>input_sequence_62983
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----ATGCGGCCGGCCGTGACGCACGACGACCTGTCCCTCCGCAAGGCGCAGGAGCGCCGGGCGGGGCGCTCCGGCAGCC
AGATCGCCGTCGCCCTCGTCGCGCTCTCCGTGCTCTGCGGCCTCGTCAGCTTCATCCTCTGCCTCGCCGCCGAGGGCTCG
CGCTCCGAGGTACGCGCGCACCCCGACCAACCAACACGCGGCTTTGC----------TAGCTCGTG--------------
---CTGATGCTGCCTGGGCTTGGCACTCT---GCAGGTGTCCAACTACCTGATGACCGTGGCCGGGAGCGAGGCGCAGGT
GGAGCTGTGCTTCTACAACGGCAGCGGCCGCTCGGCGCTCGCCTTCTCCATCGGCGCCTTCCTGCTGCTGGCCGTCGCCA
TGTTCGCCGTGCACGGCTACATGCTGCTCGCCGTCGCTTCGCCGGACTCCGCCGCCGCTGGCCTCGCCGTCGCCGAGGAC
CACCCCCGCGTGTCCTCCGCCACCAACACCCTCACCTGGCAAACCTGCTGCCTCTTCTTCGTCACGTGGTACCAACATTA
CTTCAAG-----------------CATGCATTGGGCAAGAT---TGATGGTGTGGATTCATAATAAACACTGA----TCG
ATGGGTGCAGGATTTGCTTCGGGCTCGCGGAGGTGCTGCTCATGATCGGGATCGGGGTGGAGTCCGGCCACGTCAGCGAC
TGGCGGAGGCCGCGGCAGGTGTGCCACCGGGTGCGCCCGGGGATGTTCGCGGCGGCGGGGATACTGGGGCTCATCACCGT
CGTCGTTGGCTTCGTCGTCTACGTGACCGCGGTGCACACGCAGAAGCTGCTGAGGCAGCACGGCGGCGGCCACTACCCGC
CGCACCCCGGCAGCGCCCCGTACCCCAGCG------------------TCCAGCAGCACCACCTGCAGCCGCCCGTGTCG
TACCCACCACACCCGGCCCCGCACCCACACCCTCATCCGGCGCCGAATGCGCCGGAGATTACGGCGGCCGCGTGCCAGGT
GCAGTCCAGCAACGCGTGGTGCATCACCAAGGACAAGGAGTACACCGATGTTTGA-------------------------
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>chr3D_1_TraesCS3D01G178600
AGTGGCCCAAGATGAGGAGCAAGAACACAATGTTTGTGGAATTGAGCCAATAGAAGTTTGTCTCATTAATGCTTCTGAAA
AGATTGATGACTTGCATGAGACCTAATGGTTTCCCAACATCTATTTGAAAAATAATCCGGTGAATCCATCCGACGCGGGG
GGATGTCGCTAGGCATTTGATTGATAGCGTCACTTACTTCCTCCTTGGAGAAATGATCGGCATGCCCAAGTACCAATGGT
CGTCCTATATCCATATTATTAAGGTAAACAGGAGTCGGGATAATGTTCAAATGCACTCCACTATTCAGCTCCACACAAGT
GCATGTCGGT------AGGAGTGCAAGCTGATTCATCACCAATGTAATGGGGTACCCATGGGCCATGGCACTGCCGACCT
TGCATCTGTTTTCTTCAAAA----AAA----AAAAAATCCTAGCCCTTTCTCTTACCTATAGGTTGCCTCGTTGGCGCTA
CAAAGCGCAGATGCTCCGCGTCGCTTTCCCGAAAAGGCACCGCGGCGAATTACCCACCCCAGCGGAAAGAAGAAGGTGCC
CTCCTCTCCGCCTCATCACT----------GGTGAAAAAGAAGGAAAGGCGAAACGAATCGGAATGTCTCCCACCGCGGC
ACGGCGCAAGAAACCCCGATCCCC-----TCACCCACGCTCCCATCCCATGCATCATCGCCATGCCAT-CCATGGATTCC
TCCCGTGCGGCGTCTCCCAACCCAAGTTCCTAACCCCACCCACACCC------ACACCCAGCAACCCCAATTCCTTCCTC
TCCCACCAACGCAACCACATATTCTGTCGTCGCCGTCACCTTGACGGCTAGACGCGGTTAGAGACCGACCGGCCCCATAT
ATACCATACGTGACTGGGCAACATCGTATCCGGCCGTGGAAAGGAGAAGCCTAGCCTAACTGCGAGGAGTGAGGTCGGTA
CCGGCTTAGC---CAGCAATCTGCAGGTGAATTG---GGGCACTAA--CAGCAGCAGCAGCATCAATCAAGTGAGGATTT
CACAATGCGGCCGGCCGTGACGCACGACGACCTGTCCCTCCGCAAGGCGCAGGAGCGCCGGGCGGGGCGCTCCGGCAGCC
AGATCGCCGTCGCCCTCGTCGCGCTCTCCGTGCTCTGCGGCCTCGTCAGCTTCATCCTCTGCCTCGCCGCCGAGGGCTCG
CGCTCCGAGGTACGCGCGCACCCCGACCAACCAACACGCGGCTTTGC----------TAGCTCGTG--------------
---CTGATGCTGCCTGGGCTTGGCACTCT---GCAGGTGTCCAACTACCTGATGACCGTGGCCGGGAGCGAGGCGCAGGT
GGAGCTGTGCTTCTACAACGGCAGCGGCCGCTCGGCGCTCGCCTTCTCCATCGGCGCCTTCCTGCTGCTGGCCGTCGCCA
TGTTCGCCGTGCACGGCTACATGCTGCTCGCCGTCGCTTCGCCGGACTCCGCCGCCGCTGGCCTCGCCGTCGCCGAGGAC
CACCCCCGCGTGTCCTCCGCCACCAACACCCTCACCTGGCAAACCTGCTGCCTCTTCTTCGTCACGTGGTACCAACATTA
CTTCAAG-----------------CATGCATTGGGCAAGAT---TGATGGTGTGGATTCATAATAAACACTGA----TCG
ATGGGTGCAGGATTTGCTTCGGGCTCGCGGAGGTGCTGCTCATGATCGGGATCGGGGTGGAGTCCGGCCACGTCAGCGAC
TGGCGGAGGCCGCGGCAGGTGTGCCACCGGGTGCGCCCGGGGATGTTCGCGGCGGCGGGGATACTGGGGCTCATCACCGT
CGTCGTTGGCTTCGTCGTCTACGTGACCGCGGTGCACACGCAGAAGCTGCTGAGGCAGCACGGCGGCGGCCACTACCCGC
CGCACCCCGGCAGCGCCCCGTACCCCAGCG------------------TCCAGCAGCACCACCTGCAGCCGCCCGTGTCG
TACCCACCACACCCGGCCCCGCACCCACACCCTCATCCGGCGCCGAATGCGCCGGAGATTACGGCGGCCGCGTGCCAGGT
GCAGTCCAGCAACGCGTGGTGCATCACCAAGGACAAGGAGTACACCGATGTTTGAATGCCTGAGCCTGACACAATGAATG
GTCGAAGAAGTGCAGAGACGATGAGCCTGACACAATGAATGGTCGAAGAAGTGCAGAGACGATGCACGTAAAATTCCTTT
TCGTTTTCGAACAATTGCTTGCTGATTTG----------AGCAATTGGATTATTATTTGCTGATATGTAAAATAATTTGT
TTGTACAAGGACAATATTCATGTTTTAACTTGTTA-TTATGCTGTTCATTTGGCCTGCCAACACTGTAATCACAATGCCC
TTGTCAAGATTGGAACATGCAAATCAAAATTGATCACACAACAAAACTGAGCAACGACACAGGTATACTAATAATTAAGT
GAAAGCTGGCATTGACATGTTCGGACAAACTGCAACTCACTTCATTCCTGAAGAACCCCACAA-ACCAAACCATTCAAGA
ATTGTCCCCTAAATGCCTCGCAGAGTTGCAGAAGCTTAAA-CTCAGGCTATACAGTAGCAAAATAGTGCACACCATACTA
AAGATGC-AAACCCCTACATAGTAGCCTGATAAAAAAGACCCAGACTCCTCAAGTTTGACGATTATACTCCTCTTACAAA
CGCTGCGATATTGATACCCAGGACCAGTTGCTTCCTTGAAAATCTTCAGCTTATTGGACCCACCACAACCATGACCTTAC
CCCACACACCGACTAGACCAAATGGTGACAACTGCAGCGACAAGGGAATTACCACCATTGGTCAAATCTGCAAAAGGAAT
TTAAAATTATATTATTGGTTGTCTCTTTGCTCAAAAGCTGATTCATGCTACCATATCGAGCAAATATGACGAGAGAAACA
ACAAATATGGTTATATGTTGAGAGTACCGACCTGTATTCAGCCCAAGTTCAGATCAGGGTTGCCACCTTGGCCAAAGTCA
AAGGCAACACCTGTGGGAGCTTCCATAGTTGCCCCCATCGCATCATCTTCCTCCTCCATCCAGTAAGCCTCGAGAATCTT
CACAGCCTTCTCATAGATTTCATTGTTAT
>chr3B_254
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-------------TATTATTAACATAAACAGGAGTCGAGATAATGGTCAGATGCGCTCCACTGTTCAGCTCCACACAAGT
GCATGTCGGTAGCGGTAGGAGTGCAAGCTGATTCATCACCAATGCAGTGGG-TACCCATGGGCCATGGCACTGCCGACCT
TGCATCTGTTTTCTTCCAAATAAAAAA----TAAAAATCCTAGCCCTTTCTCTTACCTATAGGTTGCCTCGTTGGCGCTA
CAAAGCGCAGATGCTGCGCGTCGCTTTCCCCAAAAGGCACCGCGGCGAATTACCCACAGCAGCGGAAAGAAGAAGGTGCC
C----CTCCTCCTCATCATCACCGGTGAAAGGTGAAAAAGAAGGAAAGGCGAAACGAATCGGAATGTCTCCCACCGCGGC
ACGGCGCAAGAAACCCCGATCCCCCTCACTCACTCACGCTCCCATCCCATGCATCATCGCCATGCCATGCCATGGATTCC
TCCCGTGCGGCGTCTCCCAACCCAAGTTCCTAA------CCCCACCC------ACACCCATCAACCCCAATTCCTTCCTC
TCCCACCAACGCAACCACATATTCTGTCGTCGCCGTTACCTAGACGGCTAGACGCAGGTAGAGACCGACCGGCCCCATAT
ATACCATACGTGACTGGGCAACATCGTATC-------------------------------------------------A
CTGGCTTAGC---TAGCAATCTGCAGGTGAATTAATTGGGCACTAA--CATCACCAGCATCA--AATCAAGTGAGGATTT
CACAATGCGGCCGGCCGTGACGCACGACGACCTGTCCCTCCGCAAGGCGCAGGAGCGCCGGGCGGGGCGCTCCGGCAGCC
AGATCGCCGTCGGCCTCGTCGCGCTCTCCGTGCTCTGCGGCCTCGTCAGCTTCATCCTCTGCCTCGCCGCCGAGGGCTCG
CGCTCCGAGGTACGCACGCACGCACGTACG----CACGCGGCCTTGCTAGCTCGACCGTTACTGTGACTGACTGACTGAC
TGACTGGTGCTGCCTGGGCTTCTTGGCTCGCCGCAGGTGTCCAACTACCTGATGACCGTGGCCGGGAGCGGGGCGCAGGT
GGAGCTGTGCTTCTACAACGGCAGCGGCCGCTCGGCGCTCGCCTTCTCCATCGGCGCCTTCCTGCTGCTGGCCGTCGCCA
TGTTCGCCGTGCACGCCTACATGCTCCTCGCCGTCGCTTCGCCGGACTCCGCCGCCGCAGGCCTCGCCGTCGCTGAGGAC
CACCCCCGCGTGTCCTCCGCCACCAACACCCTCACCTGGCAAACCTGCTGCCTCTTCTTCGTCACATGGTACGGAAATTA
CTTTCAAGCGCCGCGAAACCATGCCATGCATTGGGCAAGAAGAATGGTGGTGTGGATTAATAATAAGAGCACACTCGTCG
ATGGGTGCAGGATTTGCTTCGGGCTCGCGGAGGTGCTGCTCATGATCGGGATCGGGGTAGAGTCCGGCCACGTCAGCGAC
TGGCGGAGGCCGCGGCAGGTGTGCCACCGGGTGCGCCCGGGGATGTTCGCGGCGGCGGGGATACTGGGGCTCATCACCGT
CGTCGTCGGCTTCGTCGTCTACGTGACCGCAGTGCACACGCAGAAGCTGCTGCGGCAGCACGGCGGCGGCCACTACGCCC
CGCACCCCGGCAGCGCCCCCTACCCCAGCGGTGCACCATACCCCGGCGTCCAGCAGCACCACCTGCAGCCGCCGGTGTCG
TACCCACCACACCCGGCCCCGCACCCACACCCTCATCCGGCGCCGAATGCGCCGGAGATCACGGCCGCCGCTTGCCAGGT
TCAGTCCAGCAACGCGTGGTGCATCACCAAGGACAAGGAGTACACCGATGTTTAAA------AGCCTAAGCCAATGAATG
GT--AAGAAGTGCAGAGACAATGAGCCTGACGCAATGAATGGTCGAACAAGAGCAGAGACAATGCACGTAAAATTCCTTT
TCGTTTTCGAACAATTGCTTGCTCATTTGTGATATAAGTAGCAATTGGATTATTATTCGCTGATATGTAAAACAATTTGT
TTGTTCAAGGACAATATTCATGTTTTAACTTGTTAATTATGCTGTTCATTTGGCCTGCCAACTCTGTAATCACAATGCCC
TTGTCAAAATTGGAACATGCAAATCAAAATTGATCAGAGAACAAAACTGAGCAACGACACAGGTATACTAATAATCAAGT
GAAAGCTGACATTGACATGTTCGGACAAACTGCAACTCACTTCATTCCTGAAGAACCCCACAA-ACCAAACCATTCAAGA
ATTGTCCCCTAAATGCCTCGCAGAGTTGCAGAAGCTTAAA-CTCAGGCTATACAGTAGCAAAATAGTGCACACCATACTA
AAGATGC-AA-CCCCTACATAGTAGCCTGATAAAAAAGACCCAGACTCCTCAAGTTTGACGATTATACTCCTCTTACAAA
CGCTGCGATATTGATACCCAGGACCAGTTGCTTCCTTGAAAATCTTCAGCTTATTGGACCCACCACAACCATGACCTTAC
CCCACGCACCGACT--ACCAAATGGTGGCAACTGCAGCGACAAGGGAATTACCACCATTGGTCAAATCTGCAAAAGGAAT
TTCAAATTATATTATTGGTTGTCTCTTTGCTCAAAAGCTGATTCACGCTACCATATCGAGCGAATATGACAAGAGAAACA
ACAAATACGGTTATATGTTGAGAGTACCGACCTGTATTCAGCCCAGGTTCAGATCAGGGTTGCCACCTTGGCCAAAGTCA
AAGGCAACACCTGTCGGAGCTTCCATAGTTGCCCCCATCGCATCATCTTCCTCCTCCATCCAGTAAGCCTCAAGAATCTT
CACAGCCTTCTCATAGATTTCATTGTTAT
>chr3A_378
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---------------------------------------------------------------CATGGCACTGCCGACCT
TGCATCTGTTTTCTTCCAAA----AAAATAAAAAAAATCGTAGCCCTTTCTCTTACCTATAGGTTGCCTCGTTGGCGCTA
CAAAGCGCAGATGCTGCGCGTCGCTTTCCCGAAAAGGCACCGCGGCGAATTACCCACCCCAGCGGAAAGAAGAAGGTGCC
CTCCTCTCCTCCTCATCACT----------GGTGAAAAAGAAGGAAAGGCAAAACGAATCGGAATGTCTCCCACCGCGGC
ACGGCGCAAGAAACCCCGATCCC-----CTCACCCACGCTCCCATCCCATGCATCATCGCCATGCCAT-CCATGGATTCC
TCCCGTGCGGCGTCTCCCAACCCAAGTTCCTAACCCCACCCACACCCACACCCACACCCAGCAACCCCAATTCCTTCCTC
TCCCACCAACGCAACCACATATTCCATCGTCGCCGTCACCTTGACGGCTAGACGCAGGTAGAGACCGACCGGCCCCATAT
ATACCATACGTGACTGGGCAACATCGTATCCGGCCGTGGAAAGGGGAAGCCTAGCCTAGCTGCGAGGAGTGAGGTCGGTA
CCGGCTTAGCTAGCAGCAATCTGCAGGTGAATTG---GGCACTAGCAGCAGCAGCAGCAGCATCAATCAAGTGAGGATTT
CGCAATGCGGCCGGCCGTGACGCACGACGACCTGTCCCTCCGCAAGGCGCAGGAGCGCCGGGCGGGGCGCTCCGGCAGCC
AGATCGCCGTCGCCCTCGTCGCGCTCTCCGTGCTCTGCGGCCTCGTCAGCTTCATCCTCTGCCTCGCCGCCGAGGGCTCG
CGCTCCGAGGTACGCACGCACGCACACCGACCAACACGCGGCCTTGCTAGCTTACTATAGCTCGTG--------------
---CTGATGCTGGCTGG----------CT---GCAGGTGTCCAACTACCTGATGACCGTGGCCGGGAGCGGGGCGCAGGT
GGAGCTGTGCTTCTACAACGGCAGCGGCCGCTCGGCGCTCGCCTTCTCCATCGGCGCCTTCCTGCTGCTGGCCGTCGCCA
TGTTCGCCGTGCACGCCTACATGCTGCTCGCCGTCGCTTCGCCGGACTCCGCCGCCGCTGGCCTCGCCGTCGCCGAGGAC
CACCCCCGCGTGTCCTCCGCCACCAACACCCTCACCTGGCAAACCTGCTGCCTCTTCTTCGTCACGTGGTACCAACATTA
CTTCAAG-----------------CATGCATTGGGCAAGAT---TGATGGTGTGGATTCATAATAAACACTGA----TCG
ATGGGTGCAGGATTTGCTTCGGGCTCGCGGAGGTGCTGCTCATGATCGGGATCGGGGTGGAGTCCGGCCACGTCAGCGAC
TGGCGGAGGCCGCGGCAGGTGTGCCACCGGGTGCGCCCGGGGATGTTCGCGGCGGCGGGGATACTGGGGCTCATCACCGT
CGTCGTTGGCTTCGTCGTCTACGTGACCGCGGTGCACACGCAGAAGCTGCTGAGGCAGCACGGCGGCGGCCACTACCCGC
CGCACCCCGGCAGCGCCCCGTACCCCAGCG------------------TCCAGCAGCACCACCTGCAGCCGCCCGTGTCG
TACCCACCATACCCGGCCCCGCACCCACACCCTCATCCGGCGCCGAATGCGCCGGAGATCACAGCGGCCGCGTGCCAGGT
GCAGTCCAGCAACGCGTGGTGCATCACCAAGGACAAGGAGTACACCGATGTTTGAATGCCTGA-----------------
----------------------------------------------------GCCGAGACGATGCACGTAAAATTCCTTT
TCGTTTTCGAACAATTGCTTGCTGATTT-------------CAATTGGATTATTATTTGCTGATATGTAAAACAATTTGT
TTGTACAAGGACAATATAAATGTTTTAACTTGTTA-TTATGCTGTTCATTTGGCCTGCCAACTCTGTAATCACAATGCCC
TTGTCAAGATTGGAACATGCAAATCAAAATTGATCACAACAAA-----------------------ACTGATAATTAAGT
GAAAGCTGACATTGCCATGTTCGGACAAACTGCAACTCACTTCATTCCTGAAGAACCCCACAAGACCAAACCATTCAAGA
ATTGTCCCCTAAATGCCTCGCAGAGTTGCAGAAGCTTAAAACTCAGGCTATACAGTAGCAAAATAGTGCACACCATACTA
AAGATGCAAA-CCCCTACATAGTAGCCTGATAAAAAAGACCCAGACTCCTCAAGTTTGACGATTATACTCCTCTTACAAA
CGCTGTGATATTGATACCCAGGACCAGTTGCTTCCTTGAAAATCTTCAGCTTATTGGACCCACCACAACCATGACCTTAC
CCCACACACCGACTAGACCAAATGGTGACAACTGCTGCGACAAGGGAATTACCACCATTGGTCAAATCTGCAAAAGGAAT
TTAAAATTATATTATTGGTTGTCTCTTTGCTCAAAAGCTGATTCATGCTACCATATCGAGCAAATATGACAAGAGAAACA
ACAAATATGGTTATATGTTGAGAGTACCGACCTGTATTCAGCCCAAGTTCAGATCAGGGTTGCCACCTTGGCCAAAGTCA
AAGGCAACACCTGTGGGAGCTTCCATAGTTGCCCCCATCGCATCATCTTCCTCCTCCATCCAGTAAGCCTCGAGAATCTT
CACAGCCTTCTCATAGATCTCATTGTTAT
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSS---------SS-------------S-------S---S----S-------S-----------------
--------------------------------------------S-S----S----------------------------
----------------S---------------------------------------------------------------
---------------S----------------------------------------------------------------
---------S----------------------------------------------------------------------
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-------------------------------------------------------S-S----------------------
--------------------------------------------S-------------S---------------------
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---------------S-----S-SS---S-------------S-------------------------------------
---------------------SSSSSS-------------------------------------------S---------
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---------------S----------------------------------------------------------------
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-----------------------------------------------------------S--------------------
-------------------------------------------------------------------S-SS---------
--SS---------------S-----------S---------------S---S----------------------------
------------------------------------------------------------------------S-------
--------------------------------------------------------------S-----------------
--------------------------------------S-----------------------------------------
--------S-----------------------------------------------------------------------
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----------S---------------------------------------------------------------------
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----------------------------------------------------------------------S---------
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>forward_496
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----------------------------------------------------------------------------GCTA
CAAAGCGCAGATGCTC----------------------------------------------------------------
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>reverse_2163
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--CGAAGAAGTGCAGAGACGATG---------------------------------------------------------
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