>input_sequence_85221
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------------------------------------------------------------------------------AT
GGAGGACAAGGGGGCGGCTGCGCCGGCGGTGCT---------GGAGA---AGGAGGCGCAGGCGGT------GGCGGCGA
CGTCGTGCTTCAAGAGGACGGTGGGCGAGGACGCGTCGCTGTTGGAGCTGGCCAAGGACCAGTACCGGCAGTTCGCGGAG
GCGCAGGGGAGGGACCACTGGGAGTGCATCAAGAACAAGGTCAGCTCCATGTTCGTCGACCCCATCTTCAGCGGCTTCAA
GCCCGACTCCACCGCCAACA---CGCCGCCGCCGCCGTCCGTCGAGTCGCAGTAG-------------------------
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>chr4A_1_TraesCS4A01G370200
ATTGGGCCGGGATCAAGAGCTAAATTATTGAACTCTGAAGACGTGAACAAAGTCATCATCGGAGCCTCAACCTACCGGCA
GCATCTCATCAACAGAAACC-TATCTAGTAACGATCGACGATGGTCTTGATGGGCCCGATGTTGGGCTCGCCGAACAGGG
CGACGCCCTGGCGGGTCCTGAGCGTCGCGTACTCGCCGGCCGCGCGGGCCTTGT--------------------------
-------GCGTCGTGTACTCGCCGGCT---------------------------------GCGCGGGCCTGGCTCTTGAG
GCTGGCCCAGTAGCGCTTCGCCGCCGCCGACGCCGCGCCCTTGATCCCCTCCGTCGTCGTCCATGGCCCCGCTCCGGCGG
C-GCCGGCGCCGGAGCAGCCTCCTCCTTGCGCGCCAGCGCCTTGAGCATGGCCTCCTCCTCCGCGGCCATGGGCGCCGCC
GCCTTGAGCATGGCCTCCGCCGCCCCCTTGGTGTCCATGGCACTCGAACGTCGC-GGCCGGGCTTGGTCGTCAAGAA---
-AATGCTATGGAACCCACCGGTGTATCGAGAAGAGGAGAGGTTTGGATATTGCC-GCTGTCGCTGATGCTGCTATGGGGT
GTGGGCGGCGAGCTGGAGTTATATAGGACAGGAGCATAGCATGCGCTTGTTTCTTGAGGAGAAAGCAAAGCTCGCGGCTT
GGAGCAGGGTGCAAGG----------------------------------------------------------------
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----------------------------------ATAGAAACAGAGACACAGAAGTAGCTCCCGTTCCGTCTGCACCCGG
GAAAGGAAATCATCGTGATCCGAACTCCGAAGTGGCCGT--------------------------TAGTTATATCCAATC
CAATCCAAGAAGGTTGGTTAACGGGGCGCTCTCTTTCTCTTCCTCTTGTTCGGTTCGGTTTCTGTTTCTGTTTCCTTCTT
TCTTTGCCCCTAGTCCAAGACGGCCAGCGCCCCCTCCCCTCCCCTGCATATA----------------------------
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---------AGCAGGCACGATCCCGCAGCCCCATGGCCTCCAAAGCAACGCAAG-----------------------CAC
AAGCAGCGACATCGTCTTCTCATCTTCACGTAGATAC--AGACAAGTTT------------------TTCGGGGCCTGAT
GGAGGACAAGGGGGCGGCTGCGCCGGCGGTGCT---------GGAGA---AGGAGGCGCAGGCGGT------GGCGGCGA
CGTCGTGCTTCAAGAGGACGGTGGGCGAGGACGCGTCGCTGTTGGAGCTGGCCAAGGACCAGTACCGGCAGTTCGCGGAG
GCGCAGGGGAGGGACCACTGGGAGTGCATCAAGAACAAGGTCAGCTCCATGTTCGTCGACCCCATCTTCAGCGGCTTCAA
GCCCGACTCCACCGCCAACA---CGCCGCCGCCGCCGTCCGTCGAGTCGCAGTAGATTGTCGTCGTTCGTTCGCCTGCCG
TCGTCCGTCTAGATGACCTATATACCGTTGCTACTTTATTATGAGGATCACGGGCATTGTTTTTAGTTGTGGGGAACTTC
TATCCTC------------AACTCGAGGAGCTGTATATTGTGGATTTTGAGTTTA-TTAAATTCTTCAAGTGATTATCTC
GAAGAAGAGCACTTTTTTTTCTTTCTCAATGTGATTTTTTGCTATATATCTTGTTTTCATGCTG----GTTGTGATGCTC
GATTT-TAGGAATTTCGTGGTATTATGTTTTATTTTCTACTTCTTGAATATATTAGTG-------CTCCTTATATGGCTC
GATTCAGAAAAAAATACTGGATTTTTTTAGTGGATCTGGATCCTTGTGAAATCCTAAGTTTTGCACTTTATTTTAAAAGA
AACTTCTCATCCACCCAAATCTCTTTACAAATGAATTGCTTTTCATGTGGTTCTCTAATAATCCTAGTCTTAACCCATAG
TGTTAAAAGAGGACGTATATGT---------------TTTGCCAGACCTGGACAAATCGCTGAAA-----ACGGTGCCTC
GCTTGAGTTTCGTCCCAGGAACCAAT---------AAGAATCCAACGAAAATGCATCACCTCACATGGTTTAACGATATA
TAATCACTTGTAGAGGGTGCCATTGTTTCCCAGACAAAATGGAAGTCCACAATTGTAAGGTCGTCCCCAACAATGCTGCT
TCACCTACCACAAAACCAAATCCTAACTACTCGCATCATGATCCTCAAGGCAAGTAAAACAACTTCCAGGAGACGAAACG
AACCCAGATGATCTCGACATTAATAAACGTTAGCATAGATTTAGATACACTCAGAGGGTGTTTGTTTCCAGGGACTTACT
GGTTTAGGGACTTAAAAAAGTCATGTCCCATCTAAACCAAACAGGAGGGACTTATAGATAGGGCTGGACCAAAAGCTCGT
AGCTCGCGAGCTTAATGAGCGCTCGATAGTTCGGCTCGTTAAGCTCGTAGCTCGCTTCTTAATGAACAG
>chr4D_63
--------------------------------------------------------------AGCCTCAACCTACTG---
GCATCTCATCAAAAGAAATCTTATCTAGCAACGATCAACGATGGTCTTGATGGGGCCGATGTTGGGCTCGCCGAAGAGGG
CGACGCCCTGGCGGGTCCTGAGCGTCGTGTACTCGCCGGCCGCGCGGGCCTTGCTCGTCATGTACTCGCCGGCCGCGCGG
GCCCTGAGCGTCGTGTACTCGCCGGCCGCGAGGGCCTTGCTCGTAGTGTACTCGCCGGCAGCGCTGGCCTGGCTCTTGAG
GCTGGCCCAGTAGCGCTCCACCGCCGCCGACGCCGCGCCCGTGATGCCCCCCGTCGTC---CATGGCCCCGCCGGGC---
---CCGGCGCCGGAGCAGCCTCCTGCTTGTGCGCCAGCGCCTTGAGCATGGCCTCCTCCTCCGCCCCCATGGGCGCCGCC
GCCTTCAGCATTGCCTCCGCCGCTCCTTTGGTGTCCATGGCACTCAGAA--CGCCGGCCGGGCTTGCTAGAGAGATCAAA
GAATGCTAGGGAATC--------GATCGAGAAGAGG--------------TGCG-GATATTGCTGCTGCGGCTATGGGGT
---GGCGGCGAGCTGGAGTTATAAAGGAGCAGGGGCGTT-------TTATTGCTTGAGAAG-----AAAGCGCGCGGCTT
GGAGCAGGGGACAAGG----------------------------------------------------------------
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----------------------------------AAGAAGCGGGGAGG--ACGAGCAGCTCCCGTTCC------------
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----------------------------CGTTTGCAC-------------------------------------------
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>chr4D_97
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----------------AACC-TATCTAGAAACGATCAACGATGGTCTTGATGGGGCCAATGTTGGGCTCGCCGAAGAGGA
CGACGCCCTGGCGTGTCCTGCGTGTCGCGTACTCGCCGGCCGCGCGGGCCT-----------------------------
----------------------------------------------------------------------GGCTCTTTAG
GCTGGCCCAGTAGCACTCCGCCGCCGCCGACGCCGCGCCCTTGATCACCTCCGTCGTC---CATGGCCTCGCCGTTGTCA
TGGCCGGCGCCGGAGCGGCCTCCTCCTTGTGCGCCAGTGCCTTCAGCATGGCCTCCTCCTCCGCCCCCATGGGCGCCGTC
GCCTTGAGCATCGCGTCCGCCGCTCCCTTGGTGTCCATGGCGCTCGAACGTCGCCGGCCGGGCCTGGTCGTCAAGAA---
-GATGGTATGGAACCGATCAATGGAGCGAGAAGAGGAGAGATTTGGATATTGCTTGCTGACGATGATGATGAACCGATCC
ATCAATCGTCAAGAGGATCGATGG-------------AGCGTGCGCTTATTTCTTGAGGAG-----AAAGCTAGCGGCTT
GGAGCAGGGTGGTTAAAAATTTCAACGAAATTTCAGTGAATTTTTTGAAATTTCGCATATTTCAGTGGGGTCCGAAATTT
CGAGGCAGACTTAAATCGATTCCAACATAAATTTAAATTATGTTAGAAATCATTAAAATTAAGTGAAATTTTAAATCTTA
AAATCCAAAATAATTTTCAAAATATACAAAATTTCCAAAATTTCGCATATTTCAGTGAGGTCCGAAATTATTTCAGTTTG
TCTAATTCACATCTAGATGTTATTTAAGGATATCACATCTAAACTCCCATAAATATATAATGCAACAACAAAAAACAGAA
AAAAACTAAGAAGAAAAAAAATAGATCACAAACAGAGTGTACATCAGATTAGATGTGACATAACTATATCACATCTATAT
GTGTCCTAGAGAGATCCAAATTATTTTATTTCCCAAGAAGCAGGGAGT--AGGAGTAGCTCCCGTTCCGTTTGCACTTG-
----GGAAATCATCATGTTCCGAACTCCGAAGTGGCCGTTAACTTGTCTTCTTATTACATCTAGCTAGTTGTATCCAATC
CAATCCAAGAAGGTA----AACGGGACGCTCTCTTTCTCG------TGTTCTGTTCTGTTTCTGTTTGCTTTCTTT----
----------------------------------TCCCCTCCCCAGCATATA----------------------------
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---------ATAAGCAGGCAC------GACCCCTGTCCACCAAAGCAACGCAACGCAAGCACAAGCACAAGCACAACCAC
AACCAGCGACATCGTCTTCTCTTCTTCACGTAGATAGATAGACAAGTTTTCCATCTCGCTTTTCCTCTTCGGGGCCTGAT
GGAGAACAAGGAGGCGGCTGCAGCGGCGGCGCCGGCCGTGCCGGAGA---AGGAGTCGCAGGCGG------------CGT
CGACGTGCTTTAAGAGGACGGTGGCCGAGGACGCGGGGCTGATGGAGCTGGCCAAGGACCAGTACCGGCAGTTCAAGGAG
GCGCAGGGGAGGGACCACTGGGAGTGCATCAAGAACAAGGTCAGCTCCATGTTCGCCGACCCCATCTTCGGCGGCTTCAA
GCCTGACTCCACCACCAACA---CGCCGCCG------TCCGTCGAGTCGCAGTAGATCGCCGTCGTCGT-----------
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>chr4A_880
TTTTTTTTCTTTCTCAATGTGATTTTTGCTATATCTTGTTTTGATGCTGGTTTTGATGCTCGATTATAGGAATTTCGTGG
TATTATGTTTCTTTTCTACTTCTTGAATATGTTAGTGCTCCTTATATGGCTCGATTCAGAGAAAATTACTGGATTTTTTC
AGAGGATCTGGATCCTTGTGAAATCCTAAGTTTTGCACTTTATTTTGAAAGAAAATTCTCATCCACCCAAATCTCTTTAC
AAACGAATTGCTTTTCCTGCGGTTCTCTAATAATCCTAGTGTTAACCCATAGTGTTAAAAGAGGACGTATATGTTTTGCC
AGACCTGAAAAATCGCTGAATACGGTGGTGCCTCGCTTGAGTTTCGTCCCAAGAAGCAATAAGAATCCAACGAAAATGCA
TCACCTCAGACTGTTTAACGATATATAATCATTTGTAGAGGGTGCCATTGTTTCCCAGACAAAATGGAGGTCTGCAATTG
TAAGGTCGTCCCCAACAATGCTGCTTCACCTACCACAAAACCAAATCCTAACTACTCGCATCATGATCCTCGAGACAAGT
AAAACAACTTCCAGGAGACGAAACGAACCAAGATGATCTCGACATTAATAAACGTTAGCATAGATTTAGGTACACTCAAC
TAAGGCCATTTCAAACCAAAAACCGATCCCCTAAAAAATAGAGGATCCGGCCAAGTAAACCAGTGGACTAAGTTTTGGTA
AACATAAATTTGCAAGAATTCAACTGAAATTTGCATACATTTAAACATAAGTTCAACCTAGTCTTGACAATCGAACATTA
AACATAAATTCAAACTTAAACTACACTAAACTTAAACTAAATTAGACTACTCATCATCATGGGCCATAGTGGAGGTTGAG
GCAATCTTTACTCGACATGCCACCACCGGTAACATTCTTCACGAAGATGGCCGCTCTGCCTCTACGAGTTCGGGTGCTCC
CGGCGGAGGTCCGGCATGTACCCTTGTCTGCGGCCTCTGTTGCAAGGTGCTCCCTCGCCTCCCGGTTCCCTCGAGCCGTC
GCCGGATCCACCACACCTGGCGTCAACGGGACGAGGTGGGCAGGCGCCGTCCCAAAAGGGAAATTGAGCCTCACGGCGGA
GTCGTGGAACTAGACTTGCCACCGGTCGTATTCGAGTGCCATCATGTGGAACGACTCGATCCACTTCCTCTTGTGGGTCT
TCCGGTCGGTGATCTCCGCCATTCATGTTCCCCACGGGCACTGCTGGATGCCGANNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACCGAGTGGGGGCCGAAGCATCGACCGTGCAGTGACGGCT
AGAGGATGCGCCTCTTGAAAGCGAACCACGGGCGTGGCAGTGCGGATCCGCGCTGCAGATTGACGGCGGGGACCTCCGGC
CACCGCGTCTGGCCATTGGAAGGAGGGGGAGGCGGCGAACGACAAGGGAGGCGCCAGCGGCAGGGCAGAGGGGAGGAGGA
GGGGAAGAGAGAGTGTGATATTTTTTACTCGGCCGGCAAGCGGTGAAGTAAATATAGGGAGAACCGCGGCGGCCGAGGAT
AATTTATCCTCCTATGAGGCCAATTGGGGATCGGTTAGATCCTGGTTAGAGAAGTAAAACCAGAAGTTTACTACTCTACC
AATTATTGGGTACTAGTTAGGTCCCGGTTAGAGGAGTGGAAGCAGAATTTTACTTCTTTATAATCGGCTATTGGGAACCG
GTTAGAAATGACCTGAGGAGCATAGTATTAGACTAGATATTCTCGCAAAAAAAGAGATTAGTTTAGATACATGACTCAAC
TAAGGGAGATTTCGGCATCATCGCATCGATAAAACTTTATCAAGGCGACTACACACATAAGTGAACTGACTGAGAAAAAG
AACTTTTACCCCCGAATCTATCTCTACTTCCTAGACTACACTTGGCACATTGGTAGCGAAGGGGATTAAAACAAGGAAGG
AACAGAGAGAAGGAGTAGTTCCCGTTCCCGTTTGCACTTGGGAAATCATCATCTCATCGGAGAAGAGAAGAAAAGTGTCC
GTTTTTACTTGTGATCCAGTCCAGTCCAAAGCTAAGAATCCGTGTTTACTTCTGCCATGGTGATGATCCGGACTCGTAGT
TTCTCGTGTGGTCGACTTGTGTTCTTATCCAATTATTATTTCCACTCGGACCCTTCTTCCTCCTCAAGATAGGCCGACCT
CCCCTGCATATAAGTAGCCAC------GCCCCCTGGCCACCAAACCAACGCAAC-----------------------CGC
AACCATCAATATCGTCTTCTTCTCTTCACGTAGA--------CAAGTTTTCAATCTCAGTTTTTAGTTCTTC------AT
GGAGAACAAGGGGGCGGCTGCGCCGGCGGCGCC---------AGAGAAGGAGGAGGCGCAGGCGGCGGCGGCGGCGGCGA
CGTCGTGCTTCAAGAGGACGGTGGGCGAGGACGCGTCGCTGTTGGAGCTGGCCAAGGACCAGTACCGGCAGTTCGCGGAG
GCGCAGGGTCGGGACCACTGGGAGTGCCTCAAGAACAAGGTCAGCTCCATGTTCGCCGACCCCATCTTCGGCGGCCTCAA
GCCCGACTCCACCGCCAACACGCCGCCGCCG------TCCGTCGAGTCGCAGTAGATCGTCGTCGTTCGTTCGCCTGCCG
CGGTTCGTCCTGCAG-----TATATCGTTGCAACTTTATTATGAGGATCATGGGCCTTGTTTTTAGCTGTGGGGAACTTG
TATTTGTATCGTCGTATTAAACTCGAGGAACTATATATTGTGGATTTTGAGTTTAATTGAATTAGTCAAGTGATTATCTC
GAAGAAGAGC----------------------------------TATATCTTGTCTACATGATTCTTTGTTTTGATGCTT
GATCCATAGGAATTTTGTGGTATGATGTT---TTTTCTACTTCTTGAAAATATGATCAGTGCTCCCTTCTTATAGGGCTC
GATTCAGAGAAAATTACTGGATTCTTTTAGAGGATCTGGATCCTTGTGAAAATT---------CACTTTGTTTTAAAAGA
AAATTCTCATCCACGCA--------------------GTTTTTCCTGTGGTTCTCC----------------------AG
TGTTGAAAGAGGACGTATGTCACTCCAATGCTATGTGTTTCCCAGACCTGAGAAAAATCATGTTGAATACACGGTGCCTC
GCACGAGTTTCGTACGTCCCAGGCAAAGCAGCAACAAGAATCCAACGAAAACGCAACACCTGAGACTGTTTAACGAT---
--ATCACTTGTAGCGACAAAAAGGTAGGCCTG-----------------CAATTGGAAGGTCGTCCCCAACAATGCTGCT
TCACCTAGCACAAAACCAAATCCTAACTACTCGCATCATGAT--------------------------------------
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>SNPs
S--SSSSSSSSSSSS-SS-SS-SS--SSSS-SS---SSSSSS-SSSSSSSSS-SSSSSSSS----------------SSS
------------S---------------S-------------------------S--------------------S----
-----------------------------------------------------S--------------------------
--------------------------S-------------------------------------S---------------
-----------------S----------------------------------------S-S-----------SSS--SSS
S---------------------------------------------------------------S---------------
-----------S--------------------------------------------------------------------
---------------S-S--S--S-----------------------------S--------------------------
S-S--------------------S-----SS---S-S---S---------------------SS-S--------------
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-----------------------------------SS--S-SS-S-SSSS--S-----------------S-----SS-S
SSSS----------S--S----------------------------------------------------S---------
--------------SSSSS------S-------------SSSSSSS-----S----S----------SSS--SSS-SSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----------S-----------------------------------
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----------SS--SSS-S-SSSSSSS-----S-----S--------------S--------------------------
--S------------------S--------------S-------------------------------------------
----S------------------------S--S--------------------------------S--------------
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-------------------------------------------------------S-------------S----------
-------------------------------SSSSSS--------------------S----------------------
SS--S----SS-SS-SSSSS----S------S------------------S----S----------S------------S
---SSSS----------------------S--S-------------------------S----SS---------------
----------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----------S-S----S-S-------S-------S
---SS----------S-------S-----SSS----------------S----S-SSS---------S------S-----
--------S----S---------S------S--------------------SSSSSSSSSSSS------S----------
--S-----------S--SSSSSSSSSSSSSSSSSSSS-S-----S----------SSSSSSSSSSSSSSSSSSSSSSS--
----S-------------S-SS------------------S---------SSS---SSSS--SSS---------------
--SS---------S-SSSSS-SSS-S-------------------------S---S-----S-S-SS----------SSS
SS-----------S-SSSSSS-SSSSSS--SSSSSSSSSSSSSSSSSSS------S------------------------
-------S----------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_664
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----GCGGCGAGCTGGAGTTATAT--------------------------------------------------------
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>reverse_3907
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------------------------------------------------------------------CAGGAGACGAAACG
AACCCA--------------------------------------------------------------------------
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