>input_sequence_59431
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-------ATGGACGAGTGGTTCTTCTCCGTCGACCGGGACGACGACGACGACCTGCTGAGCCTGATGGGCCTCCTCTCGC
CCCCGCCCGCGGTGGTGCACCAGGGCAGCGCCTTCGCGCCGTACCAGCGGCGTAGTACGGCGACGTCA---TTGCTCGTG
TCCCCGGGCCGGCGGCAGCGCGCGCGGGGCAGAGCCAACGCCCACCGGAGCATGCACGAGTACTT------GAGGCGCAT
GAATGGCCTTGAGTCGTCTCCCCAGGGGACATCTTCGGGAGCACGAGCGGCGCCGCCGGCGAAGGAGCCGATCGAGCCGC
AGGTGCCGCGCAGCTCGGCGTTCCGGCACATCACGCGGGAGCGGCTGCGGCGGGAGCGCCTCAGCCAGGGCTACGCCGAC
ATCCGCGCCCTCCTGCCACCGGGACGGGCACCAAACGTACGTACATTGATTACAATCAATCGGTCGCTGAACTGCAGCTG
CAACTGCAAGTGACACGAGCAATTCTCTTCTCCTCGTACGTACGCAGGGTGCCAAGAACTTTGTCCTCGCCGCGGCGGTC
GACTACATCAGGGAGCTGGAGGGGAGGAAGGGCCGGCTTGGCGCGCGGCATGCAGAGCTGGTGAGATCGTCTGAATCAGA
CGGCGCGTCCGGCGGCGGCATGGTGGTCAAGGTGCGCGGCGAGGGCGGGTGTTCTTCTATGGTTGGCGCACTTGAGGCGG
TGCTCCGGCGGCTCAAGGCCATGCAGGAGCTGCGGGTGACGGAGATCCGGTCGTGGTGCTGTGACGGCGCCATGTGCATG
GACGTCGCGGTCGCGGTGGAGTCCACGGTAGGTGCGCGGGAAAACGTAATCCGACTTTAGTTCTTTCGACGAATTGCTCT
CTATCACTACCCGAAAGCTACGTTAACGGACTAGTATAATATAGTCGCAGGTTGACTGCTTCTTCGGTCAGAATGAGTCA
ACGTGGTTTCATTCAGTATCATGCGAAATTAATTATACTCCGTGTATGTCGTGCGTGTAGGTATCTTCGTTCGAGGTGGA
CATGCGAATAACAAATGCCTTGATGGAGCTTGAGGAAATCAAATCCGGCCGCTTGCAGGATGCAGTGAAGCGTAGCTCCA
ACTTTAGTTGTCAAGTTGTAAGTGGTGAGCTCATGAGTTGA---------------------------------------
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>chr3D_1_TraesCS3D01G309500
GTTGATCAGGAAGTGTCAGGTTCCAAACCCCTACATTATAATTTTTTTCATGTTATTTCTCACCACCATACACTGTGTTT
GAGGTC-TTTCTCATGAGGGGGGTTTCTGCTAAAAAAA-TCCTCACGCACGGAGTACCCAACACTGTCCCCGCTCTCAGC
AGCTGACAGGTGGGTCACTGCCATGTTGGCATGCCACGCGGGCTAGACATGCGTTTGGAT-TAGAATGAGGCACCGTATT
TGCACGGCCAGACAAGTTTAAACACATATTTTGTGTATTTTACAACTTTAGACATCAAACCGAACATGCAAGACAAGTTG
AACCACCTTCAATGTATTTAACTCTAGTCGGAGTGCGTAGACATTCCATATAGAGCATGTAAACCATGCGCATGCGATCG
AAAGAAACCATCCCGCTGTTCCGCGCAGGCTGCAGCTTCCGCGA---TACTGGCCATCTCTCCCAGAACCGCATTACGGC
CAGCAATCAACGCACGCATCGTGCGTATACACCGCACGCCGAAACAA--GGAGGGCCAAGTAGAAGTTTTCAACCCTCTA
TCTGACCG------ATCGATCGGTGCT-----TTCTGAGTTTGCCTCGGGGCAGAGGACACCGAGCCCCTTCCACCGTAC
GTATATGCATGGCATACAGACTACGCGCGGGTACTGTACGGG-CCGTCTTTCTAAATGAAAAACAGGTACACCGTA----
---CACACCATGCAG--------ACGCAGTGCTGCAGTGACAAGCCATGCTGCTTCTGCTTTC--TTTT----CAGCCAG
CCAGCCTTCAAACAGTGTGCCCGGTCAAACCAAACCACCCGCGGGCGTGACAACCTTTCTTCTC------CTCCTCCTCC
TCGGTCTTTTTTTTGTCGTGCCGCCACACCCGGACGCGCGCGTATATAAGCGCAGACACGCGCGCGATCGCGGCACCACC
AACAGCGGCAACAGCGGCATGCGTGCAAGCATAGCCTCGGCATTCAGAGCACCCAGAGGCCACCGGCGAGAACTTGGTCC
TTGAGCCATGGACGAGTGGTTCTTCTCCGTCGACCGGGACGACGACGACGACCTGCTGAGCCTGATGGGCCTCCTCTCGC
CCCCGCCCGCGGTGGTGCACCAGGGCAGCGCCTTCGCGCCGTACCAGCGGCGTAGTACGGCGACGTCA---TTGCTCGTG
TCCCCGGGCCGGCGGCAGCGCGCGCGGGGCAGAGCCAACGCCCACCGGAGCATGCACGAGTACTT------GAGGCGCAT
GAATGGCCTTGAGTCGTCTCCCCAGGGGACATCTTCGGGAGCACGAGCGGCGCCGCCGGCGAAGGAGCCGATCGAGCCGC
AGGTGCCGCGCAGCTCGGCGTTCCGGCACATCACGCGGGAGCGGCTGCGGCGGGAGCGCCTCAGCCAGGGCTACGCCGAC
ATCCGCGCCCTCCTGCCACCGGGACGGGCACCAAACGTACGTACATTGATTACAATCAATCGGTCGCTGAACTGCAGCTG
CAACTGCAAGTGACACGAGCAATTCTCTTCTCCTCGTACGTACGCAGGGTGCCAAGAACTTTGTCCTCGCCGCGGCGGTC
GACTACATCAGGGAGCTGGAGGGGAGGAAGGGCCGGCTTGGCGCGCGGCATGCAGAGCTGGTGAGATCGTCTGAATCAGA
CGGCGCGTCCGGCGGCGGCATGGTGGTCAAGGTGCGCGGCGAGGGCGGGTGTTCTTCTATGGTTGGCGCACTTGAGGCGG
TGCTCCGGCGGCTCAAGGCCATGCAGGAGCTGCGGGTGACGGAGATCCGGTCGTGGTGCTGTGACGGCGCCATGTGCATG
GACGTCGCGGTCGCGGTGGAGTCCACGGTAGGTGCGCGGGAAAACGTAATCCGACTTTAGTTCTTTCGACGAATTGCTCT
CTATCACTACCCGAAAGCTACGTTAACGGACTAGTATAATATAGTCGCAGGTTGACTGCTTCTTCGGTCAGAATGAGTCA
ACGTGGTTTCATTCAGTATCATGCGAAATTAATTATACTCCGTGTATGTCGTGCGTGTAGGTATCTTCGTTCGAGGTGGA
CATGCGAATAACAAATGCCTTGATGGAGCTTGAGGAAATCAAATCCGGCCGCTTGCAGGATGCAGTGAAGCGTAGCTCCA
ACTTTAGTTGTCAAGTTGTAAGTGGTGAGCTCATGAGTTGA----TGTACTAGGAAATAGCATCACCCTTTAATTCACTA
CATGCTCCCTATGATGTGAAGACCTCTCACAAGCAATAGAGGTGTACAATTTAAGATTTTGCCCCACGATTTTAACTCGG
TCATCGTCTCGGTGGGTCCCTTTGGTCACTGCATGAGATTTTATTCTGGTCATCAGACTACTATGTTAGTTGGGAGAACA
TGAGCATTCTCAGAGTTTAGCGATTCTCGGCCGTCGGATCGTTTACTTGATGCGTTCTGGACCGTTGGATTGAGCTCCCG
GATCACCTGCGCCGTCGGATCGACCCGGAGCTACTGCTACAATGAACAGTTACTTCCGTTTCGTGCCACCGCGCGTAATT
CCAGCGCCCCCACAAGGGTATTTTTGTCATTTCGCACGTAGGCGTATAAAAGGCAGCCGCTCCCCATGGAGATAACCTAG
CCGCCGCCTCCTCGAGCACTCCCGCACTCGCGCCCGCTCCTCCCGCACGCGCGCCGCGCCCTCACCTCTCTCTCCCCTCC
AAACCCTACCCCGCCGCCGCCGCTGCTCGCCCGGGCACCCATCCCCTGCCTCACGCCACCCATCTAGAGAGATGGGGCCG
CGGGCGAAGAGGCCGACGTGCCGTCGTCTCGTCTTCTGCCGCGCCCGCCTCCCTGCCCCGCCGTCGCCGCTGCTGCTCGC
TCGGGCACCCATCCTCGGCCTCACACCACCCATCTAGAGAGATGGGGGCCACGGGTGATGAGGCCGGCGTCTCATCGTCC
CGTCTTCTGCGAGGTCGAGGAGAGCCAATCCCACCTCGCCGCGCGCAGCCGACCGGGACGGGGCCGCGGGCGAGGGGGCT
CAGCCTCGCCCCCCTCGATCTGGATGTCGCCGTCGCCGTGGTTTGCCCCCTTCGCCTCTTCTATCCAGCCGTGTAACTCG
AGCCGGCAATATCCAGCAATGGCGCGGCGGTCAACTCTGCCTTCCCGAGCCCGACGAGAAGGGGTTGCGCGGCTGTCCCT
CCCCA
>chr3A_1
GTTGATCAGGAAGTGTCAGGTTCGATACCCCTACATTATGAA-TTTTTCATGTTATTTCTCACCACCGTACACTGTGTTT
GAGGTCTTTTTTCATGAGGGGGGTTTCCGCTAAAAAAAATCCTCACGCACGGAGTACCCAACATTGTCCCTGCTCTCAGC
AACTGACAGGTGGGTCACTGCCATGCTGGCATGCCACACGGGTTAGATGTACGGGCGGATATAGAAGGAGGCACCCCATT
TACACGGCCGGGCAAGTTCAAACACTTATTTTATGTATTTTACAACTTTAAACATCAAACCGAACATGCAGGACAAGTTG
AGTCACCTTCAATGTATTTAACTTTAATCGGAGTGCGTAGACATTCCATATAGAGCATGTAAACCATGCGCATGCGATCG
AAAGAAACCATCCCGCTGTTCTGTGCAGGCTGCAGCTTCCGGGATACTACTGGCCATCTCTCCCAGAACCGCATTACGGC
CAGCAATCAACGCACGCATCGTGCGTATACACCGCACGCCGAAACAAAAGGAGGGCCAAGTAGAAGTTTTCAATCCTTCT
ATCTGAATCTGACCATCGATCGGTGCTTTCTGTTCTGATGTTGCCTCGGAGCAGAGGACACCGAGCTCCTTCCATCGTAC
GTATATGCATGGCATACAGACTACGCGCGGGTACTGTAC-GG-CCGTCTTTCTAAATGAAAAACAGGTACACCGTAGACC
GTACACACCATGCAGACGCAGACACGCAGTGCTGCAGTGAGAAGCCGTGCTGCTTCTGCTTTCACTTTTCAGCCAGCCAG
CCAGCCTTCAAACAGTGTGCCCGGTCAAACCAAACCACCCGCGGGCGTGACGACCTTTCTTCTCCTCCTCCTCCTCCTCC
TCGGTCTTTTTTTTGTCGTGCCGCCACACCTGGACGCCCGCGTATACAAGCGCAGACACGCGCGCGATCGCGGCACCACC
AACAGCGGCAACATCGGCATGCGTGCAAGCATAGCCTCGGCATTCAGAGCACCCAGAGGCCACCGG-GAGAACTTGGTCC
TTGAGCCATGGACGAGTGGTTCTTCTCCGTCGACCGGGACGACGACGACGGCCTGATGAGCCTGATGGGCCTCCTCTCGC
CCCCGCCCGCGGTGGCGCACCAGGGCAGCGCCTTCGCGCCGTACCAGCGGCGTAGTACGGCGACGTCG---TCGCTGGCG
TCCCCGGGCCGGCGGCAGCGCGCGCGGGGCAGAGCCAACGTCCACCGGAGCATGCACGAGTACCTGAGGCCGAGGCGCAT
CAATGGCCTTGAGTCGTCTCCCCAGGGGACATCTTCTGGAGCACGAGCGGCGCCGCCAGCGAAGGAGCCGATCGAGCCGC
AGGTGCCGCGCAGCTCGGCGTTCCGGCACATCACGCGGGAGCGGCTGCGGCGGGAGCGCCTCAGCCAGGGCTACGCCGAC
ATCCGCGCCCTCCTGCCCCCGGGACGGGCACCAAACGTACGTACGTTGATCACA-TCAATTGGTCGCTGAACTGCAAACG
CAAGTG-AAGTGACACGAGCATTTCTCTTCTGCACGTTCGTATGCAGGGTGCCAAGAACTTCGTCCTCGCCGCGGCGGTC
GACTACATCAGGGAGCTGGAGGGGAGGAAGGGCCGGCTTGGCGCGCGGAATGCAGAGCTGGTGAGATCGTCAGAATCAGA
CGGCGCGTCCCGCGGCGGTGTGGTGGTCAAGGTGCGCGGCGAGGGCGTGTGTTCTTCTATGGCTGGCGTGCTTGAGGCGG
TGCTCCGGCGGCTCAAAGCCATGCATGAGCTGCGGGTGACGGCGATCCGGTCGTGGTGCTGCGACGGCGCCATGTGCATG
GACGTCGCGGTCGCGGTGGAGTCAACGGTACGTGCGCCGGAAAGCCTAATCCGACTTTAGTTCTTTCGACGAATTGCTCT
CCATCAGTGCCCGA------------------------------------------------------------------
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>chr3B_402
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----AAACCATCTCGCTGTTCTGTGCTGGCTGCAGCTTCCGGGATACAGAT---CATCTCTCCCAGAACCGCATTACGGC
CAGCAATCAACGCACGCATCGTGCGTATACACCGCACGCCGAAACAA--GGAGGGCCAAGTAGAAGTTTTCAATCCTCTA
TCTGACCG------ATCGATGTGTTCT-----TTCCGATTTTGCCTCGGGGCAGAGGACACCCGTGT-------------
--------ATGGCATACAGACTACGCGCGGGTACTGTAC-GGGCCGTCTTTCTAAATGGAAAACAGGTACACCGTA----
---CACACCATGCAG--------ATGCAGTGCTGCAGTGAGAAGCCATGCTGCTTCTGCTTTCACTTTT----GAGCCAG
CCAGCCTTCAAACAGTGTGCCCGGTCAAATCAAACCACCCGCGGGCGTGACGACCTTTCTTCTCTTGTT----CTCCTGC
TCGGTCTTTTTTCTGTCGTGCCGCCTCTCCTGGACGCGCGCGTATATAAGCGCAGACACGCGCGCGATCGCGGCACCACC
AACAGCGGCAACAGCGGCATGCGTGCAAGCATAGCCTCGGCACTCAGAGCACCCAGAGGCCACCGACGAGAACTTGGTCC
TTGAGCCATGAATGAGTGGTTCTTCTCCGTCGACCGGGACGACGACGACGGCCTGATGGGCCTGATGGGCCTCCTCTCGC
CCCCGCCCGCGGTGGTGCACCAGGGCAGCGCCTTCGCGCCGTACCAGCGGCGTAGTACGGCGACGTCGTCGTTGCTCGTG
TCCCCGGGCCGGCGGCAGCGCGCGCGGGGCAGAGCCAACGTCCACCGGAGCATGGACGAGTACTT------GAGGCGCAT
GAATGGCCTTGAGTCATCTCCCCAGGGGACATCTT------------------------CGAATGAGCCGATCGAGCCGC
AGGTGCCGCGCAGCTCGGCGTTCCGGCACATCACGCGGGAGCGGCTGCGGCGGGAGCGCCTCAGCCAGGGCTACGCCGAC
ATCCACGCCCTCCTGCCCCCGGGACGGGCATCAAACGTACGTACGTTGATCACA-TCAACCGGTCGTTGAACTGCAAA--
----TGCAAGTGACACGAGGATTTCTCTTCTGCGCGTACGCACGCAGGGTGCCAAGAACTGCGTCCTCGCCGCGGCGGTC
GACTACATCAGGGAGCTGGAGGGGAGGAAGGGCCGGCTTGACGCGCGGAATGCAGAGCTGGTGAGATCGTCAGAATCAGA
CGGCGCGTCCGGCGGCGGCGTGGTGGTCAAGGTGCGCGGCGAGGGCGGGTATTCTTCTATGGCTGGCGTGCTTGAGGCGG
TGCTCCGGCGGCTCAAAGCCATGGAGGAGCTGCGGGTGACGGCGATCCGGTCGTGGTGCTGTGACGGCGCCATGTGCATG
GACGTCGCGGTCGCGGTGGAGTCCAAGGTACGTGCGCCGGAAAGCGTAATCCAACTTTAGTTCTTTCGACGAATTGCTCT
CCATCAGTGCCCGAAAGCAACGTTAACGGACTAGTATAATATAGTCGCAGGTTGACTGCTTCCTCGGTCAGAATGAGTCA
ACGTGGTTTCATTCAGTATCATGCGAAATTAATTATACTCCGTGTATGTCGTGCGTGTAGGTATCTTCGTTTGAGGCAGA
CATGCGAATAACAAATGCCTTGATGGACCTTGAGGAAATCAAATCCTGCCGCTCGCAGGATCCAATGAAGCGTACCTCCA
ACTTTAGTTGTCAAGTTGTAAGTGGTGAACTGATGAGTTGAGAGGTGTACTAAGAAATATCATCATCCTTTAATTCACTA
TATG--CCCTATGATGTGAAGCC--CTCACAATCAATAGAGGTGTACAATTTAAGATTTTGCCTCATGATTTTAACTCGA
CCATGGTCTTGATGGATCCCTTTGGTCAATGCATGAGACCTTTTTTTGGTCAT---------------------------
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>SNPs
-----------------------S-S-------------S-SS------------------------S------------
----------S----------------S-----------------------------------S------S---------
-S-----------------------S-----------S----S----SS-S--SSS----------S--------SS---
-S-------S-S------S------S------S-----------------S-------------------S---------
-SS--------------------S--S-----------------------------------------------------
---------------------S-S-----------------S--------------------------------------
-------------------------------------------------------------------------S------
--------------------------------------S---------------------------S-------S-----
---------------------------------------S----------------------------------------
----------------------------------------S---------------------------------------
---------------------------------------------------S----------------------------
------------------------------S-------------------------------------------------
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--------------------------------------------------S----S------------------------
-------------------------------------------------------------------S------------
----------------------------------------S---------------------------------------
------------------------------------S--------------------S----------------------
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-----------------S--------------------------S-----S---S---------------------SSS-
---S-----------------S---------S-S---------------------------S------------------
------------------------------------------------S----------------------S--------
-------------------S------------------------------------------S-----SS----------
----------------S-------------------------S-------------------------------------
------------------------------S------S-----S------------------------------------
-S----S-S---------S-------------------------------------------S-----------------
-----------------------------------------------------------------------S----SS--
---------------------------S------------------S------S-------S--S---------S-----
----------------------------S--S--------------------S------S-----S--------------
S---SS---------------S-SS-------S------------------------------S--S------------S
S---S----S-S---S------------S---------SS--S--S-------SSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSS
>forward_422
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--AGAAACCATCCCGCTGTTCC----------------------------------------------------------
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>reverse_2457
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--------------------------------------------------------CTGGACCGTTGGATTGAGCT----
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