>input_sequence_83863
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--------------------ATGTCTGGCGTGTGGGTGTTCAAGAACGGTGTGGTGCGCCTGGTGGAGAACCCGGGGAGC
GAGCGGACGTCGACGGTGCGACGGAAGGCGCTGCTGCACACGCCGAGCGGGCAGGTGGTGTCGTCGTACGCGACGCTGGA
GGCGAAGCTGACGGCGCTGGGGTGGGAGCGCTACTACGAGGACCCGGCGCTGTACCAGTTCCACAAGCGCGGCTGCCTCG
ACCTCATCTCGCTCCCCAGGGACTTCAACCACTTCTCCTCCGTCCACATGTACGACGTCGTCATCAAGAACAGGGAATCC
TTCCGCGTCGTCGACGCCTAG-----------------------------------------------------------
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>chr3A_1_TraesCS3A01G176100
AGAGAGTATCAATTTTGTTCTCGACAAAGGCAACATTGGTTTGATCGACCGGCCAGAAATTCCCTTTCGTGGAAAAA-CA
ATGCTGCAAAAGGTACGCAAAGATAGCTCTCATATTTCTTATTGTTTAAGTAAAGTCGAAAACTGTATGGCGAGTGAATC
CCATTCCCCTGAGAATTAGGCTAGCTCTTTTTGTTTTCCTTTCAGGAAAAAGGTGAGTAGGATTCCTCGCACAACATCAC
ATTCTTTCTTTTCAATTTTCCATATGGGAGTGCTCAAGCCATAGATTACGCATGAATTATATGTAGATCTCCCCATTGGC
AATTAACCAACGCCATCAGTTAATGTCCTGTTCTTGACGTGTCGCGGGGCGGCCGCGACACATGTCAAATTTCGTGACCT
CATGATGATCAATCACCTCATGCACTACGTAATTCTGG-AAAATAACAATATGCGTAGCATATAGCTACCTTTTTTAGCT
ACCTACCTAGCTAGAATTTCCTTCTTTCTTCCAACAAATATATTCCAGGTAGCTTATCAAGAACATAAGCTAGCTAGGCA
CATATATTCTCCCGCGCGCACTACTCAAGTTTAATGAATGTACCATATATTCTGCTTCTCTCCCATCCCTGTGCATGCAA
CCAGCTACAGCATCTTCCTGACCTAACCTAGCTACAAACTAAAGACGCCCTTCTCTTCTCTGGTGCATGCACGCGTATAT
CGACGTACTAATCACTGGCAGTATAGTATCGCAGTCGCATAAGAAATCTATGTTCTGCGGCTGTCCCCCGTATACATGTC
ACCTCTACCCCACACCATCGATAATCTAGCTTCATCCACATCCACCTCTATATATACCCCCTTCATCTCGCCCTCCCTTG
CTCCATCA--------------------------------------------------------TCCCAGTGCTAGCTCG
ACCAAGTGCATCATCTATCGTTTGTTTTCCCTCAATCTCTAAGCCGATAGAAAGGTGAGAGTT-GAGGGGTAGGTCGGCC
GACCGGAG-GGCTGTGGACCATGTCTGGCGTGTGGGTGTTCAAGAACGGTGTGGTGCGCCTGGTGGAGAACCCGGGGAGC
GAGCGGACGTCGACGGTGCGACGGAAGGCGCTGCTGCACACGCCGAGCGGGCAGGTGGTGTCGTCGTACGCGACGCTGGA
GGCGAAGCTGACGGCGCTGGGGTGGGAGCGCTACTACGAGGACCCGGCGCTGTACCAGTTCCACAAGCGCGGCTGCCTCG
ACCTCATCTCGCTCCCCAGGGACTTCAACCACTTCTCCTCCGTCCACATGTACGACGTCGTCATCAAGAACAGGGAATCC
TTCCGCGTCGTCGACGCCTAGACGGCCCTCTTCCGTCCATGCAGTCTCTCGATCTCTTCTCATCAGTTCAGCTATAGCTC
TTCTTCCATCGTTTGACTTGATTTCGCATGCAGGGTTTGTTGTTGTTAGTGATCCGGGTGTTATATATGATTGGTTGTGC
CTGATTTGGTTGGGAGGTGTAGTGTGGTAGTGGAGTGAACGAGGGTACTGTTTCTGCACACATATGTGCGTGTGGTGCC-
GAGTATATGCATAGGTTTTCGTTGTGGTGTGTATATGTATGCGTGCTG-GGGGTGTGTAAGATCTCTGTTTTGATGTAAA
TTAGTGTCCGTGTGATGACTATATATATCCACTTACGTTCATTTGCACGTTTCTCTGCATGCACATGCGTCATGCATGTT
ACCGGCCATGTTGCATGCCTAGGGAAATATATAAAGAATA-TATCATGCACGCATTGCTTCTCGTTATGATTGTTTGGTG
GTGGGGAGGGGGGTGTGGGGGTTCTGATGAAAACATAGGGAATAGACAGCCACTCCAAAAAAAAATGAAAACATATAGGG
AATAATAGGCTGACACGATGATATTTATGCTGCCTTTTTTTAGACAAATATTTAGACCGACTGATGCTAGGCAAGACAAC
CACTTACTCCACCCGTCCGCGAATAAGTGTATTTCTACCTTTTGTCCTAAATCAAACTTTG-AAATTTTTACCAACTGTA
TAAAAAAGAGTAATAACATATATGACACCAAACTGGTATATTATAAAGGTACATTTTAAAACGGATCTACTGATACTAAT
TTAGTACCATAAATGCTGCTATTTTTTTCTATAAAATTGGTCAAAGTTTTAAAACTTTAACTTAGTACAAAAACTAGATG
TGCATTTATTTGTGGACGGAGGGAGTACTTTGCTGGCATCCAAAATTGAATCGCTGAAGCTACAGCTACTGGGCCTTCGT
TTGAATCACCACAGATTAACATTTTGAGCCACAGTAAGTACATGCTTCGTCACAAATTCGGCCCA
>chr3D_1
AGAGAGTATCAATTTTGTTCTCGACAAAGGCAACATTGGCTTGATCGACCGGCCAGAAATTCCCTTTCGTGGAAAAAACA
ATGCTGCAAAAGGTGCGCAAAGATAGCTCTCATATTTCTTATTGTATAAGTAAAGTAGAAAACTGTATGGCGAGTGAATC
CTATTCTCCTGAGAATTAGGCTAGCTCTTTTTGTTTTCCTTTCAGGAAAAAGGTGGGTAGGATTCCTCGCACAACATCAC
ATTCTTTCTTTTCAATTTTCCGTATGGGAATGCTCAAGCCATAGATTACGCATGAATTATATGTAGATCTTCCCATTGGC
AATTAACCAACGCCATCAGTTAATGTCCTGTTTTTGACGTGTCGCAGGGCGGCCGCGACACATGTCAAATTTCGTGACCT
CATGATGATCAATCACCTCATGCACTACGTAATTCTGAAAAAATAACAATATGCGTAGCATATAGCTACCTTTTTTAGCT
ACCTAGCTAGCTAGAATTTCTTTCTTTTTTCCAACAAATATATTCCAGGTAGCTTATCAAGAACATAAGCTAGCTAGGCA
CATATATTCTCCCGCGCGCACTACTCAAGTTTAATGAACGTACCATATATTCTGCTTCTCTCCCATCCCTGTGCATGCAG
CCAGCTACAGCATCTTCCTGACCTAACCTAGCTACAAACTAAAGACGCCCTTCTCTTCTCTGGTGCATGCACGCGTACAT
CGACGTACTAATCACTAGCAGTACAGTATCGCAGACGCATAAGAAATCTATGTCCTGCGGCTGTCCCCCGTATACATGTC
ACCTCTACCCCACACCATCGATAAGCTAGCTTCATCCACATCCACCTCTATATATACCCCCTTCATCTCGCCCTCCCTTG
CTCCATCAATCACACTGCTACTTATTCATTAGTTTGCATCTTCCATCTCCTGAACTCCACATCGTCCCAGTGCTAGCTCG
ACCAATTGCATCATCTATCGTTTGTTTTCCCTCAATCTCTAAGCCGACAGAGAGGTGAGAGTT-GAGGGGTAGGTCAGTC
GACCGGAGGGGCTGTGGACCATGTCTGGCGTGTGGGTGTTCAAGAACGGGGTGGTGCGCCTGGTGGAGAACCCGGGGAGC
GAGCGGACGTCGACGGTGCGGCGGAAGGCGCTGCTGCACACGCCGAGCGGGCAGGTGGTGTCGTCTTACGCGACGCTGGA
GGCGAAGCTGACGGCGCTGGGGTGGGAGCGCTACTACGAGGACCCGGCGCTGTACCAGTTCCACAAGCGCGGCTGCCTCG
ACCTCATCTCCCTCCCCAGGGACTTCAACCACTTCTCCTCAGTCCACATGTACGACGTCGTCATCAAGAACAGGGAGTCC
TTCCGCGTCGTCGACGCCTAGACGCCCCTCTTCCGTCCATGCAGTCTGTCGATCTTGTCTCATCTGTTCAGCTATAGCTC
TTCTTCTATCGTTTGACTTGATTTCGCATGCAGGGTTTGTTGTTGTTAGTGATCCGGGTGTTATATATGATTGGTTGTGC
CTGATTTGGTTGGGAAGTCTAGTGTGGTAGTGGAGTGAGCGAGGGTACTGTTTTTGCACACATATGTGCGTGTGGTGCC-
GAGTATATGCATAGGTATTCGTTGTGGTGTGTATACGTATGCGTGCTG-GGGGTGTGTAAGATCTCTGTTTTGATGTAAA
TTAGTGTCCGTGTGATGAC--CATATATCCACTTACGTTCATTTGCACGTTTCTCTGCATGCACATGCGTCATGCATGTC
ACCGGCCATGTTGCATGCCTAGGGAAATATGTAAAGAATATTATCATGCACGCATTGCTTCTCGTTATGATTGTTTGGTG
GTGGGGAGGGGTGTGTGGTGGTTCTGATGAAAACATAGGGAATAGACAGTCACTCCAAA-AAAAATGAAAACATATAGAG
AATAATAGGCTGACACGATAATATTTATGCTGCCTTTTTTGAGACAAATATTTAGACTGACTGATGCTAGGCAAGACAAC
CACTTACTCCATCCGTCCGCGAATAAGTGTATTTCTACCTTTTGTCCTAAATTCAAACTTTTAATTTTTGATCAACTATA
TAGAAAAGAGTAATAACATATATGACATCAAACAGGTATATTATAAAAGTACATTTTAAAAC-GATCTACTTATACTAAT
TTAGTAC-------------------------------------------------------------------------
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>chr3B_1
AGAGAGCATCAATTTTGTTCTCGGCAAAGGCAACATTGGCTTGATCGACCGGCCAGAAATTCCCTTTCGTGGAAAAAACA
ATGCTGCAAGAGGTGCGCAAAGATAGCTCTCATATTTCTTATTGTTTAAGTAAAGTCGAAAACTGTATGGCGAGTGAATC
CTATTCCCCTGAGAATTAGGCTAGCTCTTTTTGTTTTCCTTTCAGGAAAAAGGTGGGTGGGATTCCTCGCACAACATCAC
ATTCTTTCTTTTCAATTTTCCATATGGGAATGCTCAAGCCATAGATTACGCATGAATTATATGTGGATCTCCCTATTGGC
AATTAACCAACGCCATCAGTTAATGTCCTGTTTTTGACGTGTCGCGGGGCGGCCGCGACACATGTCAAATTTCGTGACCT
CATGATGATCAATCACCTCATGCACTACGTAATTCTGG-AAAATAACAATATGCATAGCATATAGCTACCTTTTTTAGCT
ACCTAGCTAGCTAGAATTTCTTTCTTTCTTCCAACAAATATATTCCAGGTAGCTTATCAAGAACATAAGCTAGCTAGGCA
CATATATTCTCCCGCGCGCACTACTCAAGTTTAATGAACGTACCATATATTCTGCTTCTCTCCCATCCCTGTGCATGCAG
CCAGCTACAGCATCTTCCTGACCTAACCTAGCTAGAAACTAAAGACGCCCTTCTCTTCTCTGGTGCATGCACGCGTATAT
CGACGTACTAATCACTAGCAGTATAGTATCGCGGTCGCATAAGAAATCTATGTCCTGCGGCTGTCCCCCGTATACATGTC
ACCTCTACCCCACACCATCGATAAGCTAGCTTCATCCACATCCACCTCTATATATACCCCCTTGATCTCGCCCTCCCTTG
CTCCATCAATCACACTGCTACTTATTCATTAGTTTGCATCTTCCATCTCCTGAACTCCACATCGTCCCGGTGCTAGCTCG
ACCAATTGCATCATCTATCGTTTGTTTTCCCTCAATCTCTAAGCCGATAGAGAGGTGAGAGTTTGAGGGGTAGGTCGGCC
GACCGGAGGGGCTGTGGACCATGTCTGGCGTGTGGGTGTTCAAGAACGGGGTGGTGCGCCTGGTGGAGAACCCGGGGAGC
GAGCGGACGTCGACGGTGCGGCGGAAGGCGCTGCTGCACACGCCGAGCGGGCAGGTGGTGTCGTCCTACGCGACGCTGGA
GGCGAAGCTGACGGCGCTGGGGTGGGAGCGCTACTACGAGGACCCGGCGCTGTATCAGTTCCACAAGCGCGGCTGCCTCG
ACCTCATCTCCCTCCCCAGGGACTTCAACCACTTCTCCTCCGTCCACATGTACGACGTCGTCATCAAGAACAGGGAGTCC
TTCCGCGTCGTCGACGCCTAGCCAGCCCTCTTCCGTCCATGCAGTCTCTCGATCTCGTCTCGTCTGTTCAGCTATAGCTC
TTC---CATCGTTTGACTTGATTTGCCATGCAGGGTTTGTTGTT---AGTGATCGGGATGTTATATACGATTGGTTGTGC
CTAATTTGGTTGGGAAGTGTAGTGTGGTAGTGGAGTGAGCGAGGGTACTGTTTTTGCACACATATGTGCGCGTGGTGCCT
GAGTATATGCATAGGTTTTCGTTGTGGTGTGTATATGTATGCGTGCTGTGGGGTGTGTAAGATCTCTGTTTTGATGTAAA
TTAGTGTCCGCGTGATGAC--TATATATCCATTTACGTTCATTTGCACGTTTCTCTGCATGCACATGCATGATGCATGGC
ACCAGCCATGT---------------------------------------------------------------------
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>SNPs
---------------------------------------S----------------------------------------
--------------S-----------------------------------------------------------------
-S-----------------------------------------------------S------------------------
-----------------------------S--------------------------------------------------
--------------------------------S-----------------------------------------------
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-----S--------------S-----------------------------------------------------------
--------------------------------------S----------------------------------------S
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----------------S------------------------------------S--------------------------
------------------------S-------------------------------------------------------
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-----S---------------------------------------------S----------------------------
-------------------------------------------------S------------------------------
--------------------S--------------------------------------------S--------------
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----------S-----------------------------------------------------------------S---
--------------------------------------------------------S-------S---------------
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---------------S----------------------S--------------S--------------------------
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-------------------SS----------------------------------------------------------S
------------------------------S-------------------------------------------------
-----------S------S------------------------------S---------S------------------S-
-------------------S--------------------S----------------S----------------------
-----------S----------------------------------------SS--SS--S---S----S-S-----S--
--S------------------------S-----S-------------S--------------S--------S--------
-------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_966
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------------------------------------------------------------------CCAGTGCTAGCTCG
ACCAAG--------------------------------------------------------------------------
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>reverse_2012
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-----------CCCGTCCGCGAATAAGTGTA-------------------------------------------------
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