>input_sequence_85981
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-----------------------------------------------------------------ATGGCTTCGATCGTG
CTGCTGCTGTCGGAGCTGCTCGGCGGCGCGGGGAGCACCAGCATGCTGGAGGCCAGCTGCTACATGGGCGGCCACAGCCT
GCGGGAGTTCCGGCCCGCGGCGGCGGCCACGGGCGACCGGGCGCCGCCGGAGCCGAAGCTG------------TCCACGG
AGGCCAAGGATGAGGAGC---CGTCGTCGTTGGACCTGGAGGATCTCTCCACCGTGTCCAGGATATCGGTGGACGTGATG
TGGCCCTGA-----------------------------------------------------------------------
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>chr3B_1_TraesCS3B01G212400
TCTATTTTCTATTATTTTACACCATAGACATGACATCAACTTCCCAACCGCCACTCTCTTCCTCCCCTCCCCTTGCACTG
CTGTCAGGACCCTAAAACCAGGCTAACTTGGATGGCAGTATAATCACCAGATTGGTCCATCACCTCCT---CTCCGCATA
GGCATAATGTCGGTTTTATATGACTTTACTGTTGTTGATAGGTCGGTTTTTATCTTTTTCTTTTTGCTAGAATGTTGGTG
GTTGGTTGTGTGCATCTTAGCTCTGCAGGGGTCAGATGTTGCTCATCATGCTTTCTATGCACTCGATACTAAATTTTAAG
TTAATAAAAGCAGCATTTATGAT---AAAAAAAATCCCTCTTTTCATTTTCATCATGAACGGATATATATTCTCTATTAC
CGGGTTAGCCACGTGGAAAATGGAAAATGTCCTAGCCTTTCTATCCATCAGGCTGTTGTACCGGCACCACCTAACGTCGG
TAGAGTAGAGCAAGTGAGCAAACCAGGAACCTGGACAAGGACACACACAGGATCAGCCGATCCGTCCGCCATCACCGCAC
GGGAC--------------ACGGCATAATACCAGGCATCAGCTCACGCCAGCTGCACTCCAAAGTTGAGAAAACCCACGT
CTCCCAGAAAAAACAAACAAATGGCAAGTTGACAACGACAACACAAGGGGCCGTAGCTTTCTCCGCCCTCCGTTTCGGCC
GAAACCCAGCGGCCGTCAGCT----CGCTCGCTTCCTACCAAACAAGGCGGCGGCCATTCATGGCGTGCGCGCGGAGCCG
TAGACGTCCAAAACCACAGCGGACACGGCCCACCGTTGCCTGCCCGCGCGCATATAAAGACCACACACCCTTCC-TTTAG
CCGCAGCGCCATAATTTCCGAGCTGCTAGCGCTACAGTCCCCATCAACAGTTCAGGCTTACAGTACAGCTAGTTGCAGTA
CCACGCGAGTACACCACCAAGCCAACGCCCAACAGAGAGGTAGTCGTGCCACTGGGTCTGGGAGGATGGCTTCGATCGTG
CTGCTGCTGTCGGAGCTGCTCGGCGGCGCGGGGAGCACCAGCATGCTGGAGGCCAGCTGCTACATGGGCGGCCACAGCCT
GCGGGAGTTCCGGCCCGCGGCGGCGGCCACGGGCGACCGGGCGCCGCCGGAGCCGAAGCTG------------TCCACGG
AGGCCAAGGATGAGGAGC---CGTCGTCGTTGGACCTGGAGGATCTCTCCACCGTGTCCAGGATATCGGTGGACGTGATG
TGGCCCTGAGCCTGCCGCCAGCTCCCGCTGACTCGG------GAGGTCCATTCGCCTCGAGGTTCCTCTGTGTTTTTGTT
GCCGACGACGAAGAAGAGACGTCATGTGATTCCTCGTTGCCTCGAGTTCTATGAAATGGAGATGTAAATATGCAAAGCCA
CCGCTGAATGTACTCCTTTTGTTCCTTCTTGTCCCATGACTTTTCCTACACACAGTTCCTTCGGGGATTCAACCGTCTGA
TCAGAGAA----CGACCGAACTCGTTTGCGACTTATTTTCCTCGTAATAATCGACCGGGTACTGACAATGATCCCATGCT
AATTGCAGAATTATATGGTTCTCGTAATCGGGCGGATAATGACAGTCCATCGAGCGGGTATACCCACCC--ACCTTCCCT
GCGTGGACTACAGAAAACAACGCATTTTCCATATACAAACTTGTAATCCATTCTGAGATATTGCTGTAACTGAACTTTCT
GTACTTTTAACAGCGCATTTTTTGTTGTCTTGGCCTTGCAAGGCATTGTTCAGGTAAACCACAAGAGCTCTGTAGTTTTT
AAGTCCCACATTACAAATAACGTCAAACAGAATTGCAAATAGTATCAAAGACCATACTGCTCCATGGGCGGTGGGTTGTC
TTCGGTAGTTCGATTCCAAGCATATCTGCCATTACTGCAATTTTGTCGATGTATATTTTAAGCAACCATTGCGTGTGGTT
TAGCAGAAACGTTTGCTAGGATATAATATAACTATGTGGGAAGAGGTTACTGGAAAATATTGGTGGCCTTGCACAGCTCA
TACACCGGCGGAGTGACCTTCAAGAAACCGCTGGAAGTTCTAAAACCACCACAGAGCAGCCTAGAGTAATTGCCCACAAC
GATTGTTCATATTACAAACCCGACCGTGATTTCCCTACAAAGCAATCATGCCTACTCCCTCCGATCCTAAATAATTGTCT
TTCTAGAGATTTCAACAAGTGACTACATACGAAGCAAAATGAGTGAACCTACACTCTAAAA
>chr3A_84
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---TCAGGACCCTAGACCTAGGCTAACTTGGATGGCAGCATAATCACCAAACTGGTCCATCACCTCCTTCTCTCTACATA
GGCCTAGTGTCAGTTTTATATGACTTTACTGCTGCCGATATGTCTGTTTCTATCTTCTTTTTTTTGCTAGAATATTGGTG
GTTGGTTGTGTGCATTTTAGGTCTGCAGTGGTCAGATGTTGCTCATCATGCCTTCTATATGCTCGATACTAAATTTTAAG
TTAATAAAAGCAGCATTTATGATAGAAAAAAAATCCCCTCTTTACATTTTCATTTTGAGCGGATATATATTCTCTATTAC
CGGGTTAGCCACGTGGAAAATGGAAAATGC----------CTATCCATCAGGCTGTTGTACCGGCACCACCTAACGTCGG
TAGAGTAGAGCAAGGCAGCAACCCAGGAACCTGGACAAGGACACACACAGGATCACCTGATCCGTCCGAGCCATCAC---
----CGCACCGCACGGGACACGGCATAATACCATGCATCAGCTCACGCCAGCTGCACTCCAAAG---AGAAAAACCACGT
CTCCCAGAAAAAACAAA----TGGCAAGTTGACAACGACAAGACAAGGGGCCGTGGCTTTCTCCGCCCTCCGTTTCGGCC
GAAACCCAGCGGCCGTCAGCTCGCTCGCTCGCTTCCTACCAAACAAGGCGGCGGCCATTCATGGCGTGCGCGCGGAGCCG
TAGACGTCCAAAACCACAGCGGACACGGCCCACCGTTACCTGCCCGCGCGCATATAAAGACCACA--CCCTTCC-TTCAT
CCGCAGCGCCATAATTTCCGAGCTGCTAGCGCTACAGTCCCCATCAACAGTTCAGGCTTACAG-----CTAGTTGCAGTA
CTACACGAGTACACCACCAAGCCAACGCCCAACAGAGAGGTAGTGGTGCCAT------TGGGAGGATGGCTTCGATCGTG
CTGCTGCTGTCGGAGCTGCTCGGCGGCGCGGGGAGCACCAGCATGCTGGAGGCCAACTGCTACATGGGCGGCCACAGCCT
GCGGGAATTCCGGCCC---GCGGCGGCCACGGGCGAGCGGGCGCCCACGGAGCCGAAGCTGCGGGGAACAACCTCAACGG
CGGCGAAGGATGAGGAGC---CGTCGTCGTTGGACCTGGAGGATCTCTCCGCCGTGTCCAGGATATCGGTGGACGTGATG
TGGCCCTGAGCCTTCCGCTGACTCAGGAGGTCGATTCGCCTCGAGGTTGTTCTGTG-----------------TTTTGCT
GCCGAGGACGAAGAAGATGTGTCATGTGATTCCTCGTTGCCTCGAGTTCTATGAAATGAACATGTAAATATACAAAGCCA
GCGCTGAATGTTCTCCCTGTGTTCCTTTTTGTCTCGTGACTTTTT-------------CTTCGGGGATTCAACCTTCTGA
TCAGATCATAATCGACCGAACTCGTTTGCAACATTTTTTCCTCGTAGCAATCGACCGGGTACTGACAATAATCCCATGCT
AATTGCAGAATTAAATGGTTCTCGTAATCGGGTGGATAATGACAGTCCATCGAGCGGGTATACCCACACCGACCTTCTCA
ACCTGGACTACAGAAAACAACGCATTTTCCCTATACAAACTTGCAATCCATT-----------CTGTAACTGAACTTTTT
GTACTTTTAACAGTGCATTTTTTGTTGTCTTGGCCTTGCAAGGCATTGTTCAGGTAAACCACAAGAGCTCTGGAGTTTTT
AAGTCCCATATTGCAAATAACATCAAACACAATTGGAAATAGTATCAAAGATCATACTATTCCATGGATGGTGGACTGTC
ATCGATAGTTCGATTCCCAGCA----------------------------------------------------------
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>chr3D_381
ATATCTG-------------------------------------------------------------------------
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--------------------------------------------------------------------------TATTAC
CGGGTTAGCCACGTGGACAATGAAAACTGGCCTAGCCTTTCTATCCATCAGGCTGTTGTACCGGCACCACCTAACGTCGG
TAGAGTAGAGCAAGGCAGCAACCCAGGAACCTGGACAAGGACACACACAGGATCAGCTGACCCGTCCGAGCCATCAC---
----C--------------ACGGCATAATACCACGCATTAGCTCACGCCAGCTGCACTCCAAAG---AGAAAAACCACGT
CTCCCAAGAAAAACAAA---ATGGCAAGTTGACAAGGACAACACAAGGGGCCGTGGCTTTCTCCGCCCTCCGTTTCGGCC
GAAACCCAGCGGCCGTCAGCTCGCTCGCTCGCTTCCTACCAAACAAGGCGGCGGCCATTCATGGCGTGCGCGCGGAGCCG
TAGACGTCCAAAACCACAGCGGACACGGCCCACCGTTACCTGCCCGCGCGCGTATAAAGACCACA--CCCTTCCCTTTAG
CCGCAGCGCCATAATCTCCGAGCTGCTAGCGCTACAGTCCCCATCAACAGTTCAGGCTTACAG-----CTAGTTGCAGTA
CTACACGAGTACACCACCAAGCCAACGCCCAACAGAGAGGTTGTAGTGCCAT------TGGGAGGATGGCTTCGATCGTG
CTGCTGCTGTCGGAGCTGCTCGGCGGCGCGGGAAGCACCAGCATGCTGGAGGCCAGCTGCTACATGGGCGGCCACAGCCT
GCGGGAGTTCCAGCCC---GCGGCGGCCAACGGCGAGCGGGCGCCGGCGGAGCCGAAGCTGCGGGGAACAACCTCAACGG
AGGTGAAGGATGAGGAGCCGTCGTCGTCGTTGGACCTGGAGGATCTCTCCGCCGTGTCCAGGATATCGGTGGACGTGATG
TGGCCCTGAGCCTGCCGCCAGCTCCCGCTGACTCGG------GAGGTTGCTCTGTG-----------------TTTGCTT
GCCGAGGACGAAGAAGAGATGTGATGTGGTTCCTCGTTGCCTCGAGTTCTATGAAATGAAGATGTAAATATGCAAAGCCA
CCGCTGAATGTTCTCCCTGTGTTCCTTTTCGTCTCGTGACTTTCT-------------CTTTGGGGATTCAACCATCTGA
TCAGATCATAATCAACCGAACTCGTTTGCAACATTTTTTTCTCGTAATAATCGACCGGGTACTGACAATAATCCCATGCT
AATTGCAGAACTAAATGGTTCTCGTAATCGGGCGGATAATGACAGTCCATCCAGCGGGTATACCCACCC--ACCTTCTCT
GCGTGGACTGCAGAAAACAACACATTTTCCGTATACAAACTTGCAGTCCAGTCTGAGATATTGCTGTAACTGAACTTTTT
GTACTTTTAACAG--CATTTTTTTTTGTCTTGGCCTTGCAAGGCATTGTTCAGGTAAACCACAAGAGCTCTGGAGTTTTT
AAGTCCCACATTACAAATAACATCAAACAGAATTGCAAATAGTATCAAAGATCATACTACTCCATGGGTGGTGGGTTGTC
TTTGATAGTTCGATTCCAAGCATATCTGCCATTCCTGCGATTTTGTCGATGTATATTTTAAGCAACCATTGCGTGTGGTT
TAGCAGAAACGTTTGCTAGG-----ATATAACTATGTGGGAAGAGGTTACTGGAAAATATTGGTGGCCTTGCACAGATCA
TACACCGGCGGAGTGACCTTCAAGAAACCGCTGGAAGTTCTAAAACCACCACAGAGCAGCCTAGAGTAATTGCCCACAAC
GATTGTTCATATTACAAGCCCGACAGTGATTTCCCTACAAAGCAAGCATGCCTA--------------------------
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>SNPs
SSSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSS-----------S-S-S-------------------S----------S-S----------------------SS----
---S--S----S-------------------S--SS----S---S----S------S--S-------------S------
---------------S----S-------S----------------------S------SSS-------------------
---------------------------------SS--------S---------SS---S---------------------
-----------------------------S--------------------------------------------------
--------------SS-----S-----------------------------------S----------SSSSSS-SSSSS
SSSS-----------------------------S------------------------------SSS------S------
-----------------SSS----------------------------------S-------------------------
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-------------------------------------S---------------------------SS-------------
---------------------------------------------------------------SSSSS------------
-S--S---------------------------------------S------SSSSSSS----------------------
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----------------SSS-----------------S---------S----------------------------S----
----S---------------------------------------------S-----------------------------
-----------------------------------------------SSS-SS-SSSSSSSSSSSSSSSSSSS-------
-----S-------------S--------------------------------------S---------------------
-----------S----S-S--------S-----S-S--------SSSSSSSSSSSSSS----------------S-----
-----SS----------------------S--S-S----------------------------------S----------
-------------S---------------------------------------------------------------S--
------------------------------S------------S----------------------------------S-
-------------S----------------------------------------------------------S-------
---------------------S-----------------------------S------S---------S-----------
----S----------------------------S----S-----------------------------------------
--------------------SSSSS---------------------------------------------------S---
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-----------------S------S--------------------S--------SSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_256
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----------------------------------------------------------------------------GGTG
GTTGGTTGTGTGCATC----------------------------------------------------------------
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>reverse_1352
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-----------------------------------------------------------------------GTTTTTGTT
GCCGACGACGA---------------------------------------------------------------------
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