CLUSTAL X (1.81) multiple sequence alignment input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 TCTTTGTGCGCATGCCCTAAGGACCAGCTCCCCGGAGCCGCAGCCGTGAC chr3D_570 TAATTC-TT----------------------------------------- chr3D_571 AAATAATTA----------------------------------------- chr5D_572 ATTAATTTT----------------------------------------- chr2A_574 TAA----TT----------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 -------------------------------------------------- chr3B_579 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 -------------------------------------------------- chr3D_581 -------------------------------------------------- chrUn_581 -------------------------------------------------- chr1D_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr2A_581 -------------------------------------------------- chr7D_583 -------------------------------------------------- chr6D_583 -------------------------------------------------- chr2D_584 -------------------------------------------------- chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 TCA----------------------------------------------- SNPs -----S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 CGTTGAATTCTTGAATCGATCTGAAGAACTTGAACCAAATATCACCTTTG chr3D_570 -------------------------------------------------- chr3D_571 -------------------------------------------------- chr5D_572 -------------------------------------------------- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 -------------------------------------------------- chr3B_579 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 -------------------------------------------------- chr3D_581 -------------------------------------------------- chrUn_581 -------------------------------------------------- chr1D_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr2A_581 -------------------------------------------------- chr7D_583 -------------------------------------------------- chr6D_583 -------------------------------------------------- chr2D_584 -------------------------------------------------- chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 CGTACATAGGACGAGAAATCCTAACCTCGCCACCCCGAGGAGCTGGCAGC chr3D_570 -------------------------------------------------- chr3D_571 -------------------------------------------------- chr5D_572 -------------------------------------------------- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 -------------------------------------------------- chr3B_579 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 -------------------------------------------------- chr3D_581 -------------------------------------------------- chrUn_581 -------------------------------------------------- chr1D_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr2A_581 -------------------------------------------------- chr7D_583 -------------------------------------------------- chr6D_583 -------------------------------------------------- chr2D_584 -------------------------------------------------- chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 AATCTACGCCAGAGCTCCGTCTAATCCGTTCCAACGAACGAACTTGAGGA chr3D_570 -------------------------------------------------- chr3D_571 -------------------------------------------------- chr5D_572 -------------------------------------------------- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 -------------------------------------------------- chr3B_579 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 -------------------------------------------------- chr3D_581 -------------------------------------------------- chrUn_581 -------------------------------------------------- chr1D_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr2A_581 -------------------------------------------------- chr7D_583 -------------------------------------------------- chr6D_583 -------------------------------------------------- chr2D_584 -------------------------------------------------- chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_177 -------GCCAGAGCTCCGTCTAATCC----------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GGGTCGGAGCCCGAAAGACTGCCTCGAAGAAGAACCGCCACCATCGGTCC chr3D_570 -------------------------------------------------- chr3D_571 -------------------------------------------------- chr5D_572 -------------------------------------------------- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 -------------------------------------------------- chr3B_579 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 -------------------------------------------------- chr3D_581 -------------------------------------------------- chrUn_581 -------------------------------------------------- chr1D_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr2A_581 -------------------------------------------------- chr7D_583 -------------------------------------------------- chr6D_583 -------------------------------------------------- chr2D_584 -------------------------------------------------- chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 AAACGTCGCCCATGCGAGGACTTAAACCCTACCAATCTACTAGCCGGATC chr3D_570 -------------------------------------------------- chr3D_571 -------------------------------------------------- chr5D_572 -------------------------------------------------- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 -------------------------------------------------- chr3B_579 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 -------------------------------------------------- chr3D_581 -------------------------------------------------- chrUn_581 -------------------------------------------------- chr1D_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr2A_581 -------------------------------------------------- chr7D_583 -------------------------------------------------- chr6D_583 -------------------------------------------------- chr2D_584 -------------------------------------------------- chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 TGGGGCACCAGAAATCCCCTCCCCGCCACCGGCCGCCGGAGCGGCAGGCA chr3D_570 -------------------------------------------------- chr3D_571 -------------------------------------------------- chr5D_572 -------------------------------------------------- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 -------------------------------------------------- chr3B_579 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 -------------------------------------------------- chr3D_581 -------------------------------------------------- chrUn_581 -------------------------------------------------- chr1D_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr2A_581 -------------------------------------------------- chr7D_583 -------------------------------------------------- chr6D_583 -------------------------------------------------- chr2D_584 -------------------------------------------------- chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 ----------------------------------------------GGCA reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 TAGGAGAGGCGAATCCACGGGCTCGCCGGTGGAGATCGAGGGAAGGAAGA chr3D_570 -------------------------------------------------- chr3D_571 -------------------------------------------------- chr5D_572 -------------------------------------------------- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 -------------------------------------------------- chr3B_579 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 -------------------------------------------------- chr3D_581 -------------------------------------------------- chrUn_581 -------------------------------------------------- chr1D_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr2A_581 -------------------------------------------------- chr7D_583 -------------------------------------------------- chr6D_583 -------------------------------------------------- chr2D_584 -------------------------------------------------- chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 TAGGAGAGGCGAATCC---------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 CTTTCACTAGTCGCCTTCCGAGAGGGGAAAGAAAAACTTAATGATTTGAC chr3D_570 -------------------------------------------------- chr3D_571 -------------------------------------------------- chr5D_572 -------------------------------------------------- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 -------------------------------------------------- chr3B_579 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 -------------------------------------------------- chr3D_581 -------------------------------------------------- chrUn_581 -------------------------------------------------- chr1D_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr2A_581 -------------------------------------------------- chr7D_583 -------------------------------------------------- chr6D_583 -------------------------------------------------- chr2D_584 -------------------------------------------------- chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GACTATTAACTCGCATAAAATTTGTGAATATTATTCCTTTTAAATTTCCT chr3D_570 -------------------------------------------------- chr3D_571 -------------------------------------------------- chr5D_572 -------------------------------------------------- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 -------------------------------------------------- chr3B_579 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 -------------------------------------------------- chr3D_581 -------------------------------------------------- chrUn_581 -------------------------------------------------- chr1D_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr2A_581 -------------------------------------------------- chr7D_583 -------------------------------------------------- chr6D_583 -------------------------------------------------- chr2D_584 -------------------------------------------------- chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GATGAATATTAGTTGTGCACAAGCACTTAACTACATATCACCCATATGTA chr3D_570 -------------------------------------------------- chr3D_571 -------------------------------------------------- chr5D_572 -------------------------------------------------- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 -------------------------------------------------- chr3B_579 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 -------------------------------------------------- chr3D_581 -------------------------------------------------- chrUn_581 -------------------------------------------------- chr1D_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr3A_581 -------------------------------------------------- chr2A_581 -------------------------------------------------- chr7D_583 -------------------------------------------------- chr6D_583 -------------------------------------------------- chr2D_584 -------------------------------------------------- chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 TATCAATGATATATGCAGGTAATTAATTAAGGGTTAATTATCCTTTTGCC chr3D_570 -----------------------------AGGGTTAATTATCCTTTTGCC chr3D_571 ----------------------------AAGGGTTGATTATCCTTTTGCC chr5D_572 -----------------------------TGGGTTAATTATCCTTTTGCC chr2A_574 -----------------------------AGGGTTAATTATCCTTTTGCC chr1D_578 ---------------------------TAAGGGTTAATTATCCTTTTGCC chr2A_578 ---------------------------TAAGGGTTAATTATCCTTTTGCC chr5D_579 ----------------------------AAGGGTTAATTATCCTTTTGCC chr3B_579 ----------------------------AAGGGTTAATTATCCTTTTGCC chr2A_580 -----------------------------AGGGTTAATTATCCTTTTGCC chr2A_580 -----------------------------AGGGTTAATTATCCTTTTGCC chr1A_580 -----------------------------AGGGTTAATTATCCTTTTGCC chr5D_581 ------------------------------GGGTTAATTATCCTTTTGCC chr3D_581 ------------------------------GGGTTAATTATCCTTTTGCC chrUn_581 ------------------------------GGGTTAGTTATCCTTTTGCC chr1D_581 ------------------------------GGGTTAATTATCCTTTTGCC chr3A_581 ------------------------------GGGTTAATTATCCTTTTGCC chr3A_581 ------------------------------GGGTTAATTATCCTTCTGCC chr2A_581 ------------------------------GGGTTAATTATCCTTTTACC chr7D_583 --------------------------------GTTAATTATCCTTTTGCC chr6D_583 --------------------------------GTTAATTATCCTTTTGCC chr2D_584 ---------------------------------TTAATTATCCTTTTGCC chrUn_624 -------------------------------------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSS----------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 CTCAGTTGTGTCCATGTGCTCAGTTTTGCCCTCAGATGCGAATTGTGCTC chr3D_570 CTCAGTGGTGTCCGTGTGCTTAGTTTTGCCCTCAGATGCGAATTGTGCTC chr3D_571 CTTAGTGGTGTCCATGTACTCAGTTTTGCCCTCAGATGCGAATTATGCTC chr5D_572 CTTAGTGGTGTCCGTGTGCTCAGTTTTGCCCTCAGATGCGAATTGTGCTC chr2A_574 CTCAATGGTGTTCATGTACTCAGTTTTGCCCTCAGATGCGAATTGTGCTC chr1D_578 CTCAGTGGTGTCCATGTACTCAGTTTTGCCCTCAGATGTGAATTGTGCTC chr2A_578 CTCAGTGGTGTCCATGTACTCAGTTTTGCCCTCAGATGCGAATTGTGCTC chr5D_579 CTCAGTGGTGTCCATGTGCTCAGTTTTGCCCTCAGATGCGAATTGTGCTC chr3B_579 CTCAGTGGTGTCCATGTGCTCAGTTTTGCCCTCAGATGCGAATTGTGCTT chr2A_580 CTCAGTGGTGTCCATGTGCTCAGTTTTGCCCTCAGATGCGAATTATGCTC chr2A_580 CTCAGTGGTGTCCATGTGCTCAGTTTTGCCCTCAGATGCGAATTGTGCTC chr1A_580 CTCAGTGGTGTCTCTGTGCTCAGTTTTGCCCTCAGTTGTCAATCGTGCTT chr5D_581 CTCAGTGGTGTCTGTGTGCTCAGTTTTGCCCTCAGATGCGAATTGTGCTC chr3D_581 CTCAGTGGTGTCCATGTGCTCAGTTTTGCCCTCGGGTGCGAATCGTGCTC chrUn_581 CTCAGTGGTGTCCGTGTGCTCAGTTTTTCCCTCAGATGCGAATTGTGCTC chr1D_581 CTCAGTGGTGTCCGTGTGCTCAGTTTTGCCTTCAGATGTGAATTGTGCGC chr3A_581 CTCAATGGTGTCCGTGTGCTTAGTTTTGCCCTCAGACGCGAATTATGCTC chr3A_581 CTCAATGGTGTCTGTGTGCTCAGTTTTGCCCTCAGATGTGAATTGTGCTC chr2A_581 CTCGTTGGTGTCCATGTACTCAGTTTTGCCCTCAGATGCGAATTGTGCTC chr7D_583 CTCAGTGGTGTCCGTGTGCTCAGTTTTGCCCTCAGATGCGAATTGTGCTC chr6D_583 CTCAGTGGTGTCCGTGTGCTCAGTTTTGCCCTCAGATGCGAATTGTGCTT chr2D_584 CTCAC---TGTCCATGTACTCAGTTTTGCCCTCAGATGTGAATTGTGCTC chrUn_624 -----------------------TTTTGCCCTCAGATGCGAATTGTGCTC chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs ------S------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 AGTTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCCGTGAACTCTGCCAT chr3D_570 AGTTTTGCCCCTAGTCCATGCGCACCGACTCGTTCCGTGAACTCTGCCGT chr3D_571 AGTTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCCGTGAACTCTGCCGT chr5D_572 AGTTTTGCCCCTAGTCCGTGTGCACCGACTCGTTCCGTGAACTCTGTCGT chr2A_574 AGTTTTGCCCCTAGTTCGTGCGCACCGACTCGTTCCGTGAACTCTGCCGT chr1D_578 AGTTTTGCCCCTAGTCTGTGCGCACCGACTCGTTCCGTGAACTCTGCCGT chr2A_578 AGTTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCCGTGAACTCTGCCGT chr5D_579 AGTTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCCGTGAACTCTGCCGT chr3B_579 AGTTTTGCCCCTAGTCCATGCGCACCAACACTTTCCGTGAACTCTGCCGT chr2A_580 AGTTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCTGTGAACTCTGCCGT chr2A_580 AGTTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCCGTGAACTCTGCCGT chr1A_580 AGTTTTACCCCTAGTCTGTCCGCACCGACTCATTCCGTGAACACTGCCGT chr5D_581 AGTTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCCGTGAACTCTGCCGT chr3D_581 AGTTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCCGTGAACTCTGTCAT chrUn_581 AGTTTTGCCCCTAGTCCGTGCGCACTGACTCGTTCCGTGAACTCTGCCGT chr1D_581 AGTTTTGTCCCTAGTCCGTGTGCACCGGCACGTTCCGTGAACTCTGCCGT chr3A_581 AATTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCCATGAACTCTGCCGT chr3A_581 AGTTTTGCCCCTAGTCTGTGCGCACTGACTCGTTCCATGAACTCTGCCGT chr2A_581 AGTTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCCGTGAACTCTGCCGT chr7D_583 AGTTTTGCCCCTAGTCCGTGTGCACCGACTCGTTTCGTGAACTCTGCCGT chr6D_583 ACTTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCCGTGAACTCTGTCGT chr2D_584 AGTTTTGCCCCTAGTCCGTGCGCACCGACTCGTTCCGTGAACTCTTCCGT chrUn_624 AGTTTTGCTCCTAGTCCGTGCGCACCGACTCGTTCCGCGAACTCTGCCGT chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 CTCCGTCAGGTCAACCTTTTGACTCGGCCCTTACAGGTGGGACAAGGCGG chr3D_570 CTTCGTCAGGTCAACGTTTTGACTCGGCCCTTGCAGGTGGGACCAGGCGG chr3D_571 CTCCATCAGGTCAACCTTTTGACTCCGCCCTTACAGGTGGGACCAGGTGG chr5D_572 CTCCGTCAGGTCAACCTTTTGACTCGGCCCTTACAGGTGGGACCAGGCGG chr2A_574 CTCCGTCAGGTCAACCTTTTGACTCGGCCCTTACAGGTGGGACCAGGCGA chr1D_578 CTCCGTCAGGTCAACCTTTTGACTCGGCCCTTACAGGTGGGACCAGGCGG chr2A_578 CTCCATCAGGTCAACCTTTTGACTCGGCCCTTACAGGTGGGACCAGGCGG chr5D_579 CTCCGTCAGGTCAACCTTTTGACTCGGCCCATATAGGTGGGACCAGGTGG chr3B_579 CTCCGTCAGGTCAACCTTTTGACTCGGCCCTTACAGGTGGGCCCAGGCGG chr2A_580 CTCCGTCAGGTCAACCTTTTGACTCAGCCCTTACAGGTGGGACCAGGCGA chr2A_580 CTCCGTCAGGTCAACCTTTTGACTCCGCCCTTACAGGTGGGACCAGGCGA chr1A_580 CTCCGTCAGGTCAACGTTTTGACTCGGCC-ATACAGGTGGGACCAGGCGG chr5D_581 CTCCGTCAGGTCAACGTTTTGACTCGGCCCTTGCAGGTGGGACCAGGCGG chr3D_581 CTCCATCAGGTCAACCTTTTGACTCAGCCCTTACAGGTGGGACCAGGCGG chrUn_581 GTCCGTCAGGTCAACCTTTTGACTCGGCCCTTACAGGTGGGACCGGGCGG chr1D_581 CTCCGTCAGGTCAACCTTTTGACTCGGCCCTTACAGGTGGGACCAAGCGG chr3A_581 CTCCGTCAGGTCAACATTTTGACTCGGCCCTTAGAGGTGGGACCAGGCGG chr3A_581 CTCCGTTAGGTCAACGTTTTGACTCGGCCCTTACAGGTGGGGCCAAGCGG chr2A_581 CTCCATCAGGTCAACCTTTTGACTCGGCCCTTACAGGCGGGACCAGGCGG chr7D_583 CTCCGTCAGGTCAACGTTTTGACTCGGCCCTTATAGGTGGGACCAGGCGG chr6D_583 CTCCGTCAGGTCAACCTTTTGACTCGGCCCTTACAGGTGGGACCAGGTGG chr2D_584 CTCCGTCAGGTCAACCTTTTGACTCGGCCCTTACAGGTTGGACCAGGCGG chrUn_624 CTCCGTCAGGTCAACCTTTTAACTCGGCCCTTACAGGTGGGACCAGGCGG chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------S------ forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 CAGAGACGGCCAATTCTATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chr3D_570 CAGAGACGGCCAATTCTATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chr3D_571 CAGAGACGGCCAATTCTATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chr5D_572 CAAAGACGGCTAATTATATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chr2A_574 CAGAGACGGCCAATTTTATTCAGAATGTTACACGCGTGGCTTGTGGGACC chr1D_578 CAGAGACGGCCAATTTTATTCAGACTGTTGCACGCGTGGCTTGTGGGACC chr2A_578 CAGAGACGGCCAATTTTATTCAGACCGTTGCACGCATGGCTTGTGGGACC chr5D_579 CAGAGACGGCCAATTCTATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chr3B_579 CAGAGACGGCCAATTCTATTCAGACCATTGCACGCGTGGCTTGTGGGACC chr2A_580 CAGAAACGGCCAATTTTATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chr2A_580 CAGAAACGGCCAATTTTATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chr1A_580 CAGAGACGCGCTAGACGA-TCAGACCGTTGCTCTCGTGGCTTGTGGGACA chr5D_581 CAGAGACGGCCAATTCTATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chr3D_581 CAGAGACGCCCTAGACGA-TCAGACCGTTGCACGAGTGGCTTGTGGGACC chrUn_581 CAGAGACCGCCAATTCCATTCAGACCGTTGCATGCGTGGCTTGTGGGACC chr1D_581 CAGAGACAGCCAATTTTATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chr3A_581 CAAAGACGGTCAATTCTATTCAAACCGTTGCACGCGTGGCTTGTGGGACC chr3A_581 CAGAGACT-------------------TTGCACGCGTGGCTTGTGGGACC chr2A_581 CAGAGACGACCAATTTTATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chr7D_583 CAGAGACGGACAATTCTATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chr6D_583 CAGAGACGGCCAATTCCATTCAGACCGTTGCACGCGTGGCTTGTGGGATC chr2D_584 CAGAGACGGCCAATTCTATTCAGACCGTTGCACGCGTGGCTTGTGGGACC chrUn_624 CAGAGATGGCCAATTCTATTCAGACCGTTGCACGTGTGGCTTGTGGGACC chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 CAACAGAGAGC---------------CGTTG----------------CGG chr3D_570 CAGCAGAGAGC---------------CGTTG-AGCAGAGAGCCGTTGCGG chr3D_571 CAGCAGAGAGC---------------CGTTG----------------CGG chr5D_572 CAGCAGAGAGC---------------CGTTG----------------CGG chr2A_574 CAGCAGAGAGC---------------CGTTGG---------------CGG chr1D_578 CAGCAGAGAGC---------------CTTT-G---------------CGG chr2A_578 CAGCAGAGAGC---------------CGTT-G--------------GCGG chr5D_579 CAGCAGAGAGC---------------CGTT-GAGCAGAGAGCCGTTGCGG chr3B_579 CAGCAGAGAGT---------------CGTG-GAGCAGAGAGCCGTTGCGG chr2A_580 CAGCAGAGAGC---------------CGTTGG---------------CGG chr2A_580 CAGCAGAGAGC---------------CGTT-G--------------GCGG chr1A_580 CAGCAAAGAGTCGTTGAGCAGAGGAACGTT-G---------------CGG chr5D_581 CAGCAAAGAGC---------------CGTT-G---------------CGG chr3D_581 CAGCAGAGAGC---------------CGTT-GAGCAGAGAGCCCTTGCGG chrUn_581 TAGCAGAGAGC---------------CTTT-GAGTAGAGAGTCGTTGCGG chr1D_581 CAGCAGAGAGC---------------TGTT-GAGCAGAGAGCCGTTGCGG chr3A_581 CAGCAGAGAGC---------------CGTT-GAGCAGAGAGCCATTGCGG chr3A_581 CAGCAGAGAGC---------------CGTT-G---------------CGG chr2A_581 CAGCAGAGAGC---------------CGTT-A--------------GCGG chr7D_583 CAAGAGAGAGC---------------CGTT-GAGCAGAGAGTCGTTGCGG chr6D_583 CAGCAGAGAGC---------------CGTT-GAGTAGAGAGCTGTTGCGG chr2D_584 CAGCAGAGAGC---------------CTTT-GAGTAGAGAGCCGTTGCGG chrUn_624 CAGCAGAGAGC---------------CGTT-GAGCAGAGAGCCATTGCGA chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GTGTGCTATAT-AAGCGGGC----GA----CACACAGCGGCGGTGACCAC chr3D_570 GTGTGCTATATAAAGCAGGC----GA----CACACAGCGGCGGTGACTAC chr3D_571 GTGTGCTATAT-AAGCGGGC----GA----CA----GCGGCGGTGACCAC chr5D_572 GTGTGCTATAT-AAGCGGGC----GA----CACACAGCGGCGGTGACCAT chr2A_574 GTGTGCTATAT-AAGCGGGC----GA----CA----GCGGCGGTGACCAC chr1D_578 GTGTGCTATAT-AAGCGGGC----GA----CA----GCGGCGGTGACCAC chr2A_578 GTGTGCTATAT-AAGCGGGC----GA----CA----GCGGCGGTGACCAC chr5D_579 GAGTGCTATAT-AAGCGGGC----GA----CACACAACGGCGGTGACCAC chr3B_579 GTGTGCTATAT-AAGCGGGC----GA----AA----GCGGCGGTGACCAC chr2A_580 GTGTGCTATAT-AAGCGGGC----GA----CA----GCGGCGGTGACCAC chr2A_580 GTGTGCTATAT-AAGCGGGT----GA----CA----GCGGCGGTGACCAC chr1A_580 GTGTGCGATAT-AAGCGGGC----GA----CACAGAGCGGCGGTGACCAC chr5D_581 GTGTGCTATAT-AAGCGGGC----GA----CACACAGCGGCGGTGACCAC chr3D_581 TTGTGCTATAT-AAGTGGGC----GACAGACA----GCGGCGGTGACCAC chrUn_581 GTGTGCTATAT-AAGCGGGC----GA----CACACAGCGGCGGTGATAAC chr1D_581 GTGTGCTATAT-AAGCGGGC----GA----CA----GCGGCGGTGACCAC chr3A_581 GTGTGCTATAT-AAGCGGGC----GA----CACATAGCGGCGGTGACCAT chr3A_581 GTGTGCTATAT-AAGCAGGC----GA----CACACAGCGGCGGTGACCAC chr2A_581 GTGTGCTATAT-AAGCGGGC----GA----CA----GCGGCGGTGACCAC chr7D_583 GTGTGCTATAT-AAGCGGGC----GA----CACACAGCGGCGGTGACCAC chr6D_583 GTGTGCTATAT-AAGCGGAC----GA----CACACAGCGACGGTGACCAC chr2D_584 GTGTGCTATAT-AAGCGGGCGACAGA----CA----GCGGCGATGACCAC chrUn_624 GTGTGCTATAT-AAGCGGGC----GA----CA----GCGGCGGTGACCAC chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GGCGACAAAGAGCACGGCGGTGACCACGGC-------------------- chr3D_570 GGCGGCAGAGAGCACGTCGGTGACCACGGC-------------------- chr3D_571 GGCGATAGAGAGCACGGCGGTGACCACGGACACAGAGAGAGAGA------ chr5D_572 GGCGACAGAGAGCACAGCGGTGACCACGGCA------------A------ chr2A_574 GGCGACAGAGAGCACGGCAATGACCACGGC-------------------- chr1D_578 GGCGACAAAGAGCACGGCGGTGACCATGGC-------------------- chr2A_578 GACGACAGAGAGCACGACGGTGACCACGGC-------------------- chr5D_579 GGCGACAGAGAGCACGGCGGTGACCACGGC-------------------- chr3B_579 GGTGACAGAGAGCACGGCAGTGACCAC----------------------- chr2A_580 GGCGACAGAGAGCACAACAGTGACCACGGC-------------------- chr2A_580 GGCGACAGAGAGCACCGCAGTGAGCACGGC-------------------- chr1A_580 GGCGACAGAGAGAGCG-----------GGC----------GACA------ chr5D_581 GGTGACAGAGAGCATGGCGGTGACCACGGC----------GAGA------ chr3D_581 GGCGATAGAGAGCACGGCGGTGACCACGGC----------GACA------ chrUn_581 GGCGACAGAGAGCACGGCGGTGACAACAGC----------GAGA------ chr1D_581 GGCGACAGAGAGCACGACGGTGACCACGGC-------------------- chr3A_581 GGCGACAAAGAGCACGACGGTGACCACGGC----------GAGAGAGAGA chr3A_581 GGCGACAGAGAGCCCGACGATGACCACGGC----------GAGA------ chr2A_581 GGCGACAGAGAGCACATCAGTGACCACGAC-------------------- chr7D_583 GGCGACAGAGAGCACGGCGGTGACCACGGC----------GAGA------ chr6D_583 GGCGAGAGAGAGCACGGCGGTGACCACGGC----------GAGA------ chr2D_584 GGCGACAGAGAGCACGGCG------------------------------- chrUn_624 GGCGACAGAGAGCACGGCGGTGACCACGGC-------------------- chr1A_906 -------------------------------------------------- chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 ---------------------GAGAGAGAGAGAGCACGGCGGTGACCACT chr3D_570 ---------------------GAGAGAGAGAGAGCACGGA---------- chr3D_571 -------------------GAGA--------------------------- chr5D_572 -------------------GAGA--------------------------- chr2A_574 ---------------------GAGAGAGAGAGAGCACGGC---------- chr1D_578 ---------------------GAGAGAGAG-------------------- chr2A_578 -------------------------------------------------- chr5D_579 ---------------------GA--------------------------- chr3B_579 --------------------AGC--------------------------- chr2A_580 ---------------------GA--------------------------- chr2A_580 ---------------------GA--------------------------- chr1A_580 -------------------GAGA----------GCGCGGCAGTGACCACG chr5D_581 -------------------GAGAGAGAGAGAGAGCACGGCGGTGACCACG chr3D_581 -------------------GAGA----------GCATGGCGGTGACCACG chrUn_581 -------------------GAGA--------------------------- chr1D_581 ---------------------GA--------------------------- chr3A_581 GCACGACGGTGACCACGGCGAGA--------------------------- chr3A_581 -------------------GAGA------GAGAGCACGGCGGTGACCACG chr2A_581 ---------------------GA--------------------------- chr7D_583 -------------------GAGA------GAGAGCACGGCGGTGACCATG chr6D_583 -------------------GAGA--------------------------- chr2D_584 --------------------AGA--------------------------- chrUn_624 ---------------------GA--------------------------- chr1A_906 ------------------------------------CGGCGGTTACCACG chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------S forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GC----GAGAGA-G-------------------------AGAG------- chr3D_570 -------------------------------------------------- chr3D_571 ------GAGAGA-G-------------------------AGAG------- chr5D_572 ------GAGAGA-G-------------------------AGAG------- chr2A_574 -------------------------------------------------- chr1D_578 ---------------------------------------GGAG------- chr2A_578 --------GAGA-G-------------------------AGAG------- chr5D_579 ------GAGAGA-G-------------------------GGAG------- chr3B_579 ------GAGAGA-G-------------------------AGAG------- chr2A_580 ------GAGAGA-G-------------------------AGAGCACGGCG chr2A_580 ------GAGAGA-G-------------------------AGAGCATGGCG chr1A_580 GT--------GA-T-------------------------GGAG------- chr5D_581 GC----GAGAGA-G-------------------------AGAG------- chr3D_581 GC--------GAGG-------------------------AGAG------- chrUn_581 ------GAGAGA-G-------------------------AGAG------- chr1D_581 ------GAGAGA-G-------------------------AGAG------- chr3A_581 ------GAGAGA-G-------------------------AGAG------- chr3A_581 GCGAGAGAAAGA-G-------------------------AGAG------- chr2A_581 ------GAGAGA-GAGCACAACGGTGGCAAGCTAGCTGTGGAG------- chr7D_583 GC----AAGAGA-G-------------------------AGAG------- chr6D_583 ------GAGAGA-G-------------------------AGAG------- chr2D_584 ------GAGAGA-G-------------------------AGAG------- chrUn_624 ------GAGAGA-G-------------------------AGAG------- chr1A_906 ------GAGAGA-G-------------------------AGAG------- chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 --------------------AGCACGGCGGTGGGAAG------------- chr3D_570 ----------------------------GGTGGGAAG------------- chr3D_571 --------------------AGCACGACGGTGGGAAG------------- chr5D_572 --------------------AGCACGGCGGTGGGAAG------------- chr2A_574 ----------------------------GGCGGGAAGCTAGCTGTGGAGG chr1D_578 --------------------AGCATGGCGGTGGGAAG------------- chr2A_578 --------------------AGCACGGCGGCGGGAAG------------- chr5D_579 --------------------AGCACGGCGGTGGGAAG------------- chr3B_579 --------------------AGCACGGCGGCGGGAAG------------- chr2A_580 GCGGGAAGCTAGCTGTGGAGGGCGCGGTGGTGGGAAG------------- chr2A_580 GCGGGAAGCTAGCTGTAGAGGGCACGGCGGTGGGAAG------------- chr1A_580 --------------------AGAGCGGCGGTGGGAAG------------- chr5D_581 --------------------AGCATGGCGGTGGGAAG------------- chr3D_581 --------------------AGAGCGGCGGTGGGAAG------------- chrUn_581 --------------------AGCACGTCGGTGAGAAG------------- chr1D_581 --------------------AGCACGGCGGTGGGAAG------------- chr3A_581 --------------------AGCACGGCGGTGGGAAG------------- chr3A_581 --------------------AGCACGGAGGTAGGAAG------------- chr2A_581 --------------------GGCGCGGCGGTGGGAAG------------- chr7D_583 --------------------AGCACAGCGGTGGGAAG------------- chr6D_583 --------------------AGCACGGCGGTGAGAAG------------- chr2D_584 --------------------AGCACGACGGTCGGAAG------------- chrUn_624 --------------------AGCACGGCGGTGGGAAG------------- chr1A_906 --------------------AGCACGGCGGTGGGAAG------------- chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 ----------------CTAGCTGTGGAGGGCG------------------ chr3D_570 ----------------CTAGCTGTGGAGGGCG------------------ chr3D_571 ----------------CTAGCTGTGGAGGGCG------------------ chr5D_572 ----------------CTAGCCATGGAGGGCG------------------ chr2A_574 GCGCGGCGGTGGGAAGCTAGCAGTGGAGGGCG------------------ chr1D_578 ----------------CTAGCTGTGGAGGGCG------------------ chr2A_578 ----------------CTAGCTGTGGAGGGCGCGGCGGTGGGAAGCTAGC chr5D_579 ----------------CTAGCTGTGGAGGGCGCGGCGG------------ chr3B_579 ----------------CTAGATGTGGAGGGCGCGG--------------- chr2A_580 ----------------CTAGCAGTGGAGGGCGCGGCGG------------ chr2A_580 ----------------CTAGCAGTGGAGGGCGCGGCGG------------ chr1A_580 ----------------ATAGCTATGGAGGGTG------------------ chr5D_581 ----------------CTAGCTGTGGAGGGCG------------------ chr3D_581 ----------------CTAGCTGTGGAGGGCG------------------ chrUn_581 ----------------CTAGCTGTGGAGGGCG------------------ chr1D_581 ----------------CTAGCTGTGGAGGGCG------------------ chr3A_581 ----------------CTAGCTGTGGAGGGCA------------------ chr3A_581 ----------------CTAGTTGT-GAGGGTG------------------ chr2A_581 ----------------CTAGCTGTGGAGGGCG------------------ chr7D_583 ----------------CTAGCTGTGGAGGGCG------------------ chr6D_583 ----------------CTAGCTATGGAGGGCG------------------ chr2D_584 ----------------CTAGCTGTGGAGGGCG------------------ chrUn_624 ----------------CTAGCTGTGGAGGGCG------------------ chr1A_906 ----------------CTAGCTGTGGAGGGCG------------------ chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 -----------CGGC-----------------------------GGCGTT chr3D_570 -----------CGGC-----------------------------GGCGTT chr3D_571 -----------CGGC-----------------------------GGCGTT chr5D_572 -----------CGGC-----------------------------GGCGTA chr2A_574 -----------CGGC-----------------------------GGCGTT chr1D_578 -----------CGGCGGTGGGAAGCTAGCTGTGGAGGGTGTGGCGGCATT chr2A_578 AGTGAAGGGCGTGGC-----------------------------GGCGTT chr5D_579 ----------------------------------------------CGTT chr3B_579 --------------T-----------------------------GGCGTT chr2A_580 ----------------------------------------------CGTT chr2A_580 ----------------------------------------------CGTT chr1A_580 -----------TGTC-----------------------------GGCGTT chr5D_581 -----------CGGC-----------------------------GACGTT chr3D_581 -----------TGGC-----------------------------GGCGTT chrUn_581 -----------CGGC-----------------------------GGCGTT chr1D_581 -----------CGGC-----------------------------GGCGTT chr3A_581 -----------CGGT-----------------------------GGTGTT chr3A_581 -----------CTGC-----------------------------GGTGTT chr2A_581 -----------CGAC-----------------------------GACGTT chr7D_583 -----------CGGC-----------------------------GGTGTT chr6D_583 -----------CGGC-----------------------------GGCGTT chr2D_584 -----------CGGC-----------------------------GGCGTT chrUn_624 -----------CGGC-----------------------------GGCGTT chr1A_906 -----------CGGT-----------------------------GGCGTT chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------ATGTCTTCCTCAAGCTCCCGCGCCA chr5D_1_TraesCS5D01G012600 GAGATCCCCTTCGGCTTCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr3D_570 GAGATCCCCTTCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr3D_571 GAGATCCCCTTCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr5D_572 GAGATCCCCTTCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr2A_574 GAGATCCCCTTCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr1D_578 GAGATCCCCTTCGGCTCCGAGCTCCATGTCTTACTCAAGCTCCCGTGCCA chr2A_578 GAGATCCCCTTCGGCTCTGAGCTCCATGTCTTCCTCAAGCTCTCGCGCCA chr5D_579 GAGATCCCCTTCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr3B_579 GAGATCCCCTTCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCTCGCGCCA chr2A_580 GAGAT-CCCTTCGACTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr2A_580 GAGAT-CCCTTCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr1A_580 GAGATCCCCGTCGGCTCCGAGCTTGATGTCTTCTTCAAGCTCCCGCGCCA chr5D_581 GAGATCCCCTTTGGCTCCGAGCTCCATGTCTTCCTCTAGCTCCCGCGCCA chr3D_581 GAGATCCCCTTCGGCTCTGAGCTCCATGTCTTCCTCAAGCTCCCGCACCA chrUn_581 GAGATCCCCTTCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr1D_581 GAGATCCCCTTCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr3A_581 GAGATCGCCTTCGGCTCCGCGCTCCATGTCTTCCTCAAGCTCCTGCGCCA chr3A_581 GAGATCCCCTTTGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr2A_581 GAGATCCCATTCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr7D_583 GAGATCCCCTTCAGCTCCGAGCTCCATGTCTTGCTCAAGCTCCCGCGCCA chr6D_583 GAGATCCCC-TCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr2D_584 GAGATCCCTTTCGGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chrUn_624 GAGATCCCCTTCAGCTCCGAGCTCCATGTCTTCCTCAAGCTCCCGCGCCA chr1A_906 GAGAACCCCTTCGGCTCCGAGCTCCATGTCTTCCTTAGGCTCCCGCGCCA chr7D_1233 -------------------------------------------------- SNPs ----------------S--------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTCTGT chr5D_1_TraesCS5D01G012600 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTCTGT chr3D_570 CCTCATGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTCTGT chr3D_571 CCTCGCGGATGCAGAGCCGGGTGCGTGTGGACATGCGTGTCTTCGTCTGT chr5D_572 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTTTGT chr2A_574 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCATCTGT chr1D_578 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATTCCTGTCTTCGTCTGT chr2A_578 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCATGTCATCGTCTGT chr5D_579 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTTTGT chr3B_579 CCTCGCGGATGCAGAGCCGGGTGCGTGTGGACATGCCTGTCTTCGTCTGT chr2A_580 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTCTGT chr2A_580 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTCTGT chr1A_580 CCTCGCGGATGCAAAGCCTAGCGCGCATGCAGATGTCGATCTTTGTTAGT chr5D_581 CCTCACGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTCTGT chr3D_581 CCTCGCGGATGCAGAGCCGGGCGCATATGGACATGTCAGTCTTCGTCTGT chrUn_581 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTCTGT chr1D_581 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTCTGT chr3A_581 CCTCACGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCATCTGT chr3A_581 CCTCACGGATGCAGAGCCGGGCACGTGTGGACATGCCTGTCTTCGTCTGT chr2A_581 CCTCACGGATGCAGAGCCGGACGCGTGTGGACATGCCTGTCTTCGTCTAT chr7D_583 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTCTCT chr6D_583 CCTCGCGGATGTAGAGCCGGGCGCGTGTGGACATGCCTATCTTCGTCTGT chr2D_584 CCTCGCGGATGCAGAG-CGGGCGCGTGTGGACATGCCTGTCTTCGTCTGT chrUn_624 CCTCGCGGATGCAGAGCCGGGCGTGTGTGGACATGCCTGTCTTCGTCTGT chr1A_906 CCTCGCGGATGCAGAGCCGGGCGCGTGTGGACATGCCTGTCTTCGTCTGT chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 CCGCGGTGCCGGGCGGGCGTTGTTCGGAGGGTTTCTCACACACCGAGGAA chr5D_1_TraesCS5D01G012600 CCGCGGTGCCGGGCGGGCGTTGTTCGGAGGGTTTCTCACACACCGAGGAA chr3D_570 CCACGGTGCCGGGCGGGCGTTGTTCGAAGGGTTTCTCACACACCGAGGAA chr3D_571 CCGCGGTGCCGGGCGGGTGTTGTTCGGAGGGTTTCTCACACACCGAGGAA chr5D_572 CTGCGGTGCCGGGCGGGCGTTGTTCGGAGGGTTTCTCACACACCGAGGAA chr2A_574 TCGCGGTGCCGGGCGGGCGTTGATCGGAGGGTTTCTCACACAACGAGGAA chr1D_578 CCGCAGTGCCGGGCGGGCGTTGATCGGAGGGTTTCTCACACACCGAGGAA chr2A_578 CCGCAGTGCCGGGCGGGCGTTGATCGGAGGGTTTCTCAGACACCGAGGAA chr5D_579 CCGCGGTGCCGGGCGGGCGTTGTCCGGAGGGTTTCTCACACACCGAGGAA chr3B_579 CTGTGGTGCCGAGCGGGCGTTGTTCGGAGGGTTTCTCACACACTGAGGAA chr2A_580 CCGCGGTGCCGGGCGGGCGTTGATCGAAGGGTTTCTCAGACACCGAGGAA chr2A_580 CTGTGGTGCCGGGCGGGCGTTGATCGGAGGGTTTCTCAGACACCGAGGAA chr1A_580 CCGCGGTGCCGGGCGGGCATTGATCGGAGGGTTTCTCACACACCGAAGAA chr5D_581 CCGCTGTGCCAGGCGGGCGTTGTTCGGAGGGTTTCTCACACATCGAGGAA chr3D_581 CCGCGGTGCCGGGCGGGTGTTGATCGGAGGGTTTCTCACACACCGAGGAA chrUn_581 CCGTGGTGCCGGGCGGGCGTTGTTCGGAGGGTTTCTCACACACTGAAGAA chr1D_581 CCGCAGTGCCGGGCGGGCGTTGATCGGAGGGTTTCTCACACACCGAGGAA chr3A_581 CTGTGGTGCCGGGCAGGCGTTGTTCGGAGGGTTTCTCACACACCGAGGAA chr3A_581 CCCCGGTGCCGGGCGAGCGTTGTTCGGAGGGTTTCTCACACATCGAGGAA chr2A_581 CCGCGGTGCCGGGCGGGCGCTGATCGGAGTGTTTCTCACACACCGAGGAA chr7D_583 CCGCGGTGCCGGGCGGGCGTTGTTCGGAGGGTTTCTCACACACTGAGGAA chr6D_583 CCGCGGTGCCGGGCAGGTGTTGTTCGGAGGGTTTCTCACACACCGAGGAA chr2D_584 CCACGGTGCCGGGCGGGCGTTGATCGGAGGGTTTCTCACACACCGAGGAA chrUn_624 CCGCGGTGCCGGGCGGCCGTTGTTCGGAGGGTTTCTCACACACCGAGGAA chr1A_906 CCGCGGTGCCGGGTGGGCATTGTTCCGAGGGTTTCTCACACACCGAGGAA chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 CCAGAATCGTCCGTTCTACGTGTGCAGCGAGAATGGGGTAAGAATCGGGG chr5D_1_TraesCS5D01G012600 CCAGAATCGTCCGTTCTACGTGTGCAGCGAGAATGGGGTAAGAATCGGGG chr3D_570 CCAGAATCGTCCGTTCTACGTGTGCAGCGAGAATGGGGTAAGAATCAGGG chr3D_571 CCAGAATCGTCTATTCTACGTGTGCACCGAGAATGGGGTAAGAATCGGGG chr5D_572 CCAGAATCGTTCGTTCTACGTGTGCAGCGAGAATGCGGTAAGAATCGGGG chr2A_574 CCAAAATCGTCCGTTCTACATGTGCGGCGAGAATGGGGTAAGAATCGGGG chr1D_578 CCAGAATCGTCCGTTCTACGTGTGTAGCGAGAATGGGGTGAGAATCAGGG chr2A_578 CCAGAATCGTCCGTTCTACGTGTGCAACGAGAATGGGGTAAGAATCGAGG chr5D_579 CCAGAATCATCCGTTCTACGTGTGCAGCGAGAATGGGGTAAGAATCGGGG chr3B_579 CTAGAATCATTCGTTCTACGTGTGCAGCGAGAATGGGGTAAGAATCGAGG chr2A_580 CAAGAATCGTCCGTTCTATGTGTGCAGCGAGAATGGGGTAAGAATCGGGG chr2A_580 CCAGAATCATCCGTTCTACGTGTGCAGCAAGAATGGGGTAAGAATCGGGG chr1A_580 CCATAATCGTCTGTTCTACGTGTGCAGTGAGAATGGGGTAAGAATCGGGG chr5D_581 CCAGAATCGTCCGTTCTACATGTGCAGCGAGAATGGGGTAAGAATCGGGG chr3D_581 CCATAATCGTCCATTCTACGTGTGCAACAAGAATGGGGTAAGAATCGGGG chrUn_581 CCAGAATCGTCAGTTCTACGCGTGCAGCGATAATGGGATAAGAATTGGTG chr1D_581 CCAGAATCGTCCGTTCTACATGTGCAGCGAGAATGGGGTAAGAATCGGGG chr3A_581 CCATAATTGTCCGTTCTACGTGTGCAGCGAGAATGGGGTAAGAATCGGGG chr3A_581 CCAGAATCATCCGTTCTACAGGTGCAGCGAGAATGGGGTAAGAATCGGGG chr2A_581 CCAGAATCGTACGTTCTACGTGTGCAGCGAGAATGGGGTAAGAATCGGGG chr7D_583 CCAGAATCGTCCGTTCTACGTGTGCAGCGAGAATGGGGTAAGAATCGGGG chr6D_583 CCATAATCGCCCGTTCTACGTGTGCAACGAGAATGGGGTAAGAATCGGGG chr2D_584 CCAGAATCGTCCGTTCTACGTGTGCAGCGAGAATGGGGTAAGAATCGGGG chrUn_624 CCAGAATCGTCCGTTCTACGTGTGCAACGAGAATGGGGTAAGAATCGGGG chr1A_906 CCAGAATCGTCCGTTCTACGTGTGTTGCGAGAATGGGGTAAGAATCAGGG chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 CAATTGCACCATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGATCTAT chr5D_1_TraesCS5D01G012600 CAATTGCACCATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGATCTAT chr3D_570 CAATTGCACCATTTTCGTAGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr3D_571 CAATTGCATCATTTTCGTGGCCGGGATCTTTGAGCAATGGGTTGATCTGC chr5D_572 CAATTGCACCATTTTCATGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr2A_574 AAATTGCACCATTTTAGTGGTCGGGATCTTTGAGAAATGGGTTAATCTGT chr1D_578 CAATTGCACCATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGATCTAT chr2A_578 CAATTGCACCATTTTCGTGGTTGGGATCTTTGAGCAATGGGTTGATCTGT chr5D_579 CAATTGCACCATTTTCGTGGTCGAGATCTTTCAGCAATGGGTTGATCTGT chr3B_579 CAATTGCACCATTTTCGTGGTTGGGATCTTTGAGCAATGGGTTGATCTGT chr2A_580 CAATTGCACCATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr2A_580 CAATTGCACCATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr1A_580 CAATTGCACCATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr5D_581 CAATTGCACCATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr3D_581 TAATTGCACCATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chrUn_581 CAATTG-ACCACTTTCGTGGTCAGGATCTTTGAGCAATGGGTTGATCTGT chr1D_581 CAATTGCACCATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGAGCTGT chr3A_581 CCATTGCAACATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr3A_581 CAATTGCACCATTTTCATGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr2A_581 CAATTGCACCATTTTCATGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr7D_583 CAATTGCACCATTTTGGTGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr6D_583 CAATTGCACCATTTTCGTGGTCGGGGTCTTTGAGCAATGAGTTGATCTGT chr2D_584 CAATTGCACCATTTTCATGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chrUn_624 CAATTGCACCATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr1A_906 CAATCACACCATTTTCGTGGTCGGGATCTTTGAGCAATGGGTTGATCTGT chr7D_1233 -------------------------------------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 TTAGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTTTGGC chr5D_1_TraesCS5D01G012600 TTAGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTTTGGC chr3D_570 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCAATGCTCTGGC chr3D_571 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr5D_572 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr2A_574 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr1D_578 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr2A_578 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr5D_579 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr3B_579 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGTTCTGGC chr2A_580 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr2A_580 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr1A_580 TTGGCGTTCATGCAGGTGAAATGTTGGTTCCTTTGGGTCGATGCTCTGGC chr5D_581 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr3D_581 TTGGCGTTCATGCAGGTGAAATGCTTCTTTCTTTGGATCGATGCTCTAGC chrUn_581 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr1D_581 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr3A_581 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGTC chr3A_581 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGTC chr2A_581 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr7D_583 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr6D_583 TTGGTGTTCATGTAAGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr2D_584 TTGGTGTTCATGCAGGTGACGTGCTTCTTTCTTTGGGTCGATGCTCTGGC chrUn_624 TTGGTGCTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr1A_906 TTGGTGTTCATGCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC chr7D_1233 -----------GCAGGTGACATGCTTCTTTCTTTGGGTCGATGCTCTGGC SNPs --S------------------------------------------S---- forward_177 -------------------------------------------------- reverse_1453 --AGTGTTCATGCAGGTGACATG--------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGTGCA chr5D_1_TraesCS5D01G012600 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGTGCA chr3D_570 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGTGCA chr3D_571 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGCAGAATGGTTGCGCA chr5D_572 CAAGACTCTGATGAATGAAATGCAAGAAGAGCATGAAGAATGGTTGTGCA chr2A_574 CAAGACTCTGATGAATGAACTGCAAGAAAAGCATGAAGTATGGTTGCGCA chr1D_578 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGCGCA chr2A_578 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGCGCA chr5D_579 CAAGACTCTGATGAATGAAATGCAAGAAGAGCATGAAGAATGGTTGTGCA chr3B_579 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGCGCA chr2A_580 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGCGCA chr2A_580 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGCGCA chr1A_580 CAAGACTCTGATGAATGAACTGCAAGAATAGCATGAAGAATGGTTGCCCA chr5D_581 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGTGCA chr3D_581 CAATAATCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGTGCA chrUn_581 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGTGCA chr1D_581 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGCGCA chr3A_581 CAAGACTTTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGTGCA chr3A_581 CAAGACTCTGATGAACGAACTGCAA-----GCATGAAGAATGGTTGTGCA chr2A_581 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGCGCA chr7D_583 CAAGACTCTGATGAATGAACTGCAAGAATAGCATGAAGAATGGTTGTGCA chr6D_583 CAAGACTCTGATGAATGAACTGCAAGAAGATCATGAAGAATGGTTGTGCA chr2D_584 CAAGACTCTGATGAATGAACTGCAAGAAGAGCATGAAGAATGGTTGCGCA chrUn_624 CAAGACTCTGATGAATGAACTGCAAGAAGAACATGAAGAATGGTTGCGCA chr1A_906 CAAGACTCTGATGAATGAACTTCAAGAAGAGCATGAAGAATGGTTGCGCA chr7D_1233 CAAGACTCTGATGAATGAACTACAATAAGAGCATGAAGAATGGTTGCGCA SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 TGCTGCCACGAACGGCAGTGGCCGCAGCACGAGCTCTTGAAGAAGAGATG chr5D_1_TraesCS5D01G012600 TGCTGCCACGAACGGCAGTGGCCGCAGCACGAGCTCTTGAAGAAGAGATG chr3D_570 TGCTGCCACGAACGGCAGTGGCCGCAGCACGAGCTCCGGAAGAAGAGATG chr3D_571 TGCTGCCACGAACGGTAGTGGCCGCAGCACGAGCTCCGGAAGAAGAGATG chr5D_572 TGCTGCCACGAATGGCAGTGGCCGCAGCACGAGCTCCGGAAGAAGAGATG chr2A_574 TGCTGCCACGAACGGCAGTGGCCGCACCACGAGCTCCGGAAAAAGAGATG chr1D_578 TGCTGCCACGAACGGCAGTGGCCGCAGCACGAGCTCTGGAAGAAGAGATG chr2A_578 TGCTGCCACGAACGGCAGTGGCCGCACCACGAGCTCCGGAAGAAGAGATG chr5D_579 TGCTGCCACGAATGACAGTGGCCGCAGCACGAGCTCCGGAAGAAGAGATG chr3B_579 TGCTGCCACGAACGGCAGTGGCCGCAGCACGAGCTCCGAAAGAAGAGATG chr2A_580 TGCTGCCACGAACGGCAGTGGCCGCACCACGAGCTCCGAAAGAAGGGATG chr2A_580 TGCTGCCACGAATGGCAGTGGCCGCACCACGAGCTCCGGAAGAAGGGATG chr1A_580 TGCTGCCATGAACGGCAGTGGCCGCAACACAAGCTCCGGAAGAACAGACG chr5D_581 TGCTGCCACGAATGACAGTGGCCGCAGCACGAGCTCCGGAAGAAGAGATG chr3D_581 TGCTGCCACGAACAGCAGTGGCCGCAGCACGAGCTCCGGAAGAAGAGATG chrUn_581 TGCTGCCACGAACGGCAGTGGCCGCAGCACGAGCTCGGGAAGAAGAGATG chr1D_581 TGCTGCCACGAACGGCAGTGGCCGCAACACGAGCTCCGGAAGAAGAGATG chr3A_581 TGCTGCCACGAACGGCAGTGGCCGCAGCACGAGCTCCGGAAGAAGAGATG chr3A_581 TGCTACCACGAACGGCAGTGACCGCAACACGAGCTCTGGAAGAAGAGATG chr2A_581 TGCTGCCACGAACGGTAGTGACCACAACACGAGCTCCGGAAGAAGAGATG chr7D_583 TGCTGCCATGAACGGCAGTGGCCGCAGCACGAGCTCCGGAAGAAGAGATG chr6D_583 TGCTGCCACGAACGGCAGTGGCCGCAGCACGAGCTCCGGAAGAAGAGATG chr2D_584 TGCTGCCACGAACGGCAGTGGCCGCAACACGAGCTCCGGAAGAAGAGATG chrUn_624 TGCTGCCACGAACGGCAGCGGCCGTAGCACGAGCTCCGGAAGAAGAGATA chr1A_906 TGCTGCCACGAACGGCAGTGGCTGCAACACGAGCTCCAGAAGAAGAGATG chr7D_1233 TGCTGCCACGAATGGCAGTGGCCGCAGCACGAGCTCCGAAAGAAGAGATG SNPs -------------------------------------S------------ forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 GAGGGTGAAGCATGCACTGACAGAGAGCTAGCCGTTGAGCTTAGCATGTT chr5D_1_TraesCS5D01G012600 GAGGGTGAAGCATGCACTGACAGAGAGCTAGCCGTTGAGCTTAGCATGTT chr3D_570 GAGGGCGAAGCACGCACTGACAGAGAGCTAGTTGTTGATCTTAGGATGTT chr3D_571 GAGGGCGAAGCACGCACTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT chr5D_572 GAGGGCGAAACACGCACTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT chr2A_574 GAGGGCGAAGCACGCACTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT chr1D_578 GAGGGCGAAGCACGCACTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT chr2A_578 GAGGGCGAAGCACGCACTGACAGAGAGCTAGCTATTGAGCTTAGGATGTT chr5D_579 GAGGGCGAAGCATGCACTGACAGAGAGCTAGCTGTTGAACTTAGGACGTT chr3B_579 GAGGGCGAAGCACGCACTGACAGAGAGCTAGCCGTTGAGCTTAGGATGTT chr2A_580 AAGGGCGAAGCACGCACTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT chr2A_580 GAGGGCGAAGCACGCACTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT chr1A_580 GGGGGCGAAGCATGCAATGATAGAGAGCTAGCTGTTGAGCTTAGGATGTT chr5D_581 GAGGGTGAAGCACGCACTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT chr3D_581 GAGGGCGAAGCACGCACTGACAGGGAGCTAGCTGTTGAGCTTAGGATGTT chrUn_581 GAGGGTGAAGCATGCACTGACAGAGAGCTAGCTATTGAGCTTAGGATGTT chr1D_581 GAGGGCGAAGCACGCACTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT chr3A_581 GAGGGCGAAGCACACACTGATAGAGAGCTAGCTGTTCAGCATAGGATGTT chr3A_581 GAGGGCGAAGCACGCACTGACAGAGAGCTAGTTGTTGAGCTTAGGATGTT chr2A_581 GAGGGCGAAGCACGCACTGGCAGAGAGCTAGCTATTGAGCTTAGGATGTT chr7D_583 GAGGGCGAAGCATGCACTGGCAGAGAGCTAGCTGTTGATCTTAGGATGTT chr6D_583 GAGGGCGAAGCATGCACTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT chr2D_584 GAGGGCGAAGCACGCACTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT chrUn_624 AAGGGCGAAGCACGCACTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT chr1A_906 GAGGGCGAAGCACACACTGACAGAGAGCTAGCTGTTGAGCTTAGGATATT chr7D_1233 GAGGGCGAATCACGCATTGACAGAGAGCTAGCTGTTGAGCTTAGGATGTT SNPs --------------------------------------------S----- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr5D_1_TraesCS5D01G012600 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr3D_570 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr3D_571 GAAGAAGAAGGTTAGGAAGCTTGAAGATGAAGCACAAATACCAATACTCA chr5D_572 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATAGCCA chr2A_574 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr1D_578 GAAGAAGAAGGTTAGGAAGCTTAAAGATCAAGCAC---TACCAATACCCA chr2A_578 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr5D_579 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr3B_579 GAAGAAGAAGGTTAGGAAGCCTGAAGATCAAGCACAAATACCAATACCCA chr2A_580 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr2A_580 GAAGAAGAAGGTTAGGAAGCTTGAAGATAAAGCAC---TACCAATACCCA chr1A_580 GAAGAAGATGGTTAGGAAGCTTGAAGATCAAGCACA------AATACCCA chr5D_581 GAAGAAGAAGGTTAGGAAACTTGAAGATCAAGCAC---TACCAATACCCA chr3D_581 GAAGAAGAAGGTTAGGAAGCTTGAAGATCGAGCACAAATACCAATACCCA chrUn_581 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr1D_581 GAAGAAGAAGGTTAGTAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr3A_581 GAAGAAGAAGGTTAGGAAGCTTGAAGATCGAGCAC---TACCAATACCCA chr3A_581 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATAACCA chr2A_581 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr7D_583 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr6D_583 GCAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCAC---TACCAATACCCA chr2D_584 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCACAAATACCAATACCCA chrUn_624 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCACGAATACCAATACCCA chr1A_906 GAAGAACAAGGTTAGGAAGCTTGAAGATCAAGCACAAATACCAATACCCA chr7D_1233 GAAGAAGAAGGTTAGGAAGCTTGAAGATCAAGCACAAATACCAATACCCA SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 TTTGCAAATACTTTTGGGCATTTGTAGGTATGGTAATCGCATTGGTTGTA chr5D_1_TraesCS5D01G012600 TTTGCAAATACTTTTGGGCATTTGTAGGTATGGTAATCGCATTGGTTGTA chr3D_570 TTTGCAAATACTTTTGGGCATTTGTAGGTATGATAATCGCACTGGTTGTA chr3D_571 TTTGCAATTAATTTTGGGCATTTGTAGGTATGGTAATTA-------TGTA chr5D_572 TTTGCAATTACTTTTGGTCATTTGTAGGTATGGTAATCGCACTGGTTGTA chr2A_574 TTTGCAAATACTTTTGGGCATTTGTAGGTATGGTAATCGTACTGGTTGTA chr1D_578 TTTGCAAATACTTTTGGGCATTTGTAGGTATGGTAATCGCACTGGTTGTA chr2A_578 TTTGCAAATACTTTTGGGCATTTGTAGGTATTGTAATCGCATTGGTTGTA chr5D_579 TTTGCAAATACTTTTGGGCATTTGTAGGTATGGTAATCGCGCTGGTTGTA chr3B_579 TTTGCAATTACTTTTGGGCATTTGTAGGTATGGTAATCGCACTGGTTGTA chr2A_580 TTTGCAAATACTTTTGGGCATTTGTAGGTATGGTAATCGCACTGGTTGTG chr2A_580 TTTGCAAATACTTTTGGGCATTTGTAGGTATGGTAATCGCACTGGTTGTA chr1A_580 TTTGCAATTACTTTTGGGCATTCGTTGGTATGGTAATCACACTGGGTGTA chr5D_581 TTTGCAAATACTTTTGGGCATTTGTAGGTATGGTAATCACACTGGTTGTA chr3D_581 TTTGCCATTACTTTTGGGAATTTGTATGTATGGTAATCGCACTGGTTGTA chrUn_581 TTTGCAATTACTTTTGGGCATTTGTAGGTATGGTAATCGCACTGGTTGTA chr1D_581 TTTGCAAATACTTTTGGGCATTTGTAGGTATGGTAATCGCACTGGTTGTA chr3A_581 TTTGCAAATACTTTTGGGCATTTGTAGGTATGGTGATCGCACTAGTTGTA chr3A_581 TTTGCAAATACTTTTTGGCATTCATAGGTATGGTAATCACACTGGTTGTA chr2A_581 TTTGCAAATACTTTTGTGCATTTGTAGGTATGGTAATCGCACTGGTTGTA chr7D_583 TTTGCAAATACTTTTGGGCATTTGTAGGTATGGTAATCGCACTGGTTGTA chr6D_583 TTTGCAATTACTTTTGGGCATTTGTAGGTATGGTAATCACACTGGTTGTA chr2D_584 TTTGCAATTACTTTTGGGCATTTGTAGGTATGGTAATCGCATTGGTTGTA chrUn_624 TTTGCAATTACTTTTGGGCATTTGTAGGTATGGTAATCGCACTGGTTGTA chr1A_906 TTTGCAATTAATTTTGGGCATTTGTAGGTATGGTAATCGCACTGGTTGTA chr7D_1233 TTTGCAATTACTTTTGGGCATTTATAGGTATGGTAATCGCACTGGTTGTA SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 ATGTTCAAAATGTATGGAAAGGCATGA----------------------- chr5D_1_TraesCS5D01G012600 ATGTTCAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAAGC-T chr3D_570 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAAGC-T chr3D_571 ATGTTGAAAATGTATGGAAAGGCTTGAATTATGGAGGAATTTGTAAGC-T chr5D_572 ATGTTAAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAAGC-T chr2A_574 ATGTTGAAAATGTATGGAAAGACATGAATTATGGAGGAATTTGTAATC-T chr1D_578 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAATC-T chr2A_578 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAATC-T chr5D_579 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGTAATTTGTAAGC-T chr3B_579 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAAGC-T chr2A_580 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAATC-T chr2A_580 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAATC-T chr1A_580 ATGTTGAAATTGTATGGAAAGGCATGAATTATGGAGGAATTAGTAAGT-T chr5D_581 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAATC-T chr3D_581 ATGTTGAAATTGTATGGAAAGGCATGAATTATGGAGGAATTTGTAAGC-T chrUn_581 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAAGC-T chr1D_581 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAATCTT chr3A_581 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAATCTT chr3A_581 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAATCTT chr2A_581 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAATCTT chr7D_583 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTATAATCTT chr6D_583 ATGTTGAAAACGTATGGAAAGGCATGAATTATGGAGGAATTTGTAAGCTT chr2D_584 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGATTTTGTAAGCTT chrUn_624 ATGTTGAAAATGTATGGAAATGCATGAATTATGGAGGAATTTGTAAGCTT chr1A_906 ATGTTGAAAATGTATGGAAAGGCATGAATTATGGAGGAATTTGTAAGCTT chr7D_1233 ATGTTGAAAATGTATGGAAAGGCGTGAATTATGGAGGAATTTGTAAGCTT SNPs -----S-------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 TGAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGGTCAAAGTTGTTT chr3D_570 TGAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGTTAAAAGTTGTTT chr3D_571 TGAAATTGTATGAGAAATTCACCTAGTTTAAATATTGGTCAAAGTTGTTT chr5D_572 TGAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGGTCAAAGTTGTTT chr2A_574 TGAAATTGTTTGAGAAATTCACCTAGTTTAAATGTTGGTTAAAGTTGTTT chr1D_578 TGAAATTGTATGAGAAATTCACATAGTTTAAATGTTGGTCAAAGTTGTTT chr2A_578 TGAAATTGTTTGAGAAATTCACCTAGTTTAAATGTTGGTTAAAGTTGTTT chr5D_579 TGAATTTGTA----------ACCTAGTT------TTAGTCAAAGTTGTTT chr3B_579 TGAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGGTCAAATTTGTTT chr2A_580 TGAAATTGTTTGAGAAATCCACCTAGTTTAAATGTTGGTTAAAGTTGTTT chr2A_580 TGAAATTGTTTGAGAAATCCACCTAGTTTAAATGTTGGTTAAAGTTGTTT chr1A_580 TGAAATTCTATGAGAAATTCACCTTATTTAAATGTTGGTCAAAGGTTTTT chr5D_581 TGAAATTGTATGAAAA-TTCACATAGCTTAAATGTTGGTCAAAGTTGTTT chr3D_581 -GAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGGTCAAAGTTGTTT chrUn_581 TGAAATTGTATGAGAAATTCACCTAGATTAAATGTTGGTCAAAGTTGTTT chr1D_581 -GAAATTGTATGAGAAATTCACCTATTTTAAATGTTGGTCAAAGTTGTTT chr3A_581 -GAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGGTCAAAGTTGTTT chr3A_581 -GAAATTGTATGAGAAATTCACCTAGTTCAAATGTTGGTCAAAGTTATTT chr2A_581 -GAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGGTCAAAGTTGTTT chr7D_583 -GAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGGTCAAAGTTGTTT chr6D_583 -GAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGGTCAAAGTTGTTT chr2D_584 -GAAATTGCATGAAAAATTCGCCTAGTTTAAATGTTGGTCAAAGTTCTTT chrUn_624 -GAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGGTCAAAGTTGTTT chr1A_906 -GAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGGTCAAAGTTGTTT chr7D_1233 -GAAATTGTATGAGAAATTCACCTAGTTTAAATGTTGGTCAAAGTTGTTT SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 AAA-----------TGTTG------------AA--AA-AAGAAGAGA--A chr3D_570 GAA-----------TGTT------------GAA--AA-AA-A-GAGA--A chr3D_571 AAA-----------TGTTG------------AA--AA-AA-A-GAGA--A chr5D_572 AAA-----------TGTTG------------AA--AA-AA-A-GAGA--A chr2A_574 AAA-----------TGTTG------------AAACAA-AA-A-GAGA--A chr1D_578 AAA-----------TGTTG-----------GAA--AA-AA-A-GAGA--A chr2A_578 AAA-----------TGTTG-----------AAA-CAA-AA-A-GAGA--A chr5D_579 AAA-----------TGTTG------------AA--AA-AA-A----A--A chr3B_579 GTTGAA-------------------------AA--AA-AG-A-GATA--A chr2A_580 AAAGGTTGTTTAAATGTTG-----------AAA-CAA-AA-A-GAGA--A chr2A_580 AAA-----------GGTTGTTTAAATATTGAAA-CAA-AA-A-GAGA--A chr1A_580 AAA-----------TGCTG------------AA--GA-AATG-GAGA--A chr5D_581 AAA-----------TGTTG-------------A--AA-AA-A-TAGA--A chr3D_581 AAA-----------TGTTG-------------A--AA-AA-AAGAGA--A chrUn_581 AAA-----------TGTTG-------------A--AA-AA-AAGAGA--A chr1D_581 AAA-----------TGTTG-------------A--AA-AA-AAGAGA--A chr3A_581 AAA-----------TGTTG-------------A--AA-AA-AAGAGA--A chr3A_581 AAA-----------TGTTG-------------A--AA-AA-A--AGA--A chr2A_581 AAA-----------TGTTG-------------A--AA-AA-A-GAGA--A chr7D_583 AAA-----------TGTTG-------------A--AA-AA-A-GAGA--A chr6D_583 AAA-----------TGTTG-------------A--AA-AA-A--AGA--A chr2D_584 AAA-----------TGTTG-------------A--AAAAA-A-GAGA--A chrUn_624 AAA-----------TGTTG-------------A--AAAAA-A--AGA--G chr1A_906 AAA-----------TGTTG-------------A--AAAAA-A-GAGA--A chr7D_1233 AAA-----------TGTTG-------------A--AA-AA-A--AGAGAA SNPs ----------------------------------------S--------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GAAGTGACCAACATTTAAATACGTTG--A-AAAAA--GG----AGAAGAA chr3D_570 GAAGTGACCAACATTTAAATATGTTG--AA--AAAA-GG----AGAAGAA chr3D_571 GAAGTGACCAACATTTAAATATGTTG--AA--AAAA-------AGAAGAA chr5D_572 GAAGCGACCAACATTTAAATATGTTG--AAAAAAA--GG----AGAAGAA chr2A_574 GAAGTGACCAACATTTAAATATGTTG--G-AAAAA--AG----AGAAGAA chr1D_578 GAAGTGACCAACATTTAAATATGTTG--AA--AAA--GG----AGAAGAA chr2A_578 GAAGTGACCAACATTTAAATATGTTG--GA--AAAA-AG----AGAAGAA chr5D_579 GAAGTGACCAACATTTAAATATGTTG--AA--AAAA-GG----AGAAGAA chr3B_579 GAAGTGACCAATATTTAAATATGTTG--AA--AAAG-GG----AGAAGAA chr2A_580 GAAGTGACCAACATTTAAATATGTTG--GA--AAAA-AG----AGAAGAA chr2A_580 GAAGTGACCAACATTTAAATATGTTG--GA--AAAA-G-----AGAAGAA chr1A_580 GAAATGACCAACAATTAAATATGTTG--AA--AAA--GGGGAGAAAAAAA chr5D_581 GAAGTGACCAACATTTAAATATGTTG--AA--AAAACA-----AGAAGAA chr3D_581 GAAGTGACCGACATTTAAATATGTTG--AA--AAA-GGG----AGAAGAA chrUn_581 GAAGTGACCAACATTTAAATATGTTC-AAA--AAAA-GG----AGAAGAA chr1D_581 GAAGTGACCAACATTTAAATATGTTG--AA--AAAA-GG----AGAAGAA chr3A_581 GAAGTGACCAACATTTAAATATGTTG--AA--AAAA-GG----AGAAGAA chr3A_581 GAAGTGACCAACATTTAAATATGTTGGAAA--AAAA-GG----AGAAGAA chr2A_581 GAAGTGACCAAAATTTAAATATGTTG--AA--AAAA-GG----AGAAGAA chr7D_583 GAATTGACCAACATTTAAATATGTTG--AA--AAAA-GG----AGAAGAA chr6D_583 GAAGTGACCAACATTTAAATATGTTC--AA--AAAAGG-----AGAAGAA chr2D_584 GAAGTGACCAACATTTAAATATGTTG--AA--AAAAGGG----AGAAGAA chrUn_624 AAAGTGACCAACATTTAAATATGTT---AA--AAAA-GG----AGAAGAA chr1A_906 GACGTGACCAACATTTAAATATGTTG--AA--AAAAGGG----AGAAGAA chr7D_1233 GAAGTGACCAACTTTTAAATATGTTG--AA--AAAAGGG----AGAAGAA SNPs ---------------------S---------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr3D_570 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGT chr3D_571 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr5D_572 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr2A_574 ATTAGGAATTCAAAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr1D_578 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr2A_578 ATTAGGAATTCAGAAAGTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr5D_579 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTAA chr3B_579 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAACTCTCTGCTCTAC chr2A_580 ATTAGGAATTCAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr2A_580 ATTAGGAATTCAGAAAC--------------------------------- chr1A_580 ATGAGAAATTCAGAAAC-TTTGATCAATGAAATGCAACTCTCTGCTCTGC chr5D_581 ATGAGGAATTCAGAGACTTTTGATCAATGAAGTGCAGCTCTCTGCTCTGC chr3D_581 ATGAGGAATTCAAAAACTTTTGATCAATGAAATGCAGCTCTTTGTTCTGC chrUn_581 ATGAGGAATTCAGAAACTTTTGATCGATGAAATGCAGCTCTCTGCTCTGC chr1D_581 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr3A_581 ATGAGGAATTCAAAAACTCTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr3A_581 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr2A_581 ATGAGGAATTAAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr7D_583 ATGAGGAATTAAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCCGC chr6D_583 ATGAGGAATTAAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr2D_584 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAACTCTCTGCTCTGC chrUn_624 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC chr1A_906 ATGAGGAATTCAGAAACTTTTGATCAATGAAATACAGCTCTCTGCTCTGC chr7D_1233 ATGAGGAATTCAGAAACTTTTGATCAATGAAATGCAGCTCTCTGCTCTGC SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 CTTTCTGTCAAAAAAA--GGTTCCTCTGTGGGCCAAATTCAGAGCGTAGA chr3D_570 CTTTCTATAAAAAAAA--GGTTCCTCT-TGGGCCAAATTCAGAGTGTAGA chr3D_571 CTTTCTGTCAAAAAAA--GGTTCTTCTGTGGGCCAAATTCAGAGCGTAGA chr5D_572 CTTTCTGTCAAAAAAA--GGTTTCTTTGTGGGCCAAATTCAGACCGTAGA chr2A_574 CTTTCTGTCCAAAAAAA-GGTTGCTCT-TGGGCCAAATTCAGAGCGTAGA chr1D_578 CTTTCTCTCAAAAAAA--GGTTGCTCT-TGGGCCAAATTCAGAGCGTAGA chr2A_578 CTTTCTGTCCAAAAAAAAGGTTGCTCT-TGGGCCAAATTCAGAGCGTAGA chr5D_579 CTTCCTGTCAAAAAAAA-GGTTCCTCTGTGGGCCAAATTCAGAGCGTAGA chr3B_579 CTTTCTGTCAAAAAAAA-GGTTCCTCTGTGGGCCAAATTCAGAGTGTAGA chr2A_580 CTTTCTGTCCAAAAAAA-GGTTACTCT-TGGGCCAGATTCAGAGCGTAGA chr2A_580 -------------------------------------------------- chr1A_580 CTTTTCTG-TAAAAAAA-GGTTTCTATATGGGTCAAATTCAGAGCGGAGA chr5D_581 CTTTCTGTCAAAAAAA--TGTTGCTCT-TGGGCCAAATTCAGAGCGTAGA chr3D_581 CTTTCTGTCAAAAAAA--GGTTCCTCTGTGGGCCAAATTCAGAGCGTAGA chrUn_581 CTTTCTGTCAAAAAAAA-GGTTCCTCTGTGGGCCAAATTCAGAGCGTAGA chr1D_581 CTTTCTATCAAAAAAA--GGTTGCTCT-TGGGCCAAATTCAGAGCGTAGA chr3A_581 CTTTCTGTCAAAAAAA--GGTTGCTCT-TCGGCCAAATTCGGAGCGTAGA chr3A_581 CTTTCTGTCCAAAAAAAAGGTTGATCT-TGGGCCAAATTCAGAGTGTAGA chr2A_581 CTTTCTGTCAAAAAAAA-GATTGCTCT-TGGACCAAATTCAGAGCGTAGA chr7D_583 CTTTCTGTAAAAAAAA--GGTTGCTCT-TGGGCCAAATTCAGAGCGTAGA chr6D_583 CTTTCTGTCAAAAAAAA-GGTTCCTCTCTGGGCCAAATTCAGAGCGTAGA chr2D_584 CTTTTTGTCAAAAAAAA-GGTTCCTCTGTGGGCCAAATTCAGAGCGTAGA chrUn_624 CTTTCTATATAAAAAAA-GGTTCCTTTGTGGGCCAAATTCAGAGCGTAGA chr1A_906 CTTTATGTCAAAAAAAAAGGTTCCTCTATGGGCCAAATTCACAGCGTAGA chr7D_1233 CTTTCTGTAAAAAAA---GGTTCCTCTGTGGGCCAGATTCAGAGCGTAGA SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GCAAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr3D_570 GCCAAGTGCAGGCTAGACTAATGGGCCAACTACATCCAATTAGGCCCATT chr3D_571 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr5D_572 GCCAAGTGCAGGCTAGACTAATGGGCCAATTGCATCCAATTAGGCCCATT chr2A_574 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr1D_578 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr2A_578 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr5D_579 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr3B_579 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr2A_580 GCCAAGTGCAGGCTAGACTAATGGGCCAATTGCATCCAATTAGGCCCATT chr2A_580 -------------------------------------------------- chr1A_580 GCCAAGTGCCGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr5D_581 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr3D_581 GCCAAGTGCTGGCTAGACTAATGGGCCAACCGCATCCAATTAGGCCCATT chrUn_581 GCCAAGTGCAGGCTAGACTAATGGGCCAACTACATCCAATTAGGCCCATT chr1D_581 GCCAAGTGCAGGCTAGGTTAATGGGCCAACTACATCTAATTAGGCCCATT chr3A_581 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr3A_581 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr2A_581 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr7D_583 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr6D_583 GCCAAGTGCAGGCTTGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr2D_584 GCCAAGTGCAGGCTAGACTAATGGGCCAACTACATCCAATTAGGCCCATT chrUn_624 GCCAAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT chr1A_906 GCCAAGTGCAGGCTAGACTAATGGGCCAACTACAACCAATTAGGCCCATT chr7D_1233 GCCCAGTGCAGGCTAGACTAATGGGCCAACTGCATCCAATTAGGCCCATT SNPs --S----------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 CGGGGG-T------------TCTCTTGCGTTTTTTTTCTGTTTTC-TTTT chr3D_570 CGGGGG-T------------TCTCTTGCGTG-TTTTTCTGTTTTC-TGTT chr3D_571 CGGGGG-T------------TCTCTTGCGTG-TTTTTCTGTTTTC-TGTT chr5D_572 CGGGGG-T------------TCTCTTGCGTG-TTTTTCTGTTTTC-TGTT chr2A_574 CGGGGG-T------------TCTCTTGCGTA-TTTTTCTGTTTTC-TATT chr1D_578 CGGGGG-T------------TCTCTTGCGTG-TTTTTCTGTTTTC-TGTT chr2A_578 CGGGGT-T------------TCTCTTGCGTA-TTTTTCTGTTTTC-TATT chr5D_579 CGGGGG-T------------TCTCTTGCGTG-CTTTTTTGTTTTC-TGTT chr3B_579 CGAGGG-T------------TCTCTTGCGTG-TTTTTCTGTTTTC-TTTT chr2A_580 CGGGGG-T------------TCTCTTGCGTA-TTTTTCTGTTTTC-TATT chr2A_580 -------------------------------------------------- chr1A_580 CGGGGG-TGGGCAAATGAGATCTCTTGCGTG-TTTTTCTGTTTTC-TGTT chr5D_581 CGGGGG-T------------TCTCTTGCGTG-TTTTTCTGTTTTC-TGTT chr3D_581 CGGGGG-T------------TCTCTTGCGTG-TTTTTCTGTTTTC-TGTT chrUn_581 CGGGGG-T------------TGTCTTGCGTG-TTTTTCTGTTTTC-TGTT chr1D_581 CGGGGGGT------------TCTCTTGCATG-TTTTTCTGTTTTC-TGTT chr3A_581 CGGGGG-T------------TCTCTTGCGTG-TTTTTCTGTTTTTTTGTT chr3A_581 TGGGGG-T------------TCTCTTGCATG-TTTTTCTGTTTTC-TGTT chr2A_581 CGGGGG-T------------TCTCTTGCGTA-TTTTTCTATTTTC-TGTT chr7D_583 CGGGAG-T------------TCTTTTGCGTG-TTTTTCTGTTTTC-TGTT chr6D_583 CGGGGG-T------------TCTCTAGCGTG-TTTTTCTGTTTTC-TATT chr2D_584 CAGGGG-T------------TCTCTTGCGT--TTTTTCTGTTTTC-TATT chrUn_624 CGGGGGGT------------TCTCTTGCGTGTTTTTTCTGTTTTC-TGTT chr1A_906 CGGGGGAT------------TCTCTTGCGTG-TTTTTCTATTTTC-TGTT chr7D_1233 CGAGGG-T------------TCTCATGTGTG-TTTTTCTATTTTC-TTTT SNPs ------------------------------S------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- chr3D_570 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- chr3D_571 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- chr5D_572 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- chr2A_574 CTGATTTAATTTAGGCAGTAAACCA-------TAATGCTGAAACTTTTT- chr1D_578 CTGATTTAATTTAGGCAGTAATTCA-------TAATGCTGAAACTTTTT- chr2A_578 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- chr5D_579 GTGATTTAATTTAGGCGGTAAATCA-------TAATGCTGAAACTTTTT- chr3B_579 CTGATTTAATTTAGGCAGTAACTCA-------TAATGCTGAAACTTTTT- chr2A_580 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGGAACTTTTTT chr2A_580 -------------------------------------------------- chr1A_580 CTGATTTAGTTTAGGTAGTAAATCATTTTATTTAATGCTGAAACTTTTTT chr5D_581 CTGATTTAAATTAGGTAGTAAATCA-------TAATGATGAAACTTTTT- chr3D_581 CTAATTTAATTTAGGCACTAAATCA-------TAATGCTAAAACTTTTT- chrUn_581 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTATTT- chr1D_581 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- chr3A_581 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- chr3A_581 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- chr2A_581 CTGATTTAATTTAGGTAGTAAATCA-------TAATGCTGAAACTTTTT- chr7D_583 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- chr6D_583 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTAAAACTTTTA- chr2D_584 CTAATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- chrUn_624 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- chr1A_906 CTGATTTAATTTAGGCAGTACATCA-------TAATGCTGAAACTTTTT- chr7D_1233 CTGATTTAATTTAGGCAGTAAATCA-------TAATGCTGAAACTTTTT- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GTGGAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGGTTAGAA-A- chr3D_570 GTGGAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGGTTAGAA-A- chr3D_571 GTGGAAGCTAATTGAATTATTCCAAAGCCAAACAATTAAGTTTAGAA-T- chr5D_572 GTGGAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGCTTAGAA-TC chr2A_574 GTGGAAGCTAATTGAATTATTCCGGAGCCAAACAATTAAGATTAGAA-A- chr1D_578 ATGGAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGGTTAGAA-T- chr2A_578 GTGGAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGGTTAGAA-T- chr5D_579 GTGGAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGGTTAGAA-T- chr3B_579 GTGCAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGTTTAGAA-T- chr2A_580 TTGGAAGCTAATTGAATTATTCCGGAGCCAAACAATTAAGGTTCGAA-T- chr2A_580 -------------------------------------------------- chr1A_580 GTGGAAGCTAATTGAATTATTCGAGAGCCAAACAATTAAGTTTAGAATT- chr5D_581 GTGGAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGGTTGGAC-A- chr3D_581 ATGGAAGCTAATTGAATTATTCCACAGCCAAACAATTAAGTTTAGAA-T- chrUn_581 GTGGAAGCTAATTAAATTATTCCAGAGCCAAACAATTAAGGTTAGAA-T- chr1D_581 GTGGAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGGTTAGAA-A- chr3A_581 GTGGAAGCTAATTGAATTATTCCAGAGGCAAAAAATTAAGGTTAGAA-A- chr3A_581 GTGGAAGCTAATTGAATTATCCCAGAGCCAAACAATTAAGATTAGAA-A- chr2A_581 GTGGAAGCTAATTGAATTGTTCCAGAGCCAAACAATTAAGGTTAGAA-A- chr7D_583 GTGGAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGGTTAGAA-A- chr6D_583 GTGGAAGCTAATTGAATTATTACAGAGCCAAACAATTAGGGTTAGA---- chr2D_584 GTGAAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGTTTAGAA-T- chrUn_624 GTGGAAGCTAATTGAATTATTCGAGAGCCAAACAATTAAGTTTAGAA-T- chr1A_906 GTGGAAGCTAATTGAATTATTCCAGAGCCAAACAATTAAGTTTAGAA-T- chr7D_1233 GTGGAAGCTAATTGAATTATTCCAAAGCCAAACAATTAAGTTTCAAA-A- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 -TTTTTT-GGAGCTG-------------------TTAAATATTTAATAGC chr3D_570 -TTTTTT-GGAGCTG-------------------TTCAATATTTAATAGC chr3D_571 -TTTTTT-GGAGCTG-------------------TTAAATATTTAATAGC chr5D_572 TTTTTTT-GGAGTTG-------------------TTAAATAATTAATAGC chr2A_574 -TTTTTT-GGAGCTG-------------------TTAA------------ chr1D_578 -TTTTTT-GGAGCTGTTAAATATTTAATAGCAATTTAA------------ chr2A_578 -TTTTTT-GGAGCTG-------------------TTAA------------ chr5D_579 -TTTTTT-GGAGCTGTTGAATATTTAATAGCAATTTAA------------ chr3B_579 -TTTTTTTGAAGCTGTTAAATATTTAATAGCAATTTAA------------ chr2A_580 -TTTTTT-GGAGCTGTT-------------------AA------------ chr2A_580 -------------------------------------------------- chr1A_580 -TTTTTTTGGAGCTGTTAAATATTTAATACCAATTAAA------------ chr5D_581 --TTTTTTGGAGCTGTTAAATATTTAATAGCAATTTAA------------ chr3D_581 -TTTTTTTGGAGCTGTTAGATATTTAATAGCAATTTAA------------ chrUn_581 -TTTTTT-GGAGCTGTTAAATATTTGATAGCAATTTAA------------ chr1D_581 --TTTTTTGGAGCTGTTAAATATTTAATAGCAATTTAA------------ chr3A_581 --TTTTTTGGAGCTATTAAATATTTAATATCAATTTAA------------ chr3A_581 --TTTTTTGGAGCTGTTAAATATTTAATAGCAATTTAA------------ chr2A_581 --TTTTTTGGAGCTG-------------------TTAA------------ chr7D_583 -TTTTTT-AGAGCTGTTAAATATTTAATAGCAATTTAA------------ chr6D_583 -TTTTTTTGGAGCTGTTTAATATTTAATAGCAATTTAA------------ chr2D_584 --TTTTTTCGAGCTGTTAAATATTTACTAGCAATTTAA------------ chrUn_624 --TTTTTTGGAGCTGTTAAATATTTAATAGCAATTTAA------------ chr1A_906 --TTTTT-GGAGGTGTTAAATATTTAATAGCAATTTAA------------ chr7D_1233 -AAAATT-GGAGTTGTTAAATATCTAATAGCAATTTAA------------ SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 AATTTAATTACTCCAATTCAAATACAC--TGTGATTTAAATCAAAGACCA chr3D_570 AATTTAATTACTCCAATTCAAATACAC--CGTGATTTAAATCAAAGACCA chr3D_571 AATTTATTTACTCCAATTCAAATACAC--CGTGATTTAAATCAAAGACCA chr5D_572 AATTTAATTACTCCAATTCAAATACAC--CGTGATTTAAATCAAAGACCA chr2A_574 -------TTAATACAATTCAAATACAC--CGTGATTTAAATCAAAGACCA chr1D_578 -------TTAATCCAATTCAAATACAC--CGTGATTTAAATCAAAGACCA chr2A_578 -------TTAATCCAATTCAAATACAC--TGTGATTTAAATCAAAGACCA chr5D_579 -------TTACTCCAATTCAAATACAC--CGTGATTTAAATCAAAGACCA chr3B_579 -------TTACTCCAATTCAAATATAC--CGTGATTTAAATCAAAGACCA chr2A_580 -------TTAATCCAATTCAAATACAC--CGTGATTTAAATCAAAGACCA chr2A_580 -------------------------------------------------- chr1A_580 -------TTACTACAATTCAAATACAT--CGTGATTTAAATCAAAGACCA chr5D_581 -------TTAATCCAATTCAAATACAC--CATGATTTAAATCAAAGACCA chr3D_581 -------TTACTCCAATTCAAATACAC--CATGATTTAAATCAAAGACCA chrUn_581 -------TTACTCTAATTCAAATACAC--CGTGATTTAAACCAAAGACCA chr1D_581 -------TTAATCCAATTCAAATACACCATGTGATTTAAATCAAAGACCA chr3A_581 -------TTACTCCAATTCAAATACAC--CGTGATTTAAATCAAAGAACA chr3A_581 -------TTACTCCAATTCAAATACAC--CGTGATTTAAATCAAATACCA chr2A_581 -------TTAATCCAATTCAAATACAC--CGTGATTTAAATCAAAGACCA chr7D_583 -------TTACTCCAATTCAAATACAC--CGTGATTTAAATCAAAGACCA chr6D_583 -------TTACTCCAATTCAAATACAC--CATGATTTAAATCAAAGACCA chr2D_584 -------TTACTCCAATTCAAATACAC--CGTGATTTAAATCAAAGACCA chrUn_624 -------TTACTCCAATTCAAATACAC--CTTGATTTAAATCAAAGACCA chr1A_906 -------TTACTCCAATTCAAATACAC--CGTGATTTAAATCAAAGACCA chr7D_1233 -------TTACTCCAATTCAAATACAC--CGTGATTTAAATCAAAGACCA SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 AAATGTCATGGAAAATGTGCCTCAGCTCTGGT-----------------G chr3D_570 AAATGTCATGGAAAATGTCCCTCAGCTCTGGTAGAGGTTTACACCTGGTG chr3D_571 AAATGTCATGGAAAATGTGCCTCAGCTCTGGTAGAGGTTTATACCTGGTG chr5D_572 AAATGTCATGGAAAATGTGCCTCAGCTCTGGTAGAGGTTTACACCTGGTG chr2A_574 AAATGTCATGGAAAATATGCCTCAGCTCTGGTAGAGGTTTACGCCAGGTG chr1D_578 AAATGTCATGGAAAATGTGCCTCAGCTCTGGTAGAGGTTTACACCTGGTG chr2A_578 AAATGTCATGGAAAATGTACCTCAACTCTGGTAGAGGTTTACGCCAGGTG chr5D_579 AAATGTCACGGAAAATGTGCCTCAGCTCTAGTAGAGGTTTACACCTGGTG chr3B_579 AAATGTCATGGAAAATGTGCCTCAGCTCTGGTAGAGGTTTACACCTGGTG chr2A_580 AAATGTCATGGAAAATGTGGCTCAGCTCTGTTAGAGGTTTACGCCAGGTG chr2A_580 -------------------------------------------------- chr1A_580 AAATGTCATGGAAAATGTGCCTTAGCT------------TACACTTGGTG chr5D_581 AAATGTCATGGAAAATGTGCCCCAGCTCTGGTAGAGGTTTACACCTGGTG chr3D_581 AAATGTCATGGAAAATGTGCCTCAGCTCTGGTAGAGGTTTACACCTGGTG chrUn_581 AAATGTCATGGAAAATGTGCCTCAGCTCTGGTAGAGGTTTACACCTGGTG chr1D_581 AAATGTCATGGAAAATGTGCCTCAGCTCTGGTAGAGGTTTACACCTGGTG chr3A_581 AAATGTCATGGAAAATGTGCCTCAGCTCTAGTAGAGGTTTACACCTGGTG chr3A_581 AAATTTCATGGAAAATGTGCCTCAGCTCTGGTAGAGGTTTACACCTGGTG chr2A_581 AAATATCATGGAAAATGTGCCTCAGCTCTGGTAGAGGTTTACACCTCGTT chr7D_583 AAATGTCATGGAAAATGTGCCTCAGCTCTGGTAGAGGTTTACACCTGGTG chr6D_583 AAATGTCATGGAAAATGTGCCTTAGCTCTTGTAGAGGTTTACACCTGGTG chr2D_584 AAATGTCATGGAAAATGTGCCTCAGCTCTGGTAGAGGTTTACACCTGGTG chrUn_624 AAATGTCATGGAAAATGTGCCTCATCTCTGGTAGAGGTTTACACCTGGTG chr1A_906 ATATGTCATGGAAAATGCGCCTCAGCTCTGGT-----------------G chr7D_1233 AATTGTCATGGAAAATGTGCCTCGGCTCTGGTAGAGGTTTACACCTGGTG SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 CCAAAATAAATGAACA-TTTTT-TAAGGGCATTACATTGAGA-AAAAAAT chr3D_570 CCAAAATAAATGAACA-TTTTT-TAAGGGCATTACATTGAGA-AAAAAAT chr3D_571 CCAAAATAAATGAACA-TTTTT-TAAGGGCATTACATTGAGA-AAAAAAT chr5D_572 CCAAAATAAATGAACA-TTTTT-TAAGGGCATTACATTGAGA-AAAAAAT chr2A_574 CCAAAATAAATGAAC--ATTTT-TAAGGGCATTACATTGAGA-AAAACAT chr1D_578 CCAAAATAAATGAACA-TTTTT-TAAGGGCATTACATTGA-A-AAATAAT chr2A_578 CCAAAATAAATGAAC--ATTTT-TAAGGGCATTACATTGAGA-AAAACAT chr5D_579 CCAAAATAAATGAACA-TTTTT-TAAGGGCATTACATTGAGA-AAAAAAT chr3B_579 CCAAAATAAATGAACA-TTTTT-TATGGGCATTACATTGAGA-AAAAA-T chr2A_580 CCAAAATAAATGAACA-ATTTT-TAAGGGCATTACATTGAGA-AAAACAT chr2A_580 -------------------------------------------------- chr1A_580 CCCAAATTAATGAACATTTTTG--AAGGGCATTACATTGAG---AAA-AA chr5D_581 CCAAAATAAATGAACA-TTTTT-TAAGGGCATTACATTGAGA-AAAACAT chr3D_581 CCAAAAATAATGAACATTTTTA--AAGGGCATTACATTGAG---AAA-AA chrUn_581 CCAAAATAAATGAACA-TTTTTTTAAGGGCATTACATTGAGAAAAAT-AT chr1D_581 CCAAAATAAATGAAATTTTTTT--AAGGGCATTACATTCAG---AAA-AA chr3A_581 CCAAAATAAATGAACA-TTTTT-TAAGGGCATTACATTCAGAAAAAA-AT chr3A_581 CCAAAATAAATGAACA-TTTTT--AAGGGCATTACATTGAG---AAA-AA chr2A_581 CCAAAATAAATGAACA-TTTTT-TAAGGGCATTGCATTGAGAGAAAA-AT chr7D_583 CCAAAATAAATGAACA-ATTTT-TAAGGGCATTACATTGAGA-AAAA-AT chr6D_583 CCAAAATAAATGAACA-TTTTT-TAAGGGCATTACATTGAGA-AAAA-AA chr2D_584 CCAAAATAAATGAAGA-TTTTT-TAAGGGCATTACATTAAGAAAAAA-AT chrUn_624 CCAAAATAAATGAACA-TTTTT-TAAGAGCATTACATTGAGA-AAAA-AT chr1A_906 CCAAAATAAATGAAC--ATTTT-TAAGGGCATTACATTGAGAAAGAA-AT chr7D_1233 CCAAAATAAATGAACA-TTTTT-TAAGGGCATTACATTGAGAGAAAA-AT SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 AAT---ATGTCT--AAAATAA-TGAAGGGTGGAAAATGCACAAAAAATT- chr3D_570 AAT---TTGTCT--A-AAAAA-TGAAGGGTGGAAAATGCATAAAAAATT- chr3D_571 ATT---TTTTCT--AAAAAAA-TGAAGGGTGGAAAATGCACAAAAAATT- chr5D_572 AAT---TTGTCT--A-CAAAAATGAAGGTGGGAAAATGCACAAAAAATT- chr2A_574 AAT---TTGTCT--AAAAAAA-TGAAGGGTGGAAAATGCATAAAAAATT- chr1D_578 AAT---TTTTCT--AAAAAAA-TGAAGGGTGAAAAATGCACAAAAAATT- chr2A_578 AAT---TTGTCT--AAAAAAA-TGAAGGGTGGAAAATGCACAAAAAATT- chr5D_579 AAT---TTGTCT--AAAAAAA-TGAAGGGTGGAAAATGCTCAAAAAATT- chr3B_579 ATT---TTGTCT--AGAAAAA-TGAAGGGTGGAAAGTGCACAAAAAGTT- chr2A_580 AAT---TTGTCT---AAAAAA-TGAAGGGTGGAAAATGCACAAAAAATT- chr2A_580 -------------------------------------------------- chr1A_580 AAT---TTGTCT---AAAAAA-TGAAGGGTGGAAAATGCATAAAAA-TT- chr5D_581 AAT---TTGTCT---AAAAAA-TGAAGGGTGGAAAATGCACAAAAAATT- chr3D_581 AATAATTTATCT---AAAAAA-TGAAGGGTGGAAAATGAACAAAAAATT- chrUn_581 AAT---TTGTCT--AAAAAAA-TGAATGGTGGAAAATGCACAAAAAATT- chr1D_581 AATAATTTGTCT--AAAAAGA-TGAAGGGTGGAAAATGCACAAAAAATT- chr3A_581 AAT---TTGTCT---AAAAAA-TGAAGGGTGGAAAATGCACAAAAAATT- chr3A_581 AATAATTTGTCT--A--AAAA-TGAAGGGTGGAAAATGCACAAAAAAAT- chr2A_581 AAT---TTGTCTAAA--AAAA-TGAAGGGTGGAAAATGCACAAAAAATT- chr7D_583 AAT---TTGCCT-AA--AAAA-TGAAGGGTGGAAAATGCACAAAAAATT- chr6D_583 A-----TTGTCT-AA--AAAA-TGATGGGTGGAAAATGCACAAAAAATT- chr2D_584 AAT---TTGTCT-AA--AAAA-TGAAGGGTGAAAAATGCACAAAAAATT- chrUn_624 AAT---TTGTCTAAA--AAAA-TGAAGGGTGGAAAATGCACAAAAAATT- chr1A_906 AAT---TTGTCT-AA--AAAA-TGAAGGGTGGAAAATGAACAAAAAAATG chr7D_1233 AAT---TTGTCTAAA--AAAA-TGAAGGGTGGAAAATGCACAAAAAATT- SNPs ------S-----------S------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GGTGCGACTGGGGACTCGAACCCAGGACC-GCGTGGGTTTGTGGCGTTTA chr3D_570 GGTGCGGCTGGGGACTCGAACCCAGGACC-GCGTGTGTTTGTGGCGTTTA chr3D_571 GGTGCGGCTGGGGACTCAAACCCAGGACC-GTGTGGCTTTGTGGCGTTTA chr5D_572 GGTGCGACTGGGGACTCTTACCCAGGACC-GCGTGGTTTCGTGGCGTTTA chr2A_574 GGTGCGGCTGGGGACTCGAACCCAAGACCCGCATGGGTTTGTGGTGTTTA chr1D_578 GGTGCGGCTGGGGACTCGAACCCAGGACT-GCGTGGGTTTGTGGTGTTTA chr2A_578 GGTGCGGCTGGGGACTCGAACCCAGGACC-GCGTGGGTTTGTGGTGTTTA chr5D_579 GGTGCGGCTGGGGACTCGAACCCAGGACC-GCGTGGGTTTGTGGCGTTTA chr3B_579 GGTGCGGCTGGGGACTCGAACCCAGGACC-TCGTGGGTTTGTGGCGTTTA chr2A_580 GGTGCGGCTGGGGACTCGAACCCAGGACC-GCGTGGTTT-GTGGTGTTTA chr2A_580 -------------------------------------------------- chr1A_580 GGTGTGGCT-GGGACTCGAACCAAGGAGC-ACGTGGTTTTGTGGCATTTA chr5D_581 GGTGCGGCTGGGGACTCAAACCCAGGACC-GCGTGGGTTTGTGGCATTTA chr3D_581 GGTGTGGCTGGGGACTCGAACCCAGGACC-GCGTGGGTTTGTGGCGTTTA chrUn_581 GGTGCGGCTGGGGACTCGAACCCAGGACC-GCGTGGTTTTGTGGCGCTTA chr1D_581 GGTGCGGCTGGGGACTCGAACCCAGGACT-GCGTGGGTTTGTGGTGTTTA chr3A_581 GGTGCGGCTGGGGACTCGAACCCAGGACC-GCGTGGGTTTGTGGCGTTTA chr3A_581 GGTGCGGCCAGGGACTCCAACCCAGGACC-GCATGGGTTTGTGGCGTTTA chr2A_581 GGTGCGGCTGGGGACTCGAACCCAGGACC-GCGTGGGTTTGTGGTGTTTA chr7D_583 GGTGCGGCTGGGGACTCGAACCCAGGACC-GCGTGGGTTTGTGGCGTTTA chr6D_583 GGTGCGGCTGGGGACTCGAACCCAAGACC-GCATGGGTTTGTGGCGTTTA chr2D_584 GGTGCGGTTGGGGACTTGAACCCAGGACC-GCGTGGGTTTGTGGTGTTTA chrUn_624 GGTGCGGCTGGGGACTCGAACCCAGGACC-GCGTGGGTTTGTGGCATTTT chr1A_906 GGTGCGGCTGGGGACTCGAACCCAGGACC-GCATGGGTTTGTGGCATTTA chr7D_1233 CGTGCGGATGGGGACTCGAACCCAGGACC-GCATGGGTTTGTGGCGTTTA SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GGGCTGCGCTGGTAACCGCTAGGACAGATGGAAAGACTTTGACATGGGTA chr3D_570 AGGCTGCGCTGGTAACCGCTAGGACAGATGGAAAGACTTTGACATGGGTA chr3D_571 GGGCTGCGCTGGTAACCGCTAGGACAGATGGAAAGACTTTGACATGGGTA chr5D_572 GGGCTGCGTTGGTAACCGCTAGGACAGATGGAAAGACTTTGACATGGGTA chr2A_574 GGGCTGCGCTGGTAACCGCTAGAACAAATGACAAGACTTTGACATGGGTA chr1D_578 GGGCCGCGCTGGTAATCGCTAGGACAGATGGCAAGACTTTGACATGGGTA chr2A_578 GGGCTACGCTGGTAACCGCTAGGACAGATGGCAAGACTTTGACATGGGTA chr5D_579 GGGCTGTGCTGGTAACCGCTAGGACAGATATAAAGACTTTGACATGGGTA chr3B_579 GGGCTGCGCTGGTAACCGCTAGGACAGATGGAAATACTTTGACATGGGTA chr2A_580 CGGCTGCGCTGGTAACCGCTAGGACAGATGGCAAAACTTTGAGATGGATA chr2A_580 -------------------------------------------------- chr1A_580 GGGCTGCGTTGGTAACCGCTAGGGCAGATGGAAATACTTTGACATGGTTA chr5D_581 GGGCTGC--TGGTAACCGCTAGGATAGATGGAAAGACTTTGACATGGGTA chr3D_581 GGGCTGCGCTTGTAACCGCTAGGACAGATGGAAAGACTTTGACATGGGTA chrUn_581 AGGCTGCACTGGTAACCACTAGGACAGATGGAAAGACTTTGACATGGGTA chr1D_581 GGGCTGCGCTGGTAACCGCTAGGACAGATGGCATGACTTTGACATGGGTA chr3A_581 GGGTTGCGCTGGTATCCGCTAGGACAGATGGAAAGACTTTGACATGGGTA chr3A_581 GGGTTGCGCTGGTAACCGCTAGGACAGATGGAAAGGCTTTGACATGCGTA chr2A_581 GGGCTGCGCTGGTAACCGCTAGGACAGATGGCAAGACTTTGACATGGGTA chr7D_583 GGGCTGCGCTAGTAACCTCTAGGACAGATGGAAAGACTTTGACAAGGGTA chr6D_583 GGGCTGCTCTGGTAACCGCTAGGACAGATGGAAAGACTTTGACATGGGTA chr2D_584 GGGCTGCGCTGGTAACCGCTAGGACAGACGGAAAGACTTTGACATGGGTA chrUn_624 GGGCTGCGCTGGTAACCACTAGGACAGATGGAAAGACTTTGACATGGGTA chr1A_906 GGGCTGCACTGGTAACCGCTAGGACAGATGGAAAGACTTTGACATGGGCA chr7D_1233 GGGCTGCACTGCTAACCGCTAGGACAGATGGAAAGACTTTGACATGGGTA SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GGGAAGGAAGGTATACATAGTGAGACCA---------------------- chr3D_570 GGGAAGGAAGGTATACATAGTGAGACCG---------------------- chr3D_571 GGGAAGGAAGGTATACATAGTGAGACCG---------------------- chr5D_572 GGGAAGGAAGGTATACATAGTGAGACCG---------------------- chr2A_574 GGGAAGGAAGGTATACATAGTGAGACTA---------------------- chr1D_578 GGGAAGGAAGGTATACATAGTGAGACTG---------------------- chr2A_578 GGGAAGGAAGGTATACATAGTGAGAC------------------------ chr5D_579 -GGAAGGAAGGTATACATAGTGAGACCG---------------------- chr3B_579 GGGAAGGAAGGTATACATAGTGAGACCG---------------------- chr2A_580 GGGAAGGAAGGTATACATAGTGAGATTT---------------------- chr2A_580 -------------------------------------------------- chr1A_580 GGGAAGGAAGCTATACATAGTGAGATCGTGACTTGGTTTGGCTTTTAAAA chr5D_581 GGGAAGGAAGGTATACATAGTGAGACCG---------------------- chr3D_581 GGGAAGGAAGTTATACATAGTGAGACCG---------------------- chrUn_581 GGGAAGGAATGTATACATAGTGAGGCCA---------------------- chr1D_581 GGGAAGGAAGGTATACATAGTGGGACCG---------------------- chr3A_581 GGGAAGGAAGGTATACATAGTGAGACCG---------------------- chr3A_581 GGAAAGGAAGGTATACATAGTAAGACCG---------------------- chr2A_581 GGGAAGGAAGGTATACATAGTGAGACTG---------------------- chr7D_583 GGGAAGGAAGGTATACATAGTGAGACCG---------------------- chr6D_583 GGGAAGGAAGGTATACATAGTGAGACCG---------------------- chr2D_584 GGGAAGGAAGGTATACATAGTGAGACCG---------------------- chrUn_624 GGGAAGGAAGGTATACATAGTGAGACCG---------------------- chr1A_906 GGGAAGGAAGGTATACATAGT----------------------------- chr7D_1233 GGGAAGGAAGGTATACATAGTGAGACCG---------------------- SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 --------------TGAATGTTTGCACACGCGTGAGAGTGGTTTTCCTTT chr3D_570 --------------TGAATGTTTGCATGCGTGTGAGAGTGGTTTTCCTTT chr3D_571 --------------TGAATGTTTGCACACGCGTGAGAGTGGTTTTCCTTT chr5D_572 --------------TGAATGTTTGCACACGCGTGAGAGTGGTTTTCCTTT chr2A_574 --------------TGAATTTTT--------------------------- chr1D_578 --------------TGAA-------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 --------------TGAATGTTTGCACACGCGTGAGAGTGGTTTTCCTTT chr3B_579 --------------TGAATGTTTGCACACGCATGAGAGTGGTTTTCCTTT chr2A_580 --------------TGAATTTTT--------------------------- chr2A_580 -------------------------------------------------- chr1A_580 ACGCATGTTTGTACTGAATGTTTGCATACGCGTGAGATTGGTTTTCCTTT chr5D_581 --------------TGAATGTTTGCACATGCGTGAGAGTGGTTTTCCTTT chr3D_581 --------------TGAATGTTTGCACACGCGTGAGAGTGGTTTTCCTTT chrUn_581 --------------TGAATGTTTGCACACGCGTGAGAGTGGTTTTCCTTT chr1D_581 --------------TGAATGTTTGCACACGCGTGAGAGTGGTTTTCCTTT chr3A_581 --------------TGAATGTTTGCACACGCGTGAGAGTGGTTTTCCTTT chr3A_581 --------------TGAATGTTTGCACACGCATGACAATGGGTTTCCTTT chr2A_581 --------------TGAA-------------------------------- chr7D_583 --------------TGAATGTTTGCACACGCGTGAGAGTGGTTTTCCTTT chr6D_583 --------------TGAATGTTTGCACACGCGTGAGAGTGGTTTTCCTTT chr2D_584 --------------TGAATGTTTGCACACGTGTGAGAGTGGTTTTCCTTT chrUn_624 --------------TGAATGTTTGCACACGCGTGAGAGTGGTTTTCCTTT chr1A_906 -------------------------------------------------- chr7D_1233 --------------TGAATGTTTGCACACGCATGAGAGTGGTTTTCCTTT SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GTTTTGCACTGAAAATT-------TGGAGGGTTGG--------AA----- chr3D_570 GTTTTGCACTGAAATTT-------TGGAGGGTTGG--------AAGGTTG chr3D_571 GTTTTGCACTGAAATTT-------TGGAGGGTTGG--------AA----- chr5D_572 GTTTTGCACTGAAATTT-------TGGAGGGTTGG--------AA----- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 GTTTTGCACTCAAATTT-------TGGAGGGTTGG--------AA----- chr3B_579 GTTTTGCACTGAAATTT-------TGGGGGGTTGG--------AA----- chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 GTTTAC--------TTT-------TGGAGGGTTGG--------AA----- chr5D_581 GTTTTGCATAGAAATTTGGAGGGTTGGAATGTTGA--------AA----- chr3D_581 GTTTTGCATTGAAATTT-------TGGAGGC-TGG--------AA----- chrUn_581 GTTTTGCACTGAAATTT-------TGGAGGGTTGG--------AA----- chr1D_581 GTTTTGCACTGAAATTT-------TGGAGGGTTGGAAAGTTGAAA----- chr3A_581 GTTTTGCACTGAAATTT-------TGGAGGGTTGGAAGGTTGAAA----- chr3A_581 GTTTTGCACTGAAATTT-------TGGAGGGTTGGAAGGTTGAAA----- chr2A_581 -------------------------------------------------- chr7D_583 GTTTTGCACTGAAATTT-------TGGAGGATTGGAAGGATGAAA----- chr6D_583 GTTTTGCACTAAAATTT-------TGGAGGGTTGG--------AA----- chr2D_584 GTTTTGCACTGAAATTT-------TGGAGGGTTGG--------AA----- chrUn_624 GTTTTGCACTGAAATTT-------TGGAGGGTTGG--------AA----- chr1A_906 -------------------------------------------------- chr7D_1233 GTTTTGCACTGAAATTT-------TGGAGGGTTGG--------AA----- SNPs --------------S----------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 --------------ATTTGGAGGGTTGGAAACGT---------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 ---ACGTATGTTTGCACTGCCACTTGATTTTGGTTAGAGTGGCACTTGGT chr3D_570 AAAACGTATGTTTGCACTGCCATATGATTTTGGTTAGAGTGGCACTTGGT chr3D_571 ---ACGTATGTTTGCACTGCCACATGATTTTGGTTAGAGTGGCACTTGGT chr5D_572 ---ACATATGTTTGCACTGCCACATGATTTTGGTTAGAGTGGCACTTGGT chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 ---ACGTATGTTTGCACTGCCACATGATTTTGGTTAGAGTGGCACTTGGT chr3B_579 ---ATGTATGTTTGCACTGCCACATGATTTTGGTTAGAGTGGCACTTGGT chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 ---ACGTATGTTTGCACTGCCATATGATTCTGGTTAGAGTGACACTTTGT chr5D_581 ---ACGTATGTTTGCACTGCCACATGATTTTGGTTAGAGTGGCACTTGGT chr3D_581 ---ATGTATGTTTGCACTGCCACATGATTTTGGTTAGAGTGGCACTTGGT chrUn_581 ---ACGTATGTTTGCACTGCCACATGATTTTGGTCAGAGTGGCACTTGGT chr1D_581 ---ACGTATGTTTGCATTGCCACATGATTTTGGTTAGAGTGGCACTTGGT chr3A_581 ---GCGTATGTTTGCACTGCCACATGATTTTGGTTAGAGTGGCACTTGGT chr3A_581 ---ACGTATGTTTGCACTGCCACATGATTTTGGTTAGAGTGGCA------ chr2A_581 -------------------------------------------------- chr7D_583 ---ACGTATGTTTGCACTGCCACATGATTTTGATTAGAGTGGCA------ chr6D_583 ---ACGTATGTTTGCACTGCCACATGATTTTGGTTAGAGTGCCA------ chr2D_584 ---ACGTATGTTTGCACTGCCACATGATTTTGGTTAGAGTGGCA------ chrUn_624 ---ACGTATGTTTGCACTGCCACATGATTTTGGTTAGAGTGGCA------ chr1A_906 -------------------------------------------------- chr7D_1233 ---ACGTATGTTTGCACTGCCACATGATTTTGGTTAGAGTGGCA------ SNPs -----------------------S-------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 TTAGGGTTAGAGT-----------------------GGCACATGGTTTAG chr3D_570 TTAGGGTTAGAGT-----------------------GGCACTTGGTTTAG chr3D_571 TTAGGGTTAGAGT-----------------------GGCACTTGGTTTAG chr5D_572 TTAGGGTTAGAGT-----------------------GGCACTTGGTTTAG chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 TTAGGGTTAGAGT-----------------------GGCACTTGGTTTAG chr3B_579 TTAGGGTTAGAGT-----------------------GGCACTTGGTTTAG chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 TTAGGGTT------------------------------------------ chr5D_581 TTAGGGTTAGAGG-----------------------GGCACTTGGTTTAG chr3D_581 TTAGG--------------------------------------------- chrUn_581 TTAGGTTTAGAGT-----------------------GGCACTTGGTTTAG chr1D_581 TTAGGGTTAGAGT-----------------------GGCACCTGGTTTAG chr3A_581 TTAGGGTTAGAGTGGCACTTGGTTTAGGGTTAGAGTGGCACTTGGTTTAG chr3A_581 ----------------------------------------CTTGGTTTAG chr2A_581 -------------------------------------------------- chr7D_583 -----------------CTTGGTTTAGGGTTAGAGTGGCACATGGTTTAG chr6D_583 -----------------CTTGGTTTAGGGTTAGAGTCGCACTTGGTTTAG chr2D_584 -----------------CTTGGTTTAGGGTTAGAGTGGCACTTGGTTTAC chrUn_624 -----------------CTTGGTTTAGGGTTAGATTGGCACTTGGTTTAG chr1A_906 -------------------------------------------------- chr7D_1233 -----------------CTTGGTTTAGGGTTAGAGTGGCACTTGGTTTAG SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 GATTTAAA-GGAATAAATTTGCATGTTAGTTCATGACTTGTTTTTCTT-- chr3D_570 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTTGTTTTTT---T chr3D_571 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTTGGTTTTTTTTT chr5D_572 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTTGGTTTTTTT-- chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGATTT-GTTTTTTTTT chr3B_579 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTTGGTTTTTG--T chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTT-------TTTT chr3D_581 -------------------------------------------------- chrUn_581 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTT-------GTTT chr1D_581 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTT-------GTTT chr3A_581 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTT-------GTTT chr3A_581 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTT-------GTTT chr2A_581 -------------------------------------------------- chr7D_583 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTT-------GTTT chr6D_583 GATTTAAAGGGAATAAATTTGCATCTTAGTTCATGACTT-------GTTT chr2D_584 GATGTAAAGGGAATAAATTTGCATGTTAGTTCATGACTT-------GTTT chrUn_624 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTT-------GGTT chr1A_906 -------------------------------------------------- chr7D_1233 GATTTAAAGGGAATAAATTTGCATGTTAGTTCATGACTT-------GGTT SNPs ---------------------------------------------S---- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------------------- chr5D_1_TraesCS5D01G012600 ----------GAATGAAAGAGAGGGCTTCTCA-CCCCTCCGATTTTCATT chr3D_570 T---------TAATGAAAGAGAGGGCTTCTCACCCCCTCCGATTTTCATT chr3D_571 T---------GAATGAAAGAGAGGGCTTCTCACCCCCTCTGATTTTCATT chr5D_572 -----------AATGAAAGAGAGGGCTTCTCACCCCCTCCGATTTTCATT chr2A_574 -------------------------------------------------- chr1D_578 -------------------------------------------------- chr2A_578 -------------------------------------------------- chr5D_579 T---------GAATGAAAGAGAGGGCTTCTCACCCCCTCCAATTTTCATT chr3B_579 T---------GAATGAAAGAGAGGGCTTCTCACCCTCTCCGATTTTCATT chr2A_580 -------------------------------------------------- chr2A_580 -------------------------------------------------- chr1A_580 -------------------------------------------------- chr5D_581 T---------GAATGAAAGAGAGGGCTTCTCACCCCCTCCGATTTTCATT chr3D_581 -------------------------------------------------- chrUn_581 TT---TT----AATGAAAGAGAGGGCTTCTCACCCCCTCCGATTTTCATT chr1D_581 TT---TT--TGAATGAAACAGAGGGCTTCTCACCCCCTCCGATTTTCATT chr3A_581 TT---TT--TGAATGAAAGAGAGGGCTTCTCACCCCCTCCGATTTTCATT chr3A_581 TT--CTT--TGAATGAAAGAGAGGGCTTCTCACCCCCTCCGATTTTCATT chr2A_581 -------------------------------------------------- chr7D_583 TT---TTTCTGAATGAAAGAGAGGGCTTCTCACCCCCTCCGATTTTCATT chr6D_583 TT--TTT--TGAATGAAAGAGAGGGCTTCTCACCCC-TCCGATTTTCATT chr2D_584 TT--TTT--TGAATGAAAGAGAGGGCTTCTCACCCCCTCCAATTTTCATT chrUn_624 TC--TTT--TGAATAAAAGAGAGGGCTTCTCACCCCCTCCGATTTTCATT chr1A_906 -------------------------------------------------- chr7D_1233 TTTTTTT--TGAATGAAAGAGAGGGCTTCTCACCCCCTCCTATTTTTATT SNPs -------------------------------------------------- forward_177 -------------------------------------------------- reverse_1453 -------------------------------------------------- forward_366 -------------------------------------------------- reverse_2715 -------------------------------------------------- input_sequence_76473 -------------------------------------- chr5D_1_TraesCS5D01G012600 AATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT chr3D_570 AATGAAAACCATAAGTTCTCGAACTTCATGACTTGGTT chr3D_571 AATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT chr5D_572 AATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT chr2A_574 -------------------------------------- chr1D_578 -------------------------------------- chr2A_578 -------------------------------------- chr5D_579 AATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT chr3B_579 AATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT chr2A_580 -------------------------------------- chr2A_580 -------------------------------------- chr1A_580 -------------------------------------- chr5D_581 AATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT chr3D_581 -------------------------------------- chrUn_581 AATGAAAACCACAAGTTATCGAACTTCATGACTTGGTT chr1D_581 CATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT chr3A_581 AATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT chr3A_581 AATGAAAAGCACAAGTTCTGTAACTTCATGACTTGGTT chr2A_581 -------------------------------------- chr7D_583 AATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT chr6D_583 AATGAAAATCACAAGTTCTCGAACTTCATGACTTGGTT chr2D_584 AATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT chrUn_624 AATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT chr1A_906 -------------------------------------- chr7D_1233 AATGAAAACCACAAGTTCTCGAACTTCATGACTTGGTT SNPs -------------------------------------- forward_177 -------------------------------------- reverse_1453 -------------------------------------- forward_366 -------------------------------------- reverse_2715 --------------------------------------