>input_sequence_82892
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--------------------ATGTCTGGCGTGTGGGTGTTCCGCAACGGCGTGGTGAAGCTGGTGGAGAACCACCCGGCG
TCGGCGG----------------CGGGACCGCCGGGCGGCGGGGCGGTGCGGCGCAAGGCGCTGCTCCACACGCCCACGG
GGGAGGTGGTCGCCTCCTACGCCTCCCTGGAGCGCAAGCTCGTCGCGCTTGGCTGGGAGCGCTACTACGCCGGCGGGGGC
GGCGCCGCCGGCGACTGCATGCTCAGGTTCCACAAGCGCTCCTCCGTCGACCTCATCTCCCTCCCCAAGGACTTCGGCCA
GTTCAGCTCCGTCCACATGTACGACGTCGTTATCAAGAACCGCGACGCCTTCCGCGTCATCGACGTCTAG----------
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---------------------------------------------------
>chr3D_1_TraesCS3D01G444700
TAGGTTTTAGGTT-------------------------------------------------------------------
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-----------------------------------------------------------------------------TTC
GACGTCTTGGCTTCGGTGGTGGCAGCGACGCTGAATAAAGAAGCTCAAATTCCTTCCTCAACAAGGCGATCAACTGTATG
GGTGGTGATGGGTTTGGGAACTAGCCTATCGAAGCGGGGATGTCATGGTGGCGAAGGCATCCTTGTGGCGGACTTGTGTA
-----------CTGTTGCGATGACGTCTGCTCCAGCGCGGACGCGCTGA------------------------------A
GTGGTCTGCATTAACGACATCTGGAAGATGGATTGTGTCTTGGGTTTGTGGTTGGTGGAAGGCAGGTATGGTTTTCTCCT
TCGGCGTCGGGGTGACAGATTTAGAGTTCGATGGCATGTCTAGGGTGTTGCCCCGGTCAAATTAGTTCAACGACAATGGC
TTCGGCTTTGATGAGTCACCTTGAAGATCCACAAAACTGC--ATCAGTGGTGAAGCTGCATCAAGTTCCGATGAGGAG--
--GTGATCTGTCATTTTCTTTTGTGGTTGTTGTGATGGTGCAGAGGCAGGTGATGGGCATCAGTGTCAAGCTCAGGGGAT
TTTTTGGTC---TTGATTGTAATTTTCTTTCCTAGGATTGATGAATAAATTCA-------------GAGCACCAACGTCA
AATCTAAAACTTGAACCCTGATGGGCTAAAA--ATACCAGTGTACTTCTAACCATTCTACCGGTTCGCTTCTCA-CATCG
TTTACTGGTAGATCTTATCTCTATCCGATAGAGATCTTAACTAGAAAAAA--AATACCAGAGTACATATGATCGAGCACT
GTCTCGCCCAGTGTGAATAAACACGGCGGGGCCATGCGCACGTGCGCTCTCGCCATCGAGACGTAACGTACCTATCATGC
ACTGCACCGCTCGCGGCAATGCACCGGCCGCCTCTATTTATAGCCTCCCACGCCCCATCCTTTTCCACAT--CCCAGCCT
CAACAACCACCAAAGTACACACACCACACTAATCAAGTACACATCCA------GGCCACCAAGGCACCCAGCGAGCGATC
ACCATATCACACATAGCACCATGTCTGGCGTGTGGGTGTTCCGCAACGGCGTGGTGAAGCTGGTGGAGAACCACCCGGCG
TCGGCGG----------------CGGGACCGCCGGGCGGCGGGGCGGTGCGGCGCAAGGCGCTGCTCCACACGCCCACGG
GGGAGGTGGTCGCCTCCTACGCCTCCCTGGAGCGCAAGCTCGTCGCGCTTGGCTGGGAGCGCTACTACGCCGGCGGGGGC
GGCGCCGCCGGCGACTGCATGCTCAGGTTCCACAAGCGCTCCTCCGTCGACCTCATCTCCCTCCCCAAGGACTTCGGCCA
GTTCAGCTCCGTCCACATGTACGACGTCGTTATCAAGAACCGCGACGCCTTCCGCGTCATCGACGTCTAGCCTAGCTGGC
TGGCTGATGATTCGGCCATTCGATCGAAGCAAGCACAGCTAGCTCGTGCGCGCCGGCGGCCGCCACCGTCGCATCCATGT
CGTCATCGATCTCCGCTGGTTAACTTGTCCACCTTGTGTATGTGTGCGTATGTC---------------------TATAC
GTGTGTATGTATATGTACGTGGTGTATTGACGTATATATAGATATACATGCTGCGTGTCCATTGTGGTTAATTAATTCGG
AATATGTATTTGGCAACTGTGTGGCAGATTGCCAAAACGACCTAACCACCTGGCTGCCCTTTGATCCCGATCGCTCGATG
CACAGGAACCTCGCGACCTCCTCCATCCACGACCTCTGATAATATTCCTGCTGCTTCCCATCCCTGCCGCGCTCTAGTGG
AAACCTCCTCGGGTGCTGCTGCCGCAGGCTGACTGCGTCGCACCATGCCGTCGCCGTCGCGCATCGTAATCATTCCACCG
CCAGCAGCCTTTACCTGTCCGGCTGTGGAGAGGAACAGCGCGTGCTCGAGTCCTCTCGCGCGATGGCGTGCTCCGGTCCA
GTGTGCCGCCGGCCGGCCGGCGCCCTCTCCTCTCGCGCCATGGCGTGCTCCAGTCCAGTATGCGCCTAGTCGTCCGGCAT
CCTCTTCTCTCGCGTGATGGCGTGCTCCAGTCCAGTTCGCCCTCGGCTGGCTGGCGTGCTCTCCTCTCGCGCGATGGAAT
TGGAGGCAAGTGCAGTTCCAGCACCCACCACCAGGTCAGTTCATGTCCGCCTACATGCCTGCGAGCTGCTTGTGTTTATG
CCAATATGGTTTTCCTTGTTCACCGACAGCCTCTAGTGGCAGTTTACATAATCTGTCCACCTCCTCATCGTTTAATGCTC
ACCAACTAACCCACATTGAACGATCACAGTCGATGAATGAATGCATCTGAACATTCCAGCCACACCACAAACTAGTGCAG
AGCAGAGCATCCAACGCGTTTCTCCCTTTAGTTTGGCTTGCTTGTTTGTTT
>chr3A_1
CTCATCATTGTTTACTGGTAGAACTTATCTCTATCCGATAGAGATCTTAACTAGAGAAAAATACTTGAGTACTTATATTC
GATCGAGCAA--TCTCTCGCTCAGAGTGAATAAACACGGCGGGGCCATGCGCCCGTGGGCTCTCGCCATCAAGACGAT--
GCACGTATCATGCAGTGCACCGCTCACAGCAATG-ACTGACCGCAGTATAGATGCAGACGCTCATAAGCCACGTGTAAAG
CGTTTTCCTCTCTGGTGCCAGGTGACTAGAATACTAG-----CCGCTGTTAGGAGAGGCCAATCTTTCGGCACCGTCCTT
TGGTGGCTCCCGTCGGCCGACAACCTCGCAGTCGTCGATGGTCAAGGGGGTCGCCTGATCCCGTGCGCC-----------
--------------------------------------------------------------------------------
-------------------------CGGATCATGTAGCTTTAGGTTTTAGGGGCTTAGTGGCTTAGATTTTGGGTCATTC
GACATCTTGGCTTCGGCGGTGGCAGCGATGCTGAATAAAGAAGCTCAAATTCCTTCCTCAACAAGGCGATCAACTGTATG
AGTGGTGATGGGTTTGGGAACTAGCCTATCCAAGCGGGCATGTGGTGGTGGCGACGACATTCTTGTGGCGGACTTGTGTA
-----------CTGTTGCGACGACGTCTGTTCCAGCGCGGACGCGCTGA------------------------------A
GTGGTCTGCATTAACGGCATCTAGAAGACGGATTGTGTGTTGGGTTTGTGGTTGGTGGAAGGCAGGTATGATTTTCTCCT
CCGGCATCGGGATGATAGATCTAGAGTTCGACGGCATGTCCAGGGTGTTACCCCGGTCTAATTAGTTCAACGACAATGGC
TTCGGTTCTAGTGAGTAACCTTGGAGATCCACAAAACTGC--ATCAGTAGTGAAGCTGGGTCAAGTTCCGATAAGGAG--
--GTGATCTGTC-TTTTTTTTTGTGGTTGTTGTTGTGGTGCAGAGGTAGGTGATGGGCATCAGTGTCAAGTTCAGGGGAT
TTTTTGGTC---TTGATTGTAATTTTCTTTCCTGGGATTGACGAATAAATTCAA-------------AGCACCAACATTA
AGTCTAAAACTTGAATCCTGATGGGTTAG--AGATACCAGTATACTTCTAACCATTCTACCGGTCTGCTTCTCA-CATCG
TTTACTGGTAGATCTTATCTCTATCCGATAGAGATCTTAACTAGAAAAAA--AATACCAGAGTACATATAATCGAGCACT
GTCTCGCCCAGTGTGAATAAACACGGCGGGGCCATGCGCGCGTGCGCTCTCGCCATCGAGACGTAACGTACGTATCATGC
AGTGCACCGCTGGCGGCAATGCACCGGCCGCCTCTATTTATAGCCCACCACGCCCCATCCTTTTCCACAT--CCCAGCCT
CAACAACCACCAAAGTACACACGCCACACTAATCAAGTACACATCCA------GGCCACCAAGCCACCCAGCGAGCGATC
ACCATATCACACATAGCGCCATGTCTGGCGTGTGGGTGTTCCGCAACGGGGTGGTGAAGCTGGTGGAGAACCACCCGGCG
TCGGCGG----------------CGGGACCTCCCGGCGGCGGGGCGGTCCGGCGCAAGGCGCTGCTGCACACGCCCACGG
GGGAGGTGGTCGCCTCCTACGCCTCGCTGGAGCGCAAGCTCCTCGCGCTCGGCTGGGAGCGCTACTACGCCGGCGGGGGT
GGCGCCGCCGGCGACTGCATGCTCAGGTTCCACAAGCGCTCCTCCGTCGACCTCATCTCCCTCCCCAAGGACTTCGGCCA
GTTCAGCTCCGTCCACATGTACGACGTCGTCATCAAGAATCGCGACGCCTTCCGCGTCATCGACGTCTAGCTGAGCTAGC
TGGCTGATC---CGGCCATTCTAT-GAAGCAAGCACGGCTAGCTCGTGCGCGCCGGCGGCCGCCACCGTCGCATCCATGT
CGTCATCGATCTCCGCTGTTTAACTTGTCCTCCTTGTGTCTGTGTG------------TACGTACCCTGCACGTATATAC
GTGTGTATGTATATGTAC--------------------------------------------------------------
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---------------------------------------------------
>chr3B_1
CATTG-----TTTACTGGTAGGACTTATCTCTATCCGATAGAGATCTTAACCGGAGAAAAATACTTGAGTACTTATATTC
GATCGAGCACTCTCTCTCGCTCAGAGTGGATAAACACGGCGGGGCCATGCGCCCATGCGCTCTCCCCATCGAGACGTAAC
GCACGTATCATGCAGTGCACCGCTCGCAGCAATGCACTGGCTGCAGTACATACGCAAACGCTTATAAGCCACGCACGAAC
CGTTTTCCTCTCTAGTGCCAGGCGACTAGAACCCTAGCCTACCCGCTGTCGGGAGAGGCCAATCTTTTGGCTCCGTCCTC
CNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNCGTGCGGATCAGGTAGCTTTAGGTTTTAGGGCCTTAGTGCCTTAGGTTTTGGGTCGTTC
GACGTCCTGGCTTCGACGGCGACAACGACGCTGAATAAAGAAGCTCAAATTCCTCCCTCGATGAGGCGATCAACTCTATG
GTTGGTGATGGAATTGGGAACTAGTCTATCCAAGCGGGGATGTTGTGGTGGCGGCGTCATCCTTGTGGCAGACATGTGTA
CTCGGGCTTCGCTGTTGCGATGACGTCTGCTCCAGCGCGGACGGGGAGCTTGGGAGATAATCAAGGAGCTGATGTAGATA
GTGGTCTGTATTAATGACATCTAGAAGACGAATTGTGTAGTGGGTTCGTGGTTGGTGGAAGGCAGGCATAATTTTCTCCT
CCGACGTTGGCGTGACAGA---------------CATGTCCAGGGTGTTGCCCTAGTCTAATTCGTTCAACGGCAATGAC
TTCGCCTTTGGTGAGTCACCTTGGAGACCCACAAAGCTGTAAATCAGCGGTGAAGCTACGTCGAGTTCGGATGAGGATGC
ATGTGATCTCTCATTTTTTCCATTGGTGGTTGCTGTGTTGCAGAGGCAGGTGATGGACGTCGATGTCAAGCTCAGGGGAC
TCTTCCACAGTGTTGACTGTAATTTTCTTTCCTGTGATTGATGAATAAATTCCAAAAAAAAAATGCGAGCACCAGCTTCA
AGTTTAAGACTTAAATGACCCTGGTAGGCATAGATACCACTGTACTTCTAACCGTTCTACCGGTTCGCTTCTCATCATTG
TTTACTGGTAGATCTTATCCCTATCCGATAGAAATCTTAACTAGAAAAAACAAATACCAGAGTACATGTATTCGAGCACT
GTCTCGCCCAGAGTGAATAAACACGGCGGGGCCATGCCC-CGTGCGCTCTCGCCATCGAGACGTAACGTACGTATCATGC
AGTGCACCGCTCGCGGCAATGCACCGGCCGCCTCTATTTATAGCCTCCCACGCCCCATCCTTTTCCACAT--CCCAGCCT
CAACAACCACCAAAGTACACACACCACACTAATCAAGTACACATCCA------GGCCACCAAGCCACCGAGCGAGCGATC
ACCATATCACACATAGCGCCATGTCTGGCGTGTGGGTGTTCCGCAACGGGGTGGTGAAGCTGGTGGAGAACCACCCCGCG
TCGGCGG----------------CGGGGCCACCGGGAGGCGGGGCGGTCCGGCGCAAGGCGCTACTGCACACGCCCACGG
GGGAGGTGGTCGCCTCCTACGCCTCCCTGGAGCGCAAGCTCGTCGCGCTTGGCTGGGAGCGCTACTACGCCGGCGGGGGC
GGCGCCGCCGGCGACTGTATGCTCAGGTTCCACAAGCGCTCCTCCGTCGACCTCATCTCCCTCCCCAAGGACTTCGGCCA
GTTCAGCTCCGTCCACATGTACGACGTCGTTATCAAGAACCGCGACGCCTTCCGCGTCATCGACGTCTAGCTGAGCTAGC
TGGCTGATC---CGGCCATTCGAT-GAAGCAAGCACAGCTAGGTCGTGCAAGCCGGCGGCCGCTACCGTCGCATCCATGT
CGTCATCGATCTCCGCTGGTTAACTTTTCCACCTTGTGTACGTGTGTGTATGTGTGTGTACGTAACCTGCACGTATATAC
GTGTGTATGTATATGTACGTTGTGTATTGACGTATATGTAGATATACATGATGCTTGTGCATTGTGGTTGATTAATT---
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>chr3A_749
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GTCTCGCCCAGAGTGAATAAACACGGCGGGGTCATGCCCG-GTGCGCTCTCGCCATCGAGACGTAACGTCCGTATCAGGC
AGTGCACTGCTCGCGGCAATGCACCGGTCGCCTCTATTTATAGCCTCCCACGCCCCATCCTTTTCTACAT--CCCAGGCT
CAACAATCACCAAAGTACACACACCACACTAATCAAGTACACATCCAGATCCAGGCCATCAAGTTACCCAGAGAAAGATC
ACCATATCACACATAGCGCCATGTCTGGCGTGTGGGTGTTCCGCAACGGGGTGGTGAAGCTGGTGGAGAACCACCCGGCG
TCGGCGG----------------CGGGACCTCCCGACGGCAGGGCGGTCTGGCGCAAGGCGCTGCTGCACACGCCCACGG
GGGAGGTGGTCGCCTCCTACGCCTCGCTGGAGCGCAAGCTCGTCACGCTCGGCTGGGAGCGCTACTATGCCGGTGGGGGC
GGCACCGCCGGTGACTGCATGCTCAGGTTCCACAAGCGCTCCTCTGTCGACCTCATCTCCCTCCCCAAGGACTTCGGCCA
GTTCAGCTCCGTCCACATGTATGACATCGTCATCAAGAGCCGCGACGCCTTCCGCGTCATCGACGTCTAGGCTTGCTGGC
TGGCTGATCGTCCAGCCATTCGATAGAAGCAAGCACAGCTAGCTCGTGCGCGCTGGCCGCCGCCACCGTCGCATCC----
--TCATCGATCTCCGCGGGTTAACTTTTCCACCTTGTGTATGTGTG------------TACGTGCCCTGCACGTATATGC
GTGTTTATGTATATGTACATGGTGTATTGACGTATATGTAGATATACATGCTGCGTGTGTATTGTGGTTAATTA------
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---------------------------------------------------
>chr3A_749
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GTCTCGCCCAGAGTGAATAAACACGGCGGGGTCATGCCCG-GTGCGCTCTCGCCATCGAGACGTAACGTCCGTATCAGGC
AGTGCACTGCTCGCGGCAATGCACCGGTCGCCTCTATTTATAGCCTCCCACGCCCCATCCTTTTCTACAT--CCCAGGCT
CAAAAATCACCAAAGTACACACACCACACTAATCAAGTACACATCCAGATCCAGGCCATCAGGTTACCCAGAGAAAGATC
ACCATATCACACATAGCGCCATGTCTGGCGTGTGGGTGTTTCGCAACGGGGTGGTGAAGCTGGTGGAGAACCACCCGGCG
TCGGCGGTGGGACCTCCCGACAGCGGG----------------CCGGTCTGGTGCAAGGCGCTGCTGCACACGCCCACGG
GGGAGGTGGTCGCCTCCTATGCCTCGCTGGAGCGCAAGCTCGTCGCGCTCGGCTGGGAGCGCTACTATGCTGGTGGGGGT
GGCGCCGCCGGCGACTGCATGCTCAGGTTCCACAAGCGCTCGTCCGTCGACCTC--------------------------
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---------------------------------------------------
>chr3B_842
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-------------CGGTAATGTACCGGCA-CCTCTATTTATAGCCTCCCACGCCCCATCCTTTTCCGCATCCCACAGCCT
CAACAACAACCCAAG--CACAGAGCGCACTGATCAAGTACACATCCG------GGCTCTCAAGCTACCCGGAGAAAGATC
ACCATATCACACATAGCGCCATGTCTGGCGTGTGGGTGTTCCGCAACGGGGTGGTGAAGCTGGTGGAGAACCACCCCGCG
TCGGCGG----------------CGGG----------------GCGATGCGGCGCAAGGCGCTGCTCCACACGCCCACTG
GGGAGGTGGTCGCCTCCTACGCCTCCCTGGAGTGCAAGCTCGTCGCACTCGGCTGGGAGCGCTACTACGCCGTCAGGGGC
GGCGCCGCCGGCGACTGCATGCTCAAGTTCGACAAGCGCTCCTCCGTCGACCTCATCTCCCTCCCCAAGGACTTCGGCCA
GTTCAGCTCCGTTCACATGTACGACGTCTTCATCAAGAACCGCGACGCCTTCTGCGTCATCGACGTCTAGCCTAGCTGGC
TGGCTGAAGATTCGGCCATTCGATCGAAGTAAGCACGGCTAGCTCGTCCGCGCCGGCGGCCGCCACCGTCGCATCCATGT
CGTCATCGATCTCCGCTGGTTAACTTTTCCACCTTGTCTA----------------------------------------
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---------------------------------------------------
>chr5A_1584
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AATATGTATTTGGCAACTGTGTCGCAGATTGCCAAAACAACCTAACCACCTGGCTGCCCTTCGATCCCGATCGCTAGATG
CACAGGAACTTCACGACCTCCTCCATCCACGACCTCTGATAATAGTACCACTGCTTTCCATTCCTGCCGCACTCTAGTGG
CAACCTCCTCGGGTGCCGCTGCTGCAGGCTGACCGTGTCACACCATACCGCCGCCGCCGCGCATCCTAATCATTCCACCG
CCGATAGCCTTCCCCTGTGCGGCTGTGGAGAGGA-CATCGCATGCTCCAGTCCTCTCACGCGATGGCATGCTCTAGTCCA
GTGTCACGCTGGTCGGCCGGTGCCCTCTCCTCTCGCGCAATGGCGTGCTCTAGTCCAGCATGCGCCTAGTCATCCGGCAT
CCTCTTCTCTCGCGTGATG-------------------------------------------------------------
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-------------------------------GATGAATGAATGCATCTGAATGTTCCAGCCACACCACAAACTAGTGCAG
ATCAGAGCATCCAAAGCGTTTCTCCCTTTAGTTTGGCTTGCTTGTTTGTTT
>SNPs
S-SS-SS-S-S---------------------------------------------------------------------
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----------------S---------------------------------------------------------------
------------------------------S------------SS---------S-S-----------------------
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----------------------S-----S---------S-------------------------------S---------
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-------------------------------------------------
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----------------------------------------------S------S--------------------------
-------------------------------------S--------------------S------------------SSS
----------------------S---------------S----------------------S-------------S----
---------S--S-------------------------------S-S-SS------S----S--------S---------
S---------------S-----S----------S-S---S------S---S-----S--------S--------------
--SSS------SS-----S---------------S--S---S-----S---------S---------S-----SS-----
----SS---S--S-------S-----------------S-----------S-------S------------S--------
-------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------------------SS---------------------------
-S------------S------------------------------------
>forward_684
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------------------------CCTATCGAAGCGGGGATGTC------------------------------------
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---------------------------------------------------
>reverse_2715
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--------------------------------------------------------------------------TGGAAT
TGGAGGCAAGTGCA------------------------------------------------------------------
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---------------------------------------------------
