>input_sequence_73096
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--------ATGGGCATGGCCACCGCAGCCGCCGCGACGACGGCCGCTCCGGACAGGCTCCGGCAGCCGTGCAGGCCGAGG
CCGGCGGCGCAGATCTCCTCCTCCAAGAACCGCGCGCCCAAGGCGCCCGTGGTGATCGCGCACGAGTGCCCCAGCGCGAT
GCGCGCCCACGTCCTGGAGGTGCCCGCCGGGCGCGACGTCCTGTCGTGCGTCGCGGCGTTCGCGCGGCGGGGGCGCTGCG
GCGCGCTGGTGCTGGGCGCCGCCGGGCACGTCGCGGACGTCGTGCTCAGGGAGCCGGCGCTGGTGCTCCGGGGCACGACG
GAGATCCTGAGCCTGGCAGGGTGCTTCTTCCCGTCTCCCTCGGCGTCAGCGGCGGGCGTCGCGGTGTTCCTGGCCGGGCC
GCGAGGCAGCGTGCTGGGCGGCGCCGTCGCGGAGGGAGGGCTCGTGGCCGCCGGTCCGGTGGTGGTGATGGTGGCCACGT
TTGTCGCGGCTGCGATCGACCGGTTGCCTCTGGTGAAGGGGGACGGATCCTCCAAGGCGGACGGGAGCGACGTGCACGGC
GTGGCCGGACAGTGGCGGTGCGGCGGCCAGCCGCTGCAGCAACAGTGCGGATGGGCGCCGCTGCGTCGGAAGCTGGGCGC
GAAGAGCTGA----------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G173400
TTGAAATTTTGAAAATCTAAATGTTTTCAATTTTTGTTCGGGAGTTTAATTTTTTCACCTTTTGAAATTTTGTTCTGGAA
TTACAAAAATTTCCCCGTATCAAAAAATTGTTCATGATTTTCGAAAATGTGGCAGTTTTTAATAAAATTGTTCACGGTAT
TCAAAAGTAGTTGCGTTTCACAAAACATCCGGGTTGTTTTTTGTTTTGAAAAATGCGTTTGAAATTTCAAAAAAATCGGA
TCTGTGCTCGGTAGTTTGTGCTTAAAGGTTTGCGCTGTGTTGTGAGTATTAAAGCTTGCTATGTCTGCTGGTAGTAGCGC
ATTGACGCTAGGACGAGATTCTCGGTTCAATCCCAGCTCGGCGCTTTAATTTTTTGGCTACAGTTCTCGATCGGGTCTTT
ATTTTGGACCTACAGTTCTCAATCGGGCCGGCCCAATCGTAAACCGCCTGTGCGTGCGAGCGACGACCTGCCGCAGAGAG
CGGCAGGTAGGAGCTCCCCAATTTCTGAACAGATCTGTTAGGTTCCTGCTGTTAAGTGGACGAATCGATCCCGGTTCCTT
TGATATGCTCTTCCATATGCCCATTTCGACAAATGGATGTTTTTT-CTGACACATGCGGTGTGGAGCCTGACTTGAAAAT
TTTGGTG-CCGGCAGGACCATTGATTCTTGA-------GAATGATTCATCCCACAAAGCAATTTTAGTACTGTACCAAAC
ATGAAGTAAAAGTGTAAAACATGAACCACCTCGCACAACAAACAGACGCGCCATACCTACTCTG----------------
-------------------CGCCGCGGAAAATGTTTTACAAAACACACACACAGTACAGTTGGGAGCTTGTTAGGATGTT
CGAACACTTTACCACTAAACTACTCATCACGCGTATTTCCCTGCTTAACAGCTTATACTCGTACTTCGAACAACACCGAC
CCCGCCCTTAAAAAGCCATCTAACCCCTGTAATTAACCTCCACAAAGGACGTGCAGAAGCACACACAA----AAATAATC
TTTTTACCATGGGCATGGCCACCGCAGCCGCCGCGACGACGGCCGCTCCGGACAGGCTCCGGCAGCCGTGCAGGCCGAGG
CCGGCGGCGCAGATCTCCTCCTCCAAGAACCGCGCGCCCAAGGCGCCCGTGGTGATCGCGCACGAGTGCCCCAGCGCGAT
GCGCGCCCACGTCCTGGAGGTGCCCGCCGGGCGCGACGTCCTGTCGTGCGTCGCGGCGTTCGCGCGGCGGGGGCGCTGCG
GCGCGCTGGTGCTGGGCGCCGCCGGGCACGTCGCGGACGTCGTGCTCAGGGAGCCGGCGCTGGTGCTCCGGGGCACGACG
GAGATCCTGAGCCTGGCAGGGTGCTTCTTCCCGTCTCCCTCGGCGTCAGCGGCGGGCGTCGCGGTGTTCCTGGCCGGGCC
GCGAGGCAGCGTGCTGGGCGGCGCCGTCGCGGAGGGAGGGCTCGTGGCCGCCGGTCCGGTGGTGGTGATGGTGGCCACGT
TTGTCGCGGCTGCGATCGACCGGTTGCCTCTGGTGAAGGGGGACGGATCCTCCAAGGCGGACGGGAGCGACGTGCACGGC
GTGGCCGGACAGTGGCGGTGCGGCGGCCAGCCGCTGCAGCAACAGTGCGGATGGGCGCCGCTGCGTCGGAAGCTGGGCGC
GAAGAGCTGAACCGTATGCACCGAGTGGAGAATATAGATTGGGCCGTCATATTGTTCGTTGGCAAGCAGGCCGAAGTGGA
GTTTTGGTCCAAGCTTTGAAAAAAAAAATCCATGTTCT---------------------GCTTTTATCTTCTTTGGCTGT
GAGACAACAGAAACTTTTCAATGTCTCGAAAGAAACACAAACTTTTCATGAAGATACAGTATTAAAAATACTCCCTACGT
CCACAAACATGAGATGTTTTGGATATCTCAACATGGATTATATATACAGACTAAATGAGTGAACG---------------
----------------TACATTTGATTGAGAAAAAAGGTAGAACATCTTATATTTGTGAACAGAG------GGAGTAACA
TAT-AAGGTGCAATCTTGCATGGTAGCTGCAAAACATCCTAGAGCATTTTGTTATCTAGTGCCATGAATATCCCAACCAT
TGTCTTCATCCAAATGTTTATGCATTTATAAAATTCATCGAGAGTAAAAGGACAAC-ATCCAATGTGATTCTAAAGCTCT
CCTACTTTTGCGAGGAATGTCAATGCATCAGAAGTGCCTGCATCAGTAACCTTACCCAGCAAAGTTCCCTTGTAACTTGT
TTTCAGTACCTTCTCTTTCTCTCACACCTAAACATCTTCCGATCAGCAAAAATGCAGCTTTCACCAAACAGCTCTAAAAG
AAGACGTTTTGGCTCTCCAACTATCAAACTGACACATGCTCAAGATCGCTGAAGATGTCGCAACAAGATCGGGTACCACA
ACTCACAACATTGCACAGAAAAATAAAGATACATATATAATACTCCCTCCGCCCCGAATTACTTGTCTTAAATTTGTCTA
GATAGATACTAGCGCTA----GCTAGCAGCC----------------AAATCTAAGACAAGCAATTTGA----GAGGTAA
TATACACCTGCACAATCTACACGCACGCTAGCAGCCAAAGCCCAAAGGCTATTGTTGAGTATACTGATCATGTCAGTTCT
GGAACAAACAGCATTAATCTGAAGAAGAGAATGTCATGCAGATAATACAACTCC
>chr3B_535
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------------------------------------------------------AGTGGACGAATCGATCCCGGTTCCTT
TGATC-GCTCTTCCATATACCCATTTCGACGAATGGATGTTTTTT-CTGC--AATGTGGTGTGGAGACTGACTTGAAAAT
TCTGGTGCCCGGCAGAACCATTGATTCTTGA-------GAATGATTCAGCCCACAAAGCAATTTTAGTACTGTACCAAAC
ATGAAGTAAAAGTGTAAAACATGAACCACCTCGCACAACAAACTCA----CCATACCTACTCCGAGCCGCGAGTTCTAAA
AAAAGAAAAAAAAACTCCACGCCGCGGAAAATGTTTTACAAAACACACAGACAGTACAGTTGGGAGCTAGTTAGGATGTT
CGAACACTTTACCACTAAACTACTCATCACGCATATTTCCCTGCTTAACAGCTTATACTCGTACTTCTAACAACACCGAC
CCCGCCCTTAAAAGGCCATCTAACCCCTGTAATTAACCTCCACAAAGGACGTGCAGAAG----CACAA----AAATAATC
TTTATACCATGGGCATGGCCACCGC---------GACGACGGCCGCTCCGGACAAGCTCCGGCAGCCGTGCAGGCCGAGG
CCGGCGGCGCAGATTCCCTCCTCCAAGAACCGCGTGCCCAAGGCGCCCGTGGTGATCGCGCACGAGTGCCCCAGCGCGAT
GCGCGCCCACGTCCTGGAGGTGCCCGCCGGGCGCGACGTCCTGTCGTGCGTCGCGGCGTTCGCGCGGCGGGGGCGCTGCG
GCGCGCTGGTGCTGGGCGCGGCCGGGCACGTCGCGGACGTCGTGCTCAGGGAGCCGGCGCTGGTGCTCCGGGGCACGACG
GAGATCCTGAGCCTGGCGGGGTGCTTCTTCCCGTCTCCCTCTGCGTCAGCCGCGGGCGTCGCGGTGTTCCTGGCCGGGCC
GCGAGGCAGCGTGCTGGGCGGCGCCGTCGCGGACGGAGGGCTCGTGGCCGCCGGTCCGGTGGTGGTGATGGTGGCCACGT
TTGTCGCGGCTGCGATCGACCGGTTGCCGCTGGTGAAGGGGGACGAATCCTCCAAGGCGGAGGGGAGCGACGTGCACGGC
GTGGCCGGACAGTGGCGGTTCGGCGGCCAGCCGCTGCAGCAACAGTGCGGATGGGCGCCGCTGTGTCGGAAGCTGGGCGC
GAAGAGCTGAACCATATGCACCGAGTGGAGAATATAGATTGGGCCGAGACACTGTGCGTTGGCAAGCAGGCCGAAGTGGA
GTTTTGGTCCAAA-----------------CATGTTCTGCTTTTATCTTTTTTACGTGAGCTTTTATATTCTTTGGCTGC
CAGACACCAGAAACTTTTCGTGATGATACAGC---------------------ATACAGTATTAAATAACTAGCCTAAAA
A-------------------------------------------------------------------------------
-----------------------------------------AACTTCTTATATTTTGAGACCGAGATAGTAGGAGTAACA
TAT-AAGGTGCAAGCGTGCAAGGAAGTTGCAGAACATCCTAGAGCATTTTGATATCTAGATCCATGAATGCCCCTACCAT
TGTCTTCATCCAAATGTTTTTTCATTTATAAAATTCATCAAGAAAAAAATGAAAAAAATGCAATGTGATCCTAGTACTCT
CCTACTTTTGCGAGGAATTTCAATGCATCAGAAGTGCCAGCATCAGTTACCTTACCCAGCAAAGTTCCCTTCTAACTTGT
TTTCAGTACCTTCTCTTTCGCTCACACCTAAACATCTTCCGATCAGCAAAAATGCAGCTTTCACCAAACAGCTCTAAAAG
AAGACGTTTTGGCTCTCCAACTATCAAACTGACACATGCTCAAGGTCGCTGAAGATGTCGCAACAAGATCAGGTACCACA
ACTCACAACGTTGCACAGAAAAATAAAGATACATATATAATACTCCATCCGCCCCGATTTACTTGTCTTAAATTTGTCTA
GATAGATATGTATGTACTAACGCTAGCAGCC----------------AAATCTAAGACAAGTAATCTGAGACGGAGGTAA
TATACACCTGCACAATCTACACACACGCTAGCAGCCAAAGCCCAAAGGCTATTATTGAGTTGACTGATCATGTCAGTTCT
GGAACAAACAACATTAATCTGATGAAGAGAATGTCATGCAGATAATACAACTCC
>chr3A_555
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--------------------------------------------------------------------------TTCCTT
TGATAGGCTCTTCCATATGCCCATTTCAACAAATGGATGTTTTTTTCTGC--CATGTGGTCTGGAGCCTGACTTGAAAAT
TTTGGTGCCCGGCAGAACCATTGATTCTTGAATCTTGAGAATGATTCATCCCACAAAGCAATTTTAGTCCTGTACCAA--
ATGAAGTAAAAGTGTAAAACATGAACCACCTCGCACAACAAACTCA----CCATACCTACTCCG----------------
-------------------CGCCGCGGAAAATGTTTTACAAAACACACA--CAGTACAGTTGGGAGCTTGTTAGGATGTT
CGAACACTTTACCACTAAACTACTCATCACGCGTATTTCCCTGCTTAACAGCTTATACTCGTACTTCGAACAACACCGAC
CCCGCCCTTAAAAAGCCATCTAACCCCTGTAATTAACCTCCACAAGGGACGTGCAGAAG----CACACACACAAAAAATC
TTTTTACCATGGGCATGGCCACCGCAGCCGCCGCGACGACGGCCGCTCCGGACAAGCTCCGGCAGCCGTGCAGGCCGAGG
CCGGCGGCGCAGATCTCCTCCTCCAAGAACCGCGGGCCCAAGGCGCCGGTGGTGATCGCGCACGAGTGCCCCAGCGCGAT
GCGCGCCCACGTCCTGGAGGTCCCCGCCGGGCGCGACGTCCTGTCGTGCGTCGCGGCGTTCGCGCGGCGCGGGCGCTGCG
GTGCGCTGGTGCTGGGCGCGGCCGGGCACGTCGCGGACGTCGTACTCAGGGAGCCGGCGCTGGTGCTCCGCGGCACGACG
GAGATCCTGAGCCTGGCAGGGTGCTTCTTCCCGTCTCCCTCGGCGTCAGCGGCGGGCGTCGCGGTGTTCCTGGCCGGGCC
GCGAGGCAGCGTCCTGGGCGGCGCCGTCGCGGAGGGAGGGCTCGTGGCCGCCGGTCCGGTGGTGGTAATGGTGGCCACGT
TTGTCGCGGCTGCGATCGACCGGTTGCCGCTGGTGAAGGGGGACGAATCCTCCAAGGCGGACGGGAGCGACGTGCACGGC
GTGGCCGGACAGTGGCGGTGCGGCGGCCAGCCGCTGCAACAACAGTGCGGATGGGCGCCGCTGTGTCGGAAGCTGGGCGC
GAAGAGCTGAACCCTATGCACCGAGTGGAGAATATATATTGGGCCGTCATATTGTTCGTTGGCAAGCAGGCCGATGTGGA
GTTTTGGTCCAAGCTTTGAAAAAAAAAATCCATGTTCTGC----------------------TTTATCTTCTTTGGCTGT
GAGACAACAGAAACTTTTCAATGTCTCAAAAGAAACACGAACTTTTCATGAAGGTACAGTGTTAAAAATACTCCCTACGT
TCACAAACATGAGATGTTTTGGATATTTCAATATGGATTATATATACAGACTAAATGAGTGAACGAACACACTAGAACGT
ACGTATATCTATGTAGTACATTTGATTGAGAAAAAAGGTAGAACATCTTATATTTGTGAATGGAG------GGAGTAACA
TATAAAGGTGCAATCTTGCATGGTAGCTGCCAAACATCCTAGAGCATTTTGATATCTAGTGCCATGAATATCCCAACCAT
TGTCTTCATCCAAATGTTTATGCATTTATAAAATTCATCGAGAGAAAAAGGACAAC-ATCCAATGTGATTCTAAAGCTCT
CCTACTTTTGTGAGGAATGTCAATGCATCAGAAGTGCCAGCATCAGTTACCTTACCCAGCAAAGTTCCCTTCTAATTTGT
TTTCAGTACCTTCTCTTTCTCTCACACCTAAACATCTTCCGATCAGCAAAAATGCAGCTTTCACCAAACAGCTCTAAAAG
AAAACGTTTTGGCTCTCCAACTATCAAACTGACACATGCTCAAGGTCGCTGAAGATGTCGCAACAAGATCAG-TACCACA
ACTCACAACGTTGCACAGAAAAATAAAGATACATATATAATACTCCCTCCGCCCTGAATTACGTGTCTTAAATTTGTCTA
GATAGATATGTATGTAATAACGTGTCTAGATACATCTGTATCTAGAAAAATCTAAGACAAGTAATTTGAGACGGAGGTAA
TATACACCTGCACAATCTACACATATGCTAGCAGCCAAAGCCCAAAGGCTATTATTGAGTTTACTGATCATGTCAGTTCT
GGAACAAACAGCATTAATCTGAAGAAGAGAATGTCATGCAGATAATACAACTCC
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------------------------
-----S-------------------------------------------SSS----S-----------------------
---------------S----------------------------------------------------------------
-------------------------------------------SS-SSSS------------S-----------------
-------------------------------------------------S------------------------------
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-----------------------------------------------------------SSSS-----------------
------------------------------------------------------S-------------------------
----------------------------------S---------------------------------------------
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-------------------S------------------------------------------------------------
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----------------------------S----------------S----------------------------------
---------------------------------------------------------------S----------------
-------------S------------------------------------------------------------------
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---------------------------S----------S-----------------------------------------
S-------------------------S----S------------------------------------------------
-------------------------------------------------------------S------------------
---------------------------------------------------S----------------------------
--------------------------------------------S-----------------------------------
--------------------------------------S--------S-----------------------S--------
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--------------------------------------------S-------------------------S---------
---------S----------------------------------------------------------------------
--------SSSSS-SS---------------------------------------------S------------------
----------------------S------------------------------S------S-------------------
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>forward_765
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-------------------------CCACCTCGCACAACAAACAG-----------------------------------
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>reverse_2445
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--------------------------------------------ATCGCTGAAGATGTCGCAAC----------------
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