>input_sequence_63002
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--------------------------------------------------------ATGGACGGGAAGCTGCCGCCGCCC
AACCCCAACCTCCCGTACCGGGAGGACTGCTGGAGCGAGGGCGAGACGGCCGCCCTCGTCGACGCCTGGGGGTCGCGGTA
CATCGACCTCAACCGCGGCAGCCTCCGCCAGCCGCAGTGGCGCGAGGTCGCCGACGCCGTCAACACCCGCCCGGGGGCCT
CCGCGCGCCGCCGGCCCCCGCGCACCGACATCCAGTGCAAGAACCGGGTCGATACCCTCAAGAAGAAGTACAAGGCCGAG
CGGGCGCGGGGCGGGCCCTCCCCCTGGCCCTTCTACCGCCAGCTCGACGTCCTCGTCGGCCCGACCCTCTCGGCC---GC
CGCCGCCAAGAAGCCCTCCCCGCCCCGCGCGCTTCCCATGCTGCGGAGGCGCATGTCGCCCTCTCGCTCCCCGTCGCCGC
CCTCGCCGGCGCCGCCGATGGCGCTCCCCCTGCCCAACTACCGCCGCGGGTCCAACCTCCCGGCCGCTGACCTCTTCCAT
AAGGCCGCCGCAGCTGCGGCCGCTGCGGATTCTGACTCGGACGATGGCTACAATAACAACA---ACTATGACGACGACGA
GGGCTCGCAGCAATCGGCCTCGCGCTCAGTGTCGTCTCACTCTGGTGGTAACGGTCCTCCTGTTCTTGGCAGTGGTGGGG
GCGGCGGTGGCGGCAACAAAAGGAAGAGGGGCGGGGCTGGAGGTTTTGGGGAGCTAGCGATGGCAATGGAGACATTCGCT
GAGATGTATGAGCGCATGGAGGCTGCCAAGCAGAGGCATGCAGAGGAGATGGAGAAGCAGCGGATCAAGTTCCTCAAGGA
TCTGGAGCTCAAGCGGATGCAGGCTTTCGTGGACATGCAGCTTCAACTTTCGAGGGTAAAGCAAGCCAAGAACGGTACCT
CGGAGATGCTCATGTCTCTTGCTGCACTGCCGTTCCTCAGCAACCCTGCTTACCTCTGATATAAGAGTTTAGGTAAGGAA
TTTGGCCTCTTAAAGTCAGATTTTAGGTTACTGTAATAGA----------------------------------------
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>chr3A_1_TraesCS3A01G271400
CATGTATGGGGCAGTTTGTGTGTGCATTCCGGCTGTGGGGTTTCTTCCATCGAACGAAACCGTTCGGTGGGATCGATCGC
TCGTGCCGAACGTCTCGTTCGGTTTGGGGGATCTCCAGAACGAACGCGTGGACATTAATGGCGTCCAAACATTTTTACTC
TCTTCGTTTTGTTTAGTCCGCACATTACTTTTGACTAATTTATTTTATAAAGTTTGATTAAGTTTATAGAAAATAATATA
AAAATTACAATAAAATATCTATATAATGTGAAA--ATACATTCAATAATGAATCTAGTGAAATTGATTTGGTATTGTATA
TGTTAATATTTTTCTTCATAAATTTGGTCAAAATTTATAAAGTTTAATTTCAGAGAAAAGCTAATACGAGGAAGCTGAAG
AGCCGAAATCGCCGCCTCAATACACGGCGGCCCCACCTCTACGCACCCATCCATGACCATGCATCCCCGAAGTCTGCGAA
CCCACGTCGCCACTCGCCACCCCGCCTCTGTCGCTCGCTCGCTCGCTCGGACTGTTTCTCTCTCCTTTTCGGCGCCCGAA
AACCAAAGAGACGCAGCGCGCGCACGCCGACCGAACGTCGGCCAGCCGAG------CCGTCCCGTACGTATGGAGTCCCC
CCTGGGCACGGCATCCGTCCCGCACCGCGACGTGCCGCGCCGGCCAACCGTGCCTTCCGATTTTAATTCGGCTCCACTCC
CGACGGCCGGTCAGTCAAACCCGCGCCCCCA-CCCATCCAACGGCGGCCGTTCCCCACTGCCTCCGCCCGCTCCCCTCCC
ATCCACGTGCCCACCGCGTCCGCCTCCCTCACGGTCACGGCCCACGGGCCGCCGCTCCCCACCTCGCCGCCCGTCCGCTC
CCCTCTTTTATTCCCCTCCCCCCTCGTCGCCAGCCGCCCCCGACTCGCATCCATCCGTC---TCCAGCCACCGAGAGGGG
AAATTAGTCCAGACTTTTAGGGTTTCCT--GAGAGAGAGATCTGGGAGGGC--GCCATGGACGGGAAGCTGCCGCCGCCC
AACCCCAACCTCCCGTACCGGGAGGACTGCTGGAGCGAGGGCGAGACGGCCGCCCTCGTCGACGCCTGGGGGTCGCGGTA
CATCGACCTCAACCGCGGCAGCCTCCGCCAGCCGCAGTGGCGCGAGGTCGCCGACGCCGTCAACACCCGCCCGGGGGCCT
CCGCGCGCCGCCGGCCCCCGCGCACCGACATCCAGTGCAAGAACCGGGTCGATACCCTCAAGAAGAAGTACAAGGCCGAG
CGGGCGCGGGGCGGGCCCTCCCCCTGGCCCTTCTACCGCCAGCTCGACGTCCTCGTCGGCCCGACCCTCTCGGCC---GC
CGCCGCCAAGAAGCCCTCCCCGCCCCGCGCGCTTCCCATGCTGCGGAGGCGCATGTCGCCCTCTCGCTCCCCGTCGCCGC
CCTCGCCGGCGCCGCCGATGGCGCTCCCCCTGCCCAACTACCGCCGCGGGTCCAACCTCCCGGCCGCTGACCTCTTCCAT
AAGGCCGCCGCAGCTGCGGCCGCTGCGGATTCTGACTCGGACGATGGCTACAATAACAACA---ACTATGACGACGACGA
GGGCTCGCAGCAATCGGCCTCGCGCTCAGTGTCGTCTCACTCTGGTGGTAACGGTCCTCCTGTTCTTGGCAGTGGTGGGG
GCGGCGGTGGCGGCAACAAAAGGAAGAGGGGCGGGGCTGGAGGTTTTGGGGAGCTAGCGATGGCAATGGAGACATTCGCT
GAGATGTATGAGCGCATGGAGGCTGCCAAGCAGAGGCATGCAGAGGAGATGGAGAAGCAGCGGATCAAGTTCCTCAAGGA
TCTGGAGCTCAAGCGGATGCAGGCTTTCGTGGACATGCAGCTTCAACTTTCGAGGGTAAAGCAAGCCAAGAACGGTACCT
CGGAGATGCTCATGTCTCTTGCTGCACTGCCGTTCCTCAGCAACCCTGCTTACCTCTGATATAAGAGTTTAGGTAAGGAA
TTTGGCCTCTTAAAGTCAGATTTTAGGTTACTGTAATAGACTT--GGGATTGATGATGTGTCTTTGTATGCTATATTGCC
TTATGTGGAACCAATGCAGATGTTCTGATATGCTTAGGTGTTCACCCATGTTGAACATATGTAACCAGAGATCTAGGCTA
CCTTTTATTTGTGCAAAGCAATGCTCAAGTAATTGTATGTTTGGCGATTTTGCATTATGAGAGACCAAGGCCTGACTTAT
GATAGCGACTAGCGATCTAGGAGATATTAGTCAGTTGATGATACACCCCCTGGAAATCCTAGATAATGAATGTTTTGCGT
GTAGTCTCCCAGTGTGTTGCTGCATCTGCGTCGTCTGGTCGGCTCGCCGCCACGCACACGCGATTGCTCTGCGTATAGGC
GAATTGTTTAATTTGTTGATGATGCATCTCATCTTCTGTTCGGTCAAATTCTTAGTTATCAGGTCCTCTTTGATCTGATC
TGATAAATTCTAATGGTCGACTCTTGTGTATGCCAGTTTAGAATTTGTGGTTATATGCTTATATTAGATACATTGGTTTC
TGATTCATAGT-------TTTCTGTTGTGAGTAGGAAATGCTGAAAATCTTTTCTCTAGTGTTATGCTGATTTGATGTTA
AGTTTTTGT---TTTGTTTTATATTGGAAGCATTTGAAGATCTTCTTTTGTACTGGGGTTTCATGCTTAGATTAGTTAAG
CTGGTGATGAATGAGTATTGTT-GCTTGGTAGATTATGGAGTGGGCTGTGAGATAGTTTCCCATTAGATCCTGGTCGCCG
CCTTCCTTCTTCTTTCGCCAATAGGCTGAAGTACAATTGCCAATATTTCCTAAATTCTGAGAGGAATTTGTTTCAAATAT
GTTAAAATTTGGTCTCTAATTATCACATATTCTTGTTTGTCAGCTTTGATCATGTGGTGCACATGTTGATCATCTATTCT
TGTGATACTGGCCTTTATTAGGTGTTGATACTATGATGTTATTTGTTTATTAACTGTTACAGTCCGTTAGGGATGTGTTA
CCAACTTGTCGTA
>chr3B_3
--TGTATGGGGTGATTTGTGTGTGCATTCGGGCTGTGGGGCTTCTCCCATCGAATGAAATCGTTCGGTGGGATTGATCGC
TCGTACCGAATGTCTCGTTCGGTCTGGGGGAACTCCAGAACGAACATGTAGGTATTATCTGCGTTCTAACATTTTTACTC
CCTTCGTTTTGTTTAGTCCGCACATTACGTTTGACTGA--TTTTTTTTAAAGTTTGACTAAATTTATAGAAAAAAATATG
AAAATTATAATAAAATATCTATACGATGTGAAA--ATACATTCAATAATAAATCTAGCGGTATTGATTTGGTACGC----
---TAATATTTTTTAT-ATAAATTTGGTCAAAGTTTATAAAGTTTAATTTGAGACGAAAGCTAATACGAGGAAGGCGAAG
AGTCGAAATCGTCGCCTCAATACACGGCGGCCCCACCTCTACGCACCCATCGATGACCATCCATCCCCGAAGTCTCCGAA
CCCACG-------TCGCCACCCCGCCTCTGTCGCTCGCTCGCTCGCTCGGACTGCTTCTCTCTCCTTTTCGGCCCG--AA
AACCAAAGAGACGCAGCGCGCGCACGCCGACCGAACGTCGGCCAGCCGAGGCCGAGCCGTCCCGTACGTATGGAATCCCC
CCTGGGCACGGCATCCGCGT----CCGCGACGTGCCGCGCCGGCCAACCGTCCCTCCCGATTTTAATTCGGCTCCACCCC
CGACGGCCGGTCAGTCAAACC--CGCCCCCA-CCCATCCAACGGCGGCCGTTCCCCAATGCCTCCGCCCGCTCCCCTCCC
ATCCACGTGCCCACCGCGTCCGCCTCCCTCACGGTCACGGCCCACGGGCCGCCGCTCCCCACCTCGCCGCCCGTCCGCTC
CCCTCTTTTATTCCCCTCCCCCCTCGTCGCCAGCCGCCCCCGACTCGCATCCATCCATC---TCCAGCCACCGAGAGGGG
AAATTAGTCCAGACTTTTAGGGTTTCCT--GAGAGAGAGATCTGGGAGGGC--GCCATGGACGGGAAGCTGCCGCCGCCC
AACCCCAACCTCCCGTACCGGGAGGACTGCTGGAGCGAGGGCGAGACGGCCGCCCTCGTCGACGCCTGGGGGTCGCGATA
CATCGACCTCAACCGCGGCAGCCTCCGCCAGCCGCAGTGGCGCGAGGTCGCCGACGCCGTCAACACCCGCCCGGGGGCCT
CCGCGCGCCGCCGGCCCCCGCGCACCGACATCCAGTGCAAGAACCGGGTCGATACCCTCAAGAAGAAGTACAAGGCCGAG
CGGGCGCGGGGCGGGCCCTCGCCCTGGCCCTTCTTCCGCCAGCTCGACGTCCTCGTCGGCCCGACCCTCTCGGCC---GC
CGCCGCCAAGAAGCCCTCCCCGCCCCGCGCGCTTCCCATGCTGCGGAGGCGCATGTCGCCCTCTCGCTCCCCGTCGCCGC
CCTCGCCGGCGCCGCCGATGGCGCTCCCCCTGCCCAACTACCGCCGCGGGTCCAACCTCCCGGCCGCTGACCTATTCCAT
AAGGCCGCCGCAGCTGCGGCTGCCGCGGATTCCGACTCGGACGATGGCTACAATAACAACAACAACTATGACGACGACGA
GGGCTCGCAGCAATCGGCCTCGCGCTCAGTGTCGTCTCACTCTGGTGGTAACGGTCCTCCTGTTCTTGGCGGTGGTGGGG
GCGGCGGTGGCGGCAACAAAAGGAAGAGGGGCGGGGCCGGAGGTTTTGGGGAGCTAGCGATGGCTATGGAGACATTCGCT
GAGATGTATGAGCGCATGGAGGCTGCCAAGCAGAGGCATGCAGAGGAGATGGAGAAGCAGCGGATCAAGTTCCTCAAGGA
TCTGGAACTCAAGCGGATGCAGGCTTTCGTGGACATGCAGCTTCAACTTTCGAGGGTAAAGCAAGCCAAGAACGGTACCT
CGGAGATGCTCATGTCTCTTGCTGCACTGCCGTTCCTCAGCAACCCTGCTTACCTCTGATATAAGAGTTTAGGTAAGGAA
TTTGGCCTCTTAAAGTCAGATTTTAGGTTACTGTAATAGACTTAGGGGACTGATGATGTGTTTTTGTATGCTATATTGCC
TTATGTGGAACCAATGCAGATGTTCTGATATGCTTAGGTGTTCACCCATTTTGAAC--ATGTAACCAGAGATCTAGGCTA
TC--TTATTTGTGCAAAGCAATGCTCAAGTAATTGTATGTTTAGCGATTTTGCATGATGAGAGACCAAGGCTTGACTTAT
GATAGCGACTAGCGATCTAGGAGATATTAGTCAGTTGATAG---ACCCCCTGGAAATCCTAGATAATGAATGTTCTGTGT
GTAGTCTCCCAGTGTGTTGCTGCATCTGCGTCGTCTGGTCAGCTCGCCGCCACGCACACGCGATTGCTCTGCGTATAGGC
GAATGGTTTAATTTTTTGATGATGCATCTCATCTTCTGTTCGGTCAAATTCTTAGTTATCAGGTCTTCTTTGATCTGATC
TGATAAATTCTAATGGTCGACTCTTGTGCATGCCAGTTTAGAATTTGTGGTCATATGCTTATATTAGATACATAGGTTTC
TGATTCATGGT-------TTTCTGTTGTGAGTAGGAAATGCTCAAAATCTTTTCTCTGGTGTTATGCTGACTTGATTTTA
AGTTTTTGGTTATTTGTTTTATATTGGAAGCATTTGAAGATCTTCTTTTGTACTGGGCTTTCATGCTTAGATTAGTTGAG
CTGGTGATGAATGAGTATTGTGAGCTTGGTAGATTATGGAGTGGGCT------TAGTTTCCCATTAGATCCTGGTCGCTG
CCTTCCTTCTTCTTTCGCCAATAGGCTGAAGTACAATCGCCAATATTTCGTAAATTCTGAGAGGAATTTGTTTCAAATAT
GTTAAAATTTGGTCTCTAATTATCACATATTCTTGTTTGTCAGCTTTGATCATGTGGTGCACATGCTGATTGTCTATTCT
TGTGATACTGGCCTTTATTAGGTGTTGATACTATGATGTTATTTGTTTATTAACTGTTAGAGTCCGTTAGAGACGTGTTA
CCAACTTGTCGTA
>chr3D_15
--------------TTTGTGTGTGCATTCGGGCAATGGGGCTTCTCCCATCGAACGAAATCGTTTGGTGGGATTGATTGC
TCGTACCGAACATCTTGTTCGGTCTGGGGGATCTCCAGAACGAACATGTAG-------------------------ACTC
CCTTCATTTTGTTTAGTCCGCACATTACATTTGACTGA-TTTTTTTATAAAGTTTGACTAAGTTTATAGAAAATAATATC
AAAATTACAATAAAATATCTGTATGGTGTGAATGTATATATTCAATAATGAATCTAGTGGTATTGATTTGGTATTGTATA
TGTTAACTTTTTTTCT-ATAAATTTGGTCAAAGTTTATAAAGTTCAATTTCAGACAAAACCTAATACGAGGAAGCTGAAG
AGCCGAAATCGTCGCCTCAATACACGGCGGTCCCACCTCTACGCATCCATCCATGACCATCCATCCCCGAAGTCTCCGAA
CCCACG-------TCGCCACCCCGCCTCTGTCGCTCGCTCGCTCGCTCGGACTGTTTCTCTCTCCTTTTCGGCCCGCGAA
AACCAAAGAGACGCAGCGCGCGCACGCCGACCGAACGTCGGCCA------GCCGAGCCGTCCCGTACGTATGGAGTCCC-
---------------------GCACCGCGACGTGCCGCGCCGGCCAACCGTGCCTCCCGATTTTAATTCGGCTCCACCCC
CGACGGCCGGTCAGTCAAACC--CGCCCCCACCCCATCCAACGGCGG----------------CCGCCCGCTCCCCTCCC
ATCCACGTGCCCACCGCGTCCGCCTCCCTCACGGTCACGGCCCACGGGCCGCCGCTCCCCACCTCGCCGCCCGTCCGCTC
CCCTCTTTTATTCCCCTCCCCCCTCGTCGCCAGCCGCCCCCGACTCGCATCCATCCATCATCTCCAGCCACCGAGAGGGG
AAATTAGTCCAGACTTTTAGGGTTTCCTGAGAGAGAGAGATCTGGGAGGGGGAGCCATGGACGGGAAGCTGCCGCCGCCC
AACCCCAACCTCCCGTACCGGGAGGACTGCTGGAGCGAGGGCGAGACGGCCGCCCTCGTCGACGCCTGGGGGTCGCGATA
CATCGACCTCAACCGCGGCAGCCTCCGCCAGCCGCAGTGGCGCGAGGTCGCCGACGCCGTCAACACCCGCCCGGGGGCCT
CCGCGCGCCGCCGGCCCCCGCGCACCGACATCCAGTGCAAGAACCGGGTCGATACCCTCAAGAAGAAGTACAAGGCGGAG
CGGGCGCGGGGCGGGCCCTCCCCCTGGCCCTTCTACCGCCAGCTCGACGTCCTCGTCGGCCCGACCCTCTCGGCCGCCGC
CGCCGCCAAGAAGCCCTCCCCGCCCCGCGCGCTTCCCATGCTGCGGAGGCGCATGTCGCCCTCTCGCTCCCCGTCGCCGC
CCTCGCCGGCGCCGCCGATGGCGCTCCCCCTGCCCAACTACCGCCGCGGGTCCAACCTCCCGGCCGCTGACCTCTTCCAT
AAGGCCGCTGCAGCTGCGGCCGCCGCGGATTCCGACTCGGATGATGGCTACAATA---ACAACAACTATGACGACGACGA
GGGCTCGCAGCAATCGGCCTCGCGCTCAGTGTCGTCTCACTCTGGTGGTAACGGTCCT---GTTCTTGGCGGTGGTGGGG
GCGGCGGTGGCGGCAACAAAAGGAAGAGGGGCGGGACCGGAGGTTTTGGGGAGCTAGCGATGGCAATGGAGACATTCGCT
GAGATGTATGAGCGCATGGAGGCTGCCAAGCAGAGGCATGCAGAGGAGATGGAGAAGCAGCGGATCAAGTTCCTCAAGGA
TCTGGAGCTCAAGCGGATGCAGGCTTTCGTGGACATGCAGCTTCAACTTTCGAGGGTAAAGCAAGCCAAAAACGGTACCT
CAGAGATGCTCATGTCTCTTGCTGCACTGCCGTTCCTCAGCAACCCTGCTTACCTCTGATATAAGAGTTTAGGTAAGGAA
TTTGGCCTCTTAAAGTCAGATTGTAGGTTACTGTAATAGACTTAGGGGATTGATGCTGTGTCTTTGTATGCTATATTGCC
TTATGTGGAACCAATGCAGATGTTCTGATATGCTCAGGTGTTCACCCATTTTGAAC--ATGTAACCAGAGGTCTAGGCTA
CC--TTATTTGTGCAAAGCAATGCTCAAGTAATTGTATGTTTAGTGATTTTGCATGATGAGAGACCAAGGCTTGACTTAT
GATAGCGACTAGCGATCTAGGAGATATTAGTCAGTTGATGATACACCCCCTGGAAATCCTAGATAATGAATGTTTTGCGT
GTAGTCTCCCAGTGTGTTGCTGCATCTGCGTCGTCTGGTCGGCTTGCCACCACGCACACGCAATTGCTCTGCTTATAGGC
GAATGGTTTAATTTGTTGATGATGCATCTCATCTTCTGTTCTGTCAAATTCTTAGTTATCAGGTCCTCTTTGATCTGATC
TGATAAATTCTAATGGTCGACTCTTGTGTATGCCAGTTTAGAATTTGTGGTTATATGCTTATATTAGATACATAGGTTTC
TGATTCATGGTTTTCTCTTTTCTGTTGTGAGTAGGAAATGCTCAAAATCTTTTCTCTAGTGTTATGCTGATTTGATGTTA
AGTTTTTGT---TTTGTTTTATATTGGAAGCATTTGAAGATCTTCTTTTTTACTGGGGTTTCATGCTTAGATTAGTTAAG
CTGGTGATGAACGAGTATTGTTAGCTTGGTAGATTATGGAGTGGGCTGTGAGATAG-TTTCCATTAGATCCTGGTCGCCG
CCTTCCTTCTTCTTTTGCCAATAGGCTGAAGTACAATTGCCAATATTTCCTAAATTCTGAGAGGAATTTGTTTCAAATAT
GTTAAAATTTG----CTAATTATCACATATTCTTGTTTGTCAGCTTTGATCATGTGGTGCACATGCTGATTGTCTATTCT
TGTGATACTGGCCTTTATTAGGTGTTGATACTATGATGTTATTTGTTTATTAACTGTTACAGTCCGTTAGTGATGTGTTA
CCAACTTGTCGTA
>SNPs
SS---------SSS---------------S----------S----S-------------S-------------S------
----S------------------S---------------------SS--S-SS----SSS----S-S-------------
S---------------------------S-------S-S--S---------------S---------------------S
------------------------S----------------------------------SS-------------------
-------------SS-S---------------S---------------------S-------------------------
-----------S------------------------------------------------S--------------S----
------SSSSSSS------------------------------------------------------------S-S----
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-----------------SSSS----------------------------------S---------------------S--
---------------------SS----------------------------------S----------------------
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--------------------------------------------------------S-----------------------
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-----------------------------------------------------------------------------S--
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-----------------------S--------S-----------------------------------------------
----------------------------------------------------------------------S---------
-------------------------------------S------------------------------------------
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-------------------------------------------------S------SS----------------------
--SS--------------------------------------S------------S---------------S--------
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----S---------------------------------------------------------------------------
-------------------------------------------------------------------------S------
--------S---------------------------------S-------------------------------------
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-----------------------------------------------------------------S----SS--------
----------------------------------------------------------------------S---------
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>forward_145
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---------------------------------------------GCGTGGACATTAATGGCGTC---------------
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>reverse_1553
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--------------------------------TGACTCGGACGATGGCTACA----------------------------
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>forward_476
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--------------------------------------------------------CCATGCATCCCCGAAGTCTG----
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>reverse_1718
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-------------------------------------TGGAGGTTTTGGGGAGCTAG-----------------------
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>forward_488
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--------------------------------------------------------------------GAAGTCTGCGAA
CCCACGTC------------------------------------------------------------------------
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>reverse_2216
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-------------------------------------------------------TATGAGAGACCAAGGCCTGAC----
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