CLUSTAL X (1.81) multiple sequence alignment input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 ACAGGATTTGAACCTGTGACATTTTGTACCCAAAACAAACGCGCTACCAA chr3B_1 ACAGGATTTGAACCTGTGACATTTTGTACCCAAAACAAACGCGCTACCAA chr3D_1 ACAGGATTTGAACCTGTGACATTTTGTACCCCAAACAAACGCGCTACCAA chr2D_1 ACATGATTTGAACCTGTGACATTTTGTACCCAAAACAAACGCGCTACCAA chr1D_1 ACAGGATTTGAACCTGTGACATTTTGTACCCAAAACAAACGCGCTACCAA chrUn_1 ACAGGATTTGAACCTGTGACATTTTGTACCCAAAACAAACGCGCTACCAA chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 GCTGCGCTACATCCCTTTTCCAAATTAAATTGTTGTACAATGCCATTGTA chr3B_1 GCTGCGCTACATCCCTTTTCGAAATTAAATTGTTGTACAATGCCATTGTA chr3D_1 GCTGCGCTACATCCCTTTTCCAAATTAAATTGTTGTACAATGCCATTGTA chr2D_1 GCTGCGCTACATCCCTTTTCCAAATTAAATTGTTGTACAATGCCATTATA chr1D_1 GCTGCGCTACATCCCTTTTCCAAATTAAATTGTTGTACAATGCCATTGTA chrUn_1 GCTGCGCTACATCCCTTTTCCAAATTAAATTGTTGTACAATGCCATTGTA chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 CTCAATTCCTGTCTTCTTTTCCACATCATAATTTTCTTCTTCTTTCTATT chr3B_1 CACAATTCCTGTCTTCTTTTCCACATCATAATTTTCTTGTTCTTTCTATT chr3D_1 CACAATTCCTGTCTTCTTTTCCACATCATA-----------------ATT chr2D_1 CACAATTCCTGTCTTCTTTTCCACATCATAATTTTCTTCTTCTTTCTATT chr1D_1 CACAATTCCTGTCTTCTTTTCCACATCATAATTTTCTTCTTCTTTCTATT chrUn_1 CACAATTCCTGTCTTCTTTTCCACATCATAATTTTCTTCTTCTTTCTATT chr1D_123 ----------------------ACATCATAATTTTCTTCTTCTTTCTATT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -S------------------------------------------------ forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TTCTTCTTCTTTCTTTCTCTATCTATATATAGAACCCTCGTGTCATTTCT chr3B_1 TTCTTCTTCTTTCTTTCTCTATCTATATATAGAACCCTCATGTCATTTCT chr3D_1 TTCTTCTTCTTTCTTTCTCTATCTATATATAGAACCCTCGTGTCATTTCT chr2D_1 TTCTTCTTCTTTCTTTCTCTATCTATATATAGAACCCTCATGTCATTTCT chr1D_1 TTCTTCTTCTTTCTTTCTCTATCTATATATAGAACCCTCGTGTCATTTCT chrUn_1 TTCTTCTTCTTTCTTTCTCTATCTATATATAGAACCCTCGTATCATTTCT chr1D_123 TTCTTCTTCTTTCTTTCTCTATCGATATATAGAACCCTCGTGTCATTTCT chr5D_152 -TCTTCTTCTTTCTTTCTCTATCTATATATAGAACCCTCGTGTCATTTCT chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TCTTTTTGGTCTCATATAATTAAGGAATTATATACATATAAAATCCAATA chr3B_1 TCTTTTTGGTCTCATATAATTAAGGAATTATATACATATAAAATCCAATA chr3D_1 TCTTTTTGGTCTCATATAATTAAGGAATTATATACATATAAAATCCAATA chr2D_1 TCTTTTTGGTCTCATATAATTAAGGAATTATATACATATAAAATCTAATA chr1D_1 TCTTTTTGGTCTCATATAATTAAGGAATTATATACATATAAAATCCAATA chrUn_1 TCTTTTTGGTCTCATATAATTAAGGAATTATATACATATAAAATCCAATA chr1D_123 TCTTTTTGGTCTCATATAATTAAGGAATTATATACATATAAAATCCAATA chr5D_152 TATTTTTGGTCTCATATAATTAAGGAATTATATACATATAAAATCCAATA chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TAATTTCGCCTATAAAGGAAGGATTACTTTTCCTTGCTAATATATAGGAA chr3B_1 TAATTTGGCCTATAAAAGAAGGATTACTTTTCCTTGGTAATATATAGGAA chr3D_1 TAATTTCGCCTATAAAAGAAGGATTACTTTTCCTTGCTAATATATAGGAA chr2D_1 TAATTTCTCCTATAAAGGAAGGATTACTTTTCCTTGGTAATATCTAGGAA chr1D_1 TAATTTCGCCTATAAAAGAAGGATTACTTTTCCTTGCTAATATATAGGAA chrUn_1 TAATTTCGCCTATAAAAGAAGGATTACTTTTCCTTGCTAATATATAGGAA chr1D_123 TAATTTCACCTATAAAAGAAGGATTACTTTTCCTTGCTAATATATAGGAA chr5D_152 TAATTTCGCCTATAAAAGAAGGATTACTTTTCCTTGCTAATATATAGGAA chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 GAAGGGGTCATCTTTTTCTTTTTTAGGGATAGGAAAATTTCGTCAATATG chr3B_1 GAAGGGGTCATCTTTTTCTTTTTTAGGGATAGGAAAATTTCGTCGATATG chr3D_1 GAAGGGGTCATCTTTTTCTTTTTTAGGGATAGGAAAATTTCGTCGATATG chr2D_1 GAAGGGGTCATCTTTTTCTTTTTTAGGGATAGGAAAATTTCGTCGATATG chr1D_1 GAAGGGGTCATCTTTTTCTTTTTTAGGGATAGGAAAATTTCGTCGATATG chrUn_1 GAAGGGGTCATCTTTTTCTTTTTTAGGGATAGGAAAATTTCGTCGATATG chr1D_123 GAAGGGGTCATCTTTTTCTTTTTTAGGGATAGGAAAATTTCGTCGATATG chr5D_152 GAAGGGGTCATCTTTTTCTTTTTTAGGGATAGGAAAATTTCGTCGATATG chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs --------------------------------------------S----- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 GTTCATTTTATATATAGCATAACAATCTTGGGCAAGAGTTTATGATCATA chr3B_1 GTTCATTTTATATATAGCATAACAATCTTGGGCAAGAGTTTATGATCATA chr3D_1 GTTCATTTTATATATAGCATAACAATCTTGGGCAAGAGTTTATGATCATA chr2D_1 GTTCATTTTATATATAGCATAACAATCTTGGGCAAGAGTTTATGATCATA chr1D_1 GTTCATTTTATATATAGCATAACAATCTTGGGCAAGAGTTTATGATCATA chrUn_1 GTTCATTTTATATATAGCATAACAATCTTGGGCAAGAGTTTATGATCATA chr1D_123 GTTCATTTTATATATAGCATAACAATCTTGGGCAAGAGTTTATGATCATA chr5D_152 GTTCATTTTATATATAGCATAACAATCTTGGGCAAGAGTTTATGATCATA chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TATGTATTCCAACAAGGAAGGAGGATTTTCAATGCGGGATATAAAAACAT chr3B_1 TATGTATTCCAACAAGGAAGGAGGATTTTCAATGCGGGATATAAAAACAT chr3D_1 TATGTATTCCAACAAGGAAGGAAGATTTTCAATGCGGGATATAAAAACAT chr2D_1 TATGTATTCCAACAAGGAAGGAGGATTTTCAATGTGGGATATAAAAACAT chr1D_1 TATGTATTCCAACAAGGCAGGAGGATTTTCAATGCGGGACATAAAAACAT chrUn_1 TATGTATTCCAACAAGGAAGGAGGATTTTCAATGCGGGATATAAAAACAT chr1D_123 TATGTATTCCAACAAGGAAGGAGGATTTTCAATGCGGGATATAAAAACAT chr5D_152 TATGTATTCCAACAAGGAAGGAGGATTTTCAATGCGGGATATAAAAACAT chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 ATCTCTCTGTAGCACCCGTGCTAAGTACTCTATGGTTTGGTGCTTTAGCA chr3B_1 ATCTCTCTGTAGCACCCGTGCTAAGTACTCTATGGTTTGGTGCTTTAGAA chr3D_1 ATCTCTCTGTAGCACCCGTGCTAAGTAGTCTATGGTTTGGTGCTTTAGCA chr2D_1 ATCTCTCTGTAGCACCCATGCTAAGTACTCTATGGTTTGGTGCTTTAGCA chr1D_1 ATCTCTCTCTAGCACCCGTGCTAAGTACTCTATGGTTTGGTGCTTTAGCA chrUn_1 ATCTCTCTGTAGCACCCGTGCAAAGTACTCTATGGTTTGGTGCTTTAGCA chr1D_123 ATCTCTCTGTAGCACCCGTGCTAAGTACTCTATGGTTTGGTGCTTTAGCA chr5D_152 ATCTCTCTGTAGCACCCGTGCTAAGTACTCTATGGTTTGGTGCTTTAGCA chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 GGTTTATTGATAGAAATTAATCGTTTATTCCCAAATGCTTTGTCATTCCC chr3B_1 GGTTTATTGATAGAAATTAATCGTTTATTCCCAGATGCTTTGTCATTCCC chr3D_1 GGTTTATGGATAGAAATTAATCGTTTATTCCCAGATGCTTTGTCATTCCC chr2D_1 GGTTTATTGATAGAAATTAATCGTTTATTCCCAGATGCTTTGTCATTCCC chr1D_1 GGTTTATTGATAGAAATTAATCGTTTATTCCCAGATGCTTTGTCATTCCC chrUn_1 GGTTTATTGATAGAAATTAATCGTTTATTCCCAGATGCTTTGTCATTCCC chr1D_123 GGTTTATTCATAGAAATTAATCGTTTATTCCCAGATGCTTTGTCATTCCC chr5D_152 GGTTTATTGATAGAAATTAATCGTTTATTCCCAGATGCTTTGTCATTCCC chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs ---------------------------------S---------------- forward_551 -----------------------------CCCAAATGCTTTGTCATTCCC reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TTTTTTT-TAATTCTAGTTATTGCTATGGGAGGGATAGATTTCTTCGTGA chr3B_1 -TTTTTT-TAATTCTAGTTATTGCTATGGAAGGGATAGATTTCTTCGTGA chr3D_1 -TTTTTT-TAATTCTAGTTATTGCTATGGGAGGGATAGATTTCTTCGTGA chr2D_1 -TTTTT--TAATTCTAGTTATTGCTATGGGAGGGATAGATTTCTTCGTAA chr1D_1 -TTTTTTTTAATTCTAGTTATTGCTATGGGAGGGATAGATTTCTTCGTGA chrUn_1 -TTTTTTTTAATTCTAGTTATTGCTATGGGAGGGATAGATTTCTTCGTGA chr1D_123 -TTTTTTTTAATTCTAGTTATTGCTATGGGAGGGATAGATTTCTTCGTGA chr5D_152 -TTTTTTTTAATTCTAGTTATTGCTATGGGAGGGATAGATTTCTTCGTGA chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs S------------------------------------------------- forward_551 T------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TATGACAAAATTTGATCCTTTTCAATCTTTTTTTAGTATCGGAAGGAAA- chr3B_1 TATGACAAAATTTGATCCTTTTCAATCTTTTTTTAGTATCGGAAGGAAA- chr3D_1 TATGACAAAATTTGATCCTTTTCAATCTTTTTTTAGTATCGGAAGGAAA- chr2D_1 TATGAAAAT-TTTGATCCTTTTCAATCTTTTTTTAGTATCGGAAGGAAA- chr1D_1 TATGACAAAATTTGATCCTTTTCAATCTTTTTTTAGTATCGGAAGGAAA- chrUn_1 TATGACAAAATTTGATCCTTTTCAATCTTTTTTTAGTATCGGAAGGAAA- chr1D_123 TATGACAAAATTTGATCCTTTTCAATCTTTTTTTAGTACCGGAAGGAAAA chr5D_152 TATGACAAAATTTGATCCTTTTCAATCTTTTTTTAGTATCGGAAGGAAA- chr5D_614 --------------ATCCTTTTCAATCTTTTTTTAGTATCGGAAGGAAA- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 A-AGAAAGAAAAGATGGATTGGATTGAACCTCAGAGTCATTAAAAATTTG chr3B_1 A-GGAAAGAAAAGATGGATTGGGTTGAACCTCAGAGTCATTAAAAATTTG chr3D_1 A-AGAAAGAAAAGATGGATTGGGTTGAACCTCAGAGTCATTAAAAATTTG chr2D_1 AAAGAAAGAAAAGATGGATTGGGTTGAACCTCAGAGTCATAAAAATTTTG chr1D_1 A-AGAAAGAAAAGATGGATTGGGTTGAACCTCAGAGTCATTAAAAATTTT chrUn_1 A-AGAAAGAAAAGATGGATTGGGTTGAACCTCAGAGTCATTAAAAATTTT chr1D_123 A-AGAAAGAAAAGATGGATTGGGTTGAACCTCAGAGTCATTAAAAATTTG chr5D_152 A-AGAAAGAAAAGATGGATTGGGTTGAACCTCAGAGTCATTAAAAAATTT chr5D_614 A-AGAAAGAAAAGATGGATTGGGTTGAACCTCAAAGTCATTAAAAATTTG chr1D_1220 -------------------------------------------------- SNPs ----------------------S--------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 GTAAACCCCATTTTTGAAAATAGAAATTCAATTTAAAGGGGTACCCAAGC chr3B_1 GTAAACCCCATTTTTGAAAATAGAAATTCAATTTAAAGGGGTACCCAAGC chr3D_1 GTAAACCCCATTTTTGAAAATAGAAATTCAATTTAAAGGGGTACCCAAGC chr2D_1 GTAAACCCCATTTTTGAAAATAGAAATTCAATTTAAAGGGGTACCCAAGC chr1D_1 GTAAACCCCATTTTTGAAAATAGAAATTCAATTTAAAGGGGTACCCAAGC chrUn_1 GTAAACCCCATTTTTGAAAATAGAAATTCAATTTAAAGGGGTACCCAAGC chr1D_123 GTAAACCCCATTTTTGAAAATAGAAATTCAATTTAAAGGGGTACCCAAGC chr5D_152 GTAAACCCCATTTTTGAAAATAGAAATTCAATTTAAAGGGGTACCCAAGC chr5D_614 GTAAACCCCATTTTGGAAAATAGAAATTCAATTTAAAGGGGTACCCAAGC chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TAAATAAGACCTCAGAAATCAGAGCATAGAAAAGGCGGGGCTGGCTAATT chr3B_1 TAAATAAGGCCTCAGAAATTAGAGCATAGAAAAGGCGGGGCTGGCTAATT chr3D_1 TAAATAAGGCCTCAGAAATCAGAGCATAGAAAAGGCGGGGCTGGCTAATT chr2D_1 TAAATAAGGCCTCAGATATCAGAGCATAGAAAAGGCGGGGCTGGCTAATT chr1D_1 TAAATAAGGCCTCAGAAATCAAAGCATAGAAAAGGTGGGGCTGGCTAATT chrUn_1 TAAATAAGGCCTCAGAAATCAGAGCATAGAAAAGGTGGGGCTGGCTAATT chr1D_123 TAAATAAGGCCTCAGAAATCAGAGCATAGAAAAGGCGGGGCTGGCTAATT chr5D_152 TAAATAAGGCCTCAGAAATCAGAGCATAGAAAAGGTGGGGCTGGCTAATT chr5D_614 TAAATAAGGCCTCAGAAATCAGAGCATAGAAAAGGCGGGGCTGGCTAATT chr1D_1220 -------------------------------------------------- SNPs --------S----------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 AAATGAAAGGATTTCGAACCAAAATCTTTGCTAATTCGACAAGGATTGTA chr3B_1 AAATGAAAGGATTTCGAACCAAAATCTTTGCTAATTCAACAAGGATTGTA chr3D_1 AAATGAAAGGATTTCGAACCAAAATCTTTGCTAATTCGACAAGGATTGTA chr2D_1 AAATGAAAGGATTTCGAACCAAAATCATTGCTAATTCGACAAGGATTGTG chr1D_1 AAATGAAAGGATTTCGAACCAAAATCTTTGCTAATTCGACAAGGATTGTA chrUn_1 AAATGAAATGATTTCGAACCAAAATCTTTGCTAATTCGACAAGGATTGTA chr1D_123 AAATGAAAGGATTTCGAACCAAAATCTTTGCTAATTCGACAAGGGTTGTA chr5D_152 AAATGAAAGGATTTCGAACCAAAATCTTTGCTAATTCGACAAGGATTGTA chr5D_614 AAATGAAAGGATTTCAAACCAAAATCTTTGCTAATTCGACAAGGATTGTA chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TTCTTTAATTATTTCTCTATTTTTTATTACTTAATTTAAGAAT--AAAAA chr3B_1 TTCTTTAATTATTTCTCTATTTTTTATTACTTAATTTAAGAAT--AAAAA chr3D_1 TTCTTTAATTATTTCTCTATTTTTTATTACTTAATTTAAGAAT--AAAAA chr2D_1 TTCTTTAATTATTTCTCTATTTTTTATTACTTAATTTAAGAATAAAAAAA chr1D_1 TTCTTTAATTATTTCTCTATTTTTTATTACTTAATTTAAGAAT--AAAAA chrUn_1 TTCTTTAATTATTTCTCTATTTTTTATTACTTAATTTAAGAAT--AAAAA chr1D_123 TTCTTTAATTATTTCTCTATTTTTTATTACTTAATTTAAGAAT---AAAA chr5D_152 TTCTTTAATTATTTCTCTATTTTTTATTACTTAATTTAAGAATA-AAAAA chr5D_614 TTCTTTAATTATTTCTCTATTTTTTATTACTTAATTTAAGAATA-AA-AA chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 AATTATTCTAATGAATTTTATTCTTCTTCTTCGGATTCAAAATAGAAGAA chr3B_1 AAATATTCTAATGAATTTTATTCTTCTTCTTCGGATTCAAAATAGAAGAA chr3D_1 AATTATTCTAATGAATTTTATTCTTCTTCTTCGGATTCAAAATAGAAGAA chr2D_1 AATTATTCTAATGAATTTTATTCTTCTTCTTCGGATTCAAAATAGAAGAA chr1D_1 AATTATTCTAATGAATTTTATTCTTCTTATTCGGATTCAAAATAGAAGAA chrUn_1 AATTATTCTAATGAATTTTATTCTTCTTCTTCGGATTCAAAATAGAAGAA chr1D_123 AATTATTCTAATGAATTTTATTCTTCTTCTTCGGATTCAAAATAGAAGAA chr5D_152 AATTATTCTAATGAATTTTATTCTTCTTCTTCGGATTCAAAATAGAAGAA chr5D_614 AATTATTCTAATGAATTTTATTCTTCTTCTTCGGATTCAAAATAGAAGAA chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TAAAAGAATAAGTAGAAGAATTAAGTTAAGTCAATCCGAAAACAAAAGGA chr3B_1 TGAAAGAATAAGTAGAATAATTAAGTTAAGTCAATCCAAAAAGAAAAGGA chr3D_1 TAAAAGAATAAGTAGAAGAATTAAGTTAAGTCAATCCAAAAAGAAAAGGA chr2D_1 TAAAAGAATAAGGAGAAGAATTAAGTTAAGTCAATCCAAAAAGAAAAGGA chr1D_1 TAAAAGAATAAGTAGAAGAATTAAGTTAAGTCAATCCAAAAAGAAAAGGA chrUn_1 TAAAAGAATAAGTAGAAGAATTAAGTTAAGTCAATCCAAAAAGAAAAGGA chr1D_123 TAAAAGAATAAGTAGAAGAATTAAGTTAAGTCAATCCAAAAAGAAAAGGA chr5D_152 TAAAAGAATAAGTAGAAGAATTAAGTTAAGTCAATCCAAAAAGAAAAGGA chr5D_614 TAAAAGAATAAGTAGAAGAATTAAGTTAAGTCAATCCAAAAAGAAAAGGA chr1D_1220 -------------------------------------------------- SNPs -------------------------------------S----S------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -----ATGGCCAAGGGAAAAGATGTTAGAATCAGAGTTATTTTGGAATGC chr5D_1_TraesCS5D01G009500 GGTTCATGGCCAAGGGAAAAGATGTTAGAATCAGAGTTATTTTGGAATGC chr3B_1 GGTTCATGGCCAAGGGAAAAGATGTTAGAATCAGAGTTATTTTGGAATAC chr3D_1 GGTTCATGGCCAAGGGAAAAGATGTTAGAATCAGAGTTATTTTGGAATGC chr2D_1 GGTTCATGGCCAAGGGAAAAGATGTTAGAATCAGAGTTATTTTGGAATGC chr1D_1 GGTTCATGGCCAAGGGAAAAGATGTTAGAATCAGAGTTATTTTGGAATGC chrUn_1 GGTTCATGGCCAAGGGAAAAGATGTTAGAATCAGAGTTATTTTGGAATGC chr1D_123 GGTCCATGGCCAAGGGAAAAGATGTTAGAATCAGAGTTATTTTGGAATGC chr5D_152 GGTTCATGGCCAAGGGAAAAGATGTTAGAATCAGAGTTATTTTGGAATGC chr5D_614 GGTTCATGGCCAAGGGAAAAGATGTTAGAATCAGAGTTATTTTTGAATGC chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 ATTAGTTGTGTTCGAAAAGGTGCCAATGAGGAATCGACGGGGATTTCTAG chr5D_1_TraesCS5D01G009500 ATTAGTTGTGTTCGAAAAGGTGCCAATGAGGAATCGACGGGGATTTCTAG chr3B_1 ATCAGTTGTGTTCAAAAAGGTGCCAATGAGGAATCGACGGGGATTTCTAG chr3D_1 ATCAGTTGTGTTCGAAAAGGTGCCAATGAGGAATCGACGGGGATTTCTAG chr2D_1 ATCAGTTGTGTTCGAAAAGGTGCCAATGAGGAATCGACGGGGATTTCTAG chr1D_1 ATCAGTTGTGTTCGAAAAGGTGCCAATGAGGAATCGACGGGGATTTCTAG chrUn_1 ATCAGTTGTGTTCGAAAAGGTGCCAATGAGGAATCGACGGGGATTTCTAG chr1D_123 ATCAGTTGTGTTCGAAAAGGTGCCAATGAGGAATCGACGGGGATTTCTAG chr5D_152 ATCAGTTGTGTTCGAAAAGGTGCCAATGAGGAATCGACGGGGATTTCTAG chr5D_614 ATCAGTTGTGTTCGAAAAGGTGCCAATGAGGAATCGACGGGGATTTCTAG chr1D_1220 -------------------------------------------------- SNPs --S----------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 ATATAGTACTCAAAAGAATCGCCACAATACACCCGG-------------- chr5D_1_TraesCS5D01G009500 ATATAGTACTCAAAAGAATCGCCACAATACACCCGG-------------- chr3B_1 ATACAGTACTCAAAAGAATCGCCACAATACACCCGG-------------- chr3D_1 ATATAGTACTCAAAAGAATCGCCACAATACACCCGG-------------- chr2D_1 ATATAGTACTCAAAAGAATCGCCACAATACACCCGG-------------- chr1D_1 ATATAGTACTCAAAAGAATCGCCACAATACACCCGG-------------- chrUn_1 ATATAGTACTCAAAAGAATCGCCACAATACACCCGG-------------- chr1D_123 ATATAGTACTCAAAAGAATCGCCACAATACACCCGGACAATTAGAATTCA chr5D_152 ATATAGTACTCAAAAGAATCGCCACAATACACCCGG-------------- chr5D_614 ATATAGTACTCAAAAGAATCGCCACAATACACCCGG-------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 AAAAATTTGTCGTTATTGTCGCAAGCATACGACTCATCACGAAATAAAGA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 AATAGGAACATCGTGTGTTCGATCTTTCCAAACAACAGAAAGAGTAAGAA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 CTTCATATTTAATATATAAAGAAAACATAGTATAGAATACAAAATACAAA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 TCAACTCATCCGATTTCCGGTAGATATTATTTCATATGTATAGAGGGTAT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 TCATATACTATAATATGAATCAAATAAGATATGGATCAAAGAAAAACTAC chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 TTCTTCTGGATCCTAAATTAATAAAATAAAGAAGTGAATTTTCAAATTTT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 CAAATTTTAAATAAGGAATAAATCATGTATACATCTAAACAACCTTTTCT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 TAAATCTAAGCAACCCTTTAGTAAATCCAAGCAAACTTTTAATAAATCCA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 AGCAACCCTTTCGTAAATCCAAGCAAACTTTTCGTAAATTCAAGCAACCT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 TTTCGTAAATCTAAACAACCTTTTCGTAGGCGTCCCCGGATTGGCCCGGG chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 AGATCGAATTGATTATAGAAACATGAGTTTAATTAATAGATTTATTAGTG chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 AACAAGGAAAAATATTATCGAGACGAATAAATAGATTAACCTTGAAACAA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 CAACGATTAATTACTCTTGCTATAAAACAGGCTCGTATTTTATCTTTCTT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 ACCGTTTCGTAACTATGAGAACGAAAAGCAATTTCAAGCCCAGTCAATTT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 CAATAATTACAGGTTCTAGACCCAGAAAAAATAGACATATTCCTCAATTA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 ACGCAAAAGTACAATTCCAATAAAATAAAGATCATCAATTAAAAGTATAA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 ATAAAGTAATATACTGGAATAAAAAAAGATGAATTCCCGGAGAGGGAACT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 CCGGGAAGATACAATAAATTAAGATTAAGTGGTAGGAATCAACGAGCTGG chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 ATTACTTTCTTTATAATATATATAGGTCTGGCCCTTTCGAATTCGAATAA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 AACATCAACAATCGGAACTTAAGTTCCGGTTGTTGTTTCTTAAATTTTGG chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 TTGTTGTTTCTTAAGTTTCGATTGGAATTGTACTTTTGCGTTAATTGAGG chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 AATATGTCTATTTTTTCTGGGTCTAGAACCTGTAATTATTGAAATTGACT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 GGGCTTGAAATTGCTTTTCGTTCTCATAGTTACGAAACGGTAAGAAAGAT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 AAAATACGAGCCTGTTTTATAGCAAGAGTAATTAATCGTTGTTGTTTCAA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 GGTTAATCTATTTATTCGTCTCGATAATATTTTTCCTTGTTCACTAATAA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 ATCTATTAATTAAACTCATGTTTCTATAATCAATTCGATCTCACGGGCCA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 ATCCGAGGACGCCTACGAAAAGGTTGTTTAGATTTACGAAAAGGTTGCTT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 GAATTTACGAAAAGTTTGCTTGGATTTACGAAAGGGTTGCTTGGATTTAT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 TAAAAGTTTGCTTGGATTTACTAAAGGGTTGCTTAGATTTAAGAAAAGGT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 TGTTTAGATGTATACATGATTTATTCCTTATTTAAAATTTGAAAATTTGA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 AAATTCACTTCTTTATTTTATTAATTTAGGATCCAGAAGAAGTAGTTTTT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 CTTTGATCCATATCTTATTTGATTCATATTATAGTATATGAATACCCTCT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 ATACATATGAAATAATATCTACCGGAAATCAGATGAGTTGATTTGTATTT chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 TGTATTCTATACTATGTTTTCTTTATATATTAAATATGAAGTTCTTACTC chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 -------------------------------------------------- chrUn_1 -------------------------------------------------- chr1D_123 TTTCTGTTGTTCGAAAAGGTGCCAATGAGGAATCGACGGGGATTTCTAGA chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -----------------------------------ACAATTAGAATTCAA chr5D_1_TraesCS5D01G009500 -----------------------------------ACAATTAGAATTCAA chr3B_1 -----------------------------------ACAATTAGAATTCAA chr3D_1 -----------------------------------ACAATTAGAATTCAA chr2D_1 -----------------------------------ACAATTAGAATTCAA chr1D_1 -----------------------------------ACAATTAGAATTCAA chrUn_1 -----------------------------------ACAATTAGAATTCAA chr1D_123 TATAGTACTCAAAAGAATCGCCACAATACACCCGGACAATTAGAATTCAA chr5D_152 -----------------------------------ACAATTAGAATTCAA chr5D_614 -----------------------------------ACAATTAGAATTCAA chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 AAATTTTTGTCGTTATTGTCGCAAGCATACGACTCATCATGAAATAAAGA chr5D_1_TraesCS5D01G009500 AAATTTTTGTCGTTATTGTCGCAAGCATACGACTCATCATGAAATAAAGA chr3B_1 AAATTTTTGTCGTTATTGTCGCAAGCATATGACTCATCACGAAATAAAGA chr3D_1 AAAATTTTGTCGTTATTGTCGCAAGCATACGACTCATCACGAAATAAAGA chr2D_1 AAATTTTTGTCCTTATTGTCGCAAGCATACGACTCATCACGAAATAAAGA chr1D_1 AAATTTTTGTCGTTATTGTCGCAAGCATACGACTCATCACGAAATAAAGA chrUn_1 AATTTTTTGTCGTTATTGTCGCAAGCATACGACTCATCACGAAATAAAGA chr1D_123 AAAATTTTGTCGTTATTGTCGCAAGCATACGACTCATCACGAAATAAAGA chr5D_152 AAAAATTTGTCGTTATTGTCGCAAGCATACGACTCATCACGAAATAAAGA chr5D_614 AAAAATTTGTCGTTATTGTCGCAAGCATATGACTCATCACGAAATAAAGA chr1D_1220 -------------------------------------------------- SNPs ---------------------------------------S---------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 AATAG--------------------------------------------- chr5D_1_TraesCS5D01G009500 AATAGGAACATCGTGTGTTCGATCTTTCCAAACAACAGAAAGAGTAAGAA chr3B_1 AATAGGAACATCGTGTGTTCGATCTTTCCAAACAACAGAAAGAGTAAGAA chr3D_1 AATAGGAACATCGTGTGTTCGATCTTTCCAAACAACAGAAAGAGTAAGAA chr2D_1 AATAGGAACATCGTGTGTTCGATCTTTCCAAACAACAGAAAGAGTAAGAA chr1D_1 AATAGGAACATCGTGTGTTCGATCTTTCCAAACAACAGAAAGAGTAAGAA chrUn_1 AATAGGAACATCGTGTGTTCGATCTTTCCAAACAACAGAAAGAGTAAGAA chr1D_123 AATAGGAACATCGTGTGTTCGATCTTTCCAAACAACAGAAAGAGTAAGAA chr5D_152 AATAGGAACATCGTGTGTTCGATCTTTCCAAACAACAGAAAGAGTAAGAA chr5D_614 AATAGGAACATCGTGTGTTCGATCTTTCCAAACAACAGAAAGAGTAAGAA chr1D_1220 -----------------------CTTTTCGAACAACAGAAAGAGTAAGAA SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 CTTCATATTTAATATATAAAGAAAACATAGTATAGAATACAAAATACAAA chr3B_1 CTTCATATTCAATATATAAAGAAAACATAGTATAGAATACAAAATACAAA chr3D_1 CTTCATATTTAATATATAAAGAAAACATAGTATAGAATACAAAATACAAA chr2D_1 CTTCTTATTTAATATATAAAGAAAACATACTATAGAATACAAAATACAAA chr1D_1 CTTCATATTTAATATATAAAGAAAACATAGTATAGAATACAAAATACAAA chrUn_1 CTTCATATTTAATATATAAAGAAAACATAGTATAGAATACAAAATACAAA chr1D_123 CTTCATATTTAATATATAAAGAAAACATAGTATAGAATACAAAATACAAA chr5D_152 CTTCATATTTAATATATAAAGAAAACATAGTATAGAATACAAAATACAAA chr5D_614 CTTCATATTTAATATATAAAGAAAACATAGTATAGAATACAAAATACAAA chr1D_1220 CTTCATATTTAATATATAAAGAAAACATAGTATAGAATACAAAATACAAA SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TCAACTCATCTGATTTCCGGTAGATATTATTTCATATGTATAGAGGGTAT chr3B_1 TCAACTCATCTGATTTCCGGTAGATATTATTTCATATGTATAGAGGGTAT chr3D_1 TCAACTCATCTGATTTCCGGTAGATATTATTTCATATGTATAGAGGGTAT chr2D_1 TCAACTCATCTGATTTCCGGTAGATATTATTTCATATGTATAGAGGGTAT chr1D_1 TCAACTCATCTGATTTCTGGTAGATATTATTTCATATGTATAGAGGGTAT chrUn_1 TCAACTCATCTGATTTCCGGTAGATATTATTTCATATGTATAGAGGGTAT chr1D_123 TCAACTCATCTGATTTCCGGTAGATATTATTTCATATGTATAGAGGGTAT chr5D_152 TCAACTCATCTGATTTCCGGTAGATATTATTTCATATGTATAGAGGGTAT chr5D_614 TCAACTCATCTGATTTCCGGTAGATATTATTTCATATGTATAGAGGGTAT chr1D_1220 TCAACTCATCTGATTTCCGGTAGATATTATTTCATATGTATAGAGGGTAT SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TCATATACTATAATATGAATCAAAT------------------------- chr3B_1 TCATATACTATAATATGAATCAAAT------------------------- chr3D_1 TCATATACTATAATATGAATCAAAT------------------------- chr2D_1 TCATATACTATAATATGAATCAAATAAGATAAGATATGGATCAAAGAAAA chr1D_1 TCATATACTATAATATGAATCAAAT-----AAGATATGGATCAAAGAAAA chrUn_1 TCATATACTATAATATGAATCAAAT------------------------- chr1D_123 TCATATACTATAATATGAATCAAAT------------------------- chr5D_152 TCATATACTATAATATGAATCAAAT------------------------- chr5D_614 TCATATACTATAATATGAATCAAAT------------------------- chr1D_1220 TCATATACTATAATATGAATCAAAT------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 A------------------------------------------------- chr1D_1 ACTACTTCTTCTGGATCCTAAATTAATAAAATAAAGAAGTGAATTTTCAA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 ATTTTCAAATTTTAAATAAGGAATAAATCATGTATACATCTAAACAACCT chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TTTCTTAAATCTAAGCAACCCTTTAGTAAATCCAAGCAAACTTTTAATAA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 ATCCAAGCAACCCTTTCGTAAATCCAAGCAAACTTTTCGTAAATTCAAGC chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 AACCTTTTCGTAAATCTAAACAACCTTTTCGTAGGCGTCCTCGGATTGGC chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 CCGGGAGATCGAATTGATTATAGAAACATGAGTTTAATTAATAGATTTAT chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TCCTTATTTAAAATTTGAAAATTTGAAAATTCACTTCTTTATTTTATTAA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TTTAGGATCCAGAAGAAGTAGTTTTTCTTTGATCCATATCTTATTTGATT chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 CATATTATAGTATATGAATACCCTCTATACATATGAAATAATATCTACCG chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 GAAATCAGATGAGTTGATTTGTATTTTGTATTCTATACTATGTTTTCTTT chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 ATATATTAAATATGAAGTTCTTACTCTTTCTGTTGTTTGGAAAGATCGAA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 CACACGATGTTCCTATTTCTTTATTTCGTGATGAGTCGTATGCTTGCGAC chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 AATAACGACAAAATTTTTTGAATTCTAATTGTCCGGGTGTATTGTGGCGA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TTCTTTTGAGTACTATATCTAGAAATCCCCGTCGATTCCTCATTGGCACC chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TTTTCGAACACAACTGATGCATTCCAAAATAACTCTGATTCTAACATATT chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TTCCCTTGGCCATGAACCTCCTTTTCTTTTTGGATTGACTTAACTTAATT chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 ATTCTACTTATTCTTTTATTCTTCTATTTTGAATCCGAAGAAGAAGAATA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 AAATTCATTAGAATAATTTTTTTTTATTCTTAAATTAAGTAATAAAAAAT chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 AGAGAAATAATTAAAGAATACAATCCTTGTCGAATTAGCAAAGATTTTGG chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TTCGAAATCCTTTCATTTAATTAGCCAGCCCCGCCTTTTCTATGCTCTGA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TTTCTGAGGCCTTATTTAGCTTGGGTACCCCTTTAAATTGAATTTCTATT chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TTCAAAAATGGGGTTTACCAAATTTTTAATGACTCTGAGGTTCAACCCAA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TCCATCTTTTCTTTCTTTTTCCTTCCGATACTAAAAAAAGATTGAAAAGG chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 ATCAAATTTTGTCATATCACGAAGAAATCTATCCCTTCCATAGCAATAAC chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TAGAATTAAAAAAAAGGATTTCGAACCAAAATCTTTGCTAATTCGACAAG chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 GATTGTATTCTTTAATTATTTCTCTATTTTTTATTACTTAATTTAAGAAT chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 AAAAAAAAATTATTCTAATGAATTTTATTCTTCTTCTTCGGATTCAAAAT chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 AGAAGAATAAAAGAATAAGTAGAATAATTAAGTTAAGTCAATCCAAAAAG chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 AAAAGGAGGTTCATGGCCAAGGGAAAAGATGTTAGAATCAGAGTTATTTT chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 GGAATGCATCAGTTGTGTTCGAAAAGGTGCCAATGAGGAATCGACGGGGA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 TTTCTAGATATAGTACTCAAAAGAATCGCCACAATACACCCGGACAATTA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 GAATTCAAAAAATTTTGTCGTTATTGTCGCAAGCATACGACTCATCACGA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 AATAAAGAAATAGGAACATCGTGTGTTCGATCTTTCCAAACAACAGAAAG chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 AGTAAGAACTTCATATTTAATATATAAAGAAAACATAGTATAGAATACAA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -------------------------------------------------- chr3B_1 -------------------------------------------------- chr3D_1 -------------------------------------------------- chr2D_1 -------------------------------------------------- chr1D_1 AATACAAATCAACTCATCTGATTTCTGGTAGATATTATTTCATATGTATA chrUn_1 -------------------------------------------------- chr1D_123 -------------------------------------------------- chr5D_152 -------------------------------------------------- chr5D_614 -------------------------------------------------- chr1D_1220 -------------------------------------------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 ---------------------------------AAGATATGGATCAAAGA chr3B_1 ---------------------------------AAGATATGGATCAAAGA chr3D_1 ---------------------------------AAGATATGGATCAAAGA chr2D_1 --------------------------------TAAGATATGGATCAAAGA chr1D_1 GAGGGTATTCATATACTATAATATGAATCAAATAAGATATGGATCAAAGA chrUn_1 ---------------------------------AAGATATGGATCAAAGA chr1D_123 ---------------------------------AAGATATGGATCAAAGA chr5D_152 ---------------------------------AAGATATGGATCAAAGA chr5D_614 ---------------------------------AAGATATGGATCAAAGA chr1D_1220 ---------------------------------AAGATATGGATCAAAGA SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 AAAACTACTTCTTCTGGATCCTAAATTAATAAAATAAAGAAGTGAATTTT chr3B_1 AAAACTACTTCTTCTGGATCCTAAATTAATAAAATAAAGAAGTGAATTTT chr3D_1 AAAACTACTTCTTCTGGATCCTAAATTAATAAAATAAAGAATTGAATTTT chr2D_1 AAAACTACTTCTTCTGGATCCTAAATTAATAAAATAAAGAAGTGAATTTT chr1D_1 AAAACTACTTCTTCTGGATCCTAAATTAATAAAATAAAGAAGTGAATTTT chrUn_1 AAAACTACTTCTTCTGGATCCTAAATTAATAAAATAAAGAAGTGAATTTT chr1D_123 AAAACTACTTCTTCTGGATGCTAAATTAATAAAATAAAGAAGTGAATTTT chr5D_152 AAAACTACTTCTTCTGGATCCTAAATTAATAAAATAAAGAAGTGAATTTT chr5D_614 AAAACTACTTCTTCTGGATCCTACATTAATAAAATAAAGAAGTGAATTTT chr1D_1220 AAAACTACTTCTTCTGGATCCTAAATTAATAAAATAAAGAAGTGAATTTT SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 CAAATTTTCAAATTTTAAATAAGGAATAAATCATGTATACATCTAAACAA chr3B_1 CAAATTTTCAAATTTTAAATAAGGAATAAATCATGTATACATCTAAACAA chr3D_1 CAAATTTTCAAATTTTAAATAAGGAATAAATCATGTATACATCTAAACAA chr2D_1 CAAATTTTCAAATTTTAAATAAGGTATAAATCATGCATACATCTAAACAA chr1D_1 CAAATTTTCAAATTTTAAATAAGGAATAAATCATGTATACATCTAAACAA chrUn_1 CAAATTTTCAAATTTTAAATAAGGAATAAATCATGTATACATCTAAACAA chr1D_123 CAAATTTTCAAATTTTAAATAAGGAATAAATCATGTATACATCTAAACAA chr5D_152 CAAATTTTCAAATTTTAAATAAGGAATAAATCATGTATACATCTAAACAA chr5D_614 CAAATTTTCAAATTTTAAATAAGGAATAAATCATGTATACATCTAAACAA chr1D_1220 CAAATTTTCAAATTTTAAATAAGGAATAAATCATGTATACATCTAAACAA SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 CCTTTTCTTAAATCAAAGCAACCCTTTAGTAAATCCAAGCAAACTTTTAA chr3B_1 CCTTTTCTTAAATCTAAGCAACCCTTTAGTAAATCCAAGCAAAATTTTAA chr3D_1 CCTTTTCTTAAATCTAAGCAACCCTTTAGTAAATCCAAGCAAACTTTTAA chr2D_1 CCTTTTCTTAAATCTAAGCAACCCTTTAGTAAATCCAAGCAAACTTTTAA chr1D_1 CCTTTTCTTAAATCTAAGCAACCCTTTAGTAAATCCAAGCAAACTTTTAA chrUn_1 CCTTTTCTTAAATCTAAGCAACCCTTTAGTAAATCCAAGCAAACTTTTAA chr1D_123 CCTTTTCTTAAATCTAAGCAACCCTTTAGTAAATCCAAGCAAACTTTTAA chr5D_152 CCTTTTCTTAAATCTAAGCAACCCTTTAGTAAATCCAAGCAAACTTTTAA chr5D_614 CCTTTTCTTAAATCTAAGCAACCCTTTAGTAAATCCAAGCAAACTTTTAA chr1D_1220 CCTTTTCTTAAATCTAAGCAACCCTTTAGTAAATCCAAGCAAACTTTTAA SNPs --------------S----------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TAAATCCAAGCAACCCTTTCGTAAATCCAAGCAAA-TTTTCGTAAATTCA chr3B_1 TAAATCCAAGCAACCCTTTCGTAAATCCAAGCAAACTTTTCGTAAATTCA chr3D_1 TAAATCCAAGCAACCCTTTCGTAAATCCAAGCAAACTTTTCGTAAATTCA chr2D_1 TAAATCCAAGCAACCCTTTCGTAAATCCAAACAAACTTTTCGTAAATTCA chr1D_1 TAAATCCAAGCAACCCTTTCGTAAATCCAAGCAAACTTTTCGTAAATTCA chrUn_1 TAAATCCAAGCAACC----------------------------------- chr1D_123 TAAATCCAAGCAACCCTTTCGTAAATCCAAGCAAACTTTTCGTAAATTCA chr5D_152 TAAATCCAAGCAACCCTTTCGTAAATCCAAGCAAACTTTTCGTAAATTCA chr5D_614 TAAATCCAAGCAACCCTTTCGTAAATCCAAGCAAACTTTTCGTAAATTCA chr1D_1220 TAAATCCAAGCAACCCTTTCGTAAATCCAAGCAAACTTTTCGTAAATTCA SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 AGCAACCTTTTCGTAAATCTAAACAACCTTTTCGTAGGCGTCCCCGGATT chr3B_1 AGCAACCTTTTCGTAAATCTAAACAACCTTTTCGTAGGCGTCCTCGGATT chr3D_1 AGCAACCTTTTCGTAAATCTAAACAACCTTTTTGTAGGCGTCCCCGGATT chr2D_1 AGCAACCTTTTCATAAATCTAAACAACCTTTTCGTAGGCGTCCCCGGATT chr1D_1 AGCAACCTTTTCGTAAATCTAAACAACCTTTTCGTAGGCGTCCCCGGATT chrUn_1 -------------------------------------------------- chr1D_123 AGCAACCTTTTCGTAAATCTAAACAACCTTTTCGTAGGCGTCCCCGGATT chr5D_152 AGCAACCTTTTTGTAAATCTAAACAACCTTTTCGTAGGCGTCCCCGGATT chr5D_614 AGCAACCTTTTCGTAAATCTAAACAACCTTTTCGTAGGCGTCCCCGGATT chr1D_1220 AGCAACCTTTTCGTAAATCTAAACAACCTTTTCGTAGGCGTCCTCGGATT SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 GGCCCGGGAGATCGAATTGAT-ATAGAAACATGAGTTTAATTAATAGATT chr3B_1 GGCCCGAGAGATCGAATTGATTATAGAAACATGAGTTTAATTAATAGATT chr3D_1 GGCCCGGGAGATCGAATTGATTATAGAAACATGAGTTTAATTAATAGATT chr2D_1 GGCCCGGGAGATCGAATTGATTATAGAAACATGAGTTTAATTAATAGATT chr1D_1 GGCCCGGGAGATCAAATTGATTATAGAAACATGAGTTTAATTAATAGATT chrUn_1 -------------------------------------------------- chr1D_123 GGCCCGGGAGATCGAATTGATTATAGAAACATGAGTTTAATTAATAGATT chr5D_152 GGCCCGGGAGATCGAATTGATTATAGAAACATGAGTTTAATTAATAGATT chr5D_614 GGCCCGGGAGATCGAATTGATTATAGAAACATGAGTTTAATTAATAGATT chr1D_1220 GGCCCGTGAGATCGAATTGATTATAGAAACATGAGTTTAATTAATAGATT SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 -ATTAGTGAAGAAGGAAAAATATTATCGAGACGAATAAATAGATTAACCT chr3B_1 TATTAGTGAACAAGGAAAAATATTATCGAGACGAATAAATAGATTAACCT chr3D_1 TATTAGTGAACAAGGAAAAATATTATCGAGACGAATAAATAGATTAACCT chr2D_1 TATTAATGAACAAGGAAAAATATTATCGAGACGAATAAATAGATTAACCT chr1D_1 TATTAGTGAACAAGGAAAAATATTATCGAGACGAATAAATAGATTAACCT chrUn_1 -------------------------------------------------- chr1D_123 TATTAGTGAACAAGGAAAAATATTATCGAGACGAATAAATAGATTAACCT chr5D_152 TATTAGTGAACAAGGAAAAATATTATCGAGACGAATAAATAGATTAACCT chr5D_614 TATTAGTGAACAAGGAAAAATATTATCGAGACGAATAAATAGATTAACCT chr1D_1220 TATTAGTGAACAAGGAAAAATATTATCGAGACGAATAAATAGATTAACCT SNPs ----------S--------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TGAAACAACAACGATTAATTACTCTTGCTATAAAACAGGCTCGTATTTTA chr3B_1 TGAAACAACAACGATTAATTACTCTTGCTATAAAACATGCTCGTATTTTA chr3D_1 TGAAACAACAACGATTAATTACTCTTGCTATAAAACAGGCTCGTATTTTA chr2D_1 TGAAACAACAATGATTAATTACTCTTGCTATAAAACAGGCTCGTATTTTA chr1D_1 TGAAACAACAACGATTAATTACTCTTGCTATAAAACAGGCTCGTATTTTA chrUn_1 -------------------------------------------------- chr1D_123 TGAAACAACAACGATTAATTACTCTT-CTATAAAACAGGCTCGTATTTTA chr5D_152 TGAAACAACAACGATTAATTACTCTTGCTATAAAACAGGCTCGTATTTTA chr5D_614 TGAAACAACAACGATTAATTACTCTTGCTATAAAACAGGCTCGTATTTTA chr1D_1220 TGAAACAACAACGATTAATTACTCTTGCTATAAAACAGGCTCGTATTTTA SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TCTTTCTTACCGTTTCGTAACTATGAGAACGAAAAGCAATTTCAAGCCCA chr3B_1 TCTTTCTTACCGTTTCGTAACTATGAGAACGAAAAGCAATTTCAAGCCCA chr3D_1 TCTTTCTTACCGTTTCGTAACTATGAGAACGAAAAGCAATTTCAAGCCCA chr2D_1 TCTTTCTTATCGTTTCGTAAATATGAGAACGAAAAGCAATTTCAAGCCCA chr1D_1 TCTTTCTTGCCGTTTCGTAACTATGAGAACGAAAAGCAATTTCAAGCCCA chrUn_1 -------------------------------------------------- chr1D_123 TCTTTCTTACCGTTTCGTAACTATGAGAACGAAAAGCAATTTCAAGCCCA chr5D_152 TCTTTCTTACCGTTTCGTAACTATGAGAACGAAAAGCAATTTCAAGCCCA chr5D_614 TCTTTCTTACCGTTTCGTAACTATGAGAACGAAAAGCAATTTCAAGCCCA chr1D_1220 TCTTTCTTACCGTTTCGTAACTATGAGAACGAAAAGCAATTTCAAGCCCA SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 GTCAATTTCAATAATTACAGGTTCTAGACCCAGAAAAAATAGACATATTC chr3B_1 GTCAATTTCAATAATTACAGGTTCTAGACCCAGAAAA-ATAGACATATTC chr3D_1 GTCAATTTCAATAATTACAGGTTCTAGACCCAGAAAAAATAGACATATTC chr2D_1 GTCAATTTCAATAATTACAGGTTGTAGACCCAGAAAAAATAGACATATTC chr1D_1 GTCAATTTCAATAATTACAGGTTCTAGACCCAGAAAAAATAGACATATTC chrUn_1 -------------------------------------------------- chr1D_123 GTCAATTTCAATAATTACAGGTTCTAGACCCAGAAAAAATAGACATATTC chr5D_152 GTCAATTTCAATAATTACAGGTTCTAGACCCAGAAAAAATAGACATATTC chr5D_614 GTCAATTTCAATAATTACAGGTTCTAGACCCAGAAAAAATAGACATATTC chr1D_1220 GTCAATTTCAATAATTACAGGTTCTAGACCCAGAAAAAATAGACATATTC SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 CTCAATTAACGCAAAAGTACAATTCCAATCGAAACTTAAGAAACAACAAC chr3B_1 CTCAATTAACGCAAAAGTACAATTCCAACCGAAACTTAAGAAACAACAAC chr3D_1 CTCAATTAACGCAAAAGTACAATTCCAATCGAAACTTAAGAAACAACAAC chr2D_1 CTCAATTAACACAAAAGTACAATTCCAATCGAAACTTAAGAAACAACAAC chr1D_1 CTCAATTAACGCAAAAGTACAATTCCAATCGAAACTTAAGAAACAACAAC chrUn_1 -------------------------------------------------- chr1D_123 CTCAATTAACGCAAAAGTACAATTCCAATCGAAACTTAAGAAACAACAAC chr5D_152 CTCAATTAACGCAAAAGTACAATTCCAATCGAAACTTAAGAAACAACAAC chr5D_614 CTCAATTAACGCAAAAGTACAATTCC-ATCGAAACTTAAGAAACAACAAC chr1D_1220 CTCAATTAACGCAAAAGTACAATTCCAATCGAAACTTAAGAAACAACAAC SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 CAAAATTTAAGAAACAACAACCGGAACTTAAGTTCCGATTATTGATGTTT chr3B_1 CAAAATTTAAGAAACAACAACCGGAACTTAAGTTCTGATTGTTGATGTTT chr3D_1 CAAAATTTAAGAGACAACAACCGGAACTTAAGTTCCGATTGTTGATGTTT chr2D_1 CAAAATTTAAGAAACAACAACCGGAACTTAAGTTCCGATTGTTGATGTTT chr1D_1 CAAAATTTAAGAAACAACAACCGGAACTTAAGTTCCGATTGTTGATGTTT chrUn_1 -------------------------------------------------- chr1D_123 CAAAATTTAAGAAACAACAACCGGAACTTAAGTTCCGATTGTTGATGTTT chr5D_152 CAAAATTTAAGAAACAACAACCGGAACTTAAGTTCCGATTGTTGATGTTT chr5D_614 CAAAATTTAAGAAACAACAACCGGAACTTAAGTTCCGATTGTTGATGTTT chr1D_1220 CAAAATTTAAGAAACAACAACCGGAACTTAAGTTCCGATTGTTGATGTTT SNPs ----------------------------------------S--------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TATTCGAATTCGAAAGGGCCCGGCCTATATATATTATAAAGAAAGTAATC chr3B_1 TATTCGAATTCGAAAGGGCCAGACCTATATATATTATAAAGAAAGTAATC chr3D_1 TATTCGAATTCGAAAGGGCCAGACCTATATATATTATAAAGAAAGTAATC chr2D_1 TATTCGAATTCGAAAGGGCCAGACCTATATATATTATAAAGAAAGTAATC chr1D_1 TATTCGAATTCGAAAGGGCCAGACCTATATATATTATAAAGAAAGTAATC chrUn_1 -------------------------------------------------- chr1D_123 TATTCGAATTCGAAAGGGCCAGACCTATATATATTATAAAGAAAGTAATC chr5D_152 TATTCGAATTCGAAAGGGCCAGACCTATATATATTATAAAGAAAGTAATC chr5D_614 TATTCGAATTCGAAAGGGCCAGACCTATATATATTATAAAGAAAGTAATC chr1D_1220 TATTCGAATTCGAAAGGGCCAGACCTATATATATTATAAAGAAAGTAATC SNPs --------------------S-S--------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 CAGCTCGTTGATTCCTACCACTTAATCTTAAGTTGTTGTATCTTCCCGGA chr3B_1 CAGCTTGTTGATTCCTACCACTTAATCTTAATTTATTGTATCTTCCCGGA chr3D_1 TAGCTCGTTGATTCCTACCACTTAATCTTAATTTATTGTATCTTCCCGGA chr2D_1 CAGCTCGTTGATTCCTACCACTTAATCTTAATTTATTGTATCTTCCCGGA chr1D_1 CAGCTCGTTGATTCCTACCACTTAATCTTAATTTATTGTATCTTCCCGGA chrUn_1 -------------------------------------------------- chr1D_123 CAGCTCGTTGATTCCTACCACTTAATCTTAATTTATTGTATCTTCCCGGA chr5D_152 CAGCTCGTTGATTCCTACCACTTAATCTTAATTTATTGTATCTTCCCGGA chr5D_614 CAGCTCGTTGATTCCTACCACTTAATCTTAATTTATTGTATCTTCCCGGA chr1D_1220 CAGCTCGTTGATTCCTACCACTTAATCTTAATTTATTGTATCTTCCCGGA SNPs -------------------------------S--S--------------- forward_551 -------------------------------------------------- reverse_5685 ----------------------------------GTTGTATCTTCCCGGA input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 GTTCCCTCTCTGGGAATTCATCTTCTATTATTCCAGTATATTACTTTATT chr3B_1 GTTCCCTCTCCGGGAATTCATCTTTTTTTATTCCAGTATATTACTTTATT chr3D_1 GTTCCCTCTCCGGGAATTCAACTTTTATTATTCCAGTATATTACTTTATT chr2D_1 GTTCCCTCTCCGGGAATTAATCTTTTATTATTCCAGTATATTACTTTATT chr1D_1 GTTCCCTCTCCGGGAATTCATCTTTTATTATTCCAGTATATTACTTTATT chrUn_1 -------------------------------------------------- chr1D_123 GTTCCCTCTCCGGGAATTCATCTTTTATTATTCCAGTATATTACTTTATT chr5D_152 GTTCCCTCCCCGGGAATTCATCTTTTTTTATTCCAGTATATTACTTTATT chr5D_614 GTTCCCTCTCCGGGAATTCATCTTTTATTATTCCAGTATATTACTTTATT chr1D_1220 GTTCCCTCTCCGGGAATTCATCTTTTTTTATTCCAGTATATTACTTTATT SNPs ----------S-------------S------------------------- forward_551 -------------------------------------------------- reverse_5685 GTTCCC-------------------------------------------- input_sequence_87006 -------------------------------------------------- chr5D_1_TraesCS5D01G009500 TATACCTTTAATTGATGATCTTTATTTTATTGGAAATCGTGTAAAGATTA chr3B_1 TATACTTTTAATTGATGATCTTTATTTTATTGGAAATCGTGTAAAGATTA chr3D_1 TATACCTTTAATTGATGATCTTTATTTTATTGGAAATCGTGTAAAGATTA chr2D_1 TATACCTTTAATTGATGATCTTTATTTTATTGGAAATCGTTTAAAGATTA chr1D_1 TATACCTTTAATTGATGATCTTTATTTTATTGGAAATTGTGTAAAGATTA chrUn_1 -------------------------------------------------- chr1D_123 TATACCTTTAATTGATGATCTTTATTTTATTGGAAATCGTGTAAAGATTA chr5D_152 TATACTTTTAATTGATGATCTTTATTTTATTGGAAATCGTGTAAAGATTA chr5D_614 TATACCTTTAATTGATGATCTTTATTTTATTGGAAATCGTGTAATGATTA chr1D_1220 TATACTTTTAATTGATGATCTTTATTTTATTGGAA--------------- SNPs -------------------------------------------------- forward_551 -------------------------------------------------- reverse_5685 -------------------------------------------------- input_sequence_87006 ---------------- chr5D_1_TraesCS5D01G009500 TTTGGATTTGATACAG chr3B_1 TTTGGATTTGATACAG chr3D_1 TTTGGATTTGATACAG chr2D_1 TTTGGATTTGATACAG chr1D_1 TTTGGATTTGATACAG chrUn_1 ---------------- chr1D_123 TTTGGATTTGATACAG chr5D_152 TTTGGATTTGATACAG chr5D_614 TTTGGATTTGATACAG chr1D_1220 ---------------- SNPs ---------------- forward_551 ---------------- reverse_5685 ----------------