>input_sequence_58719
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----------------------------------------------ATGCGTGCGATGGGACGCGAGGCAGCAACGGCAG
TGGCGTGCTCCTCCAACAAGCCCAAGCTGCGGAGAGGGCTGTGGTCGCCGGAGGAGGACGAGAAGCTCTACAACCACATC
ATTCGCTACGGCGTCGGTTGCTGGAGCTCCGTCCCAAGGCTCGCCGGTGGGTAACGTAATCTCTTCATTCATATATGCCC
ATGCTGCTATGTACTATCTCTTGCTTGACCAAGAACTCAAATGTGTTTCCCTTAATTGTTCAGGGTTGGAGAGATGTGGT
AAGAGCTGCAGGCTAAGATGGATCAACTACCTCAGGCCTGATCTCAAGAGGGGCAGCTTCTCCCAGCAGGAGGAGGACCT
CATCGTCAGCCTGCACAAGATCCTCGGCAACAGGTAGTACAATTAGTAAGTTTTATTAGTGAGTTCACTGTTTTCCGATG
TTGATCGGAACTTGAGAAGCAGGTAAGTACGTACAGTAGTATATAGACGACGATGTTGCATACAGAAACACGTCGACACG
CCTCAACTGCACTACTCCTTTATGTTGGTTGTCAGGTGGTCCCAGATAGCGTCGCAGCTGCCAGGCCGGACCGACAACGA
GATCAAGAACTTCTGGAACTCGTGCATCAAGAAGAAGCTCCGGCAGCAGAGCATCGACCCCACCACCCACGAACCGCTCA
ATGACGCTGCCGCTGTCGCCGAGCCGCACGATGAGTGCAAGCAGCTAGTCCCCGCTGCGGAAGACGGC---------GGC
TCCGTTGGCAGCGACGATCTCCTAGCGCCGCACTCCCCGGTCGACTGCAGCTTCGATCCCATGTCCGTGACAAACGTCCC
CACAATGCACATGCAGGGCTCCTATTCCTTGTGTGACC------------------ACGCCTCCACGTACTGCGCCTACA
CAGGCGGCGGCGACAGCTCCAGCAACAGCAACGGCACCGGCACCGGCACCAGCACCTGGACCTGCGGCAATGTGGAGCCG
CTCCCGCACATGGACATGTTCCG---CGACG---CCGAGCCGTACCCATTCGACCCGACCAAGTTCAGCCCGTGGCACCA
GCAGCACGCGCCGGACGACGACCGCGGCTCCGCGGTCTTCCCGATCCGCTCGCTGTCCCGGGACCTGCCCGAGTCGTGCT
TCGAGCTCGCCCGTGGAGCCTTGGAGGACGAGTTCGACTTCATGTGA---------------------------------
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>chr3A_1_TraesCS3A01G200300
TTTCAGAGGAAGGATTCGAGAGTTCTACTGGCCTCGTTGCTACCCTCCTGGGGGCTGCCTCCA-GTTGGCGGCGCAGGCG
GTGTTCCCTCGTGTCATCCAATAGAGGTGGCGCGGCCGCTGGGATGGATTGTTCGCCAGATAGTGCTCGTTGGTGAAAAT
GTTGGGTCAGAAACTAATCGAGAAATGATGAATGATTATATTTTCAAATGATATGTACATGCATGCAACTAGACTCTAGG
CTTTGCTATCCCGGTCCACCCCGGCCATAACTAACAGCTCCAAGATTGCAGGCGACATTAAAGACACACATATTTACACA
TGTACAATAATCAGTGTGACATAAAGTCCAACTAACCATGTCGGAGAATTGAAGGGAAAGGAGCTAGAAAAAGGGCAAGG
AGGTTACCAACAATAATGATAAAAGGCTAAGCACCTTTATACAGTACACTAGACAGATGCCAACGACGATGGGGATGAGA
TGGTGCATGGGGCGGGCACATGCAGCTTGCTGGGTTTGTTGGCATGAGAGATTGATTATTGTACTTGATGGACTCTTCCC
CGCAACTCAAGCTATCTTACCTTAAATCCAACCTCCGGCCCCATCCATTAGGCCTGCCCACGGGGGCCTTGCCTATTTTC
AGTTGCTTCAACCCCACTTTACTATATGTTGCCCCCGCCTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
TCTCTCTCTCTCTCTCTCTCTTGCACAGCGGAGTGGCCCTTTTCTTTTCTTGAGTGAGCTAGCTAGCTCAGCTCCACTTT
AATTTGATTGTTAATTAAATCATTATACTATTATCTTAAGGCTCAAGCATTGTTGGAACTGCTTCTGTCTGTCTGTGTGT
GG-----CGAGATAAGTGTCGCTTTTATATCGCCTGTGCCCTGCCCTGCCGTGTCTCACCATCATTGTTGCCATCACAGG
CCGCTACCGCGCTCGCTCACTAGTCACTCCACCCGGGAGCACGCATATGCGTGCGATGGGACGCGAGGCAGCAACGGCAG
TGGCGTGCTCCTCCAACAAGCCCAAGCTGCGGAGAGGGCTGTGGTCGCCGGAGGAGGACGAGAAGCTCTACAACCACATC
ATTCGCTACGGCGTCGGTTGCTGGAGCTCCGTCCCAAGGCTCGCCGGTGGGTAACGTAATCTCTTCATTCATATATGCCC
ATGCTGCTATGTACTATCTCTTGCTTGACCAAGAACTCAAATGTGTTTCCCTTAATTGTTCAGGGTTGGAGAGATGTGGT
AAGAGCTGCAGGCTAAGATGGATCAACTACCTCAGGCCTGATCTCAAGAGGGGCAGCTTCTCCCAGCAGGAGGAGGACCT
CATCGTCAGCCTGCACAAGATCCTCGGCAACAGGTAGTACAATTAGTAAGTTTTATTAGTGAGTTCACTGTTTTCCGATG
TTGATCGGAACTTGAGAAGCAGGTAAGTACGTACAGTAGTATATAGACGACGATGTTGCATACAGAAACACGTCGACACG
CCTCAACTGCACTACTCCTTTATGTTGGTTGTCAGGTGGTCCCAGATAGCGTCGCAGCTGCCAGGCCGGACCGACAACGA
GATCAAGAACTTCTGGAACTCGTGCATCAAGAAGAAGCTCCGGCAGCAGAGCATCGACCCCACCACCCACGAACCGCTCA
ATGACGCTGCCGCTGTCGCCGAGCCGCACGATGAGTGCAAGCAGCTAGTCCCCGCTGCGGAAGACGGC---------GGC
TCCGTTGGCAGCGACGATCTCCTAGCGCCGCACTCCCCGGTCGACTGCAGCTTCGATCCCATGTCCGTGACAAACGTCCC
CACAATGCACATGCAGGGCTCCTATTCCTTGTGTGACC------------------ACGCCTCCACGTACTGCGCCTACA
CAGGCGGCGGCGACAGCTCCAGCAACAGCAACGGCACCGGCACCGGCACCAGCACCTGGACCTGCGGCAATGTGGAGCCG
CTCCCGCACATGGACATGTTCCG---CGACG---CCGAGCCGTACCCATTCGACCCGACCAAGTTCAGCCCGTGGCACCA
GCAGCACGCGCCGGACGACGACCGCGGCTCCGCGGTCTTCCCGATCCGCTCGCTGTCCCGGGACCTGCCCGAGTCGTGCT
TCGAGCTCGCCCGTGGAGCCTTGGAGGACGAGTTCGACTTCATGTGACCCCGCCACGCCCAGGCCGAGCTCATGTGTCCA
TCG------TTCCACAACCACAAACTCACACATATACAAACCTCACTACACCACCTGATGAGATGAGAAGATTGATCACC
GCTGAGAGGACCATGTGGTTTGACCACACCTATACTTTATTTCCTCTCCTCATTTTT-CTCTCTCTGCCTTTCGACCCTT
TCCCTCGAAAAAGAAGTACTTATTCAACGAAGCTGTTTAATTAATGAATACAATGGTACTCCCTCTGTAAACTAATATAA
GAGCGTTTAGATTACTAAAGTAGTGATCTAAACACTCTTATATTAGTTTACGGAGGGAGTATATACTAGAGTATATAGTA
TTGTGATCATAATAAGGGTTAGTAAATATGCATGTATACGTACCCCAATTCAGGAGGGTTTCATGTTTTGTATTCCCTCC
GTTCCTAAATATTTGTCTTTCTAGAGATTTCAACAAATGACTGCATACGAAGCAAAATGTTCACACTCTGAAATATGCCT
ATATACATCCGTGTGTGATAGTCCATTTGAAATCTTAAAAAAACAAATATTTAGAAACGGCGGGAGTATGGGAACAGTTT
AGCAACATCGGTCCATGGAATTTTAAAGCAAGTCTTTTTACCTCTTGCACTCCATCCATGGACTGCGCCCTTGGCGAAGT
ACGTGGCAAACAAGACTAGGCCTCACAATTATTAGGACGTACTTCCTTCATCCGGAATTACTTGTCGCCGAAATAGATAA
AACTGGATGTATTTAGAACTAAAATATATCTAAATACATTCATTTCTTTGACAAGTATTTCTGGACGGAGGAAGTACGTA
CTACATGGTCACTGTGTGGCGAAGTCGTGTAGCATGAGCGCGACACCGCGCGGGCAAAGTCTTGAATACGTTGTTGCTTT
GGCAACGACGTGGCAAGGCGGGGATGTACGGGGCAGCCGCGACGCAGCGTAAAGAAGCGTCAATCACATGATGTCTTGTC
GCCCCCTTTGCACG
>chr3B_1
TTTCAGAAGAAGGATTCGAGAGTTCTATAGGCCTCGCCGCTACCCTCCCTGGCGTCTGCCTTCGGTTGGCGGCGCAGGCG
ATGTTCCCTCGTGTCATCCAATAGAGGCGCGACC------GGGATTGGTTGTTCGTCTGATAGTGCTCGCTGGTGAAAAT
GTTGGGACGGAAACTAACCGAGAAATGATGAATG-TTATATTTTCAAATGATATGTACATCCATGCAACTAGACTCTAGG
CTTTGCTATTCCGGTCCACCCA-GCCCTAGCTAACAGCTCCAAGATTGCAGGCGAAATTAAACACATGCATATTTACACA
TGTACAATAATCAGTGTGACATAGAGTCCAACTAATCAAGTCGGAGAATTGGAGGGAAAGGAGCTAGAAAAAGGGCAAGG
AGGTTACCAACAATAATGATAAAAGGCTAAGCACCTTTATACAGTACACTAGACAGATGACAACGACGATGCGGATGAGA
TGGTGCATGGGGCGGGCACATGCAGCTTGCTGGGTTTGTTGGCATGAGAGATTGATTATTGTACTTGATGGACTCTTCCC
CGCAACTGAAGCTACCTTACCTTAAATCCAACCTCTGGCCCCATCCATTAGGCCTGCCCACGGGGGCCTCGCCTATTTTC
AGTTGCTTCAACCCCACTTTACT-TATGTTGCCCCCCTGCTCTCTCTCTCTCTCTCTCTCACACACACACACACACACAC
A----------------------CACAGCGCAGTGGCCCTTTTCTTTTCTTGAGTGAGCTAGCTAGCTCAGCTCCACTTT
AATTTGATTGTTAATTAAATCTTTATACAATTATCTTAAGGCTCAAGCATTGTTGGAACTGCTTG----TGTCTGTGTGT
GTGTGGCCGAGATAAGTGTCGCTTTTATATCGCCTGTGCCCTGCCCTGCCGTGTCTCACCATCATTGTTGCCATCACAGG
CCGCTACCGCGCTCGCTCACTAGTCACTCCACCCGGGAGCACGCATATGCGTGCGATGGGACGCGAGGCGGCAGCAGCAG
TGGCGTGCTCGTCCAACAAGCCCAAGCTCCGGAGAGGGCTGTGGTCGCCGGAGGAGGACGAGAAGCTCTACAACCACATC
ATTCGCTACGGCAACGGTTGCTGGAGCTCCGTCCCAAGGCTCGCCGGT----AACGTAATCTCTTCATTCATATATGCCC
ATGCTGCTATGT---ATCTCTTGCTTGACCAAGAACTCAAATGTGTTTCCCTTAATTGTTCAGGGTTGGAGAGATGTGGC
AAGAGCTGCAGGCTAAGATGGATCAACTACCTCAGGCCTGATCTCAAGAGGGGCAGCTTCTCCCAGCAAGAGGAGGACCT
CATCGTCAGCCTGCACAAGATCCTCGGCAACAGGTAGTACAATTAGTAAGTTTTATTAGTGAGTTCACTGTTTTCTGATG
TTGATCGGAACTTTAGAAGCAGGTAAGTATATACAGAAAC------ACGACGATATTACATACAGAAACACGTCGACACG
CCTCAACTGCACTACTCCTTTATGTTGGTTGTCAGGTGGTCCCAGATAGCGTCGCAGCTGCCAGGCCGGACCGACAACGA
GATCAAGAACTTCTGGAACTCGTGCATCAAGAAGAAGCTCCGGCAGCAGCGCATCGACCCCACCACCCACGAATCGCTCA
ATGACGCTGCCGCTGTCGCCGAGCCGCACGACAAGTGCAAGCAGCTAGTCCCCGCTGCGGAAGACGGCTGTTTCGGCGGC
TCTGTTGGCAGTGACGATTTCCTAGCGCCACACTCCCCGGTCGACTGCAGCTTCGACCCCATGTCCGTGACAAACGTCCC
CGCAATGCGCATGCAGGGCTCCTACTCCTTGTGTGACTACGCCGGCGTCGGCTCCGACGCCACCACGTACAGCGCCTACA
CAGGCGGCGGCGACAGCTCCAGCAACAGCAACGGCACCGGCACCGGCACC------TGGACCTGCGGCAATGTGGAGCCG
CTCCCGCACATGGACATGTTCCGCGACGACG---CCGAGCCCTACCCATTCGACCCGACCAAGTTCAGCCCGTGGCACCA
GCAGCAACCGCCGGACGACGACCGCGGCTCCGCGGTCTTCCCGATCCGCTCGCTGTCCCGGGATCTTCCCGAGTCGTGCT
TCGAGCTCGCCCGTGGGGCCTTGGAGGACGAGTTCGACTTCATGTGACCCCGCCACGCCCAGGCCGAGGTCATGTGTCCA
TCGTTCG------ACAACCACAAACTCACACATATACAAACCTCACTATACCACCTGATGAGATGAGAAGATCGATCACC
GTTGAGAGGA-CATGTGGTTTGACCACACCTATACTT-ATTACCTCTCCTCATTTTTTTTCTCTCTGCATTTCAACCCCT
TCCCTCGAAAAA-AAGTACTTAT---------------------------------TATATAAGTAC-------------
-----------------------------------------------------------------------TATATAGTA
TTGTGATCATAATAAGGGTTAGTAGATATGCATGTATACGTACCCCAATTCAAGGGGGTTTCATGTTTTGTATGGGAG--
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--------------------------------------------------------------------------CAGTTT
AGCAACATCGGTCCATGGAATTTTAAAGCAAGTATTTTTACCTCTTACACCCCATCCATGGACTGCGCCCTTCGCAAAGT
AC------------------------------------------------------------------------------
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>chr3D_546
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------------------------------------------------------------------GATGGACTCTTCCC
CGCAACTCAAGCTACCTTACCTTAAATCCAACCTCCGGCCCCATCCATTAGGCCTGCCCACGGGCGCCTTGCCTATTTTC
AGTTGCTTCAACCCCACTTTACTATATGTTGCCCCCGTCTTCTCTCTCTCTCTCTCTTGCACA-----------------
---------------------------GCGGAGTGGCCCTTTTCTTTTCTTGAGTGAGCTAGCTAGCTCAGCTCCACTTT
AATTTGATTGTTAATTTAATCTTTATACTATTATCTTAAGGCTCAAGCATTGTTGGAACTGCTTCTGTCTCTCTGTGTGT
GTGTGGCCGAGATAAGTGTCGCTTTTATATCGCCTGTGCCCTGCCCTGCCGTGTCTCACCATCATTGTTGCCATCACAGG
CCGCTACCGCGCTCGTTCACTAGTCACTCCACCCGGGAGCACGCATATGCGTGCGATGGGACGCGAGGCGGCAGCGGCAG
TGGCGTGCTCCTCCAACAAGCCCAAGCTGCGGAGAGGGCTGTGGTCGCCGGAGGAGGACGAGAAGCTCTACAACCACATC
ATTCGCTACGGCGTCGGTTGCTGGAGCTCCGTCCCAAGGCTCGCCGGTGCGTAACGTAATCTCTTCATTCATATATGCCC
ATGCTGCTATGT---ATCTCTTGCTTGACCAAGAACTCAAATGTGTTTCCCTTAATTGTTCAGGGTTGGAGAGATGTGGC
AAGAGCTGCAGGCTAAGATGGATCAACTACCTCAGGCCTGATCTCAAGAGGGGCAGCTTCTCCCAGCAGGAGGAGGACCT
CATCGTCAGCCTGCACAAGATCCTTGGCAACAGGTAGTACAATTAGTAAGTTTTATTAGTGAGTTCACTGTTTTCTGATG
TTGATCGGAACTTTAGAAGCAGGTAGGTATATACAGAAAC------ACGACGATATTGCATACAGAAACACGTCGACACG
CCTCAACTGCACTACTCCTTTATGTTGGTTGTCAGGTGGTCCCAGATAGCGTCGCAGCTGCCAGGCCGGACCGACAACGA
GATCAAGAACTTCTGGAACTCGTGCATCAAGAAGAAGCTCCGGCAGCAGAGCATCGACCCCACCACCCACGAACCGCTCA
ATGACGCTGCCGCTGATGCCGAGCCGCACGACGAGTGCAAGCAGCTAGTCTCCGCTGCGGAAGACGGCTGCTTCGGCGGC
TCTGTTGGCAGTGACGATCTCCTAGCGCCGCACTCCCCGGTCGACTGCAGCTTCGACCCCATGTCCGTGACAAACGTCCC
CACAATGCGCATGCAGGGCTCCTACTCCTTGTGTGGCTACGGCGGCGTCGGCTCCGACGCCACCACGTACAGCGCCTACA
CAGGCGGCGGCGACAGCTCCAGCAACAGCACCGGCACCGGCACCGGCACC------TGGACCTGCGGCAATGTGGAGCCG
CTCCCGCACATGGACATGTTCTG---CGACGACGCCGAGCCCTACCCATTCGACCCGACCAAGTTCAGCCCGTGGCACCA
GCAGCACGCGCCGGACGACGACCGCGGCTCCGCGGTCTTCCCGGTCCGCTCGCTGTCCCGGGACCTGCCCGAGTCGTGCT
TCGAGCTCGCCCGTGGGGCCTTGGAGGACGAGTTCGACTTCATGTGACCCCGCCACGCCCAGGCCGAGGTCATGTGTCCA
TCGTTCCACTTCCACAACCACAAACTCACACATATACAAACCTCACTATACCACCTGATGAGATGAGAAGATCGATCACC
GTTGAGAGGA-CATGTGGTTTGACCACACCTATACTT-ATTTCCTCTCCTCATTT-TTCTCTCTCTGCCTTCCAACCCCT
TCCCTCGAAAAAGAAGTACTTATTCGATGAAGCTGTTTATTTAATGAATACAATGGTATATAAGTAC-------------
-----------------------------------------------------------------------TATATAGTA
TTGTGATCATAATAAGGGTTAGTAAATATGCATGTATACGTACCCCAATTCAGGGGGGTTTCATGTTTTGTATGGGAG--
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--------------------------------------------------------------------------CAGTTT
AGCAACATCGGTCCATGGAATTTTAAAGCAAGTCTTTTTACCTCTTGCACTCCATCCATGGACTGCGCCCTTGGCAAAGT
ACGTGGCAAATGAGACTAGGCCTCACAATTATTAA---------------------------------------------
----------------------------------------------------------------------GACGTACGTA
CTACGTGGTCGCTGTGTGGCGAAGTCGTACAGCGTGAGCGCGACGCCGCGCGGGCAAAGTCTTGAATACGTTGTTGCTTT
GGCAACGACGTGGCAAGGCGGGGATGTACGGGGCAGCAACGACGCAGTGTAAAGAAGCGTCAGTCACATGATG-------
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>SNPs
-------S-------------------SS-------SS----------SS--S-SSSS-SSSS-----------------
S--------------------------S-SSS-SSSSSSS-----S-S-------S-S-----------S----------
------S-S--------S----------------S-------------------------S-------------------
---------S-----------SS---S--S-------------------------S------S---SS------------
-----------------------S-----------S--S------------S----------------------------
-----------------------------------------------------------S-----------S--------
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--------------S-----------------------------------------------------------------
-------------------------------------S----------------------S-S-S-S-S-S-S-S-S-S-
SSSSSSSSSSSSSSSSSSSSSSS---------------------------------------------------------
---------------------S----------------------------------------------------------
-S------------------------------------------------------------------------------
---------------------------------------------------------------------S---S------
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-------------------------------------------------S------------------------------
------------SSS----------------------------------------------------------------S
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---------------------------------------------------------------------------S----
-------------S---------------SS-----S-SSSSSSSS--------S-------------------------
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-------------------------------S------------------------------------------------
--S--------S--------------------------------------------S-----------------------
--------S---------------S------------S-----------------------S--------S---------
--------------------------------------------------SSSSSS------------------------
-----------------------------------------S--------------------------------------
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----------------S---------------------------------------------------S-----------
------------------------------------------------S-----------------------S-------
-S--------S--------------------------S-----------------------------------S----S-
-------------------------S-S-----------S------------------SSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------
------------------------------------------------------S------------------SSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------
---------------------------------------------------------------------------S----
----------SS----------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--S-------
----S-----S-----------------SS---S----------S-----------------------------------
-------------------------------------SS--------S--------------S----------SSSSSSS
SSSSSSSSSSSSSS
>forward_150
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--------------------------------------------------GTTCGCCAGATAGTGCTCGT----------
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>reverse_1712
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-------------------------------TGAGTGCAAGCAGCTAGTCC-----------------------------
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>forward_575
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---------------------------------------------------------------------------TTCCC
CGCAACTCAAGCTAT-----------------------------------------------------------------
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>reverse_1849
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--------ACATGCAGGGCTCCTATTCC----------------------------------------------------
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>forward_1215
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---------------------------------------------------------------------------TGCCC
ATGCTGCTATGTACT-----------------------------------------------------------------
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>reverse_3020
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-----------------------------------------------------------TCTGGACGGAGGAAGTACGT-
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