>input_sequence_82075
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------------------------------------------------------------------ATGGACGA---GGG
CAAATATCAGCAGGGCTGGCTCGCCGTCGGCCTGCCGCCGGCGCCGGTGCTCGCCGTCACCGGCATCGTGACCTTCTTCC
TCTACCTGTCGTGGCAGATGGATGAGTTCGAGGAGCAGCTGCGCCATCGCACCCAGGCAGGCTTCTGGGTGCTCATTGTG
CTGGGGCTCCTCGCCCTGGGCGTGCTCGCGCAGCATGTGCTGTTCGACGGAGAGGGGAGGGTCGCCGTGCCGGCGGCATG
GCGCGGCCAGCCCGAGGGCGGCTCCGGCACGTCGCCGTGGGGCGTCGCGGCCCTGGTGGCTCTGCTGCTGGTGCTAGTGT
CTCACAGGTCCGACTTCCAGATATTCAAGCCCCCGGGGTTTAGATGA---------------------------------
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>chr3D_1_TraesCS3D01G133900
AGTAAAACCGTGACTCTCGCGAAAGAAAAAAAAACAGAAAACGCGTTTTTGTTTTGTTTCCGAAAGGCACGGCCGTGACT
CTCGCTAAAGCACAACCGTGCCTCTCGCGAAAAAAACGTGACTTTTCACAAAAGAAAAAAAAGTAAAAGCGTTTTTTCGC
GCAAAATTTTTATTTTTCAAAATTTTCTTTTGGTTGAAACGCTAAGGAAGATCGGGGAAAAACCAAAACGTCAAAAAAAA
CCAGGAAAATAATCGTTTAAAAAGCCGAAAACGCGTGCGGAAAAATAAAAAAACAAAATCTGAAGGGAGTGTCCAGAGCG
CGACACGTGGCGAATGGCTGAGAGCGCGCTAATTGGCGCTGATTGTTGCGAGGCTCCCTAAGGAGCGCTCGTTAACTAGT
TGCTCCCCGTCTAAACAGCCCGTTCCCTTCCCACACGGGTCTGGTTGGGCCTAATGGAGGCAACCAAACACACCCTTAGT
ATTTCCAGGTTGGGCCTTTTGTGATGCCTGGCCGAGTCCAGCGTGATCAGCCCTAGTCGGCACGATATTTTCCTTCTCAA
ACAAAAAAAAGTCGGCACAATATTTCAGGTTCTCTTCCTTTTGCTCAAATAA--AAAA-GAAATCCCTTCTTTCTTTTTC
ACGGGTAGGTTTCCAACCGAAGAAATGAACGGTTTTCTCGCAAAGTAG--CATCCGGAGAAGATTGGGGAATCCTGAAAA
GGCGCCAGCGACCGACCGCCGACTGTCTCGTAGCCATCTCGAAAGCTCCCGTCAGAGAAGACACGCGGTGCCGCCTT-CT
CTTCCAGAGGCATCCATCAGCTTTCCACTCCTCATCCATGGCCACAAAAGCAAAGCGCGCACTGGCCGCGCACGTCTCTC
CTCCGGCCGTCCCCCATATAACGGCGCTGCCCGGCACACAGCAGATACGAAACACATGACCACACGCATAGCTGAGG---
----------------AAGCCAGGCACGTAGTAGATCCCAGACCGTACGT-CCAAATTAAGCTCCCATGGACGA---GGG
CAAATATCAGCAGGGCTGGCTCGCCGTCGGCCTGCCGCCGGCGCCGGTGCTCGCCGTCACCGGCATCGTGACCTTCTTCC
TCTACCTGTCGTGGCAGATGGATGAGTTCGAGGAGCAGCTGCGCCATCGCACCCAGGCAGGCTTCTGGGTGCTCATTGTG
CTGGGGCTCCTCGCCCTGGGCGTGCTCGCGCAGCATGTGCTGTTCGACGGAGAGGGGAGGGTCGCCGTGCCGGCGGCATG
GCGCGGCCAGCCCGAGGGCGGCTCCGGCACGTCGCCGTGGGGCGTCGCGGCCCTGGTGGCTCTGCTGCTGGTGCTAGTGT
CTCACAGGTCCGACTTCCAGATATTCAAGCCCCCGGGGTTTAGATGAGCG---TTTTTTTTTGAA---GGAAAGCTATGT
ATCCCGATGCAGATAACTATGATATATTATATACA-----ATAAATTAGTAG---AAGGTGTTTTTGCAAGCCTGCATGA
TGAAGCAAAATAACATAAATAAAAAAGAATTACTCCCTCGGTCCCCAGAAATTGC-TTTTGGAGGCCGAGCTC-----GG
CCTTCAAATGCAAAATTCAAAATTTATGAAAATTCATACTTTTACATTTTAAAAATTTCTGAAAAAAATACAG-AGATAG
ATAAAGGCAGAGTGCAAGTGTGTAAATTTTCAGGACGAGATACGTTGAAATGAGATGAGGGCCTTGCAAAAAGACAAAGG
GCCTTGCAAAAAGACAAATCTGAA-CTTTTTAACACATAATACAATTCATCCTCACATACTAGTAACTTGTCTATTTTGT
ATAGATCGCATTTCAATGTATTCCATCCTAAAATTTTACACACACGCCTCATATCCTTCTTTATTTGTACACTTTTTT-C
AGAATATTTTGAACCCGAATTTTTTGAATTTTGA-TTTTTTTTAAAGTTGGCCTCCATGAAAGCCAAGAGCCAAAATGTC
ATTCTCCTCCATCCC-ATAGTATAAGATGTA----AAATATTGTATCTAATACATTGCAAATATAATCGGTATATAATTG
GAGAGAGTTGTGATTGACGTTGTGTCCAATGGAAAAATGTTTACAGTCTGGGTGAAAGCGAAGGATGAGCCAAATAAGAC
GAGACAATTCCCATATGGGATCTATTATTGGGGATCTATGGGGCATCTTTTTGGGGTTGTACATCGGCTGGAGGGACAAG
TATTTGGCTTGATGCCGGAT-GCAAATCTTCATATATTCGCCGTGCGGTGATCAAGATAGAGTGTTGTGCCATGCACAGT
ATTGACGATGACGAGTCTTGGCGGCAAGGTGCAGCAGGATCTCGATGCTGGATACCGTTCAATGGGCGCGTGCAGAAGGC
ATGTTCTGTTTGGCATAGTGACGGCGTCAACGACAGA
>chr3B_476
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---------------------------------------------------------------------------TTAGT
GTTTCCAGGTTGGGCCTGTTGTGATGCCCGTCCGAGTCGAGCGCGGTCAGCCCTAGTCGGCATGATATTTCCTCCTTCTA
AAAAAAAGGAGTCGGCACGATATTTCAGGTTCTCCATCCCTTCTTCGTTTTGCTAAAATGAAATCCCTTCTTCCTTTTTC
ACGGGTAGGTTTCCAAGCGAAGAAATGAACGGTTTTCTCGCAAAGTAGAGCATCCGGAGAAGATTGGGGAATCCTGGAAA
GGCGCCAGCGACCGACCGCCGACTGTCTCGTAGCCATCTCGAAAGCTCCCGTCAGAGAAGACACGCGGTGCCGCCTT-CT
CTTCCAGAGGCATCCACCAGCTTTCCACTCCTTC-CCATGGCCACAAAAGCAAAGCGCGCACTGGCCGCCCACGTCTCTC
CTCCGGTCCTCCTCCATATAACGCCGCTGCCCGTCACACAGCAGATACGGAACACATGACCACACGCATAGCTGAGGGAA
GCCAGGCACGCAGTAGA------------------TCCCAGACCACACGTCCCAAATTAAGCTCCGATGGACGA---GGG
CAAGTATCAGCAGGGCTGGCTCGCCGTCGGCCTGCCGCCGGCGCCGGTGCTCGCCGTCACCGGCATCGTGACCTTTTTCC
TCTACCTTTCGTGGCAGATGGATGAGTTCGAGGAGCAGCTGCGCCATCGCACCCAGGCAGGCTTCTGGGTGCTCATGGTG
CTGGGACTCCTCGCCCTGGGCGTGCTCGCGCAGCATGTGCTGTTCGACGGAGAGGGGAGGGTCGCCGTGCCCGCGGCATG
GCGAGGCCAGCCCGAGGGCGGCTCCGGCACGTCGCCGTGGGGCGTCGCGGCCCTTGTGGCTCTGCTGCTGGTGCTTGTGT
CTCACAGGTCCGACTTCCAGATATTCAAGCCCCCGGGGTTTAGATGAGCATGCTTTTTTTTTCTCGATGGAAAGCTATGT
ATCCCGATGCAGATAGCTATGATATACTATTATTATATACATAAATTAGTAG---AAGGTGTTTTTGCACGTCTGCATGA
TCAAGCAAAATAACATAAATAAAAAAGAATTACTCCCTCCGTCCCCGGAAATTGCTTTTTGGAGGTCGGGAGCATGGAGG
CCTTCAAATGCAAAATTCAAAATTTATGAAAATTCATACTTTTACATTTCAAAAAATTCTGAAAAAAACTACGAAGATAG
ATGAAGGCAGAGTGCAAGTGCGTAAATTTTCAGGACGAAATGCC-------------------TTGCA------------
-------AAAAAGACAAATCTGAGCTTTTTTAACACATAATA----TCATCCCCACAAACCAGTAATTTGTCTATTTTGT
ATAGGTCGCATTTCAACGTATTTCATTCTAAAATTTTACACACACGCGTCACATCCTTATTTATTTGTACAA-TTTTT-C
AGAATATTTTGAACCCGATTTTTTTGAATTTTGAATTTTTAAAAAAGTGGGCCTCCATGAAAGACGACAGACAAAATGTC
ATTCTCCTCCATCCC-ATAATATAATATAAGATGTAAATATTGGATCTAATACATTTCAAATATAATCGGTATATAATTG
GAGAAATTTGTGATTGACGTTGTGTCCAATGAAAGAATGTTTATAGTCTGGGTGAAAGCGAAGGATGAGCCAAAGGAGAC
GATATAATTCCCATGCGGGATCTATTATTGGGGATCTATGGGGCATCTTTTTAGGGTTGTACATCGATTAGAGGGACAAT
TATTTGGCTTGATGGCTGGGCGCAGATCTTCATATATTCCGTGTGCGGTGATCAAGATGGAGTGGCGTGCCATCTACAGT
ATTGACGATGGCGAGTCTTGGCGGCAGGGTGCAGCGGGGGCTAGATGCTGGATACCGTTCAATGGGCGCGTGCAGGAGGC
AGGCCCTGTTTAGCATTGCGGTGGCTTCAACGGCAGA
>chr3A_476
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---------------------------------------------------------------------------TTAGT
GTTTCCAGGTTGGGCCTTTTGTGTTGCCCGGCCGAGTCCAGCGTGATCAGCCCTAGTCGGCATGATATTTCCTTT-----
--AAAAAAAAGTCGGCACGATATTTCAGGTTCTCTGTCCTTTCTTTCTTTTGCTAAAA-AAAATCCCTGCTTCCTCTTTC
ACGGGTAGGTTTCCAACCGAAGAAATGAACGGTTTTCCCTCAAAGTAGAGCATCCGGAGAAGATTGGGGAATCCTGAAAA
GGCGCCAGCGACCGACCGCCGACTGACTCGTAGCCATCTCGAAAGCTCCCGTCAGAGAAGACACGCGGTGCCGCCTTTCT
CTTCGAGAGGCACCCACCAGCTTTCCACTCC----CCATGGCCACAAAAGCAAAGCGCGCACTGGCCGTCCACGTCTCTC
CGGCCTGCCCTCTCCATATAACGGCGCTGCCCGGCACACAGCAGATACGAAACACATGACCACACGCATAGCTGAGG---
----------------A------------------TCCCAGACCACACGTCCCAAATTAAGCTCCGATGGACGAGGGGGG
CAAGTATCAGCAGGGCTGGCTCGCCGTCGGTCTGCCGCCGGCGCCGGTGCTCGCCGTCACCGGCATCGTGACCTTCTTCC
TCTACCTGTCGTGGCAGATGGACGAGTTCGAGGAGCAGCTGCGCCATCGCACCCAGGCAGGCTTCTGGGTGCTCATGGTG
CTGGGGCTCCTCGCCCTGGGCTTGCTCGCGCAGCACGTGCTGTTCGACGGAGAGGGGAGGGTTGCCGTGCCGGCGGCATG
GCGAGGCCAGCCCGAGGGCGGCTCCGGCACGTCGCCGTGGGGCGTCGCGGCCCTTGTGGCTCTGCTGCTGGTGCTAGTGT
CTCACAGGTCCGATTTCCAGATATTCAAG---------------------------------------------------
-----------------------------------TATATATAAATTAGAGTAGAAAGGTGTTTTTGCACGTCTGCATGA
TCAAGCAAAATAGCATAAATAAAAAAGAATTACTCCCTCCGTCCCCGGAAATTGC-TTTTGGAGGCCGAGCTCATGGAGG
CCTTCAAATGCAAAACTCAAAATTTATGAAAATTCATATATTTACATTTCAAAAAATTCTGAAAAAAATACAG-AGATAG
ATGAAGGCAGAGTGCAAGTGCGTAAATTTCAGGACAAATACGC-------TGAAATGAGGGCTTTGCA------------
-------AAAAAGACAAATCTCAGCCTTTTTAACATATAATACTATTCAT-CCCACATAACAGTCATTTGTCTATTTTGT
GTAGGTCGCATTTTAACGTATTTCATCCTAAAATTTTACACACACGCCTCACATCCTTGTTTAGTTGTACAA-TTTTTTC
AGAATAGCTTAAACCTGAT----------------TTTTTTTTGAAGTTGGCCTCCATGAAAGTCGAGAGCCAAAATGTC
ATTCTTCTCCATCCCCATAATATAAGATGTA----AAATATTGGATCTAATACATTTCAAATATAATCGGTAGATAATTG
GAGAGAGTTGTGATTGACGTTGTGTCCAACGAAAAAAAGTTTATAGTCTGGCTGAAAGCGAAAGATGAGCTAAAGGAGAC
GAGACAATTCCCATGTGGGATCTATTATTGGGGATCTATAGGGTATCTTTTTGGGG---TACATCGGCTGGAGGAAAAAA
TATTTGGCTTGGTGGTTGGGCGCAGATCTTCATATGTTCCGTGTGCGATGATCAAGATGGAATGATGTGCCATCTACAAT
ATTAACGATGGCGAGTCTTGACAGTAAGGCGCAGCGGGGTCTTAATGTTGGATAC-------------------------
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>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----
S---------------------------S---------------------------------S-------S-S--S--S-
-S----------------S----------------SS-S---SS--SSS-SS--------------------S-------
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----------------S---------------SSS----------------------------------S----------
------S-S---S-------------------------------------------------------------------
-----------------SSSSSSSSSSSSSSSSSS---------SS-------------------S--------------
---S----------------------------------------------------------------------------
----------------------------------------------------------------------------S---
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---S--------------------------------------------------S-------------------------
-------------------------------------------------S------------SSS---------------
---------------S----------S---SSSS-----------------------------------S-S--------
-S-------------------------------------S------S---------------------------------
-------------------------------------------------S-----S------------------------
--S-----------------S-----------------S--S-SSSSSSS---S--------S-----SSSSSSSSSSSS
SSSSSSS----------------S-------------------S--------S-------S-----S-------------
----S-----------S-----S----------------------------S------S------------SS-------
------------------S--------------------------------------------S-S--------------
-------------------S-----------------------S------------S-----------------------
-------------------------------S-----------S------------------------------SS----
--------------S----------------------------------------------------------------S
--------------S-S-SS----S--------------SSS----------------S-----S--------SS-----
----------S------------------------S--S---S--------------------------------S----
-S-SS------S----S-S-SS---S------S----
>forward_99
-------------------------------------------------------------------------------T
CTCGCTAAAGCACAACCGT-------------------------------------------------------------
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>reverse_1729
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------------------------------------------------AATGAGATGAGGGCCTTGCA------------
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