CLUSTAL X (1.81) multiple sequence alignment input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr5D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr5D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr5A_1 GTACGAGAAGAAGGTCGCGGAGAAGGTGTGGAGATGCAGGAGGTCTGGGG chr1D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr1D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr2D_1 GTACGAGAAGGAGGTGCCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr2D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr2D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr3D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCGGGAGGTCTGGGG chr3D_1 GTATGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr6D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr6D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTAGGG chr6D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr4D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr7D_1 GTACGAGAAGGAGGTGGCGGAGAAGGTGTGGAGAGGCAGGAGGTCTGGGG chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AATC---------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 CGGTGTCACCTGGCTTTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr5D_1 CGGTGTCACCTGGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr5D_1 CGGTGTCACCTGGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCAGAGT chr5A_1 CGGTGTCACCTGGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr1D_1 CGGTGTCACCTGGCTGTGGTGGAGGTGTTTATGTGAGAAGGAGCCGGAGT chr1D_1 CGGTGTCACCTGGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr2D_1 CGGTGTCACCTGGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr2D_1 CGGTCTCACCTGGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr2D_1 CGGTGTCACCTGGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr3D_1 CGGTGTCACCTGGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr3D_1 CGGTGTCACCTGGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr6D_1 CGGTGTCACCTGGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr6D_1 CGGTGTCAA-TGGCTGTGATGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr6D_1 CGGTGTCACCTCGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr4D_1 CGGTGTCACCTGACTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCGGAGT chr7D_1 CGGTGTCACCTGGCTGTGGTGGAGGTGTTTATGCGAGAAGGAGCCAGAGT chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs ---------------S---------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 GGAAGGAGAGGTCACAATTGGAAAGAATCGC------AAAAA--AAA-AT chr5D_1 GGAAGGAGAGGTCACAATTGGAAAGAATCGC------AAAAA--AAAAAT chr5D_1 GGAAGGAGAGGTCACAATTGGAAAGAATCGC------AAAAA--AAAT-T chr5A_1 GGAAGGAGAGGTCATAATTGGAAAGAATCGC------AAAAA------AT chr1D_1 GGAAGGAGAGGTCACAATTGGAAAGAATCGC------AAAAA--AAA--T chr1D_1 GGAAGGAGAGGTCACAATTGGAAAGAATCGC------AAAAA--AAAT-C chr2D_1 GAAAGGAGAGGTCACAATTGGAAAGAATCGC------AAAAA--AAAA-T chr2D_1 GGAAGGAGAGGTCACAGTTGGAAAGGATCGC------AAAAA--AAAT-T chr2D_1 GGAAGGAGAGGTCACAATTGGAAAGAATCGC------AAAAA--AAAT-C chr3D_1 GGAAGGAGAGGTCACAATTGGAAAGAATCGC------AAAAA--AA-T-C chr3D_1 GGAAGGAGAGGTCACAATTGGAAAGAATCGC-----AAAAAA--AAAT-C chr6D_1 GGAAGGAGAGGTCACAATTGGAAAGAATCGC----AAAAAAA--AAAT-C chr6D_1 GGAAGGAGAGGTCACAATTGGAAAGAATCGC----AAAAAAA--A--T-C chr6D_1 GGAAGGAGAGGTCACAATTGGAAAGAATCGC----AAAAAAAAAA--T-C chr4D_1 GGAAGGAGATGTCACAATTGGAAAGAATCGCAAAAAAAAA---AA--T-C chr7D_1 GGAAGGAGAGGTCACAATTGGAAAGAATCGC----AAAAA---AA--T-C chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 CATAACCCGGAGATCTCAGTTCAAAAA--AATGCTAATATATATCGATGG chr5D_1 CATAACCCGGAGATCTCAGTTCAAAAA--AATGCTAATAT----CAATGG chr5D_1 CATAACCCGGAGATCTCCGTTCAAAAA--AATGCTAATAT----CGATGG chr5A_1 CATAACCCAGAGATCTCAGTTCAAAAA--AATGCTAATAT----CGATGG chr1D_1 CATAACCCGGAGATCTCAGTTCAAAAA--AATGCTAATAT----TGATGG chr1D_1 -ATAACCCCGAGATCTCAGTTCAAAAA--AATGCTAATAT----TGATGG chr2D_1 CATAACCAGGAGATCTCAGTTCAAAAA--AATGCTAATAT----CGATGG chr2D_1 -ATAACCCGGAGATCTCAGTTC-AAAA--AATGCTAATAT----CGATGG chr2D_1 -ATAACCCGGAGATCTCAGTTC-AAAAAAAATGCTAATAT----CGATGG chr3D_1 -ATAACCCGAAGATCTCAGTTC-AAAAAA-ATGCTAATAT----CGATGG chr3D_1 -ATAACCCGGAGATCTCAGTTC-AAAAAA-ATGCTAATAT----CGATGG chr6D_1 -ATAACCCGGAGATCTCAGTTC-AAAAAA-ATGCTAATAT----CGATGG chr6D_1 -ATAACCCGGAGATCTCAGTTC-AAAAAA-ATGCTAATAT----CGATGG chr6D_1 -ATAACCCGGAGATCTCAGTTC-AAAAAA-ATGCTAATAT----CGATGG chr4D_1 -ATAACCCGGAGATCTCAGTTC-AAAAAA--TGCTAATAT----CGATGG chr7D_1 -ATAACCCGGAGATCTCAGTTC-AAAAAA-ATGCTAATAT----CGATGG chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs ----------------------------------------SSSS------ forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 AGGGGTGATTTTCTTCAATAGGTGGAAAACATAGAAAATATTGGTTGTTA chr5D_1 AGGGGTGATTTCCTTCAATAGGTGGAAAACATAGGAAATATTGGTTGTTA chr5D_1 AGGGGTGGTTTCCTTCAATAGGTGGAAAACATAGGAAATATTGGTTGTTA chr5A_1 -GGGGTGATTTCCTTCAATAGGTGGAAAGCATAGGAAATATTTGTTGTTA chr1D_1 AGGGGTGATTTCCTTCAATAGGTGGAAAACATAGGAAATATTGGTTGTTA chr1D_1 AGGGGTGATTTCCTTCAATAGGTGGAAAACATAGGAAATATTGGTTGTTA chr2D_1 AGGGGTGATTTCCTTCAATAGGTGGAAAACATAGGAAATATTGGTTGTTA chr2D_1 AGGGGTGATTTCCTTCAATAGGTGGAAAACATAGGAAATATTGGTTGTTA chr2D_1 AGGGGTGATTTCCTTCAATAGGTGAAAAACATAGGAAATATTGGTTGTTA chr3D_1 AGGGGTGATTTCCTTCAATAGGTGGAAAACATAGGAAATATTGGTTGTTA chr3D_1 AGGGGTGATTTCCTTCAATAGGTGGAAAACATAGGAAATATTGGTTGTTA chr6D_1 AGGGGTGATTTCCTTCAATAGGTGGAAAACATAGGAAATATTGGTTGTTA chr6D_1 AGGGGTGATTTCCTTCAATAGGTGGAAAACATAGGAAATATTGGTTGTTA chr6D_1 AGGGGTGATTTCCTTCAATAGGTGGAAAACATAGAAAATATTGGTTGTTA chr4D_1 AGGGATGATTTCCTTGAATAGGTGGAAAACAGAGGAAATATTGGTTGTTA chr7D_1 AGGGGTGATTTCCTTCAATAGGTGGAAAACATAGGAAATATTGGTTGTTA chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -----------S-------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAGCTGATTTCT chr5D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAATTGATTTCT chr5D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAACTGATTTCT chr5A_1 TAAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAACTGATTTCT chr1D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTGGGATTTTTGAACTGATTTCT chr1D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAACTGATTTCT chr2D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAACTGATTTCT chr2D_1 TCAAGGAAAGATAAAAATTTAGGAAAGTTAGGATTTTTGAACTGATTTCT chr2D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAACCGATTTCT chr3D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAACTGATTTCT chr3D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAACTGATTTCT chr6D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAACAGATTTCT chr6D_1 TCAAGGAAAGGTAAAAAATTAGGAAAGTTAGGATTTTTGAACTGATTTCT chr6D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAACTGATTTCT chr4D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAACTGATTTCT chr7D_1 TCAAGGAAAGGTAAAAATTTAGGAAAGTTAGGATTTTTGAACTGATTTCT chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs ----------------------------------------S--------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 ATGCAAATGGGGTTTTATTGTTTGGTAACGTGATATCAGTACCTGCCCGT chr5D_1 ATGCAAATGGGGTTTTATTGTTTGGTAACGTGATATCAGTACCTGCCCGT chr5D_1 ATGCAAATGGGGTTTTATTGTTTGGTAACGTGATATCAGTACCTGCCCGT chr5A_1 ATGCAAATGGGATTTTATTGGTTGGTAACGTGATATCAGTACCTACTCGT chr1D_1 ATGCAAATGGGGTTTTATTGTTTGGTAACGTGATATCAGTACCTGCCCGT chr1D_1 ATGCAAATGGGGTTTTATTGTTTGGTAACATGATATCAGTACCTGCCCGT chr2D_1 ATGCAAATGGGGTTTTATTGTTTGGTAACGTGATATCAGTACCTGCCCGT chr2D_1 ATGCAAATGGGGTTTTATTGTTTGGTAACGTGATATCAGTACCTGCCCGT chr2D_1 ATGCAAATGGGGTTTTATTGTTTGGTAACGTGATATTAGTACCTGCTCGT chr3D_1 ATGCAAATAGGGTTTTATTGTTTGGTAACGTGATATCAGTACCTGCCCGT chr3D_1 ATGCAAATGGGGTTTTATTGTTTGGTAACATGATATCAGTACCTGCCCGT chr6D_1 ATGCAAATGGGGTTTTATTGTTTGGTAACGTGATATCGGTACCTGCCCGT chr6D_1 ATGCAAATGAGGTTTTATTGTTTGGTAACGTGATATCAGTATCTGCCCGT chr6D_1 ATGCAAATAGGGTTTTATTGTTTGGTAACGTGATATCAGTACCTGCCTGT chr4D_1 ATGCAAATGGGGTTTTATTGTTTGGTAACGTGATATCAGTACCTGCCCGT chr7D_1 ATGCAAATGGGGTTTTATTGTTTGGTAACGTGATATCAGTACCTGCCCGT chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 TTGTGACGTGTCTGATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr5D_1 TTGTGACGTGTCTGATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr5D_1 TTGTGACGTGTCTGGTTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr5A_1 TTGTGACGTGTCTGATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr1D_1 TTGTGACGTGTCTGATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr1D_1 TTGTGACGTGTCTGATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr2D_1 TTGTGACGTGTCTGATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr2D_1 TTGTGACGTGTCTGATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr2D_1 TTGTGACGTGTCTGATTAAGAAAGTTTGCAAATGTTAAGAAACTATTCAT chr3D_1 TTGTGACGTGTCTGATTAGGAAAGTTCGCAAATGTTAAGAAACTATTTAT chr3D_1 TTGTGACGTGTCTGATTAAGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr6D_1 TTGTGACGTGTCTGATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr6D_1 TTGTGACGTGTCTGATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr6D_1 TTGTGACGTGTCTTATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr4D_1 TTGTGACGTGTCTGATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr7D_1 TTGTGACGTGTCTGATTAGGAAAGTTTGCAAATGTTAAGAAACTATTTAT chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 TGGGAGAAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAACAA chr5D_1 TGGGAGGAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAACAA chr5D_1 TGGGAGGAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAACAA chr5A_1 TGGGAGGAAAGTTGTGACATGTCTGTTATTTGTTTCC-----CAAAACAA chr1D_1 TGGGAGGAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAACAA chr1D_1 TGGGAGAAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAACAA chr2D_1 TGGGAGGAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAACAA chr2D_1 TGGGAGGAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAAAAA chr2D_1 TGGGAGGAAAGTTGTGGCGTGTCTGTTATTTGTTTCC-----TAAAATAA chr3D_1 TGGGAGGAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAACAA chr3D_1 TGGGAGGAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAACAA chr6D_1 TGGGAGGAAAGTTGTGACGTGTCTGTTATTTGTTTCCTAAAATAAAACAA chr6D_1 TGGGAGGAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAACAA chr6D_1 TGGGAGGAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAACAA chr4D_1 TGGGAGGAAAGTTATGACGTGTCAGTTCTTTG-TTCC-----TAAAACAA chr7D_1 TGGGAGGAAAGTTGTGACGTGTCTGTTATTTGTTTCC-----TAAAACAA chr5A_411 ---------------------TCTGTTATTTGTTTTC-----CAAAACAA chr1D_411 ---------------------TCTTTTATTTGTTTCC-----TAAGACAA chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr5D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr5D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr5A_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr1D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr1D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr2D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr2D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr2D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr3D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr3D_1 ATTTCACTAATAAGAGAAATCGGTTGATTTAGATAAGTTAGGAAAGTTAG chr6D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr6D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr6D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr4D_1 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr7D_1 AATTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr5A_411 ATTTCACTAATAAGAGAAATCGATTGATTTAGATAAGTTAGGAAAGTTAG chr1D_411 ATTGAACCAATAAAAGGAATATATTGATTTAGATAAGTTAGGAAAGCTAG chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 ATTAAAATGTATTATTTGTTTCTTGAAA---------------TCTAAGA chr5D_1 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTAAGA chr5D_1 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTAAGA chr5A_1 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTG---------- chr1D_1 ATTAAAATGTATTATTTGTTTCGTGAAAATCTGTTATTTGTTTCCTAAGA chr1D_1 ATTAAAATGTATTATTTGTTTTCTGAAAATCTGTTATTTGTTTCCTAAGA chr2D_1 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTAAGA chr2D_1 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTAAGA chr2D_1 ATTAAAATGTATTATTTGTTTC-TGAAAATCTGTTATTTGTTTTCTAAGA chr3D_1 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTAAGA chr3D_1 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTAAGA chr6D_1 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTAAGA chr6D_1 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTAAGA chr6D_1 ATTAAAATGAATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTAAGA chr4D_1 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTAAGA chr7D_1 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTATTTCCTAAGA chr5A_411 ATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTTCTAAGA chr1D_411 ATTAAAATGTATTATTTTTTTCCTGAAAATCTGGTATTTGTTTCCTAAGA chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs ----------------------S--------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 CAAATTGAATCAA------------------------------------- chr5D_1 CAAATTGAACCAA------------------------------------- chr5D_1 CAAATTGAACCAA------------------------------------- chr5A_1 -------AACCAATAAAAGGAATCGATTGATTA----------------- chr1D_1 CAAATTGAACCAATAAAAGGAATCAATTGATTTGCATAATTTAAGGAAGT chr1D_1 CAAATTGAACCAA------------------------------------- chr2D_1 CAAATTGAACCAA------------------------------------- chr2D_1 CAAATTGAACCAA------------------------------------- chr2D_1 CAAATTGAATCAA------------------------------------- chr3D_1 CAAATTGAACCAA------------------------------------- chr3D_1 CAAATTGAACCAA------------------------------------- chr6D_1 CAAATTGAACCAATAAAAGGACTCGATTGATTTGCATAATTTAAGGAAGT chr6D_1 CAAATTGAACCAA------------------------------------- chr6D_1 CAAATTGAACCAA------------------------------------- chr4D_1 CAAATTGAACCAA------------------------------------- chr7D_1 CAAATTGCACCAA------------------------------------- chr5A_411 CAAATTGAACCAA------------------------------------- chr1D_411 CAAATTGAACCAA------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 TATATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTA chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 TAGATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTCCTA chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr5D_1 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr5D_1 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr5A_1 ------------------------------------GCATAATTTAAGGA chr1D_1 AGACAAATTGAATCAATAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr1D_1 ----------------TAAAAGGAATCAATTGATTTGCATAATTTAAGGA chr2D_1 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr2D_1 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr2D_1 ----------------CAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr3D_1 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr3D_1 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr6D_1 AGACAAATTGAACCAATAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr6D_1 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr6D_1 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGAA chr4D_1 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr7D_1 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGAA chr5A_411 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr1D_411 ----------------TAAAAGGAATCGATTGATTTGCATAATTTAAGGA chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 AGTTAGATTAAAATGTATTATTTGTTT----------------------C chr5D_1 AGTTAGATTAAAATGTATTATTTGTTTTCTGAAAATCCGTTATTTGTTTC chr5D_1 AGTTAGAT------------------------------------------ chr5A_1 AGTTAGATTAAAATGTATTATTTGTTT----------------------- chr1D_1 AGTTAGAT------------------------------------------ chr1D_1 AGTTAGATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTC chr2D_1 AGTTAGATTCAAATGTATTATTTGTTTCCTGAAAATTTGTTATTTGTTTC chr2D_1 AGTTAGATTAAAATGTATTATTTGTTTCCTGAAAATATTTTATTTGTTTC chr2D_1 AGTTAGATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTC chr3D_1 AGTTAGATTAAAATGTATTATTTGTTTCTTGAAAATCTGTTATTTGTTTT chr3D_1 AGTTAGAT------------------------------------------ chr6D_1 AGTTAGAT------------------------------------------ chr6D_1 AGTTAGATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTC chr6D_1 AGTTAGATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTT chr4D_1 AGTTAGATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTC chr7D_1 AGTTAGAT------------------------------------------ chr5A_411 AGTTAGATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTC chr1D_411 AGTTAGATTAAAATGTATTATTTGTTTCCTGAAAATCTGTTATTTGTTTC chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 CTGAGACAAATTGAACCAATAAAAGGAATCGATTGATTTGCATAATTTAA chr5D_1 CTAAGACAAATTGAACCAATAAAAGGAATCGATTGATTTGCATAATTTAA chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 CTAAGACAAATTGAACCAATAAAAAGAATCGATTGATTTGCATAATTTAA chr2D_1 CTAAGACAAATTGAACCAATAAAAGGAATCGATTGATTTGCATAATTCAA chr2D_1 CTAAGACAAATTGAACCAATAAAAGGAATCGATTGATTTGCATAATTTAA chr2D_1 CTAAGACAAATTGAACCAATAAAAGGAATCGATTGATTTGCATAATTTAA chr3D_1 CTAAGACAAATTGAACCAATAAAAGGAATCGATTGATTTGCATAATTTAA chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 CTAAGACAAATTGAACCAATAAAAGGAATCGACTGATTTGCATAATTTAA chr6D_1 CTAAGACACATTGAACCAATAAAAGGAATCGATTGATTTGCATAATTTAA chr4D_1 TTAGGACAAATTGAACCAATAAAATGAATCGATTGATTTGCATAATTTAA chr7D_1 -------------------------------------------------- chr5A_411 CTATGACAAATTGAACCGATAAAAGGAATAGATTAATTTGCATAATTTAA chr1D_411 CTAAGACAAATTGAACCAATAAAAGGAATGGATTGATTTGCATAATTTAA chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs --S----------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 GAAAGTTAGATCCGTGATTTATTATACGTTAGGAAAGTTCTGGTTGTAAT chr5D_1 GGAAGTTAGATCCATGATTTGTTATACGTTAGGAAAGTTCTGGTTGTAAT chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -----------CCGTGATTTGTTATACGTTAGGAAAGTTCTGGTTGTAAT chr1D_1 GGAAGTTAGATCCGTGATTTGTTATACGTTAGGAAAGTTCTGGTTGTAAT chr2D_1 GGAAGTTAGATCCGTGATTTGTTATACGTTAGGAAAGTTCTGGTTGTAAT chr2D_1 GAAAGTTAGATCCGTGATTTGTTATACGTTAGGAAAGTTCTGGTTGTAAT chr2D_1 GGAAGTTAGATCCGTGATTTGTTATACGTTAGGAAAGTGCTGGTTGTAAT chr3D_1 GGAAGTTAGATCCGTGATTTTTTATACGTTAGGAAAGTTCTGGTTGTAAT chr3D_1 -------------------------------------------------- chr6D_1 -----------CCGTGATTTGTTATACGTTAGGAAAGTTCTGGTTGTAAT chr6D_1 GGAAGTTAGATCCGTGATTTGTTATACGTTAGGAAAGTTCTGGTTGTAAT chr6D_1 GGAAGTTAGATCCGTGATTTGTTATACGTTAGGAAAGTTCTGGTTGTAAT chr4D_1 GAAAGTTAGATCCGTGATTTGTTATACGTTAGGAAAGTTCTGGTTGTAAT chr7D_1 -------------------------------------------------- chr5A_411 GGAAGTTAGATCCGTGATTTGTTATACGTTAGGAAAGTTTTGGTTGTAAT chr1D_411 GAAAGTTATATCCGTGATTTATTATACGTTAGGAAAGTTCTGGTTGTAAT chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 AAAGAGTGAAGAGAAAAATAAACCGATGGATCGGGGTGGGAGGGGGTGGT chr5D_1 AAAGAGTGGAGAGAAAAATAAACCGATGGACCAGGGTGGGAGGGGGTGGT chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 AAAGAGTGGAGAGAAAAATAAACCGATGGACCGGGGTGGGAGGGGGTGGT chr1D_1 AAAGAGTGGAGAGAAAAATAAACCGATGAACCAGGATGGGAGGGGGTGGT chr2D_1 AAAGAGTGAAGAGAAAAATAAACCGATGGACCAGGGTGGGAGGGG-TGGT chr2D_1 AAAGAGTGGAGAGAAAAATAAACCGATGGACCAGGGTGGGAGGGG-TGGT chr2D_1 AAAGAGTGGAGAGAAAAATAAACCGATGGACCAGGGAGGGAGGGGGTGG- chr3D_1 AAAGAGTGGAGAGAAAAATAAACCGATGGACCAGGGTGGGAGGGGGTGGT chr3D_1 -------------------------------------------------- chr6D_1 AAAGAGTGGAGAGAAAAATAAACCGATGGACCAGGGTGGGAGGGGGTGGT chr6D_1 AAAGAGTGGAGAGAAAAATAAACCGATGAACCAGGGTGGGAGGGGGTGGT chr6D_1 AAAGAGTAGAAAGAAAAATAAACCGATGGACCAGGGTGGGAGGGGATGGT chr4D_1 AAAGAGTGGAGAGAAAAATAAACCA------------------------- chr7D_1 -------------------------------------------------- chr5A_411 AAAGAGTGGAGAGAGAAATAAATCGATA---------------------- chr1D_411 AAAGAGTGGAGAGAAAAATAAACCGATG---------------------- chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs ------------------------------S------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 GGGAGGAGAGAC-AA-AAAAACCCAGCTAAAATAAACCGCGGACCAGGGT chr5D_1 GGGAGGAGAGAC-GA-AAAAAACTAGTGAAAATAAACCGCAGACCAGGGT chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 GGGAGGAGAGAC-AA-AAAAACCCAGCGAAAATAAACCGCGGACCAGGGT chr1D_1 GGGAGGAGAGAC-GGTAAAAACCCAGTGAAAATAAA-CGCGGACCAGGGT chr2D_1 GGGAGGAGAGACGAA-AAAAACCCAGCGAAAATAAACCGCGGACCAGGGT chr2D_1 GGGAGGAGAGAC-GA-AAAAAACCAGCGAAAATAAACCGCAGACCAGGGT chr2D_1 --GAGGAGAGAC-AA-AAAAA-CCAGCGAAAATAAACCGCGGA------- chr3D_1 GGGAGCAGAGAC-GA-AAAAA-CCAGCGAAAATAAACCGCGGACCAGGGT chr3D_1 -------------------------------------------------- chr6D_1 GGGAGGAGAGAT-GA-AAAAA-CCAGCGAAAATAAACCGCGGACCAGGGT chr6D_1 GGGAGGAGAGAC-AA-AAAAA-CCAGCGAAAATAAACCACGGACCAGGGT chr6D_1 GGGAGCAGAGAC-GA-AAAAAC--AGCGAAAATAAACTGTGGACCAGGGT chr4D_1 ---------------------------------------TGGACCAGGGT chr7D_1 -------------------------------------------------- chr5A_411 -----------------------------------------GACTAGGGT chr1D_411 -----------------------------------------GACCATGGT chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs ---------------------------S---------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 GGGAGGGGGTGGTGGGAGGAGAGACG-AAAA-A----------------- chr5D_1 GGGAGGGGGTGGTGGGAGGAGAGACG-AAAA-A----------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 GGGAGGGGGTGGTGGGAGGAGAGACG-AAAA-A----------------- chr1D_1 GGGAGGGGGTGGTGGGAGGAGAGACGGAAAA-A----------------- chr2D_1 GGGAGGGGGTGGTGGGAGGAGAGACG-AAAA-A----------------- chr2D_1 GGGAGGGGGTGGTGGGTGGAGAGACG-AAAA------------------- chr2D_1 --GAGGGGGTGGTGGGAGGAGAGACG-AAAA-A----------------- chr3D_1 GGGAGGGGGTGGTGGGAGGAGAGACG-AAAATA----------------- chr3D_1 -------------------------------------------------- chr6D_1 GGGAGGGGGTGGTGGGAGGAGAGACG-AAAA-A----------------- chr6D_1 GGGAGGGGGTGATGGGAGGAGAGACG-AAAA-A----------------- chr6D_1 GGGAGGGGGTGGTGGGAGGAGAGACG-AAAA------------------- chr4D_1 GGGAGGGGGTGGTGGGAGGAGAGACG-AAAA-A----------------- chr7D_1 -------------------------------------------------- chr5A_411 GGGAGGGGGTGGTGGGAGGAGAGACG-AAAA-AAAACCAGCAAAAA-AAA chr1D_411 AGGAGGGGGTGGTGGGAGGAAAGACG-AAAA-AA--CCAGCGAAAATAAA chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 ----------------------------------------------A--A chr5D_1 ----------------------------------------------A--C chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 ----------------------------------------------A--A chr1D_1 ----------------------------------------------A--A chr2D_1 ----------------------------------------------A--A chr2D_1 ----------------------------------------------AAAC chr2D_1 ----------------------------------------------A--C chr3D_1 ----------------------------------------------A--A chr3D_1 -------------------------------------------------- chr6D_1 ----------------------------------------------A--A chr6D_1 ----------------------------------------------A--A chr6D_1 ----------------------------------------------A--A chr4D_1 ----------------------------------------------A--A chr7D_1 -------------------------------------------------- chr5A_411 CCGCGGACTAGGATGAGAGGGGGTGGTGGGAGGAGAGACGAAAAACA--A chr1D_411 CCGCGGACCAGGGTGGGAGGGGGTGGTGGGAGGAGAGATG-AAAAAA--A chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 ACCAGCGAAAATAAACCGCGGAGACGATTCACCAACTCGTC-ATTAGGAG chr5D_1 -CCAGCGAAAATAAACCGTGGAGACGATTCACCAACTCGTCCATTAGGAG chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 CCCAGCGAAAATAAGCCGCGGAGACGATTCACCAACTCGTCCATTAGGAG chr1D_1 AACAGCGAAAATAAACCGCGGAGACGATTCACCAACTCATCCCTTAGGAG chr2D_1 -CCAGCGAAAATAAACCACGGGGACGATTCACCAACTCTTTCATTAGGAG chr2D_1 -CCAGCGAAAATAAACCGCAGAGACGATTCACCAACTCGTCCATTAGGAG chr2D_1 -CCAGCGAAAATAAATCGCGGAGACGATTCACCAACTCGTCCATTAGGAG chr3D_1 -CCAGCGAAAATAAACCGCGGAGACGATTCACCAACTCGTCCATTAGGAG chr3D_1 -------------------------------------------------- chr6D_1 CCCAGCGAAAATAAACCGCGGAGATGATTCACCAACTCGTCCATTAGGAG chr6D_1 -CCAGCGAAAATAAACCGCGGAGACGATTCACCAACTCGTCCATTAGGAG chr6D_1 -CCAGCGAAAATAAACCGCGGAGACGATTCACCAACTCGTCCATTAGGAG chr4D_1 -CCAGCGAAAATAAACCGCGGA---------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -CCAACGAAAATAAACCGCGGAGACGATTCACCAACTCATTCATTAGAAG chr1D_411 -CCAACAAAAATAAACCGCGGAGACAATTCACCAACTCGTCCATTAGGAC chr5A_889 -------------------------------------------------- chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 TAGAGAGATTAGTGAATTTGGGCTCCAGCCCACTAAACCCGGCCCACACT chr5D_1 TAGAGA-------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 TAGAGA-------------------------------------------- chr1D_1 TAGAGA-------------------------------------------- chr2D_1 TAGAGA-------------------------------------------- chr2D_1 TAGAGATAT----------------------------------------- chr2D_1 TAGAGA-------------------------------------------- chr3D_1 TAGAGA-------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 TAGAGA-------------------------------------------- chr6D_1 TAGAGATAATAGAAAATT-------------------------------- chr6D_1 TAGAGA-------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 TAGAGA-------------------------------------------- chr1D_411 TAGAGA-------------------------------------------- chr5A_889 ------------------TGGGCTCCAGCCCAATAAAGCCGGCCCACACT chrUn_889 --------------AATTTGGGCTCCAGCCCGATAAACCCGGCCCACACT chr3B_4451 -------------------------------------------------- SNPs ------S-----SS------------------S----------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 ATAGCATGCCCAGGCCCAT-GGGTCTACACTATCCAGTCCACCTT--GCT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ATAGCAAGTCCAGGCCCATTGGGTCCACACTATCCAATCGCACCTTGGCG chrUn_889 ATAGCATGTCCAGGCCCATTGGGTCCACACTATCCAGTCACACCTTGG-- chr3B_4451 -------------------------------------------------- SNPs --------S----------------S-------------SSS-S-----S forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ------------------------------ATGCCGCCGCAGTGGCCGTG chr5D_1_TraesCS5D01G012900 TCCAGCCTTCCACCGAATTCATCGACG-AAATGCCGCCGCAGTGGCCGTG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TCCAGCCTTCCACCTAATTCGTCGACGAAAATGCCGCCGCAGTGGCCGTG chrUn_889 ------CTACCACCGAATTCGTCGACC-AAATGCCGCCGCAGTGGCCGTG chr3B_4451 -------------------------------------------------- SNPs --------------------S----------------------------- forward_1221 -CCAGCCTTCCACCGAATTCA----------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GCTCCAGCCCGCCGCCGCCGCCGCCGCCGCTCGCCGCGCCACCCCCTTCG chr5D_1_TraesCS5D01G012900 GCTCCAGCCCGCCGCCGCCGCCGCCGCCGCTCGCCGCGCCACCCCCTTCG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GCTCCAGCCCGCCGCCGCCG---CCGCCGCTCGCCGCGCCACCCCCTTCG chrUn_889 CCTCCAGCCCGCCGCCGC------CGCCGCTCGCCGCTTCCCCCCCTTCG chr3B_4451 -------------------------------------------------- SNPs --------------------SSS--------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TCTTGCGCGGGAGACGCTGCTCCTCCTCCGTCCCCGCCTCCGTCTGCGCC chr5D_1_TraesCS5D01G012900 TCTTGCGCGGGAGACGCTGCTCCTCCTCCGTCCCCGCCTCCGTCTGCGCC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TCTTGCGCGGGAGGCGCTGCTCCTCCTCGGTCTCCACCTCCTTCTGCGCC chrUn_889 TCTCCCGCAGGAGGCGCTGCTCCTCCTCCGTCCCCGCCCCCGTCTGCGCC chr3B_4451 -------------------------------------------------- SNPs -------------S------------------------------------ forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TCGGCGCCCTCCGGCCACGCCCGCGAGCAGGTAACTAGCCCAGCTCAGCC chr5D_1_TraesCS5D01G012900 TCGGCGCCCTCCGGCCACGCCCGCGAGCAGGTAACTAGCCCAGCTCAGCC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TCGGCGCCCTCCGGCCACGCCCGCGAGCAGGTAACTACTGCTCGGCCACG chrUn_889 TCGGCGCCCTCCGGCCACGCCCGCGAGCAGGTAAGTAACCCAGCTCAGCC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------S------------ forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GCCGGCCTGCCGCCGCCCCTAGCTCCTGACTC---TGTTCGCCATGCAGG chr5D_1_TraesCS5D01G012900 GCCGGCCTGCCGCCGCCCCTAGCTCCTGACTC---TGTTCGCCATGCAGG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CCAGCTCAGCCGCCGCCCCTAGCTCCTGACGCCGGTGTTCGCCATGTAGG chrUn_889 GCCGGCCTGTCGCCGCCGCTAGCTCCTGACGCCGGTGTTCGCCATGCAGG chr3B_4451 -------------------------------------------------- SNPs ------------------------------S------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AGGATGAGCAGTCGCTGGTTGTGGTGGGCGGCGGCGCCGCCGGGGTGTAC chr5D_1_TraesCS5D01G012900 AGGATGAGCAGTCGCTGGTTGTGGTGGGCGGCGGCGCCGCCGGGGTGTAC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AGGATGAGCAGTCGCTGGTTGTGGTGGGCGGCGGCGCCGCCGGGGTGTAC chrUn_889 AGGATGGGCAGTCGCTGGTTGTGGTGGGCGGCGGCGCCGCCGGGGTGTAC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GCGTCGATAAGGGCCAAGACGCTGGCTCCCCACCTCAACGTGGTGGTCAT chr5D_1_TraesCS5D01G012900 GCGTCGATAAGGGCCAAGACGCTGGCTCCCCACCTCAACGTGGTGGTCAT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GCGTCGATAAGGGCCAAGACCCTGGCTCCCCACCTCAACGTGGTGGTCAT chrUn_889 GCGTCGATAAGGGCCAAGGCCCTGGCTCCCCACCTCAACGTGGTGGTCAT chr3B_4451 -------------------------------------------------- SNPs --------------------S----------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AGAGAAAGGGAAGTTCTTGTCCAAGGTACCATGCCAATGCCAATGTCTT- chr5D_1_TraesCS5D01G012900 AGAGAAAGGGAAGTTCTTGTCCAAGGTACCATGCCAATGCCAATGTCTT- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AGAGAAAGGGAAGTTCTTGTCCAAGGTACCAACC--ATGCCAATGCCTTG chrUn_889 CGAGAAAGGCAAGTTCTTGTCCAAGGTACCAACC--ATGCCAATATCTTG chr3B_4451 -------------------------------------------------- SNPs -------------------------------SS-SS-------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ATTTCCATTGGACTGGAAAAAGGCTACCGCTATGGTGTTCCTTAAGTATG chr5D_1_TraesCS5D01G012900 ATTTCCATTGGACTGGAAAAAGGCTACCGCTATGGTGTTCCTTAAGTATG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ATTTCCATTGGACTGAAAAT---CTACTGCTATGGTGTTGCTTAAGTATG chrUn_889 GTTTCCATTGGGTTGAAAA---GCTACTCCTATGCTGTTCCTTCGGCGTG chr3B_4451 -------------------------------------------------- SNPs ---------------S---SSS-----S---------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TATGAATTGTTGGAATGGA-TGGCTGCAGGTCAAGATCTCCGGCGGCGGG chr5D_1_TraesCS5D01G012900 TATGAATTGTTGGAATGGA-TGGCTGCAGGTCAAGATCTCCGGCGGCGGG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ----AATTGCTGGAATGGA-TGGCTGCAGGTCAAGATCTCCGGCGGAGGG chrUn_889 ----AATTGCTCGAATTTACTGGTTGCAGGTCAAGATCTCCGGCGGCGGG chr3B_4451 -------------------------------------------------- SNPs SSSS-----S---------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CGGTGCAATGTCACCAACGGGCACCATCTCGAGCCGTCGGTACGCGCACT chr5D_1_TraesCS5D01G012900 CGGTGCAATGTCACCAACGGGCACCATCTCGAGCCGTCGGTACGCGCACT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CGGTGCAATGTCACCAACGGGCACCAGCTCGACCCATCGGTACGTGTACG chrUn_889 CGGTGCAATGTCACCAACGGGCACCATCTCGAGCCGTCGGTATGCGCACT chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TTGCAGACTCTACTGCATCCATTGCTTTTCATAGTCCA----TATTAGTG chr5D_1_TraesCS5D01G012900 TTGCAGACTCTACTGCATCCATTGCTTTTCATAGTCCA----TATTAGTG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CCCCATACTCTGCTGCGTCGATTGCTTTTCAATTGCAT---------GCT chrUn_889 TTGCAGACTCTGCTGAATCCATTGCTTCTCATAGTCCATATTTATTAGTG chr3B_4451 -------------------------------------------------- SNPs -----------S-------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CTGTGGATTTGTAATTGTCCAAGGTACCATGCCAATGTATGCAGCTGTCT chr5D_1_TraesCS5D01G012900 CTGTGGATTTGTAATTGTCCAAGGTACCATGCCAATGTATGCAGCTGTCT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CTGCTGCATTGCAACTGTGGCCTAGACATATGCTAGGAATGCATGGTGTG chrUn_889 CTGTGGATTTGTAATTGTGGCCTAGTCATCTAGAAAGGGAAGAT------ chr3B_4451 -------------------------------------------------- SNPs ------------------SSSSSSS--SSSSS---S-S-----SSSSSSS forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GTG-------TTCTAGCCATTGTGTTGTGTCAGTCAGTTAGTTTGCTGCC chr5D_1_TraesCS5D01G012900 GTG-------TTCTAGCCATTGTGTTGTGTCAGTCAGTTAGTTTGCTGCC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TCCGTCTGTATTCTAGCCATTGTGCTGTGTCAGTCAGTGAGTTTGCTGTC chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs SSS---------------------S-------------S---------S- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CATTCACTGGCTGAATGAGATGGTGGCAATGTGTGCACCATTTCGATCAG chr5D_1_TraesCS5D01G012900 CATTCACTGGCTGAATGAGATGGTGGCAATGTGTGCACCATTTCGATCAG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CATTCATCGACTGAATTAGATGGTGGCAATGTGTGTACCATTTTGGTTCG chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs ------SS-S------S------------------S-------S-S-SS- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CAACCATAAAAAATGATTTTTACCACTACTATTTTTCAGTCAATTGTTAC chr5D_1_TraesCS5D01G012900 CAACCATAAAAAATGATTTTTACCACTACTATTTTTCAGTCAATTGTTAC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 ------------ATGATTTT------------------------------ chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TTACCGTAAAATTGATTTACGC---------------------TTATTAC chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs SS---S-----S--------SSSSSSSSSSSSSSSSSSSSSSS--S---- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ATGTGCTCTTTAAGCTTGTGATTGTCATTTATCAAATACTATTCAATTCT chr5D_1_TraesCS5D01G012900 ATGTGCTCTTTAAGCTTGTGATTGTCATTTATCAAATACTATTCAATTCT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ATGTGTTTTGTAAGTCTGCCTTTGTCACCAGTCAAATATTATTTGATCCT chrUn_889 --------------CTTTTGATTATCATTGATCAAATATTATTCGATTCT chr3B_4451 -------------------------------------------------- SNPs -----S-S-S-------------------S--------S-----S----- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CAGGGACTGGTGAGAAATTATCCTAGGGGGTACAAAGAACTCCGGGGATC chr5D_1_TraesCS5D01G012900 CAGGGACTGGTGAGAAATTATCCTAGGGGGTACAAAGAACTCCGGGGATC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CAGGGACTTGCGAGAAATTATCCTAGGGGGTACAAAGAACTCCGGGGATC chrUn_889 CAGGGACTGGCGAGAAATTACCCTAGGGGGTACAAAGAACTCCGGGGATC chr3B_4451 -------------------------------------------------- SNPs ----------S--------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CTTCTTTCGCACCCATGGGCCACAGGATACCATGCACTGGTTTTCAGATC chr5D_1_TraesCS5D01G012900 CTTCTTTCGCACCCATGGGCCACAGGATACCATGCACTGGTTTTCAGATC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CTTCTTTCGCACCCATGGGCCACAGGATACCATGCACTGGTTTTCGGATC chrUn_889 GTTCTTTCGTAGTCATGGGCCACAGGACACCATGCACTGGTTTTCAGATC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ATGGTGTGGAGCTTAAGGTAGCTTAGTTCACACCACATTTACTTCAGGAT chr5D_1_TraesCS5D01G012900 ATGGTGTGGAGCTTAAGGTAGCTTAGTTCACACCACATTTACTTCAGGAT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ATGGTGTGGAGCTTAAGGTAATCTTA----------ATTTACATCAGGAT chrUn_889 ACGGTGTGGAGCTTAAGGTAGCTTAGTGCACACCACATTTCCTTCAGGAT chr3B_4451 -------------------------------------------------- SNPs ---------------------------S---------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 C-TTGCTTGTGCATTGACTGAAGCCAGTTTACTTATCT-ATGTCTACTGT chr5D_1_TraesCS5D01G012900 C-TTGCTTGTGCATTGACTGAAGCCAGTTTACTTATCT-ATGTCTACTGT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CTTTGCTTGTGCATTGTCTGAAGCCAGTTTTTCTTATGTGTGTCTACTGT chrUn_889 C-TTGCTTGTGCATTGACTGAAGCCAGTTTACCTATCC-GTGTCTGCTGT chr3B_4451 -------------------------------------------------- SNPs --------------------------------S----S-S---------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TTTGATTGTCATGTTAGACCGAAGAGGACGGTAGAGTCTTTCCTGTCACT chr5D_1_TraesCS5D01G012900 TTTGATTGTCATGTTAGACCGAAGAGGACGGTAGAGTCTTTCCTGTCACT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TTTGATTGCCGTGTCAGACCGAAGACGATGGAAGAGTCTTTCCTGTCACC chrUn_889 TTTGATTGTCATGTCAGACCGAAGAGGACGGTAGAGTCTTTCCTGTCACT chr3B_4451 -------------------------------------------------- SNPs --------------S----------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GACAACTCTGCTTCGGTAGTAGACTGCCTGCTGAATGAGGCGAGAAGACT chr5D_1_TraesCS5D01G012900 GACAACTCTGCTTCGGTAGTAGACTGCCTGCTGAATGAGGCGAGAAGACT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GACAACTCTGCTTCGGTAGTAGACTGCCTGCTGAATGAAGCGAGAAGACT chrUn_889 GACAACTCTGCGTCGGTAGTAGACTGCCTGCTGAACGAGGCGAGAAGACT chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GGGAGGTAGCTA-ATGCTATTTGACTCTGCTGTCCGTTCCGTTATCATCC chr5D_1_TraesCS5D01G012900 GGGAGGTAGCTA-ATGCTATTTGACTCTGCTGTCCGTTCCGTTATCATCC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TGGAGGTAGCTAAATGCTATATGAATCTGCTGTCCATTCA-------TCC chrUn_889 GGGAGGTAGCTA-ATGCTATTTGACTCTGCTGCCCATTCAGTTATCATCC chr3B_4451 -------------------------------------------------- SNPs -----------------------------------S---S---------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 --------------------TTGACTCTGCTGTCCGTTCC---------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ACACACCCTTCATCACGAAGAAACAATTTCTGGAATTGAGTTCTTTTTTT chr5D_1_TraesCS5D01G012900 ACACACCCTTCATCACGAAGAAACAATTTCTGGAATTGAGTTCTTTTTTT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ACACGCCCTTCACCGCGAAGAAACAATTTCTGAAATTGAGTTC--TTTTT chrUn_889 ACACACCCTTCACCGCAAAGAAACAATTTCTGGAATTGAGTTGTTTTTTT chr3B_4451 -------------------------------------------------- SNPs ------------S-S----------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GAAGTTTCCCTGCAGGCTGGTAAATCCGTGTCCGGTGCATCTGTCGACGC chr5D_1_TraesCS5D01G012900 GAAGTTTCCCTGCAGGCTGGTAAATCCGTGTCCGGTGCATCTGTCGACGC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GAAGTTTCCCTGCAGGCTGGTAAATCCGTGTCGGGTGCATCTGTCAATGA chrUn_889 GAAGTTTCCCTGCAGGCTGGTAAATCCGTGTCCGGTGCATCTGTCGACGC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CAACGGCAAGTTTGTTGTCAAAGTTGAGAAGCGTACTATTGATTTTGTAG chr5D_1_TraesCS5D01G012900 CAACGGCAAGTTTGTTGTCAAAGTTGAGAAGCGTACTATTGATTTTGTAG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CAATGGGAAATTTCTTGTGGAAGTTCAGAAGCGTACTGTTGATTTTGTTG chrUn_889 CAACGGCAAGTTTGTTGTCAAAGTTGAGAAGCGTACTATTGATTTTGTTG chr3B_4451 -------------------------------------------------- SNPs ------------------------------------------------S- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ATTACATCAGCGCTAATTATGTCTTAGTTGCTACAGGCAGCAGCCAACAG chr5D_1_TraesCS5D01G012900 ATTACATCAGCGCTAATTATGTCTTAGTTGCTACAGGCAGCAGCCAACAG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ATTACATCGATGCCAATTATGTCTTGGTTGCGACAGGCAGTAGCCAGCAG chrUn_889 ATTACATCAACGCTAATTATGTCTTGGTTGCTACAGGCAGCAGCCAGCAG chr3B_4451 -------------------------------------------------- SNPs ---------S---------------S--------------------S--- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GTATCTGAACACTAAATAGGTGCTTACTCTACTAGACACCATAAACTCTT chr5D_1_TraesCS5D01G012900 GTATCTGAACACTAAATAGGTGCTTACTCTACTAGACACCATAAACTCTT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GTATGTG-------AATAGATGCTTACTCTACTAGACAGCAGACACAATA chrUn_889 GTATGTGAACACTAATTAGGCGCTTACTCTACTAGACACCGTAAACTAGT chr3B_4451 -------------------------------------------------- SNPs ----S------------------------------------------S-- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TCCCTTACATAT------TTCTCTTACTTGCAGGGCTACTCATTTGCTGC chr5D_1_TraesCS5D01G012900 TCCCTTACATAT------TTCTCTTACTTGCAGGGCTACTCATTTGCTGC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TACTACCTCCCTTTCATGTTCTCTTACTTGCAGGGTTACTCGTTTGCTGC chrUn_889 TCCCTTACATGT------TTCTCTTACTTGCAGGGCTACTCATTTGCTGC chr3B_4451 -------------------------------------------------- SNPs ----------S--------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GCAACACGGTCACTCTATTATTCCACCTGTGCCCAGCCTATTCACATTCA chr5D_1_TraesCS5D01G012900 GCAACACGGTCACTCTATTATTCCACCTGTGCCCAGCCTATTCACATTCA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ACAACACGGTCACTCTATTATTCCGCCTGTGCCCAGCTTATTCACATTTA chrUn_889 GCAACACGGTCACTCGATTATTCCACCGGTGCCCAGCTTATTCACATTTA chr3B_4451 -------------------------------------------------- SNPs -------------------------------------S----------S- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AAATTGCAGACAAGCGACTGGCTGATCTATCCGGGGTATTGATCCGTAAC chr5D_1_TraesCS5D01G012900 AAATTGCAGACAAGCGACTGGCTGATCTATCCGGGGTATTGATCCGTAAC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AAATTGCAGACAAGCGACTGGCTGATCTCTCTGGGGTATTGATCCATAAC chrUn_889 AAATTGCAGACAAGCGACTGGCTGATCTCTCCGGGGTATGGATCCATAAC chr3B_4451 -------------------------------------------------- SNPs ----------------------------S----------------S---- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TGCTATTGCAAATCTCATACTCACAAGTGGTGACTCACTGCACG-CAAAA chr5D_1_TraesCS5D01G012900 TGCTATTGCAAATCTCATACTCACAAGTGGTGACTCACTGCACG-CAAAA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TGCTATTGCAAATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN chrUn_889 TGCTTTTGCAAATCTCATACTCACAAGTAATACTGACTGACTGCACAAAA chr3B_4451 -------------------------------------------------- SNPs ----------------------------SS-SSSSSSSSS-SSS------ forward_1221 -------------------------------------------------- reverse_2830 -----------------------------GTGACTCACTGCACGCAAAA- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ATGATTCCCCTCCTTTTCTCCTGCCACGTAGGTTTCGTTCACAAGGGTCG chr5D_1_TraesCS5D01G012900 ATGATTCCCCTCCTTTTCTCCTGCCACGTAGGTTTCGTTCACAAGGGTCG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN chrUn_889 ATGATTCCCCTCCTTTTCTCCTGCCATGTAGGTTTCGTTCACAAGAGTCA chr3B_4451 -------------------------------------------------- SNPs --------------------------S------------------S---S forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------GTTTCGTTCACAAGGGTCG reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CA------------------------------------------------ chr5D_1_TraesCS5D01G012900 CA------------------------------------------------ chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN chrUn_889 AA------------------------------------------------ chr3B_4451 -------------------------------------------------- SNPs S------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 C------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN chrUn_889 -------------------------------------------------- chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ---------------------------------------GCAAAACTGAT chr5D_1_TraesCS5D01G012900 ---------------------------------------GCAAAACTGAT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCACGGCAAAGCTGAT chrUn_889 ---------------------------------------GCAAAATTGAT chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GCTAGATGGCATTCAGAAAAGCGCTCCTGAATTAACTCAGGTGAGCCGGA chr5D_1_TraesCS5D01G012900 GCTAGATGGCATTCAGAAAAGCGCTCCTGAATTAACTCAGGTGAGCCGGA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GCTAGATGGCATTCAGAAAAGCGCTCCTGAGTTAACTCAGGTGAGCCGAC chrUn_889 GCTAGATGGGATTCAGAAAAGCGCTCCTGAATTAACTCAGGTCAGCTGGC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------S forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 ------------------------------ATTAACTCAGGTGAGCCGGA reverse_5480 -------------------------------------------------- input_sequence_18420 CACCTTCAGCAATAGGCTCCGTCATAGATGTTTGCTTACATCAATTGTTT chr5D_1_TraesCS5D01G012900 CACCTTCAGCAATAGGCTCCGTCATAGATGTTTGCTTACATCAATTGTTT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CACCTTCAGCAATAGGCTCCGTCATAGATGTTTGCTTACATCAATTGTTT chrUn_889 CACCTTCAGCAATAGGCTCCGTCATAGATGTTTGTTTACATCAATTGTTT chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GGCCATTGCAGACTGGACCTATGTTGGTTACACATTGGGGGCTTAGTGGC chr5D_1_TraesCS5D01G012900 GGCCATTGCAGACTGGACCTATGTTGGTTACACATTGGGGGCTTAGTGGC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GCCCATTGCAGACTGGACCTATGTTGGTTACACATTGGGGGCTTAGTGGC chrUn_889 GGCCATTGCAGACTGGACCTATGTTGGTTACACATTGGGGGCTTAGTGGC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CCTGTTGTTCTTCGATTGTCTGCATGGGGAGCACGTGAACTATATCAGGA chr5D_1_TraesCS5D01G012900 CCTGTTGTTCTTCGATTGTCTGCATGGGGAGCACGTGAACTATATCAGGA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CCTGTTGTTCTTCGATTTTCTGCATGGGGAGCACGTGAACTATATCAGGA chrUn_889 CCTGTTGTTCTTCGATTGTCTGCATGGGGAGCGCGTGAACTATATCAGGA chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CAAGTACCAAGGTGAGGCCCGAAGAAATTGTACACGAGTGG--------- chr5D_1_TraesCS5D01G012900 CAAGTACCAAGGTGAGGCCCGAAGAAATTGTACACGAGTGG--------- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CAAGTACCAAGGTGAGGCCCGAAGAAATTGTACACGAATGG--------- chrUn_889 CAAGTACCAAGGTGAGGTCCAAAGAAATTGTACACGAGTGCATTTAACTC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 TGCTGTTGAATGCCTCTTGGTACTTTGTCCACGACAAGCTGAAGAAACAT chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 AGCTGGATCAATTTCTTCAGCTAAAACATGCACACTCGTGTACAATTTCT chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -----------------------------CACTACATTTTTAATACGGAA chr5D_1_TraesCS5D01G012900 -----------------------------CACTACATTTTTAATACGGAA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -----------------------------CACTACATTTTTAATACGGAA chrUn_889 TCAGCTTGTGCATTTTGTGTTCCATCAATCACTACATTTTTAATACGGAA chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CATAGCTGGATCTAGTGTTTTATTTCTTCAGCTTGTGCATTTTGTGTTCC chr5D_1_TraesCS5D01G012900 CATAGCTGGATCTAGTGTTTTATTTCTTCAGCTTGTGCATTTTGTGTTCC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CATAGCTGGATCTAGTGTTTTGTTTCTTCAGCTTGTGCATTTTGTGTTCC chrUn_889 CATAGCTGGATCTAGTGTTTTGTTTCTTCAGCTCGTGCATTTTGTGTTCC chr3B_4451 -------------------------------------------------- SNPs ---------------------S---------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ATCAATCACATGAAACTTTCCATTACAATAGTATTTTAAAACAGCATGTA chr5D_1_TraesCS5D01G012900 ATCAATCACATGAAACTTTCCATTACAATAGTATTTTAAAACAGCATGTA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ATCAATCACATGAAACTTTCCATTACAATAGTATCTTAAAACAGCATGTA chrUn_889 ATCAATCACATGAAACTTGCCATTACAATAGTATTTTAAAACAGCATGTA chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AGATCTACTCCCTCTGTCCCACAATACAAGACGTTTTTGCAAGCTAAAAC chr5D_1_TraesCS5D01G012900 AGATCTACTCCCTCTGTCCCACAATACAAGACGTTTTTGCAAGCTAAAAC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AGATCTACTCCCTCTGTCCCACAA-------------------------- chrUn_889 AGATTTACTCCCTCTGTCCCACAATACAAGACATTTTTGCAAGCTAAAGC chr3B_4451 -------------------------------------------------- SNPs --------------------------------S---------------S- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 A------TAGCTTGCAAAAACGTCCTGTATTGTGGAACGGAGGGAGTAAA chr5D_1_TraesCS5D01G012900 A------TAGCTTGCAAAAACGTCCTGTATTGTGGAACGGAGGGAGTAAA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ---------GCTTGCAAACACGTCTTGTATTGTGGAACGGAGGGAGTAAA chrUn_889 TATGTTTTAGCTTGCAAAAACGTCTTGTATTGTGGGAGAGAGGGAGTAAA chr3B_4451 -------------------------------------------------- SNPs S-----------------------S------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 ------------------------CTGTATTGTGGAACGGAGGGA----- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AGATATTGTCGAACTCATCCACTTCTCTTGTTGGAATATGTATA-TTTCT chr5D_1_TraesCS5D01G012900 AGATATTGTCGAACTCATCCACTTCTCTTGTTGGAATATGTATA-TTTCT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AGATATTGTCGAACTCATCCACTTCTCTTGTTGGAATATGTATA-TTTCT chrUn_889 AGATATTGTCGAACTCATCCGCTTCTCTTGTTGGAATATGTATATTTTCT chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TTCAACACAGCAAAGCTTGTGGTTGACTTCATACCGGACATTCACATCGA chr5D_1_TraesCS5D01G012900 TTCAACACAGCAAAGCTTGTGGTTGACTTCATACCGGACATTCACATCGA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TTCAACACAGCAAAGCTTGTGGTTGACTTCATACCGGACATTCACATCGA chrUn_889 TTCAACACAGCAAAGCTTGTGGTTGACTTCATACCTGACATTCACATCGA chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GGACGTGAAGCGGATCCTATTCCAGCACAAAGACCAACATGCGGTTCTGA chr5D_1_TraesCS5D01G012900 GGACGTGAAGCGGATCCTATTCCAGCACAAAGACCAACATGCGGTTCTGA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GGACGTGAAGCGGATCCTATTCCAGCACAAAGACCAACATGCGGTTCTGA chrUn_889 GGACGTGAAGCGGATCCTATTCCAGCACAAAGACCAACATGCGGTTCTGA chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TCTTTCCCTGTCCTTCGTTAAT--------GTCTTCATCTGA--GAGTCT chr5D_1_TraesCS5D01G012900 TCTTTCCCTGTCCTTCGTTAAT--------GTCTTCATCTGA--GAGTCT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TCTTTCCCTATCCTTCGTTAAT--------GTCTTCATCTGAGAGAGTCT chrUn_889 TCTTTCCCTGTCCTTTGTTAATGCTTTCGAGTCTTCATCTGAGAATA--T chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GAGTTCTTTTTAGAAATAGAGAATCCGAGTTTTAAATTTTTAACTCTGCT chr5D_1_TraesCS5D01G012900 GAGTTCTTTTTAGAAATAGAGAATCCGAGTTTTAAATTTTTAACTCTGCT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GAGTTCTTTTTAGAAATAGAGAATCCGAGTTTTAAATTTTTAACTCTGCT chrUn_889 GAGTTCTTTCTAGAAACAGAGAATCCGAGTTTTAAAATT-TAACTCTGCT chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TTTGAATGCCTCTTGCTTTAATAAATTAATCGACCAGTTCTTGTAAATGC chr5D_1_TraesCS5D01G012900 TTTGAATGCCTCTTGCTTTAATAAATTAATCGACCAGTTCTTGTAAATGC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TTTGAATGCCTCTTGCTTTAATAAATTAATCGACCAGTTCTTGTAAATGC chrUn_889 GTTGAATGCCTCTTGCTCTAATAAATTAATGGACCAGTTCTTGTAAATGC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 CTTCAACAAGATGGACATTGCTTTCTGTTTCTTAATATGCCTCCCTTATT chr5D_1_TraesCS5D01G012900 CTTCAACAAGATGGACATTGCTTTCTGTTTCTTAATATGCCTCCCTTATT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CTTCAACAAGATGGGCATAGCTTTCTGTTTCTTTATATGCCTCCCTTATT chrUn_889 CTTCAACAAGACGGACATTGCTTTCTGTTTCTTTATATGTCTCCCTTATT chr3B_4451 -------------------------------------------------- SNPs ---------------------------------S---------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AGGCTTTCTGAGTAAAATTTTAATGAAGATTTGCTACTGCAGATACAGAT chr5D_1_TraesCS5D01G012900 AGGCTTTCTGAGTAAAATTTTAATGAAGATTTGCTACTGCAGATACAGAT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AGGCTTTCTGAGTTCAATTTTAATGAAGATTTGCTACTGCAGATACAGAT chrUn_889 AGGCTTTCTGAGTTCAATTTTAGTGGAGATTTGCTACTGCAGATACAGAT chr3B_4451 -------------------------------------------------- SNPs -------------SS----------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ACTTATAGCCACCTTTACAACATTCTGTTTTATCTGTCATGTTGGGGTGC chr5D_1_TraesCS5D01G012900 ACTTATAGCCACCTTTACAACATTCTGTTTTATCTGTCATGTTGGGGTGC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ACTTATAGCCACCTTTACAACATTCTGTTTTATCTGTCATGTTGGGGTGC chrUn_889 ACTTATAGCCACCTTTACAACATTCTGTTTTATCAGTCATGTTGGGGTAC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TTTAACCAACCTCCGTCCGGAAATACTTGTC----ATCCATTTCTCCGAC chr5D_1_TraesCS5D01G012900 TTTAACCAACCTCCGTCCGGAAATACTTGTC----ATCCATTTCTCCGAC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TTTAACCAACCTCCGTCCAGAAATACTTGTC----ATCCATTTCTCCAAC chrUn_889 TTTAGCCAACCTCCATCCGGAAATACTTGTCGGTTATCCATTTCTCCGAC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AAGTATTTCCAGACAGAGGGAGTGTTTTGTATGACTTATGTAATTTTGTC chr5D_1_TraesCS5D01G012900 AAGTATTTCCAGACAGAGGGAGTGTTTTGTATGACTTATGTAATTTTGTC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AAGTATTTCCGGACGGAGGGAGTGTTTTGTATGATTTATGTAATTTTGTC chrUn_889 AAGTATTTCCGGACGGAGGGAGTATTTTGTATGACTCATGTAATTTTATC chr3B_4451 -------------------------------------------------- SNPs ----------S---S----------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ACAGAAATATTCCC--TGAATATTCCGATTTTCCTTGTA----------- chr5D_1_TraesCS5D01G012900 ACAGAAATATTCCC--TGAATATTCCGATTTTCCTTGTA----------- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ACAGAAATATTCCC--TGAATATTCCGGTTTTCCTTGTA----------- chrUn_889 ACAGAAATATTCCCTGTGAATATTCCGATTTTCCTTGTACTCCCTCCGTT chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 CCTAAATATAAGTCTTTGTAGAGGTTCCACTAGGTGGACTACATACGAAG chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------- chrUn_889 CAAAATGAATGAATCTAAACTTAAAATGCATCTATATACATCCGTATGCG chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------A chr5D_1_TraesCS5D01G012900 -------------------------------------------------A chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------------------------------------------------A chrUn_889 GTCTATAGTGAAATTTCTACAAAGACTTACATTTAGGAACGGAGGGAGTA chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AACATTATGGTGAAGCTGTACTAAGATTTTTTTTTTAATCTCTGCAGAAG chr5D_1_TraesCS5D01G012900 AACATTATGGTGAAGCTGTACTAAGATTTTTTTTTTAATCTCTGCAGAAG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AACATTATGGTGAAGCTGTACTAAGATT-TTTTTTTAATCTCTGCAGAAG chrUn_889 AACATTATGGTGAAGCTGAACTAAGATT-TTTTTT-AATCTCTGCAGAAG chr3B_4451 -------------------------------------------------- SNPs ----------------------------S--------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AACAAAGTAAATAACGCCTTTCCCAAGGAGTTTGGTCTGGTGAAGAGGTT chr5D_1_TraesCS5D01G012900 AACAAAGTAAATAACGCCTTTCCCAAGGAGTTTGGTCTGGTGAAGAGGTT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AACAAAGTAAATAACGCCTTTCCCAAGGAGTTTGGTCTGGTGAAGAGGTT chrUn_889 AACAAAGTAAATAACGCCTTTCCCAAGGAGTTTGGTCTGGTGAAGAGGTT chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TTGGGGATTCCTTCTAGAACAGGAGGTTGCAGTAGCTGAATCCTGGTCCT chr5D_1_TraesCS5D01G012900 TTGGGGATTCCTTCTAGAACAGGAGGTTGCAGTAGCTGAATCCTGGTCCT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TTGGGGATTCCTTCTAGAACAAGAGGTTGCAGTAGCTGAATCCTGGTCCT chrUn_889 TTGGGGTTTCCTTCTAGAACAGGAGGTTGCAGTAGCTGAATTCTGGTCCT chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TACTCAGCCCCTTAA-TTTGATGTTTTACTCAGTCGAAGTTTTCTCTTGC chr5D_1_TraesCS5D01G012900 TACTCAGCCCCTTAA-TTTGATGTTTTACTCAGTCGAAGTTTTCTCTTGC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TACTCAGCCCCTTAA-TTTGATGTTTTACTCAGTCGAAGTTTTCTCTTGC chrUn_889 TACTCAGCCCCTTAATTTTGGTGTTTTACTCAGTCGAAGTTTTCTCTTGC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AGAGTTTAGATGGTGACATGCACTGGGCCACCGTGCCAAAAAGTCATCTA chr5D_1_TraesCS5D01G012900 AGAGTTTAGATGGTGACATGCACTGGGCCACCGTGCCAAAAAGTCATCTA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AGAGTTTAGATGGTGACATGCACTGGGCCACCGTGCCAAAAAGTCATCTA chrUn_889 AGAGTTTAGATGGTGACATGCACTGGGCCACCGTGCCAAAAACTCATCTA chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AACGCGATAGCCCTTCGCTTGAAACAGTGGATGTTTGAGGTTGTTGGGAA chr5D_1_TraesCS5D01G012900 AACGCGATAGCCCTTCGCTTGAAACAGTGGATGTTTGAGGTTGTTGGGAA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AATGCGATAGCCCTTCGCTTAAAACAGTGGATGTTTGAGGTTGTTGGGAA chrUn_889 AACGCGATAGCCCTTCGTTTAAAACAGTGGATGTTTGAGGTTGTTGGGAA chr3B_4451 -------------------------------------------------- SNPs --------------------S----------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GGTATGTG----ATATCTTAAGTA---TATCCCTTGAAAAGCTCGATAGC chr5D_1_TraesCS5D01G012900 GGTATGTG----ATATCTTAAGTA---TATCCCTTGAAAAGCTCGATAGC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GGTATGTGCGTGATATCTTAAGTA---TATCACCTGAAAAGCTCGATAGC chrUn_889 GGTATGTG----ATATCTTAAGTAGTATATCACTTGAAACGCTCCATAGC chr3B_4451 -------------------------------------------------- SNPs -------------------------------S------------------ forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GGT--TTTTTGATGTATCTGTGCTCACTGATGTTCCCTCATCGTCATATG chr5D_1_TraesCS5D01G012900 GGT--TTTTTGATGTATCTGTGCTCACTGATGTTCCCTCATCGTCATATG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GGT--TTTTTGATGTATCTGTGCTCACTGATGCTCCCTCATCGTCATATG chrUn_889 GATTCTTTTTAAAGTATCTGTGCTCACTGATGTTCCTTCATCGTCATATG chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TAGGGCCAATTCAAAGATGAATTTGTGACAGCTGGAGGTGTTCCACTTTC chr5D_1_TraesCS5D01G012900 TAGGGCCAATTCAAAGATGAATTTGTGACAGCTGGAGGTGTTCCACTTTC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TAGGGTCAATTCAAAGATGAATTTGTGACAGCTGGAGGTGTTCCACTTTC chrUn_889 TAGGGCCAATTCAAAGATGAATTTGTGACAGGTGGAGGTGTTCCACTTTC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AGAGGTATTTATTAGTCGACAA-CTTAATTGCAGTTTTCACAAACATGAC chr5D_1_TraesCS5D01G012900 AGAGGTATTTATTAGTCGACAA-CTTAATTGCAGTTTTCACAAACATGAC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AGAGGTATCTATTAGTCGACAA-CTTAATGGCAGTTTTCACAAACATGGT chrUn_889 AGAGGTACTTATTAATCGACAAACTTAATTGCTGTTTTCACAAACATGAC chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TCGACTCACGAAAAATCCAAATTGTTCATCTGTTGTAAAGATATCGCTTA chr5D_1_TraesCS5D01G012900 TCGACTCACGAAAAATCCAAATTGTTCATCTGTTGTAAAGATATCGCTTA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TCAACTCACGAAAATTTCAACTTGTTCATCTGTTGTAAAGATATCGCTTA chrUn_889 TCGACTCACGAAAATTCCAACTTGTTCATCTGTTGTAAAGATATCGCTTG chr3B_4451 -------------------------------------------------- SNPs --------------S-----S----------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GCACCATGGAAAGCAAGAAGCAGCCCAATCTGTTCTTTGCAGGAGAGGTA chr5D_1_TraesCS5D01G012900 GCACCATGGAAAGCAAGAAGCAGCCCAATCTGTTCTTTGCAGGAGAGGTA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GCACCATGGAAAGCAAGAAGCAGCCCAATCTGTTCTTTGCAGGAGAGGTA chrUn_889 GCACCATGGAAAGCAAGAAGCAGCCCAATCTGTTCTTTGCAGGAGAGGTA chr3B_4451 -------------------------------------------------- SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 ACAGCACAGCTG-TCTTGAACTTGCAACCCTCTGGTTATCTTATCTTACA chr5D_1_TraesCS5D01G012900 ACAGCACAGCTG-TCTTGAACTTGCAACCCTCTGGTTATCTTATCTTACA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ACAGCACAACTGTTCTTGAACTTGCAACCCTCTGGTCATCTTATCTTACA chrUn_889 ACAGCACAACTGTTCTTGAACTTGCAACCCTCTGGTCATCCTATCTTACA chr3B_4451 -------------------------------------------------- SNPs --------S---------------------------S------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GAGTGTGATCTTGCTGTAGGTACTTAATGTCGACGGGGTCACAGGCGGGT chr5D_1_TraesCS5D01G012900 GAGTGTGATCTTGCTGTAGGTACTTAATGTCGACGGGGTCACAGGCGGGT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GAGTGTGATCTTGCTGTAGGTACTTAACGTCGACGGGGTCACGGGCGGAT chrUn_889 GAGTGTGATCTTGCTGTAGGTACTTAACGTCGACGGGGTCACCGGCGGAT chr3B_4451 -------------------------------------------------- SNPs ---------------------------S--------------S-----S- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 ------------------------------------------AGGCGGGT forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TCAATTTTCAGGTAAGAAGTAGATATCTCCACAGCGGATTAGTAAAAACT chr5D_1_TraesCS5D01G012900 TCAATTTTCAGGTAAGAAGTAGATATCTCCACAGCGGATTAGTAAAAACT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TCAATTTTCAGGTAAGGAGCAGATATTTTCTCTTCCTGGAGAGCAGTGAA chrUn_889 TCAATTTTCAGGCAAGGAGTAGATATTTTCTCTTCCTGGAGAGCAGTGAA chr3B_4451 -------------------------------------------------- SNPs ----------------S---------S-S-S-SS-SSSSSSSSS-SSSSS forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 TCAATTTTCAGG-------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TGGAGATGCTTCCATTAAAAT----TCTTTTGAAGTGGGAACAAAAAAGG chr5D_1_TraesCS5D01G012900 TGGAGATGCTTCCATTAAAAT----TCTTTTGAAGTGGGAACAAAAAAGG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TTAGT------------AAAA----ACTTTTGAAGTGAGAACACAA--GG chrUn_889 TTAGT------------AAAATAAAACTTTTGAAGTGAGAACGCAA--GG chr3B_4451 ------------------------------TGAGGTGGGAACAAAAAAGG SNPs -SSSSSSSSSSSSSSSS---S----S------------------------ forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 TTTCAACTTAGCATTTGCTCTTTGCTTTCCACAGAATGCATGGACTGGTG chr5D_1_TraesCS5D01G012900 TTTCAACTTAGCATTTGCTCTTTGCTTTCCACAGAATGCATGGACTGGTG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TTTCAACTG-GCATTTTCTCTTTGTTTTGCACAGAATGCATGGACTGGTG chrUn_889 TTTCAACTG-GCATTTTCTCTTTGTTTTGCACAGAACGCATGGACTGGTG chr3B_4451 TCTCAACTTAGCATTTGCTCTTTGCTGTCCACAGAATGCATGGACTAGTG SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 GGTATATAGCTGGGACAAGCATTGGCACATTGGCATCAAAAAGCATTCTC chr5D_1_TraesCS5D01G012900 GGTATATAGCTGGGACAAGCATTGGCACATTGGCATCAAAAAGCATTCTC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GGTATATAGCTGGGACAAGCATTGGCACATTGGCATCAAACAGCATTCTC chrUn_889 GGTATATAGCTGGGACAAGCATTGGCACATTGGCATCAAACAGCATTCTC chr3B_4451 GGTACATAGCTGGGACAAGCATTGGCACATTGGCATCAAGCAACATGCTC SNPs ----------------------------------------S--------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 AAAGAAGAGCAAGCCTGTTTGCAACTACAAGGATCTTAA----------- chr5D_1_TraesCS5D01G012900 AAAGAAGAGCAAGCCTGTTTGCAACTACAAGGATCTTAAGGACATGTATG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AAAGAAGAGCAAGCCTGTTTGCAACTACAAGGATCTTAAGGACATGTATG chrUn_889 AAAGAAGAGCAAGCCTGTTTGCAACTACAAGGATCTTAAGGACATGTATG chr3B_4451 AAAGAAGAGCAGGCTTGTTTGCAACTGTAAGCATCTTAAGGACTGGCATG SNPs -------------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 AAATCATGACAAGGAGGGT-AGAGATTCAAGGATTCTTGGTTCTTACTGG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AAATCATGACAAGGAGGG------ATTCAAGGATTCTTAGTTCTTACTGG chrUn_889 AAATCATGACAAGGAGGGT-AGTGATTCAAGGATTCCTAGTTCTTACTGG chr3B_4451 AAACCATGATAAGGTGGGGCAGTGAGTCAAGGA-------TTCGTATTGG SNPs ----------------------S---------------S----------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 CTGACAAACTTAT----AAAAACTTCTGAAAGTGTAGCTTAGCTGC---- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CTGAGTAACTTTGTAAAAACT-----TGAGAGTGTAGCTTAGCTGC---- chrUn_889 CTGACAAACTTTGTT---AAAACTTCT--GAGAGTATAAAGTTGGGTCAT chr3B_4451 CTGACAAACTTTGTAAAAAAAACTTCT--GAGTGTAGCTTAGCTGC---- SNPs -----------SS----------------S-------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -----------------------------AAGTGTAGCTTAGCTGCTAGT input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 --------------------TAGTCCACAGTATTGTAGCTC-AAAAACAA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 --------------------TAGTCCACAGTATTGTAGCT-AAAAAACAA chrUn_889 CTATTTTGGAACGGAGTGAGTAGTCCACAATATTGTAGCTAAAAAAACAA chr3B_4451 --------------------TAGTCCACAAAATTGTAGCT-A-------- SNPs ----------------------------------------S--------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 CC------------------------------------------------ input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 GCAAAGATAACCAAGATTCACATCGACTAACTGTATCGTCGTGTTGTAGT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GCAAAGATAACCAAGATTCACATCGAGTAACTGTATCGTCGTCTTGTAGC chrUn_889 GCAAAGATAACCAAGTTTCACATCGACTAACTGTATCGTCGTCTTGTAGC chr3B_4451 -------------------------------------------------- SNPs ------------------------------------------S------S forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 GACAATTTTGCTGTGGAGTAAGATCCTAGTTGAGCAACTTGTGAATCGTT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GACAATTTTGTAATGGAGTAAGATCCTAGTTGAGCAACTTGTGAATCCTT chrUn_889 GACAATTTTGCTGTGGAGTAAGATCCTAGTTGAGCAACTTGTGAATCCTT chr3B_4451 -------------------------------------------------- SNPs -----------------------------------------------S-- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 GTAGACTTGGCAGTAATAATCAGAAGATGAATATGCCCAGTGCATTCACT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GTAAACTTGGCAGTAAGAATCAGAAGATCAATATACCCAGTGCATTCATT chrUn_889 GTAAACTTGGCAGTAAGAATCAGAAGATCAATATGCCCAGTGCATTCATT chr3B_4451 -------------------------------------------------- SNPs ---S------------S-----------S-------------------S- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 GCTTTTCCTGAAGGTTGGGCTGGAATTTACAGCTAAAACACCTGATGTGC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 GCATTTCCTGA--------------------GCTACAGTACCTGGTCTAC chrUn_889 GCTTTTCCTGA-------------------AGCTACAGCACCTGGTCTAC chr3B_4451 -------------------------------------------------- SNPs -----------SSSSSSSSSSSSSSSSSSS-----S-S------S-S-S- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 TGAAACATAAAACAAAATTCCCATTGTCTAATTTAGAATGCAACAAATCA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TGAAACATAGAAC--AATTCTCATTGTCTAATCAAGAATGCAACAAATCA chrUn_889 TGAAACATAGAAC--AATTCTCATTGTCTAATCAAGAATGCAACAAATAA chr3B_4451 ------------C--AACTCTCAGTATCTAATTTAGAATGCAGCAAATCA SNPs ---------S---SS-----S----------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 ATCTCTC------------------------------AA-TGTTCCTTCT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ATTTCTTGATGTTCCTTTTGTTGCGAAAGAATTTCTTAA-TGTTCTTTTT chrUn_889 ATTTCTTGATGTTCCTTTTGTTGCGAAAGAATTTCTTAAATGTTCATTTT chr3B_4451 TC---------------------------AATCTCTTAA-TGTACCTTCT SNPs --S---S------------------------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 CACAAACAAATAGAAGGAAATTCTCATAATTTGTATAATTCAGAATGTAT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 AAAG---------------------------------AATCAGAATGCAA chrUn_889 AAAC---------------------------------AATCAGAATGCAG chr3B_4451 CACAGATAAATAAACAAGCCTTGCAAA---TTGTATAATTCTGAATTCAA SNPs ----S-S-----S-SSSSSS--SSS-SSSS-----------------S-S forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 GATTTTAGTCCCTAAATGTTCCC------------------AGATAAATA chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CAATGCAGTCCCTAAATGTCCGC------------------AC------- chrUn_889 CAATGCAGTCCCTGAATGTCCAC------------------AC------- chr3B_4451 CAATGCAGTTCCTCGATGTTCCCATGGATAAATAAGTTTCAAC------- SNPs S-S-SS------------------------------------SSSSSSSS forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 AGTTTCGACACGCTACAGGCGAAACCATAAAAGATGAAATTAC------- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -------ACTCGCTACAGATGAAACTATAACAGATGAAATTAC------- chrUn_889 -------ACTCGCTATAGATGAAACTATAACAGATGAAGTGTAATT---- chr3B_4451 -------ACTCGCTACAGACGAAACTATGGCAGATGAAACTATAACAGAT SNPs SSSSSSS--S--------S------S----S------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 ------ACACAACCAAGATTCAGGAAGGTACATCGATTAATTGTA--TCG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ------ACACAACCAAGATTCAGAAAGGTACATCGACTACTCAT---TCG chrUn_889 -----------------ACACAGAAAGGTACATCGACTAGTCGTTCGTCG chr3B_4451 GAGATGACACAACCAAGATTCAGAGAGATACATCGACTAATTGTA--TCA SNPs -----------------------S------------S------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 TCACATCATAGCAATAATTTTGCTGTGAAGCAAAAGTTCCTGGAGCAAAC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TCGCATCGTAGCAGCAATTTTGCTGTGAAGCAA--GTTC----------- chrUn_889 TCGCATCGTAGCAGCAATTTTGCTGTGAAGCAA--GTTC----------- chr3B_4451 TCGCATCATAGCAACAATTTTGTTGTGAAGCAA--GTTCCCGGAGCAAAC SNPs --S-----------S------------------SS-----S--------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 TTCTGAATTGATGCAAACTTTGCTGCAACA--ATCAGAAGACCAATGCAT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 --CTGAATTGATGCAAACTTTGGTGTAACA--ATCAGAAGACCGATGCGT chrUn_889 --CTGAATTGATGCAAACTTTGGTGTAACACAATCACAAGACCAATGCAT chr3B_4451 TTCTGAATTGATGCAAACTTTGCTGTAACA--ATCAGAAGA--------- SNPs -------------------------S------------------------ forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 TGCCTTCCAGAAGGCTAGATTGCAACAATGCAATGTCTAAA--------- chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TGCTTTCCAGAAGGTTGGATTGGAACTTACAGCTACAGCAACATAAG--- chrUn_889 TGATTTCCAGAAGGTTAGATTGGAACTTGCAGCTACAGCAACATAAAAAC chr3B_4451 -------------------------------------------------- SNPs ---S----------S-------S---SSSSSSS-SSSSS----------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 ---------TGTCTAATTCAGAGTGCAACAATGCAATGTCTAAATGTTCT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 -----TCATTGTCTAATTCAGAATGCAACAATGCAATGTCTAAATGTTCT chrUn_889 AATATTCATCGTCTAATTCAGAACGCAACAATGCAATGTCTAAAAGTTCT chr3B_4451 -------------------------------------------------- SNPs ----------------------S--------------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 CATCACATCACAGATAAATATAGAGTTTGGAAAGATAAGAACTCAACCAT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CATCACATCACAGATAAAAA---AGTTTGGAAACATAAGAACTCAACCGT chrUn_889 CATCACACCACAGATAAATA---AGTTTGGAAACA--------------- chr3B_4451 -------------------------------------------------- SNPs --------------------SSS----------S--------------S- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 GACTACACTTTCTTAACACACGCACGCTACAGGCGACGAAACTAGAACAG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 CACTACATTTTCTTAACACACACATGCTACAGGCGACGAAACTAGAACAG chrUn_889 -------TTTTCTTAACACACGCACGCTACAGGCGACGAAACTAGAACAG chr3B_4451 -------------------------------------------------- SNPs S------S------------------------------------------ forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 ATGCTTCCTTCATCCAAAAGAGAATGATTGCTCCACAAAACTGCACCTGT chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 ATGCTTCCTTCATC--AAAGAGAATGGTTGATCCACAAAACTGCACCTGT chrUn_889 ATGCTTCCTTCATCC-AAAGAGACTGGTTGCTCCACAAAACTGCACCTGT chr3B_4451 -------------------------------------------------- SNPs ---------------S----------S----------------------- forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 TCAGCTAGCTAGCTATCTATAAGTTGGTTTATTCCTGATGATATATAACG chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TCATCAGCTAGCTAAAAAG-----T-GTTTATTCCTGATGATACATAACG chrUn_889 TCAGCTAGCTAGCTATAATTAAGTT-GTTTATTCCTGACTGATGAT-ACT chr3B_4451 -------------------------------------------------- SNPs ----------------SSS------S-----------------S------ forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 -------------------------------------------------- chr5D_1_TraesCS5D01G012900 TAACCTAGCAGAAGCAGAAGCGGAAGCAGAAGCAGGCCCTAATTAAGAAC chr5D_1 -------------------------------------------------- chr5D_1 -------------------------------------------------- chr5A_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr4D_1 -------------------------------------------------- chr7D_1 -------------------------------------------------- chr5A_411 -------------------------------------------------- chr1D_411 -------------------------------------------------- chr5A_889 TAACCTAGCAGAAGAAGCAG------------------------------ chrUn_889 TAACCTAGCAGAAGCAGAAGCAGAAGCAGAAGCAG--------------- chr3B_4451 -------------------------------------------------- SNPs ---------------------S-------------SSSSSSSSSSSSSSS forward_1221 -------------------------------------------------- reverse_2830 -------------------------------------------------- forward_2390 -------------------------------------------------- reverse_3675 -------------------------------------------------- forward_2901 -------------------------------------------------- reverse_5143 -------------------------------------------------- forward_3150 -------------------------------------------------- reverse_5480 -------------------------------------------------- input_sequence_18420 --- chr5D_1_TraesCS5D01G012900 TAA chr5D_1 --- chr5D_1 --- chr5A_1 --- chr1D_1 --- chr1D_1 --- chr2D_1 --- chr2D_1 --- chr2D_1 --- chr3D_1 --- chr3D_1 --- chr6D_1 --- chr6D_1 --- chr6D_1 --- chr4D_1 --- chr7D_1 --- chr5A_411 --- chr1D_411 --- chr5A_889 --- chrUn_889 --- chr3B_4451 --- SNPs SSS forward_1221 --- reverse_2830 --- forward_2390 --- reverse_3675 --- forward_2901 --- reverse_5143 --- forward_3150 --- reverse_5480 ---