>input_sequence_67975
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-----------------------------------------ATGTCCTCCAGTGATCAGAACCCAGCGCCCACGCCCGCC
TCGGGCACCGGCGGGACGGCGCCGCCGCCGGGCAGGCCGACCACGGTCTCCTCGCAGGCGATCGACATGGGCGCTCAGGT
GCTGCAGCCGTTGAAGCCGGTGCGCCAGATGAAGCAGCACGCGTGCAGCTTCGCGCTGTACGCGCATGACATGCACCGGC
AGCTCGAGGTCCACCACTTCGTCTCCCGCCTCAACCAAGACGTCCTCCAGTGCGCCGTCTACGACTCCGACAAGCCCTCG
GCCCGCCTCATCGGTATGTCAATCGCCGGAACCACGCAGACCATTACGTTT---------------AGTTGCTTATAAAT
TTGGATGTTGCAGGTGTGGAGTACATCGTGTCGGACAAAATCTTCGAGGACCTGCCGCCGGAGGAGCAGAGGCTGTGGCA
CTCGCACGCCTACGAGGTCAAGGCCGGGCTGTGGACCGACGTGGGCGTGCCGGAGATGCTGCAGACCTCGGAGATGGCCA
GGATGGCCAAGACGTACGGCAAGTTCTGGTGCACGTGGCAGGTGGACCGCGGCGACCGGCTGCCACTCGGCGCGCCGGCG
CTCATGATGTCGCCGCAGGCCGTGGAGCCGGGCCGGGTGCGCGCCGAGCTGGTGCGCGCACGCGACGAGAGGTGCAAGGT
GGACAGCTCGGCTCGCGGGCTCAAGGCTCAGAGGGTGGAGATGGATGAGCCGGAGTGGATCAACCCAAACGCCGACTACT
GGCGGCTGCACGGCAAGGGGTTCGCCGTGGACGTCACGGCCACGGAGATGAAGCAGCACGCGCCCTTCCCTTGA------
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>chr3D_1_TraesCS3D01G283100
AGACGCACCCACATTTGACTATCAACTGATACTAAAATGGAATACAACTTGTGTTGTATTTAGGGATGGTATTTGGATGA
AGTAAATATGAAAGTTCATGTAGAAAAATTTAAGAGGCTTGTGTGTTATCCAGCCATGGAGTTTTGAAGTCCATTCTAAT
GTAGTACTCCCTTCGTTTCTTTTTAGTCTGTATATAAGATTTGATCAAAGTCAAAGTTTGTAAAGTTTGACCAATTTTGT
AGGAAAGAATATTAACATCTACAATACTAAAGCTGTTGTATGGTATGAAAATTAATTTCATGATGCATCTAACAATATTG
ATTTCATATTGTGAATCTTGATATTTTTTCTATAAACTTAGTCAAAGTTAACAAAGTTTGACTTTAATCAAAGCTTATAT
GCAGACTAAAAAGAAACGAAGGAAGTACCATGATGACTCGTAGTTGACTGAAACATCTCCTCCACTAAACGAACATGCTA
GAAAGACTGAAATTAAATTAAAATAGTGCAAGCACCGGTGCCAAATTTAAAACTTTTGCAAAAAAACCTTCAATTTTAAG
ACCTGAATTCTTGTCATCTGACAAAGCTAACCATGTGAGCTTCACTCCATGTATCCTCTTGAAAGAAGGAAGTGAACTAA
CGAAAATTTAATATAGATTGTACTGCCATACCATATGATACTATTATCCCAGCCGTCGGTCCTCCTCGGGATCCCTGTGA
GGTCAAGTATTCGGGATGATTAGCAACCAAGTTTGTGACGTGTATCGGACTTTTTTTTTTTTGCGACGTGTATCGGACTT
AGGCGCCACGTTCGGCGGTGGAAGCTCGTACTCATAGTTCTCGCGCCTTCTGCAAGCACGCCACGTCCTTCGCCTAAAGC
AGCACGCGTCACGGCGTCAGGCCAGCTTGCGCGAACGCCTCGAAGTTACGAA-GATAAGAAGACCGCGCCCTCGACTGGT
CGCTAATCAGCCTGTTGCGATCTGCCAACGCGCGAGAAGCGATGTCCTCCAGTGATCAGAACCCAGCGCCCACGCCCGCC
TCGGGCACCGGCGGGACGGCGCCGCCGCCGGGCAGGCCGACCACGGTCTCCTCGCAGGCGATCGACATGGGCGCTCAGGT
GCTGCAGCCGTTGAAGCCGGTGCGCCAGATGAAGCAGCACGCGTGCAGCTTCGCGCTGTACGCGCATGACATGCACCGGC
AGCTCGAGGTCCACCACTTCGTCTCCCGCCTCAACCAAGACGTCCTCCAGTGCGCCGTCTACGACTCCGACAAGCCCTCG
GCCCGCCTCATCGGTATGTCAATCGCCGGAACCACGCAGACCATTACGTTT---------------AGTTGCTTATAAAT
TTGGATGTTGCAGGTGTGGAGTACATCGTGTCGGACAAAATCTTCGAGGACCTGCCGCCGGAGGAGCAGAGGCTGTGGCA
CTCGCACGCCTACGAGGTCAAGGCCGGGCTGTGGACCGACGTGGGCGTGCCGGAGATGCTGCAGACCTCGGAGATGGCCA
GGATGGCCAAGACGTACGGCAAGTTCTGGTGCACGTGGCAGGTGGACCGCGGCGACCGGCTGCCACTCGGCGCGCCGGCG
CTCATGATGTCGCCGCAGGCCGTGGAGCCGGGCCGGGTGCGCGCCGAGCTGGTGCGCGCACGCGACGAGAGGTGCAAGGT
GGACAGCTCGGCTCGCGGGCTCAAGGCTCAGAGGGTGGAGATGGATGAGCCGGAGTGGATCAACCCAAACGCCGACTACT
GGCGGCTGCACGGCAAGGGGTTCGCCGTGGACGTCACGGCCACGGAGATGAAGCAGCACGCGCCCTTCCCTTGAGAGGTC
GAATGGTTGCCCAGTGAAATGCGCATCTTCTTTCAACTTCTGTTGGTTGGTCTTGTTTTTAAGGTAGAGTCGTCGGTGTA
CGGAATGGTCGGGAGATGCGAGTGAAGGTGCAAGTTGCGTTTGATTCTATATAATCCAACGTCATTTCCCCTGATTATTT
GCATTCTTTACTGCCGTGGTTTCAGCTTTGTAAATTGCAATATGTGCATGCTGTCGCATCTTGCAGCTCGAAAAACAGGG
CAGGGTCGACATGGTGGATTGTGTTGTGAGGAGTTAATTGCAGGAAACTAAGGCCAACTCTAACCGTGATTCCCTATCTC
GCGTTAGAGCAACAGGAGGGGCGCTGTAAAAACAGCGCGGAAATAGAGCATCTCCAACAGGAGCGGCGCTGTAAAAACAG
CGCGGAAATAGTGTTTTTCTGCGCCCAGCAGGGCGTTGGCTCCAACGGACACTATAAAATGCAGCGTCGGGCGCTGAAAA
AACAGCGCGCGAGCAAATCAGTGCCACGCAACACATAGTTCATATAATACAAATAATAAAAATAGATAAAAATGATATAC
AAATAATAAATATAATACAAATAATAAAAATAGATAAAAATGATATACAAATAATAAATATAGATAAAAATGATACTACG
ATGCAAACATAGTAGAAGTTACTCCTCCTCCCCAGTGGTATAGTAACGCGTCATTTCATTAAGGATCATTGTTGTCAAAA
GTCGACGCTAGTCTCAAGTCGCACTGCGCTAACGCCAGTGCCTTTCGCCTCACGCCTGTTCACTCGATCTGTGGCTCGCT
TGTAACGCCCATGATGCGGCTATATTTCCCACGTGTTGAGGCACGACTTAGAGGCATAACCGTATTGTGGTATTGTCGCA
AGAAGGGTTATCTTCACACAATCCCATGTAATGAACAAGAATGAGATAACGAGAGTGGCTTACAATCGTCATTTTCACAC
AATACATAAATTAATTTATACATCATTCAAAATC
>chr3A_780
TTTGT---------------------------------------------------------------------------
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----------------------------------------------------------------GACGTGTATCGGCCCT
CGGCGCCACGTTCTGCGGTGGAAGCTCCTACTCATAGTTCTCGCGCCTTCAGCAAGCACGCCACGTCCTGCGCCTAAAGC
AGCACGCGTCGCGGCGTCAGGGCAGCTT-CGTGAACTCCTCCAAGTTACGAC-GATAAGAAGACCGCGCCCTCGACTGAT
CGCCAATCAACCTGCTGCGATCTGCCAACGCGCGAGAAGCGATGTCCTCCAGTGATCAGAACCCAGCGCCCACGCCCACC
TCGGGCGCCGGCGGGACGGCGCCGCCGCCGGGCAGGCCGACCACGGTCTCCTCGCAGGCGATCGACATGGGCGCTCAGGT
GCTGCAGACGTTGAAGCCGGTGCGCCAGATGAAGCAGCACGCGTGCAGCTTCGCGCTGTACGCACACGACATGCACCGGC
AGCTCGAGGTCCACCACTTCGTCTCCCGCCTCAACCAGGACGTCCTCCAGTGCGCCGTCTATGACTCCGACAAGCCGTCG
GCCCGCCTCATCGGTATGTCAGCCGCCGGAGCCTCGCCGACCATTATGTTTGCGGTTTGCACGTTTGGTCGCTCATGAGC
CTGGATGTTGCAGGTGTGGAGTACATCGTGTCGGACAACATCTTCGAGGCCCTGCCGCCGGAGGAGCAGAGGCTGTGGCA
CTCGCACGCCTACGAGGTCAAGGCCGGGCTGTGGACCGACGTGGGCGTGCCGGAGATGCTGCAGACCTCGGAGATGGCCA
GGATGGCCAAGACGTACGGCAAGTTCTGGTGCACGTGGCAGGTGGACCGCAGCGACCGGCTGCCCCTCGGCGCGCCGGCG
CTCATGATGTCGCCGCAGGCCGTGGAGCCGGGCCGGGTGCGCGCCGAGCTGGTGCGCGCGCGCGACGAGAGGTGCAAGGT
GGACAGCTCCGCTCGTGGGCTCAAGGCTGAGAGGGTGGAGATGGATGAGCCGGAGTGGATCAACCCGAACGCCGACTACT
GGCGACTGCACGGCAAGGGGTTCGCCGTAGACGTCACGGACACGGAGATGAAGCAGCAGGCGCCCTTCCCTTGAGAGATC
GAATGGTTGCCCAGTGAAATGCGCGTCTTCTTTCAACTTCTGTTGGTTGGTCTTGTTTTTCC-GTAGAGTCGTGGGTGTA
CGGGACAGTCGGGAGATGTCAGTGAAGGTGCAAGTTACGTTTGATTCTATATGATCCAACGTCATTTCCCCTGATTATTT
GCATTCTTTACTGCCGTGGTTTCATCTTTGTAAATTGCAATATGTGCATGCTGTCGCATCTTGCAGCTCGAAAAACAGGA
CAGGATCGACATGGTGGATTTTGTTGTGACAAGTTAATTGCAGGAAACTAAGGCCAAC------CGTGATACCCTATCTC
GCCTCAGAG-----------------------------------------------------------------------
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>chr3B_780
TTTGA---------------------------------------------------------------------------
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----------------------------------------------------------------GACGTGTATCGGCCCT
ATGCGCCACGTTCTGCGGTGGAAGTTCCTACTCATAGTTCTCGCGCCTTCTGCAAGCACGCCACGTCCTGCGCCTAAAGC
AGCACGCGTCGCGGCGTCGCGGCAGCTTGCGCGAACGCCTCGAAGTTACGAAGGATAAGAAGACCGCGCCCTCGAGGGAT
CGCCGATCAGCCTGCTGCGATCTGCCAACGCGCGAGAAGCGATGTCCTCCAGTGATCAGAACCCAGCGCCCACGCCCACG
TCGGGCACCGGCGGGACGGCGCCGCCGCCGGGCAGGCCGACCACGGTCTCCTCGCAGGTTATCGACATGGGCGCTCAGGT
GCTGCAGCCGTTGAAGCCGGTGCGCCAGATGAAGCAGCACGCGTGCAGCTTCGCGCTGTACGCGCATGACATACACCGGC
AGCTCGAGGCCCACCACTTCGTTTCCCGCCTCAACCAGGACGTCCTCCAGTGCGCCGTCTACGACTCCGACAAGCCCTCG
GCCCGCCTCATCGGTATGTCAGTTGCCGAAGCCTCGCCGACCATTACGTTT---------------GGTTGCTTATAAAT
TTGGATGATGCAGGTGTGGAGTACATAGTGTCGGACAAAATCTTCGAGGACCTGCCGCCGGAGGAGCAGAAGCTGTGGCA
CTCGCACGCCTACGAGGTCAAGGCCGGGCTGTGGACCGACGTGGGCGTGCCGGAGATGCTGCAGACCTCGGAGATGGCCA
GGATGGCCAAGACGTACGGCAAGTTCTGGTGCACGTGGCAGGTGGACCGCGGCGACCGGCTGCCCCTCGGCGCGCCGGCG
CTCATGATGTCGCCGCAGGCCGTGGAGCCGGGCCGGGTGCGCGCCGAGCTGGTGCGCGCACGCGACGAGAGGTGCAAGGT
GGACAGCTCGGCTCGTGGGCTCAAGGCTCAGAGGGTGGAGATGGATGAGCCGGAGTGGATCAACCCGAACGCCGACTACT
GGCGGCTGCACGGCAAGGGGTTCGCCGTGGACGTCACGACCACGGAGATGAAGCAGCACGCGCCCTTCCCTTGAGAGATG
GAATGGTTGCCCAGTGAAATGCGCATCTTCTTTCAACTTCTGTT------------------------------------
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>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------S-S-
-------------S-------------S-----------------------------------------S----------
----------S----------S--------------------------------------------------------S-
---S----------S--------------------------------------------------------------S--
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---------------------S--------S--S---S----------------------------S-------------
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---------------S--------------------------------------------------S-------------
-----------------------------------------------------------------------------S--
------------------------------------------------------------SSS----------S------
---S-SS-----------SS----------------S---------------S---------------------------
------------------------S------------------------------------------------------S
----S---------------S--------SS---------------------------SSSSSS------S---------
--S-S----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_20
AGACGCACCCACATTTGACT------------------------------------------------------------
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>reverse_1311
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------------------------------ACCACGCAGACCATTACGTT------------------------------
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>forward_1302
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--CCGCCTCATCGGTATGTCAA----------------------------------------------------------
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>reverse_2637
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----------------------------------------------------------------------------CGCT
TGTAACGCCCATGATG----------------------------------------------------------------
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