>input_sequence_87498
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----------------------ATGGACAAGTCAAGGTGTCAGGGCAAGCACAGAGGAGGCCTTCGCAGAATGATGAGAG
AGCACAAGGCGAGGCTCTACATAATTCGGCGATGCATCGTCATGCTTCTTTGTCACCACGACTGA---------------
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>chr3D_1_TraesCS3D01G259100
AGCCACATCACATCCAAGTGTCTCCTCTAAAATACTGGTCAAACAAAAGCTAGCTTGGTTTTGATGCAATCACAACGTAC
AAAACCTTTTATTACAGTCAAAGCATCTAATAACCTGAAAGCAAAGGAG--AAAGTACAGTTACATTTTGCTTATTTTGG
AGTGAGAAACTGCAGATACACTCAATTTCATCTGAATTCTCCTCATTGATAGTATATGCCTGATAAGAATGCGATGTCAT
GTCCAGTCAATAGGCGGTCAGAGGG-TATACTCGCAGGCATCATCCACCACAAGTGGTCACAAAATTCTGAATCTCGTTC
CTTTTCTATGACAGCAAAAATGTGGAATGCATGCAACTTCTGCTGATAGCAT-AAACAAAACGCAATCTGCTGTGATATA
CACATGTCTGCACAACTCGGTGCAAACGAGAACACAATGAGATCATTGATGACTAGAACTTAACATTGAGACCATTGTTT
AGGG-AATCTTATCATTTGG-ACCCGTCAGGATCTCTC-GGGTTGAGAGGAGGAACTAGGATATGTATGCCCAAGGCTAG
ACAGAACCAAGTTGATGCCAACCAAGTGGGAGTG-------TTAGCAGCCATACACTTGCCTAAAGATATCACAGAGCGA
GATATCTGTATCTGCATGCAATCAGAGCGGTTCATGAGCAGGCACTATGGTCCACAGATTATCAGGGCCGCTATTCCCTA
GATCCTGCATTCAGGTTCGTCCACTCAAGTTGTCAACTGCCATGTGCACTGTGCCTGTGGAGTGGCAGCTGCCGACTTCA
GAGAAAGTTTTTTTTTTTGTTACAACATCAAAGTGGAAGATGTTGTCACAAGCTACATCTAGGCAAGGTAGCCAGTGATC
TGGCAC--------------------------------------------------------------------------
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---------------------TTTTCAGGGCCTCTCCACTATATAAGCACACCAAATGCTATGAGATTAGGCACACTAAG
CAGAGGCTATCGACAACCCAATCGCTCGTG--------------------------------------------------
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---------------------------------------------------------------TCTTTTTCTGAGCAGAA
ACCCCTTAATCGTTCAACCAGGATGGACAAGTCAAGGTGTCAGGGCAAGCACAGAGGAGGCCTTCGCAGAATGATGAGAG
AGCACAAGGCGAGGCTCTACATAATTCGGCGATGCATCGTCATGCTTCTTTGTCACCACGACTGATCAGTGACTCTGACT
CGGAATTCAGAGTGCAGATAATTCTTTGATGTGTATATTGAGGGAATATTTGATAGTTTCAGACAATTCTTTTTTTTCAT
TGATCGGTGATCAGTGTGTCTTGTTCGAGAGAAAAGACGCCAC--TTTTGTTCTGGTCTCCTTTTCAGAATTCAGTGTAT
TGGTCTGGACAATTCTTTGATGTGTATATTGAGTGGATATGCAATATAATTGTCAGACATTCTTGTTTTTTTTTTG--AG
AAATCTTGACATTCTCGTTGTGCATTTAGTAGATTATATCTGATGCAGAGGCCGGGGGTATTCCTCCTTTTCAAAAAAAT
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------------------------------------------------------------------------AAAAAAAT
AGTAGATTATATGATGCAG-----------------------------------------------------------TA
TATGGATATTACTCAACTAGTGCTCATTTTTACTTGCACAATTGATGTGTTGGTGATATTGGTTAGTCAAATGTAGTGTG
CCTGTTTTTGTTGCCATAAAGAACATTTCCATTCAATTGATATATCGAGATGATACAACCATACTGAGCGAATGCTCGAC
CTTTGCATAGCACGACGCACATAATAGTTGTTCGACCTCAACCATACAACCATCGAGGCAAATGTGATGTACCTAATGGA
ACATAATAGTTGTTCCCCAATCCGTTCCTCTATGAACCCTAGAGAGACGATCTCTTGGCCCACCGCACCACCATCTCTCC
ACTGGTAGGTCGCCCTCCACCAGCTTTGTTGGTGCGAGAGTGCAGGGAGGCCCAGATCTACCAGATGGAGCAGTATATTC
CTTGTTTGGGGATTTTAGGTAGGTTTTTGTTGTTCGTTGGTCCTTTCAACATTGGTGACAGTTGGTGTACAATACAATCT
TTTGTGGCAGCAAGTCGTTGGTGGTAGCCACGATACCGGTCTAGCGAAAAGGGTCTCCTCAAGCCTCACCATCTTGATGG
TGTCCTCTACGGCAGCGTACATGGTACGGCTACATATTTTGCCACCTGACGTTCTGACAAGTGAGGTTATGGCTCGTAGG
>chr3B_1
AGCCACATCACATCCAAGTGTCTC---TAAAATACTGGTCAAACAAAAGCTAGCTTGGTTTTGATGCAATCACAACGTAC
AAAACCTCT-----CAGTCAAAGCTACTAATAACCTGAAAGGGAAGGAGAAAAAGTACAGTTACATTTTGTTTATTTTGG
AGTGAGAAACTGCAGATACACTCAATTTCATCTGAATTATCCTCATTGATA---TATGCCTGATAAGAATGCGGTGTCAT
GTCCAGTCAATAGGAGGTCAGATATATAAACTCGCAGGCATCATCCACCACAAGTGGTCACAAAATTGTGAATCTCGTTC
CTTTTCTATGACAGCAAAAATGTGGAATGCATGCAACTTCTGCTGATAGCATTAAACAAAACGCAATCTGCTGTGATATA
CACATGTCTGCACAACTCAGTGCAAACGAGAACACAATGAGATCATTGATGACTAGAACATAGCGTTGGGACCATTGTTT
AGGG-AATCTTATCATTTGG-ACTCGTCAGGATCTCTC-GGGTTGAGAGGAGAAACTAGGATATGTATGCCCAAGGCTAG
ACAGAACCAAGTTGGTGCCAACCAAGTGGGAATGTTAGCACTTAGCAGCCATACACTTGTCTAGACATATCACAGAGCGA
GATATCTGTATCTGCATGCAATCAGAGCGGTTCATGAGCAGGCACTATGGTCCACAGATTATCAGAGCTGCTATTCCCTA
GATCCTGCATTCAGGTTCGTGCAGTCAAGTTGTCAACTGCCTTGTGCACTGTGCCTGTGAAGTGGCAGCTGCCGACTTCA
GAGAAAGGGGATTTGT---TTACAACATCAAAGTGGAAGATGTTGTCACAAGCTACAGCTAGGCAAGGTAGCCAGTGATC
TGGCAC--------------------------------------------------------------------------
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---------------------TTTTAGGTCT-TCTCCCCTATATAAGCACACCAAATGCTATGAGATTAGGCACACTAAA
CAGAGGCAATTGACAACCCAATAGGTCATG--------------------------------------------------
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---------------------------------------------------------------TCTTTTTCTGAGCAGAA
ACCCCTTAATCGTTCAAACAGGATGAACAAGTCAAGGTGCCAGGACAAGCACAGAGGAGGCCTTCGCAGAATGATGAGAG
AGCATAGGGCGAGGCTCTACATAATCCGAAGATGCATCGTCATGCTTCTTTATCACCACGACTAATCAGTGA--------
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>chr3A_42
-----------------------------------------AACAAAAGCTAGCTTGATTTTGATGAAATCACAACGTAC
AAAACCTCA-----GAGTCAAGGCCTCTAGTAACCTGAAAGCAAAGAAG-AAAAGTACATTTACATTTTGTTTATTTTGG
AGTGTGAAACTGCAGATACACTCAATTTCATCTGAATTATCCTCATTGATA---TATGCCTGATTGGAATGTGCTGTCAT
GTCCAGTCAATAGGCGGTCAGATATATATACTCGCAGGCATCATCCACCACAAGTGGTCACAAAATTGTGCATCTCATTC
CTTTTCTATGACAGCAAAAATGTGGAATGCATGCAACTTCTGCTGATAGCAT-AAACAAAACGCAATCTGCTGTGATATA
CACATGTCTGCACAACTCAGTGCAAACGAGAACACGGTGAGATCATTGATGACTAGAACATAGCATCGAGACCATTGTTT
AGGGGAATCTTATCATAACAAACTCATCAGAATCTCTCGGGGTTGAGAAGAGGAACTAAGATATGTATGCCCAAGGCTAG
ACAGAAACAAGTTGATGTCAAGCAAGTGGGAGTGC-------TAGCAGCCATACACTTGTCTAAACATATCACAGGGTGA
GATATCTGTATCTGCATGCAATCGGAGCGGTTCATGAGCAGG-----------------------------TATTCCCTA
GATCCTGCATTCAGGTTCGTCCACTCAAGTGGTCAACTGCCATGTGCACTGTGCTTGCGGAGTGGCAGCTGCCAACTTCA
GAGAAAGGA---TTTTTTGTTACAACATCAAAGTGGAATATGTTGTCACAAGCTACAGCTAGGCAAGGTAGCCAGTGATC
TGGCGAAAAGTGTCTGCAGCTACCGAGCTTCATTGCTCTTGATATTTGAATTTTTTGAAAAACACACTTTCGATGCTCAA
AAAAATCTTAAGACAAATATGTGAATACGTACACATATTCCTAAGGCCTGATAGAAATCTAGAGAAGAAATACTTTGTAT
TTTGAGAAATACAAAAAAGAGAAATTCCTGACAGAAATGGCACCTTTTTCTCCTATATACTGTCAGAAATTTGTTTTTTC
TATAGCCCAAAACAAAACGGTATTTCTACCGAAACTTTCCACGGGGATTCGGAATGTGTATATGTATCCCCGGAAAAAAA
TTCACATTTTTTTAAAACTTCAAAAATACAAATTTGAAAATGTCAAATATAGAGAGCACCGGAGCTCGGGTGCTGAAACA
CCGCTCTCGTGATCTGGCACTTTTTAGGGTT-TCTCCCCTATATAAGCGCACCAAATGCTATGAGATTAGTCACACTAAA
CAGAGGCAATTGACAACCCAATTGGCCGTGTCTTTTGTTGGAATTATGTGTCCCGCAACTATATTCAAATTACTAGGAAT
TACTAATATTCGGAATACCTCATTATGGAATTTATATACATGTACTTATGCATGGAATTACTTTACATGATTATCATGAA
ATTATTACCTGCTGGAAAGTACTTAAGTTTTGTATGCTTAAGGAAGCTGGTCGATTATCAGTGGAATACAATATACTATT
TATATTGGAAAGACTACCCGGGTACACTGGTGATTGGAAGGAGCTAGATCGTATAATTAGATTACAGCCCTAATGTTGAT
CTACATAATTAGAGAAATTTACACTCTATTATGGCGCGTTGCTCACAAGCGCGTGCTCCGGGGACATAACGGGTAGAATC
CGTTAATAGACAAATACGATCGTGGTTGGTAATTTGATCTGGACTTTATCCCGGAAACTAGTGGAAAAGACTAGGGATCT
TATATCTGTATAAGAAGTGGACTCTTTGGAAAGGCAATATAAGAAGATCCCTACCCCCTAGCCTCAGATATGCAAATTGT
AAGCGGCACCACGGATAAGCGCAGAGGAATAGGGGATAGACCGCAAACCCTAAATTTCTAACATCTTTTTCTGAGCAGAA
ACCCCTTAATCGTTCAACCAGGATGAACAAGTCAAGGTGCCAGGACAAGCACAGAGGAGGCCTTCGCAGAATGATAAGAG
AGCACAAGACGAGGCTCTACATAATCCGGCGATGCATCGTCATGCTTCTTTGTCACCACGACTAATCAGT----------
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--------GATCAGTGTGTTTTGTTCGAGTGAAAGGGCACCAATTTTTTTTTCTGGTCTCTGTCTCAGAATTCAGTGTAT
AGGTCTTGACAATTCTTTGATGTGTATATTGAGTGGATAGTTCG--TAGTTTTCAGACATTCTAGTTTTTATATTGGGAG
AAATCTTGACGTTCTAGTTGTGCATTTAGTAGATTATAATGCAATATATGGGGACGGGGCGTTTTGGAACAGTAAATTCG
TCAAAAAATCCAATTTTTTTTGTGGTGGAAGATGCTTGAGTTCGTCATGTCCTTGCAAAAATTCAGCACATTTGAACATC
TAACAAGCTCCCAGCAAAAAAGGCAAATCTGGAGTCTGTGAAAAAGTTCACTGTTTTGCATTGTTCGGACCTGATTTTTT
TTCCTGAGAGCTACTTAAATGTCCGAATGAACTGAAACTTACACAGTATCACGCATTCAAGCCTCTTTGACCACAAAAAT
ATTTGTTTTTTTAATGTTTCTATTATTATTTACTGTTCATAGGGTGTAGATGAGTCGGGGCCGAATTAGATATTTGAATA
TATGGATATTACTCAACTAGTGCTCACTTTTACTTGCACATTTGATGTGTGGGTGATACTGGTTAGTAAAATGTAATGTG
CCTATTTTTTCCTGAAAAAGGG-CATTTCCATTCGATCAATATATCAAGATGATACAACTGCATTGAGCGAATCCTAGAC
CTCTACATAGCA--------------------------------------------------------------------
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>SNPs
------------------------SSS-----------------------------------------------------
-------S-SSSSS----------S---------------------------------------------S---------
--------------------------------------S------------SSS-------------------S------
----------------------SSS------------------------------------------S------------
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------------------S----------------------------------------S--S-----------------
-----------------------S--------------------------------------------------------
-----------------------------------------------------------S-----S--------------
-----------------------------------------------------------------S--S-----------
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-------SSSS----------------------------------------------S----------------------
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-------------------------SS--SSS-----S-----------------------------------------S
-------S--S-----------S-S-------------------------------------------------------
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-------------------------S-------------S----S-----------------------------------
-------------------------S-------------------------------------S--------SSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSS-----------S---------S----S-S-S---S------S----------SS-S----------------
S-----S--------------------------------SSSSSSS--S--S-----------S------S-S-------
----------S----S----------------------SSSS-SSSSSS--SSSS---SSS-SS-SSSSSSSS---SSSS
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-------------------------------------------------------------------------S------
-S-S-S--S-S-S---SSS-------------------------------------------------------------
--------------------------S-------------S---------S-------S--------S-------S----
---S-----SSSSSS-S--S-SS-----------S--SS-------S------------SSS-S---------S--S---
--S-S-------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_265
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-----GTCAATAGGCGGTCAGAGGG-------------------------------------------------------
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>reverse_3143
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----------------------GCTTTGTTGGTGCGAGAGTG--------------------------------------
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