>input_sequence_71908
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-------------------------------------------------------------------ATGATCTCTATAG
GCGGGTCCTCGTCCTCCTCCTCCTCCGCCGCCGCCGCGGCGGGGGTCCGGATGGGCGGGGCCAAGCGGCGGGGGAAACCG
GGCGGGGCCGCCGCGCCGGGGGCCGCGGGGCCGCCGCAGACCAGGTGGCGCAGCGGCACGCAGGAGCGGATCTACGGCCG
GCGCCTGCTGGACGCGCTGCGGGCCACGCGGTCGGGCGCCGCCTCGTCC---------CCGCAGCCGCGCGCCGTCAAGG
CGGCCGCCGACTCGGCGCTGGCGCTCACGGCGCGCGGGCAGTCGCGCTGGAGCCGCGCCATCCTGCTGGCCGGCGCCGCG
TCCTGCCGCCGCCGCGTGCTCGTCAAGGCCGGCGGGAAGATCCGCCGCCACCGCCGCCCGCAGGCGCGCGCCGCCGCCGC
GGCGTCCAAGGCCGCGGCCGCCGCGTCCGCCGGCGAGCCGCCGTTGCTCAAGGAGCGGAAGGTGAAGGACCGGCTCCGCG
TGCTGGGCCGGCTCGTCCCCGGGTGCCGGAAGCTGCAGGCCCCCGACCTGCTCGAGGAGACGGCCGACTACGTGGCCGCG
CTGGAGATGCAGGTCAAGGCCATGCGCGCGCTCGCCGACGCGCTCGCCGCGGCCCAGCTGTCGTCGCCTCCCCCGCCGGC
TGCCGGCGGCGACGACGAGGCCGAGATGGAGAGGTGA-------------------------------------------
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>chr3D_1_TraesCS3D01G172700
TCATCATGAAGTGGCCCATGGATCTTGCTGCACTTCTTTTACGGTTGCATATTTATTAAAATGTTTGAGCATTTATTGCA
GCAAAAAAACTCAGCACTCAGAAACATCATTGTTATTATGAATCGCCTACTGATTCCGACTTTATCGTTGACACCTAGCA
TGAACATGACGCGTGATTTTAACAAGGTGATCGAAGATCAATACTCCCACCATTGTTGTTACGTCGGCATATTAGTTTTG
TTTAGAGTTAAAATTTATAAACCATGCCCAAGTTTGCGTGACAAAATAATAACATATACACCATGAAATCAATATCATAG
ATTCATCATTGAATATATTTTCACATCATATAGATTTGCTATTGTAAATGTTCATATTGTTTCTAACTTGGTCAAACTTT
ATACAATTTGACCTCAGTCAAAGCTAAACAAAGGGAGTACCACGACACCGTTGCAACATCCGTGAAAATAGAAGGCGTAT
CTTCCACATTTCGCCAGATCAAAAGGCTTTAACTAGAACGTTGCGAAGCACTAATACCATGGCACATTCGCAGATAAAAG
GAGCATATAAAAAAACGGAAATAAGAAAGCGGGCACTCAATAACGACCGCTGCCTACCGT--------AGCGAGCGAGCA
----GCGCGGAGGCCACGCTACAGCGCCAA-----ATTCCACACCAAACAAAGGCGCGGCGACGAACCAGCGAACGAGCA
GCCAACACCCGCACCACCTCCCCTCACCTCACCTCACCGCACTCCTCCTTGGCTCCAATGTCTGATCCACTCGCTAATCA
CCTCCACCGCACCAGCAAATAAGTACGCCCACCCCCGCGACGGAAAGCTAATCTCTCCTCCC----CCTTTCTTCTTCAT
ACTCCCACCATCTCCACCAC---CACCACCACCATCTTCTCCT---TTCTCCCACCCACCTTTAAGCCGCCCCATCCCCC
GCTGCGCTGAGTCACTTCCTCACGCCACCCGCCGATTGATTGCTCGATCGAGGTGCGGTGCGCGGCCATGATCTCTATAG
GCGGGTCCTCGTCCTCCTCCTCCTCCGCCGCCGCCGCGGCGGGGGTCCGGATGGGCGGGGCCAAGCGGCGGGGGAAACCG
GGCGGGGCCGCCGCGCCGGGGGCCGCGGGGCCGCCGCAGACCAGGTGGCGCAGCGGCACGCAGGAGCGGATCTACGGCCG
GCGCCTGCTGGACGCGCTGCGGGCCACGCGGTCGGGCGCCGCCTCGTCC---------CCGCAGCCGCGCGCCGTCAAGG
CGGCCGCCGACTCGGCGCTGGCGCTCACGGCGCGCGGGCAGTCGCGCTGGAGCCGCGCCATCCTGCTGGCCGGCGCCGCG
TCCTGCCGCCGCCGCGTGCTCGTCAAGGCCGGCGGGAAGATCCGCCGCCACCGCCGCCCGCAGGCGCGCGCCGCCGCCGC
GGCGTCCAAGGCCGCGGCCGCCGCGTCCGCCGGCGAGCCGCCGTTGCTCAAGGAGCGGAAGGTGAAGGACCGGCTCCGCG
TGCTGGGCCGGCTCGTCCCCGGGTGCCGGAAGCTGCAGGCCCCCGACCTGCTCGAGGAGACGGCCGACTACGTGGCCGCG
CTGGAGATGCAGGTCAAGGCCATGCGCGCGCTCGCCGACGCGCTCGCCGCGGCCCAGCTGTCGTCGCCTCCCCCGCCGGC
TGCCGGCGGCGACGACGAGGCCGAGATGGAGAGGTGAGGGTCCGAGCCTCGCCTC-----CGAGGGGGAGATTGATGATG
ACATGATGGCGTTGGGCTCGGGAAAATAAGGGCGATTAATTACTGGATGGATGGA----TGGATTGTTACCGCGAGAGGG
GGTCCTGGGATTCCAGGAGGGTATTGTGATTCCGACGATGATGATTGCTGCTGCTGGTGCT---GCCGCTGATTTGTAAA
TTCTTGATGCTACTACTTGTATAAGTAATGCTGCTCTGCTCCTCTC--------TTGTGTTCTTGAAATGTTCTTCC-CC
TTCTTAAACAAGAAGGGGG-ATTCCTGTGCCTGCCTGTCCCCTGCGGATTGGATTGGATT-----------ATGCTTTTG
TTTGGCTGTGCCACGGTGAATTAGGAGTTTTGTTTCTTGA--AAGTGCAATGCTAACCGTTTGATTTCATGGCTTCCTCG
AGCTGCATTCGATAGGATTCCTCGAGGCGACAATTTCTGCTCGCAAGGAAGAACAGAAATCCGAATTCGATCAGAGGGAC
GGGGACAGGAGAATTTGCGAGTGGCTCGGCTCGTAAACCATCGATGTCGTCAACCACCGCGCTTAAC------ATAACGC
TAACAAAGATCAGACAAGGCGTGAGCAGAAAGATTCCGCTGGCTGGTTCTTTCTGCTCTGGGCGCAGTCCCGGCCTGGCG
CCGGTTTCTCTGATCCGATGGGCGAGTAC-TATTATTTGCTGCCAGAAATGTGTTACTGCTGCGC----------AGTAG
TGCTGCA-----GCAGTGCACTGGCCTTCTGCGGCAAATTT-CTGGCCTGCATTTATGCACGTGAAAATGTTCCCCTGCA
GAGAGCTCGAGGGGGACAGCGATCTGAGTCGTCGTCATCCTCTCTGTTTTCCTCCTTTTCATCCTTTTAATGGAGACTGC
GAAATGTTTCTGACATGTGGCGGATGGGAAATTTGGTTGGGTGTTTCTTCGCAGAAGTA-TTCAGAAAATTCAGAAACTT
TGGCTAAGCTGAAACTCAACGAACTCCTTATCAGTTGCTTGCAATAGATATTTCAG
>chr3A_469
TAAAAGA-------------------------------------------------------------------------
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---------------------------------------------------------------------------CGTAT
CTTCCACATTTCGCCAGATCAAAAGGCTTTAACTAGAACGTTGCGAAGCACTAATACCATGGCACATTCGCAGAAAAAAG
GAGTATAAACAAAAG-GGAAATAAGAAAGCGCGCACTCAATAACGACCCCTGCCTACCATAGCGATCGAGCGAGCGAGCA
----GCGCGGAGGCCACGCTACAGCGCCAA-----ATTCCACACCAAACAAAGGCGCGGCGACGAAC--------GAGCA
GCCAACACCCGCACCACCTCCCCTCACCGCACCGCACT--ACTCCTCCTTGGCTCCAATGTCTAATCCACTCGCTAATCA
CCTCCGCCGCACCACCAAATAAGTACGCCCACCCCCGCGACGGAAAGCTAATCTCTCCTCCCTCCCCCTTTCTTCTTCAT
ACTCCCACCATCTCCACCAC---CACCACCACCATCCT---CT---TTCTCCCACCCACCTTTAAGCCGCCCCATCCCCC
GCTGCGCTGAGTCACTTCCTCACGCCACCCGCCGACTGATTGCTCGATCGAGGTGCGGTGCGCGGCCATGATCTCTATAG
GCGGGTCCTCCTCGTCCTCCTCCTCC---GCCGCCGCAGCGGGGGTCCGGATGGGCGGGGCCAAGCGGCGGGGGAAACCG
GGCGGGGCCGCCGCGCCGGGGGCCGCGGGCCCGCCGCAGACCAGGTGGCGGAGCGGCACGCAGGAGCGGATCTACGGCCG
GCGCCTGCTGGACGCGCTCCGGGCCACGCGGTCGGGCGCCGCCTCGTCC---------CCGCAGCCGCGCGCCGTCAAGG
CCGCCGCCGACTCGGCGCTGGCGCTCACGGCGCGCGGGCAGTCGCGCTGGAGCCGCGCCATCCTGCTGGCCGGCGCCGCG
TCCTGCCGCCGCCGCGTGCTCGTCAAGGCCGGCGGGAAGATCCGCCGCCACCGCCGCCCGCAGGCGCGCGCCGCCGCCGC
GGCGTCCAAGGCCGCGGCCGCCGCTTCCGCCAGCGAACCGCCGTTGCTCAAGGAGAAGAAGGTGAAGGACCGGCTCCGCG
TGCTGGGCCGGCTCGTCCCCGGGTGCCGGAAGCTGCAGGCCCCCGACCTGCTCGAGGAGACGGCCGACTACGTGGCCGCG
CTGGAGATGCAGGTCAAGGCCATGCGCGCGCTCGCCGACGCGCTCGCGGCGGCCCAGCTGTCCTCGCCTCCCCCGCCGGC
CGCCGCCGCCGCCGACGAGGCCGAGATGGAGAGGTGAGGGTCTGAGCCTCGCCTCGCCTCCGAGAGGGAGATTGATGACA
CGAT----------GGCTCGGGGAAATAAGG-CGATTGATTACTGGATGGATGGACGGATGGATTGTTACCGCGAGAGGG
GGTCCTGGGATTCCAGGAGGGTATTGTGATTCCGATGATGATGATTGCTGCTGCTGCTGCT---GCTGCTGATTTGTAAA
TTCTTGATGCTACTACTTGTATAAGTAATGCTGCTCTGCTCCTCTC--------CTGTGTTCTTGAAATGTTCTTCCTCC
TCCTGAAACAAGACGGGGGGATTCCTGTGCCTGTCTGTCTCCTGCGGATTGGATTGGATTGGAATTGGATTATGCTTTTG
TTTGGCTGTGCCACGGTGAATTAGGAGTTTTGTTTCTTGTATAAGTGCAATGCTAACCGTCTGATTTCATGGCTTCCTCG
AGCTGCATTCGATGGGATTCCTCGAGGCGGCAATTTCTGCTCGCGAGGGAGAACAGAAATCCGAATTCGATCGGATGGAC
AGAGACAAGAGAATTTGCAAGTGGCTCGGCTCGTAAACCATCGATGTCGTCAACCACCGCGCTTAAACTAACTATAACGC
TAACAAAGATCAGACAAGGCGTGAGCATAAAGATTCCGCTGGCTGGTTCTTTCTGCTCTGGGCGCAGTCCCGGCCTGACG
CCGGTTTCTCTGATCCGATGGGCGGGCGGGTATTATTTGCTGCCAGAAATGTGTTACGTACTGCTGCGCAGTACTACTAG
TGCTGCA-----GCACTG----GGCCTTCTGCGGCAAATTTTCTGGGCTGCATTTATGCACGTGAAAATGTTCCCCTGCA
GAGAGCTCGAGGGGGACAGCGATCTGAGTCGTCGTCATCCTCTCTGTTCTCCTTCTTTTCACTCTTTCAATGAAGATCGC
GAAATGTTTTTGACATGTGGAGGATGGGGAATTTGGTTGG----------------------------------------
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>chr3B_566
TATA----------------------------------------------------------------------------
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------AAAGAAAGG-GGAAATAAGAAAGCGCGCACTCAATAACGACCGCTGCCTACCGTAGCGAGCGAGCGAGCGAGCG
AGCCGCGCGGTGGCCACGTCACAGCTCCAAATTCCATTCCACACCAAACAAAGGCGCGGCGACGAAC--------GAGCA
GCCAACACCCGCACCACCTCACCTCACCTCACCGCACT--CCTCCTCCTTGGCTCCAATGTCTAATCCACTCGCTAATCA
CCTCCACCGCACCAGCAAATAAGTATGCCCACCCCCGCGACGGAAAGCTAATCTCT----CCTCCCCCTTTCTTCTTCAT
ACTCCCACCATCTCCACCACCACCACCACCACCATCTT---CTCCTTTCTCCCACCCACCTTTAAGCCGCCCCATCCCCC
GCTGCGCTGACTCACTTCCTCACGCCACCCGCCGATTGATTGCTCGATCGAGC-----TGCGCGGCCATGATCTCTATAG
GCGGGTCCTCCTCCTCGTCGTCGT------CCGCCGCGGCGGGGGTCAGGATGGGCGGGGCCAAGCGGCGGGGGAAACCG
GGCGGGGCCGCCGCGCCGGGGGCCGCGGGGACGCCGCAGACCAGGTGGCGAAGCGGCACGCAGGAGCGGATCTACGGCCG
GCGCCTGCTGGACGCGCTGCGGGCCACGCGGTCGGGCGCCGCCTCGTCCGCGCAGCCGCCGCAGCCGCGCGCCGTCAAGG
CCGCCGCCGACTCGGCGCTGGCGCTCACGGCGCGCGGGCAGTCCCGCTGGAGCCGCGCCATCCTGCTGGCCGGCGCCGCG
TCCTGCCGACGCCGCGTGCTCGTCAAGGCCGGTGGCAAGATCCGACGCCACCGCCGCCCGCAGGCGCGCGCGGCCGCCGC
GGCGTCCAAGGCCGCGGCCGCGGCGTCCGCCGGCGAGCCGCCGTTGCTGAAGGAGCGGAAGGTGAAGGACCGGCTCCGCG
TGCTGGGCCGGCTCGTCCCGGGGTGCCGGAAGCTGCAGGCGCCCGACCTGCTCGAGGAGACGGCCGACTACGTGGCCGCG
CTGGAGATGCAGGTCAAGGCCATGCGCGCGCTCGCCGATGCGCTCGCGGCGGCCCAGCTATCGTCGCCTCCCCCGCCGGC
CGCCGCCGGCGACGACGAGGCCGAGATGGAGAGGTGAGGGTCTGAGCCTCGCCTCTGAT----GGGGGAGATTGATGATG
ACATGATGGCGTTGGGCTCGGGGAAATAAGGGCGATTAATTACTGGATGGATGGA----TGGATTGTTACCGCGAGAGTG
GGTTCTGGGATTCCAGGAGGGTATTGTGATTCCGATGATGATGATTGCTGCTGCTGCTGCCGCCGCTGCTGATTTGTAAA
TTCTTGATGCTACTACTTGTATAAGTAATGCTGCTCTGCTCCTCTCTTCTTGTCTTGTGTTCTTGAAATGTTCTTCCTCC
TTCTGAAGCAAGACGGGGGGATTCCTG----TGCCTGTCTCCTGCGGATTGGATTGGATT-----------ATGCTTTTG
TTTGGCTGTGCCACGGTGAATTAGGAGTTTTGTTTCTTGTC--AGTGCAATGCTAACCGTTTGATTTCATGGCTTCCTCG
AGCTGCATTCGATAGGATTCCCCGAGGCGACAGTTTCTGCTCGCGAGGAAGAACAGAAATCCGAATTCGATCG-------
-GAGACAAGAGAATTTGCTAGTGGC------CGTAAACCATCGATGTCGTCAACCACCACGCTTAAAC------TAACGC
TAACAAAGATCAGACAAGGCGTGAGCAGAAAGATTCCGCTGGCTGGTTCTTTCTGCTCTGGGCGCAGTCCCGGCCTGACG
CCGGTTTCTCTGATCCGATGGGCGGGCGAGTATTATTTGCTGCCAGAAATGTGTTACTGCTGCGC----------AGTAG
TGCTGCAGCACTGCACTG----GGCCTTCTGCGGCAAATTT-CTGGCCTGCATTTATGCACGTGAAAATGTTCCCCTGCA
GAGAGCTCGAGGGGGACAGCGATCTGAGTCGTCGTCATCTCCTCTGTTTTCCTTGTTTCCATTCTTTTAATGGAGACTGC
GAAATGTTTTGGACATGTGGAGGATGGGGAATTTGGTTGGGTGTTTCTTCACACAAGTATTTCAGAAAATTGAGAAACTT
TGGCTAAGCTGAAACTC---------------------------------------
>SNPs
-S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----
--------------------------------------------------------------------------S-----
---S---S-S----SS---------------S------------------------------------------------
-------------------------------------------------------------------SSSSSSSS-----
---------------------------------S---SSS-----------------------S----------------
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--------------------------------------SSS---------------------------------------
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----------S---------------SSS---------------------------------------------------
--------------------------------------------------S-----------------------------
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-S------------------------------------------------------------------------------
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-----------------------------------------------S--------------------------------
S----S------------------------------------S-------------------------------------
----------------------S---------------------------------------------------------
-----------------------------------S--------------------S---------S-------------
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----S--------S-------------------------S----------------------------------------
---------------------------------------S----------------------------------------
--------------------------------------------S---------------------------S--S----
S-S----S----------S-----------------------------------------------S-------------
-----------------------------------------------------------------------------S--
------------------------S-SSS---------------------------------------------------
---------------S--SSSS----------------------------------------------------------
-----------------------------------------------------S--------S-----------------
---------S----------S-------S---------------------S--S-----------------S--------
-----------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_285
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-------------------------GCCCAAGTTTGCGTGACAAA-----------------------------------
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>reverse_2241
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GGGGACAGGAGAATTTGCGA------------------------------------------------------------
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