>input_sequence_67560
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---------------------------------------ATGACACAGCCTCCGCGACGACCCACCGCGACCGCCGAGCC
AGTCTTCCTCGGCGCCACATCCATCCCAAGTCCATGGCCCGAGCCGGCCACCAACATCCCCGTCTTTCGGCACCCGCCTC
CCCCGCCGCCGCCGCAGAAGCACCCGCACGGGAAGCACCGGTCCCGCCCCGCCCGCCTCATGCGTTCGGTGCGCGCCGCA
TTCCGTTCGTTCCCAATTCTCCCGGCACCGTCCTGCCGTGGGATGCCGTCGCTGCCCCACCTCCCGAGCCTCAACGGTGC
CAGCCTCGTCAGGAACCAGTTCCATGGCTCTACGCGCACCACGGGGACGCTGTACGGCCGCCGGCGGTCGCGCATCACCA
GCGCCTTCCACGACAACCCGGGAAGCCCGCCGGGATTGCTGTTGGAGATGTGCGTGCCGACGGCCAAGTTTATCCAGGAC
GTCAGCGCGGCCGGCATGGTGCGCGTCACGCTCGAGTGCGACAAGCAGCAGCAGTACCAGCATCAGCACGCGGGCGAAGC
GTCGCCGGCGCAACGGCAGCTTATGGACGAGCCGACCTGGTCGGCGGAGGTGAACGGCGAGAGCGTGGGGCACGCGTCTC
GGCGGGAGGCGACGGAGGAGGACGAGCGGGTGATGCGGCTGCTGTACGCCACGTCCATGGGCGCCGGCGTGCTGCCGGAC
GACGTGGCCGAGTATGCCAACGGCGAGCTCACGTACATGCGCGTGCACTTCGACCGCGTCGTGGGATCCAAGGACTCTGA
GACGTACTACGTGTACAATCCCGAGGGCACCGCCACCGGGCCGGAGCTCACCATCTTCTTCGTTAGGAATTGA-------
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>chr3A_1_TraesCS3A01G185000
AATGTGACCTTCGTGTTGGGGTAGATGCTCATCTCTGATGTCACCGCCTTCATCTTTGACTGGTCACCTCGGCCAGGTCG
CGAAATCGCCCGGGCTGAT--CTCGAGAGTTTGGCGTCATGCGAGATCCAGGAGCAGCAGGAGCCGGTTCAG-CAGACTC
AATGTTAGATCGGATCCATGAGTTGTCAGAGAAAGTCAAAATTTTCGACCCACCCACCACCCATCTCATTGCCAATGTCG
AGGAGCTCACTCTCCAAGAGGGATTCATCGAGGATGCAGAAGACATGGAGGAGGAAACCGACGAGTCCGTAGGCAACCAA
CTGTCAACACGGCACCCTCACATC-AGTGGCAGATGACTTCGAACTATGAGTTATACATGGTGGACAAGAACCCCACAAG
CCAAGGCTCGGGGCAGTGGCACGGAGAATGATCCC-GAGTACATGACGGGAGAGGAAAGTGAGCCCACAAGGGAGTCGTT
CATCTAGTGCTACATGATGTGGATGTGGAAGGAGAACCGGATGTCGGGTGCAGGGAATGAAATTGGCGGCGGCGATCAAA
AAGTGAGGGTGAGGAAG----------GGATAACCAGGCAGGAGGTGAGAAGGGGAAAGGAAAGAACTGGGATGGGTCAG
ACCTGGAGATTGGAGGGGAAATCGGGAGTTCATATTAGATTGATAAAGAAATGTCGAAATCAAGTTAACCTATAAATAAT
TATTCTTCAGCTGAGGAAAACCCAAACGTTACTTTCATGATTCCACTGAAGTACTCCGATTAACTGTCTTCTGTTTTTCG
GGCTGAACTGAGAAAGTCTAAGCAAAACAACATTTACATGCGCCTTCCTATTTTCACGTAGGGCCAATA-----GTTGGC
GCCAAGCCTATTCAAGGCATCCCTCCCCAACCGCACGTCTCTTTTCCCCCCCACATGCCCACCCACCATCGCCGCCGCCG
CGCCACCATCG---------------------------------------------------------------------
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----------------------------------------------------------------------TCGCACCCCG
CCAGACCGTCGCGCTGCCGCTGGCAGCGCCGACCACCACATGACACAGCCTCCGCGACGACCCACCGCGACCGCCGAGCC
AGTCTTCCTCGGCGCCACATCCATCCCAAGTCCATGGCCCGAGCCGGCCACCAACATCCCCGTCTTTCGGCACCCGCCTC
CCCCGCCGCCGCCGCAGAAGCACCCGCACGGGAAGCACCGGTCCCGCCCCGCCCGCCTCATGCGTTCGGTGCGCGCCGCA
TTCCGTTCGTTCCCAATTCTCCCGGCACCGTCCTGCCGTGGGATGCCGTCGCTGCCCCACCTCCCGAGCCTCAACGGTGC
CAGCCTCGTCAGGAACCAGTTCCATGGCTCTACGCGCACCACGGGGACGCTGTACGGCCGCCGGCGGTCGCGCATCACCA
GCGCCTTCCACGACAACCCGGGAAGCCCGCCGGGATTGCTGTTGGAGATGTGCGTGCCGACGGCCAAGTTTATCCAGGAC
GTCAGCGCGGCCGGCATGGTGCGCGTCACGCTCGAGTGCGACAAGCAGCAGCAGTACCAGCATCAGCACGCGGGCGAAGC
GTCGCCGGCGCAACGGCAGCTTATGGACGAGCCGACCTGGTCGGCGGAGGTGAACGGCGAGAGCGTGGGGCACGCGTCTC
GGCGGGAGGCGACGGAGGAGGACGAGCGGGTGATGCGGCTGCTGTACGCCACGTCCATGGGCGCCGGCGTGCTGCCGGAC
GACGTGGCCGAGTATGCCAACGGCGAGCTCACGTACATGCGCGTGCACTTCGACCGCGTCGTGGGATCCAAGGACTCTGA
GACGTACTACGTGTACAATCCCGAGGGCACCGCCACCGGGCCGGAGCTCACCATCTTCTTCGTTAGGAATTGATTAGTTA
ATCTTATTCTCCTCCACCCTTATTTTTCTCTTCGATTTGTTTTATCATCTC--CCCAGTCTTCTCTGTTTATTTTACGTA
TGTGTGCATAGATTGTACCGACTTATTATTATTTTAGCCTAGATTGTTTAAAATAAGTACAAAATGTA------------
---TAACTGAAATTTTTTAGAATAAAAGTTCTCGCTTGATATTATTTATAAAGGAAAATGTTATACATCCTAGGTTCGCT
CCGGAGCAAACACGCGTGATACAAAAATAGTTATGCGACGTCATGCACAAATCTCCACACACACCTCTGCTCACAAATCC
ATCATGGAGCAACCGTTCACTCCAATACTTCATCGCTCGAACGATTTTCTCATGTATATGTCACACCACCTACA-----C
CTACCTGTCCATTTTTCGA-CAATGTGCTAGCCATGGCGGCTCTCCATTTTAAGCACAAGCCGCAGTGCACCCCGGAATG
TCAATGTCGTCCTCGCCGACCACCTCCCCT---AAAAAAATCATCTCCAGATCCGGACGCCGCCTCACCGCCAGCCTCCA
AGGGCAAGACCCCGATCTTTGTCGCCGCCGCCATCAAGCCCTTGCCTTGGGTCCCTCGCTGGCGTAGCCACCGCCGCCGC
CGGCTGAGACAACGGCTATCC-TCGCTACCAATACCCAATGTCTCCCTCCCCTCGTCAATGTTTGGTCTGTGACATGTGC
AATGCGGCAGC--GCCACCCTTGTTGTTTGACCGTAGAGAGTCACCATCATCATGCACTACTAGGTTGAGGCCGCGATGG
TCGAAGTGGTTATAGCCATCTGAGTACCGCCACATCAACAACCTCGCCATCTCCCACCCTCAAGCTCCGTCGTGTCATCG
ACCTCGTCAACGTTGTCCTCCCTGTAGGGAAACGTTGCATGGAAAACAAAAAAAATTATACGGAAACGCAAGATCTATCC
ATGGAGATGCATAGCAACGAGAGGGGAGAGTGTGTCTACGTACCCTCGTAGACCATAAGTGG
>chr3D_4
---GTGACCTTCGTGTTTGGGTAGATGTTTATCTTCGATGTCGCCACCTTCATCGTTGACTGGTCACATCGGCCATGTCA
CAAATTTGCCTTGGGTTGATCCTCGAGAGTTTGGCGTCACGCTAGATCTAGGAGTAGCAGGAGCCGGTTCACCCAGACTC
AATGTTAGATCGGATCCATGAGTTGTCAGGGAAAGTCAAATTTTTTGACCCACCCACCACCCATCTCATTGCC-ATGTCG
AGGACCTCACTCTCCAGGAGGGAGTCATCGAGGAAGCAGAAGACATGGAGGAGGAAACCGACGAGTCCATAGGCAGTCAA
CCATCAACCACAGTGCCCGCATGCTAGTGGCAGGTGACTTTGACCTGTGAATTCTACGTGGTGGACACGAACCGCACAAG
CCAAGGCTCGGGA-AGTGGCATGGAGGATAATCCCTGAGTACATGACGGGAGAGGAAAGTGAG-----------------
-------------------------------GAGAACCGGATGTGGGGTGCAGGGAATGAAATCGGCAGTGGCGATCAAA
AAGTGAGGGCGGGGAAGATGCAGAGGGGGATAACCCGACATGAGGTCAGAAGGGAAAGGGAAAGAACTGGGATGGGTCAG
ACCTGGAGATTGGAGGGGAAATCAGGAGTTTAAATCAGATTGATAAAGAAATGTCCAAATCAAGTTAACC-ATAAATAAT
TTTTTTC-------------------------------------------------------------------------
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>chr3D_736
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------------------------------ACTTTCAAGATTGCACTGGAGTGCCCCGATTAACTGTCTTCTGTTATTCG
GGCTCAAGTGAGAAAGTCTAAGCAAAACAACATTTACAGGCGCCAG-CTATTTTCACGCAGGGCCAATAGACCCGTTGGC
GCCAAGCCTATTCAAGGCGTCCCTCCCCAACCGCACGTCTCTTTTCCCC-CCACATGCCCACCCACCATCGCCGCCGCCG
CGCCACCATC----------------------------------------------------------------------
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---------------------------------------------------------------------CTCGCACCCCG
CCAGACCGTCGCGCTGCCGCTGGCAGCGCCGACCACCACATGACACAGCCTCCGCGACGACCCACCGCGACCGCCGAGCC
AGTCTTCCTCGGCGCCACATCCATCCCAAGTCCATGGCCCGAGCCGGCCACCAACATCCCCGTCTTCCGGCACCCGCCTC
CCCCGCCGCCGCCGCAGAAGCACCCGCACGGGAAGCACCGGTCCCGCCCCGCCCGCCTCATGCGTTCGGTGCGCGCCGCG
TTCCGTTCGTTCCCAATTCTCCCGGCACCGTCCTGCCGTGGGATGCCGTCGCTGCCCCACCTCCCGAGCCTCAACGGTGC
CAGCCTCGTCAGGAACCAGTTCCATGGCTCCACGCGCACCACGGGGACGCTGTACGGCCGCCGGCGGTCGCGCATCACCA
TTGCCTTCCACGACAGCCCGGACAGCCCGCCGGGATTGCTGCTGGAGATGTGCGTGCCGACGGCCAAGTTTATCCAGGAC
GTCAGCGCGGCCGGCATGGTGCGCGTCACGCTCGAGTGCGACAAGCTGCAGCAGTACCAGCATCAGCACGCGGGCGAAGC
GTCGCCGGCGCAACGGCGGCTGCTGGACGAGCCGACCTGGTCGGCGGAGGTGAACGGCGAGAGCGTGGGGTACGCGTCTC
GGCGGGAGGCAACGGAGGAGGACGAGCGGGTGATGCGGTTGCTGTACGCCACGTCCATGGGCGCCGGCGTGCTGCCGGAC
GACGTGGCCGCGCATGCCAACGGCGAGCTCACGTACATGCGCGGGCACTTCGACCGCGTCGTGGGATCCAAGGACTCTGA
GACGTACTACATGTACAATCCCGAGGGCACCGCCACCGGGCCGGAGCTCACCATCTTCTTCGTTAGGAATTGATTAGTTA
ATCTTATTCTCCTCCACCCTTATTTTTCTCTTCGATTTGTTTTATCATCTCCCCCCAGCCTTCTCTGTTTATGTTACGTA
TGTGTGCATAGATTGTAGTGACTTATTATTATTTTAGCCTAGAATGTTTAAAATAAGAACAAAATGTAGCAAAATGTGAA
ATTTAACTGCAAATTGATAGAATAGGAGTTCTCGTTTGATATTATTTATAAAGGAAAATGTTATACATCCGACGTTCGCC
CCGGTGCAAACGCACGCGACACAAAAATAGTTATGCGACGTCATGCGCAAATTTCCACACACACCTCTGCCCACGAATCC
ATCATGGAGCAATCATTCGCTCCAGTACTTCATCGCTCGAACGATTTTCTCATGCATACGTCACACCACCTACATTTCCC
CTACCTATCCATTTTCCGA-CAATCTGCTAGCCATGGCGGCTCTCCATTTTAAGCACAAGCCGCAGCGCGCCCTGGAATG
TC-ATGTTGTCCTCACCGACCACCTCCCCTTG-AAAAAAATCGGCTCCAGATCCGGTCGCCTCCTCACCGCCAGCCTCCA
AGGGCAAGACCCCGATCTTTGTCACCGCTGCCATCAAGCCCTCGCCCTGGGTCCCTCGCTGGCATAGCCACCACTGCCGC
CGGCTGAGACCACGCCTATTCATCGCCACCAATAGTCAATATCCGCCTCCCCTCGTCATTCTTTGGTCTGCGACATGTGC
AATGCGGTGGCGTGCCACCCTCACTGTTTGACCGTAGAGAGTCACCATCACCATCCACTACAAGGTTGAGCCTCCGATGG
TCGAAGTGGCTATAGCCATTTGAGTACCGCCGCATCATCGACCTCGCCATCTC---------------------------
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>chr3B_767
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-------------------------------------------------------------AACTGTCTTCTGTTTTTCG
GGCTGAACTGAGAAAGTCTAAGCAAAACAACATTTACAGGCGCCTTCCTATTTTCACGCGGGGCCAATA-----GTTGGC
GCCATGCCTATTCAAGGCGTCCCTCCCCAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTCGCACCCCG
CCAGAACGTCGCGCTGCCGCTGGCAGCGCCGACCACCACATGACACAGCCTCCGCGACGACCTACCGCGACCGCCGAGCC
AATCTTCCTCGGCGCCACATCCATCCCAAGTCCATGGCCCGAGCCGGCCACCGACATCCCCGTCTTCCGGCAGCCGCCTC
CCCCGCCACCGCCACAGAAGCACCCGCACGGGAAGCACCGGTCCCGCCCCGCCCGCCTCATGCGTTCGGTGCGCGCCGCG
TTCCGTTCGTTCCCAATTCTCCCGGCACCGTCCTGCCGTGGGATGCCGTCGCTGCCCCACCTCCCGAGCCTCAACGGTGC
CAGCCTCGTCAGGAACCAGTTCCATGGCTCCACGCGCACCACGGGGACGCTGTACGGCCGCCGGCGGTCGCGCATCACCA
TCGCCTTCCAAGACAGCCCGGACAGCCCGCCGGGATTGCTGCTGGAGATGTGCGTGCCGACGGCCAAGTTTATCCAGGAC
GTCAGCGCGGCCGGCATGGTGCGCGTCACGCTCGAGTGCGACAAGCAGCAGCAGTACCAGCATCAGCACGCGGGTGAACC
GTCGCCGGCGCAACGGCGGCTGCTGGACGAGCCGACCTGGTCGGCGGAGGTGAACGGCGAGAGCGTGGGGTACGCGTCTC
GGCGGGAGGCAACGGAGGAGGACGAGCGGGTGATGCGGCTGCTGTACGCCACGTCCATGGGCGCCGGCGTGCTGCCGGAC
GACGTGGCCGAGCATGCCAACGGCGAGCTCACGTACATGCGCGGGCACTTCGACCGCGTCGTGGGATCCCAGGACTCTGA
GACGTACTACATGTACAATCCCGAGGGCACCGCCACCGGGCCGGAGCTCACCATCTTCTTCGTTAGGAATTGATTAGTTA
ATCTTATTCTCCTCCACCCTTATTTTTCTCTTCGATTTGTTTTAACATT---CCCCAGCCTTCTCTGTTTATTTTACGTA
TATGTGCATAGATTGTACTGACTTATTATTATTATAGCCTAGATCGTTTAAAATAAGAACAAAATGTA------------
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>chr3B_2027
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------------------------------------------TATTTATAAAAGAAAATGTTATACATCCGACGTTCGCC
CCGGAGAAAACACGCATGACACAAAAATAGTTATGCCACGTCATGAGCAAATCTCCACACACACCTCTACTCATGAATCC
ATCATGGAGCAACTGTTCAGTCCAATACTTCATCGCTCGAACGATTTTCTCATGCATACGTCACACCACCTACATTTCCC
CTACCTATCCATTTTTCCGCCAATCTGCTAGCCATGGCGGCTCTCCATTTTAAGCACAAGCCGCAGTGCACCCCGGGATG
TC-ATGTCGTCCTCGCCGACCACCTCCCCCTCAAAAAAAATTGGCTCCGGATCCGGTCGCCGCCTCACCGCCAGCCTCGA
AGGGCAAGACCCCGATCTTTGTTGCCGCCG-CATCAAGCCCTCGCCATGGGTCCCTTGCTAGCATAGCCACGACCACCGC
CGGCTGAGACAACGCCTATCC-TCGCTACCAATACCCAATATCTGCCTCCCCTCGTCATTGTTTGGTCTGCGTGATGTGC
AATGCGGTGGC--GCCACCCTCGCTGTTTGACCGTAGAGAGTCACCATCATCATGCACTACGAGGCTGAGGCCGTGATGG
TTGAAGTGGTTATAGCCATCTGAGTACCACCGCATCA-------------------------------------------
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>SNPs
SSS--------------S---------S-S----SS------S--S--------S------------S-------S---S
-S--S-S---SS--S-SSS--------------------S--S-----S-----S----------------S--------
-----------------------------S----------S----S---------------------------S------
----S-----------S------S----------S---------------------------------S------SS---
-SS-----SSSSSSS--SSSSSS----------S------S--S--S---S--S---S---------S-----S------
------------SS-------S----S--S---------------------------------SSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-------------S------------------S---S-S----------
---------S-S-----------------------S-S--S-----S-------S--S----------------------
-----------------------S------S-S--S-------------------S--------------S---------
-S--S-SSSSSSSSSSSSSSSSSSSSSSSS-------S----S-----S---S-S-------------------------
--------------------------------------S-------------------S---------------------
------------------S------------------------------S------------------------------
----------S---------------------------------------------------------------------
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------------------------------------------------------------------S-------------
-------------------------------------------------------------------------------S
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------------------------------S-------------------------------------------------
S--------------S-----SS------------------S--------------------------------------
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-----------------S---SS-----------------------------------------------S---------
----------S---------------------------------------------------------------------
------------S------------------------------S------------------------------------
----------S---------------------------------------------------------------------
----------------------------------------------------------S---------------------
------------------S--------------------------------------S----------------------
---------S--S--SS-------SS--------S-----------------------------------S-S------S
-------------------S--------------------------S---------------------------S-----
------------------------------------------------------S---S---------------------
------S-----------------S-------------------------------------------------------
--S---------------------------------------SS------------S-----------------------
------------------------------------------S---S----------------S--------S-------
--------------S-------------------------S---S-------------S-----------S---------
-------SS------------S-S-------------------------------------S------------------
-------------------------------S-----S-S-------------SSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_468
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------------------------------------------------GGAGAGGAAAGTGAGCCCAC------------
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>reverse_2091
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----------GTGTACAATCCCGAGGGCAC--------------------------------------------------
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>forward_472
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----------------------------------------------------AGGAAAGTGAGCCCACAAGG--------
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>reverse_2539
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----------------------------------------------------------TGTCACACCACCTACACCTAC-
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