CLUSTAL X (1.81) multiple sequence alignment input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TTTCTGGATACCGCGGCGAATGGAGCCGGGGTCGTCCTCCTCGTCGGGCT chr7D_1 TTCCTGGATACCGCGGCGAATGGAGTCGGGGTCGTCCTCCTCGTCGGGCT chr4A_1 TTCCTGGATACCGCGGCAAATGAAGCCGGGGTCGTCCTCCTCGTCGGGCT chr3B_1 TTTCTGGATACCGCGGCGAATGGAGCCGGGGTCGTCCTCCTCGTCGGGCT chr5D_1 TTCCTGGATACCGCGGCGAATGGAGCCGGGGTCGTCCACCTCGTCGGGCT chr5B_1 TTCCTGAATACCATTGCGAATGGAGCCGGAATCGTCCTCCTCGTCGGGCT chr7B_1 TTCCTGGATACCGCGGTGAATGGAGCCAGGGTTGTCCTCCTTGTCGGGCT chr1D_2 TTCTTGGATACCGCGGCGAATGGAGCCGGGGTCGTCCTCCTCGTCGGGCT chr6B_4 ---CTGGATACCGCGGCGAATGGAGCCGGGGTCGTCCTCCTTGTCGGGCT chr4B_4 ---CTGGATACCGCGGCGAATGGAGCCGGGGTCGTCCTCCTCGTCGGGCT chr2B_4 ---CTGGATACCACGGCTAATGGAGCCGGGGTCGTCCTCCTCGTCGGGCT chr1B_4 ---CTGGATACCGCGGCGAATGGAGCC-GGGTCGTCCTCCTCATCGGGCT chr2D_4 ---CTGGACGCCGTGACGGATGGAGCCGGTGTCGTCCTCGTCGTCGGGCT chr5D_11 ----------CCGCGGCGGATGGAGCCGGGGTCGTCCTCGTCGTCGGGTT chr3D_14 -------------CGGCGGATGGAGCCGGGGTCGTCCTCGTCGTAGGGTT chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 TGGGATG------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CCGGCTCGCCGGCC---ATCCGCCCCGTCAAGCCCGAGCCGGAGGAGACA chr7D_1 CCGGCTCGCCGGCC---ATCCGCCCCGTCAAGCCCGAGCCGGAGGAGACA chr4A_1 CCGGCTCGCCGGCC---ATCCGCCCCGTCAAGCCCGAGCCGGAGGAGACA chr3B_1 CCGGCTCGCCGGCC---GTCCGCCCCGTCAAGCCCGAGCCGGAGGAGACA chr5D_1 CCGGCTCGCCGGCC---ATCCGGCCCGTCAAGCCCGAGCCGGAGGAGACA chr5B_1 CCGGCTCGCTGGCC---CTCCGCCCCGTCAAGCCCGAGCCGGAGGAGACA chr7B_1 CCGGCTCGCCGGTC---CTACGCCCCGTCAAGCCCGAGCCGGAGGAGACA chr1D_2 CCGGCTCGCCGGCC---ATCCGCCCCGTCAAGCCCGAGCCGGAGGAGACA chr6B_4 TCGGCTCGCCGGCC---ATCCGCCCCGTCAAGCCGGAGCCGGAGGAGACA chr4B_4 CCGCCTCGCCGGCC---CTCCGCCCCGTCAAGCCCGAGCCGGAGGAGACA chr2B_4 TCGGCTCGCCGGCC---ATCTGCCCCGTCAAGCCCGAACCGGAGGAGACA chr1B_4 CCGGCTCGTCGGCC---ATCCACCCCGTCAAGCCGGAGCCGGAGGAGACA chr2D_4 CCGGCTCGCCAGCCGCGATACGCCCGGTCAAGCCCGAGCAGGAGGAGACG chr5D_11 CCGGCTCGCTGGCCGCGCTCCGCTCCGTCAAGCTCGAGCCAAAGGAGACG chr3D_14 CCGGCTCGCCGGCCGAGCTCCGCCCCGTGAAGCCCATGCTGGAGGAGACG chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CCACTCGGGCGCCGCGCGCGGAGCGGCGCCCTCATCAACAACGAG----- chr7D_1 CCGCTCGCGCGTCGCGCGCGGAGCGGCGCCCTCGTCATCAACGAG----- chr4A_1 CCGCTCGGGCGTCGCGCGCGGAGCGGCGCCCTCGTCATCAATGAG----- chr3B_1 CCGCTCGGGCGTCGCGCACGGAGCGGCATCCTCGTCATCAACGAG----- chr5D_1 CCGCTCGGGCGTCGCGCGCGGAGCGGCGCCCTCGTCATCAACGAG----- chr5B_1 CCGCTCGGGCGTCACGCGCGGAGCGGCGCCCTCGTCATCAACGAG----- chr7B_1 CCGCTCAGGCGTCGTGTGCGTAGCTGCGCCCTCGTCATCAACAAG----- chr1D_2 CCGCTCGGGCGTCGCGCGCGGAGCGGCGCCCTCGCCATCAACGAG----- chr6B_4 CCGCTCGGGCGTCACGCGCGGAGTGGCGCCCTCGTCATCAACGAG----- chr4B_4 CCGCTCGGGCGTCGCGCATGGAGCGGCGCCCTTGTCATCAACGAG----- chr2B_4 CCACTCGGGCGTCGCGCGCGGAGTGGCGCTCTCGTCATCAACGAA----- chr1B_4 CCGCTCGGGCGTCGCGCGCGGAGTGGCGCCCTCGTCATCAACGAG----- chr2D_4 CCGCTCCGGCGCCGCACCCGCAGCGGCGCCCTCGTCATCAACGAGGGTGC chr5D_11 TCGCTCGGGCGCCGCACCCGCAGCGGCGCCCTCGTCATCAACGAGGGTGC chr3D_14 CCGCTCGGGCGCCGCACCCGCAGAGGCGCCCTCGTCATCAACAAGGGTGC chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ---------------------------------S---S------------ forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 -------CCGTCGCCTGTGACGGCACCGACAAGGCGCTCCCTTCGCCTTG chr7D_1 -------TCGTCGCCTGCGACGGCACCGACGAGGCGCTCCCTTCGTCCTG chr4A_1 -------CCGTCGCCTGCGACGGCACTGATGAGGCGCTTCCTTCGCCTTG chr3B_1 -------CCGTTGCCTGCGACGACACCGACGAGGCGCTCCCTTCGCCTTG chr5D_1 -------CCGTCGCCTGCGACGGCACCGACGAGGCGCTCCCTTCGCCTTG chr5B_1 -------CCCTCGCCTGCGACGGCACCGA---GGCACTCCCTTCGCCTAG chr7B_1 -------CCCTCGCCTGCGACATCACCGACGAGGCGCTCCCTCCACCTGG chr1D_2 -------CCGTTGCCTGTGACGGCACCGACGAGGCGCTCCCTTCGCCTTG chr6B_4 -------CCGTCGCTTGCGACGACACCGACGGGGCGCTCCCTTCGCCTTG chr4B_4 -------CCCTCGCCTGCGATGGCACCGATGAGGCGCTCCCTCCGCCTGG chr2B_4 -------CCGTCGTCTGCGTCGGCATCGATGAGGCGCTCCCTTCGCCTTG chr1B_4 -------CCGTCGCCTGTGACGGCACCGACGAGGCGCTCCCTTCGCCTTG chr2D_4 CCGACCCTCCCCGCCTGGTCCGGCTCCGGGGAGGCGCTCCCTCCACCTGG chr5D_11 CCAGCCCTCCCCGCCTGGTCCGGCTCCGGGGAGGCGCTCCCTCCGCCTGG chr3D_14 CCGGCCCTCCCCGCCTGGTCCGGCTCCGGGGAGGCGCTCCCTCCGCCTGG chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ------------------------------S------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TCCGGCCGAAGCCCGAGCCGGACACGCCCCCCGTGAAGCCGGACACGCCG chr7D_1 TCCAGCCGAAGCCCGAGCCGGACACGCCCCGCGT---------------- chr4A_1 TCTGGCCGAAGCCCGAGCCGGACAAGCCCCCCGT---------------- chr3B_1 TCCGGCTGAAGCCCGAGCCGGACACGACCCCCGT---------------- chr5D_1 TCTGGCCGAAACCCGAGCCGGACACGCCCACCGT---------------- chr5B_1 TCCGGCTGAAGCCCGAGCCGGACATGCCGCCCGT---------------- chr7B_1 TCCAGCAAAAACCCGAGCCGAACATGCCCCCCGT---------------- chr1D_2 TCCGGCCGAAGCCCGAGCCGGACACGCCCCCCGT---------------- chr6B_4 TCCGGCCGAAGCCCAAGCCGGACGCGCCCCCGGT---------------- chr4B_4 TCCGATCGAAGCCCGAGCCGGACATGCCCCCCGT---------------- chr2B_4 TCCGGCCAAAGCCCGATCCGGACGTGCCCCCCGT---------------- chr1B_4 TCCGGCCGAAACCCGAGCCGGCCGCAGCCCCCGT---------------- chr2D_4 TCCGGCCGAAGCCCGAGCCGGGGATGCTCCCGGT---------------- chr5D_11 TCCGGTCGAAGCTCGAGCCGGGGCTGCTCCCGGT---------------- chr3D_14 TCCGGCCGAAGCCCGAGCCGGGGCTGCTCCCGGT---------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ----------------------------------SSSSSSSSSSSSSSSS forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CCCGTGAAGCCGGAGCACGCCGGCATGGTGGCCCCCGACGACGAGTCCGC chr7D_1 -----GAAGCCGGAGCACATCGGCATGGTGGCACCCGACGACGAGTCCGC chr4A_1 -----GAAGCCGGAGCATGCCGGCATGGTGGCCCCCGACGACGAGTCCGC chr3B_1 -----GAAGCCGGAGCACGCCGGCATGGTGGCACCCGACGACGAGTCCGC chr5D_1 -----GAAGCCGGAGCACATCGGCATGGTGGCACCCGACGACGAGTCCGC chr5B_1 -----GAAGCCTAAGCACGCCGGCATGGTTGCCCCCGACGACGAGTCCAC chr7B_1 -----GAAGCCGGAGCACGCCGGCATGGTGGCCCCCGACGACGAGTCCGC chr1D_2 -----GAAGCCGGAGCACATCGGCATGGTGGCACCCGATGACGAGTCCGC chr6B_4 -----GAAGCCGGAGCACGCCGGCATGGTGGCCCCCGACGACGAGTCCGC chr4B_4 -----GAAGCCGGAGCACGCCGGCATGGTGGCCCCTGACGACGAGTCCGC chr2B_4 -----GAAGCCGGAGCACGCCGGCATGGTGGCCCCCGACGACGAGTCCGC chr1B_4 -----GAAGCCGGAGCACGCCGGCATGGTGACCCTCGACGACGAGTCCGC chr2D_4 -----GAAGCCGGAGCACGTCGAGATGGCAGCCCCCGACGACGAGTCCAC chr5D_11 -----GAAGCCGGAGCACGTCGAGATGGCAGCCCCCGACGACGAGTCCGC chr3D_14 -----GAAGCCGGAGCACGTCGAGATGGCAGCCCCCGACGACGAGTCCGC chr5D_239 ---GTGAAGCCGGAGCACGTCGACGTGGCAGCCCCCGATGATGAGCCCGC chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs SSS----------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CCTCAAATGG-GCGAGGGAGGACTAAATCCGCGAGCAGGTGCGCCGCCAG chr7D_1 CCTCAAATGG-GCGAGGGAGGACTACGTCCGCAAGCAGGTGCGCCGCCAG chr4A_1 CCTCAAATGG-GCGAGGGAGGACTACGTCCGCGAGCAGGTGCGCCGCCAG chr3B_1 CCTCAAATGG-GCGAGGGAGGACTACGTCCGCGAGCAGGTGCGCCAACAG chr5D_1 CCTCAAATGG-GCGAGGGAGGACTACGTCCGCGAGCAGGTGCGCCGCCAG chr5B_1 CCTCAAATAG-GCGAGGGAGGACTACGTCCGCGAGCAGGTGCGCCGCCAA chr7B_1 ACTCAAATGG-GCGAGGTAGGACTACGTCCGCGAGCAGGTGCGCCGCCAG chr1D_2 CCTCAAATGG-GCGAGGGAGGACTACGTCCGCGAGCAGGTGCACCGCCAG chr6B_4 CCTCAAATGG-GCGAGGGAGGACTACGTCCGCGAGCAGGTGCGCCGCCAG chr4B_4 CCTCAAAT-G-GCGAGGGAGGACTACGTCCGCGAGCAGGTGCGCCGCCAG chr2B_4 CCTCAAAT-GGGCGAGGGAGGACTACGTCCGCGAGCAGGTGCGCCGCCAG chr1B_4 CCTCAGATGG-GCGAGGGAGGACTACGTCCGCAAGGAGATGCGCCGCCAG chr2D_4 CCTCAAGTGG-GCGAAGAAGGACTACGTCTGAGAGCAGGTCCGCCGCCAG chr5D_11 CCTCAAGTGG-GCGAAGGAGGACTACGTCCGGGAGCAGGTCCGCTGGCAG chr3D_14 CCTCAAGTGG-GCGAAGGAGGACTACATCCGGGAGCAGGTCCACCGGCAG chr5D_239 CCTCAAGTGG-ACGAAGGAGGACTACGTCCGGGAGCAGGTCCGCCGCCAG chr5B_314 -----------------------------CGAGAGCAGGTGCGCCGCCAG chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------S------------------------ forward_326 ------AATGGGCGAGGGAGGACTAA------------------------ reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CGTCGGGCGTACCTGGAGACCCAGGCCCACAGCCGCGCCGAGGCCCGTCG chr7D_1 CGTTGGGCTTATCTGGAGACCCAGGCCCGCAGCCGCGCCGAGGCCCGTCG chr4A_1 CATCGGGCGTACCTGGAGACCCAGGCACGCAACCGCGCCGAGGCCCGTCG chr3B_1 CGTCGGGCTTACCTGGAGACCCAGGCCCGCAGCCGCGCCGAGGCCCGTCG chr5D_1 CGCCGAGCTTACCTGGAGACCCAGGCTCGCAGCCGCGCCGAGGAGCGTCG chr5B_1 CGTCGGGCGTACCTGGAGACCCAGGCCCGTAGCCGCGCCGAGGCCCGTCG chr7B_1 CGTCGGGCGTACCTGGAGACCCAGGCCCGTAGCCGCGCTGAGGCCCGTCG chr1D_2 CGTCGGGCTTACCTGGAGATCCAGGCCCGCAGCCGCGCCGAGGCTCGTCG chr6B_4 CGTCGGGCTTACCTGGAGACCCAGGCCCGCAGCCGCGCCGAGGCCCGTCG chr4B_4 CGTCGGGCGTACCTGGAGACCCAGGCCCGTAGCCGCGCCGAGGCCCGTCG chr2B_4 CGTCGGGCTTACCTGGAGACCCAGGCCCGCAGCCGCGCCGAGGAGCATCG chr1B_4 CGTCGGGCTTACCTGGAGACCCAGGCCCGCAACCGCGCCGAGGAGCATCG chr2D_4 CGTCGGGCGTACGCGGAGCTCCAGGCCCGGCGCCGCGGG----------- chr5D_11 CGCCGGGCGTACGCGGAGCTCCAGGCCCGGCGCCGCGGG----------- chr3D_14 CGCCGGGCGTACGCGGAGCTCCAGGCCCGG----GCGGT----------- chr5D_239 CGCCGGGCGTACGCAGAGCTCCAGGCCCGGCGCCGCGGG----------- chr5B_314 CGTCGGGCATACCTGAAGACCCAGGCCCGCAGCCGCGCCGAGGCCCATCG chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ----------------------------S--------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TCGCCGCGCCGAGGAG------------------------GGCGTTATCG chr7D_1 ---------------------CTGCGCC---GAGGAGGTCGGCGTTATCG chr4A_1 TCGCCGCGCCGAGGAGCGTCGCCGCGCC---AAGGAGGGTGGCGTTATCG chr3B_1 ---------------------CCGCGCC---GAGGAAGGCGGCGTTATCG chr5D_1 ---------------------CCGTGCCGAGGAGGAGGTCGGCGTTATCG chr5B_1 ---------------------CCGCGCC---GAGGAGGGCGGCGTCATCG chr7B_1 ---------------------CTGCGCC---GAGGAGGGCGGCGTTATCG chr1D_2 ---------------------CCGCGCC---GAGGAGGTCGGCGTTCTCG chr6B_4 ---------------------CCGGGCC---GAGGAGGGCGGCGTTATCG chr4B_4 ---------------------CTGCGCC---GAGGAGGGCGGCGTTATTG chr2B_4 ---------------------CCGCGCC---GAGGAGGGCGGCGTTATCG chr1B_4 ---------------------CCGCGCC---GAGGAGGGCGGCGTTATCG chr2D_4 -------------------------CGT---GAGGAGGGCGGCGTCATCG chr5D_11 -------------------------CGC---GAGGAGGGCGGCGTCATCG chr3D_14 -------------------------CGC---GAGGAGGACAGCGTCATCG chr5D_239 -------------------------CGC---GAGGAGGGCGGCGTCATCG chr5B_314 ---------------------TCGCCGC---GCCGAGGAGGGCGTTATCG chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TCATCGACAGCGACGACGAGGTCGAGGCCGGGCCGTCATGC---GCTG-- chr7D_1 TCATCGACAGTGACAACGAGGTCGAGGCCGGGCCGTCATGC---GCTG-- chr4A_1 TCATCGACAGCGACGACGAGGTCGAGGCCGGGCCGTCATGC---GCTG-- chr3B_1 TCATCGACAGCGACGACGAGGTCGAGGCCGGGCCGTCATGC---GCTG-- chr5D_1 TCATCGACAACGACGACGAGGTCGAGGCCGGGCCGTCAAGCGCTGCTG-- chr5B_1 TCATCGACAGCGACGACGAGGTCGAGGCCGGGCCGTCAAGCGCTG----- chr7B_1 TCATCGACAGCGACGACGAGGTCGAGGCCGGGCCGTCGAGCGCTG----- chr1D_2 TCATCGACAGCGACGACGAGGTCGAGGCCGGGCCGTCATGCGCTG----- chr6B_4 TCATTGACAGCGACGACGAGGTCGAGAT-GGGCCGTCATGCGCTG----- chr4B_4 TCATCGACAGCGACGACGAGGTCGAGGCCGGGCCGTCAAGCGTTG----- chr2B_4 TCATCGACGGCGATAACGAGGTCGAGGCCGGGCCGTCATGCGATG----- chr1B_4 TCGTCGACAGTGACGACGAGGTCGAGGCCGGGCCGTCATGCGCTG----- chr2D_4 TCCTCGACAGCGATGAGGAGGACGAGGCAGGGCCGTCCAGC---GCCACC chr5D_11 TCCTTGACAGCGATGAGGAGGACGAGGCCGGGCCGTCCAGCGC-GCCACC chr3D_14 TCCTCGACAACGACGAGGAGGACGAGGCCGGGCCGTCCAGCGC-GCCACC chr5D_239 TCCTCGACAGCGACGAAGAGGATGAGGCCGGGCCGTCAAGCGC-GCCACC chr5B_314 TCATCGACTGCGATGACGAGGTCGAGGCCGGGCTGTCATGCGCTG----- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 -----TCGGCGACCCGGGCGAGGGGTGCAGTAGGGACGCCGCGGGCGAG- chr7D_1 -----TCGGCGACCCGGGCGAGGGGTGCAGCAGGGACGCCGCGGGCGAG- chr4A_1 -----TCGGCGACCCGGGCGAGGGGTGCAGCAGGGACGCCGCGGGCGAG- chr3B_1 -----TCGGTGACCCGGGCGAGGGGTGCAGCAGGGACGCCGCGGGCGAG- chr5D_1 -----TCGGCGACCCGGGTGAGGGGTGCAGCAGGGATGCCGCGGGCGAG- chr5B_1 -----TCGGCGACCCGGGCAAGGGGTGCAGCAGGGATGCCGCGGGCGAG- chr7B_1 -----TCGGCGACCCGAGCGAGGGGTGCAGCAGGGACGCCACGGGCGAG- chr1D_2 -----TCGGCGATCCGAGCGAGGGGTGCAGCAGGGACGCCGCGGGCGAG- chr6B_4 -----TCGGCGACCTGGGTGAGGGGTGTAGCAGGGACGCCGCGGGCGAG- chr4B_4 -----TCGGCGACCCGGGCGAGGGGTGCAGTAAGGACGCCGCGGGCGAG- chr2B_4 -----TCGGCGACCCGGGTGAGGGGTGCAGCAGGGACGCCGCGGGCGAG- chr1B_4 -----TCGGTAACCCGGGTGAGGGGTGCAGCAGGGACGCCGCGGGCGAG- chr2D_4 GCGCCTCGGCGACCCTGGCCAGGGCTGCAGCAGGGACGACGCCTGCCCAA chr5D_11 ACGCCTCGGCGATCCTGGCCAGGGCTGCAGCAGGGACGTCGCCGGCCCAA chr3D_14 ACGCCTCGGCGACCCTGGCCAGGGCTGCAGCAGGGACGTCGCCGGTCCAA chr5D_239 GCGCCTCGGCGACCCTGGCCAGGGCTGCAGCAGGGACGGCGCCGGCCCAA chr5B_314 -----TCGGCGACCCGAGCGAGGGGTGCAGCAGGGACGTCGCGGGCGAG- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 -------GCG--------CG-CGACGACGATGACGACG--------ACGA chr7D_1 -------GCG--------CG-CGACGACGACGACGACGGCGGCG--GCGG chr4A_1 -------GCG--------CG-CGACGACGATGACGACGA--------CGG chr3B_1 -------GCG--------CG-CGATGACGACGACGAT------G-----A chr5D_1 -------GCG--------CG-CGACGACGACGACGACGGCA-----GCGG chr5B_1 -------GCG--------CG-CGACGACGACGACGA-------------- chr7B_1 -------GCG--------CG-CGACGAGGACGACGAT------G--GCGG chr1D_2 -------GCG--------CG-CGACGACGACGACGAC------G--GCGG chr6B_4 -------GCG--------CGATGACGACGACG---GC------G--GCGG chr4B_4 -------GCG--------CG-CGACGACGACG---AC------G--GCGG chr2B_4 -------GCG--------CG-CGACGATGACG---GC------G--GCGG chr1B_4 -------GCACGCGA---CGACGACGACGGCG---GC------G--GCGG chr2D_4 GCCAGCCG--CGCGA---CGACGATGACGGCG---AC------G--GCGG chr5D_11 GCCAGCCA--CGCAATGACGACGACGACGATG---AC------GGCGCGG chr3D_14 GCCAGCCG--CGCGACAACGATGATGACGGCG---AC------G--ACGG chr5D_239 GCCAGCCGCG--------CGGCGACGACGATG---AC------G--GTGG chr5B_314 -------GCG--------CG---ACGACGACG---AC------G--ACGA chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CGACGGCA------------------TCGGCATGTAGACGGCGGCGGCGG chr7D_1 CGACTACACCCGCTTCTACAGGCTTCTCGGCATGTAGAAGGC-------- chr4A_1 TGACTACACCCGCTTCTACAGGCTTCTCGGCATGTAGACGATGGCGGCGA chr3B_1 CGACTACACCCGCTTCTACAGGCTTGTCGGCATGTAGAAGGC-------- chr5D_1 CGACTGCACCCGCTTCTACAGGCTTCTCGGCATGTAGAAGGC-------- chr5B_1 CGACTACACCCATTTCTACAGGCTTCTCGGCATGTAGGCGGC-------- chr7B_1 CGACTACACCCGCTTCTACAGGCTTCTCGGCATGTAAACGGCGGCAGCGG chr1D_2 CGACTACACCCGCTTCTACAGGCTTCTCGGCATATAAAAGGC-------- chr6B_4 CGACTACACCCGCTTCTATAGGCTTCTCGGCATGTAGACGGC-------- chr4B_4 CGACTACACCCGCTTCTACAGGCTTCTCGGCATGTAGACGGC-------- chr2B_4 CGACTACACCCGCTTCTACAGGCTTCTCGGCATGTTGGCAGC-------- chr1B_4 CGACTACACCCGCTTCTACAGGCTTCTCGGCATGTAGACGGC-------- chr2D_4 CGACTACACCCGCTTGTACAGGCTTCTCGGCATGTAGACGAC-------- chr5D_11 CGACTACACCCGCTTCTACAGGCTTCTCGGCATGTAGACGAC-------- chr3D_14 CGACTACACCCGCTTCTACAGGCTTCTCGGCATGTAGACGAC-------- chr5D_239 CGACTACACCCGCTTCTACAGGCTTCTCGGCATGTAGAGGAC-------- chr5B_314 CGACTACACCCGCTTCTACAGGCTTCTCGACATGTAGACGAC-------- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ----S--------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CGACGATGGCGGCAGCGG---------------CTAGGCGT--TTT---- chr7D_1 -------GGCGGCGGCGACGGTGGCGGCACTAGCTAGGCGT--TTTA--- chr4A_1 CGACGG-GGCGGTAGTGG---------------CTAGGCGT--TTT---- chr3B_1 -------GGCGGTGGTGACGGTGGCGGCACTAGCTAGGCGT--TTTAATA chr5D_1 -------GGCGGCGGCGACGGTGGCGGCACTAGCTAGGCGT--TTTA--- chr5B_1 -------GGCGGCAGTGG---------------CTAGGCTT--TTT---- chr7B_1 CGG---TGGCGGCAGTGG---------------CTAGGCTT--TTT---- chr1D_2 -------GGCGGCGGCGACGGTGGCGGCACTAGCTAGGCGT--TTTA--- chr6B_4 -------GGCGGCGGCGACGGTGGCGGCACTGGCTAGGCGT--TTT---- chr4B_4 -------GGCGGCGGTGACGGTGGCAGCAGTGGCTAGGCTT--TTT---- chr2B_4 -------GGCGGCGACG---GTGGTGGCACTGGCTAGGCGT--TTT---- chr1B_4 -------GGCGGTGGCGATGGTGGCACCACCGGCTAGGCGT--TTT---- chr2D_4 -------AGTGGCGGCTA-------------------------------- chr5D_11 -------GGCGACGACG---GCGGCGGTGGCGGCTAGGCGTAGTTT---- chr3D_14 -------GGCGGCGGTGGCAG------------CTAGGCGTAGTTT---- chr5D_239 -------GGCGACGGCGGCGG------------CTAGGTGTAGTTT---- chr5B_314 -------GATGGCGGCGACGATGGCGGCAACGACTAGGCAT--TTT---- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -----S-------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 AGTTCGTTTTTAA-----------TGCATG-TTTTAAAG-----TT-TTT chr7D_1 AGTTCGTTTTTAAGTTAGT--TCACGCTTG-TTTTACG---CTTTTGT-- chr4A_1 AGTTCGTTTTTAAGTTTGT--TCATGCATG-TTTTAAG---TTTTT-TTT chr3B_1 AGTTCGTTTTTAAGTTAGC--TCACGCATG-TTTTACG---CTTTTGT-- chr5D_1 AGTTCGTATTTAAGTTAGTTTTCACGCATG-TTTTACG---CTTTTGT-- chr5B_1 AGTTCGTTTTTAAATTAGT--TCATGCATG-TTTTAAG---TTTTT-T-- chr7B_1 AGTTCGTTTTTAAGTTAGT--TCATGCATG-TTTTAAG---TTTTTGT-- chr1D_2 AGTTCGTTTTTAAGTTAGT--TCACGCATG-TTTTACG---CTTTTGT-- chr6B_4 AGTTCGTTTTTAAGTTAGT--TCACGCATG-TTTTACG---TTTTTTG-- chr4B_4 AGTTTGTTTTTAAGTTAGT--TCATGCATG-CTTTAAG---TTTTTGT-- chr2B_4 AGTTCGTTTTTAAGTTCAT--TCACACATG-TTTTATG---TTTTTTG-- chr1B_4 AGTTCGTTTTTAAGTTTGT--TCACGCATG-TTTTACG---TTTTTGT-- chr2D_4 GGCGTAGTTTAGGCGTAGT--TCAGGCGTA-GTTTGCATGTTTTCTGT-- chr5D_11 GGCGTAGC-------------T--TGCATG-TTTT-CATGTTTTCTGT-- chr3D_14 GGCGTAGTTTAGGCGTAGT--TCAGGCGTA-GTTTGCATGTTTTATGT-- chr5D_239 GCA-TAGTTTAGGCGTAGT--T--TGCATGTTTTCATG---TTTTTGT-- chr5B_314 AGTTCGTTTTTAAGTTAGT--TCATGCATG-TTTTAAG---TTTTTTT-- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs --------------------------------------S----------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TACAAATTTCAAGTAAGTTTCGCCGAGTTCGTGCAAAAGTCGCCGAATTT chr7D_1 -ATAAATTTGGACG-AAAATGGCCATGTTCATGCAAAAGTCGCCGAGTTT chr4A_1 TACAAATTTCAAGTAAGTTTCGCCGAGTTCGTGCAAAAGTCGCCGAGTTT chr3B_1 -ACAAATTTGAACAAAAAATGGTAGAGTTCATGCAAAAGTCGCCCAGTTT chr5D_1 -ACAAATTTGGACG-AAAATGGCCGTGTTCATGCAAAAGTCGCCGAGTTT chr5B_1 -ACAAATTCCGATGAAAAATGACCGAGTTCATGCAAAAGTCGTCGAGTTT chr7B_1 -ACAAATTTCGATGAAAAATGGCCGAGTTCATGCAAAAGTCGCCGAGTTT chr1D_2 -ACAAATTTGGACG-AAAATGGCCGTGTTCATGCAAAAGTCGCCGAGTTT chr6B_4 TACAAATTTGGATGCAAAATGGCCGAGTTCATGCAAAAGTCGCCGAGTTT chr4B_4 -ACAAATTTGAACGAAAAATGACTGAGTTCATGCAAAAGTCGCCGAGTTT chr2B_4 TATAAATTTGGACGAAAAATGGCCGAGTTCATGCAAAAGTCGCCGAGTTT chr1B_4 -ACAAATTTGGACGAATAATGGCCGAGTTCACGCAAAAGTCACCGAGTTT chr2D_4 -ACAAATTTCAATGAAGTT--------------------TCGCCGAGTTT chr5D_11 -ACAAATTTCAATGAAGTTTCGCCGAGTTCGTGCAAAAGTCGTTGAGTTT chr3D_14 -ACAAATTTCAATGAACTTTCGCCGAGTTCGTGCAAAAGTCGCCGAGTTT chr5D_239 -ACAACTTTTAGTGAAATTTTGCCGAGTTCGTGCAAAAGTCGCCGAGTTT chr5B_314 -ACAATTTTCAAGTAAGTTTCGCCGTGTTCGTGCAAAAGTCGCCGAGTTT chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ----------------------------------------------S--- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 GCATATATTTTGTACGC--AACATCGCCAAACCCGGGGCGACC--CGTGG chr7D_1 GAAAAAAAA-CAAGA--CGAACTTCGCCGAACCCGCGGCGACCA---TGG chr4A_1 GAATATATTTTGTACGC--AACATCGCCGAACCGGGGGCAACC--CATGG chr3B_1 AAAAAAAAA-TAAGG--CGAACTTCGCCGAACCCGCAACGACCACCGTGA chr5D_1 GAAAAAAAAACAAGA--CGAACTTCGCCGAACCCGCGGCG---ACCGTGG chr5B_1 GCAAAGAAAATAAAA--CGAACTTCGCCGAATCCGCGACG---ACCGTGG chr7B_1 GATAAAAAAATAAGA--CGAACTTCGCCGAACCCGCGGCG---ACTGTGG chr1D_2 GGAAAAAAA-TAAGA--CGAACT--------------------------- chr6B_4 GCAAAAAAA-CAAGA--CGAACTTCGCCGAACCCGCGGCG---ACCGTGG chr4B_4 GAAAAAGAAAGATGG-----ACTTCGCCGAACCCGCGGCA---ATCGTGG chr2B_4 GCAAAAAA--CAAGA--CGAATTTCGCCGAACCCACAGTG---ACCCTGG chr1B_4 GCAAAAAATAGAAAAGACGATCTTTGATGAACCCGCGGCG---ACCGTGG chr2D_4 GCATATATTTTGTACGC--AACATCGCCGAACCCGGGGCGACC--GGTGA chr5D_11 GCATATATTTTGTACGC--AACATCGCCGAACCCGGGGCGACC--GGTGG chr3D_14 GCATATATTTTGTACGC--AACATCGCCGAACCCGGGGCGACC--GGTGG chr5D_239 GCATATATTTTGTACGC--AACATCGCCGAACCCGGGGCGACC--TGTGG chr5B_314 GCATATATTTTGTACGC--AACATCGCCGTACCCGAGGCGACC--CGTGG chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ----------------------------S--------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 GCCGACGACTAGGAGCTAGGTCGCCCCCACGCGCCAAACTAGCGCCGGCT chr7D_1 GCGTGTGACTGGGAGCGAACCGAACCCCAGGGGCCGAACTAGCGCCGGCT chr4A_1 GCCAACGACTGGGAGCTAGATCGCCCCCACGGGCCAATCTAGCGCCGGCT chr3B_1 GCGTGCGACTGGGAACGAACCGAACCCCAGGGGCCGAACTAGCGTCGGCT chr5D_1 GCGTGTGACTGGGAGCGAACCGAACCCCAGGGGCCGAACTAGCGTCGGCT chr5B_1 GCATGTGACTGGGAGCGAACCGACCTCCAGGGGCCGAACTAGCGCCGGCT chr7B_1 GCGTGTGACTGGGAGCGAATCGAATCCCAGGGGCCGAATTAGCGCCGGCT chr1D_2 -------------------------------------------------- chr6B_4 GCGTGTGACTGGGTTCGAACCAAACCCCAGGGGCTGAACTAGCGCCGGCT chr4B_4 GCGTGTGACTGGCCGTGAGCCGAACCCCAGAGGCCGAATTAACGCCGGCT chr2B_4 GCGTGTGACTGGAATCGGACCGAACCCCAGGGACCGAACTAGCGCCGACT chr1B_4 GCGTGTGACTGAGATCAAACCGAACCCCAGAGACCGAACTAGCGCCGGCT chr2D_4 GCCGACGACTGGAAGCTAGGTCGCCCCCACGCGCCAATCTAGCGCCGGCT chr5D_11 GCCGACGACTGGGAGCTAGGTCGCCCCCACGCGCCAATCTAGCGCCGGCT chr3D_14 GCCGACGACTGGGAGCTAGGTCGCCCCCACGCGCCAATCTAGCGCCGGCT chr5D_239 GCCGACGACTGGGAGCTAGGTCGCCCCCACGCGCCAATCTAGCGCCGGCT chr5B_314 GCCGATGACTGGGAGCTAAGTCGTCCCCACGCGTCAATCTAGCGCCGGCT chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ----------S--------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CGTCCCCAAGGGGCTCTTTTTCGGCGCCGGGGGGGGGCCGAATCGGCTGG chr7D_1 CGCCCCCAGGCCGCTATTTTTCGGC------------------------- chr4A_1 CGTCCCCAGG-GGCTCTTTTTCGGC------------------------- chr3B_1 CGCCCCCAGGCCGTTATTTTTCGTC------------------------- chr5D_1 CACCCCCAGGCCGCTATTTTTCGGT------------------------- chr5B_1 CACCCCAG-GCCGTTC-TTTTTGGC------------------------- chr7B_1 CGCCCCCAGGCCGCTCTTTTTCGGC------------------------- chr1D_2 -------------------------------------------------- chr6B_4 CGCCCCCAGGCCGCTCTTTTTCGGC------------------------- chr4B_4 CACCCCCAGGCCGCTCTTTTTCAGC------------------------- chr2B_4 CACTCCCAGGCCGCTCTTTTTCGGC------------------------- chr1B_4 CATCTCCAGGCTGCTCTTTTTAGGCAG----------------------- chr2D_4 CGCCCCCAGGGGGCTCTTTTTCGGC------------------------- chr5D_11 CGCTCCCA-GGGGCTCTTTTTCGGC------------------------- chr3D_14 CGCCGCCATGGGGCTCTTTTTCGGC------------------------- chr5D_239 CACCCCCAGGCGGCTCTTTTTCGGC------------------------- chr5B_314 CGTCCTCAGGGGGCTCTTTTTCGGC------------------------- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs --------S----------------SSSSSSSSSSSSSSSSSSSSSSSSS forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 AGATGCTCTTATGACCCGTCCACTGGGCGCTGGATCCATGTGCCCAAGAT chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------CCTATGACCCCTACAGGGAGCGCTGGATCCAGGTGCCCAAGAT chr4A_821 ------TCTTATGACCCGTCCACTGGGCGCTGGATCCAAGTGCCCAAGAT chr7D_822 -------CTTATGACCCGTCCACTGGGCGCTGGATCCAAGTGCCCAAGAT chr7D_822 -------CTTATGAGCCGTCCACTGGGCACTGGATCCATGTGCCCAAGAT chr7A_822 -------CTTATGACCCGTCCACTGGGCGCTGGATCCAAGTGCCCAAGAT chr7A_822 -------CTTATGACCCGTCCACTGAGCGCTGGATCCAAGTGCCCAAGAT chr4A_822 -------CTTATGACCCATCCACTGGGTGCTGGATCCATGTGCCCAAGAT chr4A_822 -------CTTATGACCCGTCCACTGGGCGCTGGATCCAAGTGCCCAAGAT chr4A_822 -------CTTATGACCCGTCCACTGGGCGCTGGATCCAAGTGCCCAGGAT chr4A_822 -------CTTGTGACCCGTCCACTGGGCGCTGGATCCAAGTGCCCAAGAT chr4A_822 -------CTCATGACCCGTCCACTGGGCGCTGGATCCATGTGCCCAAGAT chr4D_824 ---------TATGACCCCTACAGGGAGCGCTGGATCCAGGTGCCCAAGAT chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs SSSSSS-------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 ACCACCGGTTGAAAGCGGAA---TCTG------GGATTCGCTTGCTGTAG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 GCCACCGGATGAATGCTTCATGTGCTCTGACAAGGAGTCCCTGGCTGTGG chr4A_821 GCCACCGGCTGAATGCTCTT---ACTG------GGAGTCATTTGCTGTAG chr7D_822 GCCACCGGCTCAAAGCATCC---TCTG------GGAGTCGCTTGCTGTAG chr7D_822 GCCACCGGCTGGAAGCTACA---TCTG------GGGCGCGCTCGCTGTAT chr7A_822 GCCACCGGCTAAAGGCGACT---TCTGTT------ATTCGCTTGCTGTAG chr7A_822 GCCACCGGCTCAAAGCAAATTCATCTC------GGAGTCGCTCGCCGTAG chr4A_822 GCCACCGGCTGAAAGCTCCTCCATCCG------GGAGTCGCTCGCTGTAG chr4A_822 GCCACCGGCTGGAAGCATCG---TCTG------GGAGTCGCTTGCTGTAG chr4A_822 GCCACCGGCTGGAAGCCCCT---ACTG------GAGGTCGCTCGCTGTCG chr4A_822 GCCACCGACTCAAAGCTCCT---ACTG------GGATTCGCTTGCTGTAG chr4A_822 GCCACCTGCTCAAAACGTCA---TCTG------GGATTCGCTGGCTATAG chr4D_824 GCCACCGGATGAATGCTTCATGTGCTCTGACAAGGAGTCCCTGGCTGTGG chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs S-------S--------S-------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 GAACCGAGCTGCTGGTGTTTGGGGTCCGCGGAAGGGTTGCCTTGAGATAT chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 GCACCGAGCTGCTTGTGTTTGGGATGGCACACATTGTG---TTCAGATAT chr4A_821 GGACCGAGCTGCTGTTGTTTTGGG---ACGGAAGGGTTGCCTTGAGATAT chr7D_822 GAACTGAGTTGCTGGTTTTTGGGAACGAGG---GGGTTGCCTTGAGATAT chr7D_822 GAACCGAGCTGCTGGTGTTTGGGGCCCACGGAAGGGTTGCCTTGAGATAT chr7A_822 GAACCGAGCTGCTGGTGTTTGTGGACCGTGGAAGGGTTGCCTTGAGATAT chr7A_822 GAACCGAGCTGCTGGTGTTTGGGGACTGCGGAAGGGTTGCCTTGAGATAT chr4A_822 GAACCGAGCTGCTGGTGTTTGGGGACCGCGGAAAGGTTGCCTTGAGATAT chr4A_822 GAACCGAGCTGCTGGTGTTTGGGGACCAGGGAAGGGTTGCCTTGAGATAT chr4A_822 GAACCGAGCTGCTGGTGTTTGGGTCCGC---AATGGATGCCTTGAGATAT chr4A_822 GAACCGAGCTGCTGGTGTTTGGGGGCTACGGAAGGGTTGCCTTGAGATAT chr4A_822 GAACCGAGCTTCTGCTGTTTGGGGAGGGCTGGCGGA------TGAGATAT chr4D_824 GCACCGAGCTGCTTGTGTTTGGGATGGCACACATTGTG---TTCAGATAT chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 AGCATCCTTACCAATTCATGGACATG---GCTGGCTGAT------GCTGA chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 AGCATCCTGACCAATTCATGGACAAG---G---------------GCTGA chr4A_821 AGCATCCTTACCAATTCATGGACATG---GCTGGCTGAT------GT--- chr7D_822 AGCATCCTTACCAATTCATGGACATGGCTG---------------GCTGA chr7D_822 AGCATCCTTACCAATTCATGGACATG---GCTGGCTGATGCGATGTA--- chr7A_822 AGCATCCTTACCAGTTCATGGACAGG---GCTGGCTGAT------GCTGA chr7A_822 AGCATCCTTACCAATTCATGGACATG---GCTGGCTGAT------GCTGA chr4A_822 AGCATCCTTACCAATTCATGGACAGG---GCTGGCTGATGCTGATGC--- chr4A_822 AGCATCCTTACCAATTCATGGACATG---GCTGGCTGAT------GC--- chr4A_822 AGCATCCTTACCAATTCATGGACAGG---GCTGGCTGAT------GC--- chr4A_822 AGCATCCTTACCAATTCATGGACATG---GCTGGCTGAT------GT--- chr4A_822 AGCATCCTTACCAATTCATGGACAGG---GCTAGTGGAT------GA--- chr4D_824 AGCATCCTGACCAATTCATGGACAAG---G---------------GCTGA chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 ----ATGAACACCCCACGGTACTTCTTTGGGTCAGCAAGTGTCGGTGAAA chr7D_1_TraesCS7D01G005100 TACGATGAACACCCCACGGTACTTCTTTGGGTCAGCAAGTGTCGGTGAAA chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 TCCCATGAACTCTCCCCGGTGCTTGTTTGGATCAACAAGCGTCGGTGAAA chr4A_821 ---GATGAACATCCGGCGGCGCTGGTTTGGGTCAGCAAGTGTCGGTGAAA chr7D_822 TGCGATGTACCCCCCGCGGTACTTGTTTGGGTCAGCAAGTGCCGGTGAAA chr7D_822 ----------CCCCCGCGGTACTTGTTTGGGTCAGCAAGTGTCGGTGAAA chr7A_822 TGCGATGAACACCCCGCGGTACTTGTTTGGGTCAGCAAGTGTCGGTGGAA chr7A_822 TGCGATGAACACCCCGCGCTACTGGTTTGGGTCAGCGAGTGTCGGTGAAA chr4A_822 ---GATGAACACCCCGCGGTTCTGGTTTGGGTCAGCAAGTGTCGGTGAAA chr4A_822 ---GATGAACACCCCACGGTACTTGTTTGGGTCAACAAGTGTCGGGGAGA chr4A_822 ---TATGAACACGCCGCGGTACTCGTTTGGGTCTGCGAGTGTTGGTGAAA chr4A_822 ---GATGAACAACCCGCGGTACTGGTTTGGGTCAGCAAGTGTCGGTGAAA chr4A_822 ---GATGAACACCCCGCGGTTCTCGTTTGGATCAGCAAGTGTTGGCGAAA chr4D_824 TCCCATGAACTCTCCCCGGTGCTTGTTTGGATCAACAAGCGTCGGTGAAA chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -S----------------------S------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 AGGCATATGTCGCGGGAGGCGTCGA---TTCTTCGTTTCAGGC---ATTG chr7D_1_TraesCS7D01G005100 AGGCATATGTCGCGGGAGGCGTCGA---TTCTTCGTTTCAGGC---ATTG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 AGGCGTATGTCGCTGGAGGCACCGA---TGCTTCTGG---AAAGATACTG chr4A_821 AGGCATATGTCACGGGAGGCGTTGA---TTCTTCTGA---AAGGATATTG chr7D_822 AGGCGTATGTCGCGGGAGGCAAGGT---TTCTTACGTTAGTTAC---TTG chr7D_822 AGGCGTATGTCGCGGGAGGCGCTGA---TTCTTCTC---ATAATATATTG chr7A_822 AGGTGTATGTCGCGGGAGGCAAGGA---TTCTTCTCGTAATAATGTATTG chr7A_822 AGGCGTATGTCGCGGGAGGCAAGGA---TTCTTCTTG---TAATGTGTTG chr4A_822 AGGCGTATGTCGTGGGAGGCGCTGA---TTCTTCTGG---TAATGTACTG chr4A_822 AGGCGTATGTCGCGGGAGGCGTTGA---TTCTTCGCGTAGTTAC---TTG chr4A_822 AGGCGTATGTCGCGGGAGGCTATGG---TTCTTCTGG---TAATGTATTG chr4A_822 AGGCGTATGTCGCGGGAGGCAAGGATTCTTCTTCTGG---TAATGTATTA chr4A_822 AGGCGTATGTCGTGGGAGGCGCTGA---TTATTCTCG---TAATGTATTG chr4D_824 AGGCGTATGTCGCTGGAGGCACCGA---TGCTTCTGG---AAAGATACTG chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs --------------------------------------S-SSS------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 AGCTGCGCAGAGATGTATGACTCGGAGACACATACTTGGACACCCCTTCC chr7D_1_TraesCS7D01G005100 AGCTGCGCAGAGATGTATGACTCGGAGACACATACTTGGACACCCCTTCC chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 AGCTCTGCAGAGATGTATGACTCTGTGACACACACTTGGACACCCCTTCC chr4A_821 AGCTCCGCTGAGATGTATGACTCGGAGATACATACTTGGACACCCCTTCC chr7D_822 AGCTCCGCAGAGATGTATGACTCGGAGGCACATACTTGGACACCCCTTCC chr7D_822 AGCTCCGCAGAGATGTACGACTCAGAGACACATACTTGGACACCCCTTCC chr7A_822 AGGTCTGCAGAGATGTATGACTCGGAGACACATACTTGGACACCCCTTCC chr7A_822 ATCTCCGCAGAGATGTATGACTCGGAGACGCATACTTGGACACCCCTTCC chr4A_822 AGCTCTGCAGAGATGTATGACTCAGAGACACATACTTGGACACCCCTTCC chr4A_822 AGCTCCGCAGAGATGTATGACTCGGAGACACATACTTGGACACCCCTTCC chr4A_822 AGCTCCGCAGAGATGTATGACTCGGAGACACATACTTGGACACCCCTTCC chr4A_822 AGCTCTGCAGAGATGTATGACTCCGAGAAATATACTTGGACACCCCTTCC chr4A_822 AGCTCCGCAGAGATGTATGACTCAGAGGCACATACTTGGACACCCCTTCC chr4D_824 AGCTCTGCCGAGATGTATGATTCTGTGACACACACTTGGACACCCCTTCC chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ----S--------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 CAGCATGAATAGGGCTAGGAGAAAATGTTCTGGTGCGTTCATGGACGGCA chr7D_1_TraesCS7D01G005100 CAGCATGAATAGGGCTAGGAGAAAATGTTCTGGTGCGTTCATGGACGGCA chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 CAGCATGAATAGGGCTAGGAAGATGTGTTCTGGTGTGTTCTTGGATGGCA chr4A_821 CAGCATGAATAGGGCTAGGTACAAATGCTCTGGCGTGTTCATGGATGGCA chr7D_822 CAACATGAATAGGGCTAGGCACAAATGCTCTGGTGCGTTCATGGATGGCA chr7D_822 CAGCATGAATAGCGCTAGGTACAGATGCTCTGCCGCGTTCATGGACGGCA chr7A_822 CAGCATGAATAGGGCTAGGATGGGATGCTCTGGTGCGTTCATGGACGGCA chr7A_822 CAGCATGAATAGGGCTAGGTACGGATGCTCTGGCGCCTTCATGGACGGCA chr4A_822 CAGCATGAATAGGGCTAGGTACAGATGCTCTGGCGCATTCATGGACGGCA chr4A_822 CAGCATGAATAAGGCTAGGTACGGATGCTCTGGCGCGTTCATGGATGGCA chr4A_822 CAGCATGAATAGGGCGAGGAACGGATGCTCTGGAGCGTTCATGGACGGCA chr4A_822 AAGCATGAATAGGGCTAGGTACGGATGCTCTGGTGCGTTCATGGATGGCA chr4A_822 CAGCATGAATAGGGCTAGGTACAAATGCTCTGGCGCATTCATGGATGGCA chr4D_824 CAGCATGAATAGAGCTAGGAAGATGTGTTCTGGTGTGTTCTTGGATGGCA chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs --------------------SS---------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 AGTTCTATGTGATCGGTGGTATTAGCAGTAGAAGGGAGCTATTGACATGT chr7D_1_TraesCS7D01G005100 AGTTCTATGTGATCGGTGGTATTAGCAGTAGAAGGGAGCTATTGACATGT chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 AGTTCTATGTGATCGGTGGTGTTACCAACAACAACCAGGTACTGACATGT chr4A_821 AGTTCTATGTCATCGGTGGTAATAGCAGTAGCCGCGAGCTATTGACATGC chr7D_822 AGTTCTATGTGATCGGTGGTGTTACCCGTAGCCGCGAGCTCTTGACATGC chr7D_822 AGTTCTATGTGATCGGTGGTCTTAGCAGTAGCCACGAGTTATTGACATGC chr7A_822 AGTTCTATGTGATCGGTGGTTTTCTCAGTAGGTACGAGGTATTGACATGC chr7A_822 AGTTCTATGTGCTCGGTGGTAATAGCAGTAGTCACAAGGTATTGACATGC chr4A_822 AGTTCTATGTGATCGGTGGTTCTAGCAGTAGCCACGAGGTATTGACATGC chr4A_822 AATTCTATGTGATGGGTGGTAATAGCAGTTGCCACGAGGTATTGACATGC chr4A_822 AGTTCTATGTGATCGGTGGTCTTAGCAGTAGCCACGAGGTATTGACATGT chr4A_822 AGTTCTATGTGATCGGTGGTGTTAGCAGTAGGCACGAGGTATTGACATGC chr4A_822 AGTTCTATGTGATCGGTGGTCTTAACAGTAGCCACGAGGTATTGACATGC chr4D_824 AGTTCTATGTGATTGGTGGTGTTACCAACAACAACCAGGTACTGACATGT chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------S--S--------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 GGTGAGGAGTATGACTTGAACCGGCGGTCATGGAGGGTCATCCACAACAT chr7D_1_TraesCS7D01G005100 GGTGAGGAGTATGACTTGAACCGGCGGTCATGGAGGGTCATCCACAACAT chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 GGTGAGGAATATGACTTGAATCGGGGTTCGTGGAGGGTCATTGAGAACAT chr4A_821 GGTGAGAAGTATGACTTGAACCGGCGGTCATGGAGGGTCATCAACGACAT chr7D_822 GGTGAGGAGTATGACCTGAACCGGCGGTCATGGAGGGTCATCGACAATAT chr7D_822 GGTGAGGAGTATGACTTGAACCAGCGGTCATGGAGGCTCATCGACAACAT chr7A_822 GGTGATGAGTATGACTTGAACCGGCGGTCATGGAGGGTCATCAACGACAT chr7A_822 GGTGAGGAGTATGACTTGAACCGGCGGTCATGGAGGCTCACCGACAACAT chr4A_822 GGTGAGGAGTATGACTCGAATCTGCGATCCTGGAGGGTCATCGACAACAT chr4A_822 GGTGAGGAGTATGACTTGAACCGGCGGTCATGGAGGGTCATCCACAACAT chr4A_822 GGTGAGGAGTATGACTTGAACCGGCGGTCATGGAGGGTCATCGACAACTT chr4A_822 GGTGAGGAGTATGACTTGAACCGGCGGTCATGGAGGGTCATCGACAACAT chr4A_822 GGTGAGGAGTATGACTTGAACCGGCGGTCATGGAGGGTCATCGACAACAT chr4D_824 GGTGAGGAATATGACTTGAATCGGGGGTCATGGAGGGTCATTGAGAACAT chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 GTCTCAGGGGCTCAACCAGACATACCTGGGAGCTCCTCTGCTCCTTGCAG chr7D_1_TraesCS7D01G005100 GTCTCAGGGGCTCAACCAGACATACCTGGGAGCTCCTCTGCTCCTTGCAG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 GTCTGAGGGCCTCAATGGAGTGAC---GGGTGCTCCTCCACTCATTGCAG chr4A_821 GTCTCAGGGGCTCAACGAGACAAGCTGTGGAGCTCCTCTGCTCCTTGCAG chr7D_822 GTCTCAGGGGCTCAACAGTACAGCCATTGGTGCTCCTCCGCTCATTGCAG chr7D_822 GTCTCAGGGGCTCAACGAGACAGATGAGGGAGCCCCTCTGTGCCTTGCAG chr7A_822 GTCTCAGGGGCTCAACCTTGCACTCTGGGGAGCTCCTCCGCTCATTGCAG chr7A_822 GTCTCAGGGGATCAACGAGACAAGACTGGGAGCTCCTCTGCTCCTAGCAG chr4A_822 GTCTCAGGGGCTCAACCATACAAGCCCCTTCGCTCCTCCGCTCATTGCAG chr4A_822 GTCTCAGGGGCTCAACTGGACAGATGAGGGAGCCCCTCTGTGCCTTGCAG chr4A_822 GTCTCAGGGGCTCAACGAGACAGACGAGGGAGCTCCTCTGCTCCTTGCAG chr4A_822 GTCTCAGGGCCTCAACGAGACAATCATGGGGGCTCCTCTGCTACTTGCAG chr4A_822 GTCTCAGGGGCTCAACAATATAGCCATGGGTGTTCCTCCGCTCATTGTAG chr4D_824 GTCTGAGGGCCTCAATGGAGTGAC---AGGTGCTCCTCCACTCATTGCAG chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ----------------------S--------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 TTGTGAAGAATGAGCTTTATGCTGCAGATTACAGTGAGAATAATGGTTTG chr7D_1_TraesCS7D01G005100 TTGTGAAGAATGAGCTTTATGCTGCAGATTACAGTGAGAATAATGGTTTG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 TTGTCAACAATCAGCTCTATGCAGCTGATTACAGTGAG---AAGGATGTG chr4A_821 TTGTGAAAAATGAGCTTTATGCTGCTGATTACTGCGAG---AATGATTTG chr7D_822 TTGTGAACAATGAGCTTTATGGCGCTGATTACAGTGTGAATAATGATCTG chr7D_822 TTGTCAACAATGAGATTTATGCTGCTGATTACAGAGAG---AATGATTTG chr7A_822 TTGTGAACAATGAGCTTTATGGCGCTGATTACAAAGAG---AATGATTTG chr7A_822 TTGTGAACAATGAGCTTTATGCTGCTGATTACAGTGAGAATAATGATTTG chr4A_822 TTGTGAACAATGAGCTTTATGCTCCTGATTACAGTGAGAATAATGATTTG chr4A_822 TTCTCAACAATGAGCTTTATTGCACTGATTACAGTGAGAATAATGATTTG chr4A_822 TTGTGAAGAATGAGCTTTATGGCGCTGATTACAGTGAGAATAATGATTTG chr4A_822 TTGTAAACAGTGAGCTTTATGCTGCTGATTACAGAGAGAATAATGATTTG chr4A_822 TTTTGAAGAATGAGCTTTATGCCGCTGATTACAGTGAGAATAATGAGTTG chr4D_824 TTGTCAACAATCAGCTCTATGCAGCTGATTACAGTGAG---AAGGATGTG chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------S-------------------S---- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 AAGCAGTATGATAAGATGGACAACAAGTGGATCACTCTTGGAAAATTGCC chr7D_1_TraesCS7D01G005100 AAGCAGTATGATAAGATGGACAACAAGTGGATCACTCTTGGAAAATTGCC chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 AAGAAGTATGACAAGCTGAATAATAAGTGGATCGCTCTTGGGAAATTGCC chr4A_821 AAGCAGTATGATAAGCTGGACAACAAGTGGATCACTCTTGGAAAATTGCC chr7D_822 AAGCAGTATGATAAGCTGGACAACAAGTGGATCACTCTTGGAAAATTGCC chr7D_822 AAGCAGTATGATAAGCTGGACAACAAGTGGATCACTCTTGGAAAATTGCC chr7A_822 AACCAGTATGATAAGCTGGACAATAAGTGGATCACTCTTGGAAAATTGCC chr7A_822 AAGCAGTATGATAAGCTGGACAATAAGTGGATCATGCTTGGGAAATTGCC chr4A_822 AAGCAGTATGATAAGCTGGACAACAAGTGGACCACTCTTAGGAAATTGCC chr4A_822 AAGCAGTATGATAAGCTGGACAACAAGTGGATCACTCTTGGAAAATTGCC chr4A_822 AAGCAGTATGATAAGCTGGACAACAAGTGGATCACTCTTGGAAAATTGCC chr4A_822 AAGCAGTATGATAAGCTGGACAACAAGTGGATCACTCTTGGAAAATTGCC chr4A_822 AAACAGTATGATAAGCTGGACAATAAGTGGACCACTCTTGGAAAATTGCC chr4D_824 AAGAAGTATGACAAGCTGAATAATAAGTGGATCGCTCTTGGGAAATTGCC chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ---------------S---------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 TGTACTGTCTACA---AAAGAAGGCTGGGACATGGGTTTCCGAGCGTGTG chr7D_1_TraesCS7D01G005100 TGTACTGTCTACA---AAAGAAGGCTGGGACATGGGTTTCCGAGCGTGTG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 ------------------------------------TTGCCGAACCTGTG chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 TGAACGGTCTGTGTCCATGAATGGATGGGGCCTTGCTTTCCGAGCCTGTG chr4A_821 TGTACAGTCTAAGGACAAAGATGGCAGGGACATGGGTTTCCGAGCGTGTG chr7D_822 TGTACTGTCTAAGGACAAAGATGGCTGGGACATGGGATTCCGAGCATGTG chr7D_822 TGTACAGTCTAAGC---AAGGGGGCAGGGACATGGGTTTCCGAGCATGTG chr7A_822 TCTACAGTCTAAGAAGAA---GGGCTCCGACATCCGTTTCCGAGCGTGTG chr7A_822 TGTACAGTCTAAGGAGAAAGATGGCTGGGACATGGGTTTCCGAGCGTGTG chr4A_822 TGTACAGTCTAAGATCGAAGATGGCTGGGACATAGGTTTCCAAGCGTGTG chr4A_822 TGTAGAGTCTAAGGACAA---GGGCTGCGACATGGGTTTCCAAGCGTGTG chr4A_822 TGTACAGTCTAAGGACAAAGATGGCTGGGACATGGGTTTCCGAGCATGCG chr4A_822 TGTACGGTCTAAGTACAAAGATGGCTGGGACATGGGTTTCCGAGAATGTG chr4A_822 TGTACAGTCTAAGAACAAAGATGGCTTGGACATGGGTTTCCAAGCGTGTG chr4D_824 TGAACGGTCTGTGTCGATGAATGGCTGGGGCCTTGCTTTCCGAGCCTGTG chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -----------SS--------S---------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 GTGACCGGCTGATTGTTATTGGGCGTCCAAACAATTCTAGTGACGA---- chr7D_1_TraesCS7D01G005100 GTGACCGGCTGATTGTTATTGGGCGTCCAAACAATTCTAGTGACGA---- chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 GCGACCGTGGGCGTGTGACTGGGAGCGAACCGAACCC------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 GTGACCGGCTGATTGTCATTGGAGGCCCAAGGACTTCTATTGGTGGCATC chr4A_821 GTGACTGGCTGATTGTTATTGGACCTCCAAACAATTCTACTGATGA---- chr7D_822 GTGACCGGCTGATTGTAATTGGGTCTCCAAACAATTCTAGTGATGA---- chr7D_822 GTGACCGGCTGACTGTTATTGAGCCTCCAAACAATTCTAGTGATGA---- chr7A_822 GTGACCGGCTGATTGTTATTGGGCCTCCAAACAATTCTACTGATACTGAT chr7A_822 GTGACTGGCTGATTGTTATTGGGCCTCCAAACAATTCTAGTGATGA---- chr4A_822 GTGACAGGCTGATTGTTATTGGGCCTCCAAAGAATTCTAGTGATGA---- chr4A_822 GTGACCGGCTGATTGTTATTGGGCCTCCAATCAATTCTACTGGTGA---- chr4A_822 GTGACAGGGTGATTGTTATTGGGCCTCCAATCAATTCTAGTGATGA---- chr4A_822 GTGACCGGCTGATTGTTATTGGGCCTCCAAACAATTCTACTGATGA---- chr4A_822 GTGACCGGCTGATCGTAATTGGGCCTCCAAAGAATTCTAGTGATGA---- chr4D_824 GTGACCGGCTGATTGTCATCGGAGGCCCAAGGACTTCTATTGGTGGCATC chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------S------ forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 --AAAGGTGGTTGAGCTTCATTCATGGACCCCGGATGGGCAACCACCTCT chr7D_1_TraesCS7D01G005100 --AAAGGTGGTTGAGCTTCATTCATGGACCCCGGATGGGCAACCACCTCT chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 A---------TTGAGCTTAATTCATGGGTTCCCGATGAGCAACCGCCTGT chr4A_821 --AAAGGTGGTTGAGATTCATTCATGGATCCCGAATGAGCAACCGCCTGT chr7D_822 --GAAGGCGGTTGAGCTTCATTCATGGACCCCGGATGAGCAACCGCCTTT chr7D_822 --AAAGGTGGTTGAGCTTCATTCATGGACCCCGGATGGGCATCTGCCTGT chr7A_822 TCAATGGTGGTTGAACTTCATTCATGGACCCCGGATGAGCAACCGCCTGT chr7A_822 --AAAGGAGGTTGAGCTTCATTCATGGATCCCGGATGGGCAACCGCCTGC chr4A_822 --AAAGGTGGTTGAGCTTCATTCATGGACCCCAGATGGGCAACCGCCTGT chr4A_822 --AAAGGTGGTTGAGCTTCATTCATGGACCCCGGATGGGCAACCGCCTGT chr4A_822 --AAAGGTGGTTGAGCTTCATTCATGGACGCCTGATGGGCAACCGCCAGT chr4A_822 --AAAGGTGGTGGAGCTTCATTCATGGATCCCGGATGAGGAACCGCCTGT chr4A_822 --AAAGGTGGTTGAGCTTCATTCATGGACCCCGGATGGGCAACCGCCTGT chr4D_824 A---------TTGAGCTTAATTCCTGGGTTCCCGATGAGCAACCGCCTGT chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs --------------------------------------------S---S- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 GTGGAATTTGGTTGCCACACGGCCATTC-------TTGGGCGGATT---- chr7D_1_TraesCS7D01G005100 GTGGAATTTGGTTGCCACACGGCCATTC-------TTGGGCGGATT---- chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 ---------------------------C-------AGGGGCCGAACTAGC chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 GTGGAATTTGGTTGCCACACGGCAATCC-------GGGAACTTCGTGTA- chr4A_821 GTGGAATTTGATTGCAACACGGCCATACAA-------GGACTACGA---- chr7D_822 GTGGAATTTGTTTGCCACACGCCCATAC-------GGGGGCGACCA---- chr7D_822 TTGGGATTTGGTTGCCACACGGCCATAC-------TTGGG---------- chr7A_822 GTGGAATTTGTTTGCCACACGGCCATTA-------AGGGGCGGATT---- chr7A_822 GTGGAATTTGTTTGCCACACGGCCATAC-------GTTGGCGGCTG---- chr4A_822 GTGGAATTTCGTTGCCACACGGCCATAC-------AGGGGCGGACT---- chr4A_822 GTGGAGTTTGTTTGCCACACGGCCATAC-------GGGGGCTCAAA---- chr4A_822 GTGGAGTTTGTTTGCCACACGGCCATAC-------GGGGGCAGACA---- chr4A_822 ATGCAATTTGGTTGCAACTCAGCAATTTACCAGTGAGGGGCCG-TT---- chr4A_822 GTGGAATTTGTTTGCCACACGGTCAT------------------------ chr4D_824 GTGGAATTTGGTTGCCACACGGCAATCC-------GGGAACTTCGTGTA- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -----------------------------TTTT-AAATGCGCGGTGATGG chr7D_1_TraesCS7D01G005100 -----------------------------TTTT-AAATGCGCGGTGATGG chr7D_1 --------------------------------G-CCTGGGGGGCCGAACG chr4A_1 --------------------------------GCCCTGGGGGGCCGAACG chr3B_1 --------------------------------G-CCCTGGGGGCCGAACG chr5D_1 --------------------------------GCCCTGGGGGGCCGAACG chr5B_1 --------------------------------G-TCGGGGGGGGCGAACG chr7B_1 --------------------------------GCCCTGGGGGGCCGAA-- chr1D_2 GCCGGCTCGCCTCCAAGCCGCTATTTTTCGGTG-CCCTGGGAGGCGAACG chr6B_4 --------------------------------ACCCTGGGGGGCCGAACG chr4B_4 --------------------------------GCCCTGAGGGCCG----- chr2B_4 --------------------------------GTCCTGGGGGGCCGAACG chr1B_4 --------------------------------GCGCTGGGGGGCCGAACC chr2D_4 --------------------------------GCCCTGGGG--ACGAATG chr5D_11 --------------------------------GCCCTGGGGGGCCGAACG chr3D_14 --------------------------------GCCCTGGGGGGCCGAACG chr5D_239 --------------------------------GCACTGAGGGGACGAACG chr5B_314 --------------------------------GCCCTGGGAGGCCCAACG chr4B_812 --------------------------------T-AACTGCGCCGTGATGG chr4A_821 -----------------------------GATT-ATATGCGCCGTGATGG chr7D_822 -----------------------------GATT-TTGTGCACCGTCATGG chr7D_822 ----------------------------------------------ATGG chr7A_822 -----------------------------TATT-AGATGTGCGGTGATGG chr7A_822 -----------------------------GATT-ATGTGCCCCCTGATGG chr4A_822 -----------------------------TGTT-ATGTGCGCCGTGATGG chr4A_822 -----------------------------TATT-GTTTGCGTGGTGATGG chr4A_822 -----------------------------GGTT-CTGTGTGCCGTGATGG chr4A_822 -----------------------------TTTG-TACTGCGCTGTGATGG chr4A_822 -------------------------------------------------- chr4D_824 --------------------------------T-AACTGCGCCGTGATGG chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 GTTGCTGA------------------------------------------ chr7D_1_TraesCS7D01G005100 GTTGCTGAGCAGTCAGTCCACAGAATAAATGCCGAATGCAGTGGGTGTTG chr7D_1 GCTGGAGATG---CTCT--------------------------------- chr4A_1 GCTGGAGATG---CTCT--------------------------------- chr3B_1 GCTGGAGATG---CTCTTA------------------------------- chr5D_1 GCTGGAGATG---CTCT--------------------------------- chr5B_1 GGTGGAGATG---CT----------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 GTTGGAGATG---CTCTTA------------------------------- chr6B_4 GCTGGAGATG---CTCT--------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 GCTGAAGATG---CTCT--------------------------------- chr1B_4 GCTGGAGATG---CTCTTA------------------------------- chr2D_4 GCTGGAGATG---CTCT--------------------------------- chr5D_11 GCCGGAGATG---CTCTTA------------------------------- chr3D_14 GCTGGAGATG---CTCT--------------------------------- chr5D_239 GCTGGAGATA---CTCTTA------------------------------- chr5B_314 GCCGGAGATG---CTCT--------------------------------- chr4B_812 GTTGCTGAG----------------------------------------- chr4A_821 GTTGCTGAA-------TCCACAGAATAAATACTGAATGCAGTGGGTATTT chr7D_822 GTTGCTGAG----------------------------------------- chr7D_822 GTTGCTGAG-------TCCACGGAATAAATACTGAATGCT---------- chr7A_822 GTTGCTGATC---CAATCCACAGAATAAATATTGAATTCAGTTGGTATTT chr7A_822 GTTGCTGAG-------TCGGTCA--------------------------- chr4A_822 CTTGCTGAG-------TCCACGGAATAAATACTGAATGCAGTGGGCATTT chr4A_822 GTTGCTGA------------------------------------------ chr4A_822 GTTGCTGAG----------------------------------------- chr4A_822 GTTGCTGAG-------TCAGT----------------------------- chr4A_822 -------------------------------------------------- chr4D_824 GTTGCTGAG----------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs ----------SSS--S--------------S-S-------------S--S forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 AGGAATGGATGAAGATTTCTGCCCAGTTTCAGACCTTAGTTTGTACTGAG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 ATGAATGAATGAAGATTTCTGACGAGTTCCAGACATTAGTTTATATTAAC chr7D_822 -------------------------------------------------- chr7D_822 -------------GATTTCTGCCCAGTTTCAGACCTTAGTTTGTA----- chr7A_822 ATGAGTGAATGAAGATTTCTGCCCAGTTTCAGACCTTAGT---------- chr7A_822 -------------------------------------------------- chr4A_822 ATGGATGAATAAAGATTTCTGACGAGTTTCAAACCTTAGTTTGTA----- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -S-----S-------------------------------------S-S-S forward_326 -------------------------------------------------- reverse_1948 -----------------------------------------------GAG input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CGGGTATTCAGGATGCAACCCTTGAATCCTGAAACTGCTGGTT------- chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 TGGACAGGACATCTATCTGCTGAGATTTGACGTGTTTTCCTCATTTGCAT chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs S--SS-SSSSSSS-SSSSS-SSS--S-SSSSSSSS-SSSSSSS------- forward_326 -------------------------------------------------- reverse_1948 CGGGTATTCAGGATGCA--------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 ---------------------TCCACATGTCTTTTCACTGTTGATGATTC chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 TTGGATCAACAGCTCGTGTTCTCCACATGGCTTTTCACTGTTGATGCTTC chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs -----------------------------S----------------S--- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TTATTTGGCTCCTGCAACAAAGGCATGTCTTTTCTGTTATCAACAAGGTG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 ATCTTTGGCTT---CAATAAAGGCATGTCTTCTCTATTATCGATAAGGTG chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs S-S-------SSSS---S-------------S---S-----S-S------ forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CATGCCTTT-------------------------------TTTAACCAGT chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 GGTACCTCATATTCAGTTATTCACTGCTAGTCTATTTCTCTTTATCCACT chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 ------TTT-------------------------------TTTAACCAGT chr7D_1869 ------TTT-------------------------------TTTAACCAGT chrUn_1869 ------TTT-------------------------------TTTAACCAGT chrUn_1869 ------TTT-------------------------------TTTAACCAGT chr7A_1877 ---------------------------------------------CCAGT SNPs SS-S---------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TTCCTCCATGATATGCTTTTATTCAGCTGTGTGGTTATCAGAA-TCTGAA chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 TTGCTCTATGATATGCTTTTGTTCAGTTCTGTTATTGATATGCTTCTGAA chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 TTCCTCCATGATATGCTTTTACTCAGCTGTGTGGTTATCAGAA-TCTGAA chr7D_1869 TTCCTCCATGATATGCTTTTACTCAGCTGTGTGGTTATCAGAA-TCTGAA chrUn_1869 TTCCTCCATGATATGCTTTTACTCAGCTGTGTGGTTATCAGAA-TCTGAA chrUn_1869 TTCCTCCATGATATGCTTTTACTCAGCTGTGTGGTTATCAGAA-TCTGAA chr7A_1877 TTGCTCCACGATATGCTTTTGTTCAGTTCTGTTATATCAC--CTTCTGAA SNPs -------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TGGTAATGATATGCTGTTTTGCTGGTTGTGAATATTTCCTGTTTATAATG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 TGGTATTGATATGCTGTTTTGCTGGTTGTGAATAATTGCTATTTATGATG chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 TGGTAACGATATGCTGTTTTGCTAGTTGGGAATATTTGCTGTTTATAATG chr7D_1869 TGGTAACGATATGCTGTTTTGCTAGTTGGGAATATTTGCTGTTTATAATG chrUn_1869 TGGTAACGATATGCTGTTTTGCTAGTTGGGAATATTTGCTGTTTATAATG chrUn_1869 TGGTAACGATATGCTGTTTTGCTAGTTGGGAATATTTGCTGTTTATAATG chr7A_1877 TTGTAACGATATGCCGTTTTGCTGGTTGTGAAGTTTTGCTGTTAATGATG SNPs -------------------------------------S------------ forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TGCTACGAGATTAACCTTGATACCTTCAATAAATTATTTTAGTTTTAGTT chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 TGCAACTGGATTAACCTTGGTACATTGT----ATTATTTTAGTTTTTGTT chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 TGCTACGGGACTAACCTTGATACCTTCTATACATTATTTTAGTTTTAGTT chr7D_1869 TGCTACGGGACTAACCTTGATACCTTCTATACATTATTTTAGTTTTAGTT chrUn_1869 TGCTACGGGACTAACCTTGATACCTTCTATACATTATTTTAGTTTTAGTT chrUn_1869 TGCTACGGGACTAACCTTGATACCTTCTATACATTATTTTAGTTTTAGTT chr7A_1877 TGCTAAGGGATTAACCTTCATACCTCGTA-----TAATTTAGTCTTAGTT SNPs -------S-------------------S---S------------------ forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 GCGAACTTGTTCTGGTCAATTTGTGGGGTTG--------TTTGACTGACC chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 GTGAACTTGTGATTGTCGATTTGTTGGTTT--------CTTTGACTGACG chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 GTGAACTTGTC-------------TGGTTA--------ATTTGACTGACG chr7D_1869 GTGAACTTGTC-------------TGGTTA--------ATTTGACTGACG chrUn_1869 GTGAACTTGTC-------------TGGTTA--------ATTTGACTGACG chrUn_1869 GTGAACTTGTC-------------TGGTTA--------ATTTGACTGACG chr7A_1877 CTGAACTTGTGATGGTCAAGTTGTGTGTTTGTTTGACACTTTCACTTACA SNPs -S--------SS---------------S---------------------S forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TTGTGTTTCTGTTCATATTTCCATGCAG---------GAATGTCTGACTG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 TTGTGTTTCTGTTCATATTTCCATGCAGTGGCTGCTAGAACGTCCACCCG chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 TTGTGTTTCTGTTCATATCTCCATGCAGTGGCTGCTGGAACGTCTACATG chr7D_1869 TTGTGTTTCTGTTCATATCTCCATGCAGTGGCTGCTGGAACGTCTACATG chrUn_1869 TTGTGTTTCTGTTCATATCTCCATGCAGTGGCTGCTGGAACGTCTACATG chrUn_1869 TTGTGTTTCTGTTCATATCTCCATGCAGTGGCTGCTGGAACGTCTACATG chr7A_1877 TTGTGTTTCTGTTCATATTT-CAAGCAGTGGCTGCAGGAAAGTCTGCCTG SNPs ----------------------------------------S-----S--- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 GGCACTTCATTCTCAAGTCTAAATGTCCTGTG----AGCACTGATGCTAT chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 GGCC--TCATTCTCAAGTCTAAATGTCCTATG----AGGACCAAGGCTAC chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------TCCTATG----AGCACTGATGGT-- chr7D_1869 -------------------------TCCTATG----AGCACTGATGGT-- chrUn_1869 -------------------------TCCTATG----AGCACTGATGGT-- chrUn_1869 -------------------------TCCTATG----AGCACTGATGGT-- chr7A_1877 GGCC--TTATTCTCAAGTCTAAATGTCGTCTGTCTCAGCACTGATGCTAC SNPs ---SSS-----------------------S-------------------S forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 GAAAAGAGAAGACATGAATGAGTTTGGAGGAAGTGC---------TAGTT chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 AAAAAGAGAAGACATGAATGAGTTTGGAGAAAGTGCCAGTTTG----GTT chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 ----AGAGAAGACATGAATGAGTTTTGAGGAAGTGCCAGTTTTTTTACTT chr7D_1869 ----AGAGAAGACATGAATGAGTTTTGAGGAAGAGCCAGTTTTTTTACTT chrUn_1869 ----AGAGAAGACATGAATGAGTTTTGAGGAAGTGCCAGTTTTTTTACTT chrUn_1869 ----AGAGAAGACATGAATGAGTTTTGAGGAAGTGCCAGTTTTTTTACTT chr7A_1877 AAAAGGAGGAGACATGAATGAGTTTGGAGGAAGTGCCAATTTG----GAT SNPs S------------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TTTTTAGTTGCTAGCATGCTGTGATTTATTA-TTTCAATTTGGATTCCAG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 TTTTCAGTTGCTAGCTAGCCGTGATTTCTTA-TTGCAATTTGGATTCCAG chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 TTTTTAGTTACTAGCACGCTGTGATTTCTTA-TT-CAATTTGGATTCCAG chr7D_1869 TTTTTAGTTACTAGCACGCTGTGATTTCTTA-TT-CAATTTGGATTCCAG chrUn_1869 TTTTTAGTTACTAGCACGCTGTGATTTCTTA-TT-CAATTTGGATTCCAG chrUn_1869 TTTTTAGTTACTAGCACGCTGTGATTTCTTA-TT-CAATTTGGATTCCAG chr7A_1877 TTTCGAGTTGCTAC----CTGTGATTTCTTGTTT-TAATTTGGACTCCAG SNPs ----------------S----------S------S--------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 AAATGTC----------ACTATGTCCCAACTTTATCTGTACCGTACCGTG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 AAATGTTACTATCAGTTACTATGTACCAACTTTATCTGTACCGTACCGTG chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 AAATGTTACTATCAGTTATTATGTCCCAACATTATCTGTACCATGCCGTG chr7D_1869 AAATGTTACTATCAGTTATTATGGCCCAACATTATCTGTACCATGCCGTG chrUn_1869 AAATGTTACTATCAGTTATTATGTCCCAACATTATCTGTACCATGCCGTG chrUn_1869 AAATGTTACTATCAGTTATTATGTCCCAACATTATCTGTACCATGCCGTG chr7A_1877 ATATGTTACTATCAGTTACGGTGTCCCAACTTTATCTGTACCGTAGCATG SNPs ------S------------------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TTACTATCTGTCATTTTTGAACATCAAGTTCAGTCTCTAGCTTGCCTTCT chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 TTACTATCAGTTATTTTCGAACATCAAATTCAGTCTCTAGCTTGCCCTCT chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 TTACTATCAGTTAATTTCGAACATCAAATTCAGCGTGCAGCTTGCCCTCA chr7D_1869 TTACTATCAGTTAATTTCGAACATCAAATTCAGCGTGCAGCTTGCCCTCA chrUn_1869 TTACTATCAGTTAATTTCGAACATCAAATTCAGCGTGCAGCTTGCCCTCA chrUn_1869 TTACTATCAGTTAATTTCGAACATCAAATTCAGCGTGCAGCTTGCCCTCA chr7A_1877 TTCCTATCAGTTATTTTTGAACATCAAGTTCA------------------ SNPs --------S--S----------------------------------S--- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TTTCTGTTGAAGATTTTTCAATCTCTGAATAAGGAAAACAAATTGGAAAG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 TTTCCATTCATGACTTTTTAAACTCTGAATAAAGAAAACAATTCGGAAAG chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 TTTCCATTCATTATTTTTCAAACTCTGACTAAAGAAAATAATTTGGAAAG chr7D_1869 TTTCCATTCATTATTTTTCAAACTCTGACTAAAGAAAATAATTTGGAAAG chrUn_1869 TTTCCATTCATTATTTTTCAAACTCTGACTAAAGAAAATAATTTGGAAAG chrUn_1869 TTTCCATTCATTATTTTTCAAACTCTGACTAAAGAAAATAATTTGGAAAG chr7A_1877 TTTCTGTTCAAGATTTTTCAAACACTGAATAAAGAAAACAATTTGGAAGG SNPs --------S------------S----------S--------S-------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 ATGCACATGTGTATCATTTCCTATTGACTCAGATGAATATGATCGAGTAC chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 AAGCACATGTGTATCATTGGCTATTGACTCAGATGAATATGATCGAGTAC chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 AAGCACATGTCTATCATTGCATATTGACTCCAATGAATATGACCGAGTAT chr7D_1869 AAGCACATGTCTATCATTGCATATTGACTCCAATGAATATGACCGAGTAT chrUn_1869 AAGCACATGTCTATCATTGCATATTGACTCCAATGAATATGACCGAGTAT chrUn_1869 AAGCACATGTCTATCATTGCATATTGACTCCAATGAATATGACCGAGTAT chr7A_1877 TAG--CACATCTGTCATTCCGTATAGACTCGGATGAATGTGATCAAATAT SNPs -S----------------S------------------------------- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CTTCTCGAGATGGTTGCGTAGATTTCATCTTACACAGACCATTGTGATGT chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 --------AACGGCTGGAGATGCT-------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 CTTCTCGAGATGGTTGCGTAGATTTCATCTTACACGCACAGTTGCAATGT chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 CTTCTTGGAACGGTAGCGTAGATTTCATCTTACA---------------- chr7D_1869 CTTCTTGGAACGGTAGCGTAGATTTCATCTTACA---------------- chrUn_1869 CTTCTTGGAACGGTAGCGTAGATTTCATCTTACA---------------- chrUn_1869 CTTCTTGGAACGGTAGCGTAGATTTCATCTTACA---------------- chr7A_1877 CTTCTCGAAACGGCTGCATGCATTTCATCTTACACGGACCTTTGCGATGC SNPs -----------------------------------S----S---S----- forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 GTCACAAGATATGGCAAGGTTCAGATGTATTTCTTTCCCGATGCATTTGC chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 GTCACAAGA----------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 GTCACAAGA----------------------------------------- SNPs ---------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 TTTGCATTTGGTTCCTACAAGAGAGTTTGGATTAGGTAATTAGCTGTTTC chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 -------------------------------------------------- chr7D_1_TraesCS7D01G005100 CTCAGTATTTGTCCGACGTCTAAGAAGATCTCAGACAAGACCTGCCTCTG chr7D_1 -------------------------------------------------- chr4A_1 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5B_1 -------------------------------------------------- chr7B_1 -------------------------------------------------- chr1D_2 -------------------------------------------------- chr6B_4 -------------------------------------------------- chr4B_4 -------------------------------------------------- chr2B_4 -------------------------------------------------- chr1B_4 -------------------------------------------------- chr2D_4 -------------------------------------------------- chr5D_11 -------------------------------------------------- chr3D_14 -------------------------------------------------- chr5D_239 -------------------------------------------------- chr5B_314 -------------------------------------------------- chr4B_812 -------------------------------------------------- chr4A_821 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7D_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr7A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4A_822 -------------------------------------------------- chr4D_824 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chr7D_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chrUn_1869 -------------------------------------------------- chr7A_1877 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_326 -------------------------------------------------- reverse_1948 -------------------------------------------------- input_sequence_72909 --------- chr7D_1_TraesCS7D01G005100 CCTGTAACC chr7D_1 --------- chr4A_1 --------- chr3B_1 --------- chr5D_1 --------- chr5B_1 --------- chr7B_1 --------- chr1D_2 --------- chr6B_4 --------- chr4B_4 --------- chr2B_4 --------- chr1B_4 --------- chr2D_4 --------- chr5D_11 --------- chr3D_14 --------- chr5D_239 --------- chr5B_314 --------- chr4B_812 --------- chr4A_821 --------- chr7D_822 --------- chr7D_822 --------- chr7A_822 --------- chr7A_822 --------- chr4A_822 --------- chr4A_822 --------- chr4A_822 --------- chr4A_822 --------- chr4A_822 --------- chr4D_824 --------- chr7D_1869 --------- chr7D_1869 --------- chrUn_1869 --------- chrUn_1869 --------- chr7A_1877 --------- SNPs SSSSSSSSS forward_326 --------- reverse_1948 ---------