>input_sequence_81851
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---------------------------------------------------------ATGGGGAGAACCACCATGCTTCT
CATGGCGCTGGCCCTCGCCCTCATCGCCGTCGCCCACGCGGCGCCTCCCGCGCTCCGGAAAAGCCGCTTCCTCGCGGACA
AGACCCCGCCGCCGCTGTCCTACTACGACTGCGTCAGGAAGCCCCCGTCGGTGTGCCTGGAGCCCGGGAGCCCCGGGAAC
ACGTGCTGCAAGGGCACCTGCACCAACACGCTGTCAAGCGTGGAGCACTGCGGCAACTGCAACAGGAAGTGCAAGTACGG
GGACACCTGCTGCGACGGCAAGTGCGTCGACCTCCTCAAGGACAAGAAGAACTGCGGCGAGTGCTCCAACCAGTGCGCCA
AGTCCGTCAAGTGCGAGTTCGGCATGTGCGACTACGCGGGGTGA------------------------------------
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>chr3D_1_TraesCS3D01G175000
CTTTCTCAGAAAAGGCAGTGATGCTTCTGTTGCTGTTGCAGGGATTATACCCCAATCATCACACGGACAGTAGCATCAAC
TTCTCCTACTGACAAAGTAGAGTCAACCTGCAGTACAAGCCATTTAAGGCTTCATCTAATTC-CTTCCTCTAATTAATAA
CATGTCTTTTTT------TTAGATCAAACCTGAAGGGAATCCGAAGCCAGGGGAGTTGTAAACCTGTCTGAATGTGGACT
ACATTATCAGTACAT----ATGTCATGCTGAACCATAGATGAGATGGAAAACTAACGATTACTTACTGTATCTTTCAAAC
CGAATCAACAATGCTTGAAAACTGATTTCGTGCTTCTAGACCCATTTGCCGTGCGTTGCATACCGAAGTAACATGCCTGC
AGACATTAGAAACAGTTTCCTTGTGCTCGCAACGCCGACAAAGTGCCCCTGGAGGGAGCTGCTAGGAGTTTGATCAACGG
ACGCAAGTCACAGCAGCAGTACGTGTAATCCTAAAAGCGCCACGATTTTATTACTGCAGATAGTCAACCCCTGCGCAAAT
CTGGCAGACGTGTCAAATCTTCATGAGTGTGAATGACCAGGCAGCCAATTGCCGAGAATATTCCTCCCCCGCCTGCAAAG
GCGGCAAG----ACGTACGTACGCACGCACAAGATCACCATCGCAAGCATGAATCATGTTAAAGTTGGACGAGGGGCAGA
GAAGAAATCAACCAGGAGCCGGCTGGC-TAGCTAGCTTGCAGGCCACAGCCTTGGTGCGCACACTCCCTCCCTGCACTCC
AGGCTTTTGCCGTGCAAATCAACCATGGGCAGGCATATGCATGCGCCGATGCGCCTTTGACTTTCGCCATGGCCGTCT-A
GCCCATAGTATAAGCACGGCCCCTCCCTCCCTACAACCCCCATTTCCTTCCTCATAGAGCCACCTGCCGAGCCACAAGCC
ATCAGCAGCGCACTGCCACGACCCTAAGCTCTCTCCCTCCAGCGCCACCCCACCACCATGGGGAGAACCACCATGCTTCT
CATGGCGCTGGCCCTCGCCCTCATCGCCGTCGCCCACGCGGCGCCTCCCGCGCTCCGGAAAAGCCGCTTCCTCGCGGACA
AGACCCCGCCGCCGCTGTCCTACTACGACTGCGTCAGGAAGCCCCCGTCGGTGTGCCTGGAGCCCGGGAGCCCCGGGAAC
ACGTGCTGCAAGGGCACCTGCACCAACACGCTGTCAAGCGTGGAGCACTGCGGCAACTGCAACAGGAAGTGCAAGTACGG
GGACACCTGCTGCGACGGCAAGTGCGTCGACCTCCTCAAGGACAAGAAGAACTGCGGCGAGTGCTCCAACCAGTGCGCCA
AGTCCGTCAAGTGCGAGTTCGGCATGTGCGACTACGCGGGGTGATGCCGAT---------CCGGCCATGCCCGCCATGCG
TGC-----GTGTGATCGGCGGCCACGCATATACAGTTCTGCACCCA----------CCAAGAAATAAAATCGGCAGTACG
TATATACTACGTGAGTGCATCTTAAGAAGTCCAAATTGTTTAAGGTATTTCGATTGTTGATCTCCTCGATCATATGTATA
CAAAAAAAA-GGGTACAAATGATTTATACGTCTCTCTGTTCGTCTCATGATTTACGTGTTTTATTTGTTGGACTACATAC
TATAAATACAAAGTTGTCACGTGGTATTAATAAAGTGAATAATGTTGTAATGTGTTATACAGCATATATATCATTTTTGG
GGTACCCTTAGCTCGATCAATACATATGTATATATGGATTCCTTTTTATGTATACCGAATAATGGAAACATTTTCAATGA
ATGTTTATTTGATTTAACAATCGATTCTGATGAATTTATCAAGTTTGAAAAATCTAGTTTTTTCTTGTATAGACTAGTAG
GCATCTGTACATGCCATTCGCTTAATTTGTACGACTGCTTGCAAACTGCCAATTCATAGAACTGGTCTTACTTAGGACCT
AGGATGCGTACAAACGGGAAAGTACTTAACGTAGATGCCTCCCATGGTCAACTTAATCAACTCATTTGCATGTGGCCTAC
ATTCT------TTGCATTAGTACGTGACGTGTCTGTCCAGTATCCATAGCAGCCAAATCTTTTTTTTTTTTGCGAGAACA
CAGCAGCCAAATCTGACACTAGTAATTTCCTAAGTACAGTTTACTATGATCACAGGATTTCCAATCTTTTCTTGAGGATT
TTTTCAAGAAACTGTAGAGTTTATCATCTTGGCTAGAGCAAAAAAATCAGGGTTTTAGCATAGGTGTATCCTGAACTTTA
TTTTAAGAAACATGCACCCGCAATATTCTTTTTTTTAAGAGAGGCAAAAGATTTGCCTCATTCATTATAAGAGGAATAGA
GTATATGGTCGTGTTACAACACAGACAGCGCCGTA
>chr3A_1
CTTTCTCCGGAAAGGCAATGATGCTTCTTTTA------CAGGGATTATACCGCAATCATCACACGGACAGTAGCATCAAC
TTCTCCTGCTGACAAAGT-GAGTCAACCTGCAGTACAAGCCGTTTAAGGCTTCAGCTAATTC-CTTTCTCTAATTAATAA
CATGTCAAGTTGGGTTTCTTAGATCAAACCTGAAGGGAATCCGAAGCCAGGGGAGTTCTAAACCTGTC-GAATGTGGACT
ACATGATCAATCAGTACAAATGTCATGCTGAACCATAGATGAGATGGAAAACTAACAATTACTTACCGTATCTTTCTAAC
CGGATCAACAATGCTTCAAAACAAATTTCGTGCTTCTGGACCCATTTGCCGTGCACTGCATACCGAAGTAACATGCCTGC
AGACATTAGAAAGAGTTTCCTTGTGCTCGCAACGCCGACAAAGTGCCCCTGGAGGGAGCTGCATGCTAGGCAG-------
------------------------------------GCGCCACGATTTTATTACTGCAGATAGTCAACCCCTGCGCAAAT
CTGGCAGACGTGTCAAATCTTCAGGAGTGTGAATGACCAGGCAGCCAATTGCCAAGAATATTCCGCCTCTGCCTGCAAAG
GCGGCAACGCGTACGTACGTACGCACGCACAAGATCGCCATCGCAAGCATGGATCATGCTAAAGTTGGACGAGAGGCAGA
GAAGAAATCAACCAGGAGCCGGCTAGC-GAGCTAGCTTGCAGCCCACAGCCTTGCTGCGCACACTCCCTCCCTGCACTCC
AGGCTTTTGCCGTGCAAATCAACCATGGGCAGGCATATGCATGCGCCGAGACGCCTTTGACTTTCGCCATTGCCGTCT-A
GCCCATACTATAAGCACTGCCCCTCCCTCCCTACAACCCCCATTTCCTTCCTCATAGAGCCACCTGCCGAGCCACAAGCC
ATCAGCAGCGCACTGCCACGACCCTAAGCTTTCCCCCTCCACCGCCACCCCACCACCATGGGGAGAGCCACCATGCTTCT
CATGGCGCTGGCCCTCGCCACGATCACCGTCGCCCACGCCGCGCCTCCCGCGCTCCGGCGGAGCCGCTTCCTTGCGGACA
AGCTCCCGCCGCCGCTGTCCTACTTCGACTGCGTCAGGAAGCCCCCGTCGGTGTGCCTGGAGCCCTTGAGCCCCGGGAAG
ACGTGCTGCAAGGGCACCTGCACCGACACGGAGTCCAGCGCTGAGCACTGCGGCAACTGCAACAGGAAGTGCAAGTACGG
GGACACCTGCTGCGGCGGCAAGTGCGTCGACCTCCTCAAGGACCAGAAGAACTGCGGCGAGTGCTCCAACCAGTGCGCCA
ACTCCGTCAAGTGCGAGTTCGGCATGTGCGACTACGCGGGGTGATGCCGATCCGGCGACGCCGGCCATGCCCGCCATGCG
TGCGTGCGGTGTGATCGGCGGCCACGCATATACAGTTCTGCACCCATCATGCATGACCAAGAAATAAATTCGGCAGTGCG
TATATACTACGTGAGTGCATCTTAAGAAGTCCAAATTGTTTAAGGTATTTCGATTGTTGATCTCCTCGATCATATGTATA
CAAAAAAAA-GGGTACAGATGATTTATACGTCCCTCTGTTCGTCTCATGATTTACGTGTTTTATTTGTTGGACTACATAC
TATAAATACAAAGTGGTCACGTGGTATTAATAAAGTGAATAATGTTGTAATGTGTTATA---CATATAT--GATTTTTTG
GGTACCCGTAGCTCGATCAATACATATGTATATATGGATTC-TTTTTATGTATACCGAATAGTGGAAACATTTCCAATGA
ATGTTTATTTGATTTAACAATCGATTCTGTGTATTTTACCTAGCTTGAATATTCT--TTTTTTTCTGTATAGACTAGTAG
GCAT--GTACATGCCATTCGCATTATTTGTACGACTGCTTACAAACTGCCAATTCATAGAACTGGTCTTAGTTAGGACCT
AGGACGCGTACAAACGGGAAAGTACTTAACGTAGATGCCTCCCATGGTCAACTTAATCAACTCATTTGCATGTGGCA---
----T------TTGCATTAGTACGTGACGTGTCTGTCCAGTGTCCACAACAGCCAAATCT--------------------
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>chr3B_2
TTTGCTCAGAAAAGGAAGCGATGGTTCTGTTG------CAGGGATTATACCCCAATCATCACACGGACAGTAGCATCAAC
TTCTCCTACTGACAAAGTAGAGTCAACCTGCAGTACAAGTCATTTAAGGTTCCAGCTAATTCTCTTTCTCCAAT---TAA
CATGTCAAGTTGGGTTTCTTAGATCCAACCTGAAGGGAATCCGAAGTCAGGGGAGTTCTAAACCTGTCTGAATGTGGACT
AAATGATCAGTACAT----ATGTCATGCTGAACCATAGATGAGATGGAAAACTAACAATTACTTACTGTACCTTTCAAAC
CGAATCAACAATGCTTCAAAACTAATTTCGTGCTTCTAGACCCGTTTGCCGTGCATTGCATACCGATGTAACATGCCTGC
AGACATTAGAAACAGTTTCCTTGTGCTCGCAGCGCCGACAAAGTGCCCCTGGAGGGAGCTGCTAGGAGTTTGATCAACGG
ACGCAAGTCGCAGCAGCAGTACGTGTAATCCTAAAAGCGCCACGATTTTATTACTGCAGATAGTCAACCCCTGCGCAAGT
CTGGTAGACGTGTCAAATCTTGATGAGTGTGAATGACCAGGCAGCCAATTGCTACGAATATTCCTCCCCTGCCTGCAAAG
GCGGCAAG----ACGTACGTACACACGCACAAGATCACCATCGCAAGCATGAATCATGTTAAAGTTGGACGAGAGGCAGA
GAAGAAATCAAGCAGGAGCCGGCTAGCTTAGCTAGCTTGCAGCCCACAGCCTTGCTGCGCACACTCA----CTGCACTCC
AGGCTTTTGCCGTGCAAATCAACCATGGGCAGGCATATGCATGCGCCCATGCGCCTTTGACTTTCGCCATTGCCGGCTCA
GCCCATAGTATAAGCACGGCCCTTCCCTCCCTACAACCCCCATTTCCTTCCTCATAGAGCCACCTGCCGAGCCACAAGCC
ATCAGCAGCGCACTGCCACGACCCTAAGCTCTCTCCCTCCAGCGCCACCCCACCACCATGGGGAGAACCACCATGCTTCT
CATGGCGCTGGCCCTCGCCCTCACCGCCGTCGCCCACGCGACGCCTCCCGCGCTCCGGAGGAGCCGCTTCCTTGCCGACA
AGACCCCGCCGCCGCTGTCCTACTACGACTGCGTCAGGAAGCCCCCGTCGGTGTGCCTGGAGCCCGGGAGCCCCGGGAAC
ACCTGCTGCAAGGGCACCTGCACCAACACCTTGTCCAGCGTGGAGCACTGCGGCAACTGCAACAGGAAGTGCAAGTACGG
GGACACCTGCTGCGACGGCAAGTGCGTCGACCTCCTCAAGGACAAGAAGAACTGCGGCGAGTGCTCCAACCAGTGCGCCA
ACTCCGTCAAGTGCGAGTTCGGCATGTGCGACTACGCGGGGTGATGCCGATCCGGCGACGCCGGCCATGCCCGCCATGCG
TACGTGTGGTGTGATCGGCGGCCACGCATATACAGTTCTGCACCCATCATGCATGACCAACAAATAAAATCGGCAGTACG
TATATACTACGTGAGTGCATCTTAAGAAGTCCAAATTGTTTAAGGTATTTCAATTGTTGATCTCCTCGATCATATGTATA
CAAAAAAAAAGGGTACAGATGATTTATACGTCTCTCTGTTCGTCTCATGATTTACGTGTTTTATTTGTTGGACTACATAC
TATAAATACAAAGTGGTCACGTGGTATTAATAAAGTGAATAATGTTGTAATGTGTTATA---CATATATATGATTTTTTG
GGTACCCGTAGCTCCATCAATTCATATGTATATATGGATTCTTTTTTATGTATACCGAACAATGGAAACATTTTCAATGA
AT-----------------------TCAGATGTATTTACCAAGTTTGAAC---CT--TTTTTTACGGTATAGACTAGTAG
GCAT--GTGC-TGCCATTCGC-TTATTTGTGCGACTGCTTGCAAACTGCCAATTCATAGAACTGGTCTTAGTTAGGATCT
AGGACGCGTACAAAAGGGAAAGTGCTTAACGTAGATGCCTCCCATGGTCAACTTAATCAACTCATTTGCATGTGGCA---
----TACATTCTTGCATTAGTACGTGACGTGTCTGTCCAGTATCCACAGC------------------------------
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>SNPs
--------------------------------SSSSSS------------------------------------------
------------------------------------------------------S-----------S-------------
------SSS--S---------------------------------------------S----------------------
----S---------------------------------------------------S-----------------------
----------------S------S------------------------------S-------------------------
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---------S----------------------------------------------------------------------
-----------------------------------------------------S---------------S----------
-------------------------------------------------------------------------S------
------------------------S-----------------S-----------S-------------------------
----------------------------------------------------------------------S---------
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-----------------------------------------------------------SS-----------S-------
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------------------------------S----S--------------------------------------------
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-S------------------------------------------------------------------------------
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-----------------S--------------------------------------------------------------
--------------S--------------------------------------------SSS---------S------S-
-------S---------------------------------S--------------------------------------
--------------------------------------S----------S-S---SS------SS---------------
----SS---------------S-S----------------------------------------------S---------
----S-----------------------------------------------------------------------SSSS
SSSS------------------------------------------S-------------SSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_33
-------------GGCAGTGATGCTTCTGTTGC-----------------------------------------------
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>reverse_1231
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------------------------------CTGTCAAGCGTGGAGCACT-------------------------------
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>forward_630
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--------------------------------------------------GCCGAGAATATTCCTCCCCC----------
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>reverse_2148
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-------------------------------------------------------------------TTTTGCGAGAACA
CAGCAGC-------------------------------------------------------------------------
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-----------------------------------
