>input_sequence_74862
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--------------------GACCACCGCGCCGAACAACTCTCACCGGA--ACGCAGCAAATTCCCCAGCCTTCCCTCGA
CCCAGATCCGCAAAATGGCCCGCACGAAGCAGACCGCGCGCAAGTCGACCGGCGGCAAGGCCCCGCGGAAGCAGCTGGCG
ACCAAGGCGGCGCGCAAGTCGGCGCCGGCGACCGGCGGCGTGAAGAAGCCCCACCGCTTCCGCCCCGGCACCGTCGCGCT
CCGCGAGATCCGCAAGTACCAGAAGAGCACCGAGCTGCTCATCCGCAAGCTGCCCTTCCAGCGCCTCGTCCGGGAGATCG
CGCAGGACTTCAAGACCGACCTCCGCTTCCAGAGCTCCGCCGTGTCCGCCCTGCAGGAGGCCGCCGAGGCCTACCTCGTG
GGGCTCTTCGAGGACACCAACCTCTGCGCCATCCACGCCAAGCGTGTCACCATCATGACCAAGGACATCCAGCTCGCCCG
CCGCATCCGCGGGGAGCGCGCGTAGGCGCCCTCTCGCTCCTGCTTGATCTCTTCATGCCTCATCGTGCCATGATCTAGCC
GTGCTGTAGTTTTTAGTATGTGCAATGGATGTATGAAT------------------------GAAAAGTATGCATATCT-
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>chr3D_1_TraesCS3D01G266000
TGATCCCTCTAGGTACATCTTCTACGCTTTGTGAGTTGATCAAGTTGATTCACTCTTGACTTAGTCTTGATCAACCATGA
ATCTTTTCAACTCTCTTCATTTAGATGATGTCTTGAAGATATACATGAATGATCACACAATCTTCTTCTTCAAGACATGC
TTGCAATAAGCTCAACTCTCACATGACCAATCTCTGAATAATTCCTTAATAACAACTTGGTCACCACATAAACTCCTTGA
AACCAACACATGAACTTCAAGAAATGCCTATGGACAAATCCTTCAAATATAACTCAAGGCAACTATTAGTCCATAGAGAT
TGTCATCAATTACCAAAACCAAACATGGGGCACCGTATGTTCTTTCAAAATGTATAAAATTCAGGACACAAATGAAACAA
AAACAATTTATATGGTTTGGAGGGAAATTATATCCCAACATACAAAAAATTGAATAAAGGCAAAAAGATATAGTCATCGC
AGTCGAACGTCCGGAAATTGGAATGAAGATGAAAAATACCTACTAAATAATTGAGATCCCTAAATAATTCAACAGGAATC
ACAATGGGAGATCGGCCGGCAAGAAAATTTGAGTGAAACAAATTGAAATTAGTCATATGGAATATACGTAGCAAATATGT
TCATCGCCGCTGC------------------------------AAAAAAAATGTTTTCTTTAATCATCACCTAGTGAGCT
CTCGCATTGCTAGTGCTAGCCAAACACTGCTCACA---------------------------------------------
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---------------------------------------------------------GGGCTCATGGATGGCGATCCGAC
GGCTGCCACGCCAAGAGGGCAAACAGCACAGCGATAATCCCACGGATCGCGATCCGTGGCCAACCTTCCTAACACACATC
GCCACCGTCCAATCCTCCGTAGTCCAGCGGCTGACCCAGGCCCGCGTTCCTCCGGTGCCGTGGCGCGCTGAGGCTCCCCA
AAATCCCCAAAATTTCATGGTACGCGC------GCGCCCGCCGGCCAAACC--CGCCCCTACTTAACCCCGGCGAACCCC
CCACAGATGACAGATCACCAGACCACCGCGCCGAACAACTCTCACCGGA--ACGCAGCAAATTCCCCAGCCTTCCCTCGA
CCCAGATCCGCAAAATGGCCCGCACGAAGCAGACCGCGCGCAAGTCGACCGGCGGCAAGGCCCCGCGGAAGCAGCTGGCG
ACCAAGGCGGCGCGCAAGTCGGCGCCGGCGACCGGCGGCGTGAAGAAGCCCCACCGCTTCCGCCCCGGCACCGTCGCGCT
CCGCGAGATCCGCAAGTACCAGAAGAGCACCGAGCTGCTCATCCGCAAGCTGCCCTTCCAGCGCCTCGTCCGGGAGATCG
CGCAGGACTTCAAGACCGACCTCCGCTTCCAGAGCTCCGCCGTGTCCGCCCTGCAGGAGGCCGCCGAGGCCTACCTCGTG
GGGCTCTTCGAGGACACCAACCTCTGCGCCATCCACGCCAAGCGTGTCACCATCATGACCAAGGACATCCAGCTCGCCCG
CCGCATCCGCGGGGAGCGCGCGTAGGCGCCCTCTCGCTCCTGCTTGATCTCTTCATGCCTCATCGTGCCATGATCTAGCC
GTGCTGTAGTTTTTAGTATGTGCAATGGATGTATGAAT------------------------GAAAAGTATGCATATCTG
TTTACCTTTCTCTCTGCTTAATCATATGTTCAGAATTGTTGGTGTTGTTTGGGCAATGGGAACTGAACAATCTGCACTTG
AAACCGGAGTTGCTCCTAAAATTTGGATAAACAACAGGA-TCTTCCAATCTCGATCC---TAGACATGGGAAACAATCCG
GTGTCGCCAGCACGTAAGCCGACGGTAGAAGACGCCCCAAATTCCATCCGGCAGGCGAAGCGAAATAATTCGGATGCGCG
GCTCGCCGTTTCCCAGCTCGCCCGAGGAAGCCGAAGACGTGCTCATGCGCGTATCGTTCTGCCGCGCGACTGCTCCAAGA
TGCGGGAGGACATGCTCGTGCGCATATCGGGCTGCTGGAACCCCGGAACTCGGCCGTTCAGGCGCCCTCAGACGAGATAG
ACGCGCGACTGGTCGCGATATTAGCTCCAGATGCTGTCTTCATGATGGATGAATGGTAG---------------------
-TACCAGTTTAACCAATTTATCATTTT-CTAGTTCAGTGGTAAATTAGCCCCATCTGGTTTGGTT-CAAGGTACACATTG
---CGTCAGCTTGTTTGTGGTGCTCAGAGCATTTTCAGCAGCTTCCCCACAAAAAAGAAAAAATTCTCCCCCTACAGATG
AATCCATGGAGGGTCATCATTGAATTGACTAGTTTTGGAAATGAC------------------ATTTTAATTTCTAGCTA
AGCTTAACTCATGCATAGTTCCAGATAACCTGATTAGTTGCAAAAAAGGGTTAGAAATGCATATGAATATATAACCAACT
TCAACACTATACTCAAACAGACATGTCCGGATGTGTTGGCCCACAACTTTACGGAAGCTGATCATCCAACCTGATGTATC
AAATAAAAGCGAACACTACATTTTTCAATAATATTGAGTTTTTTTTACATAGAAAATTAAAACCGGTCCAAGTCTACTCT
TCATCGGAGCGCACGTTAATGTTCCACGACTCCATGTCGTACTCCCCGTTGGAGATCGTCGGTGGAGGTCAGGTCGACAA
TCAAATCG
>chr3A_400
AAAACATG------------------------------------------------------------------------
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-------TTATATGGTTTGAAGGGAAAGTGTAACCCAACATACAAAGTTA-GAATATAGGCAAAAAGATATAGTCATTGC
AATCGAACGTCAAGAAATTAGAATGAAGGTGGAAAAGACCAACTAAATA-----------------ATTCAGCAGGAATC
ACAATAGGTGATCGGACTGCAAGAAA-TTTGAGTGAAACAAATTGAAATTAGTCGTATGGAAAATACTACTCCCTCTACA
CGCAAAAAAAATACTACTCCCTTGGATGGAAATAAGTGCTGAAAAAAAAAACGTTTTCCTTAACCATCCCCTAGTGAGCT
CTCGCATTGCTAGTGCTAGCCAAGCACTGCTCACGGGTAGTCCTGGCCATCTCAGGCCCGGCCCTGTCGGCCCACCCAGG
CCCGACCCTAAAATCCAGGACCTAGGCCCGATGAGTTTGTCCATGGGCCGGGCTTGGGCCTGAGTTTTGAGCCCATCAAC
AGGGCCTGGACGGGCATGTGCTTGACATATTGGCATTTTAAGGAAGAGGCCCGGCCCACAGCCCTAAGCCCTAAGGGTTT
TTCAGGGCTTTTTACGAGATGGGCCGGGCTTGGGCTTGAAAAGTAGGCCCGATGGTAAGGCCTGGGAGGGCCTGGGCCTC
AGTTTTCTGCCATGGGCTTTTTTAGGCCCGGCCCGGCCCATGGCCAGATATACTCACGGGCTCATGGATGGCGATCCGAT
GACTGGCACGCCAAGAGAGCAAACAACACATGGTTAGTCACACGGATCGCGATCCGTGGCCAACCT-CCTAGCGCACATC
GCCACCGTCCAACGCTCCCTAATCCAGCGGCTGACCCAGGCCCGCGTTCCTCCGGTGCCGTGGCGCGATGAGGCTTCCCA
AAATCCCCAAAATTTCATGCTATGCGCCGCGCCGCGCCCGCCGACCAATTCCGCGCCCCTACTTAACCCCGGCGAACCCG
TCCCA------AGATCCTCAGACCACCGCGCCGAACAACTCTCTCGCCAGCACGCAGCAAACTCCCCAGCCTTCCCTCGC
CCCGGATCCGT-AAATGGCCCGCACGAAGCAGACCGCGCGCAAGTCGACCGGCGGCAAGGCCCCGCGGAAGCAGCTGGCG
ACCAAGGCGGCGCGCAAGTCGGCGCCGGCGACGGGA-GCGTGAAGAAGCCCCACCGCTTCCGCCCCGGCACCGTCGCGCT
CCGCGAGATCCGCAAGTACCAAAAGAGCACGGAGCTGCTCATCCGCAAGCTGCCCTTCCAGCGCCTCGTCCGGGAGATCG
CGCATGACTTCAAGACCGACCTCCGCTTCCAGAGCTCCGCCGTCTCCGCCCTGCAGGAGGCCGCCGAGGCCTACCTCGTG
GGGCTCTTCGAGGACACCAACCTCTGCGCCATCCACGTCAAACGCGTCACCATCATGCCCAAGGACATCCAGCTCGCCCG
CCGCATCCGCGGGGAGCGCGCGTAGGCGCCCTCTCGCTCCTGCTTGGTCCCTTGAGGCCTCATCGTGCCATGATCTAGCC
GTGCTGTAGTTTTTAGTATGTGCAATGGATGTATCATGTGTTCTCTAAGTTATTATATGAATGAAAAGTACGCAGCTCTG
TTTACCTTTCTCTCTGCTTAATCATATGTTCAGAATTGTTGATGTTGTTTGGGCAATGGGAACTGAACAATCTGCACCTG
AACAAT-AGTCGCTACTAAAATTTGCATAAACA---GGAATCCTCCAATCTCTATCCATCTAGATCTGGGAAACAATCCG
--GCCGTCAGCACGTAAGCCGACGGTAGAAGCCGCCCCAAATTCCATCCGGCAAGCGAAGCGAAACAATTCGGGTCTGCG
GCTCGACGTTTCCCAGCTCGCCCGAGGAAGCGGGAGACGTGCTCATGCGCATATCGTTCTGCCGCGCGACTGGTCCAAGA
TGCGGGAGGACATGCTCGTGCACATATCGGGCTGCTGGAACCCCGGAGCTTGGCCGTTCAGG----------CGAGATAG
GCGCGCGACTGGTCGCGATATTAGCTCCAGAG---------ATGATGGATGTATGGTAG---------------------
-TACCAGTTTAATCAATTTATCATTTT-CTAGTTCAGTGGTAAATTGGCCCCATCTTGTTTGGTT-CAAGGTACAAATTG
TTGCATCAGCTTATTTGTGGTGCTCAGAGCATTTTCAGCAGCTTCCCCACAAAAAAAAAACT------CCCCTACATATG
AATCCCTGAAGGGTCGTCATTGATTTAACTAGTTTTGGAAAGGA------------------------------------
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>chr3B_703
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------------GTGCTAGCCAAGCACTGCA-------------------------------------------------
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------------------------------------------------------CACGGGCTCATGGATGACGATCCGAC
GGCTGGCACGCCAAGAGAGCAAACAGCACACGGTTAGTCACACGGATCGCGATCGATGGCCAACCT-TCCAGCGCACATC
GTCACCGTCCAACCTTCCCTAATCCAGCGGCTGACCCAGCCCCGCGTTCCTCCGGTGCCGCGGCGCGATGAGGCTTCCCC
AAATCCCCAAGATTTCATGGTACGCGC------GCGCCCGCCGGCCAAATCCGTGCCCCTACTTAACCCCGGCGAACCCC
TCCCA------AGATCCTCAAACCACCGCGCCG---AACTCTCTCGCCACCGCGCAGCAAACTCCCCAGCCTTCCCTCGC
CCCAGATCCGC-AAATGGCCCGCACGAAGCAGACCGCGCGCAAGTCGACCGGCGGCAAGGCCCCGCGGAAGCAGCTGGCG
ACCAAGGCGGCGCGCAAGTCGGCGCCGGCGACGGGCGGCGTGAAGAAGCCCCACCGCTTCCGCCCCGGCACCGTCGCGCT
CCGCGAGATCCGCAAGTACCAGAAGAGCACCGAGCTGCTCATCCGCAAGCTCCCCTTCCAGCGCCTCGTCCGGGAGATCG
CGCAGGACTTCAAGACCGACCTCCGCTTCCAGAGCTCCGCCGTCTCCGCTCTGCAGGAGGCCGCCGAGGCCTACCTCGTG
GGGCTCTTCGAGGACACCAACCTCTGCGCCATCCACGCCAAGCGCGTCACCATCATGCCCAAGGACATCCAGCTCGCCCG
CCGCATCCGCGGGGAGCGCGCGTAGACGCCCTCTCGCTCCTGCGT-------------CTCATCGTGTCATGATCTAGCC
GTGCTGTAGTTTTTAGTATGTGCAATGGATGTATCAATTGTTCTCTAAGTTATTATATGGATGAAAA------AGCTCTG
TTTACCTTTCTCTCTGCTTAATCATCTGTTCAGAATTGTTGATGTTGTTTGGGCATTGGGAACTGAACAATCTGCATCTG
-AACCGGAGTTGCTCCTAGAATTTGCATAAACAACAGGAATCTTCCAATCTCCATCCACCTAGACCTGGGAAACAAACCG
GCGCCGCCACCACGTAAGCCGACGGTAGAAGACGCCACAAATTCCATCCGGCAGGCGAAGCGAAACAATTCCGATGCGCG
GCTCGCCGTTTCCCAGCTCGCCCGAGGAAGCCGGAGACGTGCTCATGCGCATATCGTTCTGCCGCGCGACTGCTCCAAGA
TGCAGGAG--------------CATATCGGCCTGCTGGAACCCCGGAGCTCGCCTGTTCAGGCGCGCTCGGACGAGATAG
GCGCGCGACTGGTCGCGATATTAGCTCCAGATGCTGTCTTCATGATGGATGAATGGTAGAACTCGAGCGATAAGTGGCCT
TTACCAGTTTAAACGATTTATCATTTTTCTAGTTAAGTGTTAAATTGGCCCTATCCGGTTTGGTTCCAAGGTACACATTG
TTGCGTCAGCTTATTTGTGGTGCAGAGAGCATTTTCAGCAGCTTCCTCACCAAAAAAAAAAA---CTCCCTCTACAGACA
AATCCATGGAGGGTCATCATTGAATTGAGTAGTATTTTTTTTTTGCCAAAAAAATATTTTAGTATTTTAATTTTTAGCTA
AGCTTAACTCATGCACAGTTCTAGATAACCTGATTAGTTGCT-AAAATGGTTAGAAATGCATGTGAA-------------
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>SNPs
SS-S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSS------------S-------S-S--S-------------SSSSS-----S--------------------S--
-S---------SS------S--------S--S----S---S--------SSSSSSSSSSSSSSSSS-----S--------
-----S--S------S-S--------S---------------------------S-------S----SSSS-SSSSSSSS
SSSSSSSSSSSSS--------------------------------------S------S----S----S-----------
-----------------------S----------S---------------------------------------------
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-----S-----------S------------SS-S--S--S--------------------------S----S-S------
------------S-----S--S---------------------------------------------S-------S----
-------------------------------------------------S------------------------------
S-S--SSSSSS-----SS-------------------------S-SSS-------------S-----------------S
-----------S--------------------------------------------------------------------
--------------------------------S-----------------------------------------------
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-------------------------------------------S------------------------------------
--------------------------------------------S------------S----------------------
----------------------------------------------S--S---S-S------------------------
----------------------------------S-----------------------------------S---SS----
-----------------------------------------S-----------------------------------S--
-------------------------S--------------------------S------------S--------------
-S-S-------------------------------------------------------------S--------------
---------------------------------S----------------S-----------------------------
---------------------S-------------------------S-----------------S---S----------
S-------------------------------------------------------------------------------
------------S---------------------------------S---------------------------------
------------S-------------------------------------------S-----SSS---------------
--------------------------------------------S----------------------------S------
---------------S-----S-------------------SS----S--------------S----SSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSS
>forward_1222
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--CACCGTCCAATCCTCCGTAG----------------------------------------------------------
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>reverse_2962
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-CATCGGAGCGCACGTTAATG-----------------------------------------------------------
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