>input_sequence_83142
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-------------------------------------------------ATGGACACACGGGCTGCTATTGTTTGCTTCC
TCGTGGTGCTAGCACTAGTGGGTACTCCTATTTCTGCAGGTGTGTTTAATTGTGTTCGTCAAACATAATGGTTTGTGTTT
TCTTGGTGGTGCTGCTAATCTAATCTAAT-GGGGTTTTGCTGCTAATCTTCTAATATAATGGTTTGTGTTTTCTTGGTGT
TGTGCAGAT-AACTGCACGGTCGTTGACGACGGTGGGGAGTTTTTCTGCACCAAGCCCCTGTGCAAGGCCACATGCGAGG
TGTTTGCACGTGATAGGAAGGGCAACCTCAAGGACTACCACTGTGAGAAGAAGAACGCCATCAAGGCTGTTTGCTAA---
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>chr3B_1_TraesCS3B01G601900
ATGAGCCTTCAAGTTTTTCTCAACAAAAATTATAAAAAAAATTCAAGTGTATCCTCTGGTGCCGTCGCCGCCGCCCCCAC
TCTCTGAGAAATTTAGGCTCCCTCGCCTCCGGCTTCCATCTTGGCGCTCCGAGGTGGGGGGACCTCGGATCTTCAAGACC
TCTTTATTCTTCGTCAACGTCTAGTGATCATCATAGTTTTGTGAGAATAGATTTCCTCTCATTCTTGTGGTAGTGCCATG
AGATTAGAGAGTTTTT--TCCTCACGGATCCGATTATTCGGATCTGATAAGTTTATGTTGTTGTGTCCAGTTTTTTTTAT
TTGTTTGATTCTTTATGGAGGTGAAATCTTTCATCAACACTATGGTGAAGATAAAGTGATTCCACAATCTGCACTTCTAA
GAGATCATCCTCGGGCCAAGTGTGTTCATCAATCAAGGCTTCCCATATTTTTCC-ATGGGTGACTCAAGGCACTTTCAAA
AATCATTATTGGTAATGTTCGTGCGGGTAAAAGAGTGGCAACATCGTTGCTCCAGTCCAATTGCAGACTCTTTACCGAAG
TCAGTCAATTGAATTTCAATGCACAATGGTGTTTACTGTTAAAGTGGCTAGACAATTTTTTATAATAAAAAGCATGTTTT
ATTAATGTCACCGGCAACAAAAAGATGACTCCA-TTTTTT-GAATGGTCATGCCTATTTTGTAGTAGAAAATTAAAGGCC
T-TAAATATTGGATAGACATTACTCATGTATTCTTTTGCCTTTTGTCATTTAATTCCTCACCCAGCATTAAGTGCTTCCA
TTTTTGGGGTGTGACTCACCTCTATCTCTTTTGCCAAGTTTAACAAGCGTTTAAATGCTTTTATTTTTGTCCCTTTTAAC
AAGTCTATATAAGATAACACTCCAGGTACTCCAAGACATAAACATTAGTCCCATTGCCAAATTAAAGTAGACGAAGAGAA
CGCATATTT-TCCTTCCTATAGATCAAAAAAGGAGAGAA--CCCTTGGGATGGACACACGGGCTGCTATTGTTTGCTTCC
TCGTGGTGCTAGCACTAGTGGGTACTCCTATTTCTGCAGGTGTGTTTAATTGTGTTCGTCAAACATAATGGTTTGTGTTT
TCTTGGTGGTGCTGCTAATCTAATCTAAT-GGGGTTTTGCTGCTAATCTTCTAATATAATGGTTTGTGTTTTCTTGGTGT
TGTGCAGAT-AACTGCACGGTCGTTGACGACGGTGGGGAGTTTTTCTGCACCAAGCCCCTGTGCAAGGCCACATGCGAGG
TGTTTGCACGTGATAGGAAGGGCAACCTCAAGGACTACCACTGTGAGAAGAAGAACGCCATCAAGGCTGTTTGCTAATGC
AACATTTGCTAGCAGAGACTGAAATACTAGCTAGTACTCCCTCCATTTGGAATTACTTATCGCGAAAATGGATGTATCTA
GACGTATTTTAGTTCTAGATACATTCATTTTCAAGACAAGTAATTCCGAACGGAGGGAGTACTTGTTAGGCGGTACTTAC
TTCAGG----------------ATGGACCAAAACATGTTATGTATGACCTCATATTGAGAGCAAGGAATAAACAACTTAT
TACTTGATCTGTTAAATAGTCTTATTTGGAAGCCATGTGGAGTCGGTCGATGTTTTATTGTTCACTTATTTTTCGTTTGA
GTTAGTTATTTTAACTATATTTTTTTTGAAAACCATTGGGAATTAAAGGATTATCAAGTCGAATCTTATTGGATCTATCA
AGTTGAACTGTATGCTTTAGTTAGGCAAATCCTAACTACATATA--GACCTTTAGTTCAACAAGGGATTGGACTGGATTG
GTTTCGTCAGCCAACCCGGTGTTCAGTTGCAATCTCAGACT-------CACACTATAATTGAGGATATATATAATACACT
TACTTTGGTTCATCTCAGACTCTACTCCTTGCAGCATTTTACTACTTAGTTGCAATAAGGGATTCAACTCGACATGTAAT
AGAACACCAGGGATTGGATTGCCAGTTGACCTGGTGTTCTATTGCAATCTTGGGTGG-AATCACTCACT-----------
----------------AGAATTAAGGATATATAATGCACTTACTCTAGCCTATGTCAAACTCTACTCTTAGTAGCCTTTT
GCTCTTGAGTTGTAAGCGGCAATGAGTTGCCTTTTATTTGTACCGCAAGCATCATTCATATGCATCAATGTAGAAACTAC
TGGTTGTGTACAATTCGTTGCAGAGGCTT-------GTG--GGAGGGGGTGGGGGTGTTTGG-------------TTTCT
TTTTTTGGATCAAGGCAACGACAATTTTCTCGAGGGGTGCTTGGGTACACCACTGCCGTTTACAAAATGAGGACTTTTAA
TCTAGACCACTGCCGTTTACAAAATGAGGAGT
>chr1B_54
CTCGTGTT-------------------------------------------------------GTCGTCGTCGTCGCCGC
CATCTGAGAGATTTTGGTCTCCTGACCTCTACCTGCCATCTTGGCGCTAAGAGGTGGGGGGATCTCGGATCTTCAAGACC
TCTATGTTCTTCGTCAACGCCTAGTGATCATCATAGTTTTGCGAGAATAAATT-CCTCTCATTCTTTTGGCGGTGTCATG
GGGTTAGAAAGTTTTCTGTCCTCGCGGATTTGATTATTCGGATCTGATGAGTTTATGTTGACGTGTCAAGCTGTTTTTGT
TGGTTTGATTCTTTGCGGAGGTGAAATTTTTCATCGACACCATGGTGAAGATATAGTGATTCGACGGCCTGCACTTCTAG
GGTATCATCCCCGACACAAGTACGTTCATCGATCAAGGCTTCCCATCTGTTTGAGATGGGCAACTCAAGGCGCTTTCAAA
AATCATTATTGGTAATGTTCGTGCGGGTGAAAGAGTGACAATACCGTTGCTCCAGTCTAATTGCAGCCTCTTTACCGAAG
TC------------------------------------------------------------------------------
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>chr3A_560
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--AGTCAATTGAATTTCAGTGCACAATGGTGCTTGCAATTAAAGTGGCTAGACATTTTTTATAACAAAAA--CATTTTTG
ATCAATGTCACCAGCCACAAAACGATGACTCCATTTTTTT-GAATGGTCATGCTTATTTTGTAGTCGAAAATTATA-GCC
T-TAATTATTAGATAAACATCACTCATATATTCTTT-GCCTTTT-TCATTTAATTTCTCACCCAGCATTAAGTGCTTCCA
TTTTTGGGGTGTGACTCACCTCTATCTCTTTTTCTAAGTTTAACAAGGATTTAAATGCTTTTATTTTTGTCCCTTTCAAT
AAGTCTATATAAGACAACACTCCAAGCACTCCAAGACATAAACATTAGCCCCATAGCCAAATTAAAATAGACGAAGAGAA
CACATATTTTTCCTTCCTAGT--TCAAAAAAAGAGAGAA--CTCTTGGGATGGACACACGGGCTGCTATTGTTTGCTTCC
TCGTGGTGCTAGCACTTGTGGGTACTCCTATTTCTGCAGGTGTGTTTAATTGTGTTTGTCAAACACGTA-----------
---------------TAATCTAATCTAATGGGGGGTTTGTCGCTAATATTCTAATATAGTGGTTTCTGTTTTGTTGGTGT
TGTGCAGAG-AATTGCGCGGTCGTTGACGACGGCGGGGAGTTTTTCTGCACCAAGCCGCTGTGCAAGGCCACGTGTGAGG
TGTTTGCACGTGATAGGAAGGGCAGCCTCAAGGACTACCACTGTGAGAAGAAGAACGCCATGAAGGCTGTTTGCTATTGC
AACATTTGCTAGTAGAGACTGAAATACTAGCTAGTACTTGTTAC------------------------------------
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-----G----------------ATAGACCAAAATATGTTATGTATAACCTCATATTGAGAGCAAGGAATAAACAATTTAT
TACTCGATCTGATAATTACTTTTATTTGGAAGCCATGTGGAGCCGTTCGATGTTTGATTGTTCACTTATATTTCGTTTGA
GTTAGTTATTGTAACTATTTTTTTTCTAAAAACCATTAGGAATTAAACGATTATCGAGTTGAATCTTACTAGATCTATCA
AGTTGAACTGCATGCTTTAGTTAGGCAACTCCTAAGTACATATACCGACTTTTAGTTCAATAAGGGATTGGACTAGATTG
GTTTCATCAACCAACTTGGTGTTCTGTTGCAATCTTGGGTGGTGACCGCACACTATAATTGAGGATATACATAATGCACT
TACTCTGGTTCATCTCATACTCTACTCATAGTAGCTCTTTTTAGT----------------ATTTAACTTGAGATATAAT
AGAACACCAGGGATTGGATTGTCAGTTGACCCGGTGTTCTATTGCAATCTTGGGTGGCAATCACGCACT-----------
----------------AGAAATAAGGATATATAATGCACTTACTTTGGCCCATGTCAAACTCTACTCCTAGTAGCCTTTT
TCTATTTAGTTGTAAGCGACAATGAGTTGCCTTTTATTTCAACTGTAAGCATCATTCATATGTAGTAATGTAGAAACTAT
TGGTTGTGTACAATTCGGTGCATAGGAACACTGGAGGTG--TGTGTGGGGGGGAGTGTTTGGTTT--TTTTACTCTTTCT
TTCTTTGGATCAAGGGAATGCCAATTTCAGT-AGGGGTGCTTGGGTACACCACTCTCGTTAAAAAAA-------------
--------------------------------
>chr3A_560
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--AGTCAACTGAATTTCAATGCACAATGGTGTTTGCAATTAAAGTGGCTATACATTTTTTTTTATAAAAAACCATGTTTG
ATCAATGTCACCAGCGACAAAAAGATGACTCCATTT-TTT-GAATGGTCATGCTTATTTTGTAGTCGAAAATTAAA-GCC
T-TGATTATTGGATAAACATCACTCATATATTCTTT-GCCTTC-GTCATTTAATTTCTCACCCAGCATTAAGTGCTTCCA
TTTTTGGGGTGTGACTCACCTCTATCTCTTTTGCTAAGTTTAACAATCATTTAAATGCTTTTATTTTTGTCCCTTTCAAT
AAGTCTATATAAGACAACACTCCAAGCACTTCAAGACATAAACATTAGTCCCATAGCCAAATTAAAATAGACGAAGAGAA
CACATATTT-TTCCTTCTAGT--TCAAAAAAGGAGAGAA--CTCTTGGGATGGACACACGGGCTGCTATTGTTTGCTTCC
TCGTGGTGCTAACACTTGTGGGTACTCCTATTTCTGCAGGTGTGTTTAATTGTGTTTGTCAAATACGTA-----------
---------------TAATCTAATCTAAT-GGGGGTTTGTCGCTAATATTCTAATATAATGGTTTGTGTTTTCTTGGTGT
TGTGCAGCACAATTTCGCGGTCGTTGACGACGGCGGGGAGTTTTTCTGCACCAAGCCTCTATGCAAGGCCACGTGTGACG
TGTTTGCACGTGATAGGAAGGGCAGCCTCAAGGACTACCACTGTGATAAGAAGAACGCCATCAAGGCTGTTTGCTATTGC
AACATTTGCTAGTAGAGACTGAAATACTAGCTAGTACTTGTTAC------------------------------------
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-----GTAATACTTACTTCAGGATGGACCAAAATATGTTATGTATAACCTCATATTAAGAGCAAGGAATAAACAATGTAT
TACTCGATCTGTTAATTAGTTTTATTTGGAAGCCATGTG-AGCCGGTCGATGTTTGATTGTTCGCTTATATTTCGTTTGA
GTTAGTTATTGTAACTATTTTTTATAG--AAACCATTAGGAATTAAACGATTATCGAGTTGAATCTTACTAGATCTATCA
AGTTGAACCGCATGCTTTAGTTAGGCAACTCCTAAGTACATATACCGACTTTTAGTTCAATAAGCGATTGGACTAGATTG
GTTTCGTCAGCCAAATTGGTGTTCTGTTGCAATCTTGGGTGGTGACCGCACACTATAATTGAGGATATACATAATGCACT
TACTCTCGTTCATCTCATACTCTACTCCTAGTAGCACTTTTTAGT----------------ATTTAACTCGACATATAAT
AGAACACCAGGGATTGGATTGTCAGTTGACCTGGTGTTCTATTGCAATCTTGGGTGGCAATCACACACTAGAAATAAGGA
AAAAAAATTGCGAAACAGAAATAAGGATATATAATGCACTTACTCTAGCCTATGTCAAACTCTACTCCTAGTATCCTTTT
GCTATTTAGTTGTAAGCGACAATGAGTTGCCTTTTATTTCAACTGTAAGCATCATTCATGTGTAGCAATGTAGAAACTAT
TGGTTGTGTACAATTCGGTGCATAGGAACGCTGGAGGTGTATGTGGGGGGGGGAGTGTTTGGTTTCTTTTTACTCTTTTT
TTCTTTGGATCAAGGGAACGCCAATTTCATT-AGGGGTGCTTGGGTACACCACTTCTGTTTAAAAAA-------------
--------------------------------
>chr3D_560
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--AGTCAATTGAATTTCAATGCACAATGGCGTTTGCGATTAAAGTGGCTAGACATTTTTTGTAATAAAAAGA-ATGTTTG
ATCAATGTCACCGGCGACAAAA-GATGACTCCATTTTTTTTGAATGGTCATGCTTATTTTGTAGTATAAAATTAAA-GCC
CGTAATTATTGGATAAACATTACTCATATATTCTTT-GCCTTTTGTCATTTAATTTCTCACCTAACATTAAGTGCTTCCA
TTTCTGGGGTGTGACTCACCTCTATCTCGTTTGCTAAGTTTAACAAGTGTTTAAATGCTTTAATTTTTGTCCCTTTTAAT
AGGCCAATATAAGACAA---------CACTCCAAGACATAAACATTAGTCCCATAGCCAAATTAAAACAGACGAAGAGAA
CACATATTT-TCCTTCCTAGT--TCAAAAAAGGAGAGAACACCCTTGGGATGGACACACGGGCTGCTATTGTTTGCTTCC
TAGTGGTGCTAGCACTTGTGGGTACTCCTATTTCTGCAGGTATGTTTAATTATGTCCATCAAACAAGTA-----------
---------------TAATCTAATCTAAT-GGGGGTTTGCCGCTAATCTTCTAATATAATGGTTTGTATTTTCTTGGTGT
TGTACAGAT-AGTTGCACGGTCGTTGACGACGGCGGGGAGTTTTTCTGCACCAAGCCGCTGTGCAAGGCCACATGCGAGG
TGTTTGCACGTGATAGGAAGGGCAGCCTCAAGGACTACCATTGTGAGAAGAAAAACGCCATCAAGGCTATTTGCTATTGC
AACATTTGCTAGTAGAGACTGAAATACTGGCTAGTA--------------------------------------------
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>SNPs
S-SSSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----S--S--S-S--S-
SS-------S----S--SSS---SS----SSS--S-------------SS------------S-----------------
---S-S-------------S---------------------S-------S---S------------S---SS---S----
S-S-----S------S-------S-----SS-----------------S-----------SS-----S--S-S-----S-
-S------------SS-----------S-------S----S------------S--------S--SSS-----------S
-SS-------S--SSS-----SS-------S---------------S-S---SS------SS---------S--------
----------------------------S--------S---S-S-------------S--------S-------------
----------------------------------S-SS----------------S------S--SS-----S-------S
--S------------S-------------------------------------S----------------------S---
-----S---------S-----------S--------S------------------S------------------------
----------------------------------S--------------------------------------------S
--------------S---------S-S---------------------------S-----------S-------------
-S-----------------SSSS---------------------------------------------------------
----------------S------------------------------------------------SSSSSSSSSSSSSSS
SSSSSSSSSSSSSSS-------------------S-----S---------------------------------------
------------S--------------------S-----------------------S----------------------
------------------------S---------------------------------------------------S---
------------S-------------------------SSS-S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSS----------------------------S-----------S-----------------------------S----
----S----------S----S---------------------S------------S-------------S----------
----------S-------S------S-S---------S---------S-------S---S--------S-S---------
----------S-----------------S------S-------------S----------S-------------S-----
---------------SS-------S----------SS-SSS----------------------------S-----S----
----S------------S-----------S-S----S---SSSSSSSSSSSSSSSSSSSSS---S----------S----
---------------------S------------------------------------------S---------------
--------------------S----------------------------------------------S------------
---S--S-----------S--------------------SS--S-S----------------S-S--------------S
-----------------S----S---SSS------------S-S-----S---S--------------------------
--S------------S----S------SS-SS----------------------S-------S----SSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_522
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----------------------GCGGGTAAAAGAGTGGCAAC--------------------------------------
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>reverse_1484
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-------------------------------------------TTCCGAACGGAGGGAGTACT-----------------
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