>input_sequence_77129
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-------------------------------------------------------------CTGAGTTTTCTCTGGTCCG
CTCGTGTTTTAGGCGGCGTGCCCAGTTGAAAGGGACCCTTTGCTCTGCATCTGCCAA-----------------------
---CGTCGTAGGTCACCTCCTCGTATCAAGTTTCTTTGTT-CTCTGTTC-TTTGCTTGGAAGAACACAGGAGGGAGGAGC
AG--GCATGGGGAAGGTGATGAGCATGCGGCTCGCGCTGGTGGTCCTGGTGCTGGCGAGCCTCGTGCTGGCGGCCCAGGA
GGCCGACGGGGCGCGGCCAGCGTCGACCGACGGCGTTATCAGCTACGGTGCTCTCCTGCGCGGGAACGGCGCCAACACCT
CCGACGCCAGCGTCCGGCCTTCCGCGGTGGCCAACTCTTACACGCGCGGCTGCAGCAAGATCAACCGTTGCCGCGGCTGA
TGCGACGCGTGCCTGCATGCG----------TGTGTATCTCTTGCTTTGCTCGAACGTTTGAACGTTGATCCGGTGCCGT
GTGCAAGCCAGGAGTATGATGCAACA-CACTCGCTTCTTTCATGAATACAAGATC-------------------------
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----------------------------------ATGCAGTGCTGTCTCTGAA---------------------------
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>chr3A_1_TraesCS3A01G141000
CAATGCCCTTTGTCCGGTCCATTTTTTTAGCTCTTGTCTGGTCCATTTTGGTAGCCTCTCCCACGAAAGAGCAGGCAAGA
CAAGAGGAGAGTGACCCAGAAGTATGACGCACGTTGCGATCCGGGCAATCCGGCTTGGAATCAGACAATGCATTCTGGAC
ATTTATCTATTCTTATCTACAAGCGACAGATGCTGC------AATGATGATA-ATTTTGATGGACGTGAATTTTTTTGGT
CCTTGGTTGGTTGCAGGGATGCTAAGGCAGAAGCCGAGGGCGTGCTGCGGGGCGGCGGGCGTGGGGGTGTACAACTTCAA
CCTGACGTCCAAGTGCGGAGAGCCCGGCGCGTACGCGTGCGACGACCCCTCCAACCACTGGAGCTGGGACGGCATCCACC
TCACGGAGGCGTCCTACGGCCACATCGCCAGGGGCTGGCTCTACGGGCCCTTCGCCGACCCGCCCATCGTCGGCAACCGG
AACCTCGAGTA--------GCAGCACTAGTAGTAGTACACAGGCTTGTTTTTGCGTACATGCCATTGCCGCCTGCACATG
GGTGGGTCACTAC--TGTAGAGAAAG----GAAAGGAGGTCAAAGAACAGAACACACTACATGCCTTGTGCAGATTGGTT
AATTGTTAATTTATTGGTTCTGTTTGTTCACGACATGAAGGAGATTTTGGGAAAATGGGTGCAACGTCTTACATCGTTAG
AGGCGACGGCTTGGTGTTAAATACATACGCAGAGGCATATCCTTGGAGATGCATACATGCATGCGGTACAAGGAGAAAAG
AAAACAGAAGAGATAAAGAAAATTAATTGCGATATGCATAACCTCCTATCAGAATTATTAAAAAGCTACTCCCTCGGTCT
GATAATATAAGAGCGTTTTTTAATTAATGTAGTGTCAAAAACACTCCTATATTATGAGACGGAGGGAGTACAAGATAGCT
CGTGTGTTTGGAAAAGATGCAGGCTCGCTGGAAAAACAAGACCTAAACATGGCACAGGCCTCTGAGTTTTCTCTGGTCCG
CTCGTGTTTTAGGCGGCGTGCCCAGTTGAAAGGGACCCTTTGCTCTGCATCTGCCAA-----------------------
---CGTCGTAGGTCACCTCCTCGTATCAAGTTTCTTTGTT-CTCTGTTC-TTTGCTTGGAAGAACACAGGAGGGAGGAGC
AG--GCATGGGGAAGGTGATGAGCATGCGGCTCGCGCTGGTGGTCCTGGTGCTGGCGAGCCTCGTGCTGGCGGCCCAGGA
GGCCGACGGGGCGCGGCCAGCGTCGACCGACGGCGTTATCAGCTACGGTGCTCTCCTGCGCGGGAACGGCGCCAACACCT
CCGACGCCAGCGTCCGGCCTTCCGCGGTGGCCAACTCTTACACGCGCGGCTGCAGCAAGATCAACCGTTGCCGCGGCTGA
TGCGACGCGTGCCTGCATGCG----------TGTGTATCTCTTGCTTTGCTCGAACGTTTGAACGTTGATCCGGTGCCGT
GTGCAAGCCAGGAGTATGATGCAACA-CACTCGCTTCTTTCATGAATACAAGATC-------------------------
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----------------------------------ATGCAGTGCTGTCTCTGAATCAAACTGTTTAAAGCTTGACCAGATC
CGTAGAAAGCATTAGAATCCACACTACTAAATTACTTTTTTAGACAAGACACTACTAAAATACCTTTTTTAGCACTACTA
AATTACTGTTAATGCAACATTGGTCGGGCCTAATTCGACAACCCGGACCGGCCGATTTA-TTTACAAGGCCTGGACCGTT
CAGTCCGATCCATAGCGGGCCATGAGCCGGGCCGAAAGCCCGCTCAACACATCCAGGCTT----ATAGCGATAGCCAACC
CTTTATTATAACCACTTCCTCCGCTCCCAAATATAAGGCCATATTTGATAGCAAAGTATTTTCTAAGTATTTTGAAAATA
CTATAATTTTTGCAATTGCCACAGTTTTATTTACAATGAGCTGTTTGATTGCCCCTAACAATTGTGTTTTTAATATTGTA
GTATTGGGCAAACTGCAGTTTTTTCTCTGCATAAAAAAAAACCCAAACCTCTTTTTTAAAAACAGAGCTGCTGAGTGCTT
AAACACAACGGCTAAACAGCAAAATTTACAGTGTTATGCGGCAAAAGCCAAACAGGTTCTATGTATTGTGAATACTGCAA
AATACTCTGTTTTGATAAAACTATGGTATCTCACACCTACAGATAAAATTACTGTAATTTTTGATACTTTGGTTTATATA
ATACTTTGCTACAAAACACAGGCTAAGTATTTTTAGAACTTCTATGATATGGACTATATACGCGGTAAAATAAGTGAATC
TACACTTTAAAGTATGTCTATGTGCATATGTATGCAGTCTATATGGAAATCTTTAAAAAGACTTATATTTAGAAATGGAG
GGAGTAGTGATTTTCCGCTCAAATTTTTTATTATAACTAGTGATCCCCATCCCAACGGGCATCTGCACGACATGGGCTTA
TGGAACTCTTGTCGCTAATGTGGGTTGGTCGATTGTTTGGCATGCATCATCATAGGCTTATGTGTTTGTTGTGGCAAGAG
CTATGTCGTTGGTAGTCT
>chr3B_30
GCTCTC----------------------------TGTCCGGTCCATTTTAGTTGCCTCTCCCACGAAAGAGCAGGCAAAA
GGGAGGGTGT----CTGAGAAGTATGACGCACGTTGTGATCCGGGCAATCCGGGTTGGAATCGGACAACGCATTCTAGAC
ATTTGTCTAT-CTTATCTACTACTATCTGTGTGAGCGACCATAATGATAAAGGGTTGTGATGGATGT-------------
---------GTTGCAGGGATGCTGAGGCAGAAGCCGAGGGCGTGCTGCGGGGCGCCGGGCATCGGGGTGTACAACTTCAA
CCTGACGTCCAAGTGCGGCGAGCCCGGCGCGTACGCGTGCGACGACCCGTCCAACCACTGGAGCTGGGACGGCATCCACC
TCACGGAGGCCTCCTACGGCCACATCGCCAGGGGCTGGCTCTACGGCCCCTTCGCCGACCCGCCCATCGTCGGCAACCGG
AACCTCGAGTAGCACTGTAGCAGCAGTAGTACAG-------GGCTTGTTTTTGCGTACATGC-------------ACATG
GGT-----TACTGTATGTAGAGAAAG----GAAAAGAAATCAAAGAACAGA--------CATGTCTTGTGCAGATTAATT
AATTATTAATTAATTGGTTCTGTTTGTGTTATTTTATCCCTTA-------------------------------------
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----------------TTTGAAATTTATATTTTTTAAGAAAAAAAACTAAATATGATGCCGTTTC---------------
-----------------------------GTAAAAAGACGGTCTAAATAGGGCATGCGCCTCTGAGTTC-CTCTGGTCCG
CTCGTGTTTTAGGCATGGAGCCTCATCAAAAGGAACCCTTTGCTCTGCATCCCCACCAGCTTGGCACACCAATAAGGAGG
AACCGTCGTAGGTCA---CCTCGTATCAAGTTTCTTTGTTTCTCTGTTC-TTTCCTTGGAAGAACACAGGAGGGAGGAGC
AG--GCATGGGGAAGGTGAGCATGCAGCAGCTTGCGCTAGTGGCCCTGGTGCTGGCAAGCCTCGTGTTGTCGGCCCAGGA
GGCCGACGGGGCTCGGCCCGAGTCGACCGGCGGCGTCATCAGCTACCGTGCTCTCGTGCGCGGGAATAGCGCCAACACCT
CCGACGCCAACGTCCGGCCTTCTGCGGTGGCCAACCCTTACACGCGCGGCTGCAGCAAGATCAACCGTTGCCGCGGTTGA
TGCGTGCC---------TGCG----------TGTGTATCTCTTGTTTTGCTCGAACGTTCGAACGTTGATC-----CCGT
GTGCAAGCCAGGAGTATGATACAACA-CGCTCGCTTCTTTCATCAATACAAGATC-------------------------
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----------------------------------ATGCAGTGTTTTCTCTGAATCGATCTGTTTAAAGTTTGATCAAATC
CATAAAAAACATTGGCATCAACACTACCAAATCAATTT------------------------------------------
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>chr3D_30
GCTCTC----------------------------TGTCTGGTCCATTTTAGTTGCCTCTCCCACGAAAGAGCAGGCAAAA
GGGAGGGTGT----CCGAGAAGTATGACGCACGTTGTGATCCGGGCAATCCGGGTTGGAATCGGACAACGCATTCTAGAC
ATTTGTCTAT-CTTATCTAT--CTATCTGTATAAGCGACCATAATAATAATA-GTTGTGATGGATGC-------------
------TTGGTTGCAGGGATGCTGAGGCAGAAGCCGAGGGCGTGCTGCGGGGCGCCGGGCGTGGGGGTGTACAACTTCAA
CCTGACGTCCAAGTGCGGGGAGCCGGGAGCGTACGCGTGCGACGACCCGTCCAACCACTGGAGCTGGGACGGCATCCACC
TCACGGAGGCCTCCTACGGCCACATCGCCAGGGGCTGGCTCTACGGGCCCTTCGCCGACCCACCCATCGTCGGCAACCGG
AACCTCGAGTAGTACTGTAGCAGCAGTGGTACAG-------GGCTTGTTTTTGCGTACATGCCA------CCTGCACATG
GGTTTTACTACTGTATGTAGAGAAAGAAAGGAAAACAAGTCAAAGAACACA--------CATGCCTTGTGCAGATTAATT
GATTGTTAATTAATTGGTTCTGTTTG------------------------------------------------------
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>chr3D_1080
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------CGTAGGTCACCTCCTCGTATCAAGTTTCTTTGCT-CTCTGTTCTTTTCCTTGGAAGAACACAGGAGGGACAAGC
AGAGGCATGGGGAAGGTGAGCATGCCGCGGCTCGCGCTGGCGGCCCTGGTGCTGGCGAGCCTCGTGCTGTCGGCCCAGGA
GGCCGACGGGGCACGGCCCGCGTCGACCGACGGCGTCATCAGCTACAGCGCTCTCCTGCGCGGGAACAGCGCCAACACCT
CCGACGCCAGCGTCCGGCCTTCTGCGGTGGCCAACCCTTACACGCGCGGCTGCAGCAAGCTCAACCGTTGCCGCGGTTGA
CGCGCGCC---------TGCGTGTAACCGCATGTGTGCCTCTTGTTTTGCTCAAAGGTTAACATGTTGATC-----CCGT
GTGCAAGCCAGGAGTATGATGCAACAACGCTCGCTTCTTTCATCAATGCAAGATCCACCCCCTCATGTCGTTTTTCTTCA
TCTTCTTTTCCGTTTTATCCTTTTGATCGCTTTGATCAAACCCTGTATTCTTTCACCCCTCTGCTAAATCAATGCAAGCC
AGTCGAGCTGGATCTTTCAAAAAAAAAAAAGATCATGCAGTGTTGTCTCTGAATCAAGCTGTTTAAACCTTGACCAAAAC
CGTAGAAAGCATTAACATCGACACTACTACATCACTGTTAAT--------------------------------------
---------------------------GCCTAATTTGACAACCCGGACCGGCTGATTTTTTTTACCAGGCTTGGACCGTT
CGGTCCGGTCCATAGCAGGCCACGAGCCGGACCAAAAGCCCGCTCGGCACATCCAGGCTTATACATAGCGATAGCCAACC
CTTTATTATAAC--------------------------------------------------------------------
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>SNPs
SSSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSS---------------S--S-------------------------S-
SSSSS--S-SSSSS--S-------------------S----------------S--------S-----S-------S---
----S-----S---------S-SSSS-S-SSSSS--------------S----S--S-------S--SSSSSSSSSSSSS
SSSSSS-----------------S------------------------------S-------------------------
------------------S-----------------------------S-------------------------------
----------S---------------------------------------------------------------------
-------------------------S-----SSSSSSSSSS-----------------------SSSSSS----------
---SSSS-SSSSS---------------------S--S-------------SSSSSSSS-----------------SS--
-----------S---------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSS---SS----S--S-SS-S-S-S---S-SSS---S--SSSSS-S--SSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSS-S-----S-S-SS-----S-S----SSS-----------SS----------
--------------SSS-S---SSS-SS-----S-----------------SS-SSS-----------------------
-----------------------------------------------------S--------------------------
-------------------SS-SSSS-----------------S-------------------------S----------
------------S-----S-----------------S---------S--------------------S------------
----------------------S------------S----------------------------------------S---
----SSS-SSSSSSSSS---------------------------S--------------S-----------SSSSS----
----------------------------S--------------S------------------------------------
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------------------------------------------S--------------S------------------S---
---------------S---S------------S------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSS--------S----------------S-----S------S----S---------
-S-----S--------S-----S-------S--S-----------SS---------------------------------
------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSS
>forward_794
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------------------------------------------------------ACATGCATGCGGTACAAGGA------
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>reverse_2013
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------------CACTTCCTCCGCTCCCAAAT------------------------------------------------
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