CLUSTAL X (1.81) multiple sequence alignment input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 AAAACTGTGTC-TTATGATGAACGAATACTTTTTAGGCTAAAGGCGTAGG chrUn_1 AAAACTGTGTCTTTATGACGAACGAATACTTTTTAGGCCAAAGGCATAGG chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ------------------S-------------------S------S---- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TATGCAATTCTTCCCCGTATCATGATATTTATAGCTGTATAAAAGAAAAT chrUn_1 TATGCAATTATTCCCCTTATCATGATATTTATAGCTGTATAAAAGAAAAT chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ---------S------S--------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 ATGCCAATGGTACGCAATTATTCACCTTAATTACAGTTATGTCTTCATGT chrUn_1 ATGCCAATGGTACGCAATTATTCAGCTTAC---CAGTTATGTCTTCATGT chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ------------------------S----SSSS----------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 CTAGTATTATGCTTTCATATAAAAGCTAGTACTACCTGCCAAGATCAATG chrUn_1 CTAATATTATGCTTTCATATAAAAACTACTACTACCTGCCAAGATCAATG chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ---S--------------------S---S--------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TGCGGTCTCTAGGTTTACAATTGTTATGAGGTTGTTTTTTCT-----TGT chrUn_1 TGCGGTCTCTAGGTTTACAATTGTTATGAGATTATTTTTTCT-----TGT chr7A_208 --------CTAGGTTTACAATTGTTATGAGATTATTTTTTTCTTGTATGT chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ------------------------------S--S---------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 ATCAAGAAATTAACTCAAATCGATGTGGCTCACTGTTTTTT-ATAATGAG chrUn_1 ATCGAGAAATTAACTCAAAACGATGTGGCTCACTGTTTTTTTATAATAAG chr7A_208 ATTGAGAAGTTAAGCCAAATTGATGTGGCTCACTGTTTTTTTATAATAAG chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ---S-------------------------------------------S-- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TTAATTGCTGAGAAATGAGAATTAAGAATTTAAACCCCAAGACTCGTAGG chrUn_1 TTAATTGCTGAGAAATGAGAATTAAGAATTTAAAACCTAAGACTCGTAGG chr7A_208 TTTATCGCTGAGAAATGAGAATTAAGAATTTAAAACCTAAGACTCGCAGG chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ----------------------------------S--S------------ forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 GCTGTAGATCGAGACCGCCTTTTCGCAAACTACCCATATA-TTTTTTGAC chrUn_1 GCCGTAGATTGAGACCACCTTTTCATAAACTACCCTTATATTTTTTTGAC chr7A_208 GTTGTAGATTGAGACCACCTTTTCATAAACTACCCTTGTATTTTTTTGAC chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ---------S------S-------SS---------S-------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 ATAAAAAGCGATGAGTACAAGCTAA----TAAAATAATACTCTCTCCAAT chrUn_1 ATAAAAAGGAGTGAGTACAAGCTAAAATATAAAATAATACTTTCTGCGAT chr7A_208 ACAAAAAGGAGTGAGTACAAGCTAAATTATAAAATAATACTTTCTCTGAT chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs --------SSS------------------------------S-----S-- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 CCATATTACTACTTGTTGTAGCTTTATG---------------------- chrUn_1 CCATATTACTTGTCGCAGCTTTAGTTCAGTTTAATA-------------- chr7A_208 CCATATTACTTGTCGCAGCTTTAGTTCAGTTTAATACTCCCTCCGTCCGG chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ----------SS-S-SS-SSSSSS-SSS---------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr7A_208 AAATACTTGTCGCATAAATGCATAAAAATGGATGTATCTAAGAACTAAAA chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 ---------------------------------------------GAGCG chrUn_1 -------------------------------------------------- chr7A_208 TACGTCTAGATACATTCATTTCGCTGACAAGTATTTCCGGACGGAGAGAG chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ------------------------------------------------S- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TAGGGAGTAATTTTATTTGGTCTGTCTATTGGTACTCGCGTCCTCTGTCT chrUn_1 --GGTTGTAATTTTATTTGGTCAGTTTATTGGTACTCGCGTCCTCTATCA chr7A_208 TAGGTTGTAATTTTATTTGGTCAGTTTACTGGTACTCGTGTCCTTTGTCT chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ----SS----------------S--S------------------------ forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 ATCATCATGCCCGAGAAAGCCAAAACCAACACTCACCTACCTAATAGCCA chrUn_1 ATCATCGCTCCCGAGAAAACCCAAACCCAATGCTCA-----------CCT chr7A_208 ATCATCGCTCCCGCGGAAACCCAAA-CCAATGCTCA-----------CCT chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ------SSS---------S--S-----S-SSSSSSSSSSSSSSSSSS--S forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 ACCTGGTGAGAGAAGCGTGC------------------------------ chrUn_1 ACCTGGTGAGAGATGTATGCTACTACCTCCGTCCTGATTTTGTAAGTCAT chr7A_208 ACCTGGTGAGAGATATATGCTACTACCCCGGTCCTGATTTTGTAAGTCTT chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------S-SS--------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 TTTTGTATTTTGTGTCAAAGTTTGAGTATAGATTTAACTAACAAAATGTT chr7A_208 TTTTGTATTTTGTGTCAAAGTTTGACTATAAATTTAACTAACGAAATATT chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 AATGCATGCCACAAAAAATTATATCATTGGATTCGTATTTGAACATAATA chr7A_208 CATGCATGTCACCAAAAATTATATTGTTGGATTCATATTATGTTCAAATA chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 CGAATCCAACAATATAATTTTTGGTGACATGCATGAATATA-TGTTAGTT chr7A_208 TGAATCCAATGATATAATTTTTTGTGGCATGCATTAACATTTTGTTAGTT chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 AAATTTAAGGTCAAAATTTGGCATAGAATACAAAGGAGACTACTAAACTA chr7A_208 AAATTTAAGGTCAAAATTTATCACAGAATACAAAAGAGACTACTAAACCA chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 ------------TAATGTTCAGAGGTTGATTTTGAAATTAGGATGTAAAA chrUn_1 GGACGGATGTAGTAATGTTCAGAGGTTGATTTTGAAATTATGATGTAAAA chr7A_208 GGACGGAGGTAGTAATGTTCAGAGGTTGATTTTGAAATTATCATGTAAAA chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ----------------------------------------S--------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 AGAATGCATAATTTTTTTAAAAAATTATCCAAATACACAACCATATTGGT chrUn_1 A--ATACATAATTTTGAAAAAAAGAGATCCAAATACACATCCATATTGGT chr7A_208 A--AAACATAATTTTGAAAAAAAGAGATCCAAATACACATCCATATTGGC chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -SS--S---------SSS-----SSS-------------S---------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 GTGTGGATTTCAAAATCAAATTTAAAGGGAGGAAACAACAGCAATCCATT chrUn_1 GTGTGGATTTCAAAATCAGATTTAAGGGAGGAAAGT----GCAATCCATT chr7A_208 GTGTGGATTTCAAAATCAAATTTAAGGGAGGAAAGT----GCAATCCATT chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------S--SS-S--SSSSSS---------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TAATACTAGATGCCATGAAATGAAACACGTGAAATCTCTAAAATTCTTGT chrUn_1 TAATACTAGATGCCGTGAAATGAAACACGTGAAATCTCTAAAATTCTTGT chr7A_208 TAATACTAGATGCCGTGAAATGAAACACGTGAAATCTCAAAAATTCTTAT chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs --------------S----------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TGAACCTCTTAAAATCTGTGGGAAGCCAAAAAAAAAATGATCTTAAAAAA chrUn_1 TGAATCTCTTAAAATCTGTGGGAAGCCATAAAAAAAATGATCTTCAAAAA chr7A_208 TGAATCTCTTAAAATCTATGGGAAGCCA---AAAAAATGATCTTAAAAAA chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ----S-----------------------S--------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TCACAATGGTGCAAAATCCTGAAATAGATAGATTTTTGAATATGCCATAC chrUn_1 TCACAATGGTGCAAAATCTCTA---------------------------- chr7A_208 CCACAATGGTGCAAAATCCTGAAATAGATAGGTTTTTGAATATA------ chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------S-----------SSSSSSS forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 AAGATAGTACTGTTCAACAAGATAAT------------------------ chrUn_1 ---------------AACAAGATAATGCATTTTTGAAAGAGAGTGGCCTT chr7A_208 ------------TTCAACAAGATAATGCATTTTTGAAAACCGGTGGCCAC chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs SSSSSSSSSSSS-------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -----AGCCTCTGCAATCATGTGGCCGTCATACTACTAGTGTACTATTCT chrUn_1 TTAGAACCCGGGTGCCTAGGCAC--------------------------- chr7A_208 ACGACAGCCTCTGCAATCATGTGGCTACCACTGTACATGTCAGCTACTAT chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------SSS--SSS---SS--SSS---S-S- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 CG--------------------------CATCGGGAGAGTTCATCACCGT chrUn_1 -------------------------------------------------- chr7A_208 AGGATTTCTCAACGCTAGTTCAGCTCCACATCGGGAGAGTTCATCGGAGT chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs S--------------------------------------------SSS-- forward_1396 --------------------------CGCATCGGGAGAGTTCATCA---- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------CGGGAGAGTTCATCACCGT reverse_4468 -------------------------------------------------- input_sequence_49716 --------------------------------------------ATGGCT chr7D_1_TraesCS7D01G001400 CACCTGCCGGCGGCGACTGCTCCC------------------AGATGGCT chrUn_1 -------------------------------------------------- chr7A_208 AGAGCCAGAGCGCCCACTGATTTGAGCCACCCGCCGGCAGTGACATGGCT chr3B_998 -----------------------C------------------AGATGGGC chr7D_999 ------------------------------------------AGATGGGT chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs SSSSSSSSS---S-S----S-SS--------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 C------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 TCCCTGCTCATACCGCTGCTGGGCCGCGTGGCGGCCAAGGCCGGCGACGC chr7D_1_TraesCS7D01G001400 TCCCTGCTCATACCGCTGCTGGGCCGCGTGGCGGCCAAGGCCGGCGACGC chrUn_1 -------------------------------------------------- chr7A_208 TCCCTGCTCATACCGCTGCTGGGCCGCGTGGCGGCCAAGGCCGGGGACGC chr3B_998 TCGCTTCTGATGCCGCTGCTTGGCAGCGTGGCCGCTAAGGCCGGCGACGC chr7D_999 TCCCTGCTGATGCCGCTTCTGGGCAGCGTCGCCGCCAAGGCCGGCGACGC chr7B_1045 --------------------------------------GGCCGGCGACGC chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GCTGGTAGCCGAGTTGCTGCGGGCGTGGGGGCTGGACAAGGCCCGCCGGA chr7D_1_TraesCS7D01G001400 GCTGGTAGCCGAGTTGCTGCGGGCGTGGGGGCTGGACAAGGCCCGCCGGA chrUn_1 -------------------------------------------------- chr7A_208 GCTGGTGGCCGAGCTGCTGCGGGCGTGGGGGCTGGACAAGGCCCGCCGGA chr3B_998 GCTGGTGACCGAGCTGCTGCGGGCGTGGGGGCTGGATAAGTCCCGCCGGA chr7D_999 CCTCGTGGCCGAGCTGCTGCGGGCGTGGGGGCTGGACAAGTCCCGCCGGA chr7B_1045 GCTGGTCGGCGAGCTGCTGCGGGCGTGGGGGCTGGACAAGGCCCGCCGGA chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ------S------S------------------------------------ forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 AGCTTGAGCGCCACCTCGCCGCCGTCCAGTGCATCCTGCTCGACGCCGAC chr7D_1_TraesCS7D01G001400 AGCTTGAGCGCCACCTCGCCGCCGTCCAGTGCATCCTGCTCGACGCCGAC chrUn_1 ------------------CCGCTTATCAGTCCGTTCATCTAGAATCTGGC chr7A_208 AACTGGAGCGCCACCTCGCCGCCGTCCAGTGCGTCCTGCTGGACGCCGAC chr3B_998 AGCTGGAGCGCCACCTCGCCGCCGTCCAGTGCATCCTGCTCGACGCCGAC chr7D_999 AGCTGGAGCACCACCTCGCGGCCGTCCACTACATCCTGCTGGACGCCGAG chr7B_1045 AGCTGGAGCGCCACCTCGCCGCCGTCCAGTGCATCTTGCTGGACGCCGAC chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ----S--------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GCCAAGAGCCGCACCAACCCCGCCG------------------------- chr7D_1_TraesCS7D01G001400 GCCAAGAGCCGCACCAACCCCGCCG------------------------- chrUn_1 GCATTGAGATCTGTACCATGTACTATAGCACGCATTTGATTAGCATATCA chr7A_208 GCCAAGAGCCGCACAAACCCGGCCG------------------------- chr3B_998 GCCAAGAGCCGCACCAACCCCGCCG------------------------- chr7D_999 GCCAAGAGCCGCACCAACCCCTCGG------------------------- chr7B_1045 GCCAAGAGCCGCACCAACCCCGCCG------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 ATAGGTTCGACAGATTTCAACCTGGACCCATCCTAGCACTGTTTGGTATG chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 ACTGATTCCACCTATAGCAAGAAAAGAAAGGAAGATGTGGGATTTGATAC chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 TCACCGACGAGACGAGACGAAACGAGTTGTGCCCTCGACAGACCTGGTCG chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 CACTATTCCTGTGGCAGGAATCTTTCTACCGGAGCTAGCAGGCTGGTGGC chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 ATGCAACTGTATACATGCATTGGCCGCACAATATTTTAGGACTCCTTGAC chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 CGCGCGTTTGAACTGCAAAGAAAATAATCTCGCAAACCACGTACGATACA chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 GTATCTAATATTGGTTCTGTGATTGAACGAGAGACACCCGTGCATGGCTG chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 CATGTTCACGTGAATATATACTAGGTACCCATGCTTAATATTTTTATCGC chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 ATACCCAAAAAGTTGACCAACAGCCTAGCCCTGTCCCTGTCCGGCTGTCC chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 ---------------------------------------------TCAGC chr7D_1_TraesCS7D01G001400 ---------------------------------------------TCAGC chrUn_1 CTATTCATGTCTGCAAATTGCCTGCTTAATTACCTATTCATGTCATCCGC chr7A_208 ---------------------------------------------TCCGC chr3B_998 ---------------------------------------------TCCGC chr7D_999 ---------------------------------------------TCCGC chr7B_1045 ---------------------------------------------TCCGT chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -----------------------------------------------S-- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 CGGTGGGTCAAGGACCTCAAGACTGCCGCCTACCAGGCCGACGACGTCCT chr7D_1_TraesCS7D01G001400 CGGTGGGTCAAGGACCTCAAGACTGCCGCCTACCAGGCCGACGACGTCCT chrUn_1 CGCTGGATGACGGACCTCAAGACCGCCGCCTATCATGCCGACGACGTTCT chr7A_208 CATTGGGTCAAGGACCTCAAGACCGCCGCCTACCAGGCCGACGACGTCCT chr3B_998 CGCTGGATGGTGGACCTCAAGACCGCCGCCTACCAGGCCGACGACGTCCT chr7D_999 CGATGGACCAAGGACCTTAAGACCGCCGCCTACCAAGCCGAC-ACGTCCT chr7B_1045 CGATGGATCAAGGACCTCAAGACCGCCGCCTGCCAAGCCGACGACGTCCT chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs --S--------------------S-------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 CGACGGCTTCCGCTACGAGGCGCTGCGCCGCCGTGC---CACCGCCCAGT chr7D_1_TraesCS7D01G001400 CGACGGCTTCCGCTACGAGGCGCTGCGCCGCCGTGC---CACCGCCCAGT chrUn_1 CGACGACTTCCGCTACGAGGCGTTGCGACTCCGTGC---TGCA---CAGA chr7A_208 CGACGGCTTCCGCTACGAGGCGCTGCGCCGCCGTGC---CGCC---CAGA chr3B_998 CGATGACTTCCTCTACGAGGCGCTGCGCCGCCGTGC---CGCC---CAGA chr7D_999 TGACGACTTCCGCTACGAGGCGCTGCGCCGCCGTGC---CGCC---AAGA chr7B_1045 CGACGACTTCCGCCACGAGGCCCTGCGCCGCCGTGTTGGCGCC---CAGA chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ----------------------------------------S--SSS---S forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 T---------------CCACCGCTGCTCCACGGCACGCAAGGTTTGTCCT chr7D_1_TraesCS7D01G001400 T---------------CCACCGCTGCTCCACGGCACGCAAGGTTTGTCCT chrUn_1 T---------------GCGCCCCTACTCCACGGCACGCAAGGTTTGTCCT chr7A_208 T---------------ACGCCCCAGCTCCACGGCACACAAGGTTCGTCCG chr3B_998 TCCGCCGACGACGCCGCCGCCGCCGTGCCACCGCACGCAAGGTTCCCACT chr7D_999 T---------------GCGACGCTGCTACACGGCACACATGGCACGTACA chr7B_1045 G---------------CCACTCCCGCTCCACGCCGGGCAAGGTTCGTCCT chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 TGTCCTGCCTTTC------------------------------------- chr7D_1_TraesCS7D01G001400 TGTCCTGCCTTTC------------------------------------- chrUn_1 CGCCCGCTCCTTCTTTTCCCACACTTCCTCAAACTAGACGAACTGAAACA chr7A_208 TGTCCTACCTGTTCCCACCCAACTTTATTTTCAG---------------- chr3B_998 CTGTCTGGCTGTTCGGCCTCGTCCTACATGCCTTT--------------- chr7D_999 TCGTCGA-----------TCGTCCCACATTCTCTTCCATGAGTTCACCAC chr7B_1045 CGTCAAACCCCGGCAGGCTC------------------------------ chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 AAGTTTGAATGAAAATCACAAAAAATGATGCAACATATCAGCATTCGCTC chr7A_208 -------------------------------------------------- chr3B_998 ----------CCCACTCTGTCTGGCTCTGTTTTCAGTTAATCCTGCAAGT chr7D_999 CCCACCCCACCCCACCATGGCTAGCTCTGTTTTCATTTTGTAGCTAG--- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 GACAAATTCATCCAATTATTATTCAATCTTTTTTTTGTTTGTGGGTGAAT chr7A_208 -------------------------------------------------- chr3B_998 TCCTTGTAGTATATAGACAGATCACTGCCTGCAAATGAATTCCCTGCCTG chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 TATTTATTCAATCATCTGATTGCTATTCCACATGACTAGCAACTGTGCAT chr7A_208 -------------------------------------------------- chr3B_998 TAGTGCCTGCAAATTCTTATGTAAATTAAAATTCCTATGCTCGAATTCCT chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 TCTCCGCCTCTCACTTATTTGTGGTACCCTCAAGCTTGAAGCTCTGTCAA chr7A_208 -------------------------------------------------- chr3B_998 CTACTGCCTGCAAATTCATTTCCAAATAAATATTAACACTACAGATAACA chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -----------------------------------------AATTTCA-- chr7D_1_TraesCS7D01G001400 -----------------------------------------AATTTCA-- chrUn_1 TGGCGAGAGGTGGAAGGAGACAACAGCGACGATGATTTTTGTGCAGCGCA chr7A_208 -------------------------------------------------- chr3B_998 ACAAACACTTGAATATTTGGTTCACACGTTCTTTGTAGTATAATTTCA-- chr7D_999 -------------------------------------------------- chr7B_1045 ----------------------------------------TATTTTCA-- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 CTGAACTGCTGCGTTTTCTGTTTGCTTTATTCACGGATGAACTGAAAAAA chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 CGGATCGAGGACGACCCCCTCTACTGGATCGTGCCATCCCACGATCAGGG chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 GCGTGCGCTTGCCGCGAGCTACGGCCTCGGGATCGCACATGCCGCGTCCT chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 CAGGCTTGACTGAAACAACTGAAGAAAAAACTACAGACTGTCGAAACTGA chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -------------------------------------------------- chrUn_1 AACCTGACACTAAGCCTAACCTGAACCTGAAACTTGTCACGCTAGTTTAT chr7A_208 -------------------------------------------------- chr3B_998 -------------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------GTTTATTTGTTTCCAATTGGAAATGCAAGTCTTTTTA chr7D_1_TraesCS7D01G001400 -------------GTTTATTTGTTTCCAATTGGAAATGCAAGTCTTTTTA chrUn_1 TTGCTAACAATTTGTTTAAG-GTTTTATTTTGGAAA-------------- chr7A_208 -----------------------TTTCATTTGGTAATGGAAGCCTTTTAA chr3B_998 -------------GTTTAAG-GTGTTAGGTTGGAAATGTGAGCCTTTTAA chr7D_999 -------------------------------GGAAATGCAAGCATTTTAA chr7B_1045 -------------ATAAAAG-GTTTTAATTTGGAAATGGAAGCCTTCAC- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ------------------SSS----S--S-------------S-----S- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GTTTCAGTTTAAGGTTTTAAT--------TGGAAATGCAAGCCTTTCAAT chr7D_1_TraesCS7D01G001400 GTTTCAGTTTAAGGTTTTAAT--------TGGAAATGCAAGCCTTTCAAT chrUn_1 ----------------------------------ATGGCGGGCTTTTAAT chr7A_208 ATTCA--------GTTTAATT--------TGGAAATGGAAGCCTTTTAAT chr3B_998 TTTCA--------CTTTAATGTTTCGATATGGGAATGGAGGCCTCTTAAT chr7D_999 TTTTA--------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs S---SSSSSSSSS----S-S-----------------S--------S--- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 TTCTGTAGAGGGCTTTCATTTGGAAATGGATCGGAAGCCTTTCAATTTCA chr7D_1_TraesCS7D01G001400 TTCTGTAGAGGGCTTTCATTTGGAAATGGATCGGAAGCCTTTCAATTTCA chrUn_1 TTTG---------------------------------------------- chr7A_208 TTCAGTC--------TCGTTTGGAAATGGA-----ATCGTTTCGATTTCA chr3B_998 TTCT---------------------------------------------- chr7D_999 -------------------------------------------------- chr7B_1045 -------------------------------------------------- chr7D_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr4A_1493 -------------------------------------------------- chr7A_1497 -------------------------------------------------- chr4A_1509 -------------------------------------------------- chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ------SSSSSSSSS--S------------SSSSS-S-S----S------ forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 ATTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTTCATTTCAGGTGCT chr7D_1_TraesCS7D01G001400 ATTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTTCATTTCAGGTGCT chrUn_1 ---------------------AT--ATAATTGTTTTTCATTGCAGATGCT chr7A_208 GGTTAAGATACTAATTTGGAAGT--TCTGTTTGTTTTCATCTCAGATGCT chr3B_998 ---------------------GT--TTTATTTGTTCTCAATCCAGGTGCT chr7D_999 ------------------------GTTTATTTGTTTTCATTGCAGGTGTT chr7B_1045 -------------------------TTTATTTGTTATCATTTCAGGTGCT chr7D_1493 -------------------------TTTATTGGTTTTCATATCAGGCGCT chr4A_1493 -------------------------TTTGTTTGTTTTTATTTTAGGTGCT chr4A_1493 -------------------------TTTATTTGTTCTCATTCCAGGTGTT chr4A_1493 -------------------------TTTATTGGTTTTTATATCAGGCGCT chr7A_1497 -----------------------------TTTGTTTTCATTTCAGCCGCT chr4A_1509 -----------------------------------------TCAGGTGTT chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs SS--SSSSSSS-SS--SSSSSS-S-------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GGGCTATTTCACAGCCGACAGCCCGCTTCTTTTCCGTCTTTCCATGAGTA chr7D_1_TraesCS7D01G001400 GGGCTATTTCACAGCCGACAGCCCGCTTCTTTTCCGTCTTTCCATGAGTA chrUn_1 GAGCTACTTCACCACCAGCAGCCCGATTGTTTTTCGTCTCTCCATGAGCA chr7A_208 GAGCTACTTCACTGTCAATAGCCCGGTTGTTTTCCGTCTCTCAATGAGCA chr3B_998 GAGCTACTTCACCACCAATAGCCCGGTTGTTTTCCGCCTTTCAATAAGCA chr7D_999 AAGCTACTTCACCGCCCATAGCCCGGTTGTTTTCCGTCTTCACACGAGCT chr7B_1045 GACGTACCTCACAATCAATAGCCCGGTTGTTTTCCGTCTTCACATGAGTT chr7D_1493 GAGCTACTTCACCGTCAATAGTCCGGTTGTTTTCCGTCTATCCATGAGCA chr4A_1493 GACCTACTTCACCGTCAATAGTCCACTTGTTTTCCGTCTTTCCATGAGCA chr4A_1493 GAGCTACTTCACTGCCAATAGCCCGGTTGTTTTCCGTCTCTCCATGAGCA chr4A_1493 GAGCTACTTTACCGTCAATAGTCCCGTTGTTTTCCGTCTATCCATGAGCA chr7A_1497 GGGCTACTTCACCATCAATAGTCCGGTTATTTTCGGTGTTTACATGAGTT chr4A_1509 GAACTACTTCACCGTCCATAATCCGGTTGTTTTCCGTCTCTCAATGAGTA chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ------S---------S-----------S--------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GGAAGATGAAGGATGCCCTTGAGATGATAGATGAACTGGTTGCGGAGATG chr7D_1_TraesCS7D01G001400 GGAAGATGAAGGATGCCCTTGAGATGATAGATGAACTGGTTGCGGAGATG chrUn_1 GGAAGATGAAAGATGCCCTTGAAATGATAGACGAACTGGTTGTGGAGATG chr7A_208 AGAAGATGAAGAATTGCCTTGATATGATAGATGAGCTGGTTGTGGAGATG chr3B_998 GGAAGATGAAGGATGCCCTAGAGATGATTGATGAACTGGTTGTAGAGATG chr7D_999 GGAAGTTGAAGGACGTCCTTGAGACCATTGATGAACTGGTTGTGGAGACG chr7B_1045 GGAAGTTGAAGGGTGCCCTTCAAACGATTGGTGAACTTGTCGCGGAGATG chr7D_1493 GGAAGATGAAGGATGCCCTTGAGATGATAGATGAGCTGGTTGTCGAGATG chr4A_1493 GAAAGATGAAGGAGGCCCTTGACATAATAGATGAACTGGTTGTGGAGATG chr4A_1493 GGAAGATGAAGGACGCCCTTGAAATCATAGATGAACTGGTTGTGGAGATG chr4A_1493 GGAAGATGAAGGATGCCCTTGAGATGATAGATGAACTGGTTGTCGAGATG chr7A_1497 GGAAGATGAAGGGTGCCCTTCAAATGATAGATGAACTGGTTGTGGAGATG chr4A_1509 GGAAGATGAAGGATTGCCTTGATGTGATAGATGAACTGGTTGCAGAGATG chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 AACAATTTCCACTTCCTACAACGTACCGAGGCACCAACCATTGTCCATCC chr7D_1_TraesCS7D01G001400 AACAATTTCCACTTCCTACAACGTACCGAGGCACCAACCATTGTCCATCC chrUn_1 AATAACTTTCACTTCCTACAACATGCCGGGGCACCAACCATTGTTCAGCC chr7A_208 AACAATTTCCACTTCCTACAACACGCCGATGCACCAAGCATTGTTCACCC chr3B_998 AACAATTTCCACTTCCTGCAACATACCGAAGCACCATACGTTGATCATCC chr7D_999 AACAATTTCCACTTCCTACAACATACCGAAGCACCAAGCATTGATCATCC chr7B_1045 AATAATTTCCACTTCTTACAACATGCTGAGGCACCAAGCGTTGTTCGTCC chr7D_1493 AACAATTTTCACTTCCTACAACTTACCGAGACACCAACTGTTGATCATCC chr4A_1493 AACAATTTTCACTTTCTACAACATACCGAGACATCAACCATTGTTCATCC chr4A_1493 AACAAATTTCAATTCCTGCAACATAAGGAGTCACCAAGCGTTGATCATCC chr4A_1493 AACAATTTTCACTTCCTACAACTTACCGAGACACCAACTATTGATCATCC chr7A_1497 AACAATTTCCATTTCCTACAACATGTCGAGCCACGAATTATTGTTCATCT chr4A_1509 AACAAGTTCCACTTCCTACAACATATTGAGACACCAAGCACTCTCCATCC chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ----------------------S--------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GCAAACACATTCTTGTGTCGATGAATCAGAGATCATCGGCAGACAAGACG chr7D_1_TraesCS7D01G001400 GCAAACACATTCTTGTGTCGATGAATCAGAGATCATCGGCAGACAAGACG chrUn_1 GCAAACACACTCACATGTCAATGAATTACAAATCGTCGGCAGACAAGATG chr7A_208 GCAAACACACTCTCATGTTGATGAACTAGAGGTTGTTGGCAGACAAGATG chr3B_998 GCAAACACACTCTCAAGTCAATGAATCAGAGATTGTGGGCAGACAAGACG chr7D_999 ACAAACATACTCTCATGTTGATGAATCAGACATTGTGGGCAGACAAGCGG chr7B_1045 GCAAACACACTCTCTTGTCGATGAATCAGAGATTGTGGGCAGACAAGATG chr7D_1493 ACAAACACACTCTCATGTTGATGCATCAGATATAGTCGGCAGACAAGATG chr4A_1493 GCACACACACTCTCATGTTGATGAATTAGAGGTTGTCGGCAGACAATATG chr4A_1493 ACAGACACACTCTCATGTCGATGAATCAGAGATTGTGGGTAGGCAAGATG chr4A_1493 ACAAACACACTCTCATGTTGATGAATCAGATATAGTCGGCAGACAAGATG chr7A_1497 ACAAACACATTCTTGTGTCAATGAATCAGATATTGTCGGAAGACAAGATG chr4A_1509 ACAAACACATTCTCACGTCGATGAATTGGAGATTGTAGGCAAACAAGATG chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ----------------------------------S--------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 ACAAGGAACAAGTGGTGAAGATATTGCTCGACCACTCC---AACAACAGT chr7D_1_TraesCS7D01G001400 ACAAGGAACAAGTGGTGAAGATATTGCTCGACCACTCC---AACAACAGT chrUn_1 AAAAGGAACAAGTGGTGAAGATATTGCTCAACCAGTCTGATAATAGCAAC chr7A_208 AGAAGGAACGGGTGGTCAAGATATTGCTACATCACTCT---CGCAACAAC chr3B_998 AGAAGGAACAAGTGGTGAAGATGTTGCTCGACCACTCC---AACCACAAT chr7D_999 AGAAGGAACAAGTGGTGAAGATATTGCTCGACCACTCT---CACAACAAT chr7B_1045 AGAGGGAACAAGTGGTGAAGATATTGCTCGACCACAAC---AACAGTAGC chr7D_1493 AGAAGGAACAAGTGGTGAAGATATTGCTCGACCACGCC---GACAACAAC chr4A_1493 ACAAGGAACAAGTGGTGAAGATATTGCTCGGCCACTCCCATGTAAGTAAC chr4A_1493 ACAAGGAACAAGTGGTGAAGATATTGCTCGACCACTCC---AACAACAAT chr4A_1493 AGAAGGAACAAGTGGTGAAGATATTGCTCGACCACGCC---GACAACAAC chr7A_1497 ACAAGGACCAAGTGGTGAAGATTTTGCTAGACCACTCC---GCCAAAAAT chr4A_1509 AGAAGGAACAAGTGGTGAAGATATTGCTAGACCACGGC---CACAACCGT chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 AA---TGATGGACATAATGTCACGGTGCTCCCCATAGTTGGCATGGGGGG chr7D_1_TraesCS7D01G001400 AA---TGATGGACATAATGTCACGGTGCTCCCCATAGTTGGCATGGGGGG chrUn_1 AT---TGGTAATAGTGGCATCATGGTGCTCCCCATAGTTGGCATGGGGGG chr7A_208 AA---TAGTGATAACAATGTCATGGTGCTCCCCATAGTTGGTATGGGGGG chr3B_998 AA---TGGTAATGACAATGTCATGGTGCTCCCCATAATTGGCATGGGGGG chr7D_999 AA---TGACAGTAATAATGTCATGGTGCTCCCCATAGTTGGTATGGGGGG chr7B_1045 C---------ATAATAATGTCATGGTGCTCCCCGTTGTTGGTATGGGGGG chr7D_1493 GA---TAAGAATAACAATGTCATGGTGCTTCCCATAGTTGGTATGGGGGG chr4A_1493 AA---TGATAAGAATAACGTCATGGTGCTCCCTATAGTTGGTATGGGGGG chr4A_1493 AA---TGATAATAGTAATGTCATGGTGCTCCCCATAATTGGTATGGGGGG chr4A_1493 AA---TAAGAATAACAATGTCATGGTGCTTCCCATAGTTGGTATGGGGGG chr7A_1497 ---------GATAATAATGTCATTGTGCTCCCTATTGTTGGTACGGGGGG chr4A_1509 CCGAGTGATAATAATAATGTCATGGTGCTCCCCATAGTTGGTATGGGGGG chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -----------SS---------S--------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 A--ATCGGTAAGACCACCCTTGCTCAACTTGTGCACAATGACCAGAGAGT chr7D_1_TraesCS7D01G001400 A--ATCGGTAAGACCACCCTTGCTCAACTTGTGCACAATGACCAGAGAGT chrUn_1 A--ATTGGCAAAACTACCCTTGCCCAACTTGTTCACAATGATCAAAGGGT chr7A_208 A--ATTGGTAAGACCACCCTTGCTCAACTTGTGCACAATGACCAAAGGGT chr3B_998 A--ATTGGTAAGACCACACTTGCTCAACTTGTGCTCAATGACCACAGAAT chr7D_999 A--ATTGGTAAGACTACCCTTGCCCAATTTGTGCACAATGATCAGAGGGT chr7B_1045 A--ATTGGTAAGACCACCCTTGCTCAACTTGTGTACAATGACCACCGAGT chr7D_1493 A--ATTGGTAAGACTACACTTGCCCAACTTGTGCACAATGATCCGAGGGT chr4A_1493 A--ATTGGTAAGACCACACTTGCTCAACTTGTGCATAATGACCAGAGAGT chr4A_1493 A--ATCGGTAAGACCACCCTTGCTCAACTTGTGCACAATGAACAAAGGGT chr4A_1493 A--ATTGGTAAGACTACACTTGCCCAACTTGTGCACAATGATCCGAGGGT chr7A_1497 A--ATTGGTAAGACCACCCTTGCTCAACTTGTGCACAATGACCATAGAGT chr4A_1509 GGGATTGGTAAGACCACCCTTGCTCAACTTGTGTACAATGACCGGAGGGT chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GATGCATCATTTTGAGTTGGTGATATGGATCTGTGTCTCTGACAAGTTTG chr7D_1_TraesCS7D01G001400 GATGCATCATTTTGAGTTGGTGATATGGATCTGTGTCTCTGACAAGTTTG chrUn_1 GAAGGACCATTTTGAGTTGGTCTTGTGGGTATGTGTCTCTGACAAGTTCA chr7A_208 TGTGCATCACTTTGAGTTGGTCTTATGGGTATGCATCTCTGACAAGTTTG chr3B_998 GGTGCATCATTTTGAGTTAGTCTTATGGGTCTGTGTCTCTGACAAGTTCA chr7D_999 GAAGCATCATTTTGAGTTGGTCATATGGACATGTGTCTCTGACAAGTTTA chr7B_1045 CATCCACCATTTTGAGTTGGTCATATGGGTTTGTGTCTCTGACAAGTTCA chr7D_1493 GATGCATCATTTTGAGTTGGTCATATGGGTCTGTGTCTCTAACAAGTTTG chr4A_1493 GGTGCAACATTTTGAGTTGGTCTTATGGGTATGTGTCTCTGATAAGTTCA chr4A_1493 GAAGCTTCATTTTGAGTTGGTCTTATGGGCATGTGTCTCTGACAAGTTCG chr4A_1493 GATGCATCATTTTGAGTTGGTCATATGGGTCTGTGTCTCTGACAAGTTTG chr7A_1497 GGCGCATCATTTTCAGTTGGTCTTATGGGTCTGTGTCTCTGACAAGTTCG chr4A_1509 GGTGCGTCATTTTGAGTTGATCATATGGGTATGTGTCTCTAAAAAGTTTG chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ---------------------S---------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 CTATCGAAGGAATAATCCGATCTATAATAGAATTGGCCACACTGAAGAAG chr7D_1_TraesCS7D01G001400 CTATCGAAGGAATAATCCGATCTATAATAGAATTGGCCACACTGAAGAAG chrUn_1 TTATTGAAGAAATCATCCGGTCCATAATAGAAGTGGCCACCATGAAGAAG chr7A_208 TTATTGAAGAAATAATACGATCTATAATAGAAGTCGCCACGATGACCAAA chr3B_998 TTATCATGGAAATAATTCGATCTATAATACAAGTGGCCACGCTGAATAAG chr7D_999 TCGTCGAAGAAATTATTCGATCTGTAATACAAGTGGCCACATTGAACAAG chr7B_1045 TCATCCAAGAAATAATCCGATCTGTAATAGAAGTGGTCATGATGAAGAAG chr7D_1493 TTATCGAAGAAATTATTCGATCTATAATACAAGTGGTCACAATGAACAAG chr4A_1493 TTATCGAAGAAATAATCCAATCTATAATAGAAGTGGCAACGATGAAGAAG chr4A_1493 TTATCGAAGAAATAGTCCGATCTATAATAGAAGTTGCCACGATGAAGAAG chr4A_1493 TTATTGAAGAAATTATTCGATCTATTATACAAGTGGTTACAATGAACAAG chr7A_1497 TTATCGAAGAAATTATACGATCTGTAATAGAAGTGGCCACGATGAAGAAG chr4A_1509 TTATTGAAGATATAATCCGATCTATAATACAAGTGGCCACAATCAACACG chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs S--------S----------------------S----------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 TGTGGTTTGACTCAGACCGAGGCACTGCACAAGGAGCTTAGTCGGGTGTT chr7D_1_TraesCS7D01G001400 TGTGGTTTGACTCAGACCGAGGCACTGCACAAGGAGCTTAGTCGGGTGTT chrUn_1 TGTGGTTTGACTCAGATGGAGGCACTGCAGAAGGAACTCAGTAAAGTTTT chr7A_208 TGTGATTCCACTAAGATGGAGGCACTGCGGAAGCAACTTGGTGAAGTGTT chr3B_998 TGTGATTTGACCGAGATGGAGGCACTGCGGAAGGAACTTGGTCAAGTGTT chr7D_999 TGTGAATTGACTGACAAGGAGGCACTGCAGAAGAAACTTGGTGAAGTGTT chr7B_1045 TGTGATCTGACTCAGATGGAGGCACTGCAGAAGAAACTTAGTGAGGCGTT chr7D_1493 TGTGAATTGACTGAGATGGAAGCACTGCGGAAGAAACTTCGTGAACTGTT chr4A_1493 TGTGATTTGACTCAGATGGAGACACTGCAAAAGGAACTTTCTAGAGTTTT chr4A_1493 TGTGAATTGACCCATATGGAGGCACTACAGAAGAAACTTTGTGAAGTGTT chr4A_1493 TGTGAATTGACTGAGATGGAAGCACTTGAGAAGAAACTTGGTGAAGTGTT chr7A_1497 TGTGATTTGACTCAGACGGAGGCACTGCAGAAAGAACTTATTGGAGTGTT chr4A_1509 TGTGATTTGACTGAGATGGAGGCATTGCACAAGGATCTTAGTCGAGTGTT chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -----------------S-----------------S-------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GGGCAAGAAAAGGTACCTCCTGGTGCTGGATGATGTTTGGAATGAAGATA chr7D_1_TraesCS7D01G001400 GGGCAAGAAAAGGTACCTCCTGGTGCTGGATGATGTTTGGAATGAAGATA chrUn_1 GGCCAAGAAAAGGTACCTCCTAGTATTGGATGATGTTTGGAATGAAGATC chr7A_208 GGGCAGGAGAAGGTACCTCATAATTTTGGATGATGTTTGGAATGAAGATA chr3B_998 GGGCAAGAAAAGATACCTCTTAGTGCTGGATGATGTTTGGAATGAAGATG chr7D_999 GGGCAAGAAAAGGTACCTCCTAGTGTTGGATGATGTTTGGAATGAAGATA chr7B_1045 GGGCAAGAAAAAGTACCTCCTAGTGTTGGATGATGTTTGGAACGAAGATA chr7D_1493 GGGAAAGAAAAGGTACCTCCTACTGCTGGATGATGTTTGGAATGAAGATA chr4A_1493 GGGCAAGAAAAGGTACCTTCTAGTGCTGGATGATGTGTGGAATGAAGACG chr4A_1493 GGGCAAAAAAAAGTATCTCCTAGTGATGGATGATGTTTGGAATGAAGATA chr4A_1493 GGGAAAGAAAAGGTGCCTCCTAGTGTTGGATGATGTTTGGAATGAAGATA chr7A_1497 GGGAGAGAAAAAGTACCTCCTAGTGATGGATGATGTCTGGAATGAAGATA chr4A_1509 GGGCAAGAAAAGGTACCTCCTAGTGTTAGACGATATTTGGAATGAAGATG chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ---------------------S---------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GACAAAAGTGGGACGATATGAGATCAGTGTTGTGCTCACATGCTGGCCTA chr7D_1_TraesCS7D01G001400 GACAAAAGTGGGACGATATGAGATCAGTGTTGTGCTCACATGCTGGCCTA chrUn_1 GACGGAAGTGGGATGACATGAGATCATTGTTGTGCGCACATTCTAGATCG chr7A_208 GACAGAAGTGGGATGATATGAGATCATTGTTGTGCTCACATGCTGGCTCA chr3B_998 GACAGAAGTGGGATGCTATGAGATCATTGTTATGCTCACATGCTGGCTCA chr7D_999 GACAAAAGTGGGATGATATGAGATCTTTTCTATGCTCACATGCCGGCTCA chr7B_1045 GACAAAAGTGGGACGATATGAGATCTTCGTTATGCTCACATGCTGGCTCA chr7D_1493 GACAAAAATGGGATGATATGAGATCTCTGTTATGCTCACATGCTGTCTCA chr4A_1493 AACAGAAGTGGGATGCTATGAGATCACTGCTCTGCTCACATGCTGGCTCA chr4A_1493 GACACAAGTGGGATGATATGAGATCATTACTAAACTCACAGGCCGGCTCA chr4A_1493 GACAGAAGTGGGATGAGATGAGATCATTGTTGTGCTCACATGTTGGCTCA chr7A_1497 GGCAGAAGTGGGATGATATGAGATCATTGCTATGCTCACATGCTGACTCA chr4A_1509 TACAGAAGTGGGATGATATGAGATCATTGTTGTGCTCACATGCTGGCTCA chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs --------------------------S--------------------SS- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GGTAGTGTTATAATTGTGACAAGCCGCAGCGAGCAAGTTGCTTCTATCAT chr7D_1_TraesCS7D01G001400 GGTAGTGTTATAATTGTGACAAGCCGCAGCGAGCAAGTTGCTTCTATCAT chrUn_1 GGTAGTGCTGTAATTGTGACAAGCCGCAATGATCAAGTTGCTTCTATGAT chr7A_208 GGTAGTGCCATAATTGTGACAAGTCGCAGCGATCAAGTTGCTTCTATCAT chr3B_998 GGTAGTGCTATAATTGTGACAAGCCGCAGCGACAAAGTTGCATCTATCAT chr7D_999 CGCAGTGCTATAATTGTGACAAGCCGTAGCAATCAAGTTGCTTCTATCAT chr7B_1045 GGCAGTGCTATAGTTGTGACAAGCCGCAGCAGTCAAGTTGCTTCTATCAT chr7D_1493 AGCAGTGCTATAATTGTTACAAGCCGCAGCGATCAAGTTGCTTCTATCAT chr4A_1493 GGTAGTGCTATAATTGTGACAAGCCGCAGCGATCAAGTTGCTTCTATTAT chr4A_1493 GGTAGTGCTATAATTGTGACAAGCCGCAGCGATCAAGTTGCCTCTATCAT chr4A_1493 GGTAGTGCAATAATTGTGACAAGCCGAAGTGATCGAGTTGCTTCTATCAT chr7A_1497 GGTAGTGCTATACTTGTGACAACCCGCAACAATCAAGTTGCTTCTATAAT chr4A_1509 GGTACTGCTATAATTGTGACAAGCCGCAGTGATCAAGTTGCTTCTATCAT chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------S------------------------S----------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GGGCACACTTCCTCCACATCAGATATCACTTCTAAACGAGGATCAATCAT chr7D_1_TraesCS7D01G001400 GGGCACACTTCCTCCACATCAGATATCACTTCTAAACGAGGATCAATCAT chrUn_1 GGGCACACTTCCACCACATCAGATGTCACTTCTAAATGAAGATCAATCAT chr7A_208 GGGCACACTTCCTCCACGCCAGATATCACTTCTAGATGAGGATCAATCAT chr3B_998 GGGCACACTTCCTCCACATCAGATATCGCTTCTAAGTGATGATCAATCAT chr7D_999 GGGCACACTTCCTCCGCATCAGATATCACTTCTAGATGAAGATCAATCAT chr7B_1045 GGGCACACTTCCTCCACATCAAATTTCACTTCTAGATGAGGATCAATCAT chr7D_1493 GGGTACACACCCTCCACATCAAATATCACTTTTAAATGAGGATCAGTCGT chr4A_1493 GGGCACACTTCCTCTGCATCATATATCACTTCTAGATGACGATCAATCAT chr4A_1493 GGGAACGCTTCCTCCACATCGCATATCTCTTCTGAATGAGGATCGGTCAT chr4A_1493 GGGCACACTTCCTCCACATATGATATTTGTTCTAAATGAGGACCAATCAT chr7A_1497 GGGTACATGTCCTCCGCATCAGATATCACTTCTAAATGAGGATCAATCAT chr4A_1509 GGGCACCATTTCTCCACATCGGATATCACTTCTGAACGAGGATCAATCAT chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GGGAGCTTTTTCACAAGAACACATTTGGAAGGGAAGCAGAAAAGCAAGAG chr7D_1_TraesCS7D01G001400 GGGAGCTTTTTCACAAGAACACATTTGGAAGGGAAGCAGAAAAGCAAGAG chrUn_1 GGGAGCTTTTTCACAAAAATGCATTTGGTAGAGAAGTGGAAAAACCAGAG chr7A_208 GGGAGCTTTTTCATAGAAACACATTTGGAAGAGGAGTGGAAAAGCAAGAG chr3B_998 GGGAGTTCTTTGACAGAAACACATCTGGAAGAGAAGTAGAAAGGCAAGAG chr7D_999 GGGAGATTTTTAAAAGAAAAGCATTTGGAATGGAAGTGGAAAAGAAAGAG chr7B_1045 GGGACCTTTTCCACAAAAACACATTTGGAAGGGGAGTGGAAAAGCGAGAG chr7D_1493 GGGAGCTTTTCAACAGAAATGCATTTGGAAGGGGAGTAGAGAAGCAAGAG chr4A_1493 GGGAGCTTTTTCATAGAAAAGCATTTGGAAGTGAAGTGGAAAAGAATGAG chr4A_1493 GGGAGCTTTTTCAGAGAAACACATTTCAAAGGGAAGCAGAAAAGCAAGAG chr4A_1493 GGGAGCTTTTTCGTAGAAGCACATTTGGAAGCGGAGTGGAAAAACAAGGG chr7A_1497 GGCAGCTTTTTCGTAGAAAAACATTTGGAAGTGATGTGGAAAAACAAGAA chr4A_1509 GGGAGCTTTTTCATAGAAACACATTTGGAAGGCAGGTGGAAAAGCACGAG chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ----------------S--------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 GAATTAGTTTCAATGGCTAAAAGTATTCTCCACAAGTGTAAGGGATTGCC chr7D_1_TraesCS7D01G001400 GAATTAGTTTCAATGGCTAAAAGTATTCTCCACAAGTGTAAGGGATTGCC chrUn_1 GAATTCAACTCAATAGCTAAGAGTATTTTACACAAGTGTAAGGGGTTGCC chr7A_208 GAATTGATTTTAACGGCTAAGAATATTGTCCATAAGTGTAAGGGATTGCC chr3B_998 GAATTTATTTCAGTCGCAAAGAACATTGTTGACAAGTGTAAAGGATTGCC chr7D_999 GAATTGATTTCAGTCGCAAAGAGTATTGTTCATAAGTGTAAGGGATTGCC chr7B_1045 GAATTGGTTTCAATGGCTAAGAGTATTGTCCACAAGTGCAAGGGATTGCC chr7D_1493 AAACTGATTTCAATGGCCAAGAGTATTGTCCACAAGTGTAAGGGATTGCC chr4A_1493 GAATTGATTTCAGTGGCAAAGAACATTGTCCGCAAGTGTAAGGGATTGCC chr4A_1493 GAATTGATTTCAATCGCAAAGAACATTGTCCACAAGTGTAAGGGATTGCC chr4A_1493 GAATTGATTTCAGTTGCTAAGAGTATTCTCCATAAGTGCAAGGGATTGCC chr7A_1497 GAATTGATTTCAGTCAAAAAGAACATTGTTCATAAGTGTAAGGGATTGCC chr4A_1509 GAATTTATTTCAATGGCTAAGGGTATTGTCCACATGTGTAAGGGATTGCC chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -----S--------------S----------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 TCTCGCTATCAAGACCATAGCAGCTTTACTTCGTTCGAAGCATCAAAGTC chr7D_1_TraesCS7D01G001400 TCTCGCTATCAAGACCATAGCAGCTTTACTTCGTTCGAAGCATCAAAGTC chrUn_1 TCTTGCTATCAACACAGTGGCAACTTTACTTCATTCAAAGCATCACAGTC chr7A_208 TCTTGCTATCAAAACAATGGCAGCTTTACTTCTCTCAAAGCATCACAATC chr3B_998 TCTTGCTATCAAGACCATAGCCGCTTTACTTCCTTCGAAGAATCACAATC chr7D_999 TCTTGCTATCAAGACCATAGCAGCTTTACTTCGCTCGAAACATCACAGTC chr7B_1045 TCTTGCTATCAAGACCATGGCAGCTTTACTCTCTTCGAAGCATCACAGTC chr7D_1493 TCTTGCCATCAAGACTATAGCAGCTTTACTTTGTTCCAAGAATCACAGTC chr4A_1493 ACTTGCTATCAAGACCATAGCAGCTTTACTTCGCTCGAAGCATCATAGTC chr4A_1493 TCCTGCTATCAAGACCATAGCCGCTTTACTTCGTTCGAAGCATCACAGTC chr4A_1493 TCTTGCTATCAAGACCATATCTGCTTTACTTCAGTCGAAGCATCATACTC chr7A_1497 TCTTGCTATCAAGACCATAGCAGCTTTACTTCGTTCGAAGCATCATAGTC chr4A_1509 TCTTGCTATCAAGACCATAGCAGCTTTACTTCGTTTGAAGCATCACAATC chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ---S-----------------------------------------S---- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 AGTGGTTTTCTGTTTTGGATAGTGATGTCTGGAAGAATGACATCCTCGCA chr7D_1_TraesCS7D01G001400 AGTGGTTTTCTGTTTTGGATAGTGATGTCTGGAAGAATGACATCCTCGCA chrUn_1 AGTGGGTTTCTATTTTGAACAGTGATGTTTGGAAGAATGACGTCCTGGCA chr7A_208 AGTGGCTTGCTGTTCTAGATAGTGATGTCTGGAAGAATGGCATTCTCGCA chr3B_998 AGTGGTTTTCTGTTCTGGATAGCGATGTATGGAAAGATGACATTCTCACA chr7D_999 AGTGGTTTTCTGTTCTCCATAGTGATGTCTGGAAAGATGACATCCTCACA chr7B_1045 AGTGGCTTTCTGTTCTAGATAGTGATGTTTGGAAAGATAACATCGTCACA chr7D_1493 ATTGGTTTTCTATTGTTGATAGTGATGTATGGAAGAGTGACATCCTC--- chr4A_1493 AGTGGTCTTCTGTTGTGGATAGTGATGTCTGGAAAGATGACATCCTCACA chr4A_1493 AGTGGTTTTCTGTTCTGGATAGTGATGTCTGGAAAGATGAAATCCTCACA chr4A_1493 AATGGTTCTCTGTTCTGGATAGTGATGTCTGGAAAGATGATATCATCACA chr7A_1497 AGTGGTTTTCTGTTCTGGAGAGTGATGTCTGGAAAGATGACATCCTTGCA chr4A_1509 AGTGGGTTTCCGTTCTGAATAGTGATGTCTGGAAAGATCACATCCTCACA chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 ---GCTGGGATTGTACCTGCACTACAGCTAAGCTATGATCACTTGTCATC chr7D_1_TraesCS7D01G001400 ---GCTGGGATTGTACCTGCACTACAGCTAAGCTATGATCACTTGTCATC chrUn_1 ---ACTGGGATTGTACCTGCTCTACAGCTGAGCTATGATCACTTGTCATC chr7A_208 ---ACTGGGATTGTACCTGCCCTACAACTGAGCTATGATCACTTGTCATC chr3B_998 ACTACTGGGATTGTACCTGCACTACGACTGAGCTATGATCATTTGTCATC chr7D_999 GCTACTGGTATTATACCTGCACTGAAGCTGAGTTATGATCACTTGTCATC chr7B_1045 ACTACTGGGATTGTACCTGCACTACAACTAAGCTATGATCACTTGTCATC chr7D_1493 GCTACTGGGATTGCACCTGCACTACACCTGAGCTATGATCACTTGTCAGC chr4A_1493 GTTACTGGTATTGTACCTGCACTACAACTTAGCTATGACCACTTGTCATC chr4A_1493 TCTACTGCTATTGTACCTGCACTACAGCTGAGCTATGATCACTTGTCATC chr4A_1493 TCTACCGGAATTGTACCCGCACTACAGCTAAGCTATTATAACTTGTCATC chr7A_1497 ACTATTGGGATTGTACCTGCACTACAGCTAAGCTATGATCACTTGTCATT chr4A_1509 ACTACTGGGATTGTACCTGCACTACAGCTAAGCTATGATCACTTGTCATC chr4A_2458 -------------------------------------------------- chr6D_2487 -------------------------------------------------- chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ---S---------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 ---GCTGGGATTGTACCTGCACT--------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 AGAAGCAAAAGTATGTTTTTTCCTTCTGTGCTATTTTCCCCAAGGATAG- chr7D_1_TraesCS7D01G001400 AGAAGCAAAAGTATGTTTTTTCCTTCTGTGCTATTTTCCCCAAGGATAGC chrUn_1 AGAAGCAAAATTATGTTTTT-CATTCTGTGCTATTTTCCCCAAGGATAGC chr7A_208 AGAAGAGAAAATATGTTTTT-CCTTCTGTGCTATTTTCCCAAAAGATAGC chr3B_998 AGAGGAAAAAATATGCTTTT-CCTTTTGTTCTATTTTCCCCAAGGATAGC chr7D_999 CGAAGCAAAACTATGCTTCT-CCTTTTGTGCTATTTTCCCCAAGGATAGC chr7B_1045 GGAGGAAAAAATATGTTTTT-CCTTTTGTGCTATTTTCTCCAAAGATAGC chr7D_1493 AGAAGAAAAAATATGCTTTG-CATTATGTGCTATTTTCCCCAAGGATAGC chr4A_1493 CGAAGCACAAATATGCTTCT-CCTTTTGTGCTATTTTCCCCAAGGATAGC chr4A_1493 CGAAGAAAAAATATGCTTCT-CCTTCTGTGCTC-TTTTCCCAAGGATAGC chr4A_1493 GGAAGCAAAAACATGCTTTT-CATTCTGTGCTATTTTCCCCAAGGATAGC chr7A_1497 TGAAGCAAAAATTTGTTTTT-CCTTTTGTGCTATTTTCCCCAAGGATAGC chr4A_1509 AGAAGCAAAAATATGCTTTT-CTTTCTGTGCTATTTTCCCCAAGGATAGC chr4A_2458 -GAAGAAAAAATATGCTTCT-CCTCCTGTGATCTTTTCCCCAAGGATAGC chr6D_2487 ------------------------------CTATTTTCTCCAACGATAGC chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs ----------S---------S----------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 CCGATGGATAAAGACATGTTAATCCAGTTATGGATGGCAAATGACTTTAT chrUn_1 CCGATGGATACAAACATGTTAATCCAGCTTTGGATGGCAAATGACTTTAC chr7A_208 CCGATGGATAAAGACATGTTAATCCAACTATGGATTGCAAATGACTTTAT chr3B_998 CCAATGGATAAAGACATGTTAATCCAGCTATGGATGGCAAATGACTTTAT chr7D_999 CCGATGGATAAAGACACGCTAATCCAATTATGGATGGCAAATGACTTTAT chr7B_1045 CTGATGGATAAAGACATGTTAGTCCAGATATGGATGGCAAATGACTTTAT chr7D_1493 ATGATGGATAAAGACATGTTAATCCAGCTATGGATGGCAAACGACTTCAT chr4A_1493 CTGATGGATAAAGACACACTAATCCAGTTATGGATGGCAAATGACTTTAT chr4A_1493 CTGATGGACAAAGACATGTTAATCCAGCTATGGATGGCTAATGATTTTAT chr4A_1493 ATGTTGGAGAAAGACACGTTAATCCAGCTATGGATGGCAAATGACTTTAT chr7A_1497 CCAATGGATAAAGACATGTTAATCCAATTATGGATGGCAAATGACTTTAT chr4A_1509 CCAATGGATAAAAACATGTTAATCCAGCTATGGATGGCAAATGACTTTAT chr4A_2458 CTGGTGGACAAAGACATGTTAATCCAGCTATGGATGGCTAATGACTTTAT chr6D_2487 CTGATGGATAAAGACATGTGAATCCAGCTATGGATGGCAAATGACTTTGT chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TCCATCAGAAACAAGAGGCCAACAAATTTTCGATGTGCTAGTTTGGAGAT chrUn_1 TGCATCAGAAACAATAGGCCAACAAATTTTCAATATGCTAGTCCAAAGAT chr7A_208 TGCATCAGAAACAAGAGGCCAGGAAATTTTTGATGTGCTAGTTTGGAGAT chr3B_998 TGCATCAGAAGTAAGAGGCCAGCAAATTTTTGATGTGCTAGTTTGGAGAT chr7D_999 TGCATCAGAAACAAGAGGCCAACAAATTTTTGATGTGCTAGTTTGGAGAT chr7B_1045 TGCATCAGAAACAAGAGGCCACCAAATTTTTGATGTGCTAGTTTGGAGAT chr7D_1493 TGCATCAGAAACAAGAGGCCAACAAATTTTCGATGTGCTAGTTTGGAGAT chr4A_1493 TGCATCTGAAACAAGAGGCCAACAAATTTTCGATATGCTGGTTTGGAGAT chr4A_1493 TGCATCAGAAACAAGAGGCCAACACATTTTCGATGTGCTAGTTTGGAGAT chr4A_1493 TGCATCGGAAGCAAGAGGCGAACACATTTTTGATGTGCTAGTTTGGAGAT chr7A_1497 TGTATCAGAAACAAGGGGAAACCACATTTTTGATGTGCTAGTTTGGGGAT chr4A_1509 TGCATCAGAAACAAGAGGCCAACAAATTTTTGATGCGCTAGTTTCCAGAT chr4A_2458 TGCATCAGAAACAAGATGCCAAC-----TTCGATGTGCTAGTTTGGAGAT chr6D_2487 TGCATCATAAACAAGAGGCCAACACATTTTCAATGTTCAA--TTGGAGAT chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -S------------------------------------------------ forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 GTTTCCTCCAAG---ATGTGGAGATTCAAGAGAATCTAATCTC------- chrUn_1 GTTTCCTCCAAG---ATGTGGAGATTCAAAAGAATCGTCTCTC------- chr7A_208 GTTTCCTCCAATTAGATGTGGATATTGGAGAGAATTGGCTCTC------- chr3B_998 GTTTCCTACAAG---ATGTCAAGATTCAAAAGAATCCTATGGG------- chr7D_999 GTTTTCTCCAAG---ATGTGGAGATAAAAGAGGATGC------------- chr7B_1045 GTTTCCTACAAG---ATGTAAAGATTGACAA------------------- chr7D_1493 GTTTCCTCCAAG---ATGTTGAGATTCAAAAGAATAGGATCTT------- chr4A_1493 GTTTTCTGCAAG---ATGTGGAGATTCAAAAGAATCTGCTCTCCT----- chr4A_1493 GTTTCCTCCAGG---ATGTCCAAATTAAA--------------------- chr4A_1493 GTTTTCTTCAAG---ATGTGGAGACTCAAAAAAAATTGCGCCC------- chr7A_1497 GTTTCCTCGAATTAGATGTGGAGATTCGAAGGGATCTGCTCTC------- chr4A_1509 GTTTCCTCCAAG---ATGTGGAGATTCGGAAAAATCTGTTCTA------- chr4A_2458 GTTTCCTCCAAG---ATGTCGAAATTAAA--------------------- chr6D_2487 GTTTCCTCCAAGTAGATGTGGAGAATCTTCTCTTCAAACTTCAAGATTAG chr6B_2655 -------------------------------------------------- chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 --------------TAAAT------------------------TTCAAGA chrUn_1 --------------TCAGT------------------------TTCGACA chr7A_208 --------------TGAAT------------------------TTCGAGA chr3B_998 --------------CAGAT------------------------TTAAAGA chr7D_999 -------------------------------------------------- chr7B_1045 -----------------------------------------------GGA chr7D_1493 --------------AATGA------------------------TTGGAGA chr4A_1493 ----------------TAA------------------------ATAAGGA chr4A_1493 ---------------------------------------------GAGGG chr4A_1493 --------------TGAACTTCGATATGGGAATTTTCATTCTGTTCAAGA chr7A_1497 --------------TGGAT------------------------TTGAAGA chr4A_1509 --------------TGGAT------------------------TTCGAGA chr4A_2458 ---------------------------------------------GAGGG chr6D_2487 TCTTTGTTAAAAAATATAT------------------------ATCAAGA chr6B_2655 ----------------------------------------------AAGA chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TGGGTTCATCCACCGACCAACTACTTGCAAGATGCATGATCTCATGCATG chrUn_1 TGGGTTCATCCACCGACCAACTACTTGCAAGATGCATGATCTCATGCATG chr7A_208 TGAGTCCATCCACCG---AACTACTTGCAAGATGCATGATCTTATGCATG chr3B_998 TGAGTTCTTCCGTGG---ACCTGCTTGCAAGGTGCATGATCTCATGCATG chr7D_999 ---CTACATCCATCATTCAACTACTTGCAAGACGCATGATCTCATGCATG chr7B_1045 TGACTTAATCCACAGAGTAACTACTTGCAAGATGCATGATCTCATGCATG chr7D_1493 CGAGTTCGTCCACCAACCAACTACTTGCAAGATGCATGATCTTATGCATG chr4A_1493 TGACTTCATCCACCGACCAACTACTTGCAAGATGCATGATCTCATGCATG chr4A_1493 TGTCTTCATCTACCAACCAACTACTTGCAGAATGCATGATCTCATGCATG chr4A_1493 TGAATTCATCCACCAACCAACTACTTGCAAGATGCATGATCTTATTCATG chr7A_1497 TGTGTTCATGCACCGACCAACTACTTGCAAGATGCATGATCTCATGCATG chr4A_1509 AGAATTCGTCCACCGACCAACTACTTGCAAGATGCATGATCTCATGCATG chr4A_2458 TGTCTTAATCTACCAACCAACTACTTGCAGAATGCATGATCTCATGCATG chr6D_2487 TGAGTTCATCCACAGACCAACTACCTACAAGATGCATGATCTCATGCATG chr6B_2655 TGAGTTCATCCACAAACCAACTACCTGCAAGATGGATGATCTCATGCATG chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 ATCTTGCTGAGTTCATAAGTGGAAATGATTGCTCCATTCTACAAGAATCT chrUn_1 ATCTTGCTGACTCTGTAAGCGGAAATGGTTGCTTCCACTTGCAATCATTT chr7A_208 ATCTTGCTGACTTCGTAAGCGGAAATGATTGTTTCATTTTGCAAGAATCT chr3B_998 ACCTCGCTAACTTCGTAAGCGGAAATGATTGCTCCATTCTGCAAGAATCT chr7D_999 ATCTTGCTGAGTCCGTAAGCGGAAATGATTGCTCCATTCAGCAAGAATCT chr7B_1045 ATCTTGCTGATTCCGTAAGCAGAAATGTTTGCTTCATTCTGGAAGAATCT chr7D_1493 ATCTTGCTGACTCTGTAAGCGGAAATGATTGCTCCATTCTGCAAGAATCT chr4A_1493 ACCTTGCTGAGTCAGTAAGCAGAAATGATTGCTTCATTCTGCAAGAATGT chr4A_1493 ATCTTGCTGGCTCCGTAGGCAAAAATGATTGCTCCAATCTACAAGAATCT chr4A_1493 ATCTCGCTGAATTTGTAAGCGGAAATGACTGCTCTATTCTGCAACAATCT chr7A_1497 ACCTTGCTTGCTCTGTTATCGGAAATGATTGCTCTATTCTGCAAGAATCT chr4A_1509 ATCTTGCTGACTCTGTAAGTGGAAGTGATTTCTCTATTCTACAAGAATAT chr4A_2458 ATCTTGCTGGCTCCGTAAGCAAAAATGATTGCTCCATTCTGCAAGAATCT chr6D_2487 ATCTTGCTAACTCGATAAGTGGAAATGATTGCTCCATTCTGCAAGAATCT chr6B_2655 ATCTTGCTAACTTCGTAAGTGGAAATGATTGCTCCATTCTGCAAGAATCT chrUn_2926 -------------------------------------------------- SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TCATCATGCCAAGAAATTCTGCAAGGATCAACAGAT---AGTTCATTACA chrUn_1 TCATCACGTCGACGAATTTTGGAAGGATCCATAGACGCTGGTTCATTACA chr7A_208 TCATTATCTCAAAAAATTGTGCAAGGGTCCACATATGCTACTTCCTTGCA chr3B_998 TCATCATGTCAAGAAATTATGCAAGGATCCACAAACACCTGTTCGTTACA chr7D_999 TCATCACGTCAAGAAATTATGCAAGGATCTACATATACCAGTTTATTACA chr7B_1045 TCACCATGTCAAGAAATTCTGCAAGGATCCACATACACCAATTCATTACA chr7D_1493 TCATCAAGTCAAGAAAGTCTACAAGGATCCACATATGCCAGTTCATTAGA chr4A_1493 TCATCACATCAAAAAAAAATTCAAGGATCCACAGATGCTAGTTCATTACA chr4A_1493 TCATCACGTCAGGAAATT-TGCAAGGATCCACATACACCAGTTCATTACA chr4A_1493 TCATCATGTCAAGAAAACT------------------CCAGTTCATTACA chr7A_1497 TCACCATGTCAAGAAATTCTGGAAGGACCCACATATATCAGTTCATTACA chr4A_1509 TCATCACGTCAAGATATTCTACAAGGATCCATAGATACCAGTTCATTACA chr4A_2458 TCATCACGTCAGG-AAATTTGCAAGGATCCACATACACCAGTTCATTACA chr6D_2487 TCATCATGTCAAGAAATTCTGCAAGAACCCACAGATGCCAGCTCATTACA chr6B_2655 TCATCATGTCAAGTAATTCTGCAAGAACCCACAGATGCCAGCTCATTACA chrUn_2926 -------------------------------------------------- SNPs --------S--------------------S-------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 GC----ACGAAGTTCGACATTTGTCACTTTATTATGTCTTTGGTAATACT chrUn_1 GC----ATCAGGTTCGACATTTGTCACTTGATTATGACTATTTTAATGTT chr7A_208 GC----ATGAGGTTCGACATTTGTCACTTGATCATGTTAGTACTTATACT chr3B_998 GC----ATGAGGTTCGACATTTGTCACTTGATTATGTGAGTAACAATACT chr7D_999 TC----ATGAGGTCCAACATTTGTCACTTGGTTATGTCTTTAACAGTACT chr7B_1045 GC----ATGAGGTTCAACATTTGTCACTTGATTGTGTCAGTAACAATACT chr7D_1493 GC----ATCAGGTTCGATATTTGTCACTTGATCATGTCAGCAATGATACA chr4A_1493 AC----ATGAGGTTCGACATTTGTCACTTGATTATGTCAGTAGCAATACT chr4A_1493 GCATGCATGAGGTTCACCATTTGTCACTTGATAATGTGAGTAACAATACT chr4A_1493 AA----ATGAGGTTCGACATTTGTCACTTGAGTATGTCACTGATAATACT chr7A_1497 TC----ATGAGGTTCAACACTTGTCTGTCGATTACGTCACTAATAGTACT chr4A_1509 GC----ATGAAGTTCGACATTTGTTACTTGATTATGTAAGTGATAAAACG chr4A_2458 GCATGCATGAGGTTCAACATTTGTCACTTGATTATGTGAGTAACAATACT chr6D_2487 GC----ATGAGGTTCGCCATTTGTCTCTTGATTATATCAGTAATAAAGCT chr6B_2655 GC----ATGAGGTTCGACATTTATCTCTTGATTATATCAGTAATAAGACT chrUn_2926 -------------------------------------------------- SNPs -------S---------------------S-------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 ATTGCAGTCATGGAGGACATTGTAGCTCCCCGACTCCGCACATTATTAAT chrUn_1 AAAGT---CATGATGAAAATTCTAGCTCCCGGAGCCCGCACGATATTAAG chr7A_208 GTTGCAGCCATGGAGGAAATTATCGCTCCTCGGCCCCGCACAATATTAAT chr3B_998 ATTGCAGCCATGAAGAAAATTTTAGCTCCCCGAGCCCGCACAATATTAGT chr7D_999 ATTGCAGCCATGAAAGAAATTTTAGCTCCCCGAGCCCGCACAATATTAGT chr7B_1045 ATTGCAGTAATGAAGGAAATTCTAGCTCCCCAAGCCCGCACAATATTAAT chr7D_1493 AATGCAGCCATGAAGGAAATGCTAGCTCCCCGACCCCGCACGATATTAGT chr4A_1493 ATTGCAGATATGAAGGAAATTCTAGCTCCCCACCCCCGCACAATATTAGT chr4A_1493 ATTGGAGCCATGAAGGAAATTCTAGATCCCCGAGCCCGCACAATATTAGT chr4A_1493 ATGGCAGCCATGAAGGAAATTTTGGCTCCCCTACCCCGTACGATCTTAAT chr7A_1497 ATTGCAGCCATGGAGAAAATGTTAGCTCCCCGACCCCGCACGATATTAGT chr4A_1509 ATTGCAGCTATGAAGAAAATTCTAGCTCCCCGGCCCCGCACAATATTAAT chr4A_2458 ATTATTGCCATGAAGGAAATTCTATATCTCCGAGCCGGCACAATATTAGT chr6D_2487 ATTGCAGCCATGAAGGAAATTCTAGCTCCCCGACCCTGCACAATATTAAC chr6B_2655 ATTGCAGCCATGAAGGAAATTCTAGCTCCCCGACCCCGCACAATATTAGC chrUn_2926 -------------------------------------------------- SNPs -----------------S---S------------S-------S------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -----------------CATTGTAGCTCCCCGACTCC------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 CCAAAAGGAGTTGGAGCAGAT------------------TCAG------- chrUn_1 CCAACGCCAATTGGGCTATCAACG-------------------------- chr7A_208 CCAAAGGGAGT------GGAC------------------TAGG------- chr3B_998 CCGAAGGGAGTTGGAGTGGAC------------------TAAGACTTCTC chr7D_999 CCAAAGGGAGACTTCTCTGGATAGTG---------------GA------- chr7B_1045 CCGAAGGGGGTTGGAGTGGCG------------------TAAGACTTCTC chr7D_1493 CCACCCGGACT------GGAAAGAATTTGGAATGGACTATGGG------- chr4A_1493 CCAAAGGAAGTTGGAGTGGAC------------------TGAGACTTCCT chr4A_1493 TTTGAAAAATGAATTTGGGAT------------------TGAG------- chr4A_1493 CCAAAGATATTTGAAGCGGAC------------------TATG------- chr7A_1497 CCGACAGGAGAGGAAGGGGTA------------------TGTG------- chr4A_1509 GTTCCAAAGGAAATCTTGGCT------------------TGGG------- chr4A_2458 CTTGAAAAATGAATTTGGGAT------------------TGAG------- chr6D_2487 CCAACCGGAGTGGGATTGGTC------------------TTGG------- chr6B_2655 CCAACCAGAGTGGGATTGGTC------------------TGGG------- chrUn_2926 ------------------------------------------G------- SNPs ----------------------------------------S--------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 -----------ACTCCTTTTAGTATGGCCAAGTCAAAATTTGTGTCCTTA chrUn_1 -------------TCCACTAAGAAAGTCCAAGTCAGAATTAATGTCCTTA chr7A_208 -----------AATCCTCTGAGTATGGCGAAGTCAACATTCGTGTCTTTA chr3B_998 TGGATATGGGCAAGTCTCTGAGTATGACCATGTCAAAATTCATGTCCTTG chr7D_999 -----------AAGTCTTTGGGTATGGCCATATCAAAATTCATACCCTTA chr7B_1045 TGCATATGAACAAGTCTCTGAGTATGGCCATGTCAAAATTCATGTCCCTA chr7D_1493 -----------ACTCCGCTGAGTATGGCCAAGTCAAAATTCATGTCCTTG chr4A_1493 TGGATACGGACAACTCTTTGAGTACGGCCATGTCAAAATTCGTGTCCTTG chr4A_1493 -----------ATTCCTGTGAGTATGGCTAAGTCAAAATTCATGTCCTTG chr4A_1493 -----------AATCTTCCGAGTATAGTCTGGTCAAAATTCTTGTCCGTA chr7A_1497 -----------ACTCCTCTGAGTATGGCCAGGTCAAAATTCTTGTCCTTG chr4A_1509 -----------AGTCCTCTGAATATGTCCACGTCAAAATTCATGTCCTTG chr4A_2458 -----------ATTCATGTGAGTATGGCTAAGTCAATATTCATGTCCTTG chr6D_2487 -----------ACTCCTCTGAGTATGGAGAAGTAAAAATTCATGTCCTTA chr6B_2655 -----------------------------ACGTCAAAATTCATGTCCTTA chrUn_2926 -----------ACTCCTCTGAGTGTGGCCAAGTCAAAATTCATGTCACTG SNPs -------------------S--------------------S--------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 CGAGCATTGAAGACATTCTCAATCAAGACACATATGACAAACTTAAAGCA chrUn_1 CGAGCAGTGAAGACGTTCCCAAGCATAACACAAATGACAAATTTGAAGCA chr7A_208 CGAGCATTGAAGACCTTCTCAATCAAGACACATATGACAAACATGAAGCA chr3B_998 CGAGCATTGAAGATATCGTCAATCTTAACACATATGACAAACTTGAAGCA chr7D_999 CGAGCATTGAAGACATACTCAATCAATACACATATGACAAACATGAAGCA chr7B_1045 CGAGCACTGAAGACATTGTCAATCATAACAGACATGAAAAACTTCAAGCA chr7D_1493 CGAGCATTGAGGACACGCTCAATTGAGACACGTATGGCAAGCATGAAGCA chr4A_1493 AGAACGTTGAAGACAATCTCATTCGAGACAAATATGACATGCTTGAAGCA chr4A_1493 CGAGCATTGAAGACGTTCTCAATCAGTACACACATGACAAACTTGAAGCA chr4A_1493 CGAGCATTCAAGACATTCTCAATCGAGACAAATATGACAAACTTGAAGCA chr7A_1497 CGAGCACTGAAGACATTCTTATTCGAGACACATATGACAAAGTTGAAACA chr4A_1509 CGAGCACTGAAGACAATCTCAGTCAAGACAAACATGACAAACTTGAAGCA chr4A_2458 CGAGCATTGAAGACATTCTCAATCAGTACACGCATGACAAACTTGAAGCA chr6D_2487 AGAGCATTGAAGACATTCTCAGTGAAAACCCGTATGAAAAATTTGAAGCA chr6B_2655 AGAGCATTGTAAACATTCTTAGTCAAAACCCGTATGACAAATTTGAAGCA chrUn_2926 CGAGCATTGAAGACATATTCAATCATAACACAAATGACAAACTTGAAGCA SNPs --------------------------------------------S----- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TCTTCGCTATTTAGACTGTTCTTATTCTGATATATTTGCACTACCTGAAG chrUn_1 TCTTCGCTATTTAGACTGTTCTTATTCTGATATATCTGCATTGCCTGAAG chr7A_208 TCTTCGTTATTTAGATTGTTCTTATTCCCTTATATCTGCATTGCCTGAAG chr3B_998 TCTTCGGTATCTAGATTGTTCTAATTCTGATATATCTGCACTGCCTGAAG chr7D_999 TCTTCGCTATCCAGATTGTTCTTATTCTGATATATTTGCACTGCCTGAAG chr7B_1045 TCTTCGCTATCTAGATTGTTCTTATTCTCGTTTATCTGCACTGCCTGAAA chr7D_1493 TCTTCGCTATCTAGAGTGTTGTGATTCTGATATATCTGCATTGCCTGAAG chr4A_1493 TCTTCGCTATCTAGATTGTTCTTATTCTAATATATCTTCACTTCCCGAAG chr4A_1493 TCTTCGCTATCTGGATTGTTCTGGTTCTAGTATATCTGCATTGCCTGAAG chr4A_1493 TCTTCGCTACCTAGATTGTTCTTATTCTAGTATATCTTCACTTCCTGAAG chr7A_1497 TCTTCGCTACCTAGATTGTTCTTATTCTAGTATATCTGCACTGCCTGAAG chr4A_1509 TCTTCGCTATCTAGAATTTTCTAATTCTGATATATCTGAATTGCCTGAAG chr4A_2458 TCTTCGCTATCTGGATTGTTCTGGTTCTAGTATATCTGCATTGCCTGAAG chr6D_2487 TCTTCGCTATCTAGAGTTTTCTTATTCTGATATATCAACACTGCCTAAAG chr6B_2655 TCTTCGCTATCTGGATTTTTCTTATTCTGATATATCAACACTGCCTGAAG chrUn_2926 TCTTCGCTATCTAGATTGTTCTTGTTCAGCTATATCTTCACTTCCTGAAG SNPs ------------------------------------------S------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 CCACTACCATGTTGTATAGCTTGCAAACATTGAAGCTCATTGGTTGTGAA chrUn_1 CCACCACCATGTTGTATTGCTTGCAAACATTGAAGCTCATTGGTTGTAGA chr7A_208 CCACTACCATGCTGTATAGCTTGCAAACATTAAAGCTCATTGGTTGTCGA chr3B_998 GCATTACCATGTTTTATAGCTTGCAAGCATTGAAGCTCACGGGTTGTCGC chr7D_999 CAACTGCCATGCTGTATAGCCTGCAAACATTGAAGCTCATTGATTGTCAA chr7B_1045 CCACTGCCATGTTGTATAGCTTGCAGACTTTGAAGCTCATTGGTTGTAAA chr7D_1493 CGATTACCATGTTGTATAGCCTGCAAACATTGAAGCTCATTTGTTGTGAC chr4A_1493 CCACTGCCATGTTATATAGCTTGCAAACATTGAAGCTCATTGGTTGTCAA chr4A_1493 GCATTATCATGTTGTATAGCTTGCAAACATTGAAGCTCATTGGTTGTAGT chr4A_1493 CCACTACAATGTTGTATAGTTTGAAAACATTGAAGCTCATTGGTTGTCAA chr7A_1497 CCATTACCAAGTTGTATAACCTGCAAACACTGAATCTCATGGGTTGTCGA chr4A_1509 CAACTACCATGTTGTATAGCTTGCAAACGTTAAAGCTCAGTGGTTGTCAC chr4A_2458 GCATTATCATGTTGTATAGCTTGCAAACATTGAAGCTCATTGGTTGTAGT chr6D_2487 CAACTAGCATGTTGTATAGCTTGCAAACATTGAAGCTCATTGGTTGTCAA chr6B_2655 CCACTACCATGTTGTGTAGCTTGCAAACATTGAAGCTCATTGGTTGTCAA chrUn_2926 CCACTACAATGTTGTATAACTTGCAAACACTGAAGCTCATTCAATGTACA SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 AAACTTAAGAAATTACCTGAAGGCATGAGATATATGAGTAGTCTCCGGCA chrUn_1 GAACTCAAGAAATTACCAGAAGGGATGAGATATATGAGCAGTCTTCGACA chr7A_208 TACCTGAAGAAACTGCCAGAAGAGCTGAGATATATGAGCAGTCTTCGACA chr3B_998 AAACTTGAGAAATTACCAGAAGGCATACGATATATGCTCAGCCTTCGGCA chr7D_999 AACCTGAAGAAATTACCAGAAGGCATAAGATATATGAGCAGTCTTCGGCA chr7B_1045 GAACTTAAGAAATTACCAGAAGGCATGAGATATATGATCAGCCTTCGGCA chr7D_1493 AAACTTAAGAAATTACCAGAAGGCATGAGCTATATGCTCAGTCTTCGGCA chr4A_1493 AAGCTTAAGTATTTACCAGAAGGTATGAGATATATGAGCAGTCTTCGACA chr4A_1493 GAACTTAGGAAATTACCCGAAGGCATGAGGTATATGAGCAGTCTTCGTCA chr4A_1493 AAACTTGAGAAATTGCCAAAGGGCATGGGATGTATGATCAGTCTTTGGCA chr7A_1497 AGCCTTAAGAAATTACCAGAACACATGAGATGTATGAGTAGTCTCCGACA chr4A_1509 AACCTTAAGAAATTACCAGAAGGCATGAGATGTATGAGCAGCCTTCGGCA chr4A_2458 GAACTTAGGAAATTACCCGAAGGCATGAGGTATATGAGCAGTCTTCGTCA chr6D_2487 AATCTTAAGAAATTACCAGAAAGCATGAGAT-TATGAGCAGTCTTCGGCA chr6B_2655 AATCTTAAGAAATTACCAGAAGGCATGAGATTTATGAGCAGTCTTCGGCA chrUn_2926 AAACTTGAGAAATTACCAGAAGGCATGAGATATATGACCAATCTCCGACA SNPs -----------------S-------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 CATCTTCCTCATTGGGTGTGATAGTTTGGAGCGCATGCCACAGGGTATTG chrUn_1 CATCTTCCTTGTTGGGTGTCATAGTTTGGAGCAGATGCCGCAAGGTATTA chr7A_208 CATCTTACTCGCTGGGTGTCATCGTTTGGAGCGCATGCCACAAGGTATTG chr3B_998 TATCTTCCTTAATGGGTGTCATAGTTTGGAGTGCATGCCACATGGTATTG chr7D_999 CCTCTTCCTCTCTGGGTGTGATAGTTTGAAGCGCATGCCACAAGGTATGG chr7B_1045 CATCTTCCTCATTGGGTGCAATCGTTTGGAGTACATGCCACAAGGTATCA chr7D_1493 CCTCTTCCTCATTGGGTGTTTTGATTTGGAGTGCATGCCACAAGGTATTG chr4A_1493 CATATTCCTCCTTAGTACTAATTCCTTGGAGTACATGCCAAAAGCTATTG chr4A_1493 CATCTTCCTTGTGGCGTGTCGTCGTTTGGAGCGCATGCCACAAGGTGTTA chr4A_1493 CGTCTTCCTCGTTGGTTGTCATCGTTTGGAGCACATGCCACGAGGTATTG chr7A_1497 TATCTTCCTTGTTGGGTGTAATCGTTTGGAGCGCATGCCAAAAGGTATTA chr4A_1509 CATCTTCCTTGTTGGGTGTGATCGTTTGGAGTGCATGCCACAAGGTATTG chr4A_2458 CATCTTCCTTGTGGCGTGTCGTCGTTTGGAGCGCATGCCACAAGGTGTTA chr6D_2487 CATCTTCTTCGTTGGGTGTCATCTTTTGGAGCGCATGCCAAAGGGTATTG chr6B_2655 CATCTTCCTCGTTGGGTGTCATCTTTTGGAGCGCATGCCAAAAGGTATTC chrUn_2926 CATTTTCCTCCTTGGGTGTCATCGTTTGGAGCGCATGCCACAAGGTATTG SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 GTCAGCTGAATTCTCTACAAACATTGACAAGTTATGTCATTGATAGTGAT chrUn_1 GTCAGTTGAATTCCCGACAAACGTTGACGAGTTATGTCATTGATAGTGAT chr7A_208 GTCAGATGAATTCTCTACATACATTGACGAGTTTTGTCATTGTTAGTGAT chr3B_998 GTCAGCTGAATTCTTTACAGACATTGACGGATTATGTCATTGATAGTGAT chr7D_999 GTCAGATGAATTCTCTACTGACATTGACAAATTATGTCATTGATAGTGAT chr7B_1045 ATCAGCTGAATTCTCTGCAGACACTGACGAGTTACGTCATTGATAGTGAT chr7D_1493 GTAGGCTGAATTCTCTGCAGACATTGACGAGTTATGTCATTGATAGTGAT chr4A_1493 GTCAGCTGAATTCTCTACAGACAATGACAAATTATGTCATTGACAATGAT chr4A_1493 GTCAATTGAATTCTCTAAAGACATTGACGAATTATGTCATTGATAGTGAT chr4A_1493 GTCAGCTGAATTCTCTGCGGACGTTGACAAGTTATGTCATTGATAGTGAT chr7A_1497 GTCAGCTGAATTCTCTGCAGACATTGACATGTTATGTCGTTGATAGTGAT chr4A_1509 GTCTGCTGAATTCTCTATAGACATTGACAAGTTATATCATTGATAGTGGT chr4A_2458 GTCAATTGAATTCTCTAAAGACATTGACGAATTATGTCATTGATAGTGAT chr6D_2487 GTCAGCTGAATTCTCTACAGACATTGACGAGTTATGTCATTGATAGTGAT chr6B_2655 GTCAGCTGAATTCTCTACAGACGTTGACGAGTTATGTCATTGATAGTGAT chrUn_2926 GTCAGTTGAATTCTCTACCGACATTGACAAATTATGTCTGTGATAGTGAT SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 GCAGGGCGTGGAATTGATCAACTCAAATATTTGAATCTAGGTGGCGCCCT chrUn_1 ACAGGTCGTGGAATTGATCAACTGAAAGATTTAAATCTATGTGGTGCTCT chr7A_208 GCAGGCTGCGGAATTGATCAACTGAAAGACTTGAATCTAGGTGGTGCTCT chr3B_998 GTGGGCCGTGGAATTGATCAACTGAAAGATTTGAATCTAGTTGGTGGTCT chr7D_999 GGCGGTCATGGAATTGATCAACTCAAAGATTTGAATCTAGGTGGTGATCT chr7B_1045 GCAGGTCGTGGAATTGATCAACTGAAAGATTTGAGTCTTGGTGGTGCTCT chr7D_1493 GACGGCCGTGGAATTGATCAACTGAAAGATATGAATCTAGGTGGTGGTCT chr4A_1493 ATAGGTCGTGGAATTGATCAACTAAAAGATTTGAATCTAACTGGTGCTCT chr4A_1493 GCCGGCCGTGGAATTGATCAACTGAGAGATTTGAATCTAGGTGGTAGTCT chr4A_1493 GCGAGTCGTGGAATTGTTCAACTGAAAAATTTGAATCTAGGTGGTGCTCT chr7A_1497 GTAGGCCGTGGAATTGATCAACTGGAAGATTTGAATCTAGGTGGTTCTCT chr4A_1509 GTAGGTCATGGAATTGATCAGCTGAAAGATTTGAATCTAAGTGGTGGTCT chr4A_2458 GCCGGCCGTGGAATTGATCAACTGAGAGATTTGAATCTAGGTGGTAGTCT chr6D_2487 GTAGGTAATGGAATTGTTCAACTGAAAGATTTGAATCTAGGCAGTGCCCT chr6B_2655 GCAGGTCGTGGAATTGATCAACTGAAAGATTTGAATCTAGGCGGTGCCCT chrUn_2926 GCGGGTTGTGGAATTGATCAACTGAAATATTTGAATCTTAGTGGTGCTTT SNPs -----S--------------------------------------S----- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 TTCTTTGACTGAGCTGAGAAAAGTGCATAGTGCAGAAAATGCTAAACAAG chrUn_1 TTCTTTGACTGAGCTGAGAAAAGTGCATGGTGCAGAAAATGCTAAACAAG chr7A_208 TTCTTTGACTGAGCTGAGAAAAGTGCATAGTCCAGAAAATGCTAAACAAG chr3B_998 TTCTTTGACTAAGCTGAGGAAAGTGCATAGTGCAGAAAATGCTCAACAAG chr7D_999 TTCTTTGACAGAGCTGAGAAAAGTGCGTAGTGCAGAAAATGCTAAACAAG chr7B_1045 TTCTTTGACTGAGTTGAGAAAAGTGCATAGTGCAGAAAATGCTAAAGAGG chr7D_1493 TTCTTTGACAGAGCTGAGAAAAGTGCATAGTGCAGAAAATGCTAAACAAG chr4A_1493 TTCTCTGACTAAGCTGATAAAAGTGCACAGTGTAGAAAATGCTAAACAAA chr4A_1493 TTCTTTGACAGAGCTGAGAAAAGTGCATAGTGCAGAAAATGCTAAACAAG chr4A_1493 TTCTTTGTCTGGGATAAGAAAAGTACATAGTGCAGAAAATGCTAAACAAG chr7A_1497 TCATTTGATGGCACTGGGAAAAGTGGAAAGTGCAGAAAATGCTAAACATG chr4A_1509 TTCTTTAACTGAGCTGAGAAAAGTACATGGTGCAGAAAATGCTAAACAAG chr4A_2458 TTCTTTGACAGAGCTGAGAAAAGTGCATAGTGCAGAAAATGCTAAACAAG chr6D_2487 TTCTTTGACTGAGTTGAGAAAAGTGCATGGTACAGACAATGCTAAACAAG chr6B_2655 TTCTTTGACTGAGTTGAGGAAAGTGCATGGTACAGACAATGCT-AACAAG chrUn_2926 TTATTTGACTAAGTTGATAAAAGTGCATAGTGCAGAAAATGCTAAACCAA SNPs -------------------------------------------------- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 GCAGCATCTCTACCAAGCATAATTTGAAACGATTGTCACTCGATTGGGAA chrUn_1 GCAATATGTCTGACAAGCATAATTTGAAGCGATTATCACTCGATTGGACA chr7A_208 GCAATATGTCCGCAAAGCATAATTTGAAACGATTATCACTCGATTGGGCA chr3B_998 GCAATATGTCTGCTAAGCATGATTTGAAAAGATTGTCACTCGATTGGGGG chr7D_999 GCAATATGTCCGCCAATCATAACTTGAAACGATTGTCACTCGATTGGT-- chr7B_1045 GCAGTATATCCTCCAAGCATAATTTGAAACGATTATCACTCAACTGGT-- chr7D_1493 GCAATACATTCGCCAAGCATAATTTGAAAAGATTGGCACTCGATTGGT-- chr4A_1493 GCAATATGTCTGGCAAGCATAATTTGAAACGATTGTCACTCGATTGGACA chr4A_1493 GCAATTTGTCCGCCAAGCATAATTTGAAACGATTGTTGCTCAATTGGC-- chr4A_1493 GCAATATGTCCGCCAAGCACAATTTAAAAAGATTATCACTTGATTGGT-- chr7A_1497 GGAATTTGTCTGCCAAGCATAATTTGAAACGACTATCACTTGATTGGT-- chr4A_1509 GTAATATGTCCGCCAAGCATGATTTGAAACGATTATCACTCGATTGGT-- chr4A_2458 GCAATTTGTCCGCCAAGCATAATTTGAAACGATTGTTGCTCAATTGGC-- chr6D_2487 GCAATATGTCCACAAAGCATAATTTGAAACGGTTATCACTTGATTGGGCA chr6B_2655 GCAATATGTCCACCAAGCATAATTTGAAACGGTTATCACTTGATTGGGCT chrUn_2926 GCAATATGTCCGCCAAGCATAATGTGAATCAATTGTCACTTGATTGGGAA SNPs ----S--S------------------------------------------ forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 -------------------------------------------------- chr7D_1_TraesCS7D01G001400 AA---TGGACCTTCTT---CTAGCACACATGCTGGATATGAAGTACGTAA chrUn_1 AA---TGGA---CATT---ATGGCTCATATTTTGGATATGGAGTCGATAA chr7A_208 AG---TGGA---TCTT---CCAGCACACATGTTGGATATGAAGTAGATAC chr3B_998 GAAAATATATATACATGGCG------------TGAAGTTGAAGTGGATAC chr7D_999 -A---TGGA---AATT---ATATCACAGGATATGAAGATGAAGTAGATAC chr7B_1045 -A---TGCA---CATT---ATAATACAGATATTGGAAATTAAGTACATAG chr7D_1493 -A---TGGAGGTGT------TAGAAGAAGCTATGGAGATGAAGTAGACAC chr4A_1493 GGCGGAAATTT---TG---ATACCAGAGATGTTGGGAATGAAGAAGATAC chr4A_1493 -A---TGGA---CCTG---ATAGCACAAATGATAGAGATGAGGTGGATAA chr4A_1493 -A---TGGA---TCTT---ATAGCACAAATATTGGATTTGAACTTGATAC chr7A_1497 -ACTATGGA---CCTT---CATTGACAGACATTGGATCTGAAGTGGATAC chr4A_1509 -A---TGGA---ACGT---ACAGCTCAAATTATGGAGATGAAGTTGATAC chr4A_2458 -A---TGGA---CCTG---ATAGCACAAATGATAGAGATGAGGTGGATAA chr6D_2487 AA---TGGA---CCTT---ATAGCACACATGTTGGATATGTAGTACATAC chr6B_2655 AA---TGGA---CCTT---ACAGCACACATGTTGGATATGAAGTACATAC chrUn_2926 AA---TGGA---CCTTCTTATAGCACACAAGATGGGTATGAGGTAGATGC SNPs ---------SS--------------------S--------------S--- forward_1396 -------------------------------------------------- reverse_3954 -------------------------------------------------- forward_1401 -------------------------------------------------- reverse_4468 -------------------------------------------------- input_sequence_49716 ---------------------------------------------- chr7D_1_TraesCS7D01G001400 TGATGCAGAAGGAATATTAGAGGCCCTTCGTCCTCACAAAAGGCTT chrUn_1 TATTGCAGAAGGGATATTGGAGGCTCTTCGTCCACACAAAAAGCTT chr7A_208 TAATGCAGAAGGAATATTAGATGCTCTTCATCCTCACAAAATGCTT chr3B_998 TAATGCAGAAGGAATATTAGAGGCCCTTCGTCCGCACAAAAGGCTT chr7D_999 TAATGCAGAAGGAATATTGGAGGCCCTTCGTCCTCACAAAA----- chr7B_1045 TAATGCAGAAGAGATATTAGAGGCCCTTTGTCCTCACCAA------ chr7D_1493 TAATGTAGAAGGAATATTAGAGGCCCTTTGTCCTCACAAAAGTCTT chr4A_1493 TAATGCAGAAGGAATTTTAGAGGCCCTTCGTCCTCACAAAAGGCTT chr4A_1493 TAATGCAGAAGGAATCTTAGAGGCCCTTCGTCCTCATAAAAGTCTT chr4A_1493 TAATCCAGAAGGAATATTGGAAGCCCTTTGTCCGGGCAAAAGGCTT chr7A_1497 TAATGCAGAAGGAATATTAGAGGCCCTTCGTCCTCATAAAAGGCTT chr4A_1509 AAATGCAGAAGAAATACTAGAGGCCCTTCGTCCCCACAAAAGGCTT chr4A_2458 TAATGCAGAAGGAATCTTAGAGGCCCTTCGTCCTCATAAAAGTCTT chr6D_2487 TAATGCAGAAGGAATATTAGAGGCCCTCCGTCCTCATAAAAGGCTT chr6B_2655 TAATGCAGAAGGAATATTAGAGGCCCTTCGTCCTCACAAAAGGCTT chrUn_2926 CAATGCAGAAGGAATATTAGAGGCCCTTTGTCCTCA---------- SNPs -S-------------------------------------------- forward_1396 ---------------------------------------------- reverse_3954 ---------------------------------------------- forward_1401 ---------------------------------------------- reverse_4468 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