>input_sequence_63820
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---------ATGGCGGAGTCAGCTGTCGTTCATGGGTTCCTATCCCACGCCACGTTGCCTCCACTCTCCTCTCCTCTACA
TATACAGCGCCACCCTCCCTCTTC--CCTCTCTACATCTCCCTCCTCGCTCGTAGTAACTCGAGTC----CTGCTCCCTG
CACGGTCCTCCCATTACCACGAGCGAGCGCGTGTCATCTCATACGGGCGCGCGGGGGTACGTGGTGC----TCTCTGCGC
GCGCATGGCGGCGAGCGAGCAGAGCTCCGAGTCCTCGTCCACGTCCTACGCTTCCTCCTACTCCACGTCCTCGTGCTCGC
CCAGGGCCGACGCCAAGAAGCGGCAGGACGGCGGCAACAAGCGGAAGCGCGCGGCGGCGGCGGGCGAGGAGGAGGAGGAG
GCGGCCC---CGGCGGCGGCGGCGGCGTCGTCGTCGTACCGCGGCGTGCGGATGCGGGCGTGGGGCAAGTGGGTGTCGGA
GATCAGGGAGCCGCGCAAGAAGTCCCGCATCTGGCTCGGCACCTTCCCGTGCCCGGAGATGGCCGCGCGCGCCCACGACG
CCGCCGCGCTCAGCATCAAGGGCGCCCGCGCCGTGCTCAACTTCCCGGACCTCGCGCCCGCGCTGCCCCGCCCGGCCTCC
CTCGCCCCGTGCGACGTCCAGGCCGCCGCCGCGCGCGCCGCCCTCATGCACGACCACGACCACCAGTGCTGCTCCGCCTC
AACCTCAACCTCCCCCACCGCGGCGCCGGCCTCCGCGTGCGGCAATGCGCCGGCGCCAAGCGACCAGCCGGCCGCGCGGG
ACGAGCCGGAGCATGAGCCGGAGCCGTTCCAGCCGAGCCAGGGAAGCGAGCAGCAGCTCACGGCCGCGCAGGTGGAGATG
GTGTTCGACGAGCTGGCGCCGCTGTGGGTGGAGGACGTGGTGGACTTCGCGCCGTCCGATCACTGCTGGACGGCGTACGA
TTGTCTCGACCCCCTCGGCTACCAACCTCTCCTGTGGGAGTATTAA----------------------------------
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>chr3A_1_TraesCS3A01G313100
GTAAGCTTTAATTTGTAATCTTCCTTTCTTTTTCTTCCTTATGATATTGTTTAAATTCTTTTAATTAAGAGTGAATTCTA
TTTTTTTTACCTCTTAGTTT--CACGTTTGTGACATCAACTCCTCTATTTAACACGTTTTCACATATTTGCCCAATTTAA
GCAAACTGGTGCGACAAATTATCCTATTTTTTTCTCTTTCAATGTTGATTGTACATGCCATTTTGGCTGATTTTTTTACT
GTTTTTTGATTTGCTCTTGATTTGTCAAGGGATGGGTCCCACCTGTCAATTGGGGAGCAAGAAATATGAGTGAAAAATTG
GAGTTC-----------GAACCCGAAATCTCC-CCCGCAGACAGCTAAGACTCATCCCCAGCCGAACTGAGAGCAAACCA
GACAGAACCAAACAGTAAAATAAACCAGCCAACATGGCATGCACAGTCAACACTGAAATGGAAAATAACTAAATAAAT-G
GGATAATTTGTGGCACAATTTTGCTTACATTGGGTAAAAATATATGAAAAAACTACTAAATGGGATAGTTCTCGTCACAA
ACGTGAAACATGTGGTACAAATATAATC----------------------------------------------------
---------------------------------------------------CACTCTT---TAACTAATGTATAAAAATT
ACAGTGGGGTTTTATCCTACTATTGCCCTTAGAAAAAACA---TCGAGTGAGAAATGATCATTTCTAGTTCTACTGTGCT
ATAGACGTTTTATTTATTTCTAAAACATCATATGGAGTATACTATAGTACTACTCCCTCCGTTTCAAATTACTCGTCGTG
GTTTTAGTTTAAATTTAAACTAAAACCACGACGAGTAATTTTGAACTAAAACCACGATGAGTAATTTAGAATGGAGGGAG
TAGTTTTGAAGAGGCGTGCTGCATTGTGAAAGTTGAGGGAGC-TAAGTAAATCGCTGGGAGGAATTGAATATCTAGG---
------------------------------------------------------------------TGTAGC--------
----CAGGAGAGGGAGGCATGCAGGCAGCTCCGGGCAATGCCGGTCCGTCTCTGAGAGAGAGACCATACGACCCTAATTA
T---TGATCATGGCGGAGTCAGCTGTCGTTCATGGGTTCCTATCCCACGCCACGTTGCCTCCACTCTCCTCTCCTCTACA
TATACAGCGCCACCCTCCCTCTTC--CCTCTCTACATCTCCCTCCTCGCTCGTAGTAACTCGAGTC----CTGCTCCCTG
CACGGTCCTCCCATTACCACGAGCGAGCGCGTGTCATCTCATACGGGCGCGCGGGGGTACGTGGTGC----TCTCTGCGC
GCGCATGGCGGCGAGCGAGCAGAGCTCCGAGTCCTCGTCCACGTCCTACGCTTCCTCCTACTCCACGTCCTCGTGCTCGC
CCAGGGCCGACGCCAAGAAGCGGCAGGACGGCGGCAACAAGCGGAAGCGCGCGGCGGCGGCGGGCGAGGAGGAGGAGGAG
GCGGCCC---CGGCGGCGGCGGCGGCGTCGTCGTCGTACCGCGGCGTGCGGATGCGGGCGTGGGGCAAGTGGGTGTCGGA
GATCAGGGAGCCGCGCAAGAAGTCCCGCATCTGGCTCGGCACCTTCCCGTGCCCGGAGATGGCCGCGCGCGCCCACGACG
CCGCCGCGCTCAGCATCAAGGGCGCCCGCGCCGTGCTCAACTTCCCGGACCTCGCGCCCGCGCTGCCCCGCCCGGCCTCC
CTCGCCCCGTGCGACGTCCAGGCCGCCGCCGCGCGCGCCGCCCTCATGCACGACCACGACCACCAGTGCTGCTCCGCCTC
AACCTCAACCTCCCCCACCGCGGCGCCGGCCTCCGCGTGCGGCAATGCGCCGGCGCCAAGCGACCAGCCGGCCGCGCGGG
ACGAGCCGGAGCATGAGCCGGAGCCGTTCCAGCCGAGCCAGGGAAGCGAGCAGCAGCTCACGGCCGCGCAGGTGGAGATG
GTGTTCGACGAGCTGGCGCCGCTGTGGGTGGAGGACGTGGTGGACTTCGCGCCGTCCGATCACTGCTGGACGGCGTACGA
TTGTCTCGACCCCCTCGGCTACCAACCTCTCCTGTGGGAGTATTAATTAGGCTTGCTGTAAAACACCCGCCCCTTGATTT
CCTCTCTTCTTCTTCTTTTCTTGGT-TTTGTGTGGCTTTCTAGTGCTACTTAAAATGAAGCACATTTTTCGCTTTTTCAT
TTGGTTTGCGCACGTTCGGGTC--GGTTGGGACTACTTGTAAGTTTGAGATGTTTGTGACCAATTTAGCTTAGATGTGAG
TTGAGTTTGAAC--ATAAGAATCTAATGTACATGTCAAAATAAAATAAAATTACGCGGGCTTTAGGTTACCGCAAAATTA
CGTGTTTTCTTATGGGTGAAATGAGCCAGCCTCAACATGATAGCTCTGGTGGTACTTTGGGCATGCGATGTAGTTTTCAT
GAATTAACTTGCCAAACCACCTGAGATATGTGAAGCAATTGCTTGACATTGATGTTGGCTTGCTTGTTTTAGGACACA--
-----TCAACTTTGTTGAACCTAA-TTATTTCAACAACGCGCGGATAAATTCAAACTCTTCGTGGTGTAAGCTATTGACT
CTTACTGAGCAGTAACTTATATTGCTAAGCAGGTCGATCGCTTTCGT--TACCACGTGATGAGTCTGATGACATGACTTG
GTGTGATCGATATTAGTTTGCATTGATCGATAGAGCACGCCTCCTCATTTGTACCCATGTATCTTGGG-TTTGTTTTCGA
GTTTATCGGTTTCAAATGTCTCTCATGTATTCAACCACAACATGTGTCTAAACAAGATTATCTTCTTAATCATCTCCTTA
ATTACTCTATCCCTAATTCCCTATGTAG-----------------------------------AATCATCGATATTTCGG
GTTGGAGCTGAAGAGTCATATTTTTCTTCTGAAGTGGTGGCGAAA----------ACTTCCGGCCTCTACATCGATTGAT
GCACGCGCACCTGAAGAACCTTGCTAACCATTTTTCTTCGCGTTGGTCGACCAACTAATTTCGACCCTGAGATTTTTCGT
GAACGAATCAAAGAGGGGAAGTAGTATATATATATTTTTGCGAATAAGAGGGGAAGTAGTATATAAT
>chr3D_42
-----------------------------------------TGATATTGTTTAAATTATTTTCATTAAGAGTGAATTCTA
TTTTTTTTACCTCTTAGTTACACACGTTTGTGACATCAACTGCTATATTTAACAGGTTTTCACATATTTACCCAATTTAA
GC-AACTGGTGCGACAAATTATCCTTTTTTTTTCTCTTTCAATGTTGATTGTACAAGCCATTTTGGCTGATTTTTTTTTT
ACTTTTTTATTTGCTCTTGCTTTGTCAAGGGATGGTTCCTACCTGTCAATTGGGGAGCAAGAAATATGAGTGAAAAATTG
GAGTGCGGTTTTAGTTCGATCTCAAAATCTCC-CCCGCGGACAGGTAAGACTCATCCCCGCGGAG-CTGAGAGCAAACCA
CACAAAACCAAACAGTAAAATAAACCAGCCA-------ATGCACAGTCAACACTGAAACAGAAAAAG--TAAATAAAT-G
GGATAATTTGTGGCACAATTTTGCTTACATTGAGTAAAAATATATTGAAAAACTACTAAATGGGATAATTCTTTTCACAA
ATGTGAAACATGGGGTACAAATAGAATT----------------------------------------------------
---------------------------------------------------CAATCTTTAATAATTAATTTATAAAAATT
ATAGTGGAGTTTTATCCTACCGTTGCCCTTC-AAAGAAAAATGTCGAGTGAGAAATGACTATTTCTAATTCGACTGTGCT
ATAGACGTTTT---TATTTCGAAGACAACATATA----------------------------------------------
--------------------------------------------------------------------------------
------------------CTGCGTTCTGAAATGTCAGTGAGT-CAAGTGAATCGTTGGGAGGCTCCGTTTCAAAATAGAT
GACCCAACTTTGTACTATTTAGTAGTATAAAGTTGGGTCATCTATTTTAAAACGGAGGGAGTAAGTTGTAGCAGGGCATG
GAGTCAGGAGAGGGAGGCATGCAG----CTCCGGGCCGGGCCGGTCCATCCCT--GAGAGAGACCATGCGACCCTAATTA
TTGATCA--ATGGCGGAGTCAGCTGTCGTTCATGGGTTCCTATCCCACGCCACGTTGCCTCCACTCTCCTCT-----ACA
TATACAGCACCACC-TCCCTCTTCCTCCTCGCTCTACCCCTCTACTTGCTCGCAGTAACTCTAGTTCTAGCTACTCCCTG
CACGGTCCTCCCATTACCACGAGCGAGCGCGTGTCATCTCATCTGGGCGCCCGGG-CTACGCGGTGCTCGATCTCTGCGC
GCGCATGGCGGCGAGCGAGCAGAGCTCGGAGTCCTCGTCGACGTCCTGCACTTCCTCCTACTCCACGTCCTCGTGCTCCC
CCAGGGCCGACGACAAGAA---GCAGAACGGCGGCAACAAGCGGAAGCGCGCAGCGGCGGCC---------GACGAGGAG
CCGGCCCCGGCGGCGGCGTCGTCGGCGTCGT------ACCGCGGCGTGCGGATGCGGGCGTGGGGCAAGTGGGTGTCGGA
GATCAGGGAGCCGCGCAAGAAGTCCCGCATCTGGCTCGGCACCTTCCCGTGCCCGGAGATGGCCGCGCGCGCCCACGACG
CCGCCGCGCTCAGCATCAAGGGCGCCCGCGCCGTGCTCAACTTCCCGGACCTAGCGCCCGCGCTCCCGCGCCCGGCCTCC
CTCGCCCCGTGCGACGTCCAGGCCGCCGCCGCGCGCGCCGCCCTCATGCACGACCACGACCACCAGTGCTGCTCCGCC--
----TCAACCTCCCCCGCCGCCGCTCCCGCCTCTCCGCGCGGCAATACCCCGGCGCCATGCGGCCAGCCGGCCGCGCGAG
ACGAGCCGGAGCATCAGCCG---CCGTTCCAGCCGAGCCAGGGAAACGAGCAGCAGCTCACGGCTGCACAGGTGGAGATG
GTGTTCGACGAGCTGGCGCCGCTGTGGGTGGAGGACGTGGTGGACTTCGCGCCGTCCGATCACTGCTGGACGGCGTACGA
TTGTCTCGACCCCATCGGCTTCCAGCCTCTCCTGTGGGAGTATTAGGCCTGTGCCGTACAACA--------CCTTGATTT
CCT---TTCTTCTTCTTTTCTTGGT-TTTGTGTGGTTTTCTAGTGCTGCTTAAAATGAAGCACATTTTTCGCTTTGTCAT
TTGGTTTGCG------CATGCTTGGGTTTGGACTACTTGTAAG-TTGATATGCTTGTGACCAATTTAGCTTAGATGTGAG
CTGAGTTTGAACATATAAGAATCTAATGTACATGTG------------AATTATGTGGGGTTTAGATGACCGCAAAATTA
CGGGTTTTCTTACAGGTGAAATGAACCAACCTCAACATGATAGCTCTGGTGATACTTTGGCCATGCGATGTAGTTTTCGG
GAATTAACTTGACATACCACCTCAGATATGTGACGCAATTGCTTGACAACGATGCTAGCTCGCTTGTTTTACAACACGGG
AAGCGTCATCTTTCTCGAACCTATCTTATTTCAACAACGGAG----AAATTAAAACTCGTTGTGGTATAAGCTATTGACT
TTCACTGAGCAGTAACTTATATTGCTCAACAGGTCGATCGCTTTCGTTATACCACGTGATGAGT-TGATGACATGACTTG
GTGTGGTCGCGATTAGTCTGCGTTGATCGATAGAGCACACCTCCTCTGTCGTTTGCATGGATCTTGGATTTTCTTTCCGA
GTATATTGGTTTCAAATACATCTCATGTATTCAACCACAACATGTTTCTAAACATGATTATCTTCTTAATGATCCCCTTA
ATCACTCTATCCCTGTGTAGAAACGATATAAACTACTAAGTAGCTTAATTATTCAGGGCATGAAATAATTGATATTTCAG
GCTGGAGCGGAAGAGTCTTTCTTCTTCTTTTATGCGTTCTGAAACGATGGTGAGGACTTCCGGCCTCTACATCGATTGAT
GCATGCAAAGCTGAAGAACCTTGGTAATCATTTTTCTTTGCATTAATAGACCAATTATTTTTGACACCTCAGA-------
-------------------------------------------------------------------
>chr3B_116
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-------------------------------------AACTGCTATATTTAACAGGTTTTCACATATTTACCCAATTTAA
GCAAACTGGTGCGACAAATTATCCTATTTTTTTCTCTTTAAATGTTGATTGTACATGCCATTTTGGCTGTTTTTTTTAC-
---TTTTTATTTGCTCTTGATTTGTCAAGGGATGGGTCCTACCTGCCAGTTGGGGAGCAAGAAATATGAGTGAAAAATTG
GAGTACGGCTGTAGTTTGAACCCGAAATCTCCCCCCGCAGACAGGTAAGACTCATCCCCCGCCGGACCGAGAGCAAACCA
GACAAAACCAAACAGTAAAACAAACCAGCCAATATGGCATGCACAGTCAACACTGATTCAGAAAATAAATAAATAAATGG
GGATAATTTGTGGCACAATTTTGCTTACATTGGGTAAAAGTACATGGAAAAACTACCAAATGGGACAATTCTTGTCACAA
ACGTGAAACGTGGGGTACAAATAGAATTAACCCTGATGTAATTCCATTTGTACATTTTCCTCTGACAATTATTGAAAAAG
TAGAGTTACAGTAGGGTTTTACCCTACTATTTTTCTCAAAAAAAAAGAATTCACTCTT---TAATTAATTTATAAAAATT
GTAGTGGGGTATTATCCTACCGTTGCCCTTCAAAAGAAAAATGTCGAGTGAGAAATAATTATTTCTAATTCGACCGTGCT
ATAGACGTTTT---TATTTCTAAGACAACATATA----------------------------------------------
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------------------CTGCGTTCTGAAATGTCAGGGAGTCCAAGTGAATCGTTGGGAGGAATTGAATGTCTAGG---
------------------------------------------------------------------TGTAGCAGGGCATG
GAGTCAGGAGAGGGAGGCATGCAG----CCCCGCCCGGTCCT-GTCCGACCCT--GCGAGAGACCATGCGACCCTAATTA
TTGATGATCATGGCGGAGTCAGCTGTCGTTCATGGGTTCCTATCCCACGCCACGTTGCCTCCACTCTCCTCT-----ACA
TATACAGCACCACC-TCCCTCTTCCTCCTCGCTCTACCCCTCTCCTTGCTCGCAGTAACTCGAGTC----CTACTCCCTG
CACGGTCCTCCCATTACCACGAGCGAGCGCGTGTCATCTCATACGGGCACGCGGGGCTACGTGGTGC----TCTCTGCGC
GCACATGGCGGCGAGCGAGCAGAGCTCCGAGTCCTCGTCGACGTCCTGCACTTCCTCCTACTCCACGTCCTCGTGCTCCC
CCAGGGCCGACGACAAGAA---GCGGAACGGCGGCGGCAAGCGGAAGCGCGCAGCGGCGGCC---------GACGAGGAG
CCGGCCC---CGGCGGCGGCGGCGGCGTCGT------ATCGCGGCGTGCGGATGCGGGCGTGGGGCAAGTGGGTGTCGGA
GATCAGGGAGCCGCGCAAGAAGTCCCGCATCTGGCTCGGCACCTTCCCGTGCCCGGAGATGGCCGCGCGCGCCCACGACG
CCGCCGCGCTCAGCATCAAGGGCGCCCGCGCCGTGCTTAACTTCCCGGACCTCGCGCCCGCGCTCCCTCGCCCGGCCTCC
CTCGCCCCGTGCGACGTCCAGGCCGCCGCCGCGCGCGCCGCCCTCATGCACGACCACGACCACCAGTGCTGCTCCGCC--
----TCAACCTCCCCCGCCGCCGCGCCGGACTCCGCGCGCGGCAATGCCCCGGCGCCATGCGACCAGCCGGCCGCGCGAG
ACGAGCCGGAGCATGAGCCG---CCGTTCCAGCCGAGCCAGGGAAATGAGCAGCAGCTCACGGCTGCACAGGTGGAGATG
GTGTTCGACGAGCTGGCGCCGCTGTGGGTGGAGAACGTGGTGGATTTCGCGCCGTCCGATCACTGCTGGACGGCGTACGA
TTGTCTCGACCCAATCGGCTTCCAGCCTCTCCTGTGGGAGTATTAGGCTTGG--CGTACAACA--------CCTTGATTT
CCT---TTCTTCTTCTTTTCTTGGTTTTTGTGTGGTTTTCTAGTGCTGCTTAAAATGAAGCACATTTTTCGCTTTGTCAT
TTGGTTTGCGTTTGCGCATGCTTGGGTTTGGACTACTTGTAAG-TTGAGATGTTTGTGACCAATTTAGCTTAGATGTGAG
TTGAGTTTGAACA--TAAGAATCTAATGTACATGTG------------AATTATGCGGTCTTTAGGTTACCGCAATATTA
CAGGTTTTCTTACCGGTGAAATGAACCAACCTCAACATGATAGCTCTGGTGATACTTTGGCCATGCGATGTAGTTTTCGG
GAATTAACTTGACATACCACCTCAGATATGCGACGCGATTGCTTGATAACGATGTTGGCTTGCTTGTTTT----------
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>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----------------S----S-----------------
-------------------S---------------------S--S---------S--------------S----------
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SS-----S-------------------------------S----------------------------------------
----S---------------------------------------S--------------S----S---------------
----S---------------------------S-------------------------SS--------S-----------
----------------------------------------------S--------------------S----S-------
------------S----------S---S----------------------------------------------------
----------------------------------------------------------------S----S----------
-S------------------SS--------SS---S--S--------------------S-------S---S--------
-----------SSS---------S---S-----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSS----S--S-----SS-S------S-S----S-----S---------------S---------
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------------------------SSSS--------SS------------S--SS------------S------------
------------------------------------------------------------------------SSSSS---
--------S-----S---------------S--SS-S-S-S-----S-----S-------------------S-------
--------------------------------------------------------S-----------------------
---------------------------------------S-------S-S----------------------------S-
------------S------SSS----S-------------------------S--------SSSSSSSSSS--S------
S------------------------------SSSSSS-------------------------------------------
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----------------------------------------------------------------S--S------------
------------------------------------------------------------------------------SS
SSSS------------S----S---------------S----------S---------S-------------------S-
--------------------SSS----------------------S------------------S--S------------
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-------------S------S---S--------------------SSSSS-SSSSS-SS--S-SSSSSSSS---------
---SSS-----------------------------S-----------S---------------------------S----
----------SSS-SS-SS-SS------S--------------S------------------------------------
-----------------------------------SSSSSSSSSSSSS-----S--------------------------
--S---------SS----------S---S----------------------S--------S-----------------SS
-----------S--S-------S----------S--------------SS---------------------SS----S--
--------S----S-S-------S---------------SSSSSSS-----S------S-S-----S-------------
S-S-----------------------S-S-----------------------------------S---------------
-----S---SS------S---S----------------S-------SS-S--SSS----S-------S----S---S---
--S---S----------SSS-------------------------S--------S---------------S---S-----
--S-----------SSS-SSSS-S-SSS--------------------------------------S--S--------S-
-S------S--------S-SS--S-SS-S-S-S-S-S-SSSS--S-----------------------------------
---S--SS-S-------------S---S----------S--S--SS-S------S--S---S---S-SSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_385
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---------------------------------------------TAAGACTCATCCCCAGCCGA---------------
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>reverse_2338
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-----------------GGGTCGGTTGGGACTACTTG-------------------------------------------
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