>input_sequence_84091
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-------------------------------------------------------------------------ATGGAAT
CCAAGTTCTTTCAGTTCCTGAAGCTTGTCGGAGTTGGTTTCAAAGCAAGGACAGAGCAAGGAGGCCGCGAGTTGTTTCTG
AAACTAGGTTACAGCCATGAGGTGCAGTTCACTGCTCCACCCGCCGTCCGTGTCTTCTGCTTCAAACCCAACATAATATG
CTGCACTGGCATCGACAAGCATAGAGTGCACCATTTCGCCGGAGCCGTGCGAAGCAGTAAACCTCCGGAAGTGTACAAGG
GGAAGGGCATACTGTACATCGACGAGGTCATAAAGCTGAAGCCGGGGAAGAAGCAGCAGAAGAAGTAA------------
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>chr4A_1_TraesCS4A01G258300
TCGTTGAAAGAGAAACCCATTGGCGTTT-CTATTTTATATGAAAGGCGTTGCCCAGTTCTGCAT-CAAAGGTAAATATGG
TTATCACTGGAGAGAGACTGGGTTGTCACTC-------AGCATCCATGTCCGACAGTGAGCAGCAAAGAAATGAAATACA
ACAGGAAACAAACTATGAACATGATTTCACCCAACACCCTCTACTCCTGAGTCAACTTCATTCGGCCTTCCAAGGCTACT
TCTTGAGCTGACTA-TTAGTCCATTCCCCCCCCTTTCAATACCTCTTCCAATGTTGCAAGACACAAAGCAATCTTATCCT
TAATTCCTTATGCATAGCAACAATTGGACATGACATCAAGTTCCTTTCAGTAAAATCTTGTTTTGAGTTGTCCT--GAGT
CCAACACACACATGCAAACTAATTTGGTTTTCCTAAATCACACACTATAATTTCACAGAAAATTTGGCATCAAGATGAGA
CCCAAATAGAACGTGTGCAGTACCTTCCGCTGTTCCACATACACATAAACTTTGTTCCATGGCCAGGTCTTTTCAACCGA
TTGTTCCCTACAA------GGGAGTTCACCCTGTAAGACTTGCTACTTTTTGTATAACCTGGAATATTCCCTGTTTAGAG
ACTCGACATATGCCATCGTGAACCGCCATATTCAATAGTCGGGGAACCGAGTAGAGCTTCAGAGTTTAGAGTTAGCATTT
TCATCCTCCAGTTATTTCAGTA--AGAGTTGTTTATTTGTGACCGTGCATCCTTTTTTAT--------ATGAGATTATCT
GATGAATTCATATGTATTTCTACTGAATTTCTTGTCTTGGTCTGAAAATCATTTA-TCTAAGTAGTAAGTTCTGATCTGT
ATATATGTCAAATTGTCAGTACTTGCAGCATGACCATACTCC--TGTTTGTTTACATGAGTGCTCAGTTTTGTGATGAAC
CTTTTGTCTTTGTTTTGTTAAG-GTAA-CCCGGAATCAAACATTTCATCCTCAGACAAACTTCCCTTGTTGCTATGGAAT
CCAAGTTCTTTCAGTTCCTGAAGCTTGTCGGAGTTGGTTTCAAAGCAAGGACAGAGCAAGGAGGCCGCGAGTTGTTTCTG
AAACTAGGTTACAGCCATGAGGTGCAGTTCACTGCTCCACCCGCCGTCCGTGTCTTCTGCTTCAAACCCAACATAATATG
CTGCACTGGCATCGACAAGCATAGAGTGCACCATTTCGCCGGAGCCGTGCGAAGCAGTAAACCTCCGGAAGTGTACAAGG
GGAAGGGCATACTGTACATCGACGAGGTCATAAAGCTGAAGCCGGGGAAGAAGCAGCAGAAGAAGTAACACATGG---GT
GAGCCTCCCCATTTGACTTCTAGCCTGTTGTTAAGGCGCCGCGACGCG--TTTGTTGCCGCAGAATTCATGTGGTTTTCT
CTGTGCTGGGCTAGTATGGCTAGCCCCGGTACCAGGCTGGACTTTGTAATAATACTCCGTATGCGACGTATGTGAATCGT
CTGATGAACATGCATATCGTTGG---------GTGGGGGTGGATCAGCGGATTCCAACATTTTTG-TTTTGTTTTGAGCT
GGCTGGATGTGACGTAT---CTT-CAATAGTTCAATGTGTTTGTTGCTGACACAACTCTC----CATCTTTTCTCTACAA
AATATTA-------CTCCCTCCGTTCCTAAATATAAGTCTTTTTCGAGATTTCAAATGAACTACCATATAAAGATGTATA
TAGACATATCTTAGAGTCTAGATTCACTTATTTTGCATCGCATGTAGTCATCTGTTGAAATCTCTAGAAAGACCTATATT
TAGGAATGGAGGAAGTAATAGCTAGCTACTATCACCTTGTTCCAAATTATAAGATGTTTTGGATATTTTAATATGGATTA
TGTACGGACTGAAATGAGTGAACAAGTACGCTAAAATGCGTCTATACATGCGATTTAGGAAAAAAT-TAGAACATCTTAT
AATTCAAAACTTGAGGGAGTACCTTGTTATGATATTTGTTCTTCACAAATAATTCACGGTTCTGGATGTATGCTTTGTGA
TAGTGTTTTTGTTGAATCTGCTGCTTGGGGGTGA-----TTTTCTTTTTATGTCGGCCTTGAAGGATCTTGATTAATTCA
GAAAAAGGGAAAGAGAGCTGCCCGATTAATATACTTAAATCTAGACTAAAACTGTCACAATTATCCACGGAGGGCAACAC
TCGCTGACCAAAAGGCCATCTTCAACGGCGACCTTCAAACCGTCCATGTATATCCAAACCGCGTTGTCTGGATAGCGGAA
GCCATTTAACGCGGGCTTGTACACGCATTTTCTTCTGCAAAC-GGAGACAACCATGAGGGGCTTT-
>chr4B_1
TCCTTGAAAGAGAAATCCATTGGCGTTTACTGTTTTATATGAAAGGTGTTGATCAGCTGTGCAT-AAAGC-TAAATATTG
TTATCACTGGAGAGAGGCTGGGTTATTACTCAGCAATTAGCATCCATGTCCGACACTGAGCAGCAAAGAAATGAAATACA
GCAGGATACAAACTATGAACGTGATTTGACCCAACACCCGCTATTCCTGAATCAATTTCATTGGGCCTTCCAAGCCT---
TGTTGAGTTGACTCATTAGTCCATTCCCCT-CCTTTCAATAGCTCTTCCGATGTTGTAAGAAGCAAGCAAT---------
------CTTATGCATAGCAACAATTTGACATTGATATCGATTTTTTTAAGGAAAATCTTGTTTTGAGTTGTCCAAAGAGT
CCAACTCACAGATGCAAACCTATTTGGAATTCCTAAATCATGCA-TATAATTTCACAGAAAATTTGGCATCGAGATAAGT
CCCAAATAGAACATGTG---TACCTTCCACTGTTTGATATAGACACAAACTTTGTTCTGTGGCCAGTTCTTTTCAACCGA
TTGTTCCCTACAACTACAAGGGAGTTCAGCCTGTAAGACTTGCTACTTTGTGTCTAACCTAGAATGTTCCCTGTTTAGAG
ACTCGATATATGCCATCATGAACCCCCATCTTCAATAGTCGAGGAACCGAGTAGGGCTTCAGAGTTTAGAG---------
----------GTTATTTCAGTA--AGAGTTGTTTAATTTTTACCGTTCATCCTTTGTAAT--------AAGAGATTATGT
GATGAACTCATATGTATT-CTGCTGAATCTCTTGCAGTGTTCTGAAAATAATTTA-TCTAAATACTGTC-------TTGT
ATGTATATCAAATTGTCAGTACTTGCAGCATGATCATACTCC--TGTTTATTTACATGACTGCTCTGTTT-----TGAAC
CTTTTGTCCTTGTTTTGTTAAG-GTAA-GTCAGAAAGAAATATTCCATCCTCGGACAAACTTCTCTTGTTGCAATGGAAT
CCAAGTTCTTTCGGTTCCTGAAGCTTGTCGGAGTTGGTTTCAAAGCAAGGACAGAGCAAGGAGGCCGCGAGTTGTTTCTG
AAACTAGGCTACAGCCATGAGGTGCAGTTCACCGCTCCACCCGCCGTCCGCGTCTTCTGCTTCAAACCCAACATAATATG
CTGCACTGGCATTGACAAGCATAGAGTGCACCATTTTGCCGGAGCCGTCCGAAGCAGTAAACCTCCGGAAGTGTACAAGG
GGAAGGGCATACTGTACATTGATGAGGTCATAAAGCTGAAGCCGGGGAAGAAGCAGCAGAAGAAGTAACACGTGG---GT
GAGCCTCCCCATTTGACTTCTAGCCTGCTGTTAAGGCGCCGCGTAGCG--TTTGTTGCTGCAGATTTCATGTGGTTTTCT
CTGTGCTGGGCTATTATGGCTAGCCCCGGTACCAGGCTGGACTTCGTAATAATACTCCG---------TATGTGAATCGT
CTGATGAACATGCATACCGTTGG---------GTGGGGGTGGATCAGCGGATTCCAACATTTTTG-TTTTGTTTTGAGCT
GGCTGGATGTGACGTAT---CTT-CAATAGTTCAATGTGTTTGTTGCTGACACAACTCTC----CATCTTTTCTCTACAC
AATATTAATAGCTACTCCCTCCGTCCGGAAAATACTTCCGGAAAATACTTGTCATCAAAATGAATAAAAGAGGATGTATC
TAGATGTATTTTAGTTCTACATATATTCTTTTTTGTTCATTTT------------------------AATGACAAGTATT
TTCGGACGGAGGGAGTA-------GCTACTATCACCCTGTTCCAAATTATAAGATGTTTTGGATATTTCAATATGGATTA
TGTACGGGCTGAAATGAGTGAACAAGTACACTAAAATGCGTCTATACATCCGATTTAGGGAAAAAAATAGAACATCTTAT
AATTCAAAACCTGAGGGAGTACCTTGTTATGATCTTTGTTCTTCACAAATAATTCATGGTTCTGGATGTATGCTTTGTGA
TAATGTTTTCGTTGAATCTGCTGCTTGGGGGGTGATCTTTTTTCTTTTGAAGTCCGCCTTGGAGGATCTTGATTAAAAAA
AAAAGG----AAGAGAGCTTCCCGATTAATATACTTAAATCTAGACTAAAACCGTCACACTTATCCACGGAGGGCAACAC
TGGCTGACCAAAAGGCCATCTCCAACGTCGACCCTCAAACCGCCCATGTATGTCCGGATCATGTTGTTCGGGCAGCAGAA
GCCATCCAACACGAGCATTTACACACATTTTCTTCTGCAAACCGGAGACAAACGTAAGGTGGCTTT
>chr4D_1
TCCTTGGAAGTAAAATCCTTTGGCATTTACTG-TTTATATGGAAGGCGTTGATCAGCTTTGCATCAAAGC-TAAATATAG
TTATCATTGGAGGGAGACTGGGTTAT----CATCACTCAGCATCCATGT-------TGAGCAGCAAAGAAGCGGAATACA
ACAGGAAACAAACTATGAACATGATTTGACCCAACACCCGCTACTCCTGAATCAACTTCATTGGGCCTTCCAAGCCTACT
TGTTGAGTTGACTAATTAGTCCATTCCTCT-CCTTTCAATAGCTCTTCCAATGTTGTAAGAAGCAAGCAATT--------
-------TTATGCATAGCAACAATTTGACATTGATATCAATTTTTTTCAGTAAAATCTTGTTTTGAGTTGTCCG--GAGT
CCAACTCACAGATGCAAACCTATTTGGAATTCCTAAATCACGCA-TATAATTTCACAGAAAATTTGGCATCGAGATAAGA
CCCAAATAGAACATGTGTAGTACCTTCCACTGTTTGACATAGACACAAACTTTGTTCTGTGGTCAGTTCTTTTCAACCAA
TTGTTCCCTACAA------GGGAGTTCACCCTGTAAGACTTGCTACTTTGTGTCTAACCT-------------------G
ACTCAATATATGGCATCGTGAACCCCCATCTTCAATAGTCGAGGAACCGAGTAGGGCTTCAGAGTTTTGAGTCGGTG-TT
TCATCCTGCGGTTATTTCAGTATAAGAGTTGTTTAATTGTTACAGTTCATCCTTTGCAAT--------AAGAGATTATGT
GATGAACTCATATGTATT-CTACTGAATCTCTTGCGGTGTTCTGAAAATAATTTA-TCTAAATACTGTC-------TTAT
ATA-ATATCAAATTGTCAGTACTTGCAGCATGATCATACTCC--TGTTTGTTTACATGACTGCTCAGTTTTGTGATGTAC
CTTTTGTCCTTGTTTTGTGAAG-GTAA-GCCGGAATCAAACAGTTCATCCTCAGACGAACTTCCCTTGTTGCAATGGAAT
CCAAGTTCTTTCGGTTCCTGAAGCTTGTCGGAGTTGGTTTCAAAGCAAGGACAGAGCAAGGAGGCCGTGAGTTGTTTCTG
AAACTTGGCTACAGCCACGAGGTGCAGTTCACCGCTCCACCCGCCGTCCGTGTCTTCTGCTTCAAACCCAACATAATATG
CTGCACTGGCATCGACAAGCACAGGGTGCACCATTTCGCGGGAGCCGTCCGAAGCAGTAAACCTCCGGAAGTGTACAAGG
GGAAGGGCATACTGTACATCGATGAGGTCATAAAGCTGAAGCCGGGGAAGAAGCAGCAGAAGAAGTAACACATGG---GT
GAGCTTCCCCATTTGACTTCTAGCCTGTTGTTAAGACGCCGCGCTGCATTTGTGGTTCCGCAGATTTCATGTGGTTTTCT
CTGTGCCGGATTT---TGGCAGGCCCCGGTACCAGGCTGGACCTAGTAATAATACTCTGTATGCGACGTATGTGAAACGT
CTGATGAATTTGTTGTATATGACTTGCATACCGTGGGGT-GGATCGGCGGATTCCAACTTTTTTG-TTTTGTTTTGAGCT
GGCTAGATGTGACGTAT---CTT-CAATAGTTCAATGTGTTTGTTGCTGCCACAA--CTC----CATCTTTTCTCTACAC
AATATTA-------------------------------------------------------------------------
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>chr6A_657
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----------------------------------ATAGTTGAGGAACTGAGTAGGGCTTCAGAGTTCAGAGTTGCTG-TT
TCATTCTGTATTTATTTCAGTC--AGAGTTGTTGAGGCA-TACATTTCAATCTTTGTGAGATGAAATCATGAAATTACGG
GATGTACTCGTGTATATT-GTACCGAATTTCTTGCAATGTTCTGAAAACAACCTATTTTAACTACGGTC-------CTGT
GTATACATCGAATTCTCAATACTTGCAGCATGATGGTACTCC--TGTTTCTTTACATTAGTGCTCAATTTTCTGATGAAC
CTTTTGTCCTTGTTTTGTCAAG-GTCAAGCCGGAAACAAATATTTCATCCTCGTTCGGACTTCTCATCTCGCAATGGAAG
CCAAGTTCTTTCGGTTCCTGAAGCTTGTTGGAGTTGGCTTCAAAGCCAGGACAGAGCGCGAAGGCCGCGAGTTGTTTCTG
AAACTGGGCTACAGCCATGAGGTGCAGTTCACCGCTCCACCTGCCGTCCGCGTCTTCTGCTTCAAGCCCAACATAATATG
CTGTACTGGCATTGACAAGCATAGAGTGCACCATTTCGCTGGAGCTGTCCGATGCAGTAAACCTCCAGAAGTGTACAAGG
GGAAGGGCATACTGTACATCGACGAGGTCATAAAGCTGAAGCCGGGGAAGAAACAGCAGAAGAAGTAACACATGG---GT
AAACCTCCCCATTTGACTTCTAGCTTGTT---TAGACGCCCCATCACATTTGTGGTGCCGCGGATTTCATGTGGTTTTTC
TCGTGCCGGGTTT---TGGCTAGCCCTAGTACCATGCTGGACTTCGTAATAATACTCTGTATGCTATGG----GAATCAT
CTGGTGAGCATGTACTGTATGACTTGCATACCGTGGGGGCGGATCAGCACATTTGAACATTTGTGTTTTTGTTTTGGGCT
GGCTAGATGCATGTAAC-----------AGCCCAATGTGTTTGTTGATGTCACTA--CTTTCTTCATATTTTCTCTACAC
AATATTAGCTC---------------------------------------------------------------------
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>chr6D_657
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----------------------------------ATAGTTGAGGAAATGAGTACGACTTCAGAATTCAGAGTTGCTGTTT
TCATTCTATATTTATTTCAGTA--AGAGTT--TGAAGCA-TACATTTCATTCTTTGTGAG--------ATGAAATTACGG
GATATACTCGTGTATATT-GTACCGAATCTCTTGCAATGCTCTGAAAATAGTCGA-TTTAACTATGGTC-------TTGT
GTATATATCGAATTCTCAATACTTGCAGCATGATGGTACTCCCCTGTTTCATTACATTAGTGCTCAATTTTCTGATGAAC
CTTTTGTCCTTGTTTTGTCAAAAGTAAAGTCGGAAACAAATATTTCATCCTCGGACGGACTTCTCATCTCGCAATGGAAG
CCAAGTTCTTTCGGTTCCTGAAGCTTGTTGGAGTTGGCTTCAAAGCCAGGACAGAGCGTGAAGGCCGCGAGTTGTTTTTG
AAACTAGGCTACAGCCATGAGGTGCAGTTCACGGCTCCACCTGCCGTCCGCGTCTTCTGCTTCAAGCCCAACATAATATG
CTGTACTGGCATTGACAAGCATAGAGTGCACCATTTCGCTGGAGCTGTCCGATGCAGTAAGCCTCCAGAAGTGTACAAGG
GGAAGGGCATACTGTACATCGACGAGGTCATAAAGCTGAAGCCGGGGAAGAAGCAGCAGAAGAAGTAACACATGGTGGGT
AAACATCCCCATTCGACTTCTAGCTTGTT---AAGACGTCGCATCGCATTTGTGGTGCCGCGGATTTCACGCGG-TTTTC
TCGTGCCGGATTA---TGCCTAGCCCCAGTACCGGGATGGATTTCGTAATAATACTCCGTATGCTATGT----GAGTTAT
CTGGTGAGCATGTGCTGTATGACGTGCATACCGTGGGGGCGGATCAGCACATTCAAACATTTGTGTTTTTGTTTTGGGCT
GGCTAGATGCATGTAACCTACTT-CAATAGCCTAATGTGTTTGTTGATGTCACTA--CTTTCTTCATATTTTCTCTACAC
AATATTAGCTC---------------------------------------------------------------------
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>chr6B_657
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----------------------------------ATAGTTGAGGAACTGAGTACGCCTTCAGAATTCAGAGTTGCTGTTT
TCATTCTATATTTATTTCAGTA--AGAGTT--TGACGCA-TATATTTCATTCTTTGTGAG--------ATGAAATTACGG
GATGTACTCGTGTATATT-GTACCGAATCTCTTGCAATGCTCTGAAAATAGTGGA-TTTAACTATGGTC-------TTGT
GTATATATCAAATTCTCAGTACTTGCAGCATGAGTGTACTCC--TGTTTGTTTACATTAGTGTTCAA-TTTCTGATGAAC
CTTTTGTCCTCGTTTTGTGAAG-GTAAAGTCGGAAACAAATATTTCATCCTTGGAAGGACTTCTCATCTTGCAATGGAAG
CCAAGTTCTTTCGGTTTCTGAAGCTTGTTGGAGTTGGCTTCAAAGCAAGGACCGAGCGTGAAGGCCGCGAGTTGTTTCTG
AAACTGGGCTACAGTCATGAGGTGCAGTTCACCGCTCCACCTGCCGTCCGCGTCTTCTGCTTCAAACCCAACATAATATG
CTGTACTGGCATTGACAAGCATAGAGTGCACCATTTTGCTGGAGCTGTCCGATGCAGCAAACCTCCAGAAGTGTACAAAG
GGAAGGGCATACTGTACATCGACGAGGTCATAAAGCTGAAACCGGGGAAGAAGCAGCAGAAGAAGTAACACATGG---GT
-AACCTCCCCATTTGACTTCTAGCTTGTT---TAGATACCGCATCACATTTGTGGTGCCG---ATTTCATGTGG-TTTTC
TCGTGCCGGATTG---TGGCTAGCCCCAGTGCCATGCTGGACTTCGTAATAATACTCTGTATGCTATGT----GAATCAT
CTGGTGAGCATGTACTGTATGACTTGCATACCTTGGGGGCGGATCAGCACATTCAAACATTTGTGTTTTTGTTTTGGGCT
GGCTAGATGCATGTAACCTACTTTCAATAGCCCAGTGTGTTTGTTGATGTCACTA--CTTTCTTCATATTTTCTCTATAC
AATATTAGCTC---------------------------------------------------------------------
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>SNPs
--S------------S---------------S-------------------SS---S-S------S--SSS-------S-
------------------------S-S----------------------------S------------------------
---------------------------S-----------S----------S-----------S-----------S-----
-S-----S---------------------SS----------S--------------S----SS---SSS-S-SSSSSSSS
SSSSSS-------------------S-----SSSSSSS-S--SS-----------------------------S------
-----S----S--------SS------SS------------S--S--------------------------S----S---
------------S----S----------S-----SS-----S---S-----------SS-------S-------------
-------------------------------------------------S---S------S----S--------------
------S-----------------S----S-----------S------------S------------------S-SS---
-------S---------------------------S----S-----S--------S-S--------------------S-
------S-----------S---------------SSS--S---------S-----------S--S-SSSSSSSSSS----
------S--------------------------S----------------------------------------------
--------S-------------------S-------------------------------------------S-------
------------S-------------------------------------------------------------------
--------S-----------------------S-----------------------------------------------
------------------------------------------------S-------------------------------
--------------------------------------------------------------------------------
-------------------------------------------S--------------------S---------------
-------------S------------------------------S-----------------------------------
----------------S---------------------------------------------------------------
-------------------------------------------------------------------------------S
------------------------S-SS---SSSSSSS-SSSSSSS-SS-S---SSSS--SS-SS-S-SS-S-------S
----SS---S----SSSSSSSSS-SSSS-S-----SSSSSSS-SSSSSSSSSSSSSSSSSSSSSSSS--S---SSS----
-SS-S-S-----S----SSSSSSS------------S-------------------------------S-----------
-------S---------------------S-------------------S---------S-----S--------------
----------S----------------------S----------------------S-----------------------
--S------S---------------------SSS--------------S-S---S------S--------------SSS-
S---SSSSSS---------S--------------------------------S------S--------------------
-S-------------------S-----S-----S--------S--------S---SS-S-SS-----SS--SS---S---
-----SS---S--S--S-S-----S--------------------------S-S-S---S-SS---
>forward_136
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------------------------------------TCAGCATCCATGTCCGACAG------------------------
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>reverse_2168
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-------GGAAAGAGAGCTGCCCGATT-----------------------------------------------------
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