>input_sequence_76823
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------------------------------------------------------------------------GCACAAAA
CCAA-CAAGCGAGCGCGAGCGCAGGCCA-CGCATCCATCTCATGGCGCTCCTCTCCATCCTACGCTCGTCTCCGCTGGCC
GTCCCCGCGGCCTCTTCTCGCCGCCCACCCAATCATGGTGTCTACCTACTACGCGTCAGCACCAGGGCCGCGCCGTCGTC
TCTGTCCGTGAGGTGCGAGCAGAGCAGCAAGCCGGGCGGCGGCAGCGTCGTCGACGTGTGGGCGAGCCGCCTGGCCATGA
TGAGCTTCGCCGCGGCGGTCGTCGCCGAGGTGTCCACCGGCAAGGGCTTTGTCGAG----GTACGCTCCCATGGATCGAC
CTGTCCTGTAACGCCTCGCTCTGCTGAGCTAGATGCTCGCTATTGACGGCGCTCTGCCCGCTTCGACGTGTTTTGCAGAA
TTTCGGCGTGGCAACGCCGGCGCCGGCGTTGGCGCTGGTGGTGACGGCGCTCGTCATCGGCCTGGCCGTCCTCTTCATCG
TCAGGTCCGGAGCGCAGGATTGATGGATCCATCGCACGAAATAATTGAAGACTCTTTTC---------------------
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>chr3B_1_TraesCS3B01G470200
CGCTTCT-TTCTCTTTCCCTTTTTTTCCTCTTCGACGGCCATGGATGACCTCTTGTATCCACGTGTCGTGCCCTCTTTGG
CCACCGGGACAAT----------GGCGGCCATGGGAGGATGCTGCGAATCCAAGAGGTTCAACACCGACAAGTGATTCGA
TGCCTCGGGTGCGCGTCGCGTCGGTGCCAACGAGGACAAACTAAGTTGCGACCACCGGTGGGG---GGCATGCTGCAACC
GGCCATGATAGAGCTAGGGACCGTCGGTGCGGCGTGCCGCAACCAGCGACGGGGCTGTATGCTGCAACTGGCAG-TGCAG
GATGCTTGAACCGGCTGGGAGGATGTTGCATCAGTGGTCGTACCCGACGATGGCGGCTGGCAAGTGTTGCAACCGCGTTG
GCAGAAACTGGAACCGCA--------ATCACTAGATGCTGGAACGCGACTACCGGAAGCTTTTCCCATGGTGATCACGAC
CCGGCGGGATGCTGCAACCGTGGTGTCTGGATACTGGAACCGGCACCCACCGTTGCGGCAACTAGCTACGACGACGGCTA
CGGCGGGGCGCTGCACCGACAACGAATGGTGGAACCGCAAGGCCGATTTGCTGAGATCGGCAACTCGTTTTGCTGCAAAG
GGGCGGACCACACAAGCATCGGCGCCGTAACCGTCGGGCCGGCAAACGGCGCCACGATGTTGCAAGGGG--GTGGTGGGA
GGACGTGTGTGGCGACGAGCCGACATGCCATGGAAACTAC---GAGCGAGGAGAGAGACGGTGATGTGTGTTTGTGTGTG
GGGGAAAAGGCTAGATGCCGATCCGACGGCCAAGCGCATCCAAATCAAACACATCTTACAGCTAGGAGGTGACCGGCCCA
AAACTGGCGCCGGTCGGCCGGCGCCCAGGGACATCACGTTTCTGGATTTA---GTTGCAAGACGTGCGCTGTCCGACCAT
TTT-TTCCGTGGATAGAGCGACAGCCAAACGGCCAACCGACGGCCACTCACTTCGGCTAGCTCAGGCCAGCAGCACAAAA
CCAA-CAAGCGAGCGCGAGCGCAGGCCA-CGCATCCATCTCATGGCGCTCCTCTCCATCCTACGCTCGTCTCCGCTGGCC
GTCCCCGCGGCCTCTTCTCGCCGCCCACCCAATCATGGTGTCTACCTACTACGCGTCAGCACCAGGGCCGCGCCGTCGTC
TCTGTCCGTGAGGTGCGAGCAGAGCAGCAAGCCGGGCGGCGGCAGCGTCGTCGACGTGTGGGCGAGCCGCCTGGCCATGA
TGAGCTTCGCCGCGGCGGTCGTCGCCGAGGTGTCCACCGGCAAGGGCTTTGTCGAG----GTACGCTCCCATGGATCGAC
CTGTCCTGTAACGCCTCGCTCTGCTGAGCTAGATGCTCGCTATTGACGGCGCTCTGCCCGCTTCGACGTGTTTTGCAGAA
TTTCGGCGTGGCAACGCCGGCGCCGGCGTTGGCGCTGGTGGTGACGGCGCTCGTCATCGGCCTGGCCGTCCTCTTCATCG
TCAGGTCCGGAGCGCAGGATTGATGGATCCATCGCACGAAATAATTGAAGACTCTTTTCTAG--TAGAATACAAAGTAAG
CGGAGACCTGTTTCTGAAGAACGAGCGTGCAGATCTTCTTTGCATCTGGTTTGCAAAGATTCCTGGAGATTATAATTAGC
ACTACTTCTGACTGTAAATGATCTGATGTATCATGGTACTACTGCTGTGAGCATATTCATATGGCAAATTCTGGTTCAAA
TTCAAGTGAGCCAAAGGCTTC---------TACCATTTTGTGTGTGA--------ATTCAGACTGATGCTCAAAGTTCAG
GTTCTAACACCCTGCTAATTATTCAGTTATGGAGTATGAATGTAATGTCCGTTCAGATATGTATATGCCATACATGAAGT
CCCCGAAATAAAAAAATTGCACATA--TAAAAGTAAGACATGCAAATGGACGAAAGATGTGTCTTGTGTAGAGTTATGTG
TCTGGGTAAACGTTGGTGGTACCTAGAGTCACCTGAATTCCTGATGGATTTGTTCTGCACCCAGATGATTGCTTTCTGGG
AACACTGGTCTTCCACTGGGGACATGAATACCTTTGATTTAGCCTTGTATTGATATGTACTTATGTGGTAGGTACACTGA
CTGTATGAACTTGCGATTGAAATGGAGGGAGTGCATCTTACACTTGGTAGGGTATACTGGAAGCGTGACGGCATGAG-TT
GTGCAAGTTTTGGGCCTGGCGATTTGCCTGCCTCGGAGTTGAGAAGGGGGGA-AAGAATCTGCCATGGGAGCTGTTACTT
GGTTTAAGAACCCACACAAAAATTGCATGTCCAGCACGGATTGAGATCCAGTGCCTTGACTGAGCCAAGGCACCAGCAAA
TAGTGTCGTGCCTTGCCCCCCATTTCTGTCCGTCGGATCAAGAATCGATGGTCGGATGAACATGAACAGGGGTACTGCTA
CAGGAACCATCCACAGTACAATCTGCTACAGAGTTCTTTCACAGATCGGTGCTACAGTACATAATCTACGGTGCGTGATC
TTGTCTGTCCATTTCCAATCCAACGGCCAAGTCAGCAAGGCA
>chr3A_1
CGCTTCCCTTCTCTTTCCCTTTATTTCCTCTTCGACCGCCGTGGATGACCTCTTGTATCCATGCGCCGTGCCCTCTTTCG
CCACTGGGACGACGAGTTACGACGGCGGCCATGGGAGGATGATGCGAATCCAGGAGGTTCAACACCGACAAGTGGTTCGA
TGCCTTGGGTGCGTGTCGCGTCGGTGCCAGTGGGGACAAACTAAGTTGCGACCGCCGGTGTGGGGGGGCATGCTGCAACC
GGCCATGATAGAGCTAGGGACCGTCGGTGCGGCGTGCTGCAACCCGTGGCGGGGCTGTATGCTGCAACCGGCAGTTGCAG
GATGCTTGAACCGGCTGGGAGGATGTTGCAATAGTGGTCGTACCCGACGATGGCGGCTGACAAGTGTTGCAACCGTGTTG
GCAAAAACTGGAACCATGAATCCACGGTCACTAGATGCTGGAACACGACTACCCGAAGCTTTTCCAGTGGTGACCACGAC
CCGCCGGGATGCTGCAACCGCTGTGTCTGGATATTGGAACCGGCACCCACCGTTGCGGCAACTGGCTTCGACGACGGCTA
CGGTGGGGCGCTACACCGACAATGAATGTTGGAACCGCAAGGCTGATTTGCTAGGACCGGCAGCTGGTTTTGCTGCAAAG
GGGCGGACCATGCGAGCACCGGCACCGCAACCGTCGGGCCGGCAAACGGTGCCACGATGTTGCAAGGGGAGGCGGTGGGA
GG-CGTGGGTGGCGACGAGCCGACGCACTGCG-CAACTACCGTGAGCGAGGAGAGAGGCGGCGATGCGTGTTTGCGTGCC
GGGAAAAAAGCCAGGTGCCAATCCGACGGCCAAGCGCATCCAAATCAAACACATCTTACAGCTGGGAGGCGACCGGCCCA
AAGCTGGCGCCGGTCGGCCGGCGCCCAGGGACATCACGTTTCTGGATTTATTAGTTGCAAGGCGTGCGCTGTCCGATCAT
TTT-TTCCGTGGATAGAGCGACGTCCAAACGGCCAACCGACGGCCACTCACTTCGGCTAGCTCAGGCCAGCAGCACAAAA
CCAA-CAAGCGAACGCGAGCGCAGGCCATCACATCCATCTCATGGCGCTCTTCTCCATCCTACGCTCGTCTCCGCTGGCC
GTCCCCGCGGCCTCTTCTAGCCGCCGCCCCAACCATGGTGTCTGCCTACTACGCGTCAGCACCAGGGCCGCGCCGTCATC
TCTGTCCGTGAGGTGCGAGCAGAGCAGCAAGCCGGGCGGCGGCAGCGTCGTCGACGTGTGGGCGAGCCGCCTGGCCATGA
TGAGCTTCGCCGCGGCGGTCGTCGCCGAGGTGTCCACCGGCAAGGGCTTCGTGGAGGTATGTACGCTCCCATGGATCGAC
CCGTGACGCCAT-----GCTCTGCTGGGCTAGTTGCTCACTATTGACAGCGCTCT---------GACGTGCTTTGCAGAA
CTTCGGCGTGGCAACGCCGGCGCCGGCGTTGGCGCTGGTGGTGACGGCGCTCGTCATCGGCCTGGCCGTCCTCTTCATCG
TCAGGTCGGGAGCGCAAGATTGATGGATCCATCGCACGAAATAATTGAAGACCCTTTTCTAGAATACAATACAAAGTAAG
CGGAGACCTATTTCTGAAGAACGAGCGTGCAGATCTTCTTTGCGTCTGGTTTGCAAAGATTCCTGGAGATTACAATTAGC
ATTACTTCTGACTGTAGATGATCTGATGTATCATGGTACTACTGCTGTGAGCATATTCATATGGAAAATTCTGGTTCAAA
TTCAAGTGAGCCAAAGGCTTCCGATGTTGCTACCATTCTGTGTGTGAAACTGTGAATTCAGACCGATGCTCAAAGTTCAG
GCTCTAACACCCTGTTAATGATTCGGTTA-----TATGATTGCAATGTCCGTTCAGATGTGTATATGCCATATATGAAGT
CCCTGAAATAAAAACATTGCATGTA--TAAAAGTAAAACATGCAAATGGACGAAACATGTGTCTTGTGTAGAGTTTTGTG
CGTGGGTCAACGTTGGTGGTACCTAGAGTCACCTGAATTCCTGATGGATTTCTTCTGCACCCAGATGATTGCTTTCTGGG
AACACTGGTCTTCCACTGGGGACATGAATACCTTTGATTTAGCCCTGCATG--TATGTA----TGTGGTAGGTACACTCA
CAGTATGAACTTGCGATTGAAAAGGAGGGAATGCATCTTACACT-------------TGGAAGCGTGACGGCATGAGATT
ATGCAAGTTTTGGGCCTGGCGATTTCCCTGCCTCGGAGTTGAGAAGGGGGAAAAAGAATGTGCCATGG------------
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>chr3D_8
--------TTCTCTTTCCCTTTATTTCCTCTTCGACCGCCATGGATGACCTCTTGTATCCACACATCGTGCCCTCTTTTG
CCACCGGGACGACGAGCTACGACGGCGGCCATGGGAGGATGATGTGAATCCAGGAGGTTCAGCACCGACAAGTGGTTCGA
TGCCTTGGGCGCGCGTTGCGTCGGTGCCAGCGGGGACAAACTAAGTTGCGGCCGCCGGTGTGGGGG-GCATGCTGCAACC
GGCCATGATAGAGCTAGGGACCGTCGGTGCGGCGTGCTGCAACCCATGGCGAGGCTGTATGCTGCAAACGGCAGTTGCAG
GATGCTTGAACCGGCTGGGAGGATGTTGCAATAGTGGTCGTACCCGACGATGGCGGCTAACAAGTGTTGCAACCGCGTTG
GCAAAAACTGGAACCACGAATCCACGATCACTAGATGCTGGAATGCGACTACCCGAAGCTTTTCCAGTGGTGACCATGAC
CCGACGGGATGCTGTAACCGATGTGTCTGGATATTGAAACCGGCACCCACCGTTGCGGCAACTGGCTTCGATGACGGCTA
TGGTGGGGCGCTACACCGACAACGAATGTTGGAACCGCAAGGCTGATTTGCTGGGACCGGCAGCTCGTTTTGCTGCAAAG
GGGCGGACCATGCGAGCACCGGCACCGCACCCGTCGGGCCGGCAAACGGTGTAACGATGTTGCAAGGGGAAGTGCTGGGA
GGCCGTGGGTGGCGACGAGCCGATGCGCTGCGACAACTACCGTGAGCGAGGAGAGAGACGGCGATGCGTGTTTGCTGT--
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>chr3D_763
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----------------------------------------------------------------------TTTGCGTGTG
GGGGGAAAGGCCAGATGCCGATCCAACCGCCACGCGCATCCAAATCAAACACATCTTACAGCTGGGAGGCGACCGGCCCA
AAGCTGGCGCCGGTCAGCCGGCGGCCAGGGACATCACGTTTCTGGATTTA---GTTGCAAGACGTGCGCTGTCCGATCAT
TTTTTTCCGTGGATAGAGCGACGTCCAAACGGCCAACCGACGGCCACTCACTTCGGCTAGCTCAGGCCAGCAGCACAAAA
CCAAACAAACGAGCGCGAGCGCAGGCCATCGCATCCATCTCATGGCGCTCCTCTCCATCCTACGCTCGTCTCCGCTGGCC
GTCCCCGCGGCCTCTTCTCGCCGCCCACCCAACCACGGCGTCCACCTACTACGCGTCAGCACCAGGGCCGCGCCGTC---
TCTGTCTGTGAGGTGCGAGCAGAGCAGCAAGCCGGGCGGCGGCAGCGTCGTCGACGTGTGGGCGAGCCGCCTGGCCATGA
TGAGCTTCGCCGCGGCGGTCGTCGCCGAGGTGTCCACCGGCAAGGGCTTCGTGGAGGTATGTACGCTCCCATGGATCGAC
CCGTGCCACCAT-----GCTCTGCTGGGCTAGTTGCTCGCTACTGACAGCGCTCT---------GACGTGCTTTGCAGAA
CTTCGGCGTGGCAACACCGGCGCCGGCGTTGGCACTGGTGGTGACGGCGCTCGTCATCGGCCTGGCCGTCCTCTTCATCG
TCAGGTCGGGAGCGCAAGATTGATGGATCCATCGCACGAAATAATTGAAGACCCTTTTCTAGAATACAATACAAAGTAAG
CGGAGACCTATTTCTGAAGAACGAGCGTGCAGATCTTCTTTGCATCTGGTTTGCAAAGATTCCTGGAGATTATAATTAGC
ATTACTTCTGACTGTAAATGATCTGATGTATCATGGTACTACTGCTGTGAGCATATTCATATGGAAAATTCTGGTTCAAA
TTCAAGTGAGCCAAAGGCTTCCGATGTTGCTACCATTCTGTGTGTGAAACTGTGAATTCAGACCGATGCTCAAAGTTCAG
GCTCTAACACCCTGTTAATGATTCGGTTA-----TATGATTGCAATGTCCGTTCAGATGTGTATATGCCATATATGAAGT
CCCTGAAATAAAAACATTGCATATCTCTAAAACTAAAACATGCAAATGGACGAAACATGTGTCTTGTGTAGAGTTGTGTG
CCTGGGTAAACGTTGGTGGTACCTAGAGTCACCTGAATTCGTGATGGATTTCTTCTGCACCCAGATGATTGCTTCCTGGG
AACACTGGTCTTCCACTGGCGACATGAATACCTTTGATTTAGCCCTGTATTTATATGTA----TGTGGTAGGTACACTCA
CAGTATGAACTTGCGATTGAAATGGAGGGAGTGCATCTTACACTTGGCAGGGTATACTGGAAGCGTGACAGCATGAGATT
ATGCAAGTTTTCGGCCTGGCGATTTCCCTGCCCCGGAGTTGAGAAGGGGGAA-AAGAATCTGCCATGGGAGCTATTACTT
GATTTAAGAACCCACACAAAATTTTCAGTGTTCAGCA-------------------------------------------
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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-----------
------------------------------SS---------------------------S--------------------
---S-----------S-S-----------------------------------S-----------SS------S------
---S----------------SS-----------S-----------------------------S---S------------
---S--------S---------------S--------------S---------S--S-----S-----------------
----------SS-S----S----S---S---------------------S------------------------------
--S----S----------------SS--SSS-SS---------------------------S----S-------S-----
-----------S---------------------------------------------------S-----S----------
--S-------------------------------------------------------------------------S---
----------------------SS--------------------------------------------------------
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--------------------------------S--------------------------------------------S--
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-------------------------------------------------S--S---------------------------
-S--S-S-SS-SSSSSS---------S-----S--------------S-------SSSSSSSSS------S---------
S-------------------------------------------------------------------------------
-------S--------S-----------------------------------S-------------S-------------
---------S----------------------------------------------------------------------
-S--------------------------------------------------------------S---------------
-------------------------------------S-------------------------S----------------
-S------------S----S----S----SSSSS-----S--S---------------S-------------S-------
---S----------S------S--------------S------------------S-------------------S----
S--------------------------------------------------S----------------------------
--------------------------------------------S------S-------SSSS---------------S-
-S---------------------------------------------S--------------------------------
S------------------------S------------------------S----------------------S------
-S-------------------S--S--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_416
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----------------------------------------------------------------------------GTTG
GCAGAAACTGGAACCG----------------------------------------------------------------
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>reverse_2366
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---------------------------------------------ATCCAGTGCCTTGACTGAGC---------------
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