>input_sequence_87207
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-----------------------------------------------------------ATGGACGCCCACCGTCACAGC
AGCTTCTTCTTCGTCGTCGTCGTTGCTGTCGCTGCG---ATCTTCACCATGGGCTTCGTGCGGTGTGCCGATGCCGCACG
ACCCGTGCCACCGAGCC---------------CGGCGTCCGCGCTGGTGTCGTCGTTGATGGAGATGCTACCCATGGGGC
CCAGCGGAGGAGGCGCGGGGCACTGA------------------------------------------------------
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>chr3D_1_TraesCS3D01G393500
CTCCTTCTAACCATCCAACCACAGTCCATAGGTATAGATTTTGTTTCAGACTTTTTATATTTATAGGTTGGTTCGGCCTG
ACTCTTGTATGTAGTTTCATATTTATATGGAGCCGGGGAGAGTCTCCCTGTTTTTTCTAGAAAAAAATGACTTGTGAGCT
ATGACGTACATTTTTTTTTTGCGATGAAGCTATGAC--------------------------------------------
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-------------------------------------------------------------------GTACATTTGATGG
ACCTGTGACGCCTAAACAA-TGCGTGTGTTTACTCCTGCCCTGGAAATTCGCACGACATATGTGTGGTGTGAAGCACGAT
TGGAAGGTCAAGACAAGACTTCAGGTGCTGCGTGCTTGCGTGGCGCCACATGTCGTGTGGAACACCGCCAAACACACCCG
CGTGGTTGCATGCCATGTACGACTGATTTTGCACGGAGAAGGGACGAAATATAGTTCTGCGCGCACGGCCGGTGAGCGCG
GCGCTGGTGTGTCAACCCGTACGAGTTCCGGCTGCTCCGCGAGTTCATTCCTCG---GACTTCCGAACAGCACGGCGGCA
CCCACACGAGCTTCAGGTTTCCGAGAAGCC---AAAAGTGGCCGGCGCCGGTGCGCCTCCCACACCAGACCC--------
---------TTCCTCTGTTCCAGCACGAGCACCGCAGAGTCGGGC------GGCCGGGTCAGCGCTTTTCCTCCGAGTTA
ATGTGGCGGCCGCTGCTCCCGGCGCACCGGCACGCACCGTCCGTCCGTCCAAGCCTCGTTGACCGTTTCTTCCATGTGCC
ACGGCAGAAGGGCCGGCCAGCGTTCCATACCATCACGGTGTAC-------------------------------------
-----GTGTACCGGCCAGCTACACGCCACCAGATTCTGCTCCCT------------------------------------
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------ATATATACACACACCACACGAGTCACACAA--------------------GTGGTGGAC------CAGCACCAG
CACCAGACTGCAATCTCCACACCCAGAACCAGGCGGCTAGAGATTCAGTGAGGTACGTGCGTGCGTGCGTGC--------
TCCGTAGAGTTTTCAGAGGATCGAGATCTCAGGGCACGTTCCTTTGCTTCCTGGAAGCCATGGACGCCCACCGTCACAGC
AGCTTCTTCTTCGTCGTCGTCGTTGCTGTCGCTGCG---ATCTTCACCATGGGCTTCGTGCGGTGTGCCGATGCCGCACG
ACCCGTGCCACCGAGCC---------------CGGCGTCCGCGCTGGTGTCGTCGTTGATGGAGATGCTACCCATGGGGC
CCAGCGGAGGAGGCGCGGGGCACTGATCCGCTCAAGCCGATCGTTAGCGAGAAGCGTAGTGTAGAGAGGTCTAGCTAGGG
AACGGAGTTAACGTTGCTGCTGGCAGTTCTTTGTTCTTGGTCCTCCTTCTCTTCATGGCCATCTTCACTACTCTTTTTTT
TGCCCTGCACTTGCAAGAGGTTTAGGAAGTGCCTGACATTTTATCTTAAGTAGTATTGCTGTCATGATGCAATAACATGA
TGCAAACTGCTGGCATTTAAATGGTCCGAGCTCATATAATTCCAACACAAACCAGTAGAAAGTTTCTTCCATGCATCAGT
TTTGAGTATATTTTTTTTAGAAAAGGAGGATGACCCCCGGTCTCTGCATTCGGAAGATGCATACGGCCACTTTATTGATT
ATTCTCGAGGACCTTACAAATTATTACAAACAATATACCTGAATCCACCATCTTGGCAACATATGCCGCTACTCCTATCC
ATATGATGAAGGGGTGCTAGCTGGACCACTACCTAAACCACTCACCTAAGCCTAACATCAAAAGCCGGAAACCCCAGCTG
AGCCACATACCGGGTCTGGGGCACAATCCGGTCAGACGCACTCGTGTGTCGTCGCCGCCATCTTCCACGGGTCCGTCTTC
AGAACATATTGAGGCTTGTACCTTGTCTGACCACTCTGCCATCGACGTCACCATGACGCCAGACAGCTACCTCTGTTGGG
GAACGTAGTAATTTCAAAAAAATTCTACGCACATGCAAGATCATGGTGATGCATAGCAACAAGAGGGGAAAGTGTTGTCC
ACGTACCCTCGTAGACCGAAAGCGGAAGCGTTAGCACAACGCGGTTGATGTAGTCGTACGTCTTCACGATCCGACCGATC
AAGTACCGAACGCACGACACCTCCGAGTTCAGCACACGTTCAGCTCGATGACGTCCCTCGAACTCCGATCCAGCCGAGCT
TTGAGGGAGAGTTCCGTCAGCACGACGGCGTGGTGACGATGATGATGTTCTACCGATGCAGGGCTT
>chr3A_3
--CCTCCTAACCATCCAACCATAGTCTATAGGCATAACTTTTGTTTCAGACTTTTTATATTTGTAGGTTGGTTCGGCCGG
GCTTTTGTATGTAGTTTCATATTTATATGGAGCCGAGGAGAGTCCCCCGGTTTTTAATATTAAAAAATGACTTGCGGGCT
ATGACGTACTCCCTCCGTTTTGAAATATAAGTCTTTTTAGTGATTTCACTATAAACTAAGGTGGTGTTTGGTTCTCTAGT
CCTAGGACTTTTTCTAGTCCCAACTAAAAAGTCCCTAGTCTCTAAAAAGTCTCTCCCTATTTGTTTTCAGAGACTAAAAA
ATCCCTAGTCTCTTCCTAGAGATTATTAAATGACCATGTTGCCTCTAGTATATAGAAAAATAACAATCAAACAACACCAT
GAGATGGCGAACCAATGGGTGCATGGAGGAGCATTGTTGGAAAAGTCTTCAAAAGACTCTCCTTGAGAGTCTTCTTCATT
TAGTCCCAAATGTCTAGTTTAGTTCCTAAAAAGTTCCTCCCATTTGGTAAAAAAGTCTCTAAGAGGGACTTTTTCTAGTC
CCTACACAAAAAAATCCCTGAAAACAAACATCCCCTAAATACGAATGTACTATATAGACATATTTTAAATTGTAGATTTA
TTTATTTTGCTTCGTATGTAGTTCATAGTGGAATCTCTAAAAAGAGTTATATTTAGAAACAGAGTGAGTATATTTGATGG
ACCTGTGACGTCTAAACAAC-GCGTGTGTTTACTCCTGCCATGGAATTTCGCACCGTATATGTGTGGTGTGAAGCACGAT
TCGAAGGTCAAGACCCGGA-------------------------------------------------------------
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----------------------------------CTCCGCGAGTTCATTCCTCG---GACTTCCGAACAGCACGGCGGCA
CCCACACGAGCTTCAGGTTTCAAAGAAGAACCAAAAGGTGGCCGGCGCCGGTGCGCCTCCCACACCAGATCCCTTGCTGT
CATGTCCATTTCCTCTGTTCCAGCACGAGCACAGCAGAGTCGGGCACCGGCACGCA------------------------
--------------------CCGT------------CCGTCCGTCCGTCCAAGCCTTGTTGACCGTTTCTTCCACGCGCC
GCAGCAGAAGGGACGGTCAGCCTTCCAGTCCAGCACGAGAATTTCCAACCTTGTTGGCTGCCAAGAACGGGG-CACACGG
ACACGGTGTACCGGCCAACTGCACGCCACCAGATTCTTCTCCCCATATAGGGAAAAGTCTGAATAAAACCTCGAGCTCGT
AGTTCCCGTCCAAATCAGACCCTTACCTTTTAATCCCTGAAATCAGTACCCCGTACTCATCAATCCCAGTCAATCCTAAC
CTTGCAAAATTCTAGACTAGTTTGGTGCACTAGGAAAACGCAATCCCCACCGGGATCATCCTCTTCTCTCACTAACTTGG
TGAAGCTACAGTCAGATCCATCAATCTGCATCTGCATGACGCACGCACACACAATGAAACGACGTGGCAGCTCGGTGATG
TTGGTGCCGTGTGCAGCTCCGGGAGTGGTTGTGCGACGGCAGACGAGGGGCTTGTCGGCCGGCCAGTGGCGTGCAGCCCT
GGGAAACATCTTTACCTAGCTGATTGAGCGCACGAGAGCTTGCAGAGCGCAGCTTCACGGAGAGGAAATGAGGAAGACGA
CAACAATGGCGGTGGTGCTTGATCGAGCGAGTGTGGCTGGTGTCGTCGCAGTAGCTAGCCCGACATGCTAACGACGATGG
TGGATGGAGCACGGGAAACACGAGATCCACATGGACATCACCGTCCGTACCGTATGCACGCGTCCAGGCTAGGCAGAGTG
TCCCCGCGGGGCGTGAGTGTTCCGCCGAGTTGTGCTACTCCAGAAGCCCAGATCAACCAAGCATCCAGGATAGTAGTTTG
CTGCACGTGGAAAGCTAGCTAGCCTCAAGGATCCATCAGGTGCTTTCTCTACACTTGCGTACGTGCACCTTCAAATTTGA
CCAATCGATCAACCATGCTTCAGTTCAGTAGTTAGGATCTTGGGGCAGACCATGACAAAGCCTAGGAAGTTGAGCGCGGG
CCGGCGGCCTAGGCGCTCCACAGCGCCAATGAGGCGACGCCACACACGACGGCAACCACCTCCGGTGTCTAGTACGATCA
AAGCTCCCAGACCTCTCCCTGCCCCTTCAATTCTGGCTGGCCATCTCGCATCTTTTTCTTATCGCAGACGTTTCAACAAA
GGAGAGAACGACAGGGAGGACGAGGTAGAGGAGAGGGATGGATATGACATGCGGACCTAGTATTGTCGGTGAGAGTAGCA
GGTGAACCTAGTTGCGATTGCCTTTTTCCCGGTGTGCCAAACAGGTTGAAGGTCGATATTAACCGGGATCGACAAGTATG
GGGTGCCGATTTCAGGGATTAGAAGGTGAGGGTTCAATTTCGATAGGGCGTACGAGTTCAAGGTTTTTTTCAGACTTTAC
TCCCCCATATATACACACATCAGATGACTCACACAA--------------------GTGGTGGAC------TAGCACCAG
CACCAGACTGCAATCTCCACACCCAGAACCAGGC-------GATTCCGGGAGACACCTGCGTGCATGCGTGCTCCGTAAG
TCCGTAGAGTTTTCAGAGGATCGAGATCTCAGGGCACGT-CCTTTGCTTCTTGGAAGCCATGGACGCCCACCGTAACCGC
AGCTTCTTCTTCGTCGTCGTCGTTGCTGCCGCTGCG---ATGTTCACCATGAGCTTCGTGGGGTGTGCCGACGCCGTGAG
GCCCATGCCATCGAGCCCGGCGTCCTCCACCACGGCGTCCGCGCTGGTGTCGTCGTTGATGGAGATGCTACCCATGGGGC
CCAGCGGAGGAGGCGCGGGGCACTGATCCGCTCAAGTTGATCGCTAGCGAGAAGCGTAGTTTAGAG--------------
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>chr3B_188
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---------------------------AGCTATGAC--------------------------------------------
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-------------------------------------------------------------------GTACACTTGATGG
ACCTGTGACGCCTAAACAAATGCGTGTGTTTACTCCTGCCATGGAATTTCGCACCACATATGTGTGGTGTGAAGCACGAT
TCGAAGGTCAAGACAAGACTTGAGGTGCTGCATGCTTGCGTGGCGCCACATGTCGTGTGGAACACCGCCAAACACACCCG
CGTGGTTGCATGCCATCTACGACTAATTTTGCACGGAGAAGGAACAATATACAAGTCTGCGCGCACGGCCGGTGAGCGCG
GCGCTGGCGTGTCAACCCGTCCGAGCTCCGGCTGCTCCGCGAGTTCATCATTCCTCCGACTTCCGAGCAGCACGGCGGCA
CCCACATGAGCTTCAGGCTTCCGAGGACCG---AAAGGTGGCCGGCGCCGGTGCGCCTTCCACACCAGATCCCCTGCTGT
CATGTCCATTTCCTCTGTTCCAGCACCAGCACAGCAGAGTCGGGCTCGGGCGGGCGGGTCAGCGTTTTTCCTCTGAGTTA
ATGCGGCGGCCGCTGCTCGTCCGT------------CCGTCCGTCCGTCCAAGCCTTGTTGACCGTTTCTTCCACGCGCC
ACGGCAGAAGGGACGGTCAGCGTTCCAGTCCAGCACGAGAATTTCCAACCTAGTTGGCCGCGAAGAACGGGG-CACACGG
ACACGGTGTACCGGCCAGCTGCACGCCACCAGATTCCTCTCCAT------------------------------------
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------ATATATACACACACTACACGAGTCACACAA--------------------GTGGCGGACCAGCACCAGCACCAG
CACCAGACTGCAATCTCTACACTCAGAACCGGGCGGCTAGATATTCCGGGAGATACGTGCGTGCGTGCGTGCTCTGTGA-
-------AGTTTCCAGAGGATCTAGATCGCAGGGCACGTTCCTTTGCTTCTTGGAAGCCATGGATGCCCACCGTCACCGC
AGCTTGTTCGTCGTCGTCGTCGTGGCTGTCGCTGCGATAATCTTCACCATGGGCTTCGTGCGGTGTGCCGATGCCGCACG
ACCCGTGCCACCGAGCCCGGCGTCGTCCTCAACGGCGTCCGCGCTGGTGTCGTCGTTGATGGAGATGCTACCCATGGGGC
CGAGCGGAGGAGGCGCGGGGCACTGATCCGCTCAAGTTGATCGCTGGCGAGAAGCGTAGTGTAGACAGGTCTAGCTAGGG
AACGGATGTAACGCTGCTGCTGGCAGTTCTTTGTTCTTGGTCCTCCTTCTCTACCTGGCCATCTTCACT----TTTTTTT
TGCCCTACACTTGCAAGAGGTCTAGGAAGTGTCTGACATTTTATCTAAATAGTACCGTTGACATGA--GCAATAGCATGA
TGCAA---------------------------------------------------------------------------
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>chr3B_595
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---------TTCCTGTGTTCCAGCACGAACACAGCAGAGTCGGGCTCGGGCGGCCAGGTCAGCGCTTTTGCTCTGAGTTA
ATGCGGCGGCCGCTGCTCCCGGCGCACCGGCACGCAACGTCCGTCCATCCAAGCCTTGTTGACCGTCTCTTCCACGCGCC
GCAGCAGAAGGGACGGTCAGCGTTCCAGTCCAGCACGATAATTTCCAACCTAGTTGGCCGCGAAGAACGGGGGCACACGG
ACACGCTGTACCGGCCAGCTGCACGCCACCAGATTCTTCTCCCT------------------------------------
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------ATATACACACACACCACACGAGTCACCGCGTGCCTATTGAAGAATGAGCCGTGGTGGAC------TAGCACCAG
TACCATACTGCATTCAA---------AACCGGGCTGCACGT---------------------------------------
TCCATAGGGGTTTCAGAGGATCGAGATCGTAGGGCAGGTTCTTTTGCTTGTTAGCAGCCATGGACGGCCACCGTCACCGC
AGCTTGCTCTTCTTCCTCGTCGTGGCTGTCGCTTTG---ATCCTCGCCACGAGCTTCGTGCGGTGTACCGACGCCGTGAG
GACCATGCCACCGAGCCCGGCGTCCTCCTCCACGGCGTCCGCGCTGGTGTCGTCGTTGATGGAGATGCTACCCATGGGGC
CCAACGGAGGAGGCGCGGGGCACTGATCAGCTCAAGTTGATCGCTAGCGAGAAGCGTAGTATAGA---------------
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>SNPs
SS---S---------------S----S-----S---SS------------------------S---------------S-
S--S-------------------------------S--------S---S------SS--SS-------------S-S---
---------SSSS-SSS---SSS-SS------------------------------------------------------
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----------------------------------------S-----S-------S-------------------------
-S-------------------S---------S------------------------------------------------
----------------S-------S-----------------S--S-S---S-SS-------------------------
-------S------------S----S------------------------------------------------------
-----------------------------S------S--------------------------------S----------
--------------------------------S----------------------------------------S------
---S----------------------------------------------------S-----------------S-S---
------------S---S----------SS---S----S-SSSS-------------------------------------
--------------------S----------------S------------------------------------------
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----------------------------------------------S-S---S---------------------------
--------------------------------------------------S--------------------------S--
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------------------------------------SS-----S------------------------------------
------SS-----S--------------------------------------S-S--------------SSSS-------
------S--------------S---------S--------------S--SSSSSSSSSSSSSSSSSSS------S-----
-----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_986
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------GTGTGTCAACCCGTACGAGT------------------------------------------------------
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>reverse_3878
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-------------------------------------AACGCGGTTGATGTAGTCGT-----------------------
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