>input_sequence_81288
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ATGAGGAAGGGCAGCGAGTGCACCAGGATCAGCCCGGAGACCACCACCAGCGCCAACCCTATGTTCTCCCGGCAGGCCAG
CAGGTCCGGCGCCCGGACGGAACG------------GGACGCCCGGCCGAGGCAGGCGCGCGGCGGCTGCCGCCTGCTGA
GGACCGCGCGGTGGACCGCCGCGAGGTTCTACCGGCGCGCGAGGGTGAGCGTCGTCACGGCCTTCTGGTCGGCGCCGAGC
AGGAGAGGCTCTTCCAGTTCCACTTCCAGTGCTGCTTCGCGCTCGCCGGAGTATACGCCGGCGAGGAACAGCAGCAGGCG
GCAGTCCGGGCCGGTGGCCGTCGCCGATGACTCCCACAAGAGCGAAGCCGTGGAGGAGTGCATCAGGTTCATGAACTCCT
CGTCCAGGAAGTATCGCTAG------------------------------------------------------------
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>chr3D_1_TraesCS3D01G361000
ACACGCAGAGCAGGGGGGGCCTGGCTGCCTGCCGGTCGATCGATCAGCGACGATGCATGCAGCGTCCCGTTTCCCGAGAG
AAAACGCCCCCC-GCGACTGCGCAATGATTGGCGCCCGCGGCGGCCACCGGTCCGGTCGTCCG-------CGCCATGCCG
CCCACGTCGCGTCCCATGTCACCGTGCCTCGGACGGCGCGCGCGCCCCCACCCCTGTCCCTCGCGTCGCGGCGAGCGAGA
GCACCGTCGCGTGCCCCGCCCCGTCAATTCCATGTCCCCCCGGCCGGCCCAGCGGCGG---GGCGTCGCCTTGTGTGCGC
TGGTGCGCGGCGCCATTGGCC-GGGACGGGAGGGGGTCCGGCCTGCCGGCCTCAAAAGAGCCGCCCGGCCCAGCGCCTCC
CTCGCTGCATCGACCGCGTCCTTTTCCCCCCTTTCCCTTTTCTCTCCCATTCAGGGCACCTCGGCTGGGTTCGCCAGATC
TGCTCGCGCCGCACCGCTCGCTTCCACGGGAGATATTCTCCGGCCACCACCACCACCGCTAGGCAACAAGAATATACTGC
GCCGGTGCGCCCC-ACCACCCCCTTCTTGTCGTGTTTTCTCTTCGTGAAG----GCTGCAAGCTAAAGCCTTGGCCTTGG
CGGTCAT--ATTGAAGGATCTGGAAGAGGTGATGCGTACACCTCTTC-----ATGGGGTTGCGTGATCTGATCGGGAGGA
CTACCATTTTGGTGGTCAATTAGACCAAACTTTCCTTTCACTAGCTTGTCTCCCCGCTTTGCCTCTTTTCCTTTTTCTGA
GCCATGCCTTTCATGCTCTTGTCACATACTCTTGCAGTGTGTACCAGCCTG---CTACTTTTCCTTTGAGCAGGCTACAT
AGATACTC----------TGGTCTTGCCTTGCCTTGCCTCATCATAGTATAAAACGAGGCGTGCCTAGGCCACCCTGGTG
TGTGTGATACGTAGACACTGACCCGCCATCTTGGGCTAGCAAGCAAGCAAGCTAGGCATCCATCCA---TCCGGCCGGCA
ATGAGGAAGGGCAGCGAGTGCACCAGGATCAGCCCGGAGACCACCACCAGCGCCAACCCTATGTTCTCCCGGCAGGCCAG
CAGGTCCGGCGCCCGGACGGAACG------------GGACGCCCGGCCGAGGCAGGCGCGCGGCGGCTGCCGCCTGCTGA
GGACCGCGCGGTGGACCGCCGCGAGGTTCTACCGGCGCGCGAGGGTGAGCGTCGTCACGGCCTTCTGGTCGGCGCCGAGC
AGGAGAGGCTCTTCCAGTTCCACTTCCAGTGCTGCTTCGCGCTCGCCGGAGTATACGCCGGCGAGGAACAGCAGCAGGCG
GCAGTCCGGGCCGGTGGCCGTCGCCGATGACTCCCACAAGAGCGAAGCCGTGGAGGAGTGCATCAGGTTCATGAACTCCT
CGTCCAGGAAGTATCGCTAGTT-----TTTTTGTGATTCTGTTTCTACCCTCTGCGCCGATGCTAAGCGTCTTCCCCCCT
GTAATTTCCC-CCCCTTCTTGTTCTTGGCCTTTCATCTGTGTGCGCATTTGATCTAAGCTTGCGGAAATGATACGTACGG
CCGGATGCATCTTTCTCATCTTTTTGGTGCTCTCAAATCTGTCGCTGTTCCA--TTCAACATTTGTGCCTGTGAATATTT
GTCACCTTGTGCGAGCCCAGCCACCAACGAGCTAATTTCTGGTGTTCTCCATGTG-CAATGACTTGATGCATTTG-----
----------ATCCAATAGCTTGATCTTTCTGAGAAAACATACATCTCATCGATTTTCTGTTGCAGAAACGCCTTGATCC
AATAGAGTTAACAAGATACAGAAAAAAACA-GTGCATAAGAATGTT--GGGGATTCCCAATGTACCACCCATAAGCGCAA
ACAAGATCATGGCAAGACACATCATAGAGCAACAATATCATACCTGCGTGTTGCCACGAAAACACTGCGAAAACAGATTC
ATAAATATGTGGAAAAAAAATATTAAAGACCATGATAAGTGTCATACGAGTGTCACGAACACATGGCAACTTCACACGGT
TTTGATGGCAAATTTAGTGACACGAGAATGGTTTTGGATGGAGTACACATTTTCTTAAAATATAACAAAAAGAGAAAAAA
GGAAAAAAAGACATCAAGGCACAGAATAAGAAAGCTGACCGTCCTAAACTGAAACCAACGAACAGTGCTACTGAGCCAGC
CAATTCCCACGTCACCTGATGCGATCGGCTTTGTCTCGCTAGAAACGAGACATAGTCGTTTCCGAAAAACACACGATGTA
TTTTTCTTTCTATTCCAGCCCATTTGATAGAACCTTCTTTCCACGGCTCCCATTTGGCGCGTAGGATCGCTGCATAGCGA
CCAAACGCGTACCCCTCCCATGGCTACATCCACTCAAGTACGATTGTACGTCAGCCTATTTTAGTTTTCCCCAAGTTGGA
TTGTAAG
>chr3A_1
ACACGCAGAGCAGGGGGGCCCTGCCTGCCTGCCCGTCGATCGATCAGCGACGATGCATGCAGCGCCCCACTTCCCGAGAG
AAAACGTCCCCC-GCGACTGCGCAATGATTGGCGCCCGCGGCGGCCACCGGTCCGGTCGTCCATGCATGCCGCCATGCCG
CACACGTCGCGTCCCATGTCACCGTGCCTAGAACGGCGCGCGCGCTCCCACCCCTGTCCCTCGCGTCGCGGCGAGCGAGA
GCACCGTCGCGTGCCCCGCCCCGTCAATTCCATGTCCCCCCGGCCGGCCCAGCGGCGG---GGCGTCGCCTTGC------
------GCGGCGCCATTGGCCGGGGACGGGAGGGGGTCCGGCCTGCTGGCCTCAAAAGAGCCGCCCGGCCCAGCGCCTCC
CTCGCTGCATCGACCGCGTCCTTTTCCGCCCTTTCCCTTTTCTCTCCCATTCAGGGCACCTCGGCTGCGTTCGCCAGATC
TGCTCGCGCCGTGCCGCTCGCTTCCACGGGAGATATTCTCCGGCCACCACCACCACCGCTAGGCAACAAGAATATACTGC
GCCGGTGCGCCCCCACCACCCCCTTCTTGTCGTGTTTTCTCTTCGTGAATGAAAGCTGCAAGCTAAAGCCTTGGCCTTGG
CGGTCAT--ATTGAAGGATCTGGAAGAGCTGATGCGTACACCTCTTCATGGCATGGGGTTGCGTGATCTGATCGGGAGGA
CTACCATTTTGGCGGTCAATTAGACCAAACTTTCCTTTCACTAGCTTGTCTCCCCGCTTTGCCTCTTTTTCTTTTTCTGA
GCCTTGCCTTTCATGCTCTTGTCACATACTCTTGCAGCACAGTACAGTACCAGCCTGCTTTTCCTTTGAGCAGGCTACAT
AGATACTC----------T---------------TGCCTCATCATAGTATAAAACGAGGCGTGCCTAGGCCACCCTG---
-GTGTGATACGTAGACACTGACCCGCCATCTCGGGCTAGCAAGCAAGCAAGCTAGGCATCCATA---CCTCCGGTCGGCA
ATGAGGAAGGGCAGCGAGTGCACCAGGATCAGCCCGGAGACCACCACCAGCGGCAACCCCATGTTCTCCCGCCAGGCCAG
CAGGTCCGGCGGCCGGTCGGCGGCGCCGTCGGAGCCGGACGCCCGGCCGAGGCAGCCGCGCGGAGGCTGCCGCCTGCTGA
GGACCGCGCGGTGGACCGCCGCGAGGTTCTACCAGCGCGCGAGGGTGAGCGTCGTCACGGCGTTCTGGTCGGCCCCGAGC
AGGAGAGGCTCTTCCAGTTCCACTTCCAGTGCCGCCTCACGCTCGCCGGAGTATACGCCGGCGAGGAACAGCAGCAGGCG
GCAGTCCGGGCCGGTGGTCGTCGCCGATGACTCCCACAAGAGCGAAGCCGTGGAGGAGTGCATCAGGTTCATGAACTCCT
CGTCCAGGAAGTACCGCTAGTGTTTTGTTTTTTTGATTCTGTTTCTACCCTCTGCGCGGATGCT-AGCGTCTTCCCCCCT
GTAATTTCCC-CCC-TTCTTGTTCTTGGCCTTTCATCTGTGTGCGCATTTGATCTAAGCTTGTGGAAATGATACGTACGG
CCGGATGCATCTTTCTCATCTCTTCTGTACTCTGGAATCTGTCGCTCTTACATTTTCAACACATGTGCTTGTCAATATTT
GTCACCTCGTGCGAGCCCAGCCACCGACAAGCTAATTTCCGTGATGTGGTGTGTCACAATGGCTTGATGCATTTG-----
----------ATCCAATAGTTTGATCTTTGTGAGAAAACAGGCGTCCCATCGATTTTCTGTTACAGAAACGCCTTGATCC
AATAGAGTTAACAAGATACAGAAAAAAA---GTGCATAAGAATGAATGGGAGACTCCCAATGTACCACCCATAAGTGCAA
ACAAAATCATGGCAAGACACATCATAGAGCAACAAGATCATACCGGCTTGTTGCCACGGAAACACTGCGAAAACAGATTC
ATAAATGTGTGCTGAAAAACAAATA-------------------------------------------------------
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>chr3B_1
ACACGCAGAGCAGGGGGGCCCTGGCTGCCTGCCCGTCGATCGATCAGCGACGATGCATGCAGCGTCCCGTTTCCCGAGAG
AAAACGCCCCCCCGCGACTGCGCAATGATTGGTGCCCGCGGCGGCCACCGGTCCGGTCGCCCG-------CGCCATGCCG
CACACGTCGCGTCCCATGTCACCGTGCCTCGAACGGCACGCGCGCCCCCACCCCTGTCCCTCGCGTCGCGGC------GA
GCACCGTCGCGTGCCCCGCCCCGTCAATTCCATGTTCCCCCG----GCCCAGCGGCGGGCGGGCGTCGCCTTGCGCGCGC
TGGCGCGCGGCGCCATTGGCCGGGGACGGGAGGGGGTCCGGCCTGCCGGCCTCAAAAGAGCCGCCCGGCCCAGCGCCTCC
CTCGCTGCATCGACCGCGTCCTTTTCCCCCCTTTCCCTTTTCTCTCCCATTCAGGGCACCTCGGCTGGGTTCGCGAGATC
TGCTCGCACCGCACCGCTCGCTTCCACGGGAGATATTCTCCGGCCACCACCACCACCGCTAGGCAACAAGAATATACTGC
GCCGGTGCGCCCC-ACCATCG------------------------------------------------------CTAGG
CGGTCATGTATTGAAGGATCTGGAAGAGGTGATGCGTACACCTCTTCAT--CATCGGGTTGCGTGATCTGATCGGGAGGA
CTACCATTTTGGCGGTCAATTAGACCAAATTTTCCTTTCACTAGCTTGTCTCCCCGCTTTGCCTCTTTTCCTTTTTCTGA
GCCATGCCTTTCATGCTCTTGTCACATACTCTTGCAGT----ACCACCCTG---CTGCTTTTCCTTTGAGCAGGCTGCAT
AGATACTCTTGCCTTGCCT---------------TGCCTCATCATAGTATAAAACGAGGCGTGCCTAGGCCACCCTG---
-GTGTGATACGTAGACACTGACCCGCCATCTCGGGCTAGCAAGCAA----GCTAGGCATCCTTCCATCCTCCGGTCGGCA
ATGAGGAAGGGCAGCGAGTGCACCAGGATCAGCCCGGAGACCACCACCAGCGGCAACCCTATGTTCTCCCGGCAGGCGAG
CAGGTCCGGCGCCCGGACGGAACG------------GGACGCCTGGCCAAGGCAGGCGCGCGGCGGCTGCCGCCTGCTGA
GGACCGCGCGGTGGACGGCCGCCAGGTTCTACCGGCGCGCGAGGGTGAGCGTCGTCACGGCCTTCTGGTCGGCCCCGAGC
AGGAAAGGTTCTTCCAGTTCCACTTCCAGTGCTGCTTCACGCTCGCCGGAGTATACGCCGGCGAGGAACAGCAGCAGGCG
GCAATCCGGGCCGGTGGTCGTCGCCGATGACTCCCACAAGAGCGAAGCCGTGGAGGAGTGCATCAGGTTCATGAACTCCT
CGTCCAGGAAGTACCGGTAGTT-----TTTCTGTGATTCTATTTACACCCTCTGCGCGGATGCT-AGCGTCTTCCCCCCT
GTAATTTCCCCCCC-TTCTTGATCTTGGCCTTTCATCTGTGTGCGCATTTGATCTAAGCTTGTGGAAATGATACGTACGG
CCGGATGCATCTTTCTAATCTCTTCTGTGCTCTGGAATCTGCCGCTGTTACA--TTCAACATTTGTGCTTGTCAATATTT
GTCACCTTGTGCGAGCCCAGCCACCAACGAGCTAATTTCTGGTGTTCTCCAACTTCAGATTTTGTCTTGTTAATTTTGAA
TGTCGCAATAATCCAATAGTTTGATCTTTCTGAGAAAACATGCATCCCATCGATTTTCTGTTACAGAAACGCCTTGATCC
AATAGAGTTATCAAGATACAGAAAAAAAAAGGTGCATAAGAATGAATGGGAGATTCCCAACGTACCACCCAT-AGCGCAA
ACAAAATCATGGCAAGGCACATCATAGAGCAACCAGATCATACCCCTGAG---------AAACATTGCAAAAAAAGATTC
ATAAATGTGTGCTGAAAAACAAA---------------------------------------------------------
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>SNPs
------------------S--------------S----------------------------------------------
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-S-----------------------------S------------------------------------------------
-------------------------------------------------------------------------S-S----
---S----------------------------------------------------------------------------
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-------------------------------------------------S------------------------------
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------------S-------------------------------------------------------------------
--------------------------------------SSSS--------------S-----------------------
-------------------SSSSSSSSSSSSSSS-------------------------------------------SSS
S------------------------------S------------------------------------------S-----
----------------------------------------------------S---------------------------
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-------------------------------------------------------------------------S------
--------------------------------------S-----------------------------------------
-----------------S--------------------------------------------------------------
-------------S-------------------------------------------S------S---------------
--------------S-----------------------------------------------S-----------------
---------------------S--SS-------SS--------------S------------------S---S-------
------------------------------------------------------S------S------------------
-------------------S---------------------S----S---------------S-----------------
----------------------------S---------------SS----S-----------------------------
----S------------------------------S--------S-------------S---------------------
------S----SSS-----SS-S--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSS
>forward_913
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-------------TACTCTGGTCTTGCCTTGCC-----------------------------------------------
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>reverse_2354
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---------------------------------CTTCTTTCCACGGCTCCCAT---------------------------
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