>input_sequence_81761
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-----------------------------------------------------------------ATGCGGCGACCGGCC
ATGGGAAGGGCAATGGCGCCGCTCCTCGTGCTGGCGGTCCTGGCCGTCGCGGCGGCCACGGCCGGGGCTGTTGACGGAGA
TGTCAAGTGCGCTGAGTGCGGCACGGGCACGGTGCCGGTGCCCGTGCTGCCGCCGCCGCCGCCGTACTACTACTACAGCC
CTCCGCCTCCGGCGTCCTACCCCGGTGTGTCCAACTGCCCGCCGCCGCCAGGGGGGTACATCCAGATCGGGGGCTCGGCG
CCGGGCAAAGGGCGCATGTACCCGCAGGACCCCGGGTTCATGCCATCCAGCGCGCAGCCCAGGCATGGGAGCCGCGCCGT
CCACTTCACGGTATGTTCGTTTGCGGCGTTGGCGATTCTACGGGCCTTTTGGTGA-------------------------
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>chr3D_1_TraesCS3D01G221000
CCTTTTCCAACCCAACTAGTATTAAGCTTGCTCTATCTTCTCTAGATTTGGTCAGCACGAGGGTCGAACTGCAGTATGGT
TAGGGTCAGGCCCTGAAGAAATTTTAGGCCTTCTCCTTCGGGATTGTAATGTGACTCTTACTTAATCAGTACAATCCCCT
TTACCCTGGAAAAAACTATTAAGCTAGCTCCGCGAAGAATATTCT-----AGCGCACTTGATGAGTAGCAAGCATGTGTA
GAGTGAGTTTCCACGGCAACATGCAAAATGCATTAAAAATCCGTGCCAAGCAAGCAAGCAGGCCAGGATCAATGGATGAA
T------CCAGTCACATGGCAGCCGCACACACGAGGACAGATCGGAAGCTTCTTCCCGCTTTATCAAACTTGGTACGGGG
GCGAAGCCAACTTTAAGCCAAGCTCCCCGTAGTTGGGCTCCAACGACGACTCCACGTTCCCCACACTCGCACGACGCTAG
CAGCTAGTACTAGCTTGTTGCTTGACGCGTCGTCGTCCTCGCTGCGATCGCCTCGCAGC------CGCACATGCACATGT
TGACGACCACCGCGCGCGTCGGTGGCACCCCTCCAGCGAACGCATCCATCGCGCACCGCCGCGCCGAGCTCGCTCCCATA
ATGCACGCTCATGCATGTGGCCGACCTGATCCGCGGACCCACGGATTTAGCGGCCGGCACATGGTCGTCGCTTTCGAGCC
ATACCGGAGGTTAGCCGCCAGCTCAGGAGGTACCAATGCTGCCTGCCTCCTTGATGCAGCAGTACAGTTACGCCTTCCTC
TGCTTCCAAACCTACTGCCCCCGTTCTAACGAATCCCAACTAAT--------ATTCCTCCTCCATTCTACTCCTACTTTG
TGGATCGTGACAGCATCATAAGAAGGCTGGCGGGGAGGAGGGCCAGCACGGCCACACCATAACCACCATAGCGCTTCTTA
CCGAGCCACACTACTTTCGCTCGTATAGCCTCGTAGCCAACGCCCGAACGCTCACCGTGGATAGGATGCGGCGACCGGCC
ATGGGAAGGGCAATGGCGCCGCTCCTCGTGCTGGCGGTCCTGGCCGTCGCGGCGGCCACGGCCGGGGCTGTTGACGGAGA
TGTCAAGTGCGCTGAGTGCGGCACGGGCACGGTGCCGGTGCCCGTGCTGCCGCCGCCGCCGCCGTACTACTACTACAGCC
CTCCGCCTCCGGCGTCCTACCCCGGTGTGTCCAACTGCCCGCCGCCGCCAGGGGGGTACATCCAGATCGGGGGCTCGGCG
CCGGGCAAAGGGCGCATGTACCCGCAGGACCCCGGGTTCATGCCATCCAGCGCGCAGCCCAGGCATGGGAGCCGCGCCGT
CCACTTCACGGTATGTTCGTTTGCGGCGTTGGCGATTCTACGGGCCTTTTGGTGATCGATCTGCGGCAACTGCGCGGCCA
TCGTCTCCGTTACGTGTCGCGACGGAAGGACAGAGACGTGCCGGCGTTCCATGGATCTCCTGTGTATGCATTCACCTTGT
AATAATTCTTACTGGTCATATGTTTTGTAGTTCTTGTAATACATCAAGCT-------CCTTTTTCTCAATTTTGTTTCTT
GTTACAGAACTTTTACTTGTAACAAATTAGTTGCAAATCAATGGAACTAGCAGGTCATGGTGGGTATGAGAATGTGTT-A
TTCGTGGGTGATCTTTTTGGCTTTTCTTTCTTTCTTGAAA-CAACTTTCTTCTTGTTCTTTGG-CAGAAAGGCTTCAGGC
CTGGCTGTTTAAGTATTGGATTCCCAGATCATAAAGTTTACAACTCGAAGAACCCCGCCGCAAGGGTAAGCGACTTCAAA
TGGTTTATCAACAACAACAA------------ACAACAAATGGGCAAAATGGCTAAGCTATACGACTCTTACTCACAATT
CTGCTTCCGTTTCCGGAGAAGGGAAAGTTGTGACATGATGCGATCATGCCAGTTTGTTCGAAGACCAGCTCTAAGTAGCT
TTTTCCGGATCAACTATGGCTTAGAAATTGGTGGATCTATGGGGAACGCAGTTCTTCTCACAAGGATTCCGTGCATGCAA
AATGGGCCTAGCAAGTCGTGATAATTTCATCACAATGCACATTCTTTCTCACTCCTCTTTCTTTGCAGCCGTTAATGACG
CG------------------------------------------AACTAGACAATGATCAAATGCGTGCCCCTTTTTGCT
TTGCGTACAAGTTAAAATTTTCAGCAACAAGGCTAACTATCATCAGTTTAACTTCAGCAACAAAAATGCCTAGGCTTGGA
ATGAAAGATCAGACCATGTGGAGCCTTGCCAAATCCTCTTCCACAAGCTTCTGCGAACTAGTCAAAGGCTGCGGTCCTAG
CGTAAAACGATCTTCTCTGACCACAGGGTGCAACTACACATGGCGATCGGTTGTGTCTTAGTCCCTGTCGGAATGGTGG
>chr3B_1
CCTTTTCCAACCCAACTAGTATTAAGCTTGCTC-----------------------------------------------
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------------------------------CGGGATGAATATTCT-----AGAGCACTCGATGAGTAGTAAGCATGTGTA
GAG-------------------------TGCATTAAAAATCCGTGC----CAAGCAAGCAGGCCAGGATCAATGGATGAC
ATCAAGACCAGTCACATGGCAGCCGCACACACAAGGACAGATCGGAAGCTTCTTCCCGCTTTATCAAACTTGGTACGGGG
GCGAAGCCAACTTTAAGCAAAGCTCCCCGTAGTTGGGCTCCAACGAGGAGTCCACGTTCTCCACACTCGCACGACGCGAG
CAG------CTAGCTTGTTGCTTGACGCGTCGTCGTCCTCGC--------------AGC------CGCACATGCACATGT
TGACGACCACCGCGCGCGTCGGTGGCACTCCTCCAGCGAACGCATCCATCGCGCACCGCCGCGCCGAACTCGCTCCCATA
ATGCACGCTCATGCATGTGGCCGACCTGATCCGCGGACCCACGGATTTAGCGGCCGGCACATGGTCGTCGCTTTCGAGCC
ATACCGGAGGTTAGCAGCCAGCTCAGGAGGTACCGATGCTACCTGCCTCCTTGATGCAGCAGTACAGTTACGCCTTCCTC
TGCTTCTAAACCTACTGCCCCCGTTCTAACGAATCCCAACTAAT--------ATTCCTCCTCCATTCTACTCCTACTTTG
TGGATCGTGACAGCATCATAAGAAGGCTGGCCGGGAGGAGGGCCAGCACGGCCACACCATAACCACCATAGCGGTTCTTA
CCGAGCCACACAACTTTCTCTCGTATAGGCTCGTAGCCAACGCCCGAACGCTCACCGTGTATAGGATGCGGCGGCCGGCC
ATGGGAAGAGCAATGGCGCCGCTCCTCGTGCTGGCGGTCCTCGCCGTCGCGGCGGCCAGGGCCGGGGCTCTTGACGGAGA
TGTCAAGTGCGCTGAGTGCGGCACGGGCAC------GGTGCCCGTGCTGCCGCCGCCGCCGCCGTACTACTACTACAGCC
CTCCACCTCCGGCGTCCTACCCCGGTGTCTCCAACTGCCCGCCGCCGCCAGGGGGGTACATCCAGATCGGGGGCTCGGCG
CCGGGCAAAGGGCGCATGTACCCGCAGGACCCCGGGTTCATGCCATCCAGCGCGCCGCCCAGGCATGGGAGCAGCGCCGT
CCATTTCACCGTATGTTCGTTTGCGGCGTTGGCGATTCTACGGGCCTTTTGGTGATCGATCTGCAGCAATTGCGCGGCCA
CCGTCTCCGTTACGTGTCGCGACGGAAGGACAGAGACGTGCCGGCGTTCCATGGATCTCCTGTGTATGCATTCACCTTGT
AATAATTCTTACTGGTCATATGTTTTGTAGTTCTTGCAATGCATCAAGCT-------TTTTTTTTCCTCTTAATTTTGTT
GTTACAGAACTTTTACTTGTAACAAATTAGTTGCAAATCAATGGAACTAGCAGGTAATGGTGGGTATGAGAATGTGTT-A
TTCGTGGGTGATCTTTTTGGCTTTT-TTTCTTTCTTGAAAACACCTTTCTTCTCGTTCTTTGGGCAGAAAGGCTTCAGGC
CTGGCTGTTTAACTATTGGATTCCCAGATCATAAAGTTTACAACTCAAAGAACCCCGCCGCAAGGGTAAGCGATTGTAAA
TGGTTTATCAACAACAACAA------------ACAACAAATGGGTAAAATGGCTAAGCTATACGACTGTTACTGACAATT
CTGCTTCCGTTTCTGGAGAAGGAAAAGT--TGACATGATGTGATCATGCCAGTTTGTTCAAAGACCAGCTCTAAGTAGCT
TTTTC-GGATCAACTATAGCTTAGAAATTGGTGGATCTATGGGGAA-CCAGTTCTTCTCACAAGGACTTTGTGCATGCAA
AATGGACATAGCACGTCGTGATAATTTCATCACAATGCACATTCTTTCTCACTCCTCTTTCATTGCAACTGTTAATGACA
CC------------------------------------------AACTAGACAATGATCAAATGCGTGCCCCTTTT-GCT
TTGCGTATAAGTTAAAAACTTCAGCAACAAGCCTAACTATCATCAATTTAACTTCAGCAACAAAAATGCCTAGGCTTGGA
ATGAAAGATCAGACAATGTGGAGCCTTGCCAAATCCTCTTCCACAAGCTTATGCGAACTAGTCAAAGGTTGCGGTCCTAG
CGTAAAACGATCTTCTCTAACCACAAGGTGCAACTACACATGGCGCTCGGTTGTGTCTTAGTCCCTATCGGAATGGTGG
>chr3A_159
CTTTCACCC-----------------------------------------------------------------------
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--------GCAAAAAAAACAAAGTTTGCTTCGCGATGAATATTCTACTGTAGCGCACTTGATGAGTAGCAAGCATGTGTA
GAGTGAGTTTGAGCAGCCACATGCAAAATGCATTAAAAATTCGTGCCAAGCA--------GGCCAGGCTCGATGCATGAC
ATCCAGACCAGTCACATGGCAGCCGCACACACAAGGACAGATCGGAAGCTTCTTCTCGCTTTATCAAACTTGGTACGGGG
GCGAAGCCAACTTTAAGCAAAGCTCCCCGTAGTTGGGCTCCAACGAGGACTCCACGTTCCCCACACTCGCACGACGCTCG
CAG------CTAGCTTGTTGCTTGACGCGTCGTCGTCCTCGCTGCGATCGCCTCGCAGCCGCACACGCACATGCACATGT
TGACGACCACCGCGCGCGTCGGTGGCACCCCTCCAGCGAACGCACCCATCGCGCACCGCCGCGCCGAGCTCGCCCCCATA
ATGCACGCTCATGCATGTGGCCGACCTGATCCGCGGACCCACGGATTTAGCGGCCGGCACATGGTCGTCGCTTTCGAGCC
ATACCGGAGGTTAGCCGCCAGCTCAGGAGGTACCGCTGCTACCTTTCTCCTTGATGCACCAGCACAGTTACGCCTTCGCC
TGCTTCTAAACCTACCGCCCCCATTCTAACGAATCCCAAGCTCCCAACTAACATTCCTCCTCCATTCCACTCCTACTTTG
TGGATCGTGACAGCATCATAAGAAGGCTGGCCGGGAGGAGGGCCAGCACGGCCGCACCATAACCACCATAGCGCTTCTTA
CCGAGCCACACAACTTTCGCTCCTATAGCCTCGTAGCCAACGCCCGAACGCTCATCGTGGATAGGATGCGGCGGCCGGCC
ATGGGAAGGGCAATGGGGGCGGCGCTCGTGCTGGCGGTCCTGGCCGTCGCGGCGGCCACGGCCGGGGCTGTTGACGGAGA
TGTCAAGTGCGCTGAGTGCGGCACGGGCAC------GGTGCCGGTGCTGCCGCCGCCGCCGCCGTACTACTACTACAGCC
CTCCACCTCCGGCGTCCTACTCCGGTGTGTCCAACTGCCCGCCACCACCAGGGGGATACATCCAGATCGGCGGCTCGGGG
CCGGGAAAAGGGCGCATGTACCCGCAGGACCCCGGGTTCATGCCGTCCAGCGCGCCGCCCAGGCATGGGAGCAGCGCCGT
CCACATCACGGTATGTTCGTTTGCGGCGTTGGCGGTTCTACGGGCCTTTTGGTGATCGGTCTGCAGCAGTTGCGCGGCCA
TCGTCTCCGTTACGTGTCGCGACGGAAGGACGGAGACGTGCCGGCGTTCCATGGATCTCCTGTGTATGCATTCACCTTGT
AATAATTCTTACTGGTCATATGTTTTGTAGTTCTTGCAATGCATCAAGCTTCTTCTTTTTTTGTTTCTCTCATTTTTGTT
GTTACAGAACTTTTACTTGTAACAAATTAGTTGCAAATCAATGGAACTAGCAGGTCATGGTGGGTATGAGAATGTGTT-A
TTCGTGGGTGATCTTTTTGGCTTTTTTTTCTTTCTTGAAA-CAACTTTCTTCTTGTTCTTTGGGCAGAAAGGCTTCAGGC
CTGGCTGTTTAAGTATTGGATTCCCGGATCATAAAGTTTACAACTTGAAGAACCCCACCACAAGGGTAAGCGATTTCAAA
TGGTTTATCAACAACAACAACAATAATAACAAACAACAAATAGGTAAAATGGCTAAGCTATACAGCTGTTACTGACAATT
TTGCTTCCGTTTTTGGAGAAGGGAAAGTTCTGACATGATGCGATCATACCAGTTTGTTCAAAGACCAGCTCTAAGTAGCT
TTTTG-GGATCAATTATAGCTTAGAAATTGGTGGATCTATGGGGAACCCAGTTCTTCTCACAAGGACTCTGTGCATGCAA
AATGGGCCTAGCCAGTCGTGAT-ATTTCATTACAATGCACATTCTTTCT-------------TTGCAACCGTTAATGACG
CCAACTAGACAATGATCATTGTCTAGTTTTTCCCCCCGCAAGAAAACTAGACAATGATCAAATGTGTGCCCCTTTTAGCT
TTGCGTATAAGTTAAAAACTTCATCAACAAGCCTAACTATCATCAATTTAACTTCAGCAACAAAAATGCCTAGGCTTGGA
ATGAAAGACCAGAGAATGTGGAGCCTTGCCAAATGCTCTTCCACAAGCTTATGTGAACTAGTCAAAGGTTGCGGTCCTAG
CGTAAAACGATCTTCTCTAACCACAAGGTGCAACTACACATGGCGCTCGGTTGTGTCTTAGTCCCTATCGGAATGGTGG
>chr3A_1587
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------------------GTAACAAATTAGTTGCAAATCAATGGAACTAGCAGTTCATGGTGGGTATGAGAATGTGTTTA
TCCGTGGGTGATCTTTTTGGCTTTC-TTTCTTTCTTGAAA-CACCTTTCTTCTTGTTCTTTGGGCAGAAAGGCTTCAGGC
CTGGCTGTGTACGTATTGGATTCCTAGATCATAAAGTTCACAACTCTAAGAACCCCGCCGCAAGGGTAAGCGATTTCAAA
TGGTTTATCAATAACAACAACAACAACAAC-----------GGGTAAAATGGCTAAGCTATATGACTGTTACTGACAATT
ATGCTTCTGTTTTTGGAGAAGGGAAAGTTCTGACATGACGCGATCATACCCGTTTGTTCAAAGACCAGCTCTAAGTAGCT
TTTTG-GAATCAACTATAGCTTAGAAATTGGTGGATATATGGGGAACCCAGTTCTTCTCACAAGGACTCTGTGCATGCAA
AATGGGCCTAGCGAGTCGTGAT-ATTTCATTACAATGCACATTCTTTCT-------------TTGCAACCGTTAACGACG
CCAACTAGACAATGATCATTGTCTAGTTTTTCCCCCCGCAA-AAAACTAGACAATGATCAAATGTGTGCCCCTTTTTGCT
TTGCGTATAAGTTAAAAACTTCAGCAACAAGCCTAACTATCATCAATTTAACTTCAGCAACAAAAATGCCTAGGCTTGGA
ATGAAAGACCTGACAATGTGGAGCCTTGCCAAATGATCTTCCATAAGCTTATGCGAACTAGTCAAAGGTTGCAGTCCTAG
CGTAAAAATATCTTCTCTAACCACAAGGTGCAACTACACATGGCGCTCGGTTGTGTCTTAGTCCCTATCGGAATGGTGG
>SNPs
---------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSS-S-----SS-SS---S-S---S-----S--------------------------------------------
----------SSS-S--S-------------------------------------------------------------S
S-------------------------------S-----------------------------------------------
------------------S---------------------------S---------------------------------
---SSSSSS-----------------------------------------------------------------------
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----------------------------------S-----S---------------------------------------
------S-------------------------------------------------------------------------
-------------------------------S------------------------------------------------
-----------S-------------------------------------------------------------S------
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------------------------------SSSSSS--------------------------------------------
----S---------------------------------------------------------------------------
-------------------------------------------------------S----------------S-------
----------------------------------------------------------------S----S----------
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------------------------------------S---S----------------SS-----S--SS--S-S---S--
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-------------------------S------------------------------------------------------
-------------------------------------------------------------------------S------
--------------------------------------------S----------------------S-----S------
-------------S---------------S-----------------------------S--------------------
-----S-----------S-----------------------------S------------------S--S----------
-------------------------------------------------------------S-----S------------
-S------------------------------------------------------------------------------
-------S---------SS------------S-------------S----------------------------------
--------------S-----------------------------------S-----------------S-----------
------------------S------S-------------------S--------------------S------------
>forward_63
-------------------------------------------AGATTTGGTCAGCACGAGGG-----------------
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>reverse_2067
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------------------------------------------------------------------TTCCGTGCATGCAA
AATGGG--------------------------------------------------------------------------
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