>input_sequence_82039
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------------------------------------------------------------ATGGGGGCGGACGATG---G
TCGCGACGACGACGGCTGGCAGTGCCGGCCGCTGGGGCTCCTGATCGGCCTGCCGTTCGCCGGCCTCGCGCTAGTGCTCT
CGCTCGCCGGCGCCGTCGTCTGGATCCTCGGGTGCGCGCGCGTCTCTTCCTGGCTGCTCCCTC-------ATGCATGCCA
ACCTGAACGCCTGGGTGCTTGCGACTTTGGCTTAGACTTTGGTTTCTCTGCTTCGGCTC---------------------
--TGTCTCTGAACT--TTTTTCAATTGGTAGGTCGGCGCTGAGCTGCGTGTGCCCGTGCTGCGTGTGCTGCGCGGCGGCG
GCGAACCTGGCGGTGGGCCTCGTCCAGATGCCCGTCAAGGTCATCCGCTGGTTCATCAGGCAGATCCCCTGCTAG-----
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>chr3D_1_TraesCS3D01G168400
TCCAGCGATCGAAGTAGGAGGGCTTCTCGATGCCCTTGAAGCGGCACTCAAACTCGAGCATGGTGCGGCAATCCCAGTCT
CCCCACGTAACGACGGCCAAGCGGCCGCCACATCGCTTGGTCCCTA-CCCCCGTGGTCGCCGCCTCCAGCCAAGCGTCGT
GCAGCCGGAGGGCCTGGCCGAGGTCCACGCCGCCGTCGACGTCCTCCTGCCGGATACCCGTGAGGTCCCTGCAGAACTGG
GTGAGCACGGGGTGGTGCTTCGGGCGGATGTAGCGGCGAAACGCGGACTCGAGGCGGCCTGTGGCGGCGTCGACGAGGAC
GGCGGGGAACTCGATGATCTCCTGCGGGTAGATCCGCGCGTCTTTCTGGCACGTCGCCTCGAAGTCCACCACCAAGAAGA
AATCGAAGTCTTGCTGCAGCTCATGGCCCTGCCCCTGTGCGTACGGCACTGTGCGCGCCGCCATGATCGGCGCCATCGCC
ATGTAAGCTGCGT----GCTCTGAGCAGGAGCGGATCGCCTCGCAAACTCCAGACCGGGAAAACTCGGGATTGAATCAGT
GTGAGCAAGCGAAAACCAGGGCGGCGATCTCCGCCTCTTAAAGCCACGGCACCGGAGCAAACACTGTAGGAGGCGAAATC
GGATTCATC-----TTCGTAATCGTTGGCGCAGGCGCATCCGGATCCCGGGCGGACGTGGCAACCGACCTCATGACGAGC
TTCTACGCTTTGGTAAGAACAGTTAACCAA--AACATACCAAAGGCTGTGGTTGGCGGGTGAAA-AAAGGACTGCCACGC
ACGCTGCCCGTTCGGTTCCGCTCCACTCTCCGGAGTGGAGTTCCCCCGCCCCGCA-----CGTACTCTCGGTGCTGGCAG
TTCGAGTTCAATCCACAGCGTTATTTACCAACCGTTTGGTTTC--GATTTCGGACATAGTTCCAAACTTTCAAATTCGCA
CACGCACCCACGTAGGACGCTGCGGAAGAACAACCGGCTGGAGGAGCCGGAGATCGATCGATGGGGGCGGACGATG---G
TCGCGACGACGACGGCTGGCAGTGCCGGCCGCTGGGGCTCCTGATCGGCCTGCCGTTCGCCGGCCTCGCGCTAGTGCTCT
CGCTCGCCGGCGCCGTCGTCTGGATCCTCGGGTGCGCGCGCGTCTCTTCCTGGCTGCTCCCTC-------ATGCATGCCA
ACCTGAACGCCTGGGTGCTTGCGACTTTGGCTTAGACTTTGGTTTCTCTGCTTCGGCTC---------------------
--TGTCTCTGAACT--TTTTTCAATTGGTAGGTCGGCGCTGAGCTGCGTGTGCCCGTGCTGCGTGTGCTGCGCGGCGGCG
GCGAACCTGGCGGTGGGCCTCGTCCAGATGCCCGTCAAGGTCATCCGCTGGTTCATCAGGCAGATCCCCTGCTAGGCTGC
TCAATTGTCCTTCTGGAGTAGGAAATGTTGTTATCTTGTTTTCAGTTT--TATGCATGCTTGCTGAACGAGAGGCCAGAA
ATATGATATGATCGTGTTTCTGCTTGCCACGTCTCACAACTTCATATGTATCTGCCTTG--------AACATGTTCTTTC
TCGAGACAGTTTAGGACGATGCTTTTCTTGACCCTGACACAACTTCATAT------------------------------
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------GTATCTACCTTGAAAAATCGATGACTATGTTCTGTAGAT------ATGAATCTGGATGGTTAAAAGGGGAAACG
AACGATTGCAAAAGTTAACATGAGCTCCGGTCTTTTAGGTTGCAACACATT-TGTAGTCTTAGCATCTACAACCGGACCT
CTCAAACGTCTAATCAAACAACCTGGTCACTGTCCGGACGGGTGTGAGGAGGAAAAAAGTCACCCAACCACAACCCTCAC
TTTGTCCAGACATGTCTGACAAGTCCACAAATCCCTATATCCAACTCATATGTGGGGAGTATATGGAGATGTTCGGGCAG
CCCTCCATGTAGGATGCAGCCTACCTCAGACCACCTTTTCTCTTTCGATCTTCATGCTCATCAATCATATGCATTTGACT
GGACAATTTGAAAGGATGTAGGGGACATGATTGCATGCGTGCACAAATGAAGACTC-AAACGGACACGCCCAGTCACTGG
CCGGGCACATCCACGGATGTTTGGGGGATCAAAATTAGCCAATCCCGATTATAGATGCTTTGACAAGTTTTGAGTCGGCC
TCTGGAGGTCCACCTTGACAAGGCGGTGCTAATGAAA-------------------------------------------
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-----------------------------------------------------------------TTACTTGGAAGCTAT
TCAGCATAGAAGGCCCGGCT-GAGGATTTGGCGGCCTCTCACATGAAGCTGGCTGTTTGGAACAACCGGGAACCATGGAA
GCACAAAATTTTCGCATGACCTATTGTCCAGCACTT-GGTCTAGATGACCGACATGTTGCAAAGGAGAGGATGGCCAAAT
TGAGGGCTACCCCAGTTATGCAAAAGAGAGTCGGAGACT
>chr3B_1
TCCAGCGATCGAAGTAGGAGGGCTTCTCGATGCCCTT-AAGCGGCACTCGAACTTGAGCATGGTGCGGCAATCCCAGTCT
CCCCATGTAACGACCGCCAAGCGGCCGCCGGATCGCTTGGTCCCTG-CCCCCGTCGTCGCCGCCCTCAGCCAGGCGTCGT
GCAGCCGGAGCGCCTGGCCGAGATCCACGCCGCCGTCGACGTCCTCCTGCTGGATGCCGGTGAGGTCCCTGCAGAACTGG
GTCAGCACAGGGTGGTGCTTCGGGCGGATGTAGCGGCGAAACGCGGACTCGAGGCGGCCGGTGGCGGCGTCGACGAGGAC
CGCGGGGAACTCGATGATCTCCTGCGGGTAGATCCGCGCGTCTTTCTGGCACGTCGCCTCGAAGTCCACTACCAAGAAGT
AGTCGAAATCTTGCTGCAGTTCATGGCCCTGCCCCTGTGCGTACGGCACTGTGCACGCCGCCATGTCCGCC---------
---------GCGT----GCTCTGAGCAGGAGCGGATCGCCTCGCAAACTCGAGACCGGGGAAACTCGGGATTGAATCAGT
ATGCGGAAGTAAAAACCAGGGCGGCGATCTCCGCCTCTTAAAGCCACG-CACCGGAGTAAACACTGTAGGAGGCGAAATC
GGATTCATTTTGTTTTCGTAATCGTGCGTGCAGGCACACCCGGATCCCAGGCGGACCTGGCAACCGACCTCGTGATGAGC
TTCTGCGCTTTGGTAAGAACAGTTAAGCATATAACATACCAAAGGCTGTGGTTGGCGGGGAAAA-AAAGGACTGCCACGC
ACGCTGCCCGTTCGGTTCCGCTCCACTCTCCGGAGTGGAGCTCCCCCGCCCCGCA-----CGTA--TTCGGTGCTGGCAG
TTCGAGTTCAATTCACAGCGTTATTTACCAACCGTTTGGTTTC--GGTTTCGGACTTGCTTCC-AACTTCCCAGTTCGCA
CACGCACCTACGAAGGGCGCTACGTAGGAACAACCGGCTGGAGGAGCCGGAGATCGATCAATGGAGGCGGATGAC-----
-CGCGACGACGACGGCTGGCAGTGCCGGCCGCTGGGGCTCCTGATCGGCCTGCCGTTCGCCGCCCTCGCGTTAGTGCTCT
CGCTCGCCGGCGCCGTCGTCTGGATCCTCGGGTGCGTGCGCGTCTCTTCCTGGCTACTCCCTCGACCCTCATGCATGCCA
GCCCGAACTTCTGGGTGCTTGCGACATTGGCTTAGACTTTGGTTTCTCTGCGTCGACTTTTGTCACCACCATAACGTGAG
TGTGTCTCTGAACTCCTTTTTCTCTTTGTAGGTCGGCGCTGAGCTGCGTGTGCCCGTGCTGCGTGTGCTGCGCGGCGGCG
GCGAACCTGGCGGTGGGCCTCGTCCAGATGCCCGTCAAGGTCATCCGCTGGTTTATCAGGCAGATCCCCTGCTAGGCTCG
TCAATTGTCCTTCTGGAGTAGTAAATGTTGTTATCTTCTTTTCAGTTTTATATGCATGCTTGCTGAACGAGAGGCCAGAG
ATATGATATCATCGTGTTTCTGCTTCCCACGTCTCACCTAATAAATAAAGCGACGCCGTAGAGGCAAAACATGTTCTTTC
TCGAGACAGTTTAGGACGATGCTTTTCATGACCCTGACACAACTTATGTATGTACATTTTGATAACAAGTATTTTCGGAC
GGAGGAAGTATGTATCTTGAAAAATCGATGACTATGTTATGTAGATTCGTATATGAATCTGGATGGTTAAAAGGGGAAAC
GAACTAGTATCTACCTTCAAAAATCGATGACTATGTTCTGTAGATTCCTATATGAATCTGGATGGTTAAAAGGGGAAATG
AACGATTGCAAAAGTTAACATGAGCTCCGGTCTTTTAGGGTGCAACACATTTTGTAGTCTTGGCATCTATAACCGGACCT
CTCAAACGTCTAATCAGGCAACTTGGTCACTGTCCGGACAGGTGAAAGGAGGACAAAAGTCACCCAACCACAACCCTCAC
TTTGTGCGGACATGTCCCATAAATCCACAAATCCCTATACCCAACTCATATGTGTGGAGGATATGGGATGTTCGGT--AG
CCCTTCATGTAGGATGCGGCCTACCTCGTACCACTTTTGTCTTTCTT-TCTTCATGCCCATCAATCATATGCATTTGACT
GGACAATTAGGAAGGTTGTAGAGGAGATGGTTGCATGCATGCATAAATGAAGACTCAAAACGGACACGTCCGGTCACTGA
CGGTGCACATCCACGGATG-TTTGGGGATCAAAATTAACCAATCATGGTTATATATACTCTTACAATCTTTGGGTTGGCC
TCAAGAGGTCCACCTTGACGAGGCGGTGTTGATGAAATTAAACACATTAAGGCGTGGTAGAAAGGTGGCCAACCAGCTAT
GTCACGTGGCGCATACTGGTTGGCCGTGGTGAAAAAGTTTTTGATTTTTTTAGATTGTTTTTTTATGAAAGTTAGGCTTT
TTTATTTTTTGGATAAAAGTTTTTCTAGACTTTTTCTTTTCTTTTGATGGACATGATGTCCACTGAGAATGTTTTTTTAA
ATTTAAAATGAAGATGTGCACAACTTTCTCTTAAGCGGCCCGCTAATGCAGGCCCCAACCACTGGTTACTTGGAAGCTAT
TTCGCATAGAAGGCCCAGCTAGAGGATTTGGCGGCCTCTCACATGAAGCCGGCTGTTTGGAACAACTGGGAACCATCGAA
GCACAATTTTTTTGCGTGACCCATCGTAACAGGACTGGGTGTAGATGACCAACATGTTGCAAAGGAGAGGATGGCTAAAT
TGAGGGCTACCCCAGTTATGCAAAAGAGAGCCGGAGAC-
>chr3A_1
TCCACTGATCGAAGTAGGAGGGCTTCTCGATGCCCTTGAAGCGGCACTCGAACTCGAGCATGGTGCGGCAATCCCAGTCT
CCCCACGTGACGACGGCCAATCGGCCGCCGCATCTCTTGTCCCCTGCCCCCCGTCGTCGCCGCGCTCAGCCAAGCGTCGT
GCAGCCGGAGCGCCTGGCCGAGGTCGACGCCGCCGTCGACGTCCTCCTGCCGGATGCCGGTGAGGTCCCTGCAGAACTGG
GTGAGCACGGGGTGGTGTTTCGGGCGGATGTAGCGGCGAAACGCGGACTCGAGGCGGCCGGTGGCGGCGTCGACGAGGAC
GGCGGGGAACTCGATGATCT-------GTAGATCCGCGCGTCCTTCTCGCACGTCGCCTCGAAGTCCAC----------T
AGTTGAAATCTTGCTGCAGCTCATGGCCCTGCCCCTGTGCGCACGGCACTCTGCCCGCCGCCATGATCGGCTCCATGCTG
TTCGCCAACATACCCGCGCTCTGAGCAGGAGCGGATCGCCTCGCAAACTCAGTACCGGGTAAACTCGGGATTGAATCAGT
GTGAGCAAGCGAAAACCAGGGCGGCGATATCCCCCTCTTAAAGCCGCGGCACCGGAGCAAACACTGTACGAGGCGAAATC
GGATTCATT-----TTCGTGGTCGTTCGCGCAGGCGCATCCGGATCCCAGGCGGACCTGGCAACCGACCTCATGACGAGC
TTCTACGCTTTGGTAAGAACAGTTAACCAA--AACATACCAAAGGCTGTGATTGGCGGGAAAAAGAAAGGACTGCCACGC
ACGCTGCCCGTTCGGTTTTGCGCCACTCTCCGGAGTGGAGTTCCCCCGCCCCGCACCGCACGTA--CTCGGTGCTGGCAG
TTCGAGTTCAATTCACAGCGTTCTTTACCAACCGTTTGGTTTCTCGGTTTCGGGCATAGTTCC-AACCTCCCAGTTCGCA
CACGCACCTACGTAGGACGCTGCGGAAGAACAACCGGCTGGAGGAGCCGGAGATCGATCGATGGGGGCGGACGATGGTCG
TCGCGACGACGACGGCTGGCAGTGCCGGCCGCTGGGGCTCCTGATCGGCCTGCCGTTCGCCGCCCTCGCGTTAGTGCTCT
CGCTCGCCGGCGCCGTCGTCTGGATCCTCGGGTGCGTGCGCGTCTCTTCCTGGCTGCTCCCTCGACCCTCATGCATGCCA
GCCCCATCTTCTGGGTGCTTGCGACATTGGCTTAAACTTTGGTTTCTCTGCTTCGGCTTGTTAG-----CATAACGTGAG
TGTGTGTCTGAACTCG-TTTTCTCTTGGTAGGTCGGCGCTGAGCTGCGTGTGCCCGTGCTGCGTGTGCTGCGCGGCGGTG
GCGAACCTGGCGGTGGGCCTCGTCCAGATGCCCGTCAAGGTCATCCGCTGGTTCATCAGGCAGATCCCCTGCTAGGCTGC
TCAATTGTACTTCTGA---AGTAAATGTTGTCATCTTGTTTTCAGTT---------------------------------
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>SNPs
-------------------------------------------------S------------------------------
-----------------------------S---------------S--------S---------SS--------------
----------S--------------------------------------------S--S---------------------
-----------------------------------------------------------S--------------------
---------------------------------------------------------------------S---------S
-S-----S----------------------------------------------S----------------S----SSSS
S-SSSSSSS-----------------------------------------S--------S--------------------
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--------S-----------------S---------------------S-------S-----------------------
-----------------------------------------------------------SS-------------------
----------------------------------------------------------------SS--------------
------------S---------------------------------S----------------S-----S-S-S------
--------S-----------------------------------------------------------------------
--------------------------------------------------------------S-------S---------
------------------------------------S-------------------------------------------
S--S----SS---------------S--------------------------------S---------------------
----------------------SS--------------------------------------------------------
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---------------------S---------------------------------------------------------S
---------S---------------S-----------SSSS-S-SSSSSSSSSSS-SSS---------------------
---------------------------S-----------------SSSSS------------------------------
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-----------------S------------------------------------------------------------S-
---------------------------------------S---------------------S-------S----------
----------------SS----S----------------S----SS-------S--------------------------
-----S-S--------SS-S--S----------------S--------------S----S------SSSSS-SS-SSS--
----S------------S---------SS-----S---SSSS--SSSS---------S----------------------
--------S-S----S-----S---S---S--------S----S------------------------S--S-------S
-S-S---------------S--S--------------S------SS-S-----S--S--S-S----SS----S--S----
--SS---------------S--------S-S-------------------------------------------------
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-SS-------------S--------------------------------S----------------S---------S---
------SS----S--S-----S--S--SSSSSSSS-----S---------S------------------------S----
------------------------------S-------S
>forward_400
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-----------------------------------------------------------CGAAGTCCACCACCAAGAAGA
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>reverse_2098
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-----------------AGCCTACCTCAGACCACCTT-------------------------------------------
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