>input_sequence_85987
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--------ATGTCGGGGGCACAGGGGGCGCACCCGGTCGGGGAGACGACGCCGACGACGTACGGGTCGGTGGGCGGCGGG
GAGAACCGCACGCGCACGGACCTGAGGTCGCGGGAGGACCAGGGCAACATCCAGATCGAGAAGGTGCAGGACAAGGTGGA
GGATGCCGCGTCGCGCAAGGTCGACGACAGCGCCTTCGCTGCCAGGAAGGAGCCGGGCCAGGCCGGCGACGCCGGGGCAA
CCGGCACCGGCGCGTGA---------------------------------------------------------------
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>chr3D_1_TraesCS3D01G237400
TGTGGTAGGTTAGAGGTGAAACCCATAAGATCTCG--ACCAACTCATGGTTCTGGCACATGGATAGCAAGCTTCCACGCG
CCCTGTTCATGGCTAGTTCTTTGGTGATACACCAGTCCTTCAGATCTCTTTTAACGGACTCCTCCCATGTCTAGTTCGGT
CGAACGTGTGTATGTTTCATCTCCTTCGATTTCCTCCTTTCTTGTCCAAGTTCGTGTTGTATTCCTTGTCTTCCTCTTTT
CAACCGGAGTGTTTTCAAGTTCTTTTTTTTTAGCTTTTCATGTCCTTTTTCAAGTTTTTCAATCTCTCAAGATTCTTTGG
TATCACCCCTTTGTCAAGAAGCAACTTATAGTTAAACCTCTTCCTCTTTCTTTTCCGAATCTTGTTACGAGATTCTTGGA
AGTTGAGGAGCTTACTTTTATTTGCTTCAAGGTTTTAATAAGTTTAGCTGATAGTCAACTGGATCACCTGGCCCAAAATC
CTAACTACACCACTGAAATCTACTCCCTCTGTTCACAAGTATAAAATGCTTTGGATATTTCAATATGAA-----------
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-----------------------------------TTACAATACAAACTGAAATGAGTGAACACTTTTTTT---------
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--------------------TTTGCAGAAACGACCACAGGCCAATGTGGTTTTGGCGGGCACGCCGACCATTATCATCCT
AGACGCCAGCTGACCCC------------------------------------------------GAGTTGATGTTTATC
CATTA---CTCGGCGAAACGCACACGCTCTCTGCAGCACGAAGCCTCGAGCGTCCAGCTGCGCGCGACAGCGGACACGAG
TCCAATCTAGACGCCCCGCGCAGATATATCCGAGCCATGTGTCACGCGGACACCACCCGCGTCACACCACGTCCCCATGC
CACGCGCCGATACCGCGCCGCTCGCGCTCGCTGCAGCCCAGCTATATTTATACGCCGGCCCGCTGCCGCCAGACAACACC
GGAGCCGAGCAGGAAGAGCGCACGTCGAATCAGCCAGGAGCAAGCGCATATATACATACGTGTGTGCGGTGTAGTGAAGA
CAGGCAGGATGTCGGGGGCACAGGGGGCGCACCCGGTCGGGGAGACGACGCCGACGACGTACGGGTCGGTGGGCGGCGGG
GAGAACCGCACGCGCACGGACCTGAGGTCGCGGGAGGACCAGGGCAACATCCAGATCGAGAAGGTGCAGGACAAGGTGGA
GGATGCCGCGTCGCGCAAGGTCGACGACAGCGCCTTCGCTGCCAGGAAGGAGCCGGGCCAGGCCGGCGACGCCGGGGCAA
CCGGCACCGGCGCGTGATCTGGGTTCTGTTCTGTGGCGCCCTGCCGGGCGCGCGCGTCGCACGATCTTCGATCTGGGTCG
CTGCATTTGCGCGCGGCGCGTTGTGTTTGTGTAGCGAGTTGTGTTCTGTAAAAGAGTCT--GCGTGTGAGCTCGCAATAA
T---AAGAACTGCTTGTCAGTTTGCTTAGCAAGACCATGAATTTTCTGTTCGTGCAAACACTCTGCCATCTTTTTAGATT
AGATTAGATACACTGCAAGTGTTCAGATCAACACGGGCGAGACTGATGGATTCGA---------------------GTGG
AAATGGAATGCAGCCGGGACGCACTATGCTAGCTGTAGCAAAGGCCACTATGGAAGAGCTGGGCACCAATGAATTGTAGA
AATGTAGAATCCTCCTATCGTGGCACTAACGAGCTGGTGTTCCTGTCCGGCACGACGTCGGGCGCGCACGTCCACGAGCA
CCGGGGGGCTCCTTCATGGCGATCGGGCGTGGGAAGTGCGGTGATGTCGTGGACGTCGTGGTTGCCGGAGGAGCGGGGCT
CCTACTTGACGTGGTACGGTGGTAGTGAGGAGACGACCGTGGCTCCTCCTTCACGTGTGGAGAGGCGGCGAGGGAGGCGT
CGGCCCCCGGTCACGGAGGAGCTCCAGGTGTGCTGCGTACTCGCTCATCCGTCTTCGTGAGGAGGTGCGGTTGTGTCCTC
ATAGTCGGAGGAGAGCACGACCTCCTCCTTGTCTGTCATGACGGCGGAGGAGGACGGCCCAGGAGCGGCAACGCGACTAT
CCTGCCGAGAGTTGGGAGAGAATGTGCGGCGATGAGTTCAGGTGGGACCATGAACCACGTAGTCTGGCACATATACATGG
AACTAGTCCAAACGTGTACAAACCTCGCTGGTTCCCCACATTTGGTGCCAATTTACAGGAATTTGGACTCGCGTCTCCAC
GGACATATCTGACACTGCGTTCAACGACAAAATTGATGATACGGCCGAACCATGAAGTAAATTGCAAAAAACCAGGACTC
TAA
>chr3A_4
---GGTAGGTTAGAGGTGAAACCCATAAGATCTCGCGACCAACTCATGGTTCTGGCACATGGATAGCAAACTTCCACGCG
CCATGTTCATGGCTAGTTCTTTGGTGATACACCAGTCCTTCAGATTTCCCTTAACGGACTCCTCCCATGTCTAGTTCGGT
CGAACATGTGTATGTTTCATCTCCTTTGATTCCCTGATTTCTTGTCGAAGTTCATGTTGTATTCCTTGTCTTTCTCTTTT
CAACCGGAGTGTTTTCAAGTTCTTTTTTTGTTGCCTTTCGTGTCCTTTTCCAAGTTTTTCAATCTCTCAAGATTCTTTGG
TGTCACCCCTTTGTCAAGAAGCAACTTATAGCTAAACCTCTTCCTCTTTCTTTTCCGAATCTCGTGACGAGATTCTTGTA
AGTTGAGGAGCTTACTTTTATTTGCTTCAAGGTTTTAATAAGTTCAGCTGATAGTCAACTAGACCACCTGGCCCAAAATC
CCGACTACACGACTGAAATCTACTCCCTC-------------------CTTTAGATATTTCAATATGAA-----------
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-----------------------------------TTACAATACAAACTGAAATGAGTGAACA-----------------
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>chr3B_333
CAACAA--------------------------------------------------------------------------
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---------------------CAACTTATTGCTAAACCTCTTCCTCTTTCTTTTTCGAATCTTGTGATGAGATTCTTGTA
AGTTGAGGAGCTTACTTTTATTGGCTTCAAGGTTTTAATAAGTTTAGCTGATAGTCAGCTGGATCACCTGACCCAAAATC
CTGACTACACCACTGAAATCTACTCCCTCTGTTCAAAAGTATAAAATGCTTTGGATATTTCAATATGAATCTATAGAGAT
ACTAAGCTCCCACGTATTGAAGCGCTCTGGTGCTTCGGGGTTTGTGGGGTCGTTGTGGGACCCGCATGTAAGGTTTTGTG
TTGCATAGTTTTATTTTCCCTTCTTTTTACTTTTTTATAGATTTTAATTATGAGCGCTTAATAAATTTAGGAACATTTTT
TTACATTTTTAGCTTCATTAATATTTACTACATTCATGAGTATTTTAAAGTTCATGGATATTTTTAAAGTTCATTGACAT
TTTTAAATTTTGAAACTTGTTTAATTTGCAAACATTTTTTAGTACATGAATATATTTTAAACTCATGAACATTTTCTACA
ATTCATGGTTTTCTAAATTCGCATATTTTTGAAAAAATCCTTGAACATATTTTAATTAAAATAACCTATTTATTTTCAAA
AAATAGTCCATTTTTCTGAGGGAGCAGTGGGGCGAGCGGAAAAAAGCTAACCGACCGAGAGGAATAAGGAATCAAACTAA
GCGAGCGAGATCTGGTGGGCCGGTCCATGTAAGTGTTATAGTAGCAATTCCATGATTTAAGCGTGGAATAGGACCTCTCA
AGAGGCTCAAACAACAACCACCAACTGACACCGAGACGGACACGTGTAAAGACAACATAACGACAGACCAAAAAACGTCA
TTCTCCTCTAGGGAATATTGTCTTCAGCAAGAACCCGACACGGTATACAAATAAAAAAACAACTTCATAACATAGTTAAA
ACACAAGTCAACATTGATAAAATCCAAACAAAACAATCAACCATGGCACTCTACTAGATATAAGGCTGCTGCCAATGTAT
CGGTGCTTAGATGAGGTGCTAAGCACATTAAATAGCTTAGCAACTTTACTCCCCAATGCATAAGTGCTTAGCTTATAGTT
GCTAAGCTTGCTTCATTTAATGATTTAGCAACTAAAACTCTTCATGTATTGGTGGACTTCTTTTCTTTAAATGTTTTGAC
TAGGTTCGCGCGCTTAGCATTGTTTCTTTCTGGGATTACCATATTTATCTCTTTCCTCTTAAATAACTTGCCACATCAGA
TATTTTGACTACGTGAAAGGCTTAGCACCTGTACAAGGTGGAGCATTGAGAGGGGTCTAAAAGAATTAATCCCACGAGTG
AAGAACGGCGCGGCGAAGCGCGCGTTAGCCTCTAGTTACAATACAAACTGAAATGAGTGAACAAACTCACTAAAACATGT
GATGCAATTTTTTTTTGAACATCTTATATTTGCGAATGGATGAAGTAACTGATTACAGCTTGTGTATATACATACACATT
GAACTCAGTTCCAACAAAACAATGGTCATTTCACACTCCAGCTTAGAGGGCCGTGGACGCGAGGGATAGTAACCAATGTA
TTTCTGCTGCTGGGTTCAACTTTGCAGAATCGACCACATTCCAATGTGGTTTCGGCGGGCACGCCGACCATTATCATCCT
ACGCGGCAGCTGACCCC-------------------------------------------------AGTTGATGTTTATC
CATTATTACTCGCCGAAACGCACACGCGCTCTGCAGCACGAAGCCTCGAGCGTCCAGCTGCGCGCGGCAGCGGACACGAG
TCCAATCTAGACGCCCCGGGCAGATATATCCGAGCCATGTGTCACGCGGACACCACCCGCGTCACACCACGTCCCCATGC
CACGCGCCGAGACCGCGCCGCTCGCGCTCGCCGCAGCCCAGCTAT--TTATACGCCGGCCCGCTGCCGCTGGACCACACA
GGAGCCGAGCAGG-----AGCACGTCGAATCAGCCAGGAGCAA--GCATATATACATACGTGTGTGCGGTGTAGTGAAGG
CAGGCAGGATGTCGGGGGCACAGGGGGCGCACCCGGTCGGGGAGACGACGCCGACGACGTACGGGTCGGTGGGCGGCGGG
GAGAACCGCACGCGCACGGACCTGCGGTCGCGGGAGGACCAGGGCAACATCCAGATCGAGAAGGTGCAGGACAAGGTGGA
GGACGCCGCGTCGCGCAAGATCGACGACAGCGCCTTCGCTGCCAGGAAGGAGCCGGGCCAGGCCGGCGACGCCGGGGCGA
CCGGCACCGGCGCGTGATCTGGGTTCTGT-----GGCGCCCTGCCGCGCGCGCTCGTTGCACGACCAC-------GGTCG
CTGCATTTGCGCGCGGTGCGTTGTC-TTGTGTAGCGAGTTTTGTTCTGTAAAAGAGTCT--GCGTGTGAGCTCGCAATAA
T---AA---CTGCTTCTCAGTGTGCTTAGCAAGATCATTAATTTTCTGTTCGTGCAAACACTATGCTATCTTTTT--ATT
AGATTAGATACACTGCAAGTGTTCAGATCAACCCGGGCGAGACCGATAGATTCGA---------------------G---
--------TGCAGCCGGGATGCACTATGCTAGCT--AGCAAAGGCCACTATGGAAGTGCTGGGCACCAATGAATTCTAGA
AATGTAGAATCCTCCT----------------------------------------------------------------
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>chr3A_584
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--------------------TTTGCAGAATCGGCCACAGGCCAATGTGGTTTTCGCGGGCACGCCGACCATTATCATCCT
AGACGCGGATCCGGCTTGCCTGCAGCACGGAGTTTTTTTCTCAACAAAAAAAAAAATGCAGCACGGAGTTGATGTTTATC
CATTA---CTCGGCGAAACGCACACGCTCTCTGCAGTACGGAGCCTCGAGCGTCCAGGTGCGCGCCGCAGCGGACACGAG
TCCGATCTAGACG-CCCGCGCAGATATATCCGAGCCATGTGTCACGCGGACACCACCCGCGTCACACCACGTCCCCATGC
CACGCGCCGATACCGCGCCGCTGGCGCTCGCCGCAGCTCAGCTAT--TTAAACGCCGGCCCGCTGCCGCCGGACCACACC
GGAGCCGAGCAGGA--AGAGCACGTCGAGTCAGCCAGCAGCGA--GCATATATACATACGCGTGCGAAGTGCAGTGAAGG
CAGGCAGGATGTCGGGGGCACAGGGAGCGCACCCGGTCGGGGAGACGACGCCGACGACGTACGGGTCGGTGGGCGGCGGG
GAGAACCGCACGCGCACGGACCTGCGGTCGCGGGAGGACCAGGGCAACATCCAGATCGATAAGGTGCAGGACAAGGTGGA
GGACGCCGCGTCGCGCAAGGTCGACGACAGCGCCTTCGCCGCCAGGAAGGAACCGGGCCAGGCCGGCGACGCCGGGGCGA
CCGGCACCGGCGCGTGATCTGGGTTCT---CTGTGGCACCCTGCCGCGCGCG----------------------------
--------------GGTGCGTTGTG-TTGTGTAGCGAGTTGTGTTCTGTAAAAGAGTCTCTGCGTGCGAGCTCACAATAA
TAAGAA---CTGCTTCTCAGTTTGCTTAGCAAGACCATTAATTTTCTGTTCGTGCAAACACTCTGCTATCTTTTTAGATT
AGATAGG-----CTGCAAATGTTCAGATCAACCCGGGCGAGACCGATAGATTCCTGTGGAAATGGGATAGATTCCTGTGG
AAATGGAATGCAGCCGGGACGCACTATGCTAGCT--AGTAAGGGCCGCTACGGAAGTGCTAGGCACCAATGAATTCTAGA
AATGTAGA------------------------------------------------------------------------
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>SNPs
SSS------------------------------------------------------------------S----------
--S------------------------------------------S--SS------------------------------
-----S--------------------S----S---SS---------S------S------------------S-------
-----------------------------S-S--S----S---------S------------------------------
-S-----------------------------S---------------------------------S------------S-
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--S--------------------------------S--------------------------------------------
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---------------------------------------------------------------SSS-SSS----------
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-----------------------------S--------------------------------------------------
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------------------------------------------------------------------S-------------
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-------------------------------S-------------SS-----------------------S---S-----
--------------SS--S------------------------SS----------------------------------S
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------------------------S-------------------------------------------------------
---S--------------------------------------------------------------------------S-
-----------------------------S----------------S------S---S------S-SSSSSSSSS-----
----------------S--------S------------------------------------------------------
------SSS------S----------------------S---------------------------S-------------
--------------------------------S----------S---S--------------------------------
----------------------------------SS--------------------S------------------S----
----------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSS
>forward_2400
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------------------------------------------------------------TGTGTGCGGTGTAGTGAAGA
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>reverse_3460
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-------------------GAATGTGCGGCGATGAGTTC-----------------------------------------
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