>input_sequence_69632
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----------G------------CATATAAGCCGCGGCCA-------------------------------------CTC
CGTTCCCCGGCTCGTAAGCTAAGCTAGCACAGTACTGT--------------------------GGCGACATGGCAAGGC
TCCTCCTCCTCGCCGCCGACCACGCCGCCGGAGCGCCGGGGGCGGCGAGTCTCGTCCTCGTCCTCGTCGTGGTGCTCGTC
GTCGCGGCGGTCGTCGTGTCGCTCTGCACCACCAGCACGCACGCGAAGCTGTGGGGGCGGCAGCGCGGGTCCTCCTCGTC
CGCGCCGTTGCCGAAATCGGACAGCAGCGTCGGCGCGAGCAACCGGAGGCGCCTGCTGTCGGCCACGCTGAGCGGGATCG
GCGGCAAGGCGGCCAGGATGGTGTCGTGGAACAGGCGCTCTCCGGCGCCGGGCGGCAGCAGCGACGACGAGGAGGCGGTG
GCCGATCTGGGGCTGGACGACGACGACGAGGCCGTGTGGCGGAAGGCCATCATCATGGGGGACAAGTGCCGGCCGCTCCA
GTTCTCCGGGCACATCGCCTTCGACTCCGACGGCAACCAGCTGCCCCCGCCGCCGCCGGCGGCAATCAAGAAAGCCGGCC
CCGACGTCCACGCCGAGAATTAAAATTAACATCTCGAGTTCTCGATCACCCGTGGACGGACGTTCGCG----TCAACTAA
TCAAGTCAACCGAGTCGCGGTTTCTTCTTCTCGATTTTTGGTGTACTCGTATGCACGTACGTA-GCGACGGCATGCAAAG
GTTTGGCGCGTCCGGTGTACTCGTATGCACGTACGTGAGTGAGTTGTAC-------------------------------
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>chr3B_1_TraesCS3B01G011700
AAAATTCATAAAAAATGCCTTGCCAATGAAAAAAATATGTCATCCTCTTAATGATAAAATTGTCATCCTCTTGATTAATA
ACATGTCATGGAAACAAAAATAAAAATTCCAACCTGTCAATTATTAAACTACTATCCTATTAATAATAAAAATGGCATGC
TCTTAACGATAAAACTGACATGCTCTTAG---TAAAAATGTCATGTTATTAATAATAAAAATATCATGTTATTGATAATT
AAACTGCCATCCTCTTAT-AATAAAAATACCATTTATCAATTATTAAAATGCCATGCTCTCAATAAGAAAACTGCCATAT
GAGAGTTAAAAAATATTGCCAGAATTGCGAAGAATAATTAAAAACTACCGAAGTTTTTTGCCATGGGGCATTGCAAAAAG
ACCTAAAAATTAACAGGATTTGGAACAGAAAAAAAAATGTTATGGATTAAAATGCAAATAAATTTCTGTGGTACCTAGAA
TTAAGACGCTCAGTTGAGTGGTGAGTGGTA--------------------------------------------------
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-----------------------------AGTGCCCCTTCCCCGTGCGCAGAAGATC-----------------------
-----TGGTCGTGGATTTTCTGGAGAAAAAATATGGA-GAACGCTCGGCAGGATACGTGTCACAGCGAACGACTCGATGT
GATC--GACATGGCCTCAGCCTTGCTCCAAGATTCGTGCAACGGCCGGGAAGTCGTTCCCTTGGATGGGCTCCCTGGCCG
ATGTTCGTCAGATATCATTTCCGAAAGAGA--AAAATCTACCAAGAATGAGGAACAGAGCATATGGTCCTCATTTGTTCA
AAC----------CTCAAAGGTGATTAGCTGGCCCACGCGATGCCGATGGACTTGACCGGCAGGCGGCATCTGCTGTCCG
CTAGCGCCAGTCTCCGGCGGGCGGGCGACGACCCGTAGCGTCAATCACCGTCGCCGCTGGCCCGGTCAATCTA----ACC
GGTCCTGCACGGCCGGGGAATTTGAGCGCCATGTCCAGCCACGATTCTCTTCTCCCCAGTCCAGTCTCCGGTGCCAGATC
GTGCGTGCGTG------------CATATAAGCCGCGGCCA-------------------------------------CTC
CGTTCCCCGGCTCGTAAGCTAAGCTAGCACAGTACTGT--------------------------GGCGACATGGCAAGGC
TCCTCCTCCTCGCCGCCGACCACGCCGCCGGAGCGCCGGGGGCGGCGAGTCTCGTCCTCGTCCTCGTCGTGGTGCTCGTC
GTCGCGGCGGTCGTCGTGTCGCTCTGCACCACCAGCACGCACGCGAAGCTGTGGGGGCGGCAGCGCGGGTCCTCCTCGTC
CGCGCCGTTGCCGAAATCGGACAGCAGCGTCGGCGCGAGCAACCGGAGGCGCCTGCTGTCGGCCACGCTGAGCGGGATCG
GCGGCAAGGCGGCCAGGATGGTGTCGTGGAACAGGCGCTCTCCGGCGCCGGGCGGCAGCAGCGACGACGAGGAGGCGGTG
GCCGATCTGGGGCTGGACGACGACGACGAGGCCGTGTGGCGGAAGGCCATCATCATGGGGGACAAGTGCCGGCCGCTCCA
GTTCTCCGGGCACATCGCCTTCGACTCCGACGGCAACCAGCTGCCCCCGCCGCCGCCGGCGGCAATCAAGAAAGCCGGCC
CCGACGTCCACGCCGAGAATTAAAATTAACATCTCGAGTTCTCGATCACCCGTGGACGGACGTTCGCG----TCAACTAA
TCAAGTCAACCGAGTCGCGGTTTCTTCTTCTCGATTTTTGGTGTACTCGTATGCACGTACGTA-GCGACGGCATGCAAAG
GTTTGGCGCGTCCGGTGTACTCGTATGCACGTACGTGAGTGAGTTGTACATAAAGTGTGTCATGTGCCCTTCATTTTGGA
ACAAAGTTTACGTGGCTGTGCAAATAATATAAACACGAGCCGATAAGAGGCTGTCGTTCGTCAGTCACTTGTTCTTCTTT
TGGAAGGTGTGTAGTCGAGGCACCAGTAACAGCAGGCAAAGGAGCCAACCCGGCTCAAAGCAAACAAAGCATAGCAGCAG
ATAACAAGACTATTATCAACCTGTGAAACAAACACATCTCCACTCCAGCACGCGACCCCATCTCGTTCGGATGCGTCCGT
TTAGCGTAGAACAAACGAATAGCGCGGCCAAACGCGAGGTCCCAAACGGACAAACGTCCGGATTTCGTCCGTTTTCGACC
CATTACATGCCCAAACTTGTGCCGAGTTTGGGATAAAACGGACATCACGCGGACGGGCTGGACGCACGCCCTTGTCCTCC
CCGTGGCCCATCTGTCGGGGACACTAGCACTCCATTCGCCTCCAACGCCTCCACCCGCTCTCCCCTGCCCCACCCCGTCG
CCGGCGCCGCCACTATTCTCCGGCCGCCTCCTCACTGCTCACCCCCCCCCCCCGCCCGTCCATACCAAACCACGTCCCGA
CATGGCCGCCACCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC
ACCACGCCCCCGCTTTCGTAGGAGTTTTGGCCGTCGCTTGGAGGAGATTTGGTCGTCGCCGTCGTAGCCGGTGCCAGAGG
GGATACGACCGCCGACGACGGATATGGACCACGGCAGCTTCCGTCGGGTGGTCCAGAGCGGCCAGTAGCTAGCCGCCAAC
CACCCCTAC
>chr3B_1
AAAATTCATAAAAAATGCCTTGCCAATGAAAAAAATATGTCATCCTCTTAATGATAAAATTGTCATCCTCTTGATTAATA
ACATGTCATGGAAACAAAAATAAAAATTCCAACCTGTCAATTATTAAACTACTATCCTATTAATAATAAAAATGGCATGC
TCTTAACGATAAAACTGACATGCTCTTAG---TAAAAATGTCATGTTATTAATAATAAAAATATCATGTTATTGATAATT
AAACTGCCATCCTCTTAT-AATAAAAATACCATTTATCAATTATTAAAATGCCATGCTCTCAATAAGAAAACTGCCATAT
GAGAGTTAAAAAATATTGCCAGAATTGCCAAGAATAATTAAAAACTACCGAAGTTTTTTGCCATGGGGCATTGCAAAAAG
ACCTAAAAATTAACAGGATTTGGAACAGAAAAAAAAATGGTATGGATTAAAATGCAAATAAATTTCTGTGGTACCTAGAA
TTAAGACGCTCAGTTGAGTGGTGAGTGGTA--------------------------------------------------
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-----------------------------AGTGCCCCTTCCCCGTGCGCAGAAGGTCGTGAGTTTGAATTCCTCCTCGCG
CACCTTGGTCGTGGATTTTCTGGAGAAAAAATATGGA-GAACGCTCGGCAGGATACGTGTCACAGCGAACGACTCGATGT
GATC--GACATGGCCTCAGCCTTGCTCCAAGATTCGTGCAACGGCCGGGAAGTCGTTCCCTTGGATGGGCTCCCTGGCCG
ATGTTCGTCAGATATCATTTCCGAAAGAGA--AAAATCTACCAAGAATGAGGAACAGAGCATATGGTCCTCATTTGTTCA
AAC----------CTCAAAGGTGATTAGCTGGCCCACGCGATGCCGATGGACTTGACCGGCAGGCGGCATCTGCTGTCCG
CTAGCGCCAGTCTCCGGCGGGCGGGCGACGACCCGTAGCGTCAATCGCCGTCGCCGCTGGCCCGGTCAATCTA----ACC
GGTCCTGCACGGCCGGGGAATTTGAGCGCCATGTCCAGCCACGATTCTCTTCTCCCCAGTCCAGTCTCCGGTGCCAGATC
GTGCGTGCGTGCGCGCGTGCGTGCATATAAGCCGCGGCCA-------------------------------------CTC
CGTTCCCCGGCTCGTAAGCTAAGCTAGCACAGTACTGT--------------------------GGCGACATGGCAAGGC
TCCTCCTCCTCGCCGCCGACCACGCCGCCGGAGCGCCGGGGGCGGCGAGTCTCGTCCTCGTCCTCGTCGTGGTGCTCGTC
GTCGCGGCGGTCGTCGTGTCGCTCTGCACCAGCAGCACGCACGCGAAGCTGTGGGGGCGGCAGCGCGGGTCCTCCTCGTC
CGCGCCGTTGCCGAAATCGGACAGCAGCGTCGGCGCGAGCAACCGGAGGCGCCTGCTGTCGGCCACGCTGAGCGGGATCG
GCGGTAAGGCGGCCAGGATGGTGTCGTGGAACAGGCGCTCTCCGGCGCCGGGCGGCAGCAGCGACGACGAGGAGGCGGTG
GCCGATCTGGGGCTGGACGACGACGACGAGGCCGTGTGGCGGAAGGCCATCATCATGGGGGACAAGTGCCGGCCGCTCCA
GTTCTCCGGGCACATCGCCTTCGACTCCGACGGCAACCAGCTGCCCCCGCCGCCGCCGGCGGCAATCAAGAAAGCCGGCC
CCGACGTCCACGCCGAGAATTAAAATTAACATCTCGAGTTCTCGATCACCCGTGGACGGACGTTCGCG----TCAACTAA
TCAAGTCAACCGAGTCGCGGTTTCTTCTTCTCGATTTTTGGTGTACTCG-------------------------------
-----------------------TATGCACGTACGTGAGTGAGTTGTACATAAAGTGTGTCATGTGCCCTTCATTTTGGA
ACAAAGTTTACGTGGCTGTGCAAATAATATAAACACGAGCCGATAAGAGGCTGTCGTTCGTCAGTCACTTGTTCTTCTTT
TGGAAGGTGTGTAGTCGAGGCACCAGTAACAGCAGGCAAAGGAGCCAACCCGGCTCAAAGCAAACAAAGCATAGCAGCAG
ATAACAAGACTATTATCAACCTGTGAAACAAACACATCTCCACTCCAGCACGCGACCCCATCTCGTTCGGATGCGTCCGT
TTAGCGTAGAACGGACGAATAGCGCGGCCAAACGCGAGGTCCCAAACGGACAAACGTCCGGATTTCGTCCGTTTTCGACC
CATTACATGCCCAAACTTGTGCCGAGTTTGGGATGAAACGGACATCACGCGGACGGGCTGGACGCACGCCCTTGTCCTCC
CCGTGGCCCACCTGTCGGGGACACTAGCACTCCATTCGCCTCCAACGCCTCCACCCGCTCTCCCCTGCCCCACCCCGTCG
CCGGCGCCGCCACTATTCTCCGGCCGCCTCCTTACTGCTCACCCCCCC-----GCCCGTCCATACCAAACCACGTCCCGA
CATGGCCGCCACCACGCCCCT-----------------------------------------------------------
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-----------GCTTTCGTAGGAGTTTTAGCCGTCGCTTGGAGGAGATTTGGTCGTCGCCGTCGTAGCCGGTGCCAGAGG
GGATACGACCGCCGACGACGGATATGGACCACGGCAGCTTCCGTCGGGTGGTCCAGAGCGGCCAGTAGCTAGCCGCCAAC
CACCCCTAC
>chr3D_38
-------------------------------------TGTCATCCTCTTAATAATAAAATTGACATCCTCTTGATTAATA
AATGGCATGC--AAAAAAATTAAAAATTCCAACATGTCAATAATAAAATTACCATCCTATTAATAATAAAACTGACATGC
TGTTAACAATAAAACTGACATCCTCTTAGTAATAAAAATGCCATGTTATTATTAATAAAAATATCATGTTATTGATAATA
AAACTGTCATCCTCTTATTAATAAAAATACCATTTATTAATTATTAAAATGCCATGCTCTTAATAATGAAACTGCCATAT
GAGAGTTAAAAAATATTTCCAATACGGACATGAATAAGTAAAAATTACCAAAG---TTTGCCATGGGGCATTGCAAAAAG
ACCTAAAAATTGACAGGATTTGGAACAGAAAAAAA--TGTTATGGATGAAAATGCAAATAAATTTCTATGCTGCCTATAA
TGAAAAATGCATGTGGGAAGTTTTGGAAAAACCCCTCTAAAAATAGTGATTGTTGTTCTTTCATGAATGGAAAATATTCA
GGATTTTTAGATTTTTTTTCCAGAAGAAAAAACACATTTGAAATAAATCTAGCTTTAAAATACATATAACAGTTGGGTCG
CAAATGTTCACAAAACCCTACATCAGTCGAGGGCCCCTACCCCGTGCGCAGGAGTTCCTCAGTTTGAACTCCTCCTCGCG
GACCTTGGTCGTGGATTTTTTGGAGAAAAAAAATAGA-GAACGTTCGCCAGGAAACTTTTGACAGCGAACGACTCCAGCT
GATC--TACATGGCATCGGCCTTGCGCAAAGATCCGTGCAACGGTGGGGAAGTCGTTCCCTAGGATGGGCTCCCTGGCCG
ATGTTCGTCAGATGTCGTTTCCGGAAAGAAATAAAATCTGCCAAGAA-------------------------TTTGGTCA
AACCGTCGCTTCGCTCAAAGGTGATTAGCTGGCCCACGCGATACCGATGGACTTGACCGGCAGGCGGCATCTGCTGTCTG
CTAGCGCCAGTCTCCGGCGGGCGGGCGACGACT-GTCGCGTCAATCTCCGTCGCCGCTGGCCGGGTCAAACTATCTGACT
GGTCCTGCACGGCCAAGGAATTCGAGCGCCATATCCAGCCACGA-----TTCTGTCCAGTCCAGTCTCCGGCGCCTGATC
GTGCGTACGTGC------------ATATAAGCCGCGGCTACTCTCCTTCCTGTGCGTCCGTGCTCTCTCAGTGATCTCTC
CATTCCCCGGCTTGTAACCTACTCCTTG-----------------------------------GGGCGACATGGCGAGGC
TCCTCCTCTTCGCCGCCGACCACACCGCCGGAGCACCCGGGGCGGCGACTCTCGTCCTTGTCATCCTCGTCGTCCTGGTG
GTGGCGGCGGTCGTGGTGTCTCTGTGCACCAGCAGCACGCACGAGAAGCTGTGGGGGCAGCAGCGCGGGCCCTCCTCGTC
GGCGCCGCTGGCCAAGGCGGACAGCAGCGTCGGCGCCAGCAACCGGAAGCACCTGCTGTCGGCCACGCTCAGCGGGATCG
GCGGCAAGGCGGCCAGGATGGTGTCGTGGAACAGGCGCTCTCCGTCCGGCA---GCAGCGACGACGACGAGGAGGCGGTG
GCCGCTCTGGGGCCG---GACGACGACGAGGCCGTGTGGAGGAAGGCCATCATCATGGGGGACAAGTGCCGGCCGCTCCA
GTTCTCGGGGCACATCGCCTTCGACTCCGACGGCAACCAGCTGCCCCA---GCCGCCGGCGGCAGTCAAGAAAGCCTCCC
CCGACGTCCCCGCCGAGAATTAATCAGCA----------TCTCGATTT--------------------------------
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>chr3A_535
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-----TGGTTGTGGATTTTTTGGAGAGAAAAACATAAGGAACGTGCGCTAGGAAACGCTCGACAACGAACGACTTCAGCT
GATCTATACATGGCGTCGGCCTTGCGCCAAGATCCGTGCAACTGCGTT-AAGTCGTTCGCTGGGATGGGCTCCCTGGCCG
ACGTTTGTTAGATATCATTTCCGAAGGAGG--AACAGGGCAAGC------------------ATCGTCCTCGTTTGGTCA
AACCATCGCTGCGCTCAAAGGTGATTAGCTGGCCCACGCGATACCGATGGACTTGACCGGCAGGCGGCATCTGCTGTCTG
CTAGCGCCAGTCTCCGGCGGGCGGGCGACGACCTGTACCGTCAATCGCCGTCGCCGCTGGCCGGGTCAA----TCTAACC
GGTCCTGCACGGCCAAGGAATTTGAGCGCCAT--------------------------GTCCAGTCTCCGGTGCCCGATC
GTGCGTGCGTGC------------ATATAAACCGCGGCTCATCTCCTACGCGTCCGTG------CTCTCAGTGATCTCTC
TGCTCCCCGGCTTGCAAGCTCAGCGAGTAGCCGTCTTCATAAATCGGCGAGCTCCCGGCCGTCGGGCGACATGGCGAGGC
TCCCCCTCTTCGCTGCTAACCACACCGCCGGAGCACCCGGGGCGGCGACTCTCGTCCTTGTTATCCTCGTCGTCCTGGTG
GTGGCGGCGGTCGTGGTGTCTCTGTGCACCAGCAGCACGCACGAGAAGCTGTGGGGGCAGCAGCGGGGGTCCTCCTCGTC
CGCGCCGCTGGCCAAGGCGGACAGCAGCGTCGGCGCGAGCAACCGGAAGCACCTGCTGTCGGCCACGCTCAGCGGGATCG
GCGGCAAGGCGGCCAGGATGGTGTCGTGGAACAGGCGGTCTCCGTCCGGCA---GCAGCGACGACGACGAGGAGGCGGTG
GCCGCTCTGGGGCCG---GAGGACGACGAGGCCGTGTGGAGGAAGGCCATCATCATGGGGGACAAGTGCCGGCCGCTCCA
GTTCTCCGGGCACATCGCCTTCGACTCCGACGGCAACCAGCTGCCGCCCCCGCCACCGGC---AAGCAAGAAAGCCGCCC
CCGACGTCCAAGCCAAGAACTAATCAACG----------TCTCGATCACCGGTGGATTGATGCTCGCGCGCGTCGACTAA
TCG----AATCAAGTCGCCGTTTTTTCTGCTCGATTTTGGTGCGCG-----TGTACGTACGCGCGCGACGGCAAAGGTTG
ACGA--CGCGTCCGGTGTA-------------------------------------------------------------
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>SNPs
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----------------------------S---------------------------------------------------
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----------------------------------------------S---------------------------------
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-------------------------------S------------------------------------------------
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-------------------------------------------------SS--S-------SS----------SSSSSS-
SSSSSS-------------SSSS---------------------------------------------------------
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------------SS------------------------------------------------------------------
----------------------------------S---------------------------------------------
----------S---------------------------------------------------------------------
--------------------------------S---------------SSSSS---------------------------
---------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSS-----------------S---------------------------------------------------
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>forward_1087
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----------------------------CGACCCGTAGCGTCAATCA---------------------------------
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>reverse_2888
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-------CCCCGCTTTCGTAGGAGTTT-----------------------------------------------------
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