>input_sequence_64250
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--------------------------------GCACACCCACCGCCGGTTACGTGCGCCTCGATCGCCACCGCAACAAGC
CGCCGCAGCAGCCGCGAGAGACCGGTCGACCCCGTTTCCTTGCCGTAGCGCCGCCGGGGAAGGCGAAGATGTCGTGGCAG
ACTTACGTGGACGAGCACCTGATGTGCGACATCGAGGGCCACCACCTCGCCTCCGCCGCCATCCTCGGCCACGACGGCAC
CGTCTGGGCCCAGAGCGCCGACTTCCCGTCGGTACGTAAGCCAAG-AATGGCGAATCCACTTGTTGCTATTTGGCGCCTG
CATGAGCCATGCTT----CGACGATCT-TGACATGTTTGCATGCGTGATCCAGTTCAAGCCGGAGGAGATGACCAACATC
ATGAAGGACTTCGACGAGCCGGGGACCCTCGCCCCGACCGGGCTGCTACTCGGAGACGCCAAGTACATGGTCATCCAGGG
TGAACCTGGCGCCGTCATCCGCGGCAAGAAGGTAACCATGCATGCACGTCGGATCCTTCTCATCTCTGCCCTCGCCGACC
AAACCAAACGTAAAATCAATCGCCTTTGGATCGGATCCGTTCCATTCCGTCTGTGATCGCAGGGCGCGGGAGGCATCACC
CTGAAGAAGACCGGGCAGGCGCTGGTGGTCGGCATCTACGACGAGCCCATGACCCCGGGGCAGTGCAACCTGGTGGTGGA
GAGGCTGGGCGACTACCTGGTAGAGCAGGGCATGTAGACGACGACGGCCATCACGCCACGCCGCAGCAACA---ACAATT
ACTACCGGCCAAAAGACACAGTAGATCTCCACGCG------------------CACGCATATGGGATTGTGGTTCAATTT
CTCTCGCATCCTCCTC----TAATCCTCTCTCCCTGTCCCGGCAACTACTTCGCCGATTACCACCCCTCTTGATTGATCC
GCGATATTTTTTTCCCCTTGTTTCATGATGATGAAGCCGTTCGTTTCGGCTAATAATTTTGATTTTTTCTC---------
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>chr3D_1_TraesCS3D01G277200
TTTCACTCCCCTAACCCTTTTGTGCAGCGCCCAGGCGCTGCACTAGTGCAACGCCCAGGAGCTAGGCGCTGCACTGTGTA
GTGTGGCGCCTAGCTCTCGGACGCTGCACGCTGACTTGGGCACATATGGGTGCGACGCTGGCCGTGTAGCGCCTATCTGG
AAGGCGTTGCACAGTAGATGTGGCGCAAAAGGATCAGGGAAGTGAAATAGTTTCGCAACCAGTCCATTCTGTGATTTGAT
TTCGATTATAGGTCAAAATTGTCAAATTTGTTCAAGAACAACTTGGCGACCGCTTTCGGCCAGAGTGCTGGAAAGTAAGA
TTCGGCTGACCCACACCAGTCCATCGGCGGTACGAATTGCAGGCCCAGTGTACATCCAACGTTGCTGACTCTCAACTCAC
TGGCTTGGGTCCACACCTTACTCATCACGTTATTACTAGCACCCTAAAGAAAAATAATTATCATATGTTAGTTACAAAGA
TTTACGATTATGCCCATGCTTATTGTAAACC-TTTTCTTTCAAGGGGTCGGGCCAGTTCTTTTGATGGCTTAGAAAATAA
GTTGTCTTCTCAGCTTATTC---CATAATTTGCCTCTCTCATTCATTACAGCTACACTAATTATGGAATGATTTATTATT
TAAGCTACAGAGAGGCGGATAATCAATTTAGAAGACTCAACAAATTTAAAAGAA--------------------------
--------------------------------------GAATTATTTTTTAGGCTAAAGAGAGGCGGCTTATTTTCTAAG
CTGTACGGAGAAAACTGGCCCAACGAACCAATGGCAAGGCCGAAATTGCGGCCGAATCCAGGGGTGTGTGCG----ACGT
ACGGCCGTGGGTGGGGCTCATGGGCATGGCGCATGGCAGCGCACCAAAGGAGGCGCGAAGTTGAAGGGCGAGCTCAAGAT
GGACGGGTGGTTGGGACGAAGCAGCAGTGGGGAGGGATGCAGACCTTTTTCCCCGTCCTCCTCTTCCTCTCCACTCCCAC
CCTATTTATACCGGCTTCCGCCCCCCGCGATTGCACACCCACCGCCGGTTACGTGCGCCTCGATCGCCACCGCAACAAGC
CGCCGCAGCAGCCGCGAGAGACCGGTCGACCCCGTTTCCTTGCCGTAGCGCCGCCGGGGAAGGCGAAGATGTCGTGGCAG
ACTTACGTGGACGAGCACCTGATGTGCGACATCGAGGGCCACCACCTCGCCTCCGCCGCCATCCTCGGCCACGACGGCAC
CGTCTGGGCCCAGAGCGCCGACTTCCCGTCGGTACGTAAGCCAAG-AATGGCGAATCCACTTGTTGCTATTTGGCGCCTG
CATGAGCCATGCTT----CGACGATCT-TGACATGTTTGCATGCGTGATCCAGTTCAAGCCGGAGGAGATGACCAACATC
ATGAAGGACTTCGACGAGCCGGGGACCCTCGCCCCGACCGGGCTGCTACTCGGAGACGCCAAGTACATGGTCATCCAGGG
TGAACCTGGCGCCGTCATCCGCGGCAAGAAGGTAACCATGCATGCACGTCGGATCCTTCTCATCTCTGCCCTCGCCGACC
AAACCAAACGTAAAATCAATCGCCTTTGGATCGGATCCGTTCCATTCCGTCTGTGATCGCAGGGCGCGGGAGGCATCACC
CTGAAGAAGACCGGGCAGGCGCTGGTGGTCGGCATCTACGACGAGCCCATGACCCCGGGGCAGTGCAACCTGGTGGTGGA
GAGGCTGGGCGACTACCTGGTAGAGCAGGGCATGTAGACGACGACGGCCATCACGCCACGCCGCAGCAACA---ACAATT
ACTACCGGCCAAAAGACACAGTAGATCTCCACGCG------------------CACGCATATGGGATTGTGGTTCAATTT
CTCTCGCATCCTCCTC----TAATCCTCTCTCCCTGTCCCGGCAACTACTTCGCCGATTACCACCCCTCTTGATTGATCC
GCGATATTTTTTTCCCCTTGTTTCATGATGATGAAGCCGTTCGTTTCGGCTAATAATTTTGATTTTT-TCTCCTATACGT
ATCGTTTTTGGTCATTTGGGTTGCC-GTTTGAGTTGTGGATCCGGAACAATATATATATGTGATTGCCATTGG--TTTTG
CAATATACGAGAACATTTATGTGTATTCCATCGTGTGGTCTGCCTTTTTTTTAG----CTGATCGTGTGGTCTGCTTCAA
CTCCATATACATAGTTCCTATTCTGCTCATTCTGCTACATTTGAAGAAGAAAAACAAACACA--ATTTTTTGGTCAAG--
----GAAAAAAATGATATTCACCG---AAGAATCCACTCAAATTTGATGCGCATAAACTCTTTATTT--GGC---TTAAA
AGGCCATAGCCATTTTCTTTGGACCCCAATACCGAACTAAATTGGTTGTTTGCTCTCCTCTCCTGGATCGAACGAATCTT
CCA-----------------------------------------------------------------------------
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--------------------------------------------------------------------TCTGAAAAATAC
CATATCAATAGATCGAATTTTCTTAACTTTGCCATCTTTAATACACCAATTTACCTTCAATTTTCTTACACACAACCAGG
AGAGGTAAAAACAAAGAGAAAATTGTCATCGCAAAATTTAAATTTTGCCATGGTAAACTCGATGAATTTTCCGTAGAATA
TAATATAAATTTGGAATAGTCAAATACAGAAAAAACAACGTACACAGGAAAAACTGCCATGGTATTAAACGAGAAAACAT
GGCAAACTTTGATGGAAAATGTTCTATATATCATGGTTACTTAGCAAACAAGTTTATACTTGTAATTAAGGATTTT----
-------------GTTTCAAAATGGTTTTCTGTTTTGATGGTTTTATGTACATGGCAAAAATCAGGAGGTGTTGAACAT-
-------GGTAGCATGGCAAAAAAGTTATAAATTTTTCGCCATGGCAAAAATTGTTTTATTGACATAGCAAAATTTATAG
GATTTTTGCCATGGCAAAAATTGTGTTGATGAAATGGCAAAAAATGTATTGGTAACAAGGCAAACATTATAAGATTTTTG
CCATGGAAAAATTTGTGTTGGTGACCTGGCAAAAATCCTTTGCTACGACAAAAATTGTGTTGGTA
>chr3B_273
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--------------------------------CAAGAACAACTTGGCGACCGCTTTCGGCCAGAGTGCTGGAAAGTAAGA
TTCGGCTGACCCACACCAGTCCATCGGCGGTACGAATTGCAGGCCAGTGT---ATCCAACGTTGCTGACTCTCAACTCAC
TGGCTTGGGTTCACACCTTACTCATCACGTTATTACTAGTACCCTAAAGAAAAATAATTATCATATGTTACTTACAAAGA
TTTACGATTATGCCCATGCTTATTGTAAACCCTTTTCTTCCAAGGGTTCGGGCCAGATCTTTTGATGGCTTAAAAAATAA
ATTGTCTTCTTTCCAACTTATTTCATAAGTCGCCTCTCTCATTCATTAGAGCTACACTAATTATA---------------
----------------GGATAACCAATTTAGAAGACTCAACAAATTTAAAAGATGATTTATTTTTTAAACTAGAGAGAGG
CAGATAACCAATTTAGAAGACTCAACAATTTAAAGAATGATTTATTTTTTAAGTTAGAGAGAGGCGGCTTATTTTTTACT
AC--------AAAACTGGCCCAACAAACCAATGGCAAGGCCGAAATTGCGGCCGAATCCAGAGGTGTGTGCG----ACGT
ACGGCCGTGGGTGGGGCTCATGGGCATGGCGCATGGCAGCGCACCAAAGGAGGCGCGAAGTTGAAGGGCGAGCTCAAGAT
GGACGGGTGGTTGGGACGAAGCAGCAGTGGGGATC----CAGACCTTTTTCCCCGTCCTCCTAATCCTCTCCACTCCCAC
CCTATTTATACCGGCTTCCGCCCCCCGCGATTGCACACCCACCGCCGGTTACGTGCGCCTCGATCGCCACCGCAACAAG-
--CCGCAGCAGCAGCGACAGACCGATCGACCCCGTTTCCTTGCCGGAGCACCGCCGGGGAAGGCGAAGATGTCGTGGCAG
ACTTACGTGGACGAGCACCTGATGTGCGACATCGAGGGCCACCACCTCGCCTCCGCCGCCATCCTCGGCCACGACGGCAC
CGTCTGGGCCCAGAGCGCCGACTTCCCGTCGGTGCGTAAGATAAGAAATGGCTAATCCAATTGTTGCTATTTGGCGTGTG
CATAAGCCGCCTCCA-----ACGATCTCTGACATGTTTGCATGCGTGATCCAGTTCAAGCCGGAGGAGATGACCAACATC
ATGAAGGACTTCGACGAGCCGGGGACCCTCGCCCCGACCGGGCTGCTACTCGGAGCCGCCAAGTACATGGTCATCCAGGG
TGAACCTGGCGCCGTCATCCGCGGCAAGAAGGTAACCATGCACGTCGGACT----CTTCTCATCTCTGCCCTCACCGACC
AAACCAAACGTAAAA----TCGCCGTTGGATCGGGTCCATTCCGTTCCGTCTGTGATCGCAGGGCGCGGGAGGCATCACC
CTGAAGAAGACCGGGCAGGCGCTGGTGGTCGGCATCTACGACGAGCCCATGACCCCGGGGCAGTGCAACCTGGTGGTGGA
GAGGCTGGGCGACTACCTGGTAGAGCAGGGCATGTAGACGACGACGAC---CACGCCACGCCGCAGCAACA---ACAA-T
ACTACCGGCCAAAAGACACAGTAGATCTCCACGCGTTTTTTCTAGCCGCCGCGCACGCATATGGGATTGTGGTTCAATTT
CTCTCGCATCCTCCTCTCATTAAGCCTCTCTCCCTGTCCCGGCAACTACTCCGCCGATTACCACCCCTCTTGATTGATCC
GCGATATTTTTTTCCCCTTGTTTCATGATGATGAAGCCGTTCGTTTCGGCTAATAATTTTGAATTTTTTCTTCTACC--T
ATCGTTTT-GGTCATTTGGGTTGCC-GTTTGAGTTGTGGATCCGGAACAATATATATATGTGATTGCCATTGG--TTTTG
CAATATACGAGAATATTTATGTGTATTCCATCGTGTGGTCTGCTTTTTTTTTTTTGAACTGATCGTGTGGTCTGCTTCAA
CTCCATATACATTGTTCCTACTCTGCTCCTGCAGATTCATTTGAAGAAAAAAG-CAAATGCA--ATTTTTTCGCGGTTAA
GGAAGAAAAGAAAAATGACATTCACCAAAGAATCCACTCAAATTTGATGCGCATAAATTCTTTATTTTGGGC---TTAAA
AAGCCATAGCCATTTTAGTTGGACCCCAATACCGAACCGTTCGGGGCAAGGAGTTCACCCCGCACGCGCGAACCATAATA
TATGTTGCGCGATGGCCTCCAGCGGACCAGCCCAAAA-CGCAATTCCCTTGAAGAATGTTAAGAAAAAAACATGGATTCC
AATGTTGTGGGCCCAAAAAATGCTCCTGCCTCAACCAACAAATAGAGAAAAAGACCTAAAAATGCACTAGACC--AAAAA
AAACTCCCTGAAAATAATCGAGGACATATTTAAAAAAATCTTTAGTTGTCATGACATGAAAGC----AAAAAAATTCACA
AAAATGTATGTATATAATAGGACAAAGAG----CTACAAAGTTTGACATTGAAGATGTACAACAAAATTCTGAAAAATAC
CATATCAATAGATTGAATTTTATTAACTTTGCCATCTTTAATACACCAATTTATCTGCACTTTTCTTACACACAACCAGA
AAAGGTAAAAACATAGAGAAA---GTCATCACAAAATTTAAAATTTGCCATCGTAAACTCGATGAATTTTCCGTAGAATA
TAAAATAATTTTGCAACAATATAATATAGAAAAGCAACAT---ACAGGAAAAAATGCCATGGCATTAAACAAGGAAACAT
TGCAAACTTTGATTGAAAACGTTCTATATATCATGGTAACTTAGCAAACAAGTTTATACTTGTAAATACGGATTTTTTTA
AGAGAA--GTTTTTTTTCAAAAATGTTTTGTGTTTAGGCGGTTTGATGTACATGGAAAAAATCACTAGGTGTTGAACATT
ATACATGGTG-GCATGGCAAAAAAGTTATAAGATTTTTGCCATGGCAAAAAAA--TTTAGTGACACAGCAAAATTTATAG
GATTTTTGCCATGGCAAAAATTGTGTTGGTGA---GG-AAAAATTGTATTGGTGACAAAGCTAACCTTATAAGATTTTTG
CCATGGCAAAATTTGTGTTGGTGACATTGCAAAAATCCTTTCCTATGGCAATTTTTTTGTTGGT-
>chr3A_759
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--------------------------ACCAATGGCAAGGCCGAAATTGCGGCCGAATCCACGGGTGTGTGCGACGTACGT
ACGGCTGTGGGTGGGGCTCATGTTG-------ATGGCAGCGCACCGAAGGAGGCGCGAAGTTGAAGGGCGAACTCAGGAT
GGATGGGTGGTTGGGACGAAGCAGCAGTTGGGATC----CAGACATTTCCCCCCTCGG-CCTCTTCCTCTCCTCTCCCAC
CCTATTTATACCGGCTTCCGCCCCCCGCGATTGCACACCCACCGCCGGTTACGTGCGCCTCGATCGCCACCGCGACAAGC
CGCAGCAGCAGCGA-GAGAGACCGATCGACCCCGTTTCCTTGCCGGAGCGCCGCCGGGGAAGGCGAAGATGTCGTGGCAG
ACTTACGTGGACGAGCACCTGATGTGCGACATCGAGGGCCACCACCTCGCCTCCGCCGCCATCCTCGGCCACGACGGCAC
CGTCTGGGCCCAGAGCGCCGATTTCCCGTCGGTACGT--------------CGAACCCACTCGTTGCTATTTGGCGCCTG
CATGAGCCATGCATGCGCCGACGATCTCTGACATGTTTGCATGCGTGATCCAGTTCAAGCCGGCGGAGATGGCCAACATC
ATGAAGGACTTCGACGAGCCGGGGACCCTCGCCCCGACCGGGCTGCTACTCGCAGACGCCAAGTACATGGTCATCCAAGG
TGAACCTGGCGCCGTCATCCGCGGCAAGAAGGTAACCATGCATGCACGTCGGACCCTTCTCATCTCTGCCCTCACCGACC
AAACCAAACGTAAAATCAATCGCCGTTGGATCGGATCCGTTCCATTCCGTCCGTGATCGCAGGGCGCGGGAGGCATCACC
CTGAAGAAGACCGGGCAGGCGCTGGTGGTCGGCATCTACGACGAGCCCATGACCCCGGGGCAGTGCAACCTGGTGGTGGA
GAGGCTGGGCGACTACCTGGTAGAGCAGGGCATGTAGACGACGACGACGACCACGCCACGCCGCCGCAGCACCAACAA-T
ACTACCGGCCAAAAGACACAGTAGATCTCCACGCG------------------CACGCATATGGGATTGTGGTTCAATTT
CTCTCGCATCCTCCTC----TAATCCTCTCTCCCTGTCCCGGCAACTAC--------TTACCACCCCTCTTGATTCATCC
GCGATATTTTCC-CCCCTTGTTTCATGATGATG-AGCCGTTCGTTTCGGCTAATAATTTTGATTTTTCTCTCCTATACGT
ATCGTTTT-GGTCATTTGGGTTGCCCGTTTGAGTTGTGGATCCGGAACAATATATATATGTGATTGCCATTGGTATTTTG
CAATATACGAGAATATTTATGTGTATTCCATCGTGTGGTCTGCCTTTTTTTTAG----CT---------GTCTGCTTCAA
CTCCATATACATCGTTCCTATTCTGCTCCTGCAGGATCGTTTGAAGAAAAAAG-CAAACAATATATATTTTTTCGGTTAT
GCAAGAAAAAAAAGATATTCACTG---AGGAATCCACTCAAATTTGATGCGCATAGACTCTTTATTG--GGCTTATTAAA
AGGCCATAGCCATTTTCGGCGGGGGGACGAGCCACATAAAAGATTCGTTCGATCAAACAATTTAGTCCAC----------
-ATGCTGCCCGATGGCCTCCAGCGGACCAGCCCAAAAACGCAATTCCCTCGAAGAATGTAAAAAAAAA--CATGAATTGC
AATGTTGTGGGCCCAAAAACTGCTCCCGCCTCTCCCAACAAATAGACAAAAAGACATAAAAATGCACTAGACTGAAAAAA
AAACTCCCCAAAAATAATCTAGGACAGA-TTAAAAAAATCTTTAGTTGTCAAGATATTATGAAAACAAAAAAAAACCACA
AAAATGTATTTATAGAATAGAACAAAAAGATTTCTACAAAGTTTGACATTGGTGATGTACAACAAAATTCTG-AAAATGC
CATATCAATAGATCGAATTTTCTTAACTTTGCCATCTTTAATACACCAATTTACTTGCATTTTTCTTACACACAACCAGG
AAAGGTAAAAACATAGAGAAAATTGTCATCGCAAAATTTAAATTTTGCCATGGTAAACTCGATGAATTTTCCATAGAATA
TAATATAAATTTGCAATAGTCAAATACAGCAAAAACAACATACACAGGAAAAACTGCCATGGTATTAAACGAGAAAACAT
GGCAAACCTTGATGGAAAATGTTCTATATATCATGGTTAGTTAGCAAAAAAGTTTATACTTGTAATTAAGGATTTTGTTT
AAGAAAAGGTTTTGTTTCACAATGGTTTTGTGTTTTGGCGGTTTTATGTACATGGTAAAAATCAGGAGGTGTTGAACATT
ATACATGGGTAGCATGGC-AAAAAGTTATAAGATTTTTGCCATGTCAAAAATTATTTTAGTGACATGGCAAAATTTATA-
GATTTTTGCCATGGAAAAAATTGTGTTGGTGAAATGG-AAAAAATGTATTGATAACAAGGCAAACATTATAAGATTTTTG
CCATGGAAAAATTTTTGTTGGTGA-----------------------------------------
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------------------------------------------
---------------------------------------------SSSSSSSS---------------------------
----------S----------------------------S------------------------------S---------
---------------------------------------S------S---------S---------------S-------
S---------SSS-SSS--S--------S-S-----------------S---------------SSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSS------S------------------------------S--------------------------
----------------------------------------S----------S-S--S------------------S--SS
SSSSSSSSSS--------------S-------------------------------------------------------
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---------------------------------SSSSSS-----------------------------------------
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------------S-----------S--------------------S----------------------------------
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----------------------------------------SS--------------------------------------
------------S-------------------------------------------------------------------
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-----------------------------------------------------S-------------------S------
------------------------S-------------------------------------------------------
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----------------------------------------------S-S-S---------------------------S-
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--------------------------------------------------S-----------------------------
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--------S-----------------------------------------------------------------------
-------------S------------------------------------------------------------------
------------S---------------S-S-S-S-S-----------S---SS-----------------S-SSSSS--
------------S-------------------------------------------------------------------
-----------------S-------------------S---SS--SSS-SSSS-SSS-S--S-S--SS-----S-SSS-S
SSS-----------------------------------------------------------------------------
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--------------------------------------------------------S--S--------------------
-S-----------S------------------------------------------------------------------
-------------S-------------------------S----------------------------------------
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-----------------------------S-------SS----------------S------------------------
-------------------------------SS----S---------------S-----S--------------------
----------------------------S--------S------------------------------------------
-------------------------S-S-------------S---S-S---SSS--S-------S
>forward_171
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-----------------------------------------------------------------------CCTATCTGG
AAGGCGTTGCA---------------------------------------------------------------------
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>reverse_1594
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-------------------------------------------------------------------------GCCGACC
AAACCAAACGTAA-------------------------------------------------------------------
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>forward_411
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-----------------------------------------------------------------------TCAACTCAC
TGGCTTGGGTC---------------------------------------------------------------------
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>reverse_2452
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---------------------------------------------------GCTCTCCTCTCCTGGATCGA---------
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