>input_sequence_84202
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--------------------------------------------------------------------ATGTCCGTGGCC
GTGGCGGCTCTCGCGCCCGAGCTCGCCTACGTCTGGGGCGTCGCGCCGGGAGCGCCGCTCACCAGGGCATACCCCGATGG
CAACTTCGCGGGCGGCAGCATTGGGCTGCCGCTCGACGGTCCGCCGTGGGACGCGGTCTGCGTGCCCGCCGGCCTCTTCG
GCCGGACCGTGCCCGACGTGGTCGTCCCGCTTGTTTTCGCCGTCGTGGTTGTCGCCGGCGCCACCGCCTTCACCGCCGCC
GTCGGCGTGTGGGAGGACGATGAGGACGACTTCGAGATCACCGAGGTAGGACAGGTGTAG--------------------
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>chr3D_1_TraesCS3D01G078100
CGTTAGTCGCCGCCGAATGCGCCACGTGGCAATACTTTGCTGAGTGTGACCAAATGGCCCTCAGCAAATAGTGCCTTTGC
CGAGTGTGTCATGTTTGTCGAGCAATACTGTCGGCAGCACCATGTGTTTGCCGATTCACTTACTTTGCCGAGTGCAGCTC
TCGGCGTTCTTTACTTTGCCGAGTGCCCGTGTTTTGGCTCTCGGCGAAGACGCCGACACCCGGCGTATATGAAAATTCCA
GTAGTGATCACGCGCGATCCACAGCTACCGTCACCGCCCATCGCATAGCGGAGGATCCCACCGGAGCACCTCGCCAGGCA
TGGGTTCGCCAGCTGCCGCCGCACAGCCTAGACGCCGCTGTGGCTGCCGCGCGAGGGCACCCCGCTCGAGGTGCCCCAGC
CGCCTCATGGGAGATCCGGCGTAACCCTCCTGCCCTAGCCCTTTTGGCGTCGGGCGCCGCTACCACCGCAGCCAGTGCCG
GCGGCAGCGGCGGCAAGGATCTGCCTCACGGGAGGGCTGGCGTCGCCCTGGGTGGCGGCGCGAGGGGGTCGGGAGCGAAA
GAGTCGGGGGAGTCGGGGACGTGCGGAAACGGGGCATGCAAAAGCAAAAGCATACATAGGCAGATTGGCAGATTGTAGCT
CTTGTGCCTGCATTACAGTTCCTCTGTTTGG--------AAACTGGAAACTGCAGAGGAGCAGCT--------GAGCGGA
GCAGATCGAACTTGACAATTGGAGAGTCCCAACTGCTCTGCTCCCGCCAAATCCCCTTCACCCGAAAC--ACACAAACCC
CAGACAATTGCAGCCTTGGAGAGCGCCACCTGCTCCGCTCTGCCGTGTATATATAATCTCGCTC-GCGCGGCCCTCCCCA
GGACGAAGAAA-CCTCTGTGACAGACTACAGATCGAGCACCAACATTCCAGC--------AATGGCGTCCCACTTCCCTT
CGCTCGCCGGCCTCCTCGCCCCACGCCCGCTGCTCCTCTACGCGGCCACGTGATCCGCCGTCGCCGCCATGTCCGTGGCC
GTGGCGGCTCTCGCGCCCGAGCTCGCCTACGTCTGGGGCGTCGCGCCGGGAGCGCCGCTCACCAGGGCATACCCCGATGG
CAACTTCGCGGGCGGCAGCATTGGGCTGCCGCTCGACGGTCCGCCGTGGGACGCGGTCTGCGTGCCCGCCGGCCTCTTCG
GCCGGACCGTGCCCGACGTGGTCGTCCCGCTTGTTTTCGCCGTCGTGGTTGTCGCCGGCGCCACCGCCTTCACCGCCGCC
GTCGGCGTGTGGGAGGACGATGAGGACGACTTCGAGATCACCGAGGTAGGACAGGTGTAGTACACT-------------A
TGACGCTAGATCACTC-------GAGATGTA----------------GAAATTTGTCAGGGGACAACAAAGCAGAGAC-A
AGTCTCTCTGAACTTTCCGGCAGCTG------TCTCTATA-TATGTGACACTGAAAAAGATTCAGGCATCAAAATTCCAT
GGAAGCATGATGATTATAGAGCTTCAATCA------------TGCTCGGTCGAGCTAATCAAGGATGCATATGA------
----------------------------GGGGCTGTACGTGGCTGAGTTCTACTTACTATTTTTAGTTAATATG------
----------------------------------------------------------------------------CCCG
TACGTTGCTACGGGTGACAATGCAGTTAAGCGAATCGGATAAACGATGAAGTTACATGGATGACTTCTTGAAGATGGAAT
GCGTGGATAGTATCATGAGGTGACACTAAAACCTATAAAAATTTATTCAACCATTGATAGTGTAGGCGCATCAATCATTC
TTTTTTCAGTTTGATATGTTGATATCCAAAAACAGAATTTTAGTTTAAGGATTGTTCAGATCTTCTTCAACTTTGTGCTT
CACCAACTACACGGATCGAAGACCTCTCATAGTATAATTTGGTGAAGTTGCCGAAGCTAAATCGCGAAGCTTAATATGTT
TACGACTAAAACATATTGACTAGTAATGAATCAACTATGACGATAGATCACTCAAAATGTACATACTGACTAAAATCGTG
AAACTAACCTTTGAGATTTCTGATTGTGCTGCTTCA--------------------------------------------
-----CCTTTTTCTTTTGCGGGTA--------------------------------------------------------
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-----------------------------------------------------------------------------ATT
GTGCTGCTTCACCTTTACTAGTAATG------------------------------------------------------
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---------------------------------------------------AATCAGCAGCTGGAAAATTACAAATCTTT
ACTCGTGGTTTACAGAAATCTCCATCCTTTTTTCGCGCATAAAACATAG------TATGCATATTACTT-GTTTTTTACT
CGACAACAAAATGATACAAAGATCACTTTGATTTTAAGTATACACAAAATATATTTGGTCGTTTCCACATCGGACATGAC
CACATGGTAATTCAAAGAAGAAATAAGAAAAACAG-AAAAAAGAAGAGCACGTCTC-TTTTTTACAGAAGAAATAATTAT
ACGAGTCA
>chr3D_590
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-----------------------------CGGGGCATGCAAAAGCAAAAACATACATAGGCAGATTGGCAGATTGTAGCT
CTTGTGCCTGCATTGCAGTTCCTCTGTTTGACTGTTTGGAAGCTGGAAACTGCAGAGGAGCAGCT--------GAGCGGA
GTAGATCGAACTTGACAATTGCAGAGTGCCACCTGCTCTGCTCCCGCCAAATCCCCTTCACCCAAAAC--ACACAAACCC
CAGACAATTGCAG--------GGTGCTACCTGCTCCGCTCTGCTGTGTATATAC-ATCTCGCTC-ACGCGGCCATCCCCA
GGACGAAGAAAACCTCTGTGAAAGACT--AGAGCA------------CCAAC--------AATGGCGTCCCACTTCCCCT
CGCTCGCCGGCCTCCTCGCCCCACGCCCGCTGCTCCTCTACGCGGCCACGTGGTCCGCCGTCGCCGCCATGTCCGTGGCC
GTGGCGGCTCTCGCGCCCGAGCTCGCCTACGTCTGGGGCGTCGCGCCGGGAGCGCCGCTCACCAGGGCATGCCCCGATGG
CAACTTCGCTGGCGGCAGCATCGGGCTGCCGCTCGACGGTCCGCCGTGGGACGCCGTCTGCGTGCCCGCTGGCCTCTTCG
GCCGGACCGTGCCGGACGTGGTCGTCCCGCTTGTTTTCGCCGTCGTGGTCGTCGCCGGCGCCACCGCCTTCACCGCCGCC
GTCGGCGTGTGGGAGGACGATGAAGACGACATCGAGATCACCGAGGTAGGACAGGTGTAGTAGACTAGC----------A
TGACGCTAGATCACTCGAGAATCGAGATGTACTACTCTCCAGTCTCTGAAATTTGTCAGCGG-CCACAAAGCAGAGAC-A
AGTCTTTCTGAACTTTCCGGCAATTGTCTGTCTCTGTATA-TATGTGACACGGAAGAAGTTTCAGGCAACAAAAATCTCT
CAAAGCATGATGATTATAGAGCTTCAATCA------------TGCTCGGTCGAGCTAATCAAGGATGCATATGA------
----------------------------GGGGTTGTACGTGGCTGACTTCTACTTACTTTTTTTAGTTGGCTGTACGTG-
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-------CCTTTGAGATTTCTGATTGTGCTGCTTCA--------------------------------------------
-----CCTTTTTTTCTTGCGCGTA--------------------------------------------------------
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-----------------------------------------------------------------------------ATT
GTGTTGCTTCACCTTGACTAGTAATG------------------------------------------------------
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---------------------------------------------------AATCAGCAGCTGGAAA-TTACAAATCTTG
ACTCGTGGTTTACAGAAATCTCCATCTTTTTTTCACGCATAAAACATAG------TACGCATGGTAGTACTTTTTTACCT
CGATAACAAAATGATACAAATATCACTTGGATTATATGTATACACAAAATGTATTTGGTTATTTCCACAGCGGGCATGAC
CACATGGTAATTCAAAGAACAAATAAGAAATAAAG-TAAAAAGAAGAGCACGTCTC-TTTTTTACAGAAGAAATAATTAT
ACGAGTCA
>chr3B_592
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-------------------------------GGGCATGCAAAAGCAAGAGCATCCATAGGCAGAATGTAATCC-------
CTTGTGCATGCATTCCACTTCCTCTATTCGTAAGT----AAACAGGAGACTCCAGAGGAGCAGCTGAAGTGGGGAGCGGA
GCAGATCGAACTTGACAATTGCAGAGTGCCACCTGCTCTGCTCCCGCCAAATCCCCTTCACCCAAAACGCACACAAAGCC
CAGACAATTGCAG--------AGCGCCACCTGCTCCGCTCTCCCATGTATATAC-ATCCCGCTCTGCGCGGCCCTCCCCA
GGACGAAGAAAACCTCTGTGAAAGACTACAGAGTA------------CCAAC--------AATGGCGTCCCACTTCCCCT
CGCTCGCCGGCCTCCTCGCCCCACGCCCGCTGCTCCTCTACGCGGCCACGTGGTCCGCCGTCGCCGCCATGTCCGTGGCA
GTGGCGGCTCTCGCGCCCGAGCTCGCCTACGTCTGGGGCGTCGCGCCGGGAGCGCCGCTCACCAAGGCATGCCCCGATGG
CAGCTTCGCGGGCGGCAGCATCGGGCTGCCGCTCGATGGGCCGCCGTGGGACGCCGTCTGCGTGCCCGCCGGTCTCTTCG
GCCGGACCGTGCCCGACGTGGTCGTCCCGCTTGTTTTCGCCGTCGTGGTCGTCGCCGGCGCCACCGCCTTCACCGCCGCC
GTCGGCGTGTGGGAGGACGATGAAGACGACATCGAGATCACCGAGGTGGGACAGGTGTAGTAGACTAGTAGTACTAGTAA
TGACGCTAGACCACTC-------GAGATGTACTGCTCTCCAGTTTCAGAAATTTGTCAGCGG-CAACAAAGCAGAGAC-A
AGTCTTTCTGAACTTTCCGTCAACTGTCTCTGTATATACAGTATGTGACACTGAAGAAGTTTCAGGCAACAAAAATCTCT
GAAAGCATGATGATTATAGAGCTTCAATCA------------TGCTCGGTCGAGCTAATCAAGTATGCATATGA------
----------------------------GGG--------------------------------------GCTGTACGTG-
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-------CCTTTGAGATTTCTGATTATGCTGCTTCA--------------------------------------------
-----CGTTTTTTTTTTGCGGGTA--------------------------------------------------------
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-----------------------------------------------------------------------------ATT
GTGCTGCTTCACCTTGACTAGTAATG------------------------------------------------------
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---------------------------------------------------AATCAGCAGCTGCAAA-TTACAAATCTTG
ACTCGTGATTTACATAAATCTCCATCTTTTTTTCGCGCATAAAACATAGGAGTAGTACGCACAGTACTT-TTTTTTTACT
CGACAACAAAATGATACGAAGATCACTTGGATTATATGTATACACAAAATATATTTGGTCGTTTCCGCAGCGGACATGAC
CACATGGTAATTCAAAGAAGAAATAAGAAAAACAG-AAAAAAGAAGAGCACGTCTC-TTTTTTATAGAATAAATAATTAT
ACGAGTCA
>chr3A_593
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--------------------------------GGCATGCAAAAGCAAGAGCATCCATAGGCAGAATGTAATC--------
CTTGTGCATGCATTCCAGTTCCTCCATCTGTAAACAT--------GAAACTCCATAGGAGCAGCTGAAGTGGGGAGCGGA
GTAGATATCGAACT-------------------TGCTCTGCTCCCGCCAAATCCCCTTCACCCAAAAC--ACACAAACCC
CAGACAATTGGAG--------AGTGCCACCTGCTCCGCTCTGCTATGTGTATAC-ATCTCGCTC-GCGCGGCCCTCCCCA
CGACGAAG-AAACCTCTGTGACAGACTACAGAGTA------------CCAACGTTCCAGCAATGGCGTCCAACTTCCCCT
CACTCGCCGGCCTCCTCGCCCCACGCCCGCTGCTCCTCTACGCGGCCACGTGGTCCGCCGTCGCCGCCATGTCCGTGGCC
GTGGCGGCTCTCGCGCCCGAGCTCGCCTACGTCTGGGGCGTCGCGCCGGGAGCGCCGCTCACCAGGGCATGCCCCGATGG
CAGCTTCGCTGGCGGCAGCATCGGGCTGCCGCTCGACGGCCCGCCGTGGGACGCCGTCTGCGTGCCCGCCGGCCTCTTCG
GCCGGACCGTGCCCGACGTGGTCGTCCCGCTTGTTTTCGCCGTCGTGGTTGTCGCCGGCGCCACCGCCTTCACCGCCGCC
GTCGGCGTGTGGGAGGACGATGAGGACGACATCGAGATCACCGAGGTAGGACAGGTGTAGTAGACTAGTAATCTAGT--A
TGACGCTAGATCACTC-------GAGATGTACTACTCTCCAGTTTCTGAAATTTGTCAGCGG-CAACAAAGCAGAGACGA
AGTCTTTCTGAACTTTCCGGCAACTGTCTCTGTAGCGA-A-TATGTGACACTGAAGAAGTTTCAGGCAACAAAAATCTCT
GAAAGCATGATGATTATAGAGCTTCAATCAATAATTCAATCATGCTTGATCCAGCTAATCA-GGATGCATACGAGGGAGA
TACGGCGACTCTGGTCAAATCGGTGTAGGGGTCTGTACGTGGCTTGGTTTTACTTTTCTTTTTTTGAGGGAATGCCGTTC
GGCTCACTTTCTTTCATCACATGACTGTCACATCGTTGACAAAGTCTGGAAGTAAAATAGTAGGGGGATCATCGTCCCAG
TACATTGCTACTTTTGATTCATACGTTAACTTAGCTAAATTGTGTGCCGCTCTGTTTGCATTCAGAGGACAATGACCAAA
AGAGACCTGACCAATTCTGAA-----------------------------------------------------------
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-------------AGATTTCTGAAAAATATCCACTAAAATAGCAGTATACGGTGTCCATATTTCAACAACTCCAGTGATC
TCCATCCTTTTTTTCTGATCGTGCACTAATAATGAATCAGCAACTGGAAATTACAAATCTTGACTTGTGGTTTACAGAAA
TCTGCATCCTTTTTTCCGGGCATAAAACATACTTTCTCTATTCATTTTTATAAAAGATCCGCCGGCTCACGAGTCGTTGG
ATTAGACCTAATCTAGCGTTGAACATTTTCCTCTACTTTGCAACAGACACCTTATTGCAGAAACATTTGTAACAGAGATT
GTGCTGCGGATTTTTTTACAACATAGATTATGTTGCGAGTTTGTTTTGCCACAAAGTTCTTGTTGCAGAACTTTTTTGCA
ACATAGATCTTGTTGCAGATTCTTTTCTAAGAGAGATGACGTTGCAAAAGCTTGTCTAAGTTATCGCTGTCGTGGTTTGC
AACACTGCTGCTGTTGCAAGATAAGATAAGGGGCACGTGCTTGGTAGGCAAAATCAGCAGCTGGAAA-TTACAAATCTTG
ACTCGTGGTTTACAGAAATCTCAATCTTTTTTTCACGCATAAAACATAG------TACGCATAGTACTT-TTTG-TTACT
CGACAACAAAATGATACAAAGATCACTTGGATTATAGGTATACACAAAATATATTTGGTCGTTTCCGCAGCGGAGATGAC
CACATGGTAATTCAAAGAAGAAATAAGAAAAACAGAAAAAAAAAAGAGCACATCTCTTTTTTTACAGAAGAAATAATTGT
ACAAGTCA
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------------------------------------------------
--------------S---------------S-------------------------------------------------
---------------------S-----S---S-------------------------------S----------------
-------------SSSSSSSS--------------------------------SS-------------------------
--------------------------------S-SSSSSSSSSSSSS---S---------------------------S-
----------------------------------------------------S---------------------------
----------------------------------------------------------------------S---------
---------------------S--------------------------------S-------------------------
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------------------------------S-------------------------------S-----------------
-----------------------------------------------------------S--S-----------------
-----S----------------S--------------------------------S---S--------S-----S--SS-
-S------------------------------------------------------------------------------
----------------------------------------------------------S---------SSS---------
------------------------------------------------------------------------------S-
---S-------SSS---SSSSSSS-----SSS-SSSSS--SSSSSSSSSSSS-SSS--S--SSSSSSSSS--SSSSS--S
SSSSSSS-SSSSSSS-SS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSS-------------------------------------------------------------------------
------------S-------------------------------------------------------------------
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-------------------------------------------------------------------S-----------S
--------------------------S------------------------------S-----S------S---------
----------------------------S----S--S--------------------------------S----------
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>forward_233
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-----------------------------------------------------CGACACCCGGCGTATATGAA-------
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>reverse_2050
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-------------------------------------------------GCCGAAGCTAAATCGCGAAG-----------
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