>input_sequence_77996
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-------------------------------------------------------------------ATGGCAACCAGCA
GCAGCGGCAACACGACGGTGACTCTCCGCAGCTCGGACGGCGAGGAGTTCGTGGTCCAGGCGGACACGATCGCGGCGGCG
TCGGTGCTGATCAAGAACATGCTGGAGGAAGGCTGCGCCGCCGGCGCGATCCCGCTGACCCAGGTGACGGGCCGCATCCT
GGCCCGCGTCGTCGACTACTGCAACCGCCACTACGCCGACGCCGACGCG------GCCGCGTACGTCGTGAAGACCACCT
TCTCGTCGGGCGACCCCGACCTGGATCGGTTCGACACCGACTTCGTCAGCGGCGTCGACCAGGACACGCTCTTCGACCTC
CTCCTCGCCGCCAACTACCTCGAGGTGCAGGGCCTCCTTGACCTGGCGTGCAAGACGGTGGCCGACCAGATGAGGGGCAA
GACGGTCGAGGGCATGCGCGCGCACTTCAACATCCTCAACGACTACACCAAGGAGGAGGAGGCCCAGGTCCGCAGCGAAG
TTGCATGGGCCTTCGAATGA------------------------------------------------------------
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>chr3D_1_TraesCS3D01G077800
AACTAATTTAAATATATTATTTTACATTTTTATATATAATAATTAACATTTTTTCAAATACATGTTTTTATGTCTACTTT
GTGCCATACACAATGTACTCCCTCTGTCTCTAAATATCTTCTTTCTAGAGATTTCAATGTGGACTACATACAAATGCATA
TAGACATATTTTAGAGTGTAGATTCACTCGTTTTGCTCTGTATGTAGTTCATATTAAAATCTCTAAAAAAGACTTATATT
TGGGAACGGACGGAGTACATTTTTTGTATATGCTTTAAATTTTCAAATAAGTGATTAACATTTTTT-GAAACACATGTCT
TTGAACATTGTTGTTCGAATATGTGTTAAAAATACAAATACATGTTGGATTTTT-TAATTGCTATCAAATATTT------
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-----------------------------------------------------------TGTTTTCCTCTATTTCTTCAC
CGGTTTCCTTCAGTCTTCTA--TTTTTCTTTTTTTTCACCGGTTTTATTTGTTTATTTCCCTTTTTTCCCTTTTTTTACT
TTTTTTTCGTCTATCTTTATTTTTTTCTTATTTTTCATAGGTTTTGTTTTTGCTTTTTTCTTTCATAGCGTTTCCCATTA
TGGACGCTTCTGGGGGCGAGGCTCTCCTAGGTCTCGCAATAATAAGCAAGACATAAAAGCGCAAGGTTTTTTTTTGAGAT
AGACATAAAAGCGCAAGAAGAAGGAGCATAAGATCATGTATCTGGTCCGGCCCACATTGGTAGACAGGCAGGGATATTGT
TGGTTACGTTTAGGGTGGCTTCTCGGGCCCGTGGGCCGGTTGCCATGCCCGGCTCTGT--TTACCCTTCCTGCATATGTA
TGCCATGCATCC---------------------GAATTTGTGTTCTCCCCGGCCCCACAAACCCCAAAAAAGAGCCGG--
CGCCAACTTCCCTGCCGTCTCTTCTCATCTATATATTCGAGCGCCGCGTCTCCCACCCATCGACCAATCGCTCGATCTAT
AGACCTAGTTCGACAGGAGCGATCTGCAC--------ACACGCGCG-----TAGGAGATCGATCGAGATGGCAACCAGCA
GCAGCGGCAACACGACGGTGACTCTCCGCAGCTCGGACGGCGAGGAGTTCGTGGTCCAGGCGGACACGATCGCGGCGGCG
TCGGTGCTGATCAAGAACATGCTGGAGGAAGGCTGCGCCGCCGGCGCGATCCCGCTGACCCAGGTGACGGGCCGCATCCT
GGCCCGCGTCGTCGACTACTGCAACCGCCACTACGCCGACGCCGACGCG------GCCGCGTACGTCGTGAAGACCACCT
TCTCGTCGGGCGACCCCGACCTGGATCGGTTCGACACCGACTTCGTCAGCGGCGTCGACCAGGACACGCTCTTCGACCTC
CTCCTCGCCGCCAACTACCTCGAGGTGCAGGGCCTCCTTGACCTGGCGTGCAAGACGGTGGCCGACCAGATGAGGGGCAA
GACGGTCGAGGGCATGCGCGCGCACTTCAACATCCTCAACGACTACACCAAGGAGGAGGAGGCCCAGGTCCGCAGCGAAG
TTGCATGGGCCTTCGAATGAGTAGACGCCTAGACGGACACGCATCGTCACTGCCTTCACAGGCATGGGCCTTCGAGTAGA
CGTACGGGCAAATCACTGGCC-ATCACTTTTCTTTTTCTTTGGGGGATTTGCTGCTGCCATAAACTAGCATTGATAGTTC
TTATACACATTTAATGGGAGCGCTTATATGTCAGTCACCTGAAATAAAAATTTATTTCCCCATAAGCGATTTTCTGGTTT
GCCTGA--------------------------------------------------------------------------
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------------------------------------AAAGTTTATTGTTTGCTTATGTGAATACTGCATGCCAAGAGAAA
TCAGGTAACGGGGGCTTCTATTTAGATATGCTAGATCAACACTACTCACCTGTTGAAGACACGAGATGATGGGTAAAGGG
CCAAAGGTTGGGGAAAAAAAAGCTTGGAACATGTGTTTTTCTTCTCCCTAATTGATCTGATATTCTTTAAAAAACGTTTA
TCCGATATTAGAAACCGAAAGATTGTACCCTTCTTTTGTTTATTTATGGGGAAACACTTATCATCAACCGACGGATAACT
GGGCTGCGTCCGTCACCTTCGCTGCATGACACGCGTCCCGCATACCATCCTTCAATAAACTCGCTTTTGCAACAGGAGCT
ATGCTTTCGAAACATATGCAGTGTTGCAATATTCTATGACGGGTCTACGTTTTACAACAAAACTTCTCTTGTGAATTATT
TCTGCAACAAGACCTCAGTTGCAAAAAAAAATTACAACAAAATCTCAGTTGCAAAAAAAAACAAAAAAAAAACGATGTTG
CAAAAGAAATCCGCAACAAGACCTGTGTTGCAGAAATAATTCCGCAACAAGACCTATGTTGCCGAATGGAGGCACGTTCG
GCCGTGTGATGCGGTAAATCCGACGGCTCGTGACCCGGCTGCCGGCGGACGCGTAGCACGCCCCTTTTTTATGTCTATAT
ATAATTCAAAATTTGGCAAATGAATCATTAGTAATATGTTACCAAGATTATTTTCGTGTAAGAAAATGGACCCTGATAAG
TGCCAGACGTA
>chr3A_52
---------------------------------------------------TTTCCAATACATGTTTTTATGTCTACTTT
GTGCCATACGCAATGTACTCCCTCCGTTTCTAAATATCTTCTTTTTAGAGATTTCAATATGGACTACATACGGATGCATA
TAGACATATTTTAGAATGTAGATTCACTTGTTTTGCTTCGTATGTAGTCCATATTGAAATCTCTAAAAAGAT-TTATATT
TAGGAACGCAGGGAGTACATTTTTCGTATATGTTTAAAATTTTCAAATAAGTGATTAACATTTTTTTGAAACACATGTCT
TTGAACACTTTTGTTTCAATATGTTTTAAAAATACAAATACATGTTGGACTTTTGTAAATGCTATCATAAATTTTAAAAG
TTGCAGCAACATTTGTTAACGCAACACAACCATTTTTCAGTTTATTTTGATATCTACTTCTTTCCGTACATGTACATTTT
TTGTATACATCAAAAACATTTTTATACACGTTTAACATTTTTTGTATATATATTGAGGTGTACTTTTTGCCATACATGTT
GTACATTTTTTGTATACATTAGAATCATTTTTTCAATACAAGTTTAACATGTTTCAAATGCATAAGTAACATTTATTCAT
GATTTTATGTAAACTGATGTTTATAATATATATGTTTGAAATATTTCAAAATATAAACAGAAGTAAAAATGGAAAGCGAA
AAACAGGTGCTTAAAGCTTCTGGACCACCTGCGTGCTTGGCCAGCCCATTCTCACCCGTTTCATGCGAGACTTTTTTGGT
CTCCCTATAAGCGACACACAGGTGCGCCACGTGAAGACTATATCTCACTTACAGCAAATGTTCGTTTGGTCTCATCTGAA
GCATTTTCGCCCTGCTACAGTACTGGGTCAGCCCTTGTTTTGTATGTTTTTTCCTTTCACTTCTTTCGATGGAGAAGATT
GGTCGTGGTGGTTTATGTACAAATTTCTTCCGATGTTTTTTTTGCCCTTTTTTTTATTGTGTTTTCCTCTATTTCCTCAC
CGGCTTCCTTCAGTCCTCTGTTTTTCTTTGTTTTTTCACCGGTTTTATTTGTTTCTTTCATA-----------------T
TTTTTTCTGTTGTTCTTTGTTTTTTCCTTATTTTTCAAAG--------------TTTTTCTTTCATGGCGTTTCCCATTG
TGGACGCTTCTGGAGGCGAGGTTCTCCTAGGTCTGACAATAATAAGCGAGACATAAAAGCGCAAGAT-------------
-------------------GAAGGAGCATAAGATCATGTATCTGGTCCGGCCCACATTGGCAGAC---------------
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>chr3B_731
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-------------------------------------------------------------------------------T
TGGTTACGTTTAGGGTTGCTTGTCGGGCCGGTGGGCCGGTTGCCATGGCCGGCTCTGTGTTTACCGCTCCTGC--ATGTA
TGTCATGTATCGATACAAATTCGGATTACTAAGGAATTTGTTTTCTCCCCGGCCCCACAAACCCCAACAAAAAAAGCCGC
CGCCGACTTCCCTACCGTCTCTTCTCATCTATATATTCCAGCGCCGCGTCTCTCACCCATCGATCAATCGCTCGATCAAA
AGACCTAGTTCGACCGAATAGATCGACGC--------ACGCGCGCGTAGGTTAGGTGATCGATCGAGATGGCA---AGTA
GCAGCGACAACACGACGGTGACTCTCCGCAGCGACGACGGCGAGGAGTTCGTGGTCCAGGCGGACACGATCGCGGCGGCG
TCGGTGCTGATCAAGAACATGCTGGAGGACGGCTGCGCCGCCGGCGTGATCCCGCTGACCCAGGTGACGGGCCGCATCCT
CGCCCGCGTCGTCGACTACTGCAACCGCCACTACGCCGACGCCGACGCG------GCCACGTACGTCAACAG---CACCT
TCTCGTCGGGCGACCCGGAGCTGGATCGCTTCGACACGGACTTCGTGAGCGGCATCGACCAGGACACGCTCTTCGACCTC
CTCCTCGCCGCCAACTACCTCGAGGTACAGGGTCTCCTTGACCTGGCGTGCAAGACGGTGGCCGACCAGATGAGGGGCAA
GACGGTGGAGGGCATGCGTGCGCACTTCAACATCGTCAACGACTACACCAAGGAGGAGGAGGCCCAGGTCCGCAGCGAAG
TTGCATGGGCCTTCGA-----------------------------------------------------------GTAGA
CGTACCGGCAAATCACTGGCCGATCACTTATCTTTTTCTTTGGGGGATTTGTTGCTGCCATAAACTAGCTGTGATAGTTC
TTATACACATTTAATGGGAGCGCTTATATGTCAGTCACCTGA-ATAAATATTTATTTCCCCATAAGCAATTTTCTGGTTT
GCCCCCTATCAATTTGTCGCCCCGTCAACGTATCAGAAATTGGGTGAACTAGATGATATCCCGTGCATTGCCGCAGAATC
GATCAAAATACCTAGTTCATCGAGCTTCATTGCCCTGTGCCCTATGCCCTGTGCTGCGCTCATCGACTGACCTCTTAACA
GCCGTCGTATGTCTCCATCATCTTGCGTCTCTACAACCACAACCAAAGATGCTTCCTCGCTTGGACCTCTCGAGCTTCAT
TGCCTCTGCCTCCTAATTGTGATATCATAGCTCGGTTACCCGTGCATAATGAGGTAGGAGTAATTCGGCTCATCAATTTT
TATGACATGGATGCAACCTTCTCAGTAACATCAGTGTGCAATGTGGGATGTTTGGAGGAAGGAGGAGCGCCGGTGCGGTC
CGCGGAGAAGAGATGTGGAAGAAAGAAATCCATGTGCCAATGTGCGGGTGGGCAGGAGCCGCCTACTATGTGGAAGAAGG
AAGGAGTGGGGTCAGACACGACAATCAGTGCAATGGGAAAAAACACATGATTCGTTTTGTTAAAAAGAAAATAAAAGAAT
CTATTCAGTTGGCAGATTTGTTGAGGTGGAAGGCTGAAAGTTTATTGTTTGCTTATGTGAATACTGCATGCCAAGAGAAA
TCGGGTAACGGGGGCTTCTATTTAGATATGCTAGATCAACACTACTCTCCTGTTGAAGACACGGGATGATGGGTAAAGGG
CCAAAGGTTGGGGAAAAAA--GCTTGGAACA----TTTTTCTTCTCCCTAACTGATGCGAAATTCTTCTAAA--------
-----------------AAAGGTTGTACCCTTATTTGTTTATTTACGTC-------------------------------
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-------------------------------------------------------------------------------T
ATAATTCAAAATTGGGCAAATGAATCATTAGTAATATGTTACCAAGATTACTTTCATGTAAGAAAATGGACCCTAATAAG
TGCCA------
>chr1D_916
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-------------------------------------------------CTCCCACCCGTCGACCGATTGATCGATTGAA
ACACCGAGTTCAGCAGGAGCGGTTTCGATCTCGATCGACACACGCG-----TAGGAGACCGAT------GGCA---ACTA
GCAGCGGCAAC---ACGGTCACCCTCCGCAGCTCCGACGGCGAGGAGTTCGTTGTCCAAGCGGACACGATCGCGGCGGCG
TCGGCGCTAATCAAGCACATGCTGGAGGAGGACCGCGCCGGCGGCGTGATACCGCTACCCCAGGTGACCGGCCGCATCCT
CGCCCGCGTCGTCGACTACTGCAACCGCCATTACGCCGACGCCGACGCCGACGCAGCCGCGTACGCCAATC------CCT
TCTCGTCGGGCGACCCCGACTTGGAGCGGTTCGACACCGACTTCGTCAGCGGCATCGACCAGGACACGCTCTTCCTCCTC
CTCCTTGCCGCCAAAGACCTCGACGTACAGGGGCTCCTGGACCTGGCGTGCAAGACGGTGGCCGACCAGATGAGGGGCAA
GACGGTCGAGGGCATGCGCGCACACTTCGGCATCGTCAATGACTACACCCCGGAGGAGGAGGCTGCGCTCCGCAGGGAAC
TTTCATGGGCGTTGGA----------------------------------------------------------------
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>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----S------------------------
---------S--------------S--S----------------S-------------S------------SS-------
---------------S------------S--------SS---------S------S-------------SSSS-------
-S------S-S-------------S-------S--S--------------------------------------------
-------S-S-----SS-------S------------------------S--------S--------S-S----------
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---------------------------------------------------------------------------S----
---S-----------S---S-----S-S-S------------------------S----SSSSSSSSSSSSSSSSSSSS-
------SS--SSS-----S------S-----------S--SSSSSSSSSSSSSS------------S------------S
-------------S-------S------------SS-----------S-----------------S-SSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSS-----------------------------------------S----SSSSSSSSSSSSSS-
----------------S----S-------S-----------------S-----------------SS------SS-----
--S----S---S-----------------------------S-------------------------S---S-SSSSS--
----S--------S------------------------S--------------------------------------S-S
-------------------------S-----------------------------------------------SSS--S-
----------------------------------S---------------------------------------------
-----------------------------S----------------S---------------------------------
S------------------------------------------------------------------SSS-SSSS-----
-----------------------------------------------------S--------------------------
--------------------------S-----S-----------------------------------------------
----------------------------------S---------------------------------------------
----------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----
-----S-----------------------S---------------------S-----------------SS---------
------------------------------------------S-----S------------------S------------
---SSS--------------------------------------------------------------------------
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--S--------------------------------------------S---------------S----------------
-------------------SS----------SSSS----------------S----SS--S------SS---SSSSSSSS
SSSSSSSSSSSSSSSSS----S----------S---SS--SS--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-
-------------S------------------------------------S----S------------------S-----
-----SSSSSS
>forward_1350
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--------------------------------------------------CCCACATTGGTAGACAGGCA----------
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>reverse_2227
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------------------------------------------------------------------GGCCTTCGAGTAGA
CGTACG--------------------------------------------------------------------------
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