>input_sequence_87638
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------------------------------------------------------------------------ATGCTTAC
ATTAACTAGTTATTTTGGTTTTTTACTCGTTGCTTTAACTATAACCCCAGCTCTATTTATTGGGTTGAACAAGATACACC
TTATTTGA------------------------------------------------------------------------
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>chr1B_1_TraesCS1B01G361900
TCTTGGGGATTTTCTCTAACGGGATTGTAGCCAGTACACCTGTGGGTCCTATAGCTCCTCATTCTACTCCAGCCAACTCC
GATGTTGAAGCCCCCGGAGAAACCTCGACGTCCATGAGACGCGCTCGCCTGCATGTCGACAAAGTGGACTGAGTCCACCA
GAGTAGTTGTCGAGTCCTTAGTAACCCTATTGCCCTGCAGATCCCACCTTTGTGTCATAGACTGTCATGTGTATGTTTGT
AGTAGTGTGTAGTGCTTGATTGAATGATGTGCCTTTTGTGTTGTTGCCTTGTGCATGATTGCTTGTTATTTGTGATTTGC
ATCCAGTTCCTTGGACCTTAACAAATCTCGAAGACGAGATTTTCTTAAGCGGGG---T--ACATTTTGTAACAACCCA--
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-------------------------------------------------------------------AAAATTTAACCGT
GTTTTTATGAAGTAAAATTTTGGATAGAAA-GAAAATTTTGAATTATATTAGGTCTTTTATTTATTTCAGAACCTTTTCT
-------GTTTT--------C---------AAAAATCCTTCCCTCCATGTAAAACTTTTG--AAAATATTGTGGTTTTCG
AAAGTTTTCTTAAATTCATTTCTTTTAA-ATTTTAAAATTCAGTGGGAAATAATCTTAATA-A--TAAAATTTCCCAAAC
TAAATCTTTTAATAACCTT-TTCTGACTTTTAAATGCTCCTGATGCACTATAACTATTTCAAATAAATTTTTATT---TA
ATGCCACAAAATTATGAGAGGTCCTCTGATGCCTATTGATCACTTTTATGTAAAA-ACT-CACCTTGGTCTTTTGGAAAT
TTTGAGCAAAACATCTTCTTTTCAGTTATGTCCCATCCTTACATTATAAGTACAACCCTAGTTTTCCTTACTCCAAAAAT
TCTGAAGCTT-TTCCACCTTGTAGTACCTCCAACCAAACCCTTAAGTCCAGGACATCGGCCACATTTGCATCTTCGATGT
CCACCAAATTATTCCTCCAAGTTAGGGTCCAGAAGTCCATTTCAATAAAAGTTGCTGTAATTTAACTCTTTCATGCTTAC
ATTAACTAGTTATTTTGGTTTTTTACTCGTTGCTTTAACTATAACCCCAGCTCTATTTATTGGGTTGAACAAGATACACC
TTATTTGAATTGACTGAATAATTATAATTCAGAAAAGAAAAATCTTTCTTTGGGATTCCTCACATTCTATGACTTTTTTC
CAGCTAACAAGTTTTTCCTTCTGGCAAACCAACCTTACCATCATAACTACCATCCAATGAGACTTCATACTACCAAATCT
CAGGTCCAACAGAAGTTTCTAGCTAGCCCTAGCATTCTGTCGAACAGCTTGTGGGCATGGCCGATATTTGGTAATTTGCT
GAACTTGCACTTGGCTCTAGATTGTTTTGCAAAACCAACTTGACCATCATCTCTCGATTGCAAACAAACACCATCCTACA
AAATATCAGCAGCAGAAAACCACCCTGAGGTACATTGGCAATTCGTCGAGCACGTTTCGTGCGTGTCCAAG---------
--GCACGCGTCGGCACTGAGCTCCTGTTA-----------CCTCCCCTGCCTGCACCCCACTCCATCCTGCTTCGCAAGG
CACACATGCATCTCTCCGACACCTCCCCTCGTCTCCTCGCGCCGCCCTCCACCATCCATGCCCGCCGCCCATGGTTACCG
TCTTGGCTATGCCAACGCCCAACCAGCATGGCGCGCCCCGAGCCACCAAGCTCCTCCCGTGCGTAACTACCGCTGCCACC
GCCCTCGCCTACCTCCGCCGTCCACATACCGACCTCGTCTACCTCGCCACCGTCCTCGTTTGCCATTTATGGCCGCCGCC
GCAGTCAGCTCGGGACGGCACCTTCCAAGGCGCGTG----GTCTTCGAGCCAACCAATGCGCCCTGCCATCATTGCGAGA
CGCCGCCATCCACACCGACCATCCACCAACCTGAACGGCCTCACCTGCCGCCGTAATGGCCACCACCGCCATGCTTATCT
TCGGGCGTCGCGTAACCGACCTTCTCCGGCTATATAATGCCACCTCGAGCTCGCTACGCACTTCACCACAATCCCTTCTT
CCTCTGTAAGCCTCCCGTAGGAGCAAAAACTGTTGGTGCCGAAACCCTAAACCCTAGCCTGCCCTAGCTCTACC
>chr7A_48
CCTG-----------------------------------------------TAGTTCCTCATTCTACTCTAGTCAACTCC
TATGTTGAAGCCCATGGAGAAGCCTTGACATCTGTGAGACACGCCCGACTGGATGTCGACGAAGTGGACTGAGTCCACCA
GAATAGTTGTCGAATACTTAGTAACCTTGTTGCTATGTAGATCCCACCATCGTGTCATAGACGATCACGTGTATGTTTGT
AGCAGTGTGTAGTGCTTGCTTGCACGATGCACCTTTTGTGTTATTACCTTCTGTATGATTATTTGTTAGTTCTGATTTGC
ACTTAGTTCCTCCGCTCTTAACAAATCTCGAGGACGAGATTTTCTTAAGGGGG----TTTAGAGTTTGTAC--ACCCC--
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-------------------------------------------------------------------AAAATTTAACCAT
AATTTTATTAAGTAAAATTTGGCTAGAAAT-AAAAATTTTGAATTATATTAGGTCTTTTATTTACTTCGGAACCTTTTCT
ATTTCCTAT-------TTTAA---------AAACATAATTCTCTCCATATAGATTTTTTT--AATAT---GGTGTCTTTG
GTTGTTTTCTTAC-GTCATTCCATCTAT-ATTTTAAATAACAGTAGGAAATATTTTTAGAATA--AAATTTGCCACAAAA
TAATTCTTTTAATAGCATTTTTCAATCTCTGAAATGCTTTTGTTACACTAAGAACCTTTTAAATAATTCTTTCAA---AA
TTCCACAAAAATTATGAGAGGTCAGGTGATGCCTATATATCACTTTTATGCAAAA-ACCTAAC-GTGGTATTTCGAAAAT
TTTGAGTGAAACATCCTCTTTTCAATTATATCCCTTTC---------AACTATAACCCTAATTTTCCTAGCTCTAATAAT
TCTGAAATTT-TGCCATCATATAGTCCTTCCAGCTAAACCCTTAGGTCCAGAAGATCAGCCCCATTTGCATCTTGGAAGT
CCACCAAATTATTCCTCCGAGTTTGGGTCCAGAAGTGCATTTCAATATAAGTTGC-------------------------
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>chr5D_52
---------------------------------------------------TAGCTCCTCATTCTACTCCAGCCAACTCC
GACGTTGAAGTCCCCAGAGAAGCCACAACACCCACGAGACGCGCTCGACTGGATGTCGACGAAGTGGACTGAGTCCACCA
GAGTTGTTGTCGAGTCCTTAGTAACCCTATTGCCCTATAGATCCCACCTTCGTGTGATAGATGATCATGTGTATGTTTGT
AGCAGTGTGTAGTGCTTGATTGAATGATGTTCCTTTTGTGTTGTTGCCTTGTGTATGATTTCCTGTTAGTTGTGATTTGC
ATTTAGTTCCTCCGCCCTTAACAAATCTCGAGGACGGGATTTTCTTAAGGGGGGGTGT--AGATTTTGTAACACCCC---
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------------------------------------------------------------------AAAAATGTAACCAT
GCTTTTATTAAGTAAAATTTTGACAGAAAT-AAAAATTT--AATTATATTAGGTCATTTATTAATTTTAGGATCTTTTCT
AATTTCCGTTTT--------C---------CAAAATCCTTTCCTCCATTTAAAAACTTTTGAGAAACGTTGTGGGTTTTG
AAAGTTTTCTT-G-ACCATTTCATACACCATTTTAAAATTAAGTAGGAAATATTTTTAGAATA--GAATTTTCCACAAAA
TAATTCTTTTAATAGCATA-TTCAATTTGTGAAATGTTTCTATTGCACTAAGACCCTTTAAAATAATTCTTTCAA---AA
TTCCACAAAAACTTTGAGAGGTCCTATGATGCCTATAAATAACTTTTATGCAAAA-ATCCCACCTTGGTCTTTTGAAAAT
TTTGAGCAAAACATCCTCTTTTCACATATGTCCCATTCTTTAGTTATAACTACAATCCCATTGTTCCTTGATCAATTAAT
TCTGAAATTT-CTGCATCTTATAGTCCTTCCAACTAAACCCTTAAGTCTAGAAGATCAGCTCCATTTGCATCTT------
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>chr4A_284
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-------------------------------------------TTGCTTTCTGCATATTA--TTGTTTATTGTGATATGT
ATTTAGTTCTTCCGCCCTTAACAAATCTTGAGGATGAGATTTCCTTAAGGGGG----T--AGAGTTTGTAAAACCCA---
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------------------------------------------------------------------ATAAATTTAACCAT
AATTTTATTAAGTAAAATTTGGCTAGAAAT-ATTT-TTTTAAATTATATTAGGTCTTTTATTTATTTCAGAACCTTTTCT
-------GTTTTTCCGTTTAC---------AAAAATCCTTCCTTCCATATAGAAACTTTA--AAAAT---GTGTGTTTGA
AAGTTTCTCTT-A-ATCATTTCATTTAA-ATTTTAAAATTCAGTGGGTAATTATTTTTTTATAATAAAACTTGCCCAAAC
TAATTCTTTTAATAACCTT-TTCATACTTTGAAATGTTCTTGTTGCACTATATCTATTTCAAATAATTTTTTTTATTTAG
TTCCAGAAAATGTTTGAGAGGTCCTACGGTACCTAGAGATCACTTTCATGCAAAA-ACCCAAC-TTTGTCTTTTGGAAAT
TTTGAGCAAAACATCCTCTTTTCATTTCTATCCCATCCTTAAGTTATAACTACAACCCTAATTTTCCTACCTCCAATAAT
TCTGAATTTT-T-CCACTTTATAGTCCTTCCA------------------------------------------------
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>chr3D_381
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-----------------------------------------------------------------TTGTAACACCCAAAA
ATTTCAAACCATGTTTTTATTAAGTAAAATTTTGACAAAAATAAAATTTTGAATTATATTAGGTCTTTTATTAATTCTAG
GATCTTTTCTGTTTTCTGTTTTCAAAACCGGTAGGTAGTGGATTGGGAATTGGAGTTGACAAGCTTTGATTTGAAGTTTG
AAAGTACATCAACCATCCAAAGTAGAGCCTTGGCAGAGTTCATTACAGAATGGACACCAACTCCAAACAAAGAAATACGA
GAGACCTCGCTTCCCGGCAAGGAAGCGCCCCAAGATTGGATCATGTACTTTGATTGTAACACCCAAAAAATTTAAACCAT
GTTTTTATTAAGTAAAATTTTGACAAAAAT-AAAA-TTTTGAATTATATTAGGTCTTTTATTAATTCCAGGATCTTTTCT
-------ATTTT-CTGTTTTC---------AAAA-TTCTTCCCTCCCTACAAACATTTTTGGAAAATATTGTGGG-TTTG
AAAGTTTTCTT-G-ATCATTTCATCCACCCTTCTTAAATTAAGTAGGAAATATTTTCAGAATA--AAAATTGCCACAAAA
TAATTCTTTTAATAGCATT-TTCAATATCTGGAACGCTTGTGTTGCACTAAGACCCTTTTAAATAATTCTTTCAA---AA
TTCCACAAAAAATTTGAGAGGTCCTCTGATGCCTATAGATTACTTTTATGCAAAA-ACCCGAC-TTGGTCATTTAAAATT
TTTGAGCAAAGCATCCTCTTTTCAATTCTGCCCAATTCTTCAGTTATAACTACAACCCCATTTTTTCTTGATCAATTAAT
TCTGAAATTC-CTCCATATCCTAGTCCTTCCAACTAAACCCTTAAGTCCAGAAGGGCAGCCCCAACTTCATCGTGCAAGT
CCACCAAATTATTCC-----------------------------------------------------------------
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>chr5B_382
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------------------------------------------------------------------TGTAACACCCC---
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------------------------------------------------------------------AAAAATTTAACCAT
GTTTTCATTAAGTAAAAATTTTCCAT-AAA-TAAAATTTTGAATTATATTAGGTCTTTTATTTATTTCAGAACCTTTTAT
-------GTTTT--------CCTGTTTACAAAAAACCCTTCCCTCCATATAAAACTTTTA--AAAATATTGTGGGTTGTG
AAAGTTTTCTT-G-ATCATTTCATCCACCCTTTAAAAATTCAGTAGGAAATATTTTCAGAATA--AAATTTGCCACAAAA
TAATTCTTTTAATAGCATT-CTCAATCTCTGAAATGCTTCTGTTGCACTAAGACCCTTTTAAATAATTCTTTCAA---AA
TTCCACAAAAAAATTGAGAGGTCCTCTGATGCCTATAGATCACTTTTATGCAAAA-ACCCACC-TTGGTCTTTCGAAATT
TTTGAGAAAAACATCCTCTTTTCAATTTTGTCCCATTCTTTGGTTATAACTACAACCCAATGTTTCCTTGATCAATTAAT
TCTGAATTTT-TTGCATCTTATAGTTCTTCCAAATAAACCCTTAAGTCCAGAAGATAAGCTCCATTTGCATCT-------
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>chr5B_382
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------------------------------------------------------------------TGTAACATCCC---
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------------------------------------------------------------------AAAATTTTAACCAT
GCTTTTATTAAGTAAAATTTTGATAGAAAT-AAAA-TTTTAAATTCTATTAGGTCTTTCATTTATTTCAAAACCTTTTTG
-------GTTTTCCTGTTTTC---------AAAAATCCTTCCCTCCATGTAGAAACTTTTGAAAAATATTGTGTG-TTTG
AAAGTTTTCTTAA-ATAATTCCATTTAA-CTTTTAAAATTTTGTAGGAAATATTG--------ATAATATTTTCCAAAAC
TAATTCTTTTAATGGCATT-TTCAAACTTTGAAATGCTCATGCTACACGAAAACTATTTCAAATAATTCTTTTAA---AA
TTTCACAAATTTTTTGAGAGGTCCTCTGATGCCTATAGATCACCTTCATGCAAAAAACTCAAC-TTTATCTTTTGGGAAT
TTTG-----AACATCTTCTTTTCAGTCCTGTCCCATTCTTGAGTTATAACTACAACCCCATTCTCTCTTGCTCAAATAAT
TCTGAAACTTTTTCCATCCCATAGTCCCTCAAACCAAACAATTACATCCAGGAGCTCAGCTCATTTTGAATCTAGCAAGT
CCACCAAATAATCCCCTGCAGTTTCTGTCCAGAACTGAATTCTAGTAAAAGTTGC-------------------------
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>chr1B_389
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------------------------------------------------------------------------ACCCC---
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------------------------------------------------------------------AAAATTATAACCAT
GTTTTTATGAAGTAAAACTTTGGATAGAAATATTT-TTTTGAATTATATTAGGTCTTTTATTTATTTCAGAACCTTTTTT
-------GTTTT-CTGTTTTC---------AAAAATCCTTCCCTCCATATAAAACTTTTG--AAAATATTGTTGGTTTTG
AAATTTTTCTTAAAATCATTTCTTTTAA-AATTTAAAATTCAGGAGGAAATTATTT--TTATAATAAAATTTTGCCAAAC
TAAATCTTTTAATAACCTT-TTCTGACTTTGAAATGCTCCTGTTGCACTATAGCTATTTCAAATTCATTTTTATT---TA
ATGCCACAAACTTTTGAGAG---CTGTGATGCCTATTGATCACTTTTATGTAAAA-ACCCACC-TTGGTATTTTGGAAAT
TTTGAGCAAAACATCTTCTTTTCAATTATGTCCCATTCTTATGTTATAAGTACAACCCTAGTTTTCCTTGCTCCGAAAAT
TCTGAAGCTT-TTCCACCTTGTAGTACCTTCAACCAAACCCTTAAGTCCAGGAGATCAGCCCCATTGGCATCTTGGATGT
CTACCAAATTATTCCTCCAAGTTAGGGTCCAGAAGTACATTTCAATAAAAGTTGCA------------------------
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----TAACAAGTTTTTCCTTTTGTCAAACCAACCTGACAATCATAACTAACATCCAATGAGATTTCATACTACCAAATCT
CAGGTCCAACAAAAGCTTCTAGCTAGCCCTAGCATTCTGTCGAACAGCTTGTGGGCATGGCTGATATTTGGTAACTTGCT
AAACTTGCACTTGGATCTGGCTCGTTTTGCTAAACCAACTTGATCATCCTCTCTGGGTTGCAAACAAACACCATCCTGAA
AAATCTCATCAGCAGAAAACCACCCTAAA----------------------------CGAGCGTGTCCATGGCGCGCGTT
TTGCACGCGTCGGCACCGAGCTCCTGCCGCCGCCCTGCTGCCTCCACTGACTGCACCCCACTCCCTCCTGCTTCGCCAGG
CACACATGCATCTCTCCGACACCTCCCCTCATCTCCTAGTGCCGCCGTCCACCATCCAGGAACGTCGCCCATGGCTGCCG
TCTCGGCTACGCCACTGCCCAACCAGCGTGGTGCGCCCCGAGCCACCCAGCTCCTCCCGTGCGTATCTGCGGCTG---CC
GCCCTCGCCTACCTCCGCCGGCCACGTACCGACCTCGCCTACCTCACCACCATCCTCGTTTGCCAATAATGGTCGTCGCC
GCTGTCAGCTCGGGACGGCACCGCCCAAGGCGCGTGGCATGTCTTCGAGCCAACCAGCGCGCCCTGCCATCACTGCAAGA
TGCCTCCGTCCGCACCGACCACCCACCGACCTCAACGGCCTCACCTGCCGCCGTAATGTCCACTGCCGCCATGC-TATCT
TCGGGCGCCAT-------------------------------------GCTCGGTATGCTCTTCACCACAATCCCTTCTC
CTTCTGTAAGCCTCCCGTAGGAGCAAAAAC--------------------------------------------
>SNPs
S--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----------------------------
---------------------S-------S-----------------S---S--------S-------------------
-------------------------------------S------------S-----------SS----------------
--S---------------------------S-----------------------------S-------S-----------
--SS-------SS-S----------------S-----------------S-----------S------------------
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------------------------------------------------------------------------------S-
-------------------------------S------------------------------------------------
------------------------------------------------------------------------------S-
--------------S---------------------------------------S---S------S---S----------
------------------------------S-----------S-------------------------------------
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-----------------------------------------SS--------------------------S----------
-----------------------------------------------------S---S---S------------S-----
------------------------------------S------------------SSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSS----------------S--S-----------S--S----------S------------S-----------------
-----------S---S---------------------------------------------S------------S-----
S-------------S---S-S-S-------S------------S----S-----S-S--------------------SS-
----S---S-----------------S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSS--S---------S----------
----------------S---------SSS----------------S---S--------------S-----------S---
------------------------------S------S-S------S-----------S-SS--S---------S-S---
---S-----S----SS-----------S---S---------------S-----------------S--S-S----SSS--
--------------------S----S-----------S-------S-----S-------------S-S----S--S----
--S-------------------SS--------------------------------SS--------------S---S---
S---S--S---S---------S-----S----S-------------------------S----SS---------S-----
-------S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----S--S--S-------------------S
-S----------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_46
--------------------------GTAGCCAGTACACCTGTGGG----------------------------------
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>reverse_2354
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---------------------------------ATAATGCCACCTCGAGCTCG---------------------------
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