>input_sequence_86369
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--------------ATGGGGAAGGTGAGCATGCCGCGGCTCGCGCTGGCGGCCCTGGTGCTGGCGAGCCTCGTGCTGTCG
GCCCAGGAGGCCGACGGGGCACGGCCCGCGTCGACCGACGGCGTCATCAGCTACAGCGCTCTCCTGCGCGGGAACAGCGC
CAACACCTCCGACGCCAGCGTCCGGCCTTCTGCGGTGGCCAACCCTTACACGCGCGGCTGCAGCAAGCTCAACCGTTGCC
GCGGTTGA------------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G146100
AGCGCGCACTCACCATGGTTATCGAAGCATCGCCACGACCATTGAAGCGTGCCTTGTTGCATGGCGACGGTCCTCAACGC
CGTCATGGC-ATGCCTCATCGCCCTAGTCGTTGAACCAGTGCCGTGGCCGTCGAAGTCATCATGGTCATGGCG-------
-----------------------------GTCAACCGCGTCATGGTCGTTGAAGCTGTAAACGAGCCTAACCACCTCTGC
ATGCCGTTGTAGTCTCTAA-------------------------------------------------------------
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------------------------------------------------------CCAAATGTCCTTAGTCTTTAGCTAGT
TAGCTAGTCCACGGGGAGGTTGTTAGCCACGATTGAGTCTGCACTGACCGCATGATCAATGAAAGTCT------------
-------------------------CTCTGCTGCATTGTAGCTCGTGGTCCTCCGTAA-CACCAGGATGGCTCCCCCCAT
GAAGCACTGATGGTTCGCTCCTTTGCAGCGTCGAACGCCGCTGGTCGGCTCTC--CAACCACTAACGACTGACAAAATCA
TGGCGGGTCCCCC-AAAAGCACCAGTGGCCTCTTCTACAACAGCCCTTGGTGGTCCCTATAGCATCGAGTGCCGGCAAGG
AGCGGTGGCCTGCCTGGCCTGGTGAGCACGAGCTCACCGGAGGAAGGCGCTTGGGTAGAGAGAGAGAGAGAGAGAGAGAG
AAAGAGGAGG---------CCAGGAGGGGATCCAACGCGAGGACACAGCGAGATCGATTGAGCCGAGAAGATAAGGAAGA
AAAGGGGAAGCGGTGCGCTGGTTCCATGGGACACGTGGCGCAGAAGGGAGGCGGCTTACGATGCGGCAAAATCAGTCGGA
TTAAAAGAAACGTTTCCCATAAATATGAGCACCGTTTCGAAAAAAGAAGGCCTAAATACGGCACGGG----------CCT
CTGGTCCCCTCGTGTTTTAGGCATGGAGCCTCGTTAAAACGGACCCTTTGCTCCGCATCCCCGCCACCTTGGG-CACCAG
TAAGGAGGAACCGCCGTAGGTCACCTCCTCGTATCAAGTTTCTTTGCT-CTCTGTTCTTTTCCTTGGAAGAACACAGGAG
GGACAAGCAGAGGCATGGGGAAGGTGAGCATGCCGCGGCTCGCGCTGGCGGCCCTGGTGCTGGCGAGCCTCGTGCTGTCG
GCCCAGGAGGCCGACGGGGCACGGCCCGCGTCGACCGACGGCGTCATCAGCTACAGCGCTCTCCTGCGCGGGAACAGCGC
CAACACCTCCGACGCCAGCGTCCGGCCTTCTGCGGTGGCCAACCCTTACACGCGCGGCTGCAGCAAGCTCAACCGTTGCC
GCGGTTGACGCGCGCC---------TGCGTGTAACCGCATGTGTGCCTCTTGTTTTGCTCAAAGGTTAACATGTTGATC-
----CCGTGTGCAAGCCAGGAGTATGATGCAACAACGCTCGCTTCTTTCATCAATGCAAGATCCACCCCCTCATGTCGTT
TTTCTTCATCTTCTTTTCCGTTTTATCCTTTTGATCGCTTTGATCAAACCCTGTATTCTTTCACCCCTCTGCTAAATCAA
TGCAAGCCAGTCGAGCTGGATCTTTCAAAAAAAAAAAAGATCATGCAGTGTTGTCTCTGAATCAAGCTGTTTAAACCTTG
ACCAAAACCGTAGAAAGCATTAACATCGACACTACTACATCACTGTTAAT------------------------------
-----------------------------------GCCTAATTTGACAACCCGGACCGGCTGATTTTTTTTACCAGGCTT
GGACCGTTCGGTCCGGTCCATAGCAGGCCACGAGCCGGACCAAAAGCCCGCTCGGCACATCCAGGCTTATACATAGCGAT
AGCCAACCCTTTATTATAACTAGTGATGCCCATCCCAACCGGCATCTGCGCGACATGGGCTCCTGAAATGTTTGTCGCCA
ATGTCAGAGCTAACTTGTTGCTGATGTGGGTTGGTCCATTGTTTGACATGTATCATCATAGGCTTCATGTGTTTGTTGTG
GCAAGACCTATGTCGGTGGTAGTGTACAGTGTAGTTGGAGTCATTGGCTCATAGAGGGGTGATGATAATGACACATGTAT
CAACCTTGACGATAGTCTACAGTATTGTTGGCAACCAAGTGGGCTAATGGTGCCATATGAGGTCATGTCCAGGACGACAT
TTATGGACATTTCTAACGGTTTTCATCCCTTTTTTTCTTTCCAATTAATGGAGCAAATATGTTCTTAATAAATGAAAATT
GCAAATCTTGTGCCTTGTTTAAAAAAGTGTATAAGAGTCACATGTTTAAAAAAGTCCCCGCTCCGCTCCTAGGGGGGCGG
CACGGGTGAAACCCTAGCCGCCGTCCCCGTCTCCCCTCTTCTCCATC
>chr3B_1
AGCGCTCCCTCGCCATGGTTATCGAAGCATCACCACTACCATTGAAGCATGCCTTGTTGCATGGCCACGGTCCTCAACGC
CGTCATGGCAATGCCTCGTCGCCCTAGTCGTTGAACCAATGCCGTGGCCGTCGAAGTCATCATGGTCATGGAGGCATTGC
CACGGTCATTGAAGCATTGTCGTGCGGCCGTCAACCGCGTCATGGTCGTTGAAGCTGTAAACGAGCCTAACCACCTCTGC
ATGCCGTTGTAGTCTCTAAGGGCATGTACAATGATGCTATCTTAGGACTGCCACGTAGGATAAATGATGAGGTGAAGGAG
AGAGAACCCATAAGAAAAGGCTTGTCTTCTCTTATTTAAGAAAAGACAAGAGATGATCTCTTAGCACAATATGTCTCACC
ATGTTTTTAGGAATAACTAGTTATTGAAGATAAGGCTAAGAGATGACCCATTGTAGGCATGTTTTTTTGTCATCTCTAAA
CTACATGCAAAACTTAAGATAAGACTATCTTATCAACCATTGTACATGCCCTAACCAAATCTCCCTAGTCTTTAGCTAGT
TAGCTAGTCCACAGGGAGGTTGTTAGCCACGATTGAGTCTGCACTGACCGCACGATCAATGAAAGTCTGGTGTTGCATGC
ATGTTGGCGCACGACTTAGCAGCCTCTCTGCTGCATTGCAGCTCGTGGTCCTCCGTAAACACCAGGATGGCTCCCCCCAT
GAAGCACCGACGGTTAGCTGCTTTGCAGCGTCGAACGCCGCCGGTCGGCTCTCCACAACCACTAACGACTGACAAAATCA
TGGCGGGTCCCCCCAAAAGCACCAGTGGCCTCTTTTGCAACAGCCCTTGGTGGTCCCTATAGCATCGAGCGCCGGCAAGG
AGCGGTGGCCTTCCTGGCCTGGTGAAAGCGAGCTCACCGGAGGAAGGAGCTTGGGTAGAGAGAGAGAGAGAGAGAGAGAG
AGAGAGGAGGAGGAGGAGGCCAGGAGGGGATCCAGCGCGAGGACACAGCGAGATCGATTG-GCCGAGAAGATAAGGAAGA
AAAGGGGAAGCAGTGCGCTGG-TCCATGGGACACGTGGCGCAGAAGGGAGGCGGCTTACGATGCGGCAAAATAAGTCGGA
TTAAAAGAA-----------------------------------------------------------------------
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>chr3B_778
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-------------------TAAATATGATG-CCGTTTCGTAAAAAGACGGTCTAAATAGGGCATGCGCCTCTGAGTTCCT
CTGGTCCGCTCGTGTTTTAGGCATGGAGCCTCATCAAAAGGAACCCTTTGCTCTGCATCCCCACCAGCTTGGCACACCAA
TAAGGAGGAACCGTCGTAGGTCA---CCTCGTATCAAGTTTCTTTGTTTCTCTGTTC-TTTCCTTGGAAGAACACAGGAG
GGAGGAGCAG--GCATGGGGAAGGTGAGCATGCAGCAGCTTGCGCTAGTGGCCCTGGTGCTGGCAAGCCTCGTGTTGTCG
GCCCAGGAGGCCGACGGGGCTCGGCCCGAGTCGACCGGCGGCGTCATCAGCTACCGTGCTCTCGTGCGCGGGAATAGCGC
CAACACCTCCGACGCCAACGTCCGGCCTTCTGCGGTGGCCAACCCTTACACGCGCGGCTGCAGCAAGATCAACCGTTGCC
GCGGTTGATGCGTGCC---------TGCG----------TGTGTATCTCTTGTTTTGCTCGAACGTTCGAACGTTGATC-
----CCGTGTGCAAGCCAGGAGTATGATACAACA-CGCTCGCTTCTTTCATCAATACAAGATC-----------------
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>chr3A_919
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-----------CGTCGTAGGTCACCTCCTCGTATCAAGTTTCTTTGTT-CTCTGTTC-TTTGCTTGGAAGAACACAGGAG
GGAGGAGCAG--GCATGGGGAAGGTGATGAGCATGCGGCTCGCGCTGGTGGTCCTGGTGCTGGCGAGCCTCGTGCTGGCG
GCCCAGGAGGCCGACGGGGCGCGGCCAGCGTCGACCGACGGCGTTATCAGCTACGGTGCTCTCCTGCGCGGGAACGGCGC
CAACACCTCCGACGCCAGCGTCCGGCCTTCCGCGGTGGCCAACTCTTACACGCGCGGCTGCAGCAAGATCAACCGTTGCC
GCGGCTGATGCGACGCGTGCCTGCATGCG----------TGTGTATCTCTTGCTTTGCTCGAACGTTTGAACGTTGATCC
GGTGCCGTGTGCAAGCCAGGAGTATGATGCAACA-CACTCGCTTCTTTCATGAATACAAGATC-----------------
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------------------------------------------ATGCAGTGCTGTCTCTGAATCAAACTGTTTAAAGCTTG
ACCAGATCCGTAGAAAGCATTAGAATCCACACTACTAAATTACTTTTTTAGACAAGACACTACTAAAATACCTTTTTTAG
CACTACTAAATTACTGTTAATGCAACATTGGTCGGGCCTAATTCGACAACCCGGACCGGCCGATTTA-TTTACAAGGCCT
GGACCGTTCAGTCCGATCCATAGCGGGCCATGAGCCGGGCCGAAAGCCCGCTCAACACATCCAGGCTT----ATAGCGAT
AGCCAACCCTTTATTATAAC------------------------------------------------------------
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>SNPs
-----S-S---S-------------------S----S-----------S----------------S--------------
-----------------S--------------------S--------------------------------S--------
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------------------------------------------------------------S---S---------------
------------S---------------------------------------S---------------------------
--------------------------------------S-----------------------------------------
-------S--S----S---S---------------------S--------------------------------------
----------------------------------S-S--------------------------------S----------
-----------S-------------SSS-------------------S--------------------------------
-S--------------------------------S-------------------------S-------------------
-----------S---------S--------------------------------------------------S-------
---------SSSSSSSSSS---------SSS--------S-------S--S-------S----S-S--------------
-------S------------------------S-S----S-S-----------S--------S---S-----S------S
-------------S--------------------------------S----------S----------------------
---SS-----SS---------------------S--------------S-------------------------------
--------------------S---------------------------------S-S-----------------------
-------------------------------------------------------------------S------------
--------S---S----------------SSSSSSSSSS-----SS--------------S--S---SSS-S--------
----------------------------------S--------------------S-------SSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------S--------------S---------S----
----S-S---------------SS---S---------S--S---S--SSS------------------------------
-------------------------------------------S----------------S-----SS-----S----S-
---------S-----S--------S-----S-------S--S-----------SS-------------SSSS--------
--------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_1372
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------------------------------------------------------------------------CACAGGAG
GGACAAGCAGAG--------------------------------------------------------------------
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>reverse_2428
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---------------------------TTGGCAACCAAGTGGGCTAA---------------------------------
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