>input_sequence_83132
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-----------------------------------------------------------ATGGAGGCTTGGAGGAGGAAT
GCCCTGCGCTGCGCGCTTCTCGTGCTGCTCCTCGCCATTTCAAGTGAGCGCCGCCTCCCTCGGCCACCGTCGACAGGCGA
TGTGCTTCCCGTGGCGCGTGCACGTTTCTTTCAATTTTCATTGTTTTGGCTGTGTGATTGCTTGCAGGCGGGGTGGCGAG
GGCTCAGGGGGGCGGCGAGTGCTGGAGCACGGACATGGGGTACGGCATCTGCGTGAAGCCCGGGGGGTGCAGAGCTGCCT
GCCATGCCCTCGGCAAGAACGACGGCCAGTGCAACGGGGGCTACTTCTGGCCGGTCTGCGAGTGCCTGTCTCCACACTGC
CACTAG--------------------------------------------------------------------------
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>chr3A_1_TraesCS3A01G349300
CTAGGTTTGGTATTACCCTTTAAGAAGAAGAAATTGAAAT----------------------------------------
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-----------------------------------------------------------------------------AAT
AACAAAAACAAATTAAAAAAAATAAGTTTTTATTGCGAG-GAATGAATTAATGGCATTAGTATGACTCTTTAAGAAGAAA
GATTGTTAAAAAAAGAAACTTGTA----------TGCACTAAAATTGCACCTTTTTTAGTATGCAAACAATAATCATATA
ATAGTGTAATTTTCCTAGATATTGCATGGTATTTGTGTGTATACATTTGTGCTG-CCCAACATCCC-AAAAATACCCAAA
TAATAAAACTAATAAAGGAACACA-AAAAAACAAATGCAAATAGGCATAAAAACAAAAA---AAACAAGAAAAAGAGAAC
AAAGGGA----------------------------------------CAGCCCACTAGCAAATCAACTGACCCAAATATG
TGATCTGTCAAAAACACCAGCCCAAAACAACTCAAAGAACAAACCA-GAAAAAAAAACAGAGCAGGAATATGAAAGCCAA
AATCTACGGCAAAAAGTCGAATGACCCAAAATCAATTTTCAGGCGACTTGCATTTAGCTAAAATGTGAGGGTATATACTA
TGTCGATATGTACTTTGATGCTCTTTCAGGCACTAATTTCAGTGCAAATTATGTAAAGCAAAGCTTGTGGTCTTCATTGT
GATCAGAACAGAGCACGCAATCTAATAATCAAATGGTAATCGCTTCTTTGTAGTAATTCGGAC---GAAGCAATTAGGAA
GTTCTTAAAATAGCTAGCTTGGGAGAAACCGCACAAACATAGCCTCCTATTTAGGGACATGTTTGCACCAAATCTAGGGA
GGG-ACATGTTTGTGTTGACTATCCTTGAAATGGCCCGGCTTACCCGCTTGACCTCGAGTTCTTTGAGCCTCCTATTCTC
TCTCCAAGCCTTAGGACCTCGATATATATGCAGACCGTAGCTCCTCCGACGAATGCCAATTGACCAAAATAAGGAGGAGC
CTCACCAACCAAGGAGGCCCAAACAGGACAGTTGTTGTGTACATTCTCCTGTTCCTGCCATGGAGGCTTGGAGGAGGAAT
GCCCTGCGCTGCGCGCTTCTCGTGCTGCTCCTCGCCATTTCAAGTGAGCGCCGCCTCCCTCGGCCACCGTCGACAGGCGA
TGTGCTTCCCGTGGCGCGTGCACGTTTCTTTCAATTTTCATTGTTTTGGCTGTGTGATTGCTTGCAGGCGGGGTGGCGAG
GGCTCAGGGGGGCGGCGAGTGCTGGAGCACGGACATGGGGTACGGCATCTGCGTGAAGCCCGGGGGGTGCAGAGCTGCCT
GCCATGCCCTCGGCAAGAACGACGGCCAGTGCAACGGGGGCTACTTCTGGCCGGTCTGCGAGTGCCTGTCTCCACACTGC
CACTAGGATCGGATTGGTGTTGCTACTAGGCAGGCAGGCGCCTCGTCTCCTCGTCCGTCGGT-CGTCGTCAGTTGAGCAC
CTCCACTTGAGCAGCTTCAGCCTGCGACGTTGTATCAAGTTACGGCTTAGCTATGTGTGCGTTAAAACTTGAAGTATGGT
TTGAGGCATCCCCGCCCTTTTGGCCCGCATTGTTGTTTATTTTATAATGGCAAAACAC-AAGTACGTATTGGTTTACATG
ATAAAAACTTGATCTCAAAGATTTGGCATGTTTGAACCACCCTCTTTGATTCAATTGTTATTTCTGGCATGGTCCATGC-
-----------------TTCGTGAATATGCAAAGCTTGCATATCTTTTTGTTGGTAGAAGAAGTTAGCACGTGAACAAAG
GGGGCACATCACACGGCACAACCAAAGATGATGTAAACATGGCGTCCGGAGTAGAGATACATGACATACTCGGTTCAAAC
ATAAGCTACAACACATAGCTAAACTACCGTGACCAAGAGAAGCAACCTGAACCGAAATGATGTCCCAAGTCTTGAAAATC
CATCACCGGGCATGCCAC----AAGCAAGACGAAACCTTCATGAAAGGGAGCGATGCTGACATCACTGTCATCCGATCCA
AAGAATCGAACCTGGGATTTTCCCCGGTGCTCGAAGAGGGGCACGGAGAAAGGTCGTGACAATGCCTTCATGAAGGGGAA
CGACGATGACATCGCCACCATCCTATCCGAAGAACCTCGCCGCCATCCTATCCGAAGAACCGGGTCGGGTGTTTTCCCCG
GTGCTCGAATAGGGGCACGGAGAAAGGTCGTGACAACGCCTCTATGAAGGGGAACGACGCTGACATCACCGCCGTCCTAC
CCGAAGAACCGGGTCACCGCCATCTGATTTGAAGAACTGGACCTGAGGTTTTTCCCTGGTACTCGAAGAGGAGCACAGAG
AAAGGTTGTGGCAACACCTCCAAGAAGGGGACGGCACCCTCACGTATCGCCTTTGCCAGCATCAACAAAC
>chr3B_1
CTAGGTTTGGTATTACCCTTTAAGAAGAAGAAATTGAAATGATAAGAAAACATATAATCGCCCCCGCGTCGCCCTCCTGG
CGACACGGGGGAAACCGCATCCACCGTCGCGCAACCCCCCTCCGCGCGCCCCCGCTGCGCCGCCGCCGGAGGGCCGGCCG
GCGAAGCCGCGCCGCGCCCCGGGATGGTGGCGGCGGGGCGAATCCGTTCCGCCCCCAAACCCTCCGCCCACCCCGCCCCG
CCCCAGATCTGCCACCGCCGCAGGACCACCTTCCCGCCCGTTTTCGCTGCGGCGCCGCCGGGGGGCCGGTCAGCTTGGTC
GCGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNCTGCACTCTGCCGGTCCGGCGACGGCCGCCGTGTGCTAGCCTCGGCCACAGGGTG
CCGTCCCCTGTAGTTCTCCCTCCTCCGTGCGTGGCCCAGCCCTGCTGGTGCTGCTGCCCTTGGATTGCGCGTGGGATCTG
CGGCCGGTCGCAAGGGTGTTCGCGGCATGCCATCCTGCTGGCGGCCCCCTCGCCACCGACGGCCCGTCCTCTCCCTCGAG
CCACGGCAACGGCTCTCGCGTTGGTGACGAGTATGCAATGCTAATGGTGGTCTCGAAGCCCTCAAGGCGGGTGCTTGCTG
GAGCTGCTCCGGCCCCGAAGACCTGGACCCGTGTCCCATCCGGTGTCCATGGCTGCCGGCATCCTCTGCCGGGCAGCTCC
GGCCTTGGCGACCCAGCAGCTGCGTTCCTTCCAGCTTGTCTGGCTCCCTGATGTCCCGACGACTATGGCCACGGTAGCCA
GGATCTGCGTCCATCCAGACCTTGCTTGCCGGCGTTGCCGATCGCCGTCGGCCCATCCCCTCGTGGCTTGCTTCGTGCCT
GTCCTATCCTGTATACCTCAAAGCCTTTGCTTTTGCCAGATCCAATGCTCGCGGGTTCGGAGGCGGTGCCACCCTCCGAC
GGCAGTTGTAGCCCCGCCAACCCCCTTCCGACATGGTGACTCCGACCGGCGTTGGCTTCCTCATCTTCGTTTCCAGATAC
GGTGGCTATGGGATTGCTCGGCCTCGGGCCAGGGAGAAATCCCTGCTCGGCTTGCCGATGCTGGCAGCGACGGCGTCTGC
GGATGTCGTTTCCTTCTTGGAGGCGTAATCAAGGCCCTCGGCTGCGCCCCTCTTTGAGCTCAGGAGAAACCCTAGGTCTG
GTTCCTCTGGATCGGATGGTGACGGCGTCTCGACGTCGTCCTCCTTCTTGAAGGCGCCATCTTGCTTGCTCGCGGTGTCC
TCGGTTTTGGTTCTCGAGATGTTGATGCTCTAGTTGGTCCGGCGTTGCCACTCCTGGATCAGGTTTGGTAGGTTTAGCTG
TGATGTATCCTCTCTTCGGGTCGAGCATCTCTTTTCTTTCTGCTCCGGACACCATGTTCACGCCTGTCTGCGTTCGTGTC
ATGTGTTGTACCTCTATCTGTACTCATTCTATTTCTTCTATCAATGCAATGATACGCAAGCTTTGCGTATTCGAGAAAAA
AACAAAAACAAATTAAAAC-AATAAGGTTTTATTGCGAAAGAATGAATTAATGGCATTAGTATGACTCTTTAAGAAGAAA
GATTGTTAAAAAAAAAAACTTGTACA--CAACTTTGCACTAAAATTGTACTTTTTTTAGTATGCAAACAATAATCATATA
ATAGTGTAATTTTCCCAGATATTGCATGGTATTTGTGTGTATACATTTGTGCTG-CCCAACATCCCAAAAAATACCCAAA
AAATAAAATTAATAAAGGAACACACAAAAAACAAATGCAAATAGGCATAAAAACAAAAACAAAAACAAGAAAAAGAGAAC
AAAGGGAGGGAGAGAGTGGATGGTGGGGCTGCACAGGAAATGGACTTCAACCCACTAGCAAATCAACTGACCCAAATATG
TGGTCCGTCAAAAACACCAGCCCAAAACAACTCAAAGAACAAACCAGGAAAAAAAAACAGAGCACGAATATGAAAGCCAA
AATCTACGGCAAAAAGTCGAATGACCCAAAATCAATTTTCAGGCGACTTGCATTTAGCTAAAATGTGAGGGTATATACTA
TGTCGATATGTACTTTGATGCTCTTTCAGGCACTAGTTTCAGTGCAAATTATGTAAAGCAAAGCTTGTGGTCTTCATTGT
GATCAGAACAGAGCACGCAATCTAATAATCAAATGGTAATCGCTTCTTTGTAGTAATTCGGAC---GAAGCGATTAGGAA
GTTCTTAAAATAGCTAGCTTGGGAGAAACCGCACAAACATAGCCTCCTATCTAGGGACATGTTTGCACCAAATCTAGGGA
GGG-ACATGTTTGTGTTGACTATACTTGAAATGGCCCGGCTTACCCGCTTGACCTCGAGTTCTCTGAGCCTCCTGTTCTC
TCTCCGGGCCTTAGGACCTCGATATATATGCAGAGCGTAGCTCCTCCTGTGAATGCCAATTGACCAAAATAAGGAGGAGC
CTCACCAACTAAGGAGGCCCAAACAGGACAATTGTTGTGTACATTCTCCTGTTCCTGCCATGGAGGCTTGGAGGAGGAAT
GCCCTGCGCTGCGCGCTTCTCGTGCTGCTCCTCGCCGTTTCAAGTGAGCGCCGCCTCCCTCGGTCACCGTTGACAGGCGA
TGTGCTTCCCGTGGCGCATGCATGTTTCTTTCAATTTTCATTGTTATGGCTGTGTGATTGCTTGCAGGCGGGGTGGCGAG
GGCTCAGATG---GGCGAGTGCTGGAGCACGGACATGGGGTACGGCATCTGCGTGAAGCCCGCGGGGTGTAGAGCTGCCT
GCCATGCACTCGGCAAGAACGACGGCCAGTGCAACGGGGGCTACTTCTGGCCGGTCTGCGAGTGCCTGTCTCCACACTGC
CACTAGGATCGGATTGGTGTTGCTACTAGGCAGGCAGGCGCCTCGTCTCCTT----GTCCGTCCGTCGTCAGTTGAGCAC
CTCCACTTGAGCAGCTGCAGCCTGCGACGTTGTAGCAAGTTACGGC-TAGCTACGTGTGCGTTAAAACTTGAAGTATGGT
TTGAGGCATCCCCGCCCTTTTGGCCCGCATTGCTGTTTATTTTATAAAATGGCAACACAAAGTACATATTGGTTTACATG
ATAAAAACTTGATCTCAAAGCTTTGGCATGTTCGAACCACCGTCTCTGATTTAATTATTATTTCTAGCATGCTCCATGCA
CTTGTGTTTTTCTTTTTTTCGTGAATATACAAAGTTTGCGTATCTTTTCATTGGTAGAAAAAACTAGAATGAGAACAAAG
GGGTACATCACATT--CACAACCAAAGATGACGTAAATATGGTGCCCGGATTAGAGAGATATAAGATGCTCGGTCCAAAC
AGAAGTCACAATACATCACTAAACCACCCTGACAAAGAGAAACATCCCTGACCGAAACGATGCCCCGAGTCTCTAAAAAC
GATCACCGGGTATGCCACTAGCAAACAAGATGACACCTTCATGAAGGGGAACGGCGCTGACGTTATCATCGTCCGACCCA
AAGAACCGAACCTGGGGTTTCCCCCGA-----------------------------------------------------
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-TGCTCGAAGAGGGGCACGGACATAGGTCGTCACAACGCCATCATAAAGGGGAACGACATTAACGCCGTCGCCATCCGAT
CTGAAGAACC----------------------------------------------------------------------
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>chr3D_4
---GGTTTGGTGTTACCCTTTAAGAATAAGAAATTGAAAT----------------------------------------
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-----------------------------------------------------------------------------AAT
AACAAAAAAATAG----AATAATGGGGTTTTCTTGCGAA-GAATGGATTAATGGCATCGGTATTACCTTTTAAGAAGAAA
GATAA-TAAAAAAAGAAACTTGTACAGACAACTTTGCACTAAATTCGCACCTTTTTTAGTATGCAAACAATAATCATATA
ATAGTGTAATTTTCCCACATATTGCATAGTGTTTGTGTGTATGCATTTGTACTGACCCAACATCCC-AAAG-TACCCAAA
TAATAAAACTAATAAAGGAACACA-AAAAT-------------------AAAAGAAAAT---AGGCATAAAAAAAAGAAC
AAAGGGAGGGAGAGAGTGGGGGGCTGGGCTGCACAGAAAATGGCCTTCAGCCCATTAGCAAATCAACTGACCCAAATGTG
TGGTCAGTCAAAAACATCAACCCAAAACAACTCAAAGAACAAACCAGGAAAAAAA--CAAAGCACAAATGTCAAAGCAGA
AATCTACGGCAAAAAGTCGAATGACCCAAAATCAATTTTCAGGCGACTTGCATTTAGCTAAAATGTGAGTGTATGTACTA
TGTCGATATGTACTTTGATGCTCTTTCAGGCACTAATTTCAGTGCAAATTATGTAAAGCAAAGCTTGTGGTTTTCATTAT
GATCAGAACAGAGCATGCAATCTAATCATCAAATGCTAATCGCTTCTTTGTAGTAGTAATTCATATGAAGTAATTAGGAA
GTTCTTAAAATAGCTAGCTTGGGAGTGAAGGCACAAATATGGCCTCCTATTCAGGGACATGTTTGCACCAAATCTAGGGA
AGGAACATGTTTGTGTTGACTATACTTGAAATGGCCCGGCTTACCCGCTTGACCTCGAGTTCTTTGAGCCTCCTATTCTC
TCTCCGGGCCTTAGGACCTGGATATATATGCAGACCGTAGCTCCTCCTGTGAATGCCAATTGACCAAAATAAGGAGGAGC
CTCACCAACTAAGGAGGCCCAAACAGGACAGCTGTTGTGTACATTCTCCTGTTCCTGCCATGGAGGCTTGGAGGAGGAAT
GCCCTGCGCTGCGCGCTTCTCGTGCTGCTCCTCGCCGTTTCAAGTGAGCGCCGCCTCCCTCGGTCACCGTCGACAGGCGA
TGTGCTTCCCGTGGCGCACGCATGTTTCTTTCAACTGTTAGTGTTATGGCTGTGTGATTGCTTGCAGGCGGGGTGGCGAG
GGCTCAGGGGGGCGGCGAGTGCTGGAGCACGGACATGGGGTACGGCATCTGCGTGAAGCCCGGCGGGTGCAGAGCTGCCT
GCCATGCCCTCGGCAAGAACGACGGCCAGTGCAACGGGGGCTACTTCTGGCCGGTCTGCGAGTGCCTGTCTCCACACTGC
CACTAGGATCGGATTGGCGTTGCTACTAGGCAGGCAGACGCCTCGTCTCCTCGTCCGTTCGTCCCTCGTCAGTTGAGCAC
CTTCGCTTGAGCAGCTGCAGACTGCGACGTCGTTGCAAGTTACGGCTTAGCTATGTGTGCGTTAAAACTTGAAGTATGGT
TTGAGGCATCCCCGCCCTTTTGGCCCGCATTGCTGTTTATTTTATAAAATGGCAACAC-AAGTACGTATTGGTTTACATG
ATAAAAACTTGATCTCAATGCTTTGGCATGTTTGAACCACCGTCTCTGATTCAATTGTTATTTCTGGCATGGTCCATGC-
-----------------TTCGTGAATATGCAAAGCTTGCATATCTTTTTGTTGGTAGAAGAAGTTAGCACGTGAACAAAG
GGGGCACATCACACGGCACAACCAAAGATGACGTAAACATGGTGTCCGGAGTAGAGATACATGACATACTCGGTTCAAAC
ATAAGCTACAACACATAGCTAAATTACCATGACCAAGAGAAGCAACCTGAACCGAAATGATGTCCCAAGTCTCGAAAATC
CATCACCGGACATGCCAC----AAGCAAGACGAAACCTTCATGAAAGGGAGCGATGCTGACATCACTGTCATCCGATCCA
AAGAATCGAACCTGGGATTTTCCCCGGTGCTCGAAGAGGGGCACGGAGAAAGTCCGTGACAACGCCTTCATGAAGGGGAA
CGACGATGACATCGCCATCATCCTATCCGAAGAACCTCGCCGCCATCTTATCCGAAGAACCGGGTCGGGTGTTTTCCCCG
CTGCTCGAATAGGGGCACGGAGAAAGGTCGTGACAACGCCTCCATGAAGGGGAACGACGCTGACATCGCCGCCGTCCTAT
CCGAAGAACCAGGTCACCGCCATCTGATTTGAAGAACTGGACCTGAGGTTTTTCCCTGGTACTCGAAGAGGAGCATAGAG
AAAGGTCGTGGCAACACCTCCAAGAAGGGGACGGCACCCTCACGTATCGCCTTTGCCAGCATCAACAAAC
>SNPs
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-------------------S------S-----------S-----------------------------------------
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---------------S----------------------------------------------------------------
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--S--S----------------------------------------------------------S---------------
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-----------------------S--------------------------------------------------------
-----SS----------------------------------------SSS------------------------------
---------S----------------------------------------------------------------------
------------------------------------S--------------------------S----------------
-----------------S----S----------------------S----------------------------------
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-----------------------------------------------------------S--------------------
----------------S-----------------S---------------------------------------------
--------------------------------S--------------SSSSSS---------------------------
--------------------S--------------------S---S----------------------------------
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-------------------------------S----------S-------------------------------------
----------------------------S-------------------------------------------S-------
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----------------------------------------------------SS--------S-----------------
-----------------S-----------------------------S--------------------------------
S-----------------------------------------S------------------------S-----------S
----------S----------------------------------------------------------------S----
------S---------------------------------------------------------------
>forward_2849
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------------------------------CAGACCGTAGCTCCTCCGA-------------------------------
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>reverse_3833
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------------------------------------------------------------------------TGAAAATC
CATCACCGGGCA--------------------------------------------------------------------
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