>input_sequence_81849
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-------------------------------------------------------------ATGGGGAGAACCACCATGC
TTCTCATGGCGCTGGCCCTCGCCCTCACCGCCGTCGCCCACGCGACGCCTCCCGCGCTCCGGAGGAGCCGCTTCCTTGCC
GACAAGACCCCGCCGCCGCTGTCCTACTACGACTGCGTCAGGAAGCCCCCGTCGGTGTGCCTGGAGCCCGGGAGCCCCGG
GAACACCTGCTGCAAGGGCACCTGCACCAACACCTTGTCCAGCGTGGAGCACTGCGGCAACTGCAACAGGAAGTGCAAGT
ACGGGGACACCTGCTGCGACGGCAAGTGCGTCGACCTCCTCAAGGACAAGAAGAACTGCGGCGAGTGCTCCAACCAGTGC
GCCAACTCCGTCAAGTGCGAGTTCGGCATGTGCGACTACGCGGGGTGA--------------------------------
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>chr3B_1_TraesCS3B01G199400
CCCTTTTGCTCAGAAAAGGAAGCGATGGTTCTGTTG------CAGGGATTATACCCCAATCATCACACGGACAGTAGCAT
CAACTTCTCCTACTGACAAAGTAGAGTCAACCTGCAGTACAAGTCATTTAAGGTTCCAGCTAATTCTCTTTCTCCAAT--
-TAACATGTCAAGTTGGGTTTCTTAGATCCAACCTGAAGGGAATCCGAAGTCAGGGGAGTTCTAAACCTGTCTGAATGTG
GACTAAATGATCAGTACAT----ATGTCATGCTGAACCATAGATGAGATGGAAAACTAACAATTACTTACTGTACCTTTC
AAACCGAATCAACAATGCTTCAAAACTAATTTCGTGCTTCTAGACCCGTTTGCCGTGCATTGCATACCGATGTAACATGC
CTGCAGACATTAGAAACAGTTTCCTTGTGCTCGCAGCGCCGACAAAGTGCCCCTGGAGGGAGCTGCTAGGAGTTTGATCA
ACGGACGCAAGTCGCAGCAGCAGTACGTGTAATCCTAAAAGCGCCACGATTTTATTACTGCAGATAGTCAACCCCTGCGC
AAGTCTGGTAGACGTGTCAAATCTTGATGAGTGTGAATGACCAGGCAGCCAATTGCTACGAATATTCCTCCCCTGCCTGC
AAAGGCGGCAAG----ACGTACGTACACACGCACAAGATCACCATCGCAAGCATGAATCATGTTAAAGTTGGACGAGAGG
CAGAGAAGAAATCAAGCAGGAGCCGGCTAGCTTAGCTAGCTTGCAGCCCACAGCCTTGCTGCGCACACTCA----CTGCA
CTCCAGGCTTTTGCCGTGCAAATCAACCATGGGCAGGCATATGCATGCGCCCATGCGCCTTTGACTTTCGCCATTGCCGG
CTCAGCCCATAGTATAAGCACGGCCCTTCCCTCCCTACAACCCCCATTTCCTTCCTCATAGAGCCACCTGCCGAGCCACA
AGCCATCAGCAGCGCACTGCCACGACCCTAAGCTCTCTCCCTCCAGCGCCACCCCACCACCATGGGGAGAACCACCATGC
TTCTCATGGCGCTGGCCCTCGCCCTCACCGCCGTCGCCCACGCGACGCCTCCCGCGCTCCGGAGGAGCCGCTTCCTTGCC
GACAAGACCCCGCCGCCGCTGTCCTACTACGACTGCGTCAGGAAGCCCCCGTCGGTGTGCCTGGAGCCCGGGAGCCCCGG
GAACACCTGCTGCAAGGGCACCTGCACCAACACCTTGTCCAGCGTGGAGCACTGCGGCAACTGCAACAGGAAGTGCAAGT
ACGGGGACACCTGCTGCGACGGCAAGTGCGTCGACCTCCTCAAGGACAAGAAGAACTGCGGCGAGTGCTCCAACCAGTGC
GCCAACTCCGTCAAGTGCGAGTTCGGCATGTGCGACTACGCGGGGTGATGCCGATCCGGCGACGCCGGCCATGCCCGCCA
TGCGTACGTGTGGTGTGATCGGCGGCCACGCATATACAGTTCTGCACCCATCATGCATGACCAACAAATAAAATCGGCAG
TACGTATATACTACGTGAGTGCATCTTAAGAAGTCCAAATTGTTTAAGGTATTTCAATTGTTGATCTCCTCGATCATATG
TATACAAAAAAAAAGGGTACAGATGATTTATACGTCTCTCTGTTCGTCTCATGATTTACGTGTTTTATTTGTTGGACTAC
ATACTATAAATACAAAGTGGTCACGTGGTATTAATAAAGTGAATAATGTTGTAATGTGTTATA---CATATATATGATTT
TTTGGGTACCCGTAGCTCCATCAATTCATATGTATATATGGATTCTTTTTTATGTATACCGAACAATGGAAACATTTTCA
ATGAAT-----------------------TCAGATGTATTTACCAAGTTTGAAC---CT--TTTTTTACGGTATAGACTA
GTAGGCATGTGC---TGCCATTCGC-TTATTTGTGCGACTGCTTGCAAACTGCCAATTCATAGAACTGGTCTTAGTTAGG
ATCTAGGACGCGTACAAAAGGGAAAGTGCTTAACGTAGATGCCTCCCATGGTCAACTTAATCAACTCATTTGCATGTGGC
A-------TACATTCTTGCATTAGTACGTGACGTGTCTGTCCAGTATCCACAGCGCTTGGGTGCGCCCTACCACCCCCCT
CCGACCGAAGACGAAGACTTCCTACCCTGGTGCACGGCGACCATCGCCGGTTCCCCTCGCGGCCTTCGCAAGGGTCTAGC
CACATTGGCTACGCTCACCGCTTGGTGCATCTGGAGACACCGCAACCGTTGCGTGTTCGATGGCGACTCCCCTTCCGCCT
CAAGGCTTCTTGCAGCTATCCAGGACGAGGCTAGGACCTGGGCTCGAGCTGGTGCTCGCGGACTCAATCCTTTGCTGGCA
TAGGAGCGTAGCTTTACGTTAGTTGGGCTGAGCATCCCACCCCATAAAAA
>chr3D_1
CCCCTTT-CTCAGAAAAGGCAGTGATGCTTCTGTTGCTGTTGCAGGGATTATACCCCAATCATCACACGGACAGTAGCAT
CAACTTCTCCTACTGACAAAGTAGAGTCAACCTGCAGTACAAGCCATTTAAGGCTTCATCTAATTC-CTTCCTCTAATTA
ATAACATGTCTTTTTT------TTAGATCAAACCTGAAGGGAATCCGAAGCCAGGGGAGTTGTAAACCTGTCTGAATGTG
GACTACATTATCAGTACAT----ATGTCATGCTGAACCATAGATGAGATGGAAAACTAACGATTACTTACTGTATCTTTC
AAACCGAATCAACAATGCTTGAAAACTGATTTCGTGCTTCTAGACCCATTTGCCGTGCGTTGCATACCGAAGTAACATGC
CTGCAGACATTAGAAACAGTTTCCTTGTGCTCGCAACGCCGACAAAGTGCCCCTGGAGGGAGCTGCTAGGAGTTTGATCA
ACGGACGCAAGTCACAGCAGCAGTACGTGTAATCCTAAAAGCGCCACGATTTTATTACTGCAGATAGTCAACCCCTGCGC
AAATCTGGCAGACGTGTCAAATCTTCATGAGTGTGAATGACCAGGCAGCCAATTGCCGAGAATATTCCTCCCCCGCCTGC
AAAGGCGGCAAG----ACGTACGTACGCACGCACAAGATCACCATCGCAAGCATGAATCATGTTAAAGTTGGACGAGGGG
CAGAGAAGAAATCAACCAGGAGCCGGCTGGC-TAGCTAGCTTGCAGGCCACAGCCTTGGTGCGCACACTCCCTCCCTGCA
CTCCAGGCTTTTGCCGTGCAAATCAACCATGGGCAGGCATATGCATGCGCCGATGCGCCTTTGACTTTCGCCATGGCCGT
CT-AGCCCATAGTATAAGCACGGCCCCTCCCTCCCTACAACCCCCATTTCCTTCCTCATAGAGCCACCTGCCGAGCCACA
AGCCATCAGCAGCGCACTGCCACGACCCTAAGCTCTCTCCCTCCAGCGCCACCCCACCACCATGGGGAGAACCACCATGC
TTCTCATGGCGCTGGCCCTCGCCCTCATCGCCGTCGCCCACGCGGCGCCTCCCGCGCTCCGGAAAAGCCGCTTCCTCGCG
GACAAGACCCCGCCGCCGCTGTCCTACTACGACTGCGTCAGGAAGCCCCCGTCGGTGTGCCTGGAGCCCGGGAGCCCCGG
GAACACGTGCTGCAAGGGCACCTGCACCAACACGCTGTCAAGCGTGGAGCACTGCGGCAACTGCAACAGGAAGTGCAAGT
ACGGGGACACCTGCTGCGACGGCAAGTGCGTCGACCTCCTCAAGGACAAGAAGAACTGCGGCGAGTGCTCCAACCAGTGC
GCCAAGTCCGTCAAGTGCGAGTTCGGCATGTGCGACTACGCGGGGTGATGCCGAT---------CCGGCCATGCCCGCCA
TGCGTGC-----GTGTGATCGGCGGCCACGCATATACAGTTCTGCACCCA----------CCAAGAAATAAAATCGGCAG
TACGTATATACTACGTGAGTGCATCTTAAGAAGTCCAAATTGTTTAAGGTATTTCGATTGTTGATCTCCTCGATCATATG
TATACAAAAAAAA-GGGTACAAATGATTTATACGTCTCTCTGTTCGTCTCATGATTTACGTGTTTTATTTGTTGGACTAC
ATACTATAAATACAAAGTTGTCACGTGGTATTAATAAAGTGAATAATGTTGTAATGTGTTATACAGCATATATATCATTT
TTGGGGTACCCTTAGCTCGATCAATACATATGTATATATGGATTCCTTTTTATGTATACCGAATAATGGAAACATTTTCA
ATGAATGTTTATTTGATTTAACAATCGATTCTGATGAATTTATCAAGTTTGAAAAATCTAGTTTTTTCTTGTATAGACTA
GTAGGCATCTGTACATGCCATTCGCTTAATTTGTACGACTGCTTGCAAACTGCCAATTCATAGAACTGGTCTTACTTAGG
ACCTAGGATGCGTACAAACGGGAAAGTACTTAACGTAGATGCCTCCCATGGTCAACTTAATCAACTCATTTGCATGTGGC
CTACATTCT------TTGCATTAGTACGTGACGTGTCTGTCCAGTATCCATAGC--------------------------
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>chr3A_1
CCCCTTT-CTCCGGAAAGGCAATGATGCTTCTTTTA------CAGGGATTATACCGCAATCATCACACGGACAGTAGCAT
CAACTTCTCCTGCTGACAAAGT-GAGTCAACCTGCAGTACAAGCCGTTTAAGGCTTCAGCTAATTC-CTTTCTCTAATTA
ATAACATGTCAAGTTGGGTTTCTTAGATCAAACCTGAAGGGAATCCGAAGCCAGGGGAGTTCTAAACCTGTC-GAATGTG
GACTACATGATCAATCAGTACAAATGTCATGCTGAACCATAGATGAGATGGAAAACTAACAATTACTTACCGTATCTTTC
TAACCGGATCAACAATGCTTCAAAACAAATTTCGTGCTTCTGGACCCATTTGCCGTGCACTGCATACCGAAGTAACATGC
CTGCAGACATTAGAAAGAGTTTCCTTGTGCTCGCAACGCCGACAAAGTGCCCCTGGAGGGAGCTGCATGCTAGGCAG---
----------------------------------------GCGCCACGATTTTATTACTGCAGATAGTCAACCCCTGCGC
AAATCTGGCAGACGTGTCAAATCTTCAGGAGTGTGAATGACCAGGCAGCCAATTGCCAAGAATATTCCGCCTCTGCCTGC
AAAGGCGGCAACGCGTACGTACGTACGCACGCACAAGATCGCCATCGCAAGCATGGATCATGCTAAAGTTGGACGAGAGG
CAGAGAAGAAATCAACCAGGAGCCGGCTAGC-GAGCTAGCTTGCAGCCCACAGCCTTGCTGCGCACACTCCCTCCCTGCA
CTCCAGGCTTTTGCCGTGCAAATCAACCATGGGCAGGCATATGCATGCGCCGAGACGCCTTTGACTTTCGCCATTGCCGT
CT-AGCCCATACTATAAGCACTGCCCCTCCCTCCCTACAACCCCCATTTCCTTCCTCATAGAGCCACCTGCCGAGCCACA
AGCCATCAGCAGCGCACTGCCACGACCCTAAGCTTTCCCCCTCCACCGCCACCCCACCACCATGGGGAGAGCCACCATGC
TTCTCATGGCGCTGGCCCTCGCCACGATCACCGTCGCCCACGCCGCGCCTCCCGCGCTCCGGCGGAGCCGCTTCCTTGCG
GACAAGCTCCCGCCGCCGCTGTCCTACTTCGACTGCGTCAGGAAGCCCCCGTCGGTGTGCCTGGAGCCCTTGAGCCCCGG
GAAGACGTGCTGCAAGGGCACCTGCACCGACACGGAGTCCAGCGCTGAGCACTGCGGCAACTGCAACAGGAAGTGCAAGT
ACGGGGACACCTGCTGCGGCGGCAAGTGCGTCGACCTCCTCAAGGACCAGAAGAACTGCGGCGAGTGCTCCAACCAGTGC
GCCAACTCCGTCAAGTGCGAGTTCGGCATGTGCGACTACGCGGGGTGATGCCGATCCGGCGACGCCGGCCATGCCCGCCA
TGCGTGCGTGCGGTGTGATCGGCGGCCACGCATATACAGTTCTGCACCCATCATGCATGACCAAGAAATAAATTCGGCAG
TGCGTATATACTACGTGAGTGCATCTTAAGAAGTCCAAATTGTTTAAGGTATTTCGATTGTTGATCTCCTCGATCATATG
TATACAAAAAAAA-GGGTACAGATGATTTATACGTCCCTCTGTTCGTCTCATGATTTACGTGTTTTATTTGTTGGACTAC
ATACTATAAATACAAAGTGGTCACGTGGTATTAATAAAGTGAATAATGTTGTAATGTGTTATA---CATATAT--GATTT
TTTGGGTACCCGTAGCTCGATCAATACATATGTATATATGGATTC-TTTTTATGTATACCGAATAGTGGAAACATTTCCA
ATGAATGTTTATTTGATTTAACAATCGATTCTGTGTATTTTACCTAGCTTGAATATTCT--TTTTTTTCTGTATAGACTA
GTAGGCAT--GTACATGCCATTCGCATTATTTGTACGACTGCTTACAAACTGCCAATTCATAGAACTGGTCTTAGTTAGG
ACCTAGGACGCGTACAAACGGGAAAGTACTTAACGTAGATGCCTCCCATGGTCAACTTAATCAACTCATTTGCATGTGGC
A-------T------TTGCATTAGTACGTGACGTGTCTGTCCAGTGTCCACA----------------------------
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>SNPs
---S---S-----------S--S----S----------------------------------------------------
-------------------------------------------S---------S-S----------S-------S-----
-----------------------------S--------------------S-----------------------------
-----S--------------------------------------------------------------------S-----
-----------------------------------------------S----------------------S---------
-----------------------------------S--------------------------------------------
-------------S------------------------------------------------------------------
--S-----S----------------S------------------------------S-S---------------------
--------------------------S-----------------------------------------------------
---------------S---------------S--------------------------------------S---------
---------------------------------------------------S---------------------------S
--S-----------------------S-----------------------------------------------------
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---------------------------S----------------S----------------------------------S
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------S--------------------------SS---------------------------------------------
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-----S----S-----------------------------------------------------S---------------
-------------------------------------------------------S------------------------
-------------S------------------------------------------------------------------
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------------------S------S-------------------S-----------------S----------------
-------------------------------S----S----------------S-------------S-S----------
--------S--S----------------------S---------------------------------------------
-S----------------S--------S----------------------------------------------------
---------SSSSSS---------------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_436
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----------------CAGTTTCCTTGTGCTCGCAG--------------------------------------------
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>reverse_2176
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---------------GACTTCCTACCCTGGTGCAC---------------------------------------------
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