>input_sequence_84387
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----------------------------------------------------ATGGGGTGGCTCCGCTCCCTCGTCTCCC
CGCTCAGGAAGCTCTGGTGCAACATCAACACCGTGCCGAGGAAGAGTATGTCCTCCTGTATTCGTGTTTACATGCATAAA
TACAGCCTTTGTCTCTGTTCTTCTCTCCGGTTTCTGATCGTCTGCTTGTTTGTTTG--GTTTGCAGAGAGAGGGATCTAC
ATCCTGTACGACGACGTCAAGTCGTGCCAGTGCGAGGACGTGCACGTGCTCTGGTCCATCCTCGTCGAGTCCCACGGCCT
CCCGCCGCCCACACCGCCGGTGCTCCGGCTCACGCGGTGA----------------------------------------
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>chr3A_1_TraesCS3A01G318500
AGCTAGCCGCAAAACCGCAGGATCTGCTCTCTCTTTCTCCCGACGC-GACATGGTGCGCGCGGATCCTTCAGGTGGACGG
ACGGACGGACGACCATCGCCTGAAAGGCGCCCGCACGGGCGCAGCCACGGCTCCACGAGGCGCCGTGGAGCTCACGGGGA
TTTT-ATAAAGGGATCGCGTGGATAACGAGCTCCTCTGGCCTCTGCTACG--GGGAGAGCGTCGGTGGGCCGTTGGT---
-GTGTAGTGTACGTAGTTTGGTCCATGGCTTGTCTGGTTAACTGATGCCGTGCACTGTAAGAATCACCCTGTGCGTGGAT
GC----------ATTAATTTACACGCCTGCGTGCGTGGGCTGGTCTAACCGAGCATCATGCATTTGCGAAGAAAAGGAA-
----GAGCTTCAGGTAGAAGCGTCCCTAGCTTATTAGCGACTAGTGTG--------------------------------
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-----------ATCAATCTAGTCAAGTACTCCCTCGATAAAGAAATATAAGAGCGTTTAGATCGAGTAGAAGAAAAGGCG
CAGGG-CGTGGTGAAAAGCCTTTCCTCGACTACAGGAGACACGGACACGGCAG----TTCTCTTACCAGTT-------AC
CAGTGTCGGGAGCGCGAGCGTGCGACGGAAGGCGGGTCGCACTCACACGTACGCGCGCGCGGGGGGCAG---AATAGATC
CGGGAAAACGACCACGCACCGTACGGAGATCACCGCCGCGCGCACGATTGACTGATTGATTGTGCCGCAAGGGAGTCTGG
TGTGGCAGGAGAGGCAGACAGAGCGCTCACTCCAGTCATGTGGCTGCCAAGG----ACGAAGGAAGAACAGTGTGCGTAT
GCGAGGCTTTACCCAAGTGTAAAGCAAGCCGAGCGAGCGAACGAAGCCTCTGGTCG-------CTTTACCGCCGGTCCGT
CCGACTCATGCACACATTACACGCGCACCACCATAACCACCACACCAGCAGCTCCGCGCCACCAGCCATTGCTCAGGAGG
GGCGGTATAAAGGGCGGGGAGCAGAGGACGGCCCACGGCGCGTCCGCTCAGCATGGGGTGGCTCCGCTCCCTCGTCTCCC
CGCTCAGGAAGCTCTGGTGCAACATCAACACCGTGCCGAGGAAGAGTATGTCCTCCTGTATTCGTGTTTACATGCATAAA
TACAGCCTTTGTCTCTGTTCTTCTCTCCGGTTTCTGATCGTCTGCTTGTTTGTTTG--GTTTGCAGAGAGAGGGATCTAC
ATCCTGTACGACGACGTCAAGTCGTGCCAGTGCGAGGACGTGCACGTGCTCTGGTCCATCCTCGTCGAGTCCCACGGCCT
CCCGCCGCCCACACCGCCGGTGCTCCGGCTCACGCGGTGACCGGAACGCGCCGGACGGCGGATCGCTGGCATCGGCGCGG
CGC-CCCCCGGAATAAGGAACGGCCGGCGCGGTGCCGCCGTGGCTGGCTCCATGGGAGGTGAACCAGTAATAGTATAGTA
GTAGTAGCATATGAT--TTCTGATGTAAAGAGCACATAGGAGGAGTTGTTTACAGTTCATCTGGCCTTCGTCCGGCGCCT
CTTTTGGAGCTGCTGCTGGGACGGGAGAGCGAGG---CTGCTGCGTTTGCGGCTTCTGGACGCGTGTGGTGATGGGCTTT
CTTCGAGCGCACCCCTCTTTTGAGTTTTTGATTGATTCACGCGTCGTTTTCTGTCGAGA-------CTGCACTTGGATGC
AGCCCTTTAATTCATCCCCATTACCAGGGACA-------AAAAAAGAAAGGGATCTTCAGCAATTATT--------TCAT
TGCCATTTCTGTGTTGTTTCCACTGA--------TGTTTGCTTTGCGGACATGCA-------AGTGGGTGCTTCTGGTTT
GCCTTCGCCGGAGCCGGC-------GGAGCGTACACTGTTCAAATAACC-GATCGTAGTATCAAGTGTCTGCGCTCTGCG
GTGCATCATTTGTTGCTCTGTTCTTCTCCTCTTCCAATAACTGGGGTTATGATCACTTTTTTTTTTCAGAGAGAGAAATC
TGTCTTCTTTCTGGTTGGGGTCCTGCGGATGACTTGTGAGACCTCCTAGCCAGGAAAGCGACTTTTTGTTGGACGGGGGC
ATTGGCTCCCGTTTTCTGAAATGATTCAAAAAATCATATTTCCAAGTTTCAAAAAATTCGAAAAAATGTGAAAAATTGTA
CATATTCACGATGGATCTGTGAATTTTAGTTCAAAAATATTATGGTTTGCAAGCTGCACACACAAAAAAAGCTGCACACA
AAAAAAAAATCCTGGTCCAACAACGAAAAAAAGATTGGCCCATTTTCACGTATATATTTGTTTTCATTGTCTACGCCACT
TATGAAAGTATATTGTCATGAAAATTTTCTTCAACGTGTCATATGTGTATT
>chr3D_1
AGCTAGCCGCAAAACCGCAGGATCCGCTCTTTCTTTCTCCCGATGCAGACATGGTGCGCGCGGATCCTTCAGGTGGCCGG
ACGTT--------------------GGCGCCCGCACGGGCGCAGCCACGGCTCCACAAGGCGCGATGGAGCTCACGGGGA
TTTTTATAAAGTGATCGCGTGGATAACGAGCTCGCCCGTCGGTC---ACC--GAGAGAGCGTCGGTGAGCCGTTGGT---
-GCGTGGGTTGCTTGCTG-GGTCGATCGCTTGTCTGGTTAACTGGTGCCGTGCACTGTAAGAATCACCCTGTGCCTGGAT
GC----------ATTCACACGCC--------TGCGTGGGCTGGTCTAACCGAGCATCATGCATGGCAAGGACGAAGACAA
GGGCGAGCTTCAGGTAGAAGCGTCCCTAGCTTATTAGCGTGTTTATTTAACACTGGGACTAGTGTAATCAGACAGAAGGA
ACCGGTGACTTATGGTTCTGTTGGTGCAACGTTTTCTACTTCCTTCGTTTTTTTTACTCTGCATATAAAATTTGTTTAAA
GTCAAACTAAGCAAAGTTTGATCAAATTTATAAAAAAAATATCAACATCTATGATACTAAAATTATATAGTGTGAAAATT
AATTTCATAATGCATCTAATAATATTAATTTAGTATTGTGAATGTTGATATTTTTTATTATAAATTTAATCAAATTTTAC
AAAGTTTGACTTTGAGCAAAATTTATATGCTAACTAAAAAGAAATGAAGGGAGTATTTTCTTATAGAAGATGTATATGAA
AAAATAACTAACTTTTGCAACTCCGAGGGCCAAAAACACCTCTTCAACGGATGGTGTAGATGAAAAAAAAAACATATTTT
CATCTTTCGAAGATGTAAACTACAATACCTCACGATGCAAATTTGCATCTCCACCTACAGGAGNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCATCGCCCCCCCG
CGCCGTCGCCGCTGCCCGACCTCGTTGCCCCGCGCGTCGTCGCCCACCTTCCCACGCCGTCGCTCTGACCTCGCCTGACC
CCGCTGCCGCCCGACCTTGAAGCCCCCATGCCATCCGCCCCGTTGCCACCGCCCGGCCTCGCCGCCCCCTCAAATGAAGT
ACTAATTGAAATATAGTTTTTACATCTCGATTTGCATCTTTTATTGGAGTAGCTGTTTTACATCTCCGTTTCGTCTGTTG
GAGTTGGCTCTTTTTTTAATGGAAAAAGCACTTTTTGAATATGTAAATTTTTAAATCTCTTGTTTTGCATCTTCTATTGG
AGATGCTCTTAATCAATCTAGT-----------------------------------------------AAGAAAAGGCG
CAGGGGCGTGGTGAAAGTCTGGTGCTCAACCATACGATACACGGCACAGACGGCAGCTTCTCTTGCCAGTTGCCAGTAAC
CAGTGTCGGGAGCGCGAGCGTGCGACGGAAGGCGGGTCGCGCTCACACGTACGCGCGCGCGGGGGGCAG---AATAGATC
CGGGAAAACGACCACGCACCGTACGGAGATCACCGCCGCGCGCACGATTGACTGATTGATTGTGCCGCAAGGGAGTCTGG
TGTGGCAGGGGAGG----CAGAGCGCTCACTCCAGTCATGTGGCTGCCAAGG----AGGAAGAACAGTG----------T
GCGAGGCTTTACCCAAGTGTAAAGCAAGCCGAA----CGAACGAAGCCTCTGGTCG-------CTTTACCGCCAGTCCGT
CCGACTCATGCACACATTACACGCGCACCACCACCACCACCACCGCACCAGCTCCGTGCCACCAGCCATTGCT-----GG
GGCGGTATAAAGGGCGGGGAGCAGAGGACGGCCCACGGCGCGTCCGCTCAGCATGGGGTGGCTCCGCTCCCTCGTCTCCC
CGCTCAGGAAGCTCTGGTGCAACATCAACACCGTGCCAAGGAAGAGTACGTCCGTCCGATCCTCCTGTTTGTTAC-GTAC
TTCAGATACAGTCTCTGTTCTTCTCTCCTGTTTCTGATCGTGTGCTTGTTTGTTTGGTGTTTGCAGAGAGAGGGATCTAC
ATCCTGTACGACGACGTCAAGTCGTGCCAGTGCGAGGACGTGCACGTGCTCTGGTCCATCCTCGTCGAGTCCCACGGCCT
GCCGCCGCCCACGCCGCCGGTGCTCCGGCTCACGCGGTGACCGGAACGCGTCGGACGGCGGCTGGCTGGCATCGGCGCGG
CGCTCCCCCGGAATAAGGAACGGCCGGCGCGGTGTCGCCGTGGC----TCCATGGGAGGTGAACCAGTAACAGTATAGTA
GTAGTAGCATATGATGATTCTGATGTAAAGAGCACATAGGAGTTGTTGTTTACAGTTCATCTGGCCTTCGTCCAGCGCCT
CTTTTGGAGCTGCTGCTGGGACGAGAGAGCGAGGCTGCTGCTGCGTTTGCGGCTTCTTGACGAGTGTGGTGATGGGC-TT
CTTCGAGCGCACCCCTCTTTTGAGTTTT-GATTGATTCAGGCGTCGTTTTCTGTCGAGAGTCGAGACTGCACTTGGATGC
AGCTCTTTAATTCATCCCCATTACCA--------GGGACAAAAAAGAAAGGAATCTTCAGCAATTATTCCGAACTGTCAT
TGCCATTTCTGTGTTGTTTCCACTGA--------TGTTTGCTTTACGGACATGCA-------AGTGGGTGCTTCTGGTTT
GCCTTCGCCGGAGCCGGCGGGCGGTGGAGCGTGCACTGTTCAAATAACT-GATCGTAGTACCAAGTGTCTGCGA------
-TGCATCATTTGTTGCTGTGTCTTTTTCATCTTCCAATAACTGGGTTATGAACTG--TTTTTTTTTCAGAGAGAAATATG
TT--TTCTTTCTGGTTGGGGTCTTGCGGATGACTAGTGAGACCTCCT---------------------------------
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>chr3B_1
AGCTAGCCACAAGACCGCAGGATTCGCTCTTTCTTTCTCCCGATGC-GACATGGTGCGCGCGGATCCTTCAGGTGGACTG
T-GGACGGACGACCATCGCCTGAAAGGCGCCCGCACGGGCGCAGCCACGGCTCCACGAGGCGCCATGGAGCTCACGGGGA
TTTT-ATAAAGGGATCGCGTGGATAACGAGCCCGCTCGTCGGTC---ACCGAGAGAGAGCGTCGGTGACGGTGAGTCGTC
GGTGTTGGTGTGTAGCTT-GCTCGACCGCTTGTCTGGTTAACTGGTGCCGTGCACTGTAAGAATCACCCTGTGCCTGTGC
GTGGATGCATTAATTTACACGCC--------TGCGGGGAC------------GCATCATGCATGGCCAGAAAAAAACT--
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-------------------------------------------------ACGGCGGCTTCTCTCACCAGTCGCCACTGTC
GGGAG-CGGGAGCGCGAGCGTGCGACGGAAGGCGGGTCGCGCTCACACGTACGCGCGCAAGGGGGGGCAGAAAATAGATC
CGGGAAAACGACCACGCACCGTACGGAGATCACCGCCGCGCACACGATTGACTGATTGATTGTGCCGCAAGGGAGTCTGG
TGTGGCAGGGGAGGGG--CAGAGCGCTCACTCCAGTCATGTGGCCACCAAGGAGGAAGGAAGAACAGTG----------T
GCGAGGCTTTACCCAAGTGTAAAGCAAGCCGAA----CGAACGAAGCCTCTGGGCTCTCGTCACTTTACCGCCAATCCGT
CCGACTCATGCATACATTACACGCGCATCGCCACCACCACCACCACACCAGCTCCGCGCCACCAGCCATTGCTG----GG
GGCGGTATAAAGGGCGGGGAGCAGAGGACGGCCCACGG------CGCTCAGCATGGGGTGGCTCCGCTCCCTCGTCTCCC
CGCTCAGGAAGCTCTGGTGCAACATCAACACCGTGCCCCGGAAGAGTACGTCCGTCCGATCCTCCTGTTTGTTACTGTAC
TTCAGATACGGTCTCAGTTCTTCTCTCCCTGTTCTGATCGTGTGATTTGCA----------TGCAGAGAGAGGGATCTAC
ATCCTGTACGACGACGTCAAGTCGTGCCAGTGCGAGGACGTGCACGTGCTCTGGTCCATCCTCGTCGAGTCCCACGGCCT
GCCGCCGCCGACACCGCCGGTGCTCAGGCTCACGCGGTGACCGGAACGCGTCGGACGGCGGCTGGCTGGCATCGGCGCGG
CGC-CCCCCGGAATAAGGAACGGCCGGCACGGTGTCGCCCTGGCTGGCTCCATGGGAGGTGAACCAGTAACAGTATAGTA
GTAGTAGCATATGAT--TTCTGATGTAAAGAGTACATAGGAGGAGTTGTTTACAGTTCATGTGGCCTTCGTCCAGCGCCT
CTTTTGGAGCCGCTGCTGGGACGGGAGAGCGAGGCTGCTGCGA---TTGCGGCTTGTTGACGAGTGTGGTGATGGGC-TT
CTTCGAGCGCACCCCTCTTTTGAGTTTTTGATTGATTGACGCGTCGTTTTCTG-------TCGAGACTGCACCTGGATGC
AGGTCTTTAATTCATCCCCAATTCCCCACTACTCGGGACAAAAAAGAAAGGAATATTCAGCAATTATTCTGAACTCTCAT
TGCCATTTCTGTGTTGTTTCCACTGAATCACTGATGTTTGCATTGCGCACATAGCCACATACAGTGTGTGCTTCTGGTTT
GCCTTCGCCGGAGCCGA-------TGGAGCGTACACTGTTCAAATAACTTGATCGCAGTACCACAAGTGTTTGCG-----
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>SNPs
------------------------S-----S------------S------------------------------------
----------------------------------------------------------------S---------------
---------------------------------SS-S-S-SSSSSSS--S---S-------------S------------
-----S-SS-S-S-SS--S----S--S-----------------S-----------------------------S-----
---------------S-SSSS-SSSSSSSSS--------------------------------SSS-SS-S-----SS--
---------------------------------------SS-SSSS-S--------------------------------
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----------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----------
----------------SS-SSS-S---S--S-S-S--S------SSSS-S-S----------------------------
----------------------------------------S---------------------------------------
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---------S----SSSS---------------------------------------S----S-SSSSSSSSSSSSSSS-
--------------------------------SSSSS------------------------------------S------
---------------------------------SS--------SS--S-------------------------SSSSS--
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-------------------------------------S----------S----SS-S-SSSSSSSSS--SSS-S-SSS-S
-S---SSSSS------------------S------------S--------------------------------------
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S-------------------------------------------------S----------S-S----------------
----------------------------------S-----------------------------------S---------
-------------------------------------------------------------------------S------
---------------------------------------------------------S----S--------------S--
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---S----------------------SSSSSS-------------------S----------------------------
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------------------------------------------------S-----------S-------------SSSSSS
S----------------S---SS--S--S----------------S-SSSS-SSSSS-----------------S-S--S
-SSS------------------S-----------S------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_201
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---------------------GATAACGAGCTCCTCTGGCC---------------------------------------
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>reverse_4079
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------------------------------------------------------------------------------GC
ATTGGCTCCCGTTTTCTG--------------------------------------------------------------
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---------------------------------------------------
