>input_sequence_78819
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-----ATGGAGTACGAGCCGGCGATTTTTTGCCCCAAGTGCAGGAAGAAAGCGCCGCGGTGGATTTCCTGGAGTCCGGCG
AACCCTGGAAGAAGGTACTATGCATGCGTTGAAGCTCGGGTATGCTCTGATCTGATGTGTTCTTGCGCTCGTGCTTTCTT
CTCTGATTTGCTCTGTTTTTTGGTATGCCCTCTGACGAACATTGCCG--------------------------ATTGAAC
AGCACGGCTTCATTCAGTGGCATGATGGGCCTACAACTGAATTTTTGCGTCGATTGCTGGGAGATCTTCGAGATAGAGTG
TGGAGGCTGGAGGAGGATGTTGATGCACTGTTAAATGAAGCAGATTCACGAGCTGCTGCTTTAACCGATGGAGTGATTGG
AGGAAATGAAAAAATTGCATCAGTTAGTGAGAAATGTGTTAGCAGAGAGATGTTGTTGTATGGCATTGTGCTATTTCTGT
CTGGTATGGTGGTAGGGATGATTTTAGGCTAG------------------------------------------------
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>chr3D_1_TraesCS3D01G532500
ACGACCTTCTCTACAGCATATCAATCGCCGGTGCTCACGTGGTTGGGCCCAGGCCCACGGCCAGGTTCACGGCGGCTCTA
CTTCGCCCCGGCGACGCGGAGTGGACAATCCTCGAGAGGACCCTCGAGCATGAGTATGAGCATCGGTTCCGGACCTGGTC
ACCTCGTCAACCTGTTTTGTCGTCGGTCACATACC---ACGATGGTAAGATCCTGGCCGTCATGGAGGCTGACCAACATT
GGCGCCTCGTCACACCAAACAGCAATATCGCCCGCGATGAGCTTGTCCAGAGCCAGGGGACGCCGGTGGTGCAGCTGTGG
TTTGGCAAATCCACCTGCTATTACACTTACAACCACATCCTTGAGTCCCGTGGCGAGATTCTATGGGTGTCTATTAACAG
CCCTGAGTATGA---------------------------------------CAAGGTGTCAGTGCTGGCACTCGAGGAGC
CTCTATTGTCAGAACTGTCGCCACTTGAGAAGATGAGATGGGTGAGAAAGGATGGGCGTAGTCTGGCCGACCGCGTGCTG
TTCCTCG---CGCGCCACAGTTTTGTTGTGGATGCGGGGCGGGTGCCCAACAGCCACGGTGGGTGTGCCTACTTCGTCTA
CCAAAATGGAGTGAAGTCTGTTTTGAACCCTGAGAGGGTAGTGAGCGTCCGAAACGAACCCTGAAGTCCAAATCCCTGAA
GTCCGTGTCCTGTAGTCGCTGATCCCGGATTTATTTGACCTTTAGTGCGTATTAGGAGGGGATTAGCCGACGTGGCACCG
TGGGGCGGTGGGTTTGCTACTTTAAACGCCACGTCGACTCAGCCACACATCTACAGAAGCACTCGAAGCGGGGAGGGGAA
CCAAATTAGGGTTCAGGCGAGGGGAAGAGAGTGGCGACTGGCAGGCGATTGGCGGCGGAATCGATGATGTCGTCGGCGTC
GCGTGGCTCATCTGCTTCTCGCGACGAAGGGATTCGCCGGAGAGGCGTAGCAGCAAGGTCCCCGGTGCCCTATCGGGAGG
AGACCATGGAGTACGAGCCGGCGATTTTTTGCCCCAAGTGCAGGAAGAAAGCGCCGCGGTGGATTTCCTGGAGTCCGGCG
AACCCTGGAAGAAGGTACTATGCATGCGTTGAAGCTCGGGTATGCTCTGATCTGATGTGTTCTTGCGCTCGTGCTTTCTT
CTCTGATTTGCTCTGTTTTTTGGTATGCCCTCTGACGAACATTGCCG--------------------------ATTGAAC
AGCACGGCTTCATTCAGTGGCATGATGGGCCTACAACTGAATTTTTGCGTCGATTGCTGGGAGATCTTCGAGATAGAGTG
TGGAGGCTGGAGGAGGATGTTGATGCACTGTTAAATGAAGCAGATTCACGAGCTGCTGCTTTAACCGATGGAGTGATTGG
AGGAAATGAAAAAATTGCATCAGTTAGTGAGAAATGTGTTAGCAGAGAGATGTTGTTGTATGGCATTGTGCTATTTCTGT
CTGGTATGGTGGTAGGGATGATTTTAGGCTAGTGAATCAGTTAGTAGTG-AGTTGGAGGCATTGTACTGAATTTAGAGCA
ATGTAATGGTATTTGAGACAAGTTTCAATGCAATTCTGTTTGAAAAAA-ATTCTTTTAATGAGATATGCAGTGCCATTGC
TCTCTTTTGTGCACTTTGTAGAGTAAATTTTGACAGAAAAATGAGGAAATATGTATGAAATGTTGAGAGTTTGCTGTCAA
AA-----GGAATACAAGATCATCTTGACAGATTTCTGTCAAAATGTTGAGAGTTTGTAGAGTAAAGTTTGCTGTCAAAAT
GTTGAGAATTTTCACATGGCATATATCACGATCAAACATAGACAGCAGAAAATAAGACCAACAAGTTCACATTGCATTGC
CACAAGTTCACAGGGACACACATAGACAGCAAAATAAATTCCAGTGTTTCATATAACCACATTCTAACATGGTTTTTCAC
CCAACAGCAAAATATCATGCAAAAAGAACAATTCAAAAGTTCCCACTTGCTGTGAAGAAGGGCATGAACCCTCTGACACT
GCTTGTTCCCGTTCCTCTCCCTGTAGCACTAGTTGTTGCTGTTCCTCTCCCTCTCTTTGCTCCTCTGCCCCTGCCAGTAG
AAGTGCTGCCTCCAGGTGCATCATTTGCAGTGCTTGTTCCTGGTCCTCTCACTCTCTTTGCTCCTCTGCCCCTGGCAGTA
GTTGTGCTTCCTCTAGGTGCATCATTAGCTCTAGGAGGCCTGAAACTTGTATTTGCAGGTTGAGAGCTTGAACCTGCTGC
TGACTGAAAGCTTTGAGGAGCTTGTGTCCTTGTTGCAGGTTGTGTATTTGCTGTCCTGCTTTTTAATGCCTCGGTCTGTG
CTTCCTGCAACCCAGTAACATAGCATGTAGTGTTATAATTGTTTGCAAAAAAGCAACATACAGTGCAATAATTCAATGCA
AAAACAGAGCATATAGTGTTGTACAGGAGTAAATTACCTCTGTTGCTCTAAGTTTTTTCCCTCTCTTAGCAAGAAATGC
>chr3D_5
----CCTTCTCTACAGCATCTCCACG---GCTGCTTGCGTAGTTGGACACAGGCCCACGGCCAGGTTCAGGGCGGCTCTA
CTTCGCCCCGGGGACGCAGAGTGGGCAATCCTCGAGAGGACCCTCGAGCATCAGCTTCGCTACAGGG------GCTGGCC
ACCTCCTCAACCTGTTCTGTCGTCTGTCACATACCACGACGATGGTAAGATCCTGGCCGTCATGGAGGCTGACCAATGGT
GGCGCCCTGTCACACCAAACAGCAATATCGCCCCCGATGAGCTTGCCAAGAGCCGGGGGACGCCGGTGGTGCAGGTATGG
TTTGGCCAATCCACCTCCAATTACAACT------ACATCCTTGAGTCCAGTGGCGAGATTCTATGGGTGTCTATTAACAC
CCGGGAAGTTGACAGGTATCTCATAGGGACAAACCCTTGCCTTCTCAATGTCAAGGTGTCAGTGCACGCACTCCAGGAGC
CTCTGTTGTCACAATCGTCGCCATTGGAGAAGATGAGATGGGTGAGAAGGGATGGCCGTAGTCTGGCCGACCGCGTGCTG
TTCCTCGGTACACGCCATAGCTTTGTTGTGGATGCGGGGTGGGTGCCCAATGGCAACGGCGGGTGTGCCTACTTCGTGTA
CCACAAT-------------------------------------------------------------------------
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>chr3A_5
----CCTTCTCTACAGCATCTCCACCACCGGCG---ACGTGGTTGGGCACAGGCCCACGGCCATGTTCACGGCGGCTCTA
CTTCGCCCCGGCGACGGGGAGTGGACAATCCTCGAGAGGACCCTCGAGCATAAGTACGAGCATGGGTTCCAGAGCTGGTC
ACCTCGTCAACCTGTTTTGACGTCTGTCACGTACC---ATGATGGTAAGATCCTGGCCGTCATGGAGGATGACCAACCGT
GGCGCCTCGTCACACCAAACTGCAATATCGCCCGCGATGAGCTTGTCATGAGCCCGGGGAAGCCGGCGGTGCAGCTGTGG
TTTGTCGAATCCACCTGCAATTACAGCT------ACGTCCTCGAGTCCCGTGGCGAGATTCTACGGGTGTCAATCAACGC
CTGGGAATATGACAGGTATCTCATGGGGACAAACCCCTACCTTCTCAAAGTCAAGGTGTCAGTGCAGGCACTCGATGGGC
CTCTATTGTCAGAATCGTCGCCACTCGAGAAGATGAGATGGGTGAGAAGGGATGGCCGTAGTCTGGCCGACCGCGTGCTG
TTCCTTGGTACGCGCCATAGCTTTGTTGTGGATGCGGGGCGGGTTCCCAACGTTCATGGCGGGTGTGCCTACTTCGTCTA
CCACAATG------------------------------------------------------------------------
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>chr3A_42
-----------------------------------------GTTGGACACAGGCCCACGGCCAGGTTCAGGGCGGCTCTA
CTTCGCCCCGGGGACGCAGAGTGGGCAATCCTCGAGAGGACGCTCGAGCATCAGCTTCGCTACAGAG------GCTGGCC
ACCTCCTCAACCTGTTCTGTCGTCTGTCACATACCACGACGATGGTAAGATCCTGGCCGTCATGGAGGCTGACCAATGGT
GGCGCCCCGTCACACCAAACAGCAATATCGCCCCTGGTGAGCTTGCCGAGAGCCGGGGGAAGCCCGTGGTGCAGGTGTGG
TTTGGCCAATCCACCTCCAATTACAACT------ACATCCTTGAGTCCCGTGGCGAGATTCTTTGGGTGTCTATTAACAC
CCGGGAACATGACAGGTATCTCATAGGGACAAACCCCTACCTTGTCAAAGTCAAGGTGTCAGTGCACGCACTCGAGGAGC
CTCTGTTGTCACAATCGTCGCCATTGGAGCAGATGAGATGGGTGAGAAGGGATGGTCGTAGTCTGGCCGACCGCGTGCTG
TTCCTCGGTACACGCCATAGCTTTGTTGTGGATGCGGGGCGGGTGCCCAATGGCAACGGCGGGTGTGCCTACTTCGTGTA
CCACAAT-------------------------------------------------------------------------
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>chr7B_601
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-----ATGGAGTGAAGTCTGTTTTGAATCCTGAGAGCGTAGGCAGCGACAGAAATGAACCCCGACGTCGAAATCCCTGAA
GTCTGTGTCATGTAGTCTCTAATCCCAGTCGTAATGGCCCTTTAGTGCGTATTAGGCTGGGATTAGCCGACGTGACACCG
TCTGGTGGTGGGATTGCTACTTTAAACGCCACGTCGGTTCAGCCACTTATCTTCAGAC---------GCGGGGAGGGGAA
CCAAATTAGGGTTGAGGCGAGGGGAAGAGAGAGGCGATTGGCAGACGATTGACGGCGGAAGCGACGATGTCGTCGGCGTC
GCTCGGCTCATCTGCTTCTCGCGGTGGAGGGATTCGCCGGAGAGGCGGAGCAGCAAGGTCGCCGGTGCCCTATCGGGAGG
AGCCCATGGAGTATGAGCCGGTGATTTGTTGCTCCCTGTGCAGGAAGAAAGCGCCGCGGTGGATTTCCTAGAGTCCAGCG
AACCCTGGGAGGAGGTACTATGCGTGCGTTGAAGCTCAGGTATGCTCTGATCTGCTGTGTTCTTGCGCTCGTTCTTCATT
---TGGTTTGCTCTGTTTTTTGCTATGGCCTCTGATGAGTAGTTCCATCTGACGAGTACTCCCCTCTGAAAAAATTGAAC
AGCACAGCTTCATTCAGTGGCATGATGTGCCTACAACTCTTTTTGTGCGTGGACTGCTGGGAGATCTTCGAGACAGAGTG
TGGAAGTTGGAGGCAGACATTGATGCACTGTTAACTGAAGGAGCTTCAGGAGCTGCTACTTTAACTGATGGAGTGACGAG
AGGCAACGAAAAAAATGCATCAGTTAGTGAGAAATGTGTTAGCAGAGAGATGTTGTTGTATGGCATTGTGTTATTTCTGT
CTGGTATGGTAGTAGGGATGATTTTAGGCTGGTGAATCAGGTAGTAAATAAGTTTGAGGCAATGTACTGAATGTGGAGCA
ATGTAATGTT-TTTGAGACAAGTTTGAATGCAATTCAGTTTGAAAATA-----TTTTCATGACATATGCAGTGCCATTTC
TCTGTGTACTTGGAAATATAGTGTGTGTGGAACAAGAAAA--GAGGAAATATGCATCAAATGTTCAGAGTTTGATGTAAA
AAAAACTGGAATAAAAGAACATTTTGACAGCTTTCTGTCAAAA-------------------------------------
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>chr5D_606
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----------GTGAAGTCTGTTTTGAACCCTGAGAGGGTAGTGAGCGTCCGAAACGAACCCTGAAGTCCAAATCCCTGAA
GTCCGTGTCCTGTAGTCGCTGATCCCGGATTTATTTGACCTTTAGTGCGTATTAGGAGGGGATTAGCCGACGTGGCACCG
TGGGGCGGTGGGTTTGCTACTTTAAACGCCACGTCGACTCAGCCACACATCTTCAGAAGCACTCGAAGCGGGGAGGGGAA
CCAAATTAGGGTTCAGGCGAGGGGAAGAGAGTGGCGACTGGCAGGCGATTGGCGGCGGAATCGATGATGTCGTCGGCGTC
GCGTGGCTCATCTGCTTCTCGCGGCGAAGGGATTCGCCGGAGAGGCGCAGCAGCAAGGTCCCCGGTGCCCTATCGGGAGG
AGCCCATGGAGTACGAGCCGGCGATTTTTTGCCCCAAGTGCGGGAAGAAAGCGCCGCGGTGGATTTCCTGGAGTCCGGCG
AACCCTGGAAGAAGGTACTATGCATGCGTTGAAGCTCGGGTATGCTCTGATCTGATGTGTTCTTGCGCTCGTGCTTTCTT
CTCTGATTTGCTCTGTTTTTTGGTATGCCCTCTGACGAACATTGCCG--------------------------ATTGAAC
AGCACGGCTTCATTCAGTGGCATGATGGGCCTACAACTGAATTTTTGCGTCGATTGCTGGGAGATCTTCGAGATAGAGTG
TGGAGGCTGGAGGAGGATGTTGATGCACTGTTAAATGAAGGAGATTCACGAGCTGCTGCTTTAACCGATGGAGTGATTGG
AGGAAATGAAAAAATTGCATCAGTTAGTGAGAAATGTGTTAGCAGAGAGATGTTGTTGTATGGCATTGTGCTATTTCTGT
CTGGTATGGTGTTAGGGATGATTTTAGGCTAGTGAATCAGTTAGTAGTG-AGTTGGAGGCACTGTACTGAATTTAGAGCA
ATGTAATGGTATTTGAGACAAGTTTCAATGCAATTCTGTTTGAAAAAAAATTCTTTTAATGAGATATGCAGTGCCATTGC
TCTCTTTTGTGCACTTTGTAGAGTAAATTTTGACAGAAAAATGAGGAAATATGTATGAAATGTTGAGAGTTTGCTGTCAA
AA-----GGAATACAAGATCATCTTGACAGATTTCTGTCAAAATGTTGAGAGTTCAGCAAA-------------------
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--------------------------------------------------ATATAACCACATTCTAACATGGTTTTTCAC
CCAACAACAAAATATCATGCAAAAAGAACAATTCAAAAGTTCCCACTTGCTGTGAAGAAGGGCATGAACCCTCTGACACT
GCTTGTTCCCGTTCCTCTCCCTGTAGCACTGGTTGTTGCTGTTCCTCTCCCTCTCTTTGCTCCTCTGCCCCTGCCAGTAG
AAGTGCTGCCTCCAGGTGCATCATTTGCAGTGCTTGTTCCTGGTCCTCTCACTCTCTTTGCTCCTCTGCCCCTGGCAGTA
GTTGTGCTTCCTCTAGGTGCATCATTAGCTCTAGGAGGCCTGAAACTTGTATTTGCAGGTTGAGAGCTTGAACCTGCTGC
TGACTGAAAGCTTTGAGGAGCTTGTGTCCTTCTTGCAGGTTGTGTATTTGCTGTCCTGCTTTTTAATGCCTCGGTCTGTG
CTTCCTGCAACCCAGTAACATAGCATGTAGTGTTATAATTGTTTGCAAAAAAGCAACATACAGTGCAATAATTCAATGCA
AAAACAGAGCATATAGTGTTGTACAGGAGTAAATTACCTCTGTTGCTCTAAGTTTTTTCCCTCTCTTAGCAAGAAATGC
>SNPs
SSSS---------------S--S-S-S--------S------------S-------------------------------
---------------------------------------------------S-----------S------S--S------
------------------------S----------------------------------------------------SS-
-----------------------------------------------S------S-------------------------
------S-----------S------SS-SSSSSS---------------------------------------------S
--SS--S----------------------------------------------------------S--------------
--------------SS---------S----------------------S------S------------------------
-----------------S--S------------------------------S-------S--------------------
---S----------------------------------------------------------------------------
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----------------------------------------------------S---------------------------
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-----------------------S-----------------------S--------------------------------
--S-----------------------------------------------------------------------------
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----------------------------------------S---------------------------------------
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------------------------------------------------------SSSSS-SSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------------------------
------S-------------------------------------------------------------------------
------------------------------S-------------------------------------------------
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-------------------------------S------------------------------------------------
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>forward_238
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----------------------------------------------------------GTCATGGAGGCTGACCAACA--
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>reverse_1917
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----------------------------------------------------------------------------TTGC
CACAAGTTCACAGGGA----------------------------------------------------------------
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