>input_sequence_74041
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----ATGGGCTTCCCGGTCGGCTACTCCGAGCTGCTGCTCCCCAAGCAGCTGCTCCACCTCCTCCTCCTGCTCGGCTACC
TCCGCCGCTTCCTCCTCTGGGCCTTCGACGCCGTCGGCCTCGGCGACCTGCTGGATCTCGGGGACGAGCACCT-------
-----GGCGCAGGAGCACGCGCGCGCCGACCACGCCGCCG------CGGCGCACCACGCGCTGCTGCTGCAGCACCGCCG
GCCCGAGTTCCGGCCCGTGACGGCCATGGTCA---TCGAGGAGGTGCTCCCCGTGGTGCGGTTCGACGAGCTGGAGGCCG
CGGC---------GTGCGTCGACGGGGACTGCGCCGTGTGCCTCAGCGGCATCGGCGGCGGCGACGAGGTGCGGCGGCTC
AGCAACTGCCGCCACGCCTTCCACCGGGGGTGCCTGGACCGCTGGATGGAGCACGACCAGCGCACCTGCCCGCTCTGCCG
CGCCCTGCTCATCCCCGACGAGATGGCCGGCGCTCTCTGGGCCACCGCCGCCGGCGTGCCCGACGCCTCCGACTTCGACT
TCTTCTACCTGGGCGCCTCGGCGCCA---GCCACCCCGACGCTGCTGCGGCCGCACGAGCTGCTGCTCACCGGCCTCGGC
GGCTACCAGTGA--------------------------------------------------------------------
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>chr2D_1_TraesCS2D01G393400
ATTCATGTTGTCCACACGATGAGCGCTCAATATGTTTA-GCATGCAGTTAATATCCTTAAAGGATCCAATGCCAACGA-T
TTTTAAGAATCTATCAATGACAACGTTAATTACATAATTAGCACATAAATAATATCCCACCCAATATCTGTGTGCAACCA
ATATACTGCCTAATAATTTTT--GAATGCCAGCAATTTTTTGAGAATCTATCAATGATAGTTAGTAATATCATTCAAAAT
ATTAATGCCGGCGATTTTTTGAGAATCTATCAATTATGTAATTAGCACATAAATAATATCCAAAAGATTTGTGTGCAACT
AATATACACTGCCTAATATATATTTTTTGAACTGCCTAATATTAATACCATGCATTATTACTA---GTAATTTTGAAATA
CAATCCGTTTTCTACTATGCACCCTATGCATCTAGTCGGAAATAGCACT-GAGGATCAACGTGTGCATCTACGGTACGGG
TACATGCACCGGGGTTGGGAATCGGATGAACGGTGCACGCACCCGTACGCGCGCCCGTTTCCGTTGCCAACGTGCAGTGC
ACCGACCGTTGAGGGCACACCAGTTGGGGGATCAGGAGGCGAGCGGACCACCCGCACGTCAGACGGGCCACGCGCGCGGG
GGGTCGCGGTGACACCCGGCCCGGCG------------GCGGGCGGGCCAGTCAGTCACACCGACTCGCGGGGCTGGCTG
GGATTGGGAGTCGGTCATCGGGTCAGAGTCGCGCGCACGACACACCGGTGACACCACGCCACCCAACCCCAACCCCAACC
GGA--------------CGCTGCCACCCCCACCCAGCCGGATCCTTCCCCGCGCCGCTCCTTCGCTTTTATATAAGCCGG
CCTCGCCTCGTCTCGGCCTCCCCACGCCTGCCACCACCACCACCACCAGCGCACCATCGTCCTCACACTTGCCTCTCATC
CTCCCTGCCGTGCCGAGACCGCAGCGGTCAGCAGGCGGCGCGGACGCTTCTCCTTGGC----------AAGGCGAGCGAC
AGGCATGGGCTTCCCGGTCGGCTACTCCGAGCTGCTGCTCCCCAAGCAGCTGCTCCACCTCCTCCTCCTGCTCGGCTACC
TCCGCCGCTTCCTCCTCTGGGCCTTCGACGCCGTCGGCCTCGGCGACCTGCTGGATCTCGGGGACGAGCACCT-------
-----GGCGCAGGAGCACGCGCGCGCCGACCACGCCGCCG------CGGCGCACCACGCGCTGCTGCTGCAGCACCGCCG
GCCCGAGTTCCGGCCCGTGACGGCCATGGTCA---TCGAGGAGGTGCTCCCCGTGGTGCGGTTCGACGAGCTGGAGGCCG
CGGC---------GTGCGTCGACGGGGACTGCGCCGTGTGCCTCAGCGGCATCGGCGGCGGCGACGAGGTGCGGCGGCTC
AGCAACTGCCGCCACGCCTTCCACCGGGGGTGCCTGGACCGCTGGATGGAGCACGACCAGCGCACCTGCCCGCTCTGCCG
CGCCCTGCTCATCCCCGACGAGATGGCCGGCGCTCTCTGGGCCACCGCCGCCGGCGTGCCCGACGCCTCCGACTTCGACT
TCTTCTACCTGGGCGCCTCGGCGCCA---GCCACCCCGACGCTGCTGCGGCCGCACGAGCTGCTGCTCACCGGCCTCGGC
GGCTACCAGTGAGCCGAGCCCCCGATTCGGTCCAGGCAAAATTGTCCGCCGCCGTCCAGAATGCGCAATTTTACAGGACT
GAATTGGTCTCCGCGTCCGGACGCCGGCGGGCTGCCTGGCCCCAGCCGTGTACATAGGGCGAAATGAGTAAAGTAACCGC
CCCGAAAAGGGCTAGGAGATTAGATTCTTGTTATGTATAGCTAGATTCCATCTTCCAAGTTTGCGGAGCTGTGGATCTT-
---TTCTTCTGCCAATTAAATTTGTTGATGAGTTAGGCGTTCCGGGTGCAAAATTTCGGTCCCCTTTGCTCCTTCTCTTT
CCCCGTGTTGCTCAGGC------------------------ACATATACTAGTAGTACAAATTTAGAAAGGCTTCAATCA
ACTTCCCCCGCAGAGCGTACAAATTTAGGAAGGATTTTACATCGGCCGAGGA-------TTTCTGAAACCATATGCATCC
TGGCAAGTGGCAGGAAATTTAGGCTCCGACAGTACAGCCGCAGCCTTCCCTTGATTGGATCTACTAGTGTAGTACCGTTG
TTATTG------CTACAACTGCTGACACTGAAACCCATGCAGTAGGGCAGTGGAAGAATGTTCTGGAATGCTAGTAAATT
AGGTGAAAATGAACAGATTTGAACCTTCTTTTAGAAACTTACGATACAAAATACTACAGTGCTTCCGTTTACTCCCTCCG
TCCCATAATGTAAGACGTCTTTTGACACAACACTAGTGTCAGAAAACGTCTTACATTATGGGACAGAGGGAGTATATTTT
TAGAAATTTCAATACAAACTACATACGGATGTATATAAACATACTTTAGAGGATATATTCATTCATTTTGCTCCGTATGT
ACTCCCTCCGTTTCAAAATTCTTGTCTTAGATTTGTCTAGATACAGATGTATCTAATACTAAAACGTGACTTGATACATC
CGTATTTAGACAAATTTAAGACAAGAATTTTGGGACAGAGGGAGTAGTTTCTTATTGGAATCACTAAAAAGACTTATATT
TAGGAACGAAGGG
>chr2B_7
------GTTGCCCACATGATGATCGCTCAATATATTTTTGCATGCAGTCAATGTCATTCAAAATATCAATGCCAACGATT
TTTTGAGAATCTATCAATGCCCGCGCTAATTATATAATTAGCGCATAAATAATAACCCACCTAATATCCGTGTGCAACTA
ATGTACTCCCTAATATTTTTTTAGAATGCCAGCGATTTTTGTAGAATCTATCAATGCCATTTAATATA---ATTCAAAAT
ATCAATGTCGGCGATTTTTTGAGAATCTATCAATGCG------------TAAATAATATCCAAAATATCCGTGTGCAACT
AATATAC-----------------------ACTGCCTAATCTTAACACCATGCATTATTACTACTAGTAATTTTGAAATA
ATATCTGTTTTCTACTATGCACCCTATGCATCTAGTCGGAAAGAGCAGT-AAGGATCAACGTGTGCATCTACGGTACGGA
TACATGCACCGGGGTTGGGA------TGAACGGTGCACGCACCCGTACGCGCGCCCGTTTCCGTTGCCAACGTGCAGTGC
ACCGACCGTTGAGGGCACACCAGTTGGGGGATCAGGAGGCGGGCGGACCACCCGCGCGTCAGACGGGCCACGCGCGCGGG
GGGTCGCGGTGACACCCGGCCCGGCGGCGGGCGGGCAGGCGGGCGGGCCAGTCAGTCACACCGACTCGCGGGGCTGGCTT
GGACTGGGAGTCGGTCATCGGGTCAGGGTCGCGCGCACGACACACCGGTGACACCGCGCCACCCAACCCCAACCGGACGC
ACGCTACGGTACGCTAGCGCTGCCACCCCCACCCAGGCGGATCCTTCCCCGCCCCGCTCCTTCGCTTTTATATAAGCCAC
CCTCGCCTCGTCTCGGCCTCCCCACGCCTGCCACCACCACCACCACCA---CACCATCGTCCTCACACTTGCCTCTCATC
CTCCCTGCCCTGCCGAGACTGCAGCAGTCAGCCGGCGGCGCGGACGTCTCTCCTTGGC----------A-----AGCGAC
AGGCATGGGCTTCCCGGTCGGCTACTCCGAGCTGCTGCTCCCCAAGCAGCTGCTCCACCTCCTCCTCCTGCTCGGCTACC
TCCGCCGCTTCCTCCTCTGGGCCTTCGACGCCGTCGGCCTCGGCGACCTGCTGGATCTCGGGGACGAGCACCT-------
-----GGCGCAGGAGCACGCGCGCGGCGACCACGGCGCCG------CGGAG------GC---GCTGCTGCAGCACCGCCG
GCCCGAGTTCCGGCCCGTGACGGCCATGGTCA---TCGAGGAGGTGCTCCCCGTGGTGCGGTTCGACGAGCTGGAGGCCG
CGGC---------GTGCGTCGACGGGGACTGCGCCGTGTGCCTCAGCGGCATCGGCGGTGGCGACGAGGTGCGGCGGCTC
AGCAACTGCCGCCACGCCTTCCACAGGGGGTGCCTGGACCGCTGGATGGAGCACGACCAGCGCACCTGCCCGCTCTGCCG
CGCCCCGCTCATCCCCGACGAGATGGCCGGCGCGCTCTGGGCCACCGCCGCCGGCGTGCCCGACGCCTCCGACTTCGACT
TCTTCTACCTGGGCGCCTCGGCGCCCA---CCACCCCGACGCTGCTGCGGCCGCACGAGCTGCTGCTCACCGGCCTCGGC
GGCTACCAGTGAGCC-----CCCGATTCGGTCCAGGCAACTGG--CCGCCGCCGTCCAGAATGCGCAATTTTACAGGACT
GAATTGGTCTCCGCGTCCGGACGCCGGCGAGCTGCCTGGCCCAGGCCGTGTACATAGGGCGAAATGAGTAAAGTAACCGC
CCCGAAAAGGGCTAGGAGATTAGATTCTTGTTATGTATAGCTAGATTCCATCTTCCAAGTTTGCGGAGCTGTGGATCTT-
---T-CTGCTGGCAATTAAATTTGT---TGAGTTAGGCGTTCCGCGTGCAAAATTTCTGT-CCCTTTGCTCCTTCTCTTT
CCC-GTGTTGGTCAGGCCGTTCAGCCGCTTGGCTTTTCGGTACATATACTAGTAGTACAGATTTAGAAAGGCTTCA-TCA
ACTTCCCCCGCTGAGCGTACAAATTTAGGAAGGATTTTACATCAGCCGAGGA-------TTTCTGAAACCATATGCATCC
TGGCAAGTGGCAGGAAATTTAGGCTCCGACAGTACAGCCGCAGCCTTCCCTTGATTGGATCTACTAGT--AGTACCGTTG
TTATTG------CTACAACTGCTGACACTGAAACCCATGCAGTAGGGCAGTGGAAGAATGTTCTGGAATGGTAGTAAATT
AG------------------------------------------------------------------------------
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>chr2A_403
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---------TTCTACTATGCACTCTATGCATCTAGGCGGAAAGAGCACTTAAGGATCAACGTGTGCATCTAGGGTACGGG
TACATGCACCGGGGTTGGGA------CGAACGGTGCACGCACCCGTACGCGCGCCCGTTTCCGTTGCCAACGTGCAGTGC
ACCGACCGTTGAGGGCACACCAGTTGGGGGATCAGGAGGCGGGCGGACCACCCGCGCGTCAGACGGGCCACGCGCG----
--------GTGACACCCGGCCCGGCGGCGGGCGGGCGGGCGGGCGGGCCAGTCAGTCACACCGACTCGCGGGGCTGGCCG
GGACTGGGAGTCGGTCATCGGGTCCGGGTCGCGCGCACGACACACCGGCGACGCCGCGCCACCCAACCCCAACCGGACGC
ACGCTAGC---CGCTAGCGCTGCCACCCCCACCCAGCCGGATCCTTCCCCGCCCCGCTCCTTCGCTTTTATATAAGCCGG
CCTCGCCCCGTCTCGGCCTCCCCACGCCTGCCACCACCACCAG---CA---CACCGTCGTCCTCACACTTGCCTCTCATC
CTCCCTGCCGAGG-----CCGCAGCGGTCAGCAGGCGGCGCGGACGCTTCTCCTGGGCAAGGACAGGCA-----AGCGAC
AGGCATGGGCTTCCCGGTCGGCTACTCCGAGCTTCTGCTCCCCAAGCAGCTGCTCCACCTCCTCCTCCTGCTCGGTTACC
TCCGCCGCTTCCTCCTCTGGGCCTTCGACGCCGTCGGCCTCGGCGACCTGCTGGATCTCGGGGACGAGCACCT-------
-----GCCGCAGGACCACGCGCGCGCCGACCACGCCGCCG------CGGCG------GCGCAGCTGCTGCAGCACCGGCG
GCCCGAGTTCCGGCCCGTCACGGCCATGGTCA---TCGAGGAGGTGCTCCCCGTGGTGCGGTTCGACGAGCTGGAGGCCG
CGGC---------GTGCGTCGACGGGGACTGCGCCGTGTGCCTCAGCGGCATCGGCGGCGGCGACGAGGTGCGGCG----
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-----------------------------AGCTGCCTGGCCCCAGCCGTGTACATAGGGCGAAATGAGTAAAGTAACCGC
CCCGAAAAGGGCTAGGAGATTAGATTCTTGTTATGTATAGCTAGATTCCATCTTCCAAGTTTGCGGAGCTGTGGATCTTC
CTTT-CTTCTGCCAATTAAATTTGTTGATGAGTTAGGCGTTCCGGGTGCAAAATTTGGGT-CCCTTTGCTCCTTCTCTTT
CCCCGCGTTGGTCAGGCCGTTCGGCCGCTCGGCTTTTCGTTGCATATACTAGTAGTGCAAATTTAGAAAGGCTTCA-TCA
AATCCCCCCGCTGAGCGTACAAATTTAGGAAGGATTCTACATCAGCTGAGGATTTTTCCTTTCTGAAACCATATGCATCC
TGGCAAGTGGCAGGAAATTTAGGCCCCGACAGTACAGCCGCAGCCTTCCCTTGATTGGATCTACTAGT--AGTACCGTTG
TTATTGCTACTCCTACAACTGCTGACACTGAAACCCATGCAGTAGGGCAGTGGAAGAATGTTCTGGAATGGTAGTAAATT
AGGTAAAAATGAACATATTTGGCCCTTC--TTCGAAACTTACAATACAAAATACTAC-----------------------
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>chr6B_990
GATCGACGC-----------------------------------------------------------------------
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---CATGGGCTTCCCCGTGGGATACTCGGAGCTGCTGCTCCCCCGGCTGCTCCTGCAGGCGCTCCTCCTCCTCGGCCACC
TCCACCGCTTCCTCCTCTGGGCCTTCCACGCCGTGGGCCTGGGCGACCTCATCGACCTCGGCGGCAGCGCGCCCA-----
-CGGCGGAGGAGGCGCAGTGGCACGCGCACCACGGGGCAG------CGCCC------TCGCCCTCGCTGCAGCACCGGCG
GCCCGACTTCCGCGCGCTGCCGCCGATGGCCGCCGTCGAGGAGGCGCTCCCCGTGCTGCGGTTCGACGAGCTGGTGGCGT
CCTCCCCGTCCGTGTGCGGGGACGGCGACTGCGCCGTCTGCCTCTGCGGCATCGGCGGCGGCGACGAGGTGCGGCGGCTG
TCCAACTGCCGCCACGTCTTCCACCGCGGCTGCATCGACCGCTGGATGGGGCACCAGCAGCGCACCTGCCCGCTCTGCCG
CGCCCCGCTCATGCCCGG---------CGACGCGCTCTCG---------GCCGACCTCCCGGACGCCTCCGACTACGACA
TGTCCTACCCGTCCCCGCTGCCGCTGGCGGCCACCCCCACCCTGCTGCGCCCGCACGAGCTGCTGCTCAACGGCCTGGGC
GGCTTCCAGTGAG-------------------------------------------------------------------
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>chr6D_993
---CGACGC-----------------------------------------------------------------------
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---CATGGGCTTCCCCGTGGGGTACTCGGAGCTGCTGCTCCCCCGGCTGCTCCTGCAGGCGCTCCTCCTCCTCGGCCACC
TCCACCGCTTCCTCCTCTGGGCCTTCCATGCCGTCGGCCTGGGCGACCTCATCGACCTCGGCGGCAGCGCGCCCACCGCC
ACGGCGGAGGAGGCGCAGTGGCACGCGCACCGCGGGCCGG------CGCCC------TCGCCCTCGCTGCAGCACCGGCG
GCCCGACTTCCGCGCGCTGCCGCCGATGGCCGCCGTCGAGGAGGCGCTCCCCGTGCTGCGGTTCGACGAGCTGGTGGCGT
CCTCGCCGTCCGTGTGCGGGGACGGCGACTGCGCCGTCTGCCTCTGCAGCATCGGCGGCGGCGACGAGGTGCGGCGGCTG
CCCAACTGCCGCCACGTCTTCCACCGCGGCTGCATCGACCGCTGGATGGGGCACGGGCAGCGCACCTGCCCGCTCTGCCG
CGCCCCGCTCATGCCCGG---------CGACGCGCTCTGG---------GCCGACCTCCCGGACGCCTCCGACTACGACA
TGTCCTACCCGTCCCCGCTGCCGCTGCCGGCCACCCCGACCCTGCTGCGCCCGCACGAGCTGCTGCTCAACGGCCTCGGT
GGCTTCCAGTGAG-------------------------------------------------------------------
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>chr6A_993
---CGACGC-----------------------------------------------------------------------
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---CATGGGCTTCCCCGTGGGGTACTCGGAGCTGCTGCTCCCCCGGCTGCTCCTGCAGGCGCTCCTCCTCCTCGGCCACC
TCCACCGCCTCCTCCTCTGGGCCTTCCACGCCGTCGGCCTGGGCGACCTCATCGACCTCGGCGGCAGCGCGCCCGTGCCC
ACGGCGGAGGAGGCGCAGTGGCACGCGCACCACCGACCGGCGCCCTCGCCC------TCGCCCTCGCTGCAGCACCGGCG
GCCCGACTTCCGCGCGCTGCCGCCGATGGCCGCCGTCGAGGAGGCGCTCCCCGTGCTGCGGTTCGACGAGCTGCTGGCGT
CCTCCCCGTCCGTGTGCGGCGACGGCGACTGCGCCGTCTGCCTCTGCGGCATCGGCGGCTGCCACGAGGTGCGGCGGCTG
CCCAACTGCCGCCACGTCTTCCACCGCGGCTGCATCGACCGCTGGATGGGCCACGGGCAGCGCACCTGCCCGCTCTGCCG
CGCCCCGCTCATGCCCGG---------CGACGCGCTCTGG---------GCCGACCTCCCGGACGCCTCCGACTACGACA
TGTCCTACCCGTCCCCGCTGCCGCTGGCGGCCACCCCGACCCTGCTGCGCCCGCACGAGCTGCTGCTCAACGGCCTGGGC
GGCTTCCAGTGAGC------------------------------------------------------------------
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>SNPs
SS--SS----S-----S-----S----------S---S----------S---S--S--S--SSSSS--------------
----S--------------S-SS--S------S---------S-----------S------S------S---------S-
--S----S-------S-----------------S------SS--------------SS-S---S--SSSSS---------
--S----S--------------------------SSSSSSSSSSSSSSS----------------S--SS----------
-------SSSSSSSSSSSSSSSSSSSSSSS----------S----S----------------------------------
SS---S------------------------------------S-------S-----------------------------
--------------------SSSSSS------------------------------------------------------
-----------------------------------------S-------------S------------------------
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---S----------------------S----------------------------S------------------SS-SS-
SSS-------------------------------------------------S---------------------------
------------------------------------------------SSS-----------------------------
---------------------------------------------------------------------SSSSS------
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---------------------------------------------------SSSSSS----S------------------
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-----S---------------------------S----------------------------------------------
-------------------------S------------------------------------------------------
---------------SSSSS-------------------SSSSSS-----------------------------------
-----------------------------S--------------------------------------------------
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----S-------------------------------------------------------S-------------------
----------S-----------------------------------------------------------------S---
-----------S-------------------------------S------------------------------------
--------------------------------------------------------------------SS----------
----------------------------------------------------------------------S---------
----S----------S-----SS-----SS--S---------S--------------SSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSS
>forward_747
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--------AGTCGGTCATCGGGTCAGA-----------------------------------------------------
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>reverse_2381
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------------------------------------------------------------GCTTCCGTTTACTCCCTCCG
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