>input_sequence_87100
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----------------------------------------------------------ATGGAGTAC------CGGTACA
GCAGCAGCGGCGGCGGGGGCGGCAGCTTC------GTCAAGGAGAAGAGGCCTCCGGCGAAGAGGGGTCAGGTCAAGCTC
CAGATAGCGAGGGCGCTGAGCAACCTCGTGTCTCCTGGCACCGCTGCTGACGGCTCCAAGCAGGCAAATCGCAGCAGTTT
CAGAAGGGAAACAAGCTACAACTGA-------------------------------------------------------
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>chr1A_1_TraesCS1A01G289700
CCATGCATGTTGCTTGATGATGTGGCATGCTTATATGTTAAGAGAAATATATTAGTGGGGGCTAGCTATTTAGATATAGA
AGATTCCTCTAACCTATGTAGCGCATAATCAATCCTTGGTCCACACGTGCGCCTCGCCCAAAAGTCGTGAAACGAGAGTT
AGACTCTCGGTCGACCACCGTGGTCCGTGGAAATATCTTCATCAAAAGGACGACGGTGATGAAAA------------TAT
CTTCAAGAGGATGTTGTTCGCGAAAGAATATCTGAGAGTGGAAAGCTGATATTTGTTACATTTGCCGTCCGTAGTGTTAT
ATACTTTGGTCGATGGAAACTATATCAAGTAGCATGTGTCCTACCGAAACATCTTATATTTTGATATGGAGAGAGGTAAT
ACTTCTTTTTTTCGAGAATGAGGGAGGTAATACTTACTAGTGCTAGTCACAGATCAGATGTTTTTATCTAGAGACGCACC
TACTTACTCAGGGGGTGTCGAAAAGATTAAAATCCTTCAATCTATTCAATAACTCTCTTGCTAAAAGCAAAAA--AAAAG
TCTGAAAATGAAAAAGCAGAAGAAAAAACTCTCTCTTGCTGTGCTGTTGGTTCCTTGGAACACTTCACTACTGCTTCAAA
TTCCTAGTGTGTCCGTTTCTAAAAGAACAAAAATATTCCCAGTGTGCAGGCACAAATTCTCTGGTGA-TTTAGTTCCGTG
ATCTCGTTTACACCTGGAATCTTGGATAGTTGGATTCCCCCGGTATGCAGATACGTTCAGACTTCGAACACCATGGCCCC
AAAAGCACGGCCACTTTATTCCTGCAGATATAAGTGAATAAATACGAATATAAGATGCACACACCAACTGGTGCAGGCAA
CGTACATTGCATACGCCTATAAATACCTCTACA--TCATCATCCCTTTCACAAGTGAGCACCTGGCTTCACCACACAGTA
CATACGGTGCAGCACACAACACAAAAGAAGCAGCG-AGAAGATCGGCCGGCGGAGGCGATGGAGTAC------CGGTACA
GCAGCAGCGGCGGCGGGGGCGGCAGCTTC------GTCAAGGAGAAGAGGCCTCCGGCGAAGAGGGGTCAGGTCAAGCTC
CAGATAGCGAGGGCGCTGAGCAACCTCGTGTCTCCTGGCACCGCTGCTGACGGCTCCAAGCAGGCAAATCGCAGCAGTTT
CAGAAGGGAAACAAGCTACAACTGAAC-AAGAGATTTAGATGGGTATGGTGCGCCTGTGTGGG-----------------
-------TTACTAGCTAGCTGT--TTTATTACCTATTGAGGGTTTTAGCAGGATCGTGTCCCAGTTTATAAATGGAGAAC
CTGTCTGATCCACATACACTATACTGTAACTTGGCTTGAGTGGGAAATGCTCCAAGCTTGAGCGTGCATTGTGCATGTAT
TTCAAGAAGAAATTTACATGTATATACATACAAGCTTTTGAGTATGCATGACACCCAGCG------TGTGCTTGATTAGG
AGTGCTCCTGTATGACACTTCGAGATCGATTAGTTTGATGCCAACATTTGTCTTGCACATTTTGGCAAGTTAAAGAAGAC
TACTAACTGGATGAGGGATCCAAAATAAGTGTCAGTTCACA---------AAAATAAC-TGGTAAGTTTTG--TTTTTGC
TAAATGTTGGCTTGTTAAA---TTTTTTGTAAAGCCATATATTGGCATCAAACCAACTGGCC-TTCACCCGGCAATAAAA
AAAA--GGCCTCCCGCTGCGTCGTT-------------------------------------------------------
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-----CTGTCCATTAAACATGCAAGCGCGTGTGTTCGTGGGCCGGCCCTATTCAGTTTGGTGATGTATT----CCATTAA
CAAGTGCTTCACTTGCCCGTTCCAATGATTTGTTTAGTTTTCTTTCAGGTTGTTCCGTAGTCAGTTTGTTTGTTTATACA
TAAAAGCATTAACATTGTTTAATTTCAAAAAATGAACACTGTTTTAATTACACGAAAGTTTTTCAAAAATTTATACACAT
TTCTTTAAAAATGATTTTTAAATGCATGAGCACTTTTTT----AAATGTATGAACACTTACTGTTCATCATGTATTTAAA
AAAAATTCAACTTGTGTTCAAAATGTTCACCTTGTACATAAAACTGTTCACTGTCTAGTTTTAAAATAATTTTAACATGT
ATTTTAAAAAATGCTCAGAAAACGTAT------------TTTACTACTGAAAATAGGAGGAAATGAACAAAAAGGAAATA
TAGAAAGGATAAATAAACCAGGAAGAAAACTAAAAA--------------------------------------------
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>chr1D_83
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--ATTCCTCAAACCTATGGAGCGCATAATCAACCCTTGATCCACACGTGCACCCTGCCCAAAAGTCGTGAAAAGAGAGCT
GGACTCTCGGTCGACCACCGTGGTCCGTGGAAATATCTTCATCCATAGGACGATGGTGATGAAAATATCTTCAGAAGTAT
CTTCAAGAGGATGCTGTTCGCGAAAGAATATCTTAAAGTGGAAAGCTGATATTTGTTACATTTACCGTCCATAGAGTTAT
ATACTTTGGTCGATGGAAATTATATCGAGTAGCGTGTACCCTACAAAGACGTCTTATATTTTAATACGGAGGGAGGTAAT
ACTT-------------------------------ACTAGTGCTAGTCACAGATCAGATGTTTTTATCTAGAGACATACC
TACTTACTCAGGGGGTGTCGAAAAGATTAAAATCCTTCAATCTATTCAATAACTCTCTTGCTAAAACCAAAAAACAAAAG
TCTGAAAATGAAAAAGCAGAAGAAAAAAAACTCTCTTGCTGTGCTGTTGGTTCCTTGGAACACTTCACTACTGCTTCAAA
TTCCTAGTGTGTCCGTTTCAAAAAAAT---AAATATTCCCAGTGTGCAGGCACAAATTCTCCGGTGA-TTTAGTTCCGTG
ATCCCGTTTACACTTC--------GATAGTTGGATTCCCCCGGTATGCAGATACGTTCACAATTGGAACACCATGGCCCC
AAAAGCACAGCCACTTTATTCCTGCAGATATGAGTGAATAAATACGAATATAAGATGCACACACCAACTGGTGCAGGCAA
CGTACATTGCATACGCCTATAAATACCTCTACA--TCATCATCCCTTTCACAAGTGAGCACCTGGCTTCACCACACAGTG
CAGA-GGTGCAGTACACAACACAAAAGAAGCAGAGAAGAAGATCGGACGGCGGAGGCCATGGAGTACGAGCACCGGTACA
ACAGCAGT------------GGCAGCTTG------GGCAAGGAGAAGAGGCCTCCGGCGAAGAGGGGGCAGGTCAAGCTG
CAGATAGCGAGGGCGCTGAGCAACCTCGTCTCTCCCGGCGCCGCTGCCGACGGCTCGAAGCAGGCAAATCGCAGCAGCTT
CAGAAGGGAAACAAGCTACAACTGAACCAAGGAAATTAGATGGGTATGGTGCGTCCGTGTGTCAGTGTGGGGTGCAAAAT
GGTGGTATTACTAGCTAGCTGT--TTTGTTACCTTCTGAGGGTTTTAGCAGGATGGTGTCCCAGTTTATAAATGGAGAAC
CTGTCTGATCCACTACCACTGTACTGTAACTTGGCTTGAGCGGAAATTGCTCCAAGCTTGAGTGTGCATTATGTA-----
TTCAAGAAGAAATTTAAATGTATATACAAGC-----TTTGAGTATGCATAACACCCAGCA------TGTGCTTGATTAGG
AGTGCTCCTGTATGACACTTCGAGATCGATTGGTTTGATGCCAACATTTGTCTTGCACATTTTGGGAAGTTAAGAAAAAC
TACTAACTGGATGAGGGATCCAAAATAAGTGTCGTGGCTTTAGTTAAAAAAAAAAGAACTGGTAAGTTTTATTTTTTTGC
TAAATTTTGGTTTTTCAATTTTTTTTTTGTAAAGCCATATATTGGCATCAAACCAACTGGCCTTTCACCCGGCCAAAAAA
AAAACTGGCCTCGCACTGGGTCGTT-------------------------------------------------------
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-----CTGTCCATTAAACATGCAAGCGCGTGTGTTCGTGGGCCAGCTCGATTCAGTTTGGTGATGTATCCTTCCCATTAA
CAAGTGCTTCACTTGCCGGTTCCAACGATTTGTTTTATTTTCTTTCAGGTTGTTCCGTAGAG-GTTTGTTTGTTTATACA
TAAAAGCATTGACATTGTTTAATTTCAAAATATGATCACTCTTTTAGTTACATGAATAATTTTCAAAAATTTATACACAT
TTA---AAAAATAATTTTTAAATTCTTGAGCACTTTATTTTTTAAATGCATGAACACTTACTGTTCATCATATATTAAAA
AAAAA-TCAACTTGTGTTCAAAATGGTCACCTTGTACTTAAAACTGTTCACGTCTATTTTTCTAAATAATTTTATCATGT
ATTTTTAAAAATGATCTTATACTCATAAAAGAACGTATGTTTACTACTGAAAAAT-GAGGAAATGAAGAAAAAAGAAAAA
TAGAGAAGATAAATAAGCCAGGAAGAAAACTAAAAAGAAACACCAATGAACCAGAAGAAAAATCATTGAACCAGAGTAAA
AATGGGAACCCCTAAAAAAGTATATATGGGAAAGGAAAAATAGCGGGAAAAGGGCAAACATAGGACTGCCCAATCGCCCC
TATGTGCCACATGCCGACAATTCATCGCTCTGAGTGACGAATAGGGTTTACCCTTCAGCTCATTTTTCTGTCACCCTCTT
TTTTGGGAAACTTTTCTGTTACCTAGTACAAGCCCAAGGCCGACTACATCGGAAGAGAGGCCCAAGCGAGTCTGAGCGCT
CTTATTCGGCCCGGTTCTTTTCTGTCACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNCCCTACACACAAAAAAAAAA---------------------ACTTAAGCCGTCTCCA
CTACACTAAAAAAAAAACTTAAGCCGTCTCCTCATTTCGTCATTTCCTTT-GTCACCCATACAAGTTTAGGCATTTCCCT
TTTTATAACAGATTTAATGAAAACTTTTGTGAAGAAGCAGTTTAAATAATAATAAATTTTTATGTATTTTATAAAATTTA
CGTAGTTAAAAAATATTTCATG----------AACCATTGTGTTTTTAAGAATGCCCGTATATGAAAAGATATTTTTTCT
AAAAATATATTCATCGTGTATATAAAATCAAAGGAAAAAGTGCCCACCTTAGACACGGATAGAGAGGGGCTGGGGTAGGG
AGTTGTAATATTTTTTATTATGAAGTATTGTATTCTGAACCAAACATATGTGGTACACAGGAGAACATCCTTTTAGTGAC
CGAGCTCACTGGAGCTCAGAAATTTCTAAAAATTCAAAATTCAAACTTTCCGGTTTAAAAAAATCTG--AAAAAATTGTG
CAAGTAACAAGGATGTTATGTGTATGTGTGTAAATTTTTAGGATAAAATACCTTGAAATGAGATCTGTATAAAAAAGATA
AATTCATGGTCTGGGAGGACAAATAGTATCATGTGTTAAAAAGCTCCAAATTTTTTTTTTGCACAGCCCTCATTTCAACG
TGTTTTGCCCTGAAAATTTACACACAAGTGTGTTATGCCTTCATGCATATCTGTAATTTTTTTCAATATTTGTTGATACG
TAAAAATACGAATTTTGATGAAATTCAAAAATTGAACT------------TGGAGGCCGAGCTCCAAAAGCAATTTTGGG
GCACACACAGTATAACAAAACAGTGATGTTTCTTCGATAGTTGGATTCCCCCAGCAAGCAGATACGCTCACACTTGGAAC
ACCATGACCCCAAAAGCGTAGCCACTTTATTCCTGCAGATAGAAGTGAATATAAGTAAGAATATAATAAGTGAGAAAAGA
TGCACATGCCAACTGGTCACTGGTGCGTGCGGGCAACATGCTCCTATAAGTACCTCCCTGCATCATCATCCTTTCCTCAA
GCGAGCATCTAGCTTCGATACACAAACACAACGCACAGAGAACCAAAGAATCAGGAAGGAGCAAGAAGAAGATCGAGAGG
CGATGGAGTACGAGCACCAGTACATCAGCAGCGGCAGCTTCGCCAAGGAGAAGAGGCCTCCGGCGAAGAGGGGCCAGGTC
ATGATGCAGATGGCGAGGACGCTGAGCAACCTCGTCTCGCC
>chr1B_675
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------------------------------------------------GGCACAAATTCTCCGGTGAATTTAGTTCCGTG
ATTCCGTTTACACTTC--------GATAGTTGGATTCCCCCGGTATTCAGATACGTTCACACTCGGAACGCCATGACCCC
AAAAGCACGGCCACTTTATTCCTGCAGATATAAGTGAATAAATACGAATATAGGATCCACACACCAACTGGTGCAGGCAA
CGTACATTACATACGCCTATAAATACCTCTCTAGGTCCTCACCCCCTTCACAAATGAGCACCTGGCTTCACCACAGTACA
TTACACT----GTACACAACACGAAAGAAGCAGAGAAGAAGATCGGACGGCGGAGGCGATGGAGTACGAGTACCGGTACA
ACAGCAGC------------GGCGGCGGCGGCAGCGGCAAGGAGAAGAGGCCTCCGGCGAAGAGGGGGCAGGTCAAGCTG
CAGATAGCGAGGGCGCTGAGCAACCTCGTGTCTCCCGGCGGCGCTGCCGACGGCTCGAAGCAGGCAAATCGCAGCAGCTT
CAGAAGGGAAACAAGCTACAACTGAAC-AAGAAAATTAGATGGGTATGGTGCGTCTGCGTGTAAGTATCAAAAACTATCT
TATATTATGGGATGTAGGGAGTTGTTTATTACCTTTTCAGGGTTTTGGCAGGATGGTGTCCCAGTTTATAAATGGAGAAC
CTGTCTGATCCACCACCACTCTACTCTTACTTGGCTTGAGCGGGAAATGCTCCAAGCTTGAGTGTGCATTATGCATGTAT
TTCAAGAAGAAATTTAA-TGTATATACAAGC-----TTTGAGTATGCGAAACACCCGGTCCCAGTGTGTACTTGATTAGG
AGTGCTCCTGTATGACACTTAGAGATCGATTGGTTTGATGCCAACATTTGTCTTGCACAATTTGGCAAGTTAAAAAATAC
TTCTATCTGGATGAGGGATCCAAAATAATTGTCGTGGATTTAGTTCAAAGAAAAAAAA-TGGTAAATTTTG--TTTTTGC
TAAATGTTGGTTTGTCAATTTTTTTG--GTAAAGCGATATATTGGCATCAAACCAACTGGCNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCG
TCGTCCTGTCCATTAAACACGCAAGCGCATGTGTTCGTGGGCCGGAA---------------------------------
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------------------------------TGGGTGAGGAATAGG-----CCCCTCAGTTCATTTTTCTGTCACCTTTCT
TTT--GGAAACTTTTCTGTCACCGAGTGCAAGCCCAAGGCCGA----------------------GCGAGTTTGAGTGCT
CTTATTAGGCCCGGTTCTTTGACAGCCTACAACATAGCTTCCCCCTCCTTCCGTTA------------------------
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---------------------------------AAAAAAAAAACTTGCCCCTCCTCCGCTTCTCACTTAAGCCGTCTCCC
CTACACTAAAAAAA---CTTAAGCCGTCTCCCTATTTCGTCATTTCCTTTTGTCACCCATGCGAGTTTAGCAATTTCCTT
TTTTATAATAGATTTAATGAAAACTTTTGTGAAGAAGCAGTTTAAATAATAATTAA-TTTTATGTATTTTATAAAATTTA
CGTTTTTAAAAAATATTCATGTTTTTCTTAAAAACCATTGTGTTTTTAAGAATTCCCGTATATAC-------TTTTTTCT
AAAAATATATTCATCGTGTATATAAAATCAAAGGAAAAAGTGCCCACCTTAGACACAGAGAGAGGGGGGCGGGT------
--TTGTACTATTTTTTATTACGAAGTATTATTTTTTGAACCAAACATATGTGATACACAGGAGAACTTCGCTCTGGTGAC
CGAGCTCACTTGAACTTGGAATTTTAAAAAAATAA-----TCAAACTTGCCGGTTTCAAAAAAATCTGAAAAAAATTGTG
CAAGCAACAAGGACGTTATGTGCATATGTGTACATTTTTAGGTTGAAATACCTTGAAATGAGATCTGTAT-AAAAAGACG
AATTCATGGTCTGAAAGGAACAAGCCCTCA----------------------TTTTTTCTACACAACCCTCATTTCAACA
TATTTAGCCCTGAAAATTTACACACATGTGTGTTACACCTTCATGCATGTCTGTATTTTTTTTCCAGATTTTTTGAAATG
TAAAAGTATGAATTTTGATGAAATTCAAATTTTGTATTTGGAGGCCTCCATGGAGGCCGAACTCCAAAAGCAATATTGGG
GTACACACAGTATAACAAAACAGTGATGGTTCTTCGATAGTTGGATTCCC-CAGTATGCAGATACGTTCAGACTTGGAAC
ACCATGGCCCCAAAAGCGTAGCCACTTTATTCCTGCAGATAGAAGTGAATA----TAAGAATATAATAAGTGAGACAAGA
TGCACATACCAAC-GGTCACTGGTGCGTGCAGGCAACATGCCCCTATAAATACCTCCCTGCATCACCATCCTTTCCTCAA
GCGAGCATCTAGCTTCGGCACACAAACACAACACACAGAGAACCAAAGAATCAGGAAGGAGCAAGAAGAAGATCGAGAGG
CGATGGAGTACGAGCACCAGTACATCAGCAGCAGCAGCTTCGCCAAGGAGAAGAGGCCTCCGGCGAAGAGGGGCCAGGTC
ATGATGCAGATGGCGAGGACGCTGAGCAACCTCGTGTCGCC
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SS-------S--------S-------------S-----S-----------S--SS-----------------S-----S-
S------------------------------------------S-S-------S--------------------------
-------------S-------------------S-S---------------------------S------S---S-----
-------------------S------S------S---SS-----SS-S--S-----------S---S----S--------
----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----------------------------------------SS---
------------------------------------------------------------------S-------------
----------------------------SS--------------------------------------------------
-------------------S----S-SSSS-------------------------------S------------------
---S---------S-SSSSSSSSS-----------------------------------S----S---------------
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--S-S-------S--------------------S------------S---------------------------------
S-------SSSSSSSSSSSS----------------S------------------------------S-----------S
-----------------------------------S---S-------S--------S--------------------S--
--------------------------------S-S------------------S-------SS-----------------
----------------------------------S-------------------S-------------------------
-------------SSS----S-------------------S---------------------S-------S---------
----------------S-----------SS-SSSSS-------------S---------S--------------------
-------------------------------S------------------------------------------S--S--
---------------------------------SSSS-SSS-------------S--S----------------------
----------S----S--S------------------------------------------------------S-S----
------------S-S---S-------------------------------------------------------------
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----------------------------------------------S-S-------------------S-----------
-----------------S-------S---------SS-----------------------SSS-----------------
----------S-------------------S----S----S-----S-----S---SSS---------------------
--SSSS------S----------S-S----------S-----------S----------------------S----S---
-----S-------------------S-----------S-------------SSSSSSS---SS-----------S-----
-----S-------S--SS-S-SSSSSS--------------------------SSS-----------S-----S----S-
----S-S---------S---------------------------------------------------------------
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>forward_30
----------TGCTTGATGATGTGGCATGC--------------------------------------------------
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>reverse_1077
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------------------------------------TCAAGGAGAAGAGGCCTCCG------------------------
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>forward_1041
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-------------------------------------------------------------GCGATGGAGTACCGGTACA
G-------------------------------------------------------------------------------
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>reverse_2326
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-----TTCAACTTGTGTTCAAAATGTTCACC-------------------------------------------------
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