>input_sequence_81350
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------ATGGCGAAGCTGCTGGCGGCCGGCGTCGCGTTCCTCCTGGCCCTCGCCGCAGCGGCGGCGCTGGCCCCGTCTCC
GGCCTCGGCCTTGAAGGGCGCCGGCGGGCTAGGCCTCGGCGGCGCGGCTGCGGCCGTGGTTATGCGGCGGGGCGGGCGGA
CGTGCCGGGGCACGGTGGGCGAGTGCATGGAGTACTTCGGCGTGGACGGCGAGGGCGAGAGCGAGGTGGCGGCGATGGCC
GGCAAGCGGCGGGTGCTGCAGGACGGGTCCGGGTACATCGGCTACGACGCGCTGCGGCGGGACAACGTGCCGTGCTCGCA
GCGCGGTGCCTCCTACTACAACTGCCAGCCCGGAGCCGAGGCCAACCCCTACTCCCGCGGATGCAGCGCCATCACCCAGT
GCAGGGGCTGA---------------------------------------------------------------------
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>chr3A_1_TraesCS3A01G176000
AAAAGGACCTGCATTGAATTCGCCACATGGTTAATCAGTTAAGCTAACGGCCTCTCGCTGTTGACCTGGAACACACAC--
---------ATACTGTCTAGTGCTAGTCTAGTGGCTTAGATATAGGACCATTTCA--------TTTTTGTTTTGCGGGGA
CAGGACCATTTAGTAGCTAGGAGCACTAAACGAAGCTGTCACGCAGGTACGCGTACGTCCATAGAGTATGTTGCTACTCC
ATGTCCATGAAAGGAGTAGCACTGAAGCTAGGCATCGAAAGCGCTCTCTAGCTTGTCCATCTGACACCCCCATCACGTTT
ATTATTGATGTGCCCAAGTTGTACGACGGTGCGCTGTTCATATCTACGACGTCGTACTGCTAGCCATTGATGCGCACGAG
TAAATACAGCCGAACACTCCAAATGACACTGAGAAAGTAAGCTAGCTAGTGACGGTTTGCAGCACGGAAAAGCAGGTGCA
AGTAAATCGCCCGTGTCGCACGCGGTTAGCCTCCCAAAGATGTAGCAACTTGTCGTGGCATGTGAGCAGCATAGAGATGG
GAGAATTACTCCAATTCTTCTTTTTCAG-TTTCTTTCTCCCGGGCACCTGGTCCAACACCCAGGCCAAGATGTATCGGCT
CGTCTCGTGATCCAATGTGCACGCACCGCGACGAATCGAACCATCCAATCCATGCCGAGTTACCGGGATGCTCCAAAACG
ATGGATTCGGTGACGTGCTTGGGCCGATCATACGGCGGCAATCTTGATCTCGATCCGGACCAACCAACGATCGCTGTTAC
GCCACAGTGCCACACCGACGC-----GACGCGACGCGCCATCTCTCCCTCGTCTCCCA-------------------TTC
TTTCTCTTCTCACCTACTGCGGCCGTCCCGCCATTGCCAATATAACCCGCCACCCCGCCCGAGTCC-CACACACGCCCAA
CAGCTCCACACATCGCCACGGTCTTCTTGGCTCCTCCGTCCACA-GCTAGCCAGCCCCTCCGCTCCGCTCCACCACCAGC
AGCCAAATGGCGAAGCTGCTGGCGGCCGGCGTCGCGTTCCTCCTGGCCCTCGCCGCAGCGGCGGCGCTGGCCCCGTCTCC
GGCCTCGGCCTTGAAGGGCGCCGGCGGGCTAGGCCTCGGCGGCGCGGCTGCGGCCGTGGTTATGCGGCGGGGCGGGCGGA
CGTGCCGGGGCACGGTGGGCGAGTGCATGGAGTACTTCGGCGTGGACGGCGAGGGCGAGAGCGAGGTGGCGGCGATGGCC
GGCAAGCGGCGGGTGCTGCAGGACGGGTCCGGGTACATCGGCTACGACGCGCTGCGGCGGGACAACGTGCCGTGCTCGCA
GCGCGGTGCCTCCTACTACAACTGCCAGCCCGGAGCCGAGGCCAACCCCTACTCCCGCGGATGCAGCGCCATCACCCAGT
GCAGGGGCTGATCCCCTTCATTAAACCCTGCTTCATTCCTTCTT---ACCACCTGCATGCCTCATCAATTAGTATTGCTA
TCTATCTGTAACGTAATGTAATGTAATGTAATTACAAGAAGAAGATCAAACACTTCTTGACGATGCTTGATCAATCATCA
CTGGTGGGGGTGGTGTGGTCAATCGTACCGTACGG--ATCACTGGAGGAGGCGTGGTTAATTATCGTGTCATTTGTGCCT
ATTTGGGTGAAAGTAATTAAGCTTACGCGTTCTGGTGCATCTGATTTCGGTTGTGCCCAATAAATTTGTAGACTCCTTTG
GTACGTACTTCCTTCGTCTCATATTAGTTGT----------GATACTATTTGCCTCGGTTTAACTATGGTGAATTGAATG
TGCTTCTCTGCCATGGTTTTTCTCCATTTTCTTGATTGAGC---AGGTGGCAGAGAAGTTTTTTGTGAGCCTGACATGCC
AATTCGCGGATGCTTGTCAGAAAAGAAACATCAATATCTCTCGAGTTGAGCTGTCTTTTCTGAATATATTTACCTTTCTC
CTTTCTGCCCCCTCCTTGTTTCTGGTTAGCCAATGTTTAATCAGTGCTCTGAATTA-----GTATTTGTTTTGTGCGCCC
AAAGCGATCGGCTTTTGTTTGGTG---TTAAGGGGAAAATGACTCTTCTATAGTGTTGTGGCAAAGATCGGTTCAAATGG
GTTGGTGAAAGTGGAGCTTCTTTGGCTATACTTAATTTATTCCTTGTACACTTTAACACGATTCATTTGTTAGCACCAAC
ACACAATGTCCATGTGGTTGGGCTGTCACGCTTCATCCTATCTGCAGCACTGCGGCCAATAACTAGAAGGAAGGGATCCA
TCCCCTTGTGGAATCTTACATTCGCAAGGATATCTAGAAGTGCACAAGCTCAAAAGAGGATATCTAGATATACTAGAAGA
ACATCCGTGCGTTGCAACGAGGCCACATTAACTTTAAGAGTTCAATATTAATATTCTTATACATATCAAGTGACATT
>chr3D_1
AAAAGGACCTGCATTGAATTCGCCACATGGTTAATCAGTTAAGCTAACGGCCTCTCGCTGTTGACCTGGAACACACAC--
---------A--CTGTCTAGTGCTAGTCTAGTGGCTTAGATATAGGACCATTTAGTTT-----TTTTTTTTTTGCGGGGA
CAGGACCATTTAGTAGCTAGAAGCACTAAACGAAGCTGTCACGCAGGTACGCGTACGTACATAGAGTATGTTGC------
----CCATGAAAGGAGTAGCACTGAAGCTAGGCATCGAAAGCGCTCTCTGGCTTGTCCATCTGACACCCCATA-ACGTCT
GTTATTGATGTGCCCAAGTTGTACGATGGTGCGCTGTTCATATCTACGACGTCGTACTACTAGCCATTGATGTGCACGAG
TAAATACAGCCGAACACTCGAAATGACACTAGAAAGTACATA-AGCTAGTAACGGTTTACTGAAAACAAAAGCAGATGCA
AGTC-ATCCCCAGGGTCGCACGCGGTTAACCACCCAAAGATGTAGCAACTTGTCGTGGCATGTGAGCAGCATAGAGATGG
GAGAATTACTCCAATTCTTCTTTTTCAG-TT-----CTCCCGGGCACCTGGTCCAACGCCCAAGATGCATCGGCTCGTCT
CGTCTCGTGATCCAATGTGCACGCACCGCCACGAATCGAACCATCCAATCCATACCCAGTTACCGGAATGCTCCAAAACG
ATGGATTCGGTGACGTGCTCAGGCCGATCATACGGCGGCAATCTTGATCTCGATCCGGACCAACCAACGATCGCTGTTAC
GCCACAGTGCCACACCGACGCGACGCGACGCGACGCGCCATCTCTCCTCTCCTCTCCCGGTCTCCCTCCATCTCCCTTTC
TTTCTCTTCTCACCTACTGCGTCCGTCCCGCCATTGCCAATATAACCCGCCACCCCGCCCGAGTCC-CACGCACGCCC-A
CAGCTCCACACATCGCCACGGTCTTCTTGGTTCCTCCGTCCACAGGCTAGCCAGCCCCTCCGCTCCGCTCCGCCACCTGC
AGCCAAATGGCGAAGCTGCTGCCAGCCGGCGTCGCGTTCCTCCTGGCCCTCGCCGCGGCGGCGGCGCTGGCCCCGTCCCC
GGCCTCGGCCTTGAAGGGAGCCGGCGGGCTGGGCCTCGGCGGCGCGGCGGCGGCCGTGGTGATGCGCCGGGGCGGGCGGA
CGTGCCGGGGCACGGTGGGCGAGTGCATGGAGTACTTCGGCGTGGACGGCGAGGGCGAGAGCGAGGTGGCGGCGATGGCC
GGCAAGCGGCGGGTGCTGCAGGACGGGTCCGGGTACATCGGCTACGACGCTCTGCGGCGGGACAACGTGCCGTGCTCGCA
GCGCGGGGCCTCCTACTACAACTGCCAGGCCGGCGCCGAGGCCAACCCCTACTCCCGCGGATGCAGCGCCATCACCCAGT
GCAGGGGCTGA-----TTCATTAAACCCTTCTTCATTCCTTCTT---ACC---TGCATGCCTCATCAATTAGTACTGTTA
TCTATCTGTATTC---TGTAACGTAATGTAATTACAAGAAGAAGATGAAACACTTCTTAT-GATGCTTGATCAATCACCA
CTTGC-----TGGTGTGATCAATCGTACCGTACGTAC--CACTGGAGGAGGCATGGTTAATTATTGTGTCATTTGTGCCT
ATTTGGGTGAAAGTAATTAAGCT-----------------CTGATTTCGGTTGTGCCCAATAAATTTGTAGAGTCCTTTG
GTACGTACTTCCTTCGTCTCATATTAGTTGTCGTTCAAATCGATAACATTTGCCTCGGTTTAACTATGGTGAGTTGAATG
TGCTTCTCTGCCATGGCTTTTCTCCATTTTCTTGATTGAGCTGTAGGTGGCAGCGAAATTGCCTGTGAGCCTGACATGCC
AATTCGCGGATGCTTGTCAGAAAAGAAACATCAATATCTCTCGAGTTGAGCTGTCTTTTCTGA-TATATTTACCTTTCTC
CTTTCTGCTCCCTCCTTGTTTCTGGTTGGCCAATCTTTAATCAGTGCTCTGAATTA-----GTATTTGTTTTGTGCGCCC
AAAGCGATCGGCTTTTGTTTGGTG---TTAAGGGGAAAATGACTCTTCTATAGTGTTGTGGCAAAGATCGGTTCAAATGG
GTTGGTGAAAGTGGAGCTTCTTTGGCTATACTTAAATTATTCCCTGTACACTTTAAAACGATTCATTTGTTAGGACCAAC
ACACAATGTCCAAGTGGTTGGGCTGTCACGCTTCATCCTATGTGCAGCACTGCGGCCAATAACTAGAAGGAAGGGATCCA
TCTCCTTATGGAATCTTACAGTCGCAAGGATATCTAGAAGTGCACAAGCTCAAGAGAGGATATCTGGATATAC-------
-----------------------------------------------------------------------------
>chr3B_1
AAAAGGACCTGCATTGAATTCGCCACATGGTTAATCAGTTAAGCTAACCGCCTCTCGATGTTGACATGGAACACACACTG
TTTAAGCTAA--CTGTCTACTGCTAGTCTAGTGGC-TAGATATAGGACCATTTAGTTTTTTTGTTTTTATTTTGCGGGGA
TAGGACCATTTAGTAGCTAGGAGGACTAAACGAAGCTGTCACGCAGGTACGGGTACGTACATAGAGTGTGTTG-------
---------------------CTGAAGCTAGGCATCCAAAGCGCTCTCTAGCTTGTCCATCTGACACCCCATC-------
------GATGTGCCCAAGTTGTACGATGGTGCGCTGTTCATATCTACGACGTCGTACTACTAGCCATTGATGCGCACGAG
TAAATACAGCCGAACAGTTTAAATGACACTAAGAAAGTAAGCTAGCTAGTGACGGTTTGCAGCACAGAAAAGCAGGTGCA
AGCAAATCGCCCGTGTCGCACGCGGTTAACCTCCCAAAGATGTAGCAACTTGTCGTGACATGTGAGCAGCATAGAGATGG
GAGAATTACTCCAATTCTTCCTTTTCAATTT-----CTCCCGGGCACCTGGTCCAACACCCAAGATGCATCGGCTCGTCT
CGTCTCGTGATCCAATGTGCACGCACCGCCACGA-TCGAACCATCCAATCCATGCCGAGTTACCGGGATGCTCCAAAACG
ATGGATTCGGTGACGTGCTCAGGCCGATCATACGGCGGCAATCTTGATCTCGATCCGGACCAACCAACGATCGCTGTTAC
GCCACAGTGCCACACCGACGCGACGCGACGCGACGCGCCATCTCTCCCTCCCTCCT-------------------CTTTC
TTTCTCTTCTCACCTACTGCGGCCGTCCCGCCATTGCCAATATAACCCGCCACCCCACCGCACCCCTCACACACGCCC-G
CAGCTCCACAAATCGCCACGGCTTTCTTGGTTCCTCCGTCCACAGCGAGCCA---------GCTCCGCTCCACCACCCGC
AGCCAAATGGCGAAGCTGCTGCCGGCCGGCCTCGCGTTCCTCCTGGCCCTCGCCGCGGCGGCGGCGCTGGCCCCGTCCCC
GGCCTCGGCCTTGAAGGGCGCCGGCGGGCTGGGACTCGGAGGCGCG---GCGGCCGTGGTGATGCGCCGGGGCGGGCGGA
CGTGCCGGGGCACGGTTGGCGAGTGCATGGAGTACTTCGGCGTGGACGGCGAGGGCGAGGGCGAGGTGGCGGCGATGGCT
GGCAAGCGGCGGGTGCTGCAGGACGGGTCCGGGTACATCGGCTACGACGCGCTGCGGCGGGACAACGTGCCGTGCTCGCA
GCGCGGCGCCTCCTACTACAACTGCCAGCCCGGCGCCGAGGCCAACCCCTACTCCCGCGGATGCAGCGCCATCACCCAGT
GCAGGGGCTGATTCTCTTCATTAAACCCTGCTTCATTCCTTCTTACTACC---TGCATGCCTCATCAATTAGTACTGCTA
TCTATCTGTA-----ATGTAACGTAATGTAATTACAAGAAGAAGATCAAACACTTCTTGACGATGCTTGATCAATCATCA
CCGGGTGGTGTGGTGTGATCAATCGTGCCGTACGTGTATCAGTGGAGGAGGCATGGTTAATTATTGTGTGATTTGTGCCT
ATTTGGGTGAAAGTAATTAAGCTTACGCATT------CATCTGGTTTCGGTTATGCCCAATAAATTTGTAGAGTCCTTTG
ATACGTACTTCCTTCGTCTCATATTAGTTGTCGTTCAAACCGATACTTTTTGCCTCGGTTTAACTATGGTGAATTGAATG
TGCTTCTCTGCCATGGCTTTTCTCCATTTTCTTGATTGAGCTGTAGGTGGCAGAGAAATTGCCTGTGAGC--GACATGCC
AATTCGCGGATGCTTGTCAGAAAAGAAACATCAATATCTCTCGAGTTGAGCTGTCTTTTCTGAATACATTTACCTTTCTC
CTTTCTGCTCCCTCCTTGTTTCTGGTTGGCCAATCTTTAATCAGTGCTCTGAATTAAAGGAGTATTTGTTTTCTGCGCCA
AAAGCAATCGGCTTTTGTTTGGTCTTATTAAGGGGAAAATGACTTG----TAGTGTTGTGGCAAAGATCGGTTCAAATGG
GTTGGTGAAAGTGGAGCTTCTTTGGCTA--CTTAAATTATTCCTTGTACACTTTGAAACGATTCATTTGTTAGGACCAAC
ACACAATGTCCAAGTGGTTGGGCTGTCACGCTTCATCCTATGTGCAGCACTGCGGCCAATAACTAGAAGGAAGGGATCCA
TCTCCTTGTGGAATCTGAAATTCGCAAGGATATCTAGAAGTGCACAAGCTCAAGTGAGGATATCTAGATATAC-------
-----------------------------------------------------------------------------
>SNPs
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----------SS-----------------------------------------SS-------------S-----------
----------------------------------------------------------S---------------SSSSSS
SSSS------------------------------------------------------------------SSSS----S-
S-------------------------S-------------------------------S---------------------
-------------------S----------S----------------------------------S--------------
----------------------------S---------------------------------------------------
-------------------------------SSSSS--------------------------S-SSSSSSS-SS---S--
-----------------------------S--------------------------------------------------
-------------------SS-----------------------------------------------------------
--------------------------------------------------SSSS---S----------------------
------------------------------------------------------------------------------S-
------------------------------S----------------------------------------------S--
---------------------S----------------------------------S--------------------S--
------------------------------S-----------------S-----------S-----S-------------
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------S--------------------------S----------------------------------------------
------------S-S-----------------------------------SSS---------------------S-----
----------SSSSS------S----------------------------------------------------------
----SS--S--------S----------------S-----------------S-----------S---------------
----------------------------S--SSSSSS-----------------------------------S-------
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----------------S----------------------------------------S--SSS-----------------
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--------S------------------S------S---------------------------------------------
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-----------------------------------S--------------------S----------------S------
------------S----------------------------S--------------------------------------
--S--------------------------------------------------S-------------------SSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_858
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--------------------------------------CATCTCTCCCTCGTCTCCCA----------------------
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>reverse_1902
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-------------------------------------------------------------TTTGTGAGCCTGACATGCC
A-------------------------------------------------------------------------------
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