7A_30 ATTATATAGAACTAGAGATAGTTGTCTCCTTGAAGGGAGCACCTTATTTA chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 TAGGACTGGTAGAAGAGACCGACGAATTAATCACGTGACATGTGACACTA chr7A_30 TAGGACTGGTAGAAGAGACCGACGAATTAATCACGTGACATCTGACACTA chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 ACCAAACTCCACAACCCTTTGTACTAAAATTAACATACTCCACTATTTGA chr7A_30 ACCAAACTCCACAACCCTTTGTACTAAAATTAACATACTCCACTATTTGA chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 GATTTATTTTCTCCCCAACCAAAATATCTCCACTACTTATCTTTGCACTT chr7A_30 GATTTATTTTCTCCCCAACCAAAATATCTCCACTACTTATCCTTGCACTT chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 TTGACATAGCCTGTTTTTTCAAAGAGAAAATAGAACAGGAAACATCGCAA chr7A_30 TTGACATAGCCTGTTTTTTCAAAGAGAAAATAGAACAGGAAACATCGCAA chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 AGTCTAGAAATATCTTGTCACACGTTTTTAACTAATCAAGAATTTGGGGT chr7A_30 AGTCTAGAAATATCTTGTCACACGTTTTTAACTAATCAAGAATTTGGGGT chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 TCATTGAGAAACATGCACATGCATGGGATCGTGAGGAAGGCAGCACGGGT chr7A_30 TCATTGAGAAACATGCACGTGCATGGGATCGTGAGGAAGGCAGCACGGGT chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 CCGTCAGGAGTGGCGGTTACCACTCCAACAAGAAAGGAGGCTATTGGACG chr7A_30 CCGTCAGGAGTGGCGGTTACCACTCCAACAAGAAAGGAGGCTATTGGACG chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 CACGTCGATCTGGAGTCCGATTCAGTGTGTTTTTTGTTGATGCTTCTTTC chr7A_30 CACGTCGATCTGGAGTCCGATTCAGTGTGTTTTTTGTTGATGCTTCTTTC chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 ACTCATTTAGTTTCAGTTATAATTTACATACACCAGTTTCTTGAAATGAC chr7A_30 ACTCATTTAGTTTCAGTTATAATTTACATACACCAGTTTCTTGAAATGAC chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 TGAAATTAATTATTTGCAATGAGTGAAATTATCTTTTGGAAATAATTGAA chr7A_30 TGAAATTAATTATTTGCAATGAGTGAAATTATCTTTTGGAAATAATTGAA chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 ACATGTCTTTCAATAGAAAGGAGTGAAATTGGTTTTTTGAAATGAAAGAA chr7A_30 ACATGTCTTTCAATAGAAAGGAGTGAAATTGGTTTTTTGAAATGAAAGAA chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 ATCTTTTTAGAATGATTGAAATATTTTTTTAAATAAGTGAAATGTATTTT chr7A_30 ATCTTTTTAGAATGATTGAAATATTTTTTTAAATAAGTGAAATGTATTTT chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 TTGAAATGATTGAAAACAATCTTTTAAGTGTGTGAAATCCGGTTTTATGA chr7A_30 TTGAAATGATTGAAAACAATCTTTTAAGTGTGTGAAATCCGGTTTTATGA chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 AATGAATGAAATCCAAGAGATTTTATTTCAATCGTTCATATATTTTAAAC chr7A_30 AATGAATGAAATCCAAGAGATTTTATTTCAATCATTCATATATTTTAAAC chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 TATAGTTTCATTTTTGATTTTTTTAAATATATTGAGCTCCTGGTACCAAC chr7A_30 TATAGTTTCATTTTTGATTTTTTTAAATATATTGAGCTCCTGGTACCAAC chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 ACCTTCAGAGTAAGACTAATCTTTGATACATTTAAAACACGTTTAAATTC chr7A_30 ACCTTCAGAGTAAGACTAATCTTTGATACATTTAAAACACGTTTAAATTC chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 AGTGTTTCAAGCTAGTTATTTCACTCAATGTATTTCAGTATGTGAAACTG chr7A_30 AGTGTTTCAAGCTAGTTATTTCACTCAATGTATTTCAGTATGTGAAACTG chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 GTGATTTGTCAAGCTGGTTACTTATGTGTGAAATTAGTTATTCGAAATCG chr7A_30 GTGATTTGTCAAGCTGGTTACTTATGTGTGAAATTAGTTATTCGAAATCG chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 GTATGTGAAACTTTCACTAGACCTGGCTGAGCTCTCTGGGATCCAGTGGC chr7A_30 GTATGTGAAACTTTCACTAGACCTGGCTGAGCTCTCTGGGATCCAGTGGC chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 CGTCCATTAGCGCTCATAATTTGTCTAAGATAGTTTTCAGTACATATAGT chr7A_30 CGTCCATTAGCGCTCATAATTTGTCTAAGATAGTTTTCAGTACATATAGT chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 CCCTTACATTTTGCTACTTTTATAAATGTATTTTCACATTCTCATTTTAT chr7A_30 CCCTTACATTTTGCTACTTTTATAAATGTATTTTCACATTCTCATTTTAT chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 TTTCTGCTAAGTGTTTACTGGCAGTTTATTTTTATGTTTAGATATACAAG chr7A_30 TTTCTGCTAAGTGTTTACTGGCAGTTTATTTTTATGTTTAGATATACAAG chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 TTCACTAAATGTCACCTTCACTCCTGACTGTAACCTATCTCTCGAAACCA chr7A_30 TTCACTAAATGTCACCTTCACTCCTGACTGTAACCTATCTCTCGAAACCA chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 CCATGCGTAACATAACAAAGTGCTTTGCACACTCTTAATAAAAAAAAGAT chr7A_30 CCATGCGTAACATAACAAAGTGCTTTGCACACTCTTAATAAAAAAA-GAT chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 ATACTCATTTATTCTACACACACACATTTGTCATGCTTACTCTACATTAT chr7A_30 ATACTCATTTATTCTACACACACACATTTGTCATGCTTACTCTACATTAT chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 TATTCTCTTATATTCTGTTACACACCGATCCGTCATATATTACGAATCCA chr7A_30 TATTCTCTTATATTCTGTTACACACCGATCCGTCATATATTACGAATCCA chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 GTTTTAAACCCGAGTTCTTTACACACATGTTCTTAATCCTAAACTGCATT chr7A_30 GTTTTAAACCCGAGTTCTTTACACACATGTTCTTAATCCTAAACTGCATT chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 ------------ATACATGGACATGCAAGTATGAGGGAAACTTCCAGAAA chr4A_1 ----------AAATACATGAACATGCAAGTATGAGGGAAACTTCCAGAAA chrUn_30 GTTGCCACCTAAATACATGAACATGCAAGTATGAGGAAAACTTCCAGAAA chr7A_30 GTTGCCACCTAAATACATGAACATGCAAGTATGAGGAAAACTTCCAGAAA chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------S------------------------------ forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 CATGCATGTATGCAAAACACAAATATGCGTATTCCGACAGACCACGTGGG chr4A_1 CATGCATGTATGCAAAACACGAATATGTGTATTCCGACAGACCACGTGGG chrUn_30 CATGCATGTATGCAAAACACGAATATGCGTATTCCGACAGACCACGTGGG chr7A_30 CATGCATGTATGCAAAACACGAATATGCGTATTCCGACAGACCACGTGGG chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --------------------S----------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 GATTAACGTGCGAATACTCAAAACAAATGAACATGATAAGGGCGATGAAT chr4A_1 GATTAACGTGCGAATACCCAAAACAAACGAACATGATAAGGGCGATGAAT chrUn_30 GATTAACGTGCGAATACTCAAAACAAACGAACATGATAAGGGCGATGAAT chr7A_30 GATTAACGTGCGAATACCCAAAACAAACGAACATGATAAGGGCGATGAAT chrUn_141 ------------------CAAAACAAACGAACATGATAAGGGCGATGAAT chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ---------------------------S---------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 AACCGGAGTTTCTTGATCTGATCTTGGAGAGTGCCTCTATTTGTAAGATT chr4A_1 AACCGGGGTTTCTTGATCTGATCTTGGAGAGTGCCTCTATTTGTAAGATT chrUn_30 AACCG-----TCTTGATCCGATCTTAGAGAGTGCCTCTATTTGTAAGATT chr7A_30 AACCG-----TCTTGATCCGATCTTAGAGAGTGCCTCTATTTGTAAGATT chrUn_141 AACCG-----TCTTGATCCGATCTTAGAGAGTGCCTCTATTTGTAAGATT chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ------S------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 TTTATGAGACCTACGATCCACAAGTGACACAAATAG-------------- chr4A_1 TTTATGAGACCTACGATCCACATGTGATATAGATAGGGGTGAGACTTGCA chrUn_30 TTTATGACACCTACGATCCACATGTGACACAAATAG-------------- chr7A_30 TTTATGACACCTACGATCCACATGTGACACAAATAG-------------- chrUn_141 TTTATGACACCTACGATCCACATGTGACACAAATAG-------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ----------------------S--------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 TGCTCCCTTCACATGCTCCCATCTATGCTCCCAGGTACGTGGCTTGATTT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 GATTGGAACAAAATAAAGCCCGGGCCCACCCCGTTAAAATCAGGGGGAGG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 ATGATTAGATTAGAAAGGAAAAAAAGAAAAAAAACAGTCGTAGGATGAAG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 TGGGAGGACGGACGAGAGCATGGGGAGGGAGCAGGCAAGCCGGATCCCGC chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 ------AACTCCACAAGCACTCTACTAAAATTAGTTGACTTAACAC---T chr4A_1 AGATAAAACTCTAGAAGCACTCTACTAAAATTAGTTGACTTAACATTATT chrUn_30 ------AACTCCACAAGCACTCTACTAAAATTAGTTGACTTAACAT---T chr7A_30 ------AACTCCACAAGCACTCTACTAAAATTAGTTGACTTAACAT---T chrUn_141 ------AACTCCACAAGCACTCTACTAAAATTAGTTGACTTAACAT---T chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ---------------------------------------------S---- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 GCCTATTTTGGGGTTTCTTTTCTCTCCGCGCAAAAAGTCGCCACTACTTA chr4A_1 GGCTATTTTGGGATTTATTTTCTGTCCATGCAAAATGTCGCCACTACTTA chrUn_30 GCCTATTTTGGGGTTTCTTTTCTCTCCACGCAAAAAGTCGCCACTACTTA chr7A_30 GCCTATTTTGGGGTTTCTTTTCTCTCCACGCAAAAAGTCGCCACTACTTA chrUn_141 GCCTATTTTGGGGTTTCTTTTCTCTCCACGCAAAAAGTCGCCACTACTTA chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ---------------------------S---------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 TCTCTTG----TAGTCATCCATGATCTTTATATAGAAGTGGAGATAGTTG chr4A_1 TCTCTACTACATACTCATCCTTGATCTTTATATAGATGTGGAGATAGTTG chrUn_30 TCTCTTC----TACTCATCCATGATCTTTATATAGAAGTGGAGATAGTTG chr7A_30 TCTCTTC----TACTCATCCATGATCTTTATATAGAAGTGGAGATAGTTG chrUn_141 TCTCTTC----TACTCATCCATGATCTTTATATAGAAGTGGAGATAGTTG chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ------S------S------------------------------------ forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 TCTCCTTGCAGGGAGCAC---CTCTATTTATAGGACTGTCAATTACAAGA chr4A_1 TCTCCTTGTAGGGAGCAACAACTCTATTTATAGGACTGTTAATTACAAGA chrUn_30 TCTCCTTGCAGGGAGCAC---CTCTATTTATAGGACTGTTAATTACAAGA chr7A_30 TCTCCTTGCAGGGAGCAC---CTCTATTTATAGGACTGTTAATTACAAGA chrUn_141 TCTCCTTGCAGGGAGCAC---CTCTATTTATAGGACTGTTAATTACAAGA chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ---------------------------------------S---------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 CCGACGACTCAATCATGTGACATGTGACACCAACCAAGCTCCACAACACT chr4A_1 CCGACGACTTAATCATGTGACATGTGACACCAACCAAACTCCACAACACT chrUn_30 CCGACGACTCAATCATGTGACATGTGACACCAACCAAACTCCACAACACT chr7A_30 CCGACGACTCAATCATGTGACATGTGACACCAACCAAACTCCACAACACT chrUn_141 CCGACGACTCAATCATGTGACATGTGACACCAACCAAACTCCACAACACT chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------S------------ forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 ATGTACTAAGATTAACATACTCCACTATTTGAGATTTCTTTTCTCTCCAA chr4A_1 CTGTACTAAAATTAGCGAGCGAG--------------------------- chrUn_30 CTGTACTAAAATTAACATACTCCACTACTTGAGATTTCGTTTCTCTCCAA chr7A_30 CTGTACTAAAATTAACATACTCCACTACTTGAGATTTCGTTTCTCTCCAA chrUn_141 CTGTACTAAAATTAACATACTCCACTACTTGAGATTTCGTTTCTCTCCAA chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs S--------S-----------------S----------S----------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 CCAAAATATCTCCACTACTTATCATTGATCTTTTGACATAGCCTTTTCTT chr4A_1 ------------------TTATCCTTGATCTTTTGACATAGACTTTTCTT chrUn_30 CCAAAATATCTGCACTACTTATCCTTGATCTTTTGACATAGCCTTTTCTT chr7A_30 CCAAAATATCTGCACTACTTATCCTTGATCTTTTGACATAGCCTTTTCTT chrUn_141 CCAAAATATCTGCACTACTTATCCTTGATCTTTTGACATAGCCTTTTCTT chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -----------S-----------S-------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 TTGACGATCAATCAAAAAGAGAAAAGAGAAAGAGAAATCTCACAAAGTAC chr4A_1 TCA---ATCAATCAAAAAGAGAAAAGAGAAAGAGAAATCTAACAAATTAA chrUn_30 TT---GATCAATCAAAAAGAGAAAAGAGAAAT--AAATCTCA-------- chr7A_30 TT---GATCAATCAAAAAGAGAAAAGAGAAAT--AAATCTCA-------- chrUn_141 TT---GATCAATCAAAAAGAGAAAAGAGAAAT--AAATCTCACACAGTAA chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --SSS--------------------------------------------S forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 GTGTTGGGACACGTTTTTAAGTAACCAAGAAACAAATTGGGGTTCGTGAG chr4A_1 GTCTA--GACACGTTTTTAAGTAACCAACAAAACAAATTG---------G chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GTCTA--GACACGTCTTGGGAC---------------------------G chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --S-SSS---------------------S---SS--S-S-SSSSSSSSS- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 GGTCCGTCGGGAGTGGCGGTTGGTTACCACTCCAGCTGGAAAGGAAGCTA chr4A_1 GGTTCGTGGGGAGAGGCGGTTGGTTACCACTCCAGCTGGAAAGGAAGCTG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GGTCCGTCGGGAGTGGCGGTTGGTTACCACTCCAGCTGGAAAGGAAGCTG chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------S forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 CCGGACGCACGTC----------TCGAGAGATCTCCATGCATGCACGCTA chr4A_1 CTGGACGCACGTC----------TC--------------CATGCACGCTA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CTGGACGCACGTCTCGAGAGAACTC--------------CATGCACGCTA chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -S-----------------------SSSSSSSSSSSSSS----------- forward_2535 ---------------CGCACGTCTCGAGAGATCTC--------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 CCTGTCGATCGGACTTGGCGGTTACCAACCAACCGCCAAGAACCTTCCCG chr4A_1 CCTGTCGATCGGACTTGGCGGTTACCAACCAACCGCCAAGAACCTTCCCG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CCTGTCGATCGGACTTGGCGGTTACCAACCAACCGCCAAGAACCTTCCCG chr5B_809 --------------------------AACCAACCGCCAAGACCCCTCCGG chr5A_809 --------------------------AACCAACCGCCAAGACCCCTCCCG chr5D_825 ------------------------------------------CCCTCCCG chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 GCCTCTCCTCCT--CACTCCCCCGCCGCCTATTTCACCACT-------CC chr4A_1 GCCTCTCCTCCT--CACTCCCCCGCCGCCTATTTCACCAC---------C chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GCCTCTCCTCCT--CACTCCCCCGCCGCCTATTTCACCACT-------CC chr5B_809 GCCTCTCCTCCCCCCCAGCCCCCGCCGCCTATTTCTTCACCTCTAGACCC chr5A_809 GCCTCTCCTCCC--CCAGCCCCCGCCGCCTATTTCTTCACCCGTAGGCCC chr5D_825 GCCTCTCCTCCC--GCAGCCCCCGCGACCTATTTCTTCACCCCTAGGCCC chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 CCCTCTCGCCGGCGCCGCCGCCCAATCCGCCCCA---CCACTCGCCACCG chr4A_1 CCGTCACGCCGGCGCCGCCGCCCAATCCGCTCC---TCCACTCGCCACCG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CCCTCTCGCCGGCGCCGCCGCCCAATCCGCCCCTC---CACTCGCCACCG chr5B_809 CCACCTCGCCGGCGCCGCCGCCCCATCCGTCCGTCGTCCACTCGCCATCG chr5A_809 CCACCTCGCCGGCGCCGCCGCCCCATCCGTCCGTCGTCCACCCGCCATCG chr5D_825 CCACCTCGCCGGCGCAGCCGCCCCATCCATCCGTCGTCCACCCGCCATCG chr4A_876 --CTCACGCCGGCGCCGCCGCCCAATCCGCCCCTC---CACTTGACACCG chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ---------------------------------S---------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 CCGCCCCTGCCAACTGCAGTGCCGATGCGCTGCTG---GTAGATGAATGT chr4A_1 CCGCCCTTGCCAACTGCAGTGCGGATGCGCTGCTG---GTAGATGAATGA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CCGCCCCTGCCAACTGCACTGCGGATGCGCTGCTG---GTAGATGAATGT chr5B_809 CCGCCCTTGGCACGTGCAGTGCGGATGC---GCTG---GTAGATGAATGA chr5A_809 CGGCCTTTGTCACGTGCATTGCGGATGC---GCTG---GTAGATGAATGA chr5D_825 CCGCCCTTGGCACGTGCAGCGCGGATGC---GCTG---GTAGATGAATGA chr4A_876 GCGCCCTTTGCAACTGCAGTGCGGATGC---GCTGCTGGTAGTTGAATGA chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ----------------------S--------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ---------------------------------------ATGGCAGACCA chr7D_1_TraesCS7D01G003500 GGAGTGCCTTCA---CTCTCCGCACGCTC---CATCGTAATGGCAGACCA chr4A_1 GGAGTGCCATCAAGACTCTACGCACGCGC---CACCGTAATGGCAGACCA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GGAGTGCCATCAAGACTCTCCTCACGCGC---CACCGTAATGGCAGACCA chr5B_809 GGAGTGCCATCA---CTCTGCGCACGCGC---CATCATAATGGCGGACCA chr5A_809 GGAGTGCCATCA---CTCTGCACGCGCGC---CATCATAATGGCGGACCA chr5D_825 GGAGTGGCATCA---CGCTGCGCACGCGCCATCATCATAATGGCGGACCA chr4A_876 -------------------CCGCACGCGC---CACCGTAATGGCAGACCA chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --------S------------------S---------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CCACCA------------------GCAGCAGC---AGCAGCCCCCGTCGT chr7D_1_TraesCS7D01G003500 CCACCA------------------GCAGCAGC---AGCAGCCCCCGTCGT chr4A_1 CCAGCA---------------------GCAGCAGCAGCAGCAACCGTCGT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CCACCACCACCACCACCAGCAGCAGCAGCAGC---AGCAGCCCCCGTCGT chr5B_809 CCACCA---------------------GCTGCTCCCATCGT---CGTCGT chr5A_809 CCAGCA---------------------GCTGCTCCCGACGTTGA---CGT chr5D_825 CCAGCA---------------------GCTGCTCCCGTCGTTGA---CGT chr4A_876 CCACCA---------------------GCAGC---AGCAACCCCCGTCTT chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CCGCCTGCACCAACTGCGGCACCGAGCGCGCCGTCGTCTACTGCTCCGCC chr7D_1_TraesCS7D01G003500 CCGCCTGCACCAACTGCGGCACCGAGCGCGCCGTCGTCTACTGCTCCGCC chr4A_1 TCGCATGCACCAACTGCGGCACCGAGCGCGCCGTCGTCTTCTGCTCCGCC chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CCGCCTGCACCAACTGCGGCACCGAGCGCGCCGTCGTCTACTGCTCCGCC chr5B_809 CCAGGTGCAGCAACTGCGTCACGGAGCGCGCCGTCGTCTTCTGCTTCGCC chr5A_809 GCAGGTGCAGCAACTGCGTCACCGAGCGCGCCGTCATCTTCTGCATCGCC chr5D_825 GCAGGTGCAGCAACTGCGCCACCGAGCGCGCCGTCGTCTTCTGCTTGGCC chr4A_876 CCGCCTGCACCAACTGCGCTACCGAGCGCGCCGTCGCCTACTGCTCCGCC chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CACGGCGCCCGGCTCTGCCTCGAGTGCGACGGCGCCGTGCACGGCGTCAA chr7D_1_TraesCS7D01G003500 CACGGCGCCCGGCTCTGCCTCGAGTGCGACGGCGCCGTGCACGGCGTCAA chr4A_1 GACGGCGCGCGGCTCTGCCTCGAGTGCGACGGCGCCGTGCACCGCGTCAA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GACGGCGCGCGGCTCTGCCTCGAGTGCGACGGCGCCGTGCACGGCGTCAA chr5B_809 GACGGCGCCAGGCTCTGCCTCGAGTGCGACGGCGCCGTGCACGGCGCCAG chr5A_809 GACGGCGCCAGGCTCTGCCTCGAGTGCGACGGCGCCGTGCACGGCGCCAG chr5D_825 GACGGCGCCAGGCTCTGCCTCGAGTGCGACGGCGCCGTGCACGGCGCCAG chr4A_876 GACGGCGCCAGGCTCTGCCTCGAGTGCGACTGCGCCGTGCACCGCGTCAG chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs S------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CCAGGTCACGTCCCTCCACCCGCGCGCCCCGATCTGCGACGCCTGCGGCG chr7D_1_TraesCS7D01G003500 CCAGGTCACGTCCCTCCACCCGCGCGCCCCGATCTGCGACGCCTGCGGCG chr4A_1 CCATGTCGCGTCCCTCCACCCGCGCGCCCCGATCTGCGACGCCTGCGGCG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CGATGTCACGTCCCTCCACCCGCGCGCCCTGATCTGCGACGCCTGCGGCG chr5B_809 CGAGCTCGCGAGCCTCCATTCGCGCGCCCCGCTCTGCGACGGCTGCTGCG chr5A_809 CGAGCTCGCGGGCCTCCACTCGCGCGCCCCGCTCTGCGACGGCTGCTGCG chr5D_825 CGACCTCGCGGGCCTCCACTCGCGCGCCCCGCTCTGCGACGCCTGCTGCG chr4A_876 CCCGCTCACGGCCCTCCACCCGCGCGCCCCCCTGTGCGACGCCTGCGGCG chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TCGCCCACGCCGCGATCCGCTGCCAGATGGCCGGCAACCGGTCCGCGCTC chr7D_1_TraesCS7D01G003500 TCGCCCACGCCGCGATCCGCTGCCAGATGGCCGGCAACCGGTCCGCGCTC chr4A_1 TCGCCCGCGCCGCGATCCGCTGCCAGATGGCCGGCAACCGGTCCGCGCTC chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TCGCCCGCGCCGCGGTCCGCTGCCAGATGGCCGGCAACCGGTCCACGCTC chr5B_809 CCGCGCCCGCCGCGCTCCGCTGCCAAATCGGCGCCCAGCGGGCCACGCTC chr5A_809 CCGCGCCCGCCGCGCTCCGCTACCAATTCGGCGCCCACTGGGCCACGCTC chr5D_825 CCGCGCCCGCCGCGCTCCGCTGCCAAACCGGCGCCCACCGTGCCACGCTC chr4A_876 TCGCCCGCGCCGCGATCCGGTGCCAGATCGCCGGCGCCCGGGCCACGCTC chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ------S------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TGCGGCGCCTGCGCCGACCGCCTGGCCGCGCCG---GACGGCGCCCCCAT chr7D_1_TraesCS7D01G003500 TGCGGCGCCTGCGCCGACCGCCTGGCCGCGCCG---GACGGCGCCCCCAT chr4A_1 TGCGGCGGCTGCGCCGAGCGCCTGGCCCCGCCG---GACGGCGCCTCCGA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TGCGGCGACTGCGCCGACCGCCTGGCCCCGCCG---GGCGGCGGCTCCAT chr5B_809 TGCACCGACTGCGCCGACGGCCGCGCGGACGGCCGCGGCGGCGCCTCCCT chr5A_809 TGCACCGGCTGCGCCGACGGCCGCG------------GCGGCGCCTCCCT chr5D_825 TGCGCCGGCTGCGCCGACGGCCGCG------------GCGGCGCCTCCCT chr4A_876 TGCGGCGGCTGCGCCGGCTGCCTGGCCACGCCG---GACGGCGCCTCCAT chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------S-------------------------------------S---- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CGTGGAGGAGTACACCGGGTGCCCCTCGCCCGCCGAGATGCTCCGCATCC chr7D_1_TraesCS7D01G003500 CGTGGAGGAGTACACCGGGTGCCCCTCGCCCGCCGAGATGCTCCGCATCC chr4A_1 CGTGGAGGAGTACACCGGGTGCCCCTCGCCCGCCGAGATGCTCCGCATCC chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CGTGGAGGAGTACACCGGGTGCCCCTCGCCCGCCGAGATCCTCCGCATCC chr5B_809 CGTGGAGGTTTACACCGGCTGCCCCGCGCCCGCCGAGGTCCTCCGCACCC chr5A_809 CGTGGAGGTTTACACCGGCTGCCCCGCGCCCGCCGAGGTCCTCCGCACCC chr5D_825 CGTGGAGGTTTACACCGGCTGCCCCGCGCCCGCCGAGGTCCTCCGCACCC chr4A_876 CGTGGAGGAGTACACCGGATGCCCCACGCCCGCCGAGATCCTCCACATCC chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TCTCCGTCGAGGCCCCC---------TCGTCGCAGGAGGACTTCGACGCC chr7D_1_TraesCS7D01G003500 TCTCCGTCGAGGCCCCC---------TCGTCGCAGGAGGACTTCGACGCC chr4A_1 TCTCCGTCGAGGCCCCC---------TCGTCGCAGGAGGACTTCGACGCC chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TCTCCGTCGAGGCCCCC---------TCGTCGCAGGAGGACTTCGACGCC chr5B_809 TCTCCGTCGACGCGCCG------TCATCGTCGCAGCAGGACTTCGACGCC chr5A_809 TCTCCGTCGACGCGCCGTCGTCG---TCGTCGCAGGAGGACTTCGACGCC chr5D_825 TCTCCGTCGACGCGC------CGTCATCGTCGCAGGAGGACTTCGACGCC chr4A_876 TCTCCGTCGAGGCGC------CG---TCGTCGCAGGAGGACTTCGACGCC chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TGGCTCGCCGAGAAACTGCCCGAAATCATGCAGGAGGTTCAGGTACCTCA chr7D_1_TraesCS7D01G003500 TGGCTCGCCGAGAAACTGCCCGAAATCATGCAGGAGGTTCAGGTACCTCA chr4A_1 TGGCTCGCTGAAAAGCTGCCCCAAATCATGCAGGAGGTTCAGGTACCTCA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TGGCTCGCTGAAAAGCTGCCCCAAATCATGCAGGAGGTTCAGGTACATCA chr5B_809 TGGCTCGCCGACAACCTACCCCAAATCCTACAGGATGTTCAGGTACAACA chr5A_809 TGGCTCGCCGACAACCTCCCCCAAATCCTACAGGATGTTCAGGTACA-CA chr5D_825 TGGCTCGCCCACAACCTCCCCCAAATCCTACAGGATGTTCAGGTACAACA chr4A_876 TGGCTCGCCGAAAAGCTGCCCCAAATCATGCAGGACGTTCAGGTACCTCA chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -----------S--S------S---------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ACATCTAATACTGTGCTTGGTTAATTTGCAAATTTCA-----CTCCTCCT chr7D_1_TraesCS7D01G003500 ACATCTAATACTGTGCTTGGTTAATTTGCAAATTTCA-----CTCCTCCT chr4A_1 ACATCT---------------TAATTTCTCTCAATTTCACTTCTTCTTCT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ACATCT---------------TTATTTCTAAATTTCA-----CTTCTTTT chr5B_809 TC------TACT-----GGGTTTATTTCCAAATTTCA-----CTTCTTTT chr5A_809 TC------TACT-----GGGTTTATTTCCAAATTTCA-----CTTCTTTT chr5D_825 TC------TACT-----GGGTTTATTTCCAAATTTCA-----CTTCTTTT chr4A_876 ACATCTAATACT-----TGGTTAATTTCCAAATTTCA-----CATCTT-- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ------------SSSSS----------S----------------S--S-- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TTTTTGC--------------TGCAATTGAGAGACACACTCACTCTCCCT chr7D_1_TraesCS7D01G003500 TTTTTGC--------------TGCAATTGAGAGACACACTCACTCTCCCT chr4A_1 TTTTTTGCTCCGCTATATATATGCAATTGAGAGACACACTCACTCTCCCT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TTTTTTGCTACGCTATATATATGCAATTGAGAGACACACTCACTCTCCCT chr5B_809 TTGCGCCAG--------TATGTGCAATTGTGGGAGACTCTTCT------T chr5A_809 TTGCGCCAC--------TATGTGCAATTGAGAGAGACTCTTCT------T chr5D_825 TTGCGCCAG--------TATGTGCAATTGAGGGAGACTTTTCT------T chr4A_876 ------------------------------------------------CT chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -----S-------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 GATGATCTTG--TCTTGTGTGCCAATTCTTACATGGACAGTTTGATTGCG chr7D_1_TraesCS7D01G003500 GATGATCTTG--TCTTGTGTGCCAATTCTTACATGGACAGTTTGATTGCG chr4A_1 GATGATCTTG--TCTTGTGTGCCAATTCTTACATGGACAATTTGATTGTG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GATGATCTTG--TCTTGTGTGCCAATTCTTACGTGGACAGTTTGATTGCG chr5B_809 GATCGTCTTGTTTCTTGTGTGCCAAATCTTCCTTGGACAGTTTGATTGTG chr5A_809 GATCGTCTTGTTTCTTGTGTGCCAAATCTTCCTTGGACAGTTTGATTGTG chr5D_825 GATGATCTTGTTTCTTGTGTGCCAAATCTTACATGGACAGTTTGATTGTG chr4A_876 GATGATCTTG--TCTTGTGTGCCAATTCTTATC------------TTGCG chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TGATACATTCTATTCT---------TGTGTGTG-------ATCCACTGAC chr7D_1_TraesCS7D01G003500 TGATACATTCTATTCT---------TGTGTGTG-------ATCCACTGAC chr4A_1 TGGTTC-----ATTAATTGTGTGTGTGTGTGTG-------ATCCAGTGAC chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TGATAC-----ATTCT---------TGTGTGTG-------ATCCACTGAC chr5B_809 TGATACA--------T---------TGTGTGTG-------ATCCAGCAGC chr5A_809 TGATACA--------T---------TGTGTGTG-------ATCCAGCGAC chr5D_825 TGATACA--------T---------TGTGTGTG-------ATTCAGTGAC chr4A_876 TGATAGA--------T---------TGTGTGTGTGATGAGATCCAGTGAC chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------SSSS--------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TAAATTCAGTGGGTA--GCTGCTATGTATCGATCAAGGGA---------- chr7D_1_TraesCS7D01G003500 TAAATTCAGTGGGTA--GCTGCTATGTATCGATCAAGGGA---------- chr4A_1 TAAATTCAGTGAATAGTGCTG----------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TAAATTCAGTGTGTAGTGCTGCTATGTATCGATCAAGGGAATCATCACAA chr5B_809 TAAATTCAGTGATTAGTGCTTCTATGTATCGATCAAAAGAATGATATGTA chr5A_809 TAAATTCAGTGGGTAGTGCTGCTATGTATCGATCAACGGAATGGTATATA chr5D_825 TAAATTCAGTGGGTGGTGCTGCTATGTATCGATCAAGCGAATGATATAGA chr4A_876 TAA------------------------------------------ATAGA chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------GAATGATCACAATCACATACAAAGTGAGTG-----------AG chr7D_1_TraesCS7D01G003500 -------GAATGATCACAATCACATACAAAGTGAGTG-----------AG chr4A_1 -AAGAGAGAATGATGAC-----CATACAAAGTGAGTG-----------AG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TAT--------------------ATACAAAGTGAGTG-----------AG chr5B_809 GAAGAGAGAATGATGAC-----AATACAAAGTGAGTG-----------AG chr5A_809 GAAGAGAGACTGATGAC-----AATAAAAAGTGAGTG-----------AG chr5D_825 GAGGAGAGAATGATGAC-----AATATAAAGTGAGTG-----------AG chr4A_876 GAAGAGAGAATGATCAC-----AAATTCACAATACTAAGTCACTAAATAG chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -----------------SSSSS---------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 AGTGAGTGG--------------GTGAGAATGATGACAATATATGG---- chr7D_1_TraesCS7D01G003500 AGTGAGTGG--------------GTGAGAATGATGACAATATATGG---- chr4A_1 AGTGAGTGAG----------TGAGTGAGAATGATGACAATACAGAGGCCT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 AGTGAGTGAG----------TGAGTGAGAATGATGACAATATATGG---- chr5B_809 AGAGTGTGAG----------TCAAGGGAATGATATAGGCTTGGCGCTACT chr5A_809 AGAGTGTGAGTGATTAATGATCAAGGGAATGATATAGGCTTGGTGCTACT chr5D_825 AGAGTGTGAGTGATTAATGATCAAGGGAATGATATAGGTTTGGCACTACT chr4A_876 AGTGAGTGAG----------TGGAGTACTATATGGAATT----------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --------S----------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ----------------------------------------AGTGGGGAGT chr7D_1_TraesCS7D01G003500 ----------------------------------------AGTGGGGAGT chr4A_1 TGGTATCACTACATTGTAACAAATAGTATATATATAAGCAAGTGGGGAGT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ----------------------------------------AGTGGGGAGT chr5B_809 AC------CTACATTGTAT----TGTAACAA----AAGGAAGTGGGGAGT chr5A_809 AC------CTACATTGTATATACTGTAACAA----AAGGAAGTGGGGAAT chr5D_825 AC------CTACATTGTAT----TGTAACAA----AAGAAAGTGGGGACT chr4A_876 ----------------------------------------AGTGGGGAGT chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 GTGCTATCTGTCTGTGATGTAAAACAATAATAAGGAAGATCTCTTT---- chr7D_1_TraesCS7D01G003500 GTGCTATCTGTCTGTGATGTAAAACAATAATAAGGAAGATCTCTTT---- chr4A_1 GTGCTATCTGTCTGTGATGTAAAA----AACAAGGAAGATCTCTTT---- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GTGCTATCTGTGATGT-------A----AAAAAATGAATATCTACTATCA chr5B_809 GTGCTATCTGTGATGT-------A----AAAAATGAAGATTTCTTT---- chr5A_809 GTGCTATCTGTGATGT-------A----AAAAAGGTGGATTTCTTC---- chr5D_825 GTGCTATCTGTGATGT-------A----AAAAAGGAAGATTTCTTT---- chr4A_876 GTGCTATCTGTCTGTGATGTAAAA----AAAAAGGAAGATCTCTTT---- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ------------------------SSSS--S------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CGTGATACATGGATGTAATGGTGGATCG---------------------- chr7D_1_TraesCS7D01G003500 CGTGATACATGGATGTAATGGTGGATCG---------------------- chr4A_1 CCTGATACATGCATGTGATGGTGGATCG---------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CCTGGTACATGCATGTATTGGTGGATCG---------------------- chr5B_809 CCTAATACATG----TAATGGTGGATCGATGATCTAAGGATCATATGAAT chr5A_809 CCTGATACATT----TAATGGTGGATCAATGATCTATGGATCATATGAAT chr5D_825 CCTGATACATG----TAATGGTGGATCGATGATCTAAGGATCATATGAAT chr4A_876 CCTGA--------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -S---------S-------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ----------------------------------------ATGATTAATG chr7D_1_TraesCS7D01G003500 ----------------------------------------ATGATTAATG chr4A_1 ----------------------------------------ATGATTAATG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ----------------------------------------ATGATTAATG chr5B_809 GATTAATGAAGGATAACATGTAATTGTGGGATCAGATGAAATGATTAATG chr5A_809 GGATAATGAAGGATA-----------TGGGATCATATG-AATGATTAATG chr5D_825 GATTAATGAAGGATAACATGTAATGGTGGGATCATATGAAATGATTAATG chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ATGGGTACCATGCATATTCAGTTCTCCTCTGAAAGATTGCTCAGTTTTTG chr7D_1_TraesCS7D01G003500 ATGGGTACCATGCATATTCAGTTCTCCTCTGAAAGATTGCTCAGTTTTTG chr4A_1 AAGGGTGCCATGCATACTCACTTCTCCTCTGAAAGATTGCTCAATTTTTG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 AAGGGTACCATGCATTTTCACTTCTCCTCTGAAAGATTGCTCAATTTTTG chr5B_809 AAGGTTACCATGAATGTTCTGTTCTCCTCTCAA-----------TTTTTG chr5A_809 AAGGTTACCATGAATGTTCTGTTCTCCTCTCAA-----------TTTTTG chr5D_825 GAGGTTACCATGCATGTTCAGTTCTCCTCTCAA-----------TTTTTG chr4A_876 -AGGGTACTATGCATGTAAT------------------------------ chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -S-----------------------------------------S------ forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TGGTGCCAAGCTTGGATCTTTGTC----------TGACTGATATGACTGA chr7D_1_TraesCS7D01G003500 TGGTGCCAAGCTTGGATCTTTGTC----------TGACTGATATGACTGA chr4A_1 TGGTGCCAAGCTTGGATCTTTGTTTCACTGTGATTGACTGACATGACTGA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CGGCGCCAAGCTTGGATCTTTGTC----------TGACTGACATGACTGA chr5B_809 TGGTACCAAGCTTGATCTTTATATCCA------ACTAAC----TGACTGA chr5A_809 TGGTGCCAAGCTTGATCTTTATCCAACTAACTGACTAAC----TGACTGA chr5D_825 TGGT---------------------------------------------- chr4A_876 ---------------------------------TTCACAGACATGACTGA chrUn_1857 -------------------TTGTC----------TGACTGACATGACTGA chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -----------------------------------------S-------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 GATTATCTTCTAATCGCTATTTAACGCATATGTTGGTTAGTTTGACTGTA chr7D_1_TraesCS7D01G003500 GATTATCTTCTAATCGCTATTTAACGCATATGTTGGTTAGTTTGACTGTA chr4A_1 GATTATCTTCTAATCACTATTGAACGCATATGTTGGTTAGTTTGACTGTA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GATTATCTTCTAATCGCTATTCAACGCATATGTTGGTTGGTTTGACTGTA chr5B_809 CAGTACCTTCTAATCACTATTGAACGC--ATGTTAGTTAGTTTGACTGTA chr5A_809 CAGTACCTTCTAATCACTATTGAACGC--ATGTTAGTTAGTTTGACTGTA chr5D_825 ----ACCTTCTAATCACAATTGAACGCATATGTTAGTTAGTTTGGCTGTA chr4A_876 GATTATGAACACC---------------TATGTTGGTTAGTTTGACTGTA chrUn_1857 GATTATCTTCTAATCGCTATTCAACGCATATGTTGGTTGGTTTGACTGTA chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ---------------------S---------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TAAACCACACAAAAGAGCCAAAAAAA--CTAGATAAAAATGCAGACACAT chr7D_1_TraesCS7D01G003500 TAAACCACACAAAAGAGCCAAAAAAA--CTAGATAAAAATGCAGACACAT chr4A_1 TAAACCACACAAAAAAGCCAAAAAAATTCTAGATAAAAATGCAGACACAT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TAAACCACACAGAAAAGCCAAAAAAATTCTAGATAAAAATGCAGACACAT chr5B_809 TACATCACATAAAAAGCAAAAATGAGTTCTAGAAAAATT-----ACACAG chr5A_809 TACATCACATAAAAAGCAAAAATGAGTTCTAGAAAAATT-----ACACAG chr5D_825 TACATCACATAAAAAGCAAAAATGAATTCTAGAAAAATT---AGACACGG chr4A_876 TAAACCACACAAAAAAG---AAAAAA--ATATAAAAATA---CAGGACAG chrUn_1857 TAAACCACACAGAAAAGCCAAAAAAATTCTAGATAAAAATGCAGACACAT chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --------------S----------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ATGCTACAGAACCAGTGAGAAG---------------------------- chr7D_1_TraesCS7D01G003500 ATGCTACAGAACCAGTGAGAAG---------------------------- chr4A_1 ATGCTACAGAACCAGTGAGAAG---------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ATGCTGCAGAACCAGTGAAGCCTGAAGAAACCAAAAACTTTATTTTTTGA chr5B_809 ATACTACAGAACCAGTGAACCCTCAAGAAACAAAAG-------------- chr5A_809 ATACTACAGAACGAGTGAAGCCTCAAGAAACAAAAG-------------- chr5D_825 ATACTACAGAACCAGTGAACCCTCAAGAAACAAAAG-------------- chr4A_876 ATGCTACATAACCAGTGAATTCTAAAGAAAC------------------- chrUn_1857 ATGCTGCAGAACCAGTGAAGCCTGAAGAAACCAAAAACTTTATTTTTTGA chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ------------------------------------CCTGAACAACAAAA chr7D_1_TraesCS7D01G003500 ------------------------------------CCTGAACAACAAAA chr4A_1 ------------------------------------CCTGAA-------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 AAAGGGGGAGCGAAGAAACCCAAAAAAAAAAACACAGCTGAA-------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 --------------------------AAAAAACACACCTGAA-------- chrUn_1857 AAAGGGGGAGCGAAGAAACCCAAAAAAAAAAACACAGCTGAA-------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ------------------------------------------SSSSSSSS forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 AGCACGCCTGAAGGGGTTTTTTTTTTTTACAAAATGTG--GTAATTTGAG chr7D_1_TraesCS7D01G003500 AGCACGCCTGAAGGGGTTTTTTTTTTTTACAAAATGTG--GTAATTTGAG chr4A_1 -------------GGG--TTTCTTTTTTACAAAATGTA--GTCATTTGAG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------GGA--TTTCCTTTTTACAAAATGTA--GTCATTTGAG chr5B_809 -GCACACCTGAAGGGT--TTTTTTCTTAACAAAATGTA--CTAACTTGAG chr5A_809 -GCACACCTGAAGGGG--TTTTTTCTTAACAAAATGTA--CTAACTTGAG chr5D_825 -GCACACCTGAAGGGT--TTCTTTCTTTACAAAATGTA--GTAACTTGAG chr4A_876 -------------GGA--TTTCTGTTTTACAAAAGGTACAGTAGTTTGAG chrUn_1857 -------------GGA--TTTCCTTTTTACAAAATGTA--GTCATTTGAG chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs S----S----------SS-------------------S------------ forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CATGAAAAATGTGCTGTTGCAGTCTAGCTCTTTCAAGGAAA-ACAGGGG- chr7D_1_TraesCS7D01G003500 CATGAAAAATGTGCTGTTGCAGTCTAGCTCTTTCAAGGAAA-ACAGGGG- chr4A_1 CATGAAGAATGTGCTTTTGCAGTCTAGCTTTTTCAAGGAAACACAGGGG- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 AATGAAAAATGTGCAGTTGCAATCTAGCTTTTTCAAGGAGA-ACAGGGG- chr5B_809 TATGAAAAATGTGCAATTGCAATCTTGCTTTTTCAAGGAAA-ACAGGGG- chr5A_809 TATGAAAAATGTGCAATTGCAATCTTGCTTTTTCAAGGAAA-ACAGGGG- chr5D_825 TATGAAAAATGTGCAATTGCAATCTTGCCTTTTCAAGGAAA-ACAGGGG- chr4A_876 TACGGAAAATGTGCAACTGCAATCTAGCTTTTTGAAGGAAA-ACGGGGAG chrUn_1857 AATGAAAAATGTGCAGTTGCAATCTAGCTTTTTCAAGGAGA-ACAGGGG- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -----------------------------S-------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 --ACTGCTACATACTTCATATGGGCGGAGGCTAATTGTCAATCTTCCAAT chr7D_1_TraesCS7D01G003500 --ACTGCTACATACTTCATATGGGCGGAGGCTAATTGTCAATCTTCCAAT chr4A_1 --ACCGCTACATACTTCATATGGGTCGAGGCTAATTGTCAATCTTCCAAT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 --ACTGCTACATACTTCAAATGGGTCGAGGCTAATTGTCAATCTTCCAAT chr5B_809 --ACTGTTAA-------ATATGGATCGAGACTAAGTATCGATCTTCCAAG chr5A_809 --ACTGCTAA-------ATATGGATCGAGGCTAAGTATCGATCTTCCAAG chr5D_825 --ACTGCTAA-------ATATGGATCGAGGCTAAGTATCGATCTTCCAAG chr4A_876 AAACTGCTACATACTCCATATGGACCAAGGCTAATT-------------- chrUn_1857 --ACTGCTACATACTTCAAATGGGTCGAGGCTAATTGTCAATCTTCCAAT chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------S------------------------ forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TCAGGAATCTG-AAAATAACTTTCATTTA-GTAATGGAGTATAT----GA chr7D_1_TraesCS7D01G003500 TCAGGAATCTG-AAAATAACTTTCATTTA-GTAATGGAGTATAT----GA chr4A_1 TTAAGAATCTG-AAAATAACTTTCATTTA-GTAATGGAGTATATATATGA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TTAAGAATCTG-AAAATAACTTTCATTTA-GTAATGGAGTATAT----GA chr5B_809 TTAAAAATCTGAAAAATAACTTTCATTTG-GTAATGGAGTATAT----GG chr5A_809 TTAAAAATCTGAAAAATAACTTTCATTTA-GTAATGGAGTATAT----GG chr5D_825 TTAAAAATCTGAAAAATAACTTTCATTTAAGTAATGGAGTATAT----GG chr4A_876 -------------------------------------------------- chrUn_1857 TTAAGAATCTG-AAAATAACTTTCATTTA-GTAATGGAGTATAT----GA chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -S-S---------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TAG-AGAAATTATGCCTTTCCCTAATTGAGAAAATTGTACAGGC------ chr7D_1_TraesCS7D01G003500 TAG-AGAAATTATGCCTTTCCCTAATTGAGAAAATTGTACAGGC------ chr4A_1 TAG-AGAAATGATGCCTTTCCCTAATTGAGCAAATTGTACAGAC------ chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TGG-AGAAATGATGTCTTTCCCTAATTGAGAAAATTGTACAGAC------ chr5B_809 TAAAAGAAAGGATGTCTTTCTCTAGTTGAGCGAATTGTACAAAGG----- chr5A_809 TAAAAGAAAGGATGTCTTTCTCTAGTCGAGCGAATTGTACAGAGGTAATT chr5D_825 TAAAAGAAAGGATGTCTTTCTCTAGTTGAGTGAATTGTACAGAGGTAATT chr4A_876 -------------------------------------------------- chrUn_1857 TGG-AGAAATGATGTCTTTCCCTAATTGAGAAAATTGTACAGAC------ chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ----------S-------------------------------S------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ATAACTGAATCAACTAAAAACCTTCCATCATTTCTAGCACACAATTAAAG chr7D_1_TraesCS7D01G003500 ATAACTGAATCAACTAAAAACCTTCCATCATTTCTAGCACACAATTAAAG chr4A_1 ATAATTGAATCAACTAAAAACCTTCCATCGTTTCTACCACCCAATTAAAG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ATAATTGAATCAACTAAAAACCTTCCATCATTTCTAGCACACAATTAAAG chr5B_809 -TAAATGAATCGTCTAAAAACCTTCATTTTTA----GCGCA----TAAAG chr5A_809 ATAAATGAATCGTCTAAAAAACTTCATTTTTA----GCACA----CAAAG chr5D_825 ATAAATGAATCGTCTAAAAACCTTCATTGTTA----GCACA----CAAAG chr4A_876 -------------------------------------------------- chrUn_1857 ATAATTGAATCAACTAAAAACCTTCCATCATTTCTAGCACACAATTAAAG chr5A_2243 ATAACTGAACCAACTAAAAACCTTCCTTCTTTTCTGGCACA----CAAAG chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CCAAC-AAT-GCTAGCTACAAGTGCATGCCAAGATAGCTTTCGCTGCCTC chr7D_1_TraesCS7D01G003500 CCAAC-AAT-GCTAGCTACAAGTGCATGCCAAGATAGCTTTCGCTGCCTC chr4A_1 CCAAC-AATAGCTAGCTACAAGTGCATGCCAAGATAGCTTTCGCTGCCTC chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CCAAC-AAT-GCT-------------TGCCAAGATAGCTTTCGCTGCCTC chr5B_809 CCAACAAAT-GCAAGCTACAAGTCC----CAAGATGGTTTCCGCCGCCTC chr5A_809 CCAAC-AAT-GCTAGCTACAAGTGC----CAAGATGGCTTCCGCCGCCTC chr5D_825 CCAAC-AAT-GCTAGCTACAAGTGC----CAAGATGGCTTCCGCCGCCTC chr4A_876 -------------------------------------------------- chrUn_1857 CCAAC-AAT-GCT-------------TGCCAAGATAGCTTTCGCTGCCTC chr5A_2243 CCAAC-AAT-GCTAGCTTATAAG---TGCCAAGATAGGTTTCACTGCCTC chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 --------------------------------------TTTCGCTGCCTC reverse_7010 -------------------------------------------------- input_sequence_33693 GAGGAATTGACGGCTAATTACGATTGAATATCTCTTTCTTACCTCTTAAC chr7D_1_TraesCS7D01G003500 GAGGAATTGACGGCTAATTACGATTGAATATCTCTTTCTTACCTCTTAAC chr4A_1 GACGAATCGACGGCTAATTTCGAATGAATATCTCTTTCCTACCTCTTAAC chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GAGGAATCGAAGGCTAATTCCGATTGAATATCTCTTTCTTACTTCTTAAC chr5B_809 GATGAATCGACGGCTAATTACGATTGAATATCTC--TCTTACCTCTTAAC chr5A_809 GATGAATCGACGGCTAATTACGATTGAATATCTC--TCTTACCTCTTAAC chr5D_825 GATGAATCGACGGCTAATTACGATTGAATATCTC--TCTTACCTCTTAAC chr4A_876 -------------------------------------------------- chrUn_1857 GAGGAATCGAAGGCTAATTCCGATTGAATATCTCTTTCTTACTTCTTAAC chr5A_2243 GATGAATCGACAGGTAATTACGATTGAATATCTC--TCTTACCGATTAAG chr5B_2380 ---------------------------------------TAGCTCTTAAC SNPs -------S------------------------------------------ forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 GAGGAATT------------------------------------------ reverse_7010 -------------------------------------------------- input_sequence_33693 TAGGATGGCGCATGAGTACTCATTCTGTTAATTTGTCGTGCACTCTCTCA chr7D_1_TraesCS7D01G003500 TAGGATGGCGCATGAGTACTCATTCTGTTAATTTGTCGTGCACTCTCTCA chr4A_1 TAGGATGGCGCATGAGTACTCATTCTGTTAATTTGTGGTGCACTCTCTCA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TAGGATGGCGCATGAGTACTCATTCTGTTAATTTGTCGTGCACTCTCTCA chr5B_809 TAGGATGGCGCATGAGTACTCATTGTGTTAATTTGTGGTG----CTCTCA chr5A_809 TAGGATGGCGCATGAGTACTCATTGTGTTAATTTGTGGTG----CTCTCA chr5D_825 TAGGATGGCGCATGAGTACTCATTGTGTTAATTTGTGGTG----CTCTCA chr4A_876 -------------------------------------------------- chrUn_1857 TAGGATGGCGCATGAGTACTCATTCTGTTAATTTGTCGTGCACTCTCTCA chr5A_2243 TAGGATGGTGCATGAGT-------------------GGTG----CTCTCA chr5B_2380 TAGGATGGCACATGAGTACTCATTCAGTTGATTTGTGCTG----CTCTCA SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ATACATTCATGCAGGATGGACCTCAGATATGCGATGCCAGTGGAACAACA chr7D_1_TraesCS7D01G003500 ATACATTCATGCAGGATGGACCTCAGATATGCGATGCCAGTGGAACAACA chr4A_1 ATACATTCATGGAGGATGAACCTCAGATAGACGATGCGAATGG---AACA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ATACATTCATGGAGGATGGACCTCAGATATGCGATGCGAGTGGAACAACA chr5B_809 CTACATTCATGGAGGATGGATCTCAGATCTGCGATGCGAGTGG---CACA chr5A_809 CTACATTCATGGAGGATGGATCTCAGATCTGTGATGCGAGTGG---CACG chr5D_825 CTACATTCATGGAGGATGGATCTCAGATCTACGATGCGAGTGG---CACA chr4A_876 -------------------------------------------------- chrUn_1857 ATACATTCATGGAGGATGGACCTCAGATATGCGATGCGAGTGGAACAACA chr5A_2243 ATACATTCATGGAGGATGGATCTCAAATCTGCGTTGCGAATGG---GACA chr5B_2380 ATACATTCATGGAGGATGGATCTCAAATCTGCGATGCGAATGG---GACA SNPs -----------S-------------------------S------------ forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ACAACAATAGTAGGAGATCAAAGAGGCACCAGCAGCAGCAGCTTCGGCTG chr7D_1_TraesCS7D01G003500 ACAACAATAGTAGGAGATCAAAGAGGCACCAGCAGCAGCAGCTTCGGCTG chr4A_1 ACAACAATAGTAGGAGATCAAAGGGGTACCAGCAGCAGCAGCTTCGGCTG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ACAACAATAGTAGGAGATCAAAGAGGCACCAGCAACAGCAGCTTCGGCTG chr5B_809 ACAACAATAGTAGGAGATCAAAGAGGCCCCAACAGCAGTAGCTTCGTCTG chr5A_809 ACAACAATAGTAGGAGATCAAAGAGGCCCCAGCAGCAGTAGCTTCGTCTG chr5D_825 ACAACAATAGTAGGAGATCAAAGAGGCCCCAGCAGCAGTAGCTTCGTCTG chr4A_876 -------------------------------------------------- chrUn_1857 ACAACAATAGTAGGAGATCAAAGAGGCACCAGCAACAGCAGCTTCGGCTG chr5A_2243 ACAACAATAGTAGGAGATCAAAGAGGCACCAGCACCAGCAACTTCAGCTG chr5B_2380 ACAACAATAGTAGGAGATCAAAGAGGCACCAGCATCAGCAGCTTCAATCA SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TGATGATTGGAG-------------------------------------- chr7D_1_TraesCS7D01G003500 TGATGATTGGAG-------------------------------------- chr4A_1 TGATGATTGGAA-------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TGATGATTGGAG-------------------------------------- chr5B_809 TGATGATTGGAA-------------------------------------- chr5A_809 TGATGATTGGAA-------------------------------------- chr5D_825 TGATGATTGGAA-------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 TGATGATTGGAG-------------------------------------- chr5A_2243 TGATGGTTGGAA-------------------------------------- chr5B_2380 TAATTACCTGTCTCAATATGCCAAGTTCTCCATAGTGTCTCAATATAGGA SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 AGTCGTTCCTCCTCACTGCTCTTGTTGAGAAGATGCAGCAACCACTCCCG SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------CAATGCCTGCTCA chr7D_1_TraesCS7D01G003500 -------------------------------------CAATGCCTGCTCA chr4A_1 -------------------------------------CAATGCCTGCTCA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------CAATGCCTGCTCA chr5B_809 -------------------------------------CAATGGCTGCTCA chr5A_809 -------------------------------------CAATGGCTGCTCA chr5D_825 -------------------------------------CAATGGCTGCTCA chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------CAATGCCTGCTCA chr5A_2243 -------------------------------------CAATGCCTGCTCA chr5B_2380 TCATGTATGCTCGATGTTTTCCAGCCGGGGCATCCTCCAATGCTTACTCA SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ACT----------------------------------------------- chr7D_1_TraesCS7D01G003500 ACT----------------------------------------------- chr4A_1 ACT----------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ACT----------------------------------------------- chr5B_809 ACTACCTGTGCT-------------------------------------- chr5A_809 ACTACCTGTGCT-------------------------------------- chr5D_825 ACTACCTGTGCT-------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 ACT----------------------------------------------- chr5A_2243 ACTACCTGTGCT-------------------------------------- chr5B_2380 TCGCACGCCAGAATCCTCGAGCCATCGGACATCCGCAAAAAGCGTGGAAA SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 GTATCCTCGCGTTCCACGCCACAGATCGTGCAAATGTCAGAAGTCTCGAT SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 CTTTCTCTTTGCCTTATTTTCCATTGTAGCCAGAGAGTTTGTGACAAGCC SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------T chr7D_1_TraesCS7D01G003500 -------------------------------------------------T chr4A_1 -------------------------------------------------T chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------T chr5B_809 ----------------------------------------CCACAATGTT chr5A_809 ----------------------------------------CCACAATGTT chr5D_825 ----------------------------------------CCACAATGTT chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------T chr5A_2243 ----------------------------------------CCACAATGTT chr5B_2380 GCCAAGAAAACACGCGTACCTTTGAAGGGGCAGGGCACCCCCACAATGCT SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CTGGGCTTGAGAATAC--TAATGGAGTATTTGTTGGAAATCACTCAGCTG chr7D_1_TraesCS7D01G003500 CTGGGCTTGAGAATAC--TAATGGAGTATTTGTTGGAAATCACTCAGCTG chr4A_1 CTGGGCTTGAGAATAC--TAATGGACAATTTGTTGGTCATCACTCAGCTG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CTGGGCTTGAGAATAC--TAATGGAGTATTTGTTGGTCATCACTCAGCTG chr5B_809 CTGTGCTTGAGAATAC--TAATGGAGTACTTGTTGGTCATCACTTAGCTG chr5A_809 CTGTGCTTGAGAATAC--CAATGGAGTACTTGTTGGTCATCACTTAGCTG chr5D_825 CTGTGCTTGAGAATAC--TAATGGAGTACTTGTTGGTCATCACTTAGCTG chr4A_876 -------------------------------------------------- chrUn_1857 CTGGGCTTGAGAATAC--TAATGGAGTATTTGTTGGTCATCACTCAGCTG chr5A_2243 CTGGGCTTGAGAATACTATAATGGAGTATTTGTTGGTCATCACTCAGCTG chr5B_2380 TCTCTGACAGCACGTGTGCCGTCCGGCGCCC--TGCTCATGGCGCACGAT SNPs ------------------------------------SS------------ forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------AATCACTCAGCTG forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 GGCCTTCACTCCCTTTTGAGGTACATATACACATACAGACCACTCACTCC chr7D_1_TraesCS7D01G003500 GGCCTTCACTCCCTTTTGAGGTACATATACACATACAGACCACTCACTCC chr4A_1 GACCTTCACTCAGTTTTGAGGTACATACATGA------------------ chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GGCCTTCACTCCCTTTTGAGGTACATATACACATACAGACCACTCACTCA chr5B_809 GGCCTTCACTCACTTTTGAGGTACATACATACATAC--------CACTCA chr5A_809 GGCCTTCACTCACTTTTGAGGTACATACATACACAC--------CACTCA chr5D_825 GGCCTTCACTCACTTTTGAGGTACATACATACATAC--------CACTCA chr4A_876 -------------------------------------------------- chrUn_1857 GGCCTTCACTCCCTTTTGAGGTACATATACACATACAGACCACTCACTCA chr5A_2243 GACCTTCACTTACTTTTGAGGTACATACATACTTACTTCCTCCATTTCAA chr5B_2380 GACCTGCGGTTCCTCTCGTCGAGGGCAAGGCGGTAGGCGCTCCGTACAGT SNPs -------------------------------------------------S forward_2535 -------------------------------------------------- reverse_5038 GGCCTTC------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CT------------------------------------------------ chr7D_1_TraesCS7D01G003500 CT------------------------------------------------ chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CT------------------------------------------------ chr5B_809 TT------------------------------------------------ chr5A_809 TT------------------------------------------------ chr5D_825 TT------------------------------------------------ chr4A_876 -------------------------------------------------- chrUn_1857 CT------------------------------------------------ chr5A_2243 ATTACTCGTCACAGAAATGGATGTATCTAGAACTAAAATACATCTAGATA chr5B_2380 GAAGACGCCCGTGGGATCAGGTGCCCAGGTGAGGACATCCTCAAAGCCCC SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 CA------------------------------------------------ chr5B_2380 TTGTCGACAACTTGATCTTCGTGATAACCGCAACATCCACGGGAAGGAAG SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -----------------TCCATACCTGCGACAAGTAATTCG--------- chr5B_2380 TGGCGTCGTAGGAGATCTCCATACCATCTCCCGGCATCATCCAGTAGCTC SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 TGCCACGCGTCTCAAGCGGCATGTACCTCTCGGTGACACTGGCTTGAAGG SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 --------------------CATGCAATCGCAGTGC-TAATTAGCACAAT chr7D_1_TraesCS7D01G003500 --------------------CATGCAATCGCAGTGC-TAATTAGCACAAT chr4A_1 -------------TACATATTACTAACTCACACTAAATAATTTGGATAAT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 --------------------CATTCAATCGCAGTGC-TAATTAGCACAAT chr5B_809 --------------------CGCTCACTCACACTGC-TAATTAACAAAAT chr5A_809 --------------------CGCTCACTCACACTGC-TAATTAACACAAC chr5D_825 --------------------CGCTCACTCACACTGC-TAATTAACAAAAT chr4A_876 -------------------------------------------------- chrUn_1857 --------------------CATTCAATCGCAGTGC-TAATTAGCACAAT chr5A_2243 -GAACGGAGGGAGTACATACCGCTCACTCGCACTGC-TAATTAACACAAT chr5B_2380 AGAAAGGGCGGAAGAGCCAAGGGTCCCTCCGAATGC-GAATGTGTTCCCC SNPs -----------------------S-------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TAATTATTTGCAACCCAGTTATTATTCGACGATCACA------------- chr7D_1_TraesCS7D01G003500 TAATTATTTGCAACCCAGTTATTATTCGACGATCACA------------- chr4A_1 TCATTTGCATTCCGG------TTATTCGACACTGACA------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TAATTATTTGCAACCCAGTTATTATTCGACGATCACA------------- chr5B_809 TAATTTGCATCCCAG------TTATTTGGCAATGACA------------- chr5A_809 TAATTTGCATCCCAG------TTATTTGGCAATGACA------------- chr5D_825 TAATTTGCATCCCAG------TTATTTGGCAATGACA------------- chr4A_876 -------------------------------------------------- chrUn_1857 TAATTATTTGCAACCCAGTTATTATTCGACGATCACA------------- chr5A_2243 TAATTTGCATCCCAG------TTATTTGACAAAGACA------------- chr5B_2380 GTTTCCTACCCTAAAAATCAAGCCCTTCTTGAGAAGTTCGAGGCCATGGT SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 GGATAGCGTGCCAAGTCGGCGAGGCATTACAACACAGTATCTTCAAAATT SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 -------------------------------------------------- chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 ACCATTAGGGTAGTAACTTGCCTTGAGGGCGCACAGTGAATCCGGCCGCG SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ---------ATAACATTGCGAACTTGGTTT----------AATTTCTTCA chr7D_1_TraesCS7D01G003500 ---------ATAACATTGCGAACTTGGTTT----------AATTTCTTCA chr4A_1 ---------ATACCAACTAATTACCACTTTTCTTGGTATAAATTTCTTGG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ---------ATAACATTGCGAACTTGGTTT----------AATTTCTTGA chr5B_809 ---------AATAACA---TTGCTTGGTTT----------AATTTCTTGG chr5A_809 ---------AATTACA---TTGCTTGGTTT----------AATTTCTTGG chr5D_825 ---------AATAACA---TTGCTTGGTTT----------AATTTCTTGG chr4A_876 -------------------------------------------------- chrUn_1857 ---------ATAACATTGCGAACTTGGTTT----------AATTTCTTGA chr5A_2243 ---------GTAACATTGCTTGGCGG------------------------ chr5B_2380 TAATGAGACAATAACA---TTGGCGG------------------------ SNPs ------------------------------------------------S- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CAGCAACAGCAGCACCTGCCACCATCGATCTGCCAATTCCTCTCATCAT- chr7D_1_TraesCS7D01G003500 CAGCAACAGCAGCACCTGCCACCATCGATCTGCCAATTCCTCTCATCAT- chr4A_1 CAGCAACAGCAGCAGCTGCCACCGTCGATCTGCCACATCCTCTCATCAT- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CAGGAACAGCAGCAGCTGCCACCATCGATCTGCCAATTCCTCTCATCAT- chr5B_809 CAGCAACAGCAGCAGCTGCCACCGTCAATCTGCCACA---TCTCATCAT- chr5A_809 CAGCAACAGCAGCAGCTGCCACCGTCAATCTGCCACA---TCTCATCAT- chr5D_825 CAGCAACAGCAGCAGCTGCCACCGTCAATCTGCCACA---TCTCATCAT- chr4A_876 -------------------------------------------------- chrUn_1857 CAGGAACAGCAGCAGCTGCCACCATCGATCTGCCAATTCCTCTCATCAT- chr5A_2243 ------CAACAGCAGCTGCCACCATCGATCTTCCACATCTTATCATCATC chr5B_2380 ------CAACAGCAGCTGCCACCATCGATCTTCCACATCTTATCATCAT- SNPs --------------S----------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------CATACTCATGTTATAATCCATCCTCC---TCATCATGCCAGCC chr7D_1_TraesCS7D01G003500 -------CATACTCATGTTATAATCCATCCTCC---TCATCATGCCAGCC chr4A_1 -------CATTCTCATGTTATAATCCATCCTCC---TC---GTGCCAGCC chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------CATACTCATGTTATAATCCATCCTCC---TCGTCATGCCAGCC chr5B_809 -------C---------TTACAACCCATCAACATTATC---GTGCCAGCC chr5A_809 -------CATACTCATCTTATAACCCATCGACATTGTC---GTGCCAGCC chr5D_825 -------C---------TTACAACCCATCAACATTATC---GTGCCAGCC chr4A_876 -------------------------------------------------- chrUn_1857 -------CATACTCATGTTATAATCCATCCTCC---TCGTCATGCCAGCC chr5A_2243 ATACATTCATACTCATCTTATAACCCATCCACA---TCGTCGTGCCAGCC chr5B_2380 -------CATACTCATCTTATAACCCATCCTCA---TCGTCGTGCCAGCC SNPs --------------------------------------S----------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 GGTCATGACATCGACTACTCTTCTCCAATCCATG---GGAGGCAACGATC chr7D_1_TraesCS7D01G003500 GGTCATGACATCGACTACTCTTCTCCAATCCATG---GGAGGCAACGATC chr4A_1 GGTCATGACATCGACTACTCTTCTGCAGTCCATGGGAGG---CAACGATC chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GGTCATGACATCGACCACTCTTCTCCAATCCATG---GGAGGCAACGATC chr5B_809 GGCCATGACATCGACTACTCTTCTGCAATCCATG---GG---CAACGATC chr5A_809 GGCCATGG------------TTCTGCAATCCATG---AG---CAACGATC chr5D_825 GACCATGACATCGACTACTCTTCTGCAATCCATG---GG---CAACGATC chr4A_876 -------------------------------------------------- chrUn_1857 GGTCATGACATCGACCACTCTTCTCCAATCCATG---GGAGGCAACGATC chr5A_2243 GGTCATGACATCGACTACTCTTCTACAATCCATG---GG---CAACGATT chr5B_2380 GGTCATGACATCAACTACCCTTCTGCAATCCATG---GG---CAACGATT SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ACCATCCGTCTTATCTCCTCGATGGCTTCCCTACTTTCTGCCCTTCCATG chr7D_1_TraesCS7D01G003500 ACCATCCGTCTTATCTCCTCGATGGCTTCCCTACTTTCTGCCCTTCCATG chr4A_1 ACCATCCATCGCTGCTCCTCGATGGCTTCCCTACATTCTGCCCTTCCATG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ACCATCCGTCTTATCTCCTCGATGGCTTCCCTACTTTCTGCCCTTCCATG chr5B_809 ATCATCCATCGCTGCTCCTTGATGACTTCCCTACTTTCTACCCTGCCTTG chr5A_809 ATCATCCATCGCTGCTCCTTGATGGCTTCCCTACTTTCTGCCCTGCCTTG chr5D_825 ATCATCCATCGCTGCTCCTTGATGACTTCCCTACTTTCTACCCTGCCTTG chr4A_876 -------------------------------------------------- chrUn_1857 ACCATCCGTCTTATCTCCTCGATGGCTTCCCTACTTTCTGCCCTTCCATG chr5A_2243 A------------------------------------------------- chr5B_2380 ATCATCCATCGCTGCTCCTCGATGGCTTCCCTACTTCCTGCCCTGCCTTG SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CCCCTAATGTCGCCACCGCCACCACCGGAGAACGGCACCAGCTGTCATGA chr7D_1_TraesCS7D01G003500 CCCCTAATGTCGCCACCGCCACCACCGGAGAACGGCACCAGCTGTCATGA chr4A_1 CCCCTAATGTCGCCGCCGCCACTACCGGAGAACGGCACCGGCTGTCATGA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CCCCTAATGTCGCCACAGCCACCACCGGAGAACGGCACCAGCTGTCATGA chr5B_809 CCCCTAATATCGCCGCCACCACCACCGGAGAATGGCACTGACTGTCATCA chr5A_809 CCCCTAATATCGCCGCCACCACCACCGGAGAATGGCACTGACTGTCATGA chr5D_825 CCCCTAATATCGCCGCCGCCACCACCGGAGAATGGCACTGGCTGTCATGA chr4A_876 -------------------------------------------------- chrUn_1857 CCCCTAATGTCGCCACAGCCACCACCGGAGAACGGCACCAGCTGTCATGA chr5A_2243 -------------------------------------------------- chr5B_2380 CCCCTAATATCACTGCCACCACCACCAGAGAACGGGCCTGGCTGTCATGA SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CGCCAACCAGCCATCGCAGATGCTGGCCACGGATGAGCAAGCGGCGGCGG chr7D_1_TraesCS7D01G003500 CGCCAACCAGCCATCGCAGATGCTGGCCACGGATGAGCAAGCGGCGGCGG chr4A_1 TGCCAACCAGCCATCGCAGATGCTGGCAACGGATGAGCAAGTTGCGGCTG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CGCCAACCAGCCATCGCAGATGCTGGCCACGGATGAGCAAGCGGCGGCGG chr5B_809 TGCCAACCGGCCATCACAGATGCTGACCGCGGATGAGCAAGCAGCGGTGG chr5A_809 TGCCATCCAGCTATCACAGATGCTGGCCGCGGATGAGCAAGGAGCGGTGG chr5D_825 TGCCAACCAGCCATCACAGATGCTGACCGCAGATGAGCAAGCAGCGGTGG chr4A_876 -------------------------------------------------- chrUn_1857 CGCCAACCAGCCATCGCAGATGCTGGCCACGGATGAGCAAGCGGCGGCGG chr5A_2243 -------------------------------------------------- chr5B_2380 TGCCAACCAGCCATCGCAGATGCTGGCCGCAGATGAGAAAGCAGCGGCGA SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CTCATCACCAGCAAGATCCAAGCACCATTGCTAAGAAGCGAGAGGAAAGG chr7D_1_TraesCS7D01G003500 CTCATCACCAGCAAGATCCAAGCACCATTGCTAAGAAGCGAGAGGAAAGG chr4A_1 CTCATCACCAGCAAGATCCAAGCACCATTGCTAAGAAGCGAGAGGAAAGG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CTCATCACCAGCAAGATCCAAGCACCATTGCTAAGAAGCGAGAGGAAAGG chr5B_809 CTCATCATCAGCAAGATCCGAGCACCATTAGTAAGAAGAGAGAGGAAAGG chr5A_809 CTCATCATCAGCAAGATCCGAGCACCGTTAGTAAGAAGAGAGAGGAACGG chr5D_825 CTCATCATCAGCAAGATCCGAGCACCGTTAGTAAGAAGAGAGAGGAAAGG chr4A_876 -------------------------------------------------- chrUn_1857 CTCATCACCAGCAAGATCCAAGCACCATTGCTAAGAAGCGAGAGGAAAGG chr5A_2243 -------------------------------------------------- chr5B_2380 ATCCTCATCAGCAAGATCCGAGCACCGTTAGTAAGAAGAGAGATGAAAGG SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 GACAGGGCCAAGCAAAGGTACAACGAGAAGAAGAAGAACAGAAAGTAAGT chr7D_1_TraesCS7D01G003500 GACAGGGCCAAGCAAAGGTACAACGAGAAGAAGAAGAACAGAAAGTAAGT chr4A_1 GACAGGGCCAAGCAAAGGTACAACGAGAAGAAGAAGAACAGAAAGTAAGT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GACAGGGCCAAGCAAAGGTACAACGAGAAGAAGAAGAACAGAAAGTAAGT chr5B_809 GACAGGGCCAAGCAAAGGTACAACGAGAAGAAGAAGAACAGGAAGTAAGT chr5A_809 GACAGGGCCAAGCAAAGGTACAACGAGAAGAAGAAGAACAGGAAGTAAGT chr5D_825 GACAGGGCCAAGCAAAGGTACAACGAGAAGAAGAAGAACAGGAAGTAAGT chr4A_876 -------------------------------------------------- chrUn_1857 GACAGGGCCAAGCAAAGGTACAACGAGAAGAAGAAGAACAGAAAGTAAGT chr5A_2243 -------------------------------------------------- chr5B_2380 GACAGAGCCAAGCAAAGGTACTACGAGAAGAAGAAAAACAGAAAGTAAGT SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 CTGAATTATTATTTTCAATTGACAACTCTTTAATATGCAGATG-----TT chr7D_1_TraesCS7D01G003500 CTGAATTATTATTTTCAATTGACAACTCTTTAATATGCAGATG-----TT chr4A_1 CTGACTTATTATTTTCATTTGACAACTACTTTATTTGCAGATTCC----- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CTAAATTATTATTTTCATTTGACAACTCTTTTATATGCAGATGTCTTTTT chr5B_809 CTGAATTAAT-TTATCATTTGACAACTCTTCTATATACGGACAAAAAA-- chr5A_809 CTGAATTAAT-TTTTCATTTGACAACTCTTCT---TACAGACAAAAAA-- chr5D_825 CTGGATTAAT-TTTTCATTTGACAACTCTTCTATATACAGACAAAAAA-- chr4A_876 -------------------------------------------------- chrUn_1857 CTAAATTATTATTTTCATTTGACAACTCTTTTATATGCAGATGTCTTTTT chr5A_2243 ------------------------------TTATA--CAGACATAAAA-- chr5B_2380 CTGAATTAAT-TTTTCATTTGACAACTCTTTTATA--CAGACAAAAAA-- SNPs -----------------S-------------S------------------ forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TTTTTTCAGTTGATTCGAGTTTG--------------------------- chr7D_1_TraesCS7D01G003500 TTTTTTCAGTTGATTCGAGTTTG--------------------------- chr4A_1 -TTTTTCAATTGATGTGAGCTTGA-------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TTTTTGCAATTGGTTCGAGCTTGAGTTTAAATTTGATGCAAGTCTAAGTT chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 TTTTTGCAATTGGTTCGAGCTTGAGTTTAAATTTGATGCAAGTCTAAGTT chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --------S----------S------------------------------ forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -----------------------GGTTTCA------AATTTGAATTTTGA chr7D_1_TraesCS7D01G003500 -----------------------GGTTTCA------AATTTGAATTTTGA chr4A_1 ------------------------GTTTCA------AATTTGAATTTCGA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TATTTTTTGTTTGCAACTGATGCAAGTTTGACTTTAAATTTCAATTTGGA chr5B_809 -----------AGCAATTGATG------TG------AATTTGAATTTGAA chr5A_809 -----------GGCAATTGATGCGAGTTTG------AATTCGAATTTGAA chr5D_825 -----------TGCAATTGATGCGAGTATG------AATTTGAATTTGAA chr4A_876 -------------------------------------------------- chrUn_1857 TATTTTTTGTTTGCAACTGATGCAAGTTTGACTTTAAATTTCAATTTGGA chr5A_2243 -----------GT------ATGCGAGTTTG------AATTTGAATTTGAA chr5B_2380 -----------GT------ATGCGAGTTCG------AATTTGAATTTGAA SNPs -----------------------------------------------S-- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 TGAATTTTGCAGGTTCTGCAAGCAGATCATGTATGCCTCCCGCAAAGCGA chr7D_1_TraesCS7D01G003500 TGAATTTTGCAGGTTCTGCAAGCAGATCATGTATGCCTCCCGCAAAGCGA chr4A_1 TGTATTTTGCAGGTTCTGCAAGCAGATCATGTATGCCTCCCGCAAAGCGA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TGAATTTTGCAGGTTCTGCAAGCAGATTATGTACGCCTCCCGCAAAGCGA chr5B_809 ACAATTTTGCAGGTTCTGCAAGCAGATCATGTATGCGTCCCGAAAAGCAA chr5A_809 ACAATTTTGCAGGTTCTGCAAGCAGATCATGTACGCGTCCCGAAAAGCAA chr5D_825 ACAATTTTGCAGGTTCTGCAAGCAGATCATGTACGCGTCCCGAAAAGCAA chr4A_876 -------------------------------------------------- chrUn_1857 TGAATTTTGCAGGTTCTGCAAGCAGATTATGTACGCCTCCCGCAAAGCGA chr5A_2243 ACAATGTTGCAGGTTCTGCAAGCAGATCATGTACGCATCCCGAAAAGCGA chr5B_2380 ACAATTTTGCAGGTTCTGCAAGCAGATCATGTACGCATCCTGAAAAGCGA SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 GGGCAGACACGCGGAAGCGGGTCAAGGGCAGATTCGCAAAGGCTAGCAAT chr7D_1_TraesCS7D01G003500 GGGCAGACACGCGGAAGCGGGTCAAGGGCAGATTCGCAAAGGCTAGCAAT chr4A_1 GAGCGGACACACGGAAGCGGGTCAAGGGCAGATTCGCAAAGGCTAGCAAC chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GGGCGGACACGCGGAAGCGGGTCAAGGGCAGATTCGCAAAGGCTAGCAAT chr5B_809 GGGCGGACACGCGAAAGCGAGTCAAGGGCAGATTCGCCAAGGCTACCAAT chr5A_809 GGGCGGACACACGAAAGCGAGTCAAGGGCAGATTCGCCAAGGCTACCAAT chr5D_825 GGGCGGACACACGAAAGCGAGTCAAGGGCAGATTCGCCAAGGCTACCAAT chr4A_876 -------------------------------------------------- chrUn_1857 GGGCGGACACGCGGAAGCGGGTCAAGGGCAGATTCGCAAAGGCTAGCAAT chr5A_2243 GTGCGGACACGCGAAAGCGAATTAAGGGCAGATTCGCCAAGGCTACCAAT chr5B_2380 GGACGGACGCGCGAAAGCGAATTAAGGGCAGATTCGCCAAGGCTACCAAT SNPs ----S--------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 GAACACCAACACATACTACACTCAGATGCAGGATAA-------------- chr7D_1_TraesCS7D01G003500 GAACACCAACACATACTACACTCAGATGCAGGATAAATTCACGAGCGATT chr4A_1 GAACACCAACACATACTACACTCAGATGCAGGATAAATTCACGAGC---- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GAACACCAACACATACTACACTCAGATGCAGCATAAATTCATAAGC---- chr5B_809 GAACACCAACATGTACTACACCCAGATGCAGCATAAATTCACGGTTGATT chr5A_809 GAACACCAACACATACTACACCCAGATGCAGCATAAATTCACGATTGATT chr5D_825 GAGCACCAACACATACTACACTCAGATGCAGCATAAATTCACGATTGATT chr4A_876 -------------------------------------------------- chrUn_1857 GAACACCAACACATACTACACTCAGATGCAGCATAAATTCATAAGC---- chr5A_2243 GAACACCAACACATACTACACTCAGATGCAGCATAAATTCACGATTGAAT chr5B_2380 GAACACCAACACATACTACACCCAGATGCAGCATAAATTCACGATTGAAT SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 AGGTCGAT------TTTTTCGTTCTTTTTCTCTTTTTTC-------CATT chr4A_1 -GACTAGGCCGATTTTTTCGTTCTTTTTCTCTTTTTTTC-------CATT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -GATTAGGTCGATTTTTTCGTTCTTTTTCTCCTTTTTTC-------CATT chr5B_809 AGATCTGATCGATCCTTTTTCTTTCTTTTCCCTTTTTTAC-----ATATT chr5A_809 AGATCAGATCGATCCTTTTTCTTTCTTTTCCCTTTTTTGCATATTACATT chr5D_825 AGATCAGATCGATCCTTTTTCTTTCTTTTCCCTTTTTTTCT-----TATT chr4A_876 -------------------------------------------------- chrUn_1857 -GATTAGGTCGATTTTTTCGTTCTTTTTCTCCTTTTTTC-------CATT chr5A_2243 AGATCAGATAGATCCTTTTCTTATTTTTTCTCTTTTTTATA---TATATT chr5B_2380 AGATCAGATAGATCTTTTTCTTAATTTTTCTCTTTTTTATA----ATATT SNPs --S--SSS------------S--S-------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 CGTTTTACATATAGACAGTGCATATATACACAAAAAAGCAAACATTTTTT chr4A_1 CGTTTTGCATATAGACAATGCATATATACACAAAAAAGCAAACATTTTTT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CGTTTTGCATATAGACAGTGCATATATACACAAAAAAGCAAACATTTTTT chr5B_809 CCTTTAGCATATAGACAGTGCATATACACAAAAATCAAACA-----TTTT chr5A_809 CCTTGTGCATATAGACAGTGCATATACACAAAAA---------------- chr5D_825 CCTTTTGCATATAGACAGTGCATATACACAAAAATCAAA----------- chr4A_876 -------------------------------------------------- chrUn_1857 CGTTTTGCATATAGACAGTGCATATATACACAAAAAAGCAAACATTTTTT chr5A_2243 CCTTTTGCATATAGACAGTGCATATAGACAAAAATCAAACA-----TTTT chr5B_2380 CCTTTTGCATATAGACAGTGCATATACACAAAAACCAAACA-----TTTT SNPs ------S------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 GTAGTTACATCTTCATTTTTGTCGATGTAAAATAATA--TCTCAATATTA chr4A_1 GTAGTTACATCTT--TTTTTCGGA-TGTAAA-TAATA--TCCAAATATTA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GTAGTTACATCTTCATTTTTTTATGTATAGTCA----------------- chr5B_809 TTAGTTGCATCATCATTTTTTTCTGTGTAAA-TAATGTCTCAACACATTA chr5A_809 -------------------------------------------------- chr5D_825 ----------CATCATTTTTTTCTGTGTAAA-TAATGTCTCAACACATTA chr4A_876 -------------------------------------------------- chrUn_1857 GTAGTTACATCTTCATTTTTTTATGTATAGTCA----------------- chr5A_2243 TTAGTTACATCATCATTTTTTCGC-TGTAAA-TAATGCCTCAACACATTA chr5B_2380 TTAGTTACATCAT--TTTCTTCGC-TGTAAA-TAATGCCTCAACACATTA SNPs --------------------S--SS------S---------SS------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 CAGTCGATCATGCCTAGGTAGACCACTCTTCTCCACACCACACAAATACA chr4A_1 CTGTCGATCATGCCTAGGTAGACCACTCTTTTCCACACCACACAAATACA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ------ATCATGCCTAGGTAGACCACTCTTCTCCACACCACACAAATACA chr5B_809 CAGTCAGTCATGCCTAGGTAGACCACTCTTCTCCACAGCACACAAATACA chr5A_809 -------------------------------------------------- chr5D_825 CAGTCAGTCATGCCTAGGTAGACCACTCTTCTCCACAGCACACAAATACA chr4A_876 -------------------------------------------------- chrUn_1857 ------ATCATGCCTAGGTAGACCACTCTTCTCCACACCACACAAATACA chr5A_2243 CAGTGGGTCATGCCTAGGTAGAACACTCTTGTATACAGCACACAAATACA chr5B_2380 CAGTGGGTCATGCCTAGGTAGAACACTCTTGTACACAGCACACAAATAC- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 TTATACATAGCTCTAAATTTGTGGAGAAGGCTGTTGCACCTTAGATCTTA chr4A_1 TG---CATACCTCTTAATTTGTGGAGAAGGC---TGCACCTTAGATCTTA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GTATACATAGCTCTAAATTTGTGGAGAAGGCTGTTGCACCTTAGATCTTA chr5B_809 T------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 T------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 GTATACATAGCTCTAAATTTGTGGAGAAGGCTGTTGCACCTTAGATCTTA chr5A_2243 T------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 GCCCTTTTCTCAGTTTTTTTTTTGGCATTTCTTCTTTCCTTTTTGATAGT chr4A_1 GCCCTTTTCTCAGTTTTCTTTTTGAATTTTC-TCTTTCCTTTTTGATAGT chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GCCCTTTTCTCAGTTTTTCTTTTGGCATTTCTTCTTTCCTTTTTGATAGT chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 GCCCTTTTCTCAGTTTTTCTTTTGGCATTTCTTCTTTCCTTTTTGATAGT chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 TTTGTGCTCATTCTTTTTACATAGATAGTTTTGGGACACATTCTTCTTAG chr4A_1 TTTGTGCTCATTCTTTTTACAGAGATAGTTTTGGGACACATTCTTTTTAG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TTTGTGTTCATTCTTTTTACAGAGATAGTTTTGGGACACATTCTTCTTAG chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 TTTGTGTTCATTCTTTTTACAGAGATAGTTTTGGGACACATTCTTCTTAG chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ---------------------S---------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 GGAGGTACTTATAGGAACTGGTACCAAGGTGTAATAATTCAGCCCT---T chr4A_1 GGATGTACTTAGAGGACCTGGTACCAAGGTGTAATAATTCAGCCCT---T chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GGAGGTAGTTATAGGAACTGGTACCAAGGTGTAATAATTCAACCCTGCTT chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 GGAGGTAGTTATAGGAACTGGTACCAAGGTGTAATAATTCAACCCTGCTT chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -------------------------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 GTCTATGTGTACATTCATTATTCTATCTTTGGCCTGAATAAATAGAATAA chr4A_1 GTCTATGTGTACATACGTTATTATATCTTTGGCCTGAATAAATAGAATAA chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 GTCTATGTGCACGTACATTATTCTATCTTTGGCCCGAATAAATAGAATAA chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 GTCTATGTGCACGTACATTATTCTATCTTTGGCCCGAATAAATAGAATAA chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --------------S----------------------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 TGGATTTTCATGTGTTTGTCAATACTATCTG------------------- chr4A_1 TGGATTTTCATGTG-TTGTCAATGCTATGTG------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 TGTATTTTCGTATG-TTGTCAATGCTATGTTATTTTTATGTTCAAAAGAA chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 TGTATTTTCGTATG-TTGTCAATGCTATGTTATTTTTATGTTCAAAAGAA chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --------------S--------S----S--------------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 ----------ATTTTGGTGAATGTATTCTCTGAAAGTACTGTTTCTTGAA chr4A_1 ----------ATTTTGGTGAATGTATTCTCCGAAAATATTGTTTCTTCAG chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ATTCTATGCTATTTTGGTGATTGTATTCTCTGAAAGTATTGTTTCTTCAG chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 ATTCTATGCTATTTTGGTGATTGTATTCTCTGAAAGTATTGTTTCTTCAG chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --------------------------------------S--------S-S forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 AAAGAGAGACAAATGACTCACCTAAAAGT---------ACTGCAGTCTCT chr4A_1 -AAGAGAGACAAGTGACTCACCT--------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 AAAGAGAGACAAATGACTCACCTGTGTGCATGCCTGCAACTGCAATCTCT chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 AAAGAGAGACAAATGACTCACCTGTGTGCATGCCTGCAACTGCAATCTCT chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -----------------------SSSS-S---------------S----- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 ATTACTATCAATCGATTTTGTTATTTTGCCCAGAACTCCACAAATGTCAT chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ATTACTT------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 ATTACTT------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 TTCGATCTGAAATTTTGCAGGCAATTAGAACATTCATCAATGTTCATCAC chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 AAAAAAATCAGTTTTTTTTACTATTTTTTTCGATTTTACTGTTCATGCAG chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -------------------------------------------------- chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -------------------------------------------------- chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 GAGCATATGAGCTCGGGATCAAAAGAGCACTTTTGCTCTTCTCTATACTA chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 -----------------------------------CTCTTCTATATAGTA chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 -----------------------------------CTCTTCTATATAGTA chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-------S----S-- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 ---------AGCTCGGGATCAAAAGAGCA--------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 CTTAAC-----AATAACCTAAGGTTTTATCTTTCACTTGGTTTTCGCCCC chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CAGTACTTAGAAATAACCTGAGGTTTTATCTTACACTCAGTTTTCTCCCC chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 CAGTACTTAGAAATAACCTGAGGTTTTATCTTACACTCAGTTTTCTCCCC chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -SSS---------------S------------S----SS------S---- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 ACCACCCCTTCGTCCAACCTCCAACCCCCCATTGATTTTTCCTGGTTTTT chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ACCACCCCTTCGTCCAACCTCCAACCCCCCATAGATTTTTCTGGTTTTTT chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 ACCACCCCTTCGTCCAACCTCCAACCCCCCATAGATTTTTCTGGTTTTTT chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs --------------------------------S--------SS-S----- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 CATCCCTGCTGGTTTTCATCAAACCAATATTTGATAAACCAATAAACCAA chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 CATCCCTGCTGGTTTTCATCAAACCAATA---------------AACCAG chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 CATCCCTGCTGGTTTTCATCAAACCAATA---------------AACCAG chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs -----------------------------SSSSSSSSSSSSSSS-----S forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 -------------------------------------------------- chr7D_1_TraesCS7D01G003500 ATCAATCTATGGTATGGCAATAAATTCACGGTCAGTAAATAAATTGTTTC chr4A_1 -------------------------------------------------- chrUn_30 -------------------------------------------------- chr7A_30 -------------------------------------------------- chrUn_141 ATCAATCTATGGCATGGCAATAAATTCACGATATGTAAATAAATTGTTTC chr5B_809 -------------------------------------------------- chr5A_809 -------------------------------------------------- chr5D_825 -------------------------------------------------- chr4A_876 -------------------------------------------------- chrUn_1857 ATCAATCTATGGCATGGCAATAAATTCACGATATGTAAATAAATTGTTTC chr5A_2243 -------------------------------------------------- chr5B_2380 -------------------------------------------------- SNPs ------------S-----------------S-SS---------------- forward_2535 -------------------------------------------------- reverse_5038 -------------------------------------------------- forward_4458 -------------------------------------------------- reverse_7010 -------------------------------------------------- input_sequence_33693 ----------------------------------------------- chr7D_1_TraesCS7D01G003500 TTATGGTAAAACCTGGTACATGCTAGACATCTTTGGTAACCCAATAA chr4A_1 ----------------------------------------------- chrUn_30 ----------------------------------------------- chr7A_30 ----------------------------------------------- chrUn_141 TTATGGTAAAACCTGGTACAGGTTAGACATCTTTGGTAACCCAATAA chr5B_809 ----------------------------------------------- chr5A_809 ----------------------------------------------- chr5D_825 ----------------------------------------------- chr4A_876 ----------------------------------------------- chrUn_1857 TTATGGTAAAACCTGGTACAGGTTAGACATCTTTGGTAACCCAATAA chr5A_2243 ----------------------------------------------- chr5B_2380 ----------------------------------------------- SNPs --------------------S-S------------------------ forward_2535 ----------------------------------------------- reverse_5038 ----------------------------------------------- forward_4458 ----------------------------------------------- reverse_7010 -----------------------------------------------