>input_sequence_54418
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-------------------------------------------------ATGTCGGAGAGGAAGCGCCGGGCGGGGGCAG
ATGCGGCCGCGGGGGGCTCGACCTCGAAGAAACCGCGCGGCGCCTCGGCCGCCGCATCCTACGCCCAATCCCTCCGCTCG
AAGCTCCGCCCGGACGCCTCCATCCTCGCCTCCCTCCGCGCCCTCGCCTCCGCCGCCTCCAAATCCAAGCCCGCGGCCGC
GTCCTCAGCCGGCGCGAAAGCCCTCTCCGAGGACGACCCGGCATCCGCCTCCTCCAACTACATCGTGGTCGCCGACCAGG
ACACCACCTCCGTCACCTCCCGCATCAACCGCCTCGTCCTCTCCGTCGCGCGGAGCATCCTGGCTGGCCGCGGCTTCTCC
TTCGCCGTCCCCTCCCGCGCCTCCTCGAACCAGGTATACCTCCCGGACCTCGACCGCATCGTGCTCCTCCGCCGCGAGTC
CGCGAGGCCCTTCGCCAACGTCGCCACCGCGCGCAAGGCCACCGTCACCGCGCGCGTCCTCTCCCTCGTCCACGCCGTCC
TGCGCAGGGGCATCCACGTCACCAAGAGGGATCTCTTCTACACCGACGTGAAGCTCTTCGGCGACCAGTCCCAGTCGGAC
GCCATCCTCGATGACGTCTCCTGCATGCTTGGATGCACCCGCTCGTCGCTCCATGTCGTCGCCTCTGAGAAGGGCGTTGT
GGTTGGCCGCCTCACTTTTGCTGATGACGGCGACGTCATTGACTGCACGAGAATGGGCGTCGGCGGTAAGGCCATCCCGC
CCAACATCGACAGGGTGTCAGGCATTGAGAGCGACGCTCTGTTCATCTTGCTTGTGGAGAAAGATGCTGCTTTCATGCGC
CTCGCTGAGGACCGGTTCTACAACCGTTTTCCGTGCATCATATTGACAGCAAAGGGACAGCCGGATGTTGCCACCAGGTT
GTTCTTGCGCCGGCTTAAGGTAGAGCTGAAGCTGCCGGTACTCGCATTGGTGGACTCTGATCCATATGGGCTGAAGATCT
TGTCCGTGTATATGTGCGGCTCCAAGAACATGTCGTATGACAGTGCCAATCTGACAACGCCAGATATCAAGTGGCTTGGC
GTGCGGCCAAGTGATCTGGACAAGTACAGGGTACCGGAGCAGTGCCGGCTTCCCATGACTGATCACGATATCAAGGTAGG
AAAAGAGATGCTAGAGGAAGACTTCGTAAAGCAAAATGAAGGATGGGTCAAGGAGTTGGAGACGATGTTGCGAACAAAAC
AAAAGGCTGAGATTCAGGCTCTCAGCTCCTTTGGGTTCCAGTACCTGACTGAGGTATATCTACCCCTCAAGCTGCAGCAG
GAGGACTGGATTTGA-----------------------------------------------------------------
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>chr4A_1_TraesCS4A01G105600
TGCACCCCATCCCATCAGACCTTCTTTCATAGACAAGTAGTGATGTACTCCATCCGCTTATGTTTTTTACAGTACACATA
TACTACATAATTTTGCACTACATCCCCATCTGAATTTGACTAGTATACATTGCAGTACATCATTCTAATTTTGGTTAGAT
GCGTATGACTTCATAATTTTGGCTATTTGACTGAAGGTAATTAGTCAGAACATTTACATGGATTCCTCAAAAACAAAAGA
ACGTTCACATGGCATATTTGTTGTCAATTTTTTGAGCTGGACCATCCTGTCGTCAAATGCTAGCTCCGCCACTGGCTGCG
GTGCATCACCCCCGGCGTCGAGGGTACACGTAACGTGTTCATGTGCGAACAGAAGGGAGGCACGAGCTCCTCAGATATAC
AAATGCCACAAAAATTTGCATAAATCTTGCGTATATGAACATTGAGTGCTGCTATGCACACGACATGTTCCAGCCGATTG
TTGGACGATACTGCAATTCAGGCCATCGATACCTAGTACTAGGTGCAACACAGCCACTAGATTAAGAATCGTGCTTGAAT
CGTCCAACAGCTATCGGCTGTGAAGTAGTTTCGATGAACATTTTAGATGCCTAAAAAATTCAAATTCTTTGGTATCTTCT
ACTCCCTCTGTAAACTAATATAAAAGCGTTTAGATTGAATTTATTGTTCAGGCCGGGGGTAGATGGACAGTGAGTAAAAA
AACTTCACGGAGACAGTTG----TTTTTTTTAACCTTCACGGAGACATCTGGCGGCTGGCGCACAAGAAAAAAAACGTCA
GCGAGACGTGTTGCTGGGCCGAGCTACTACGGGCTTCGTGGGCCGCGCGCTTGGCGCATAGGGTAGGTGCGGAGTGCGGA
-CCGTCTCCGTCCCTCCCATGCTC----ACCAAAGCCTCAGCCACACTCCAGTTCGAATCCCGCCGCCGTCTCCGCCGTA
GTGCCCCCCACCCCTCCTCCCCGGTGATTCCGCCTCCAGATCTCTCCACATGTCGGAGAGGAAGCGCCGGGCGGGGGCAG
ATGCGGCCGCGGGGGGCTCGACCTCGAAGAAACCGCGCGGCGCCTCGGCCGCCGCATCCTACGCCCAATCCCTCCGCTCG
AAGCTCCGCCCGGACGCCTCCATCCTCGCCTCCCTCCGCGCCCTCGCCTCCGCCGCCTCCAAATCCAAGCCCGCGGCCGC
GTCCTCAGCCGGCGCGAAAGCCCTCTCCGAGGACGACCCGGCATCCGCCTCCTCCAACTACATCGTGGTCGCCGACCAGG
ACACCACCTCCGTCACCTCCCGCATCAACCGCCTCGTCCTCTCCGTCGCGCGGAGCATCCTGGCTGGCCGCGGCTTCTCC
TTCGCCGTCCCCTCCCGCGCCTCCTCGAACCAGGTATACCTCCCGGACCTCGACCGCATCGTGCTCCTCCGCCGCGAGTC
CGCGAGGCCCTTCGCCAACGTCGCCACCGCGCGCAAGGCCACCGTCACCGCGCGCGTCCTCTCCCTCGTCCACGCCGTCC
TGCGCAGGGGCATCCACGTCACCAAGAGGGATCTCTTCTACACCGACGTGAAGCTCTTCGGCGACCAGTCCCAGTCGGAC
GCCATCCTCGATGACGTCTCCTGCATGCTTGGATGCACCCGCTCGTCGCTCCATGTCGTCGCCTCTGAGAAGGGCGTTGT
GGTTGGCCGCCTCACTTTTGCTGATGACGGCGACGTCATTGACTGCACGAGAATGGGCGTCGGCGGTAAGGCCATCCCGC
CCAACATCGACAGGGTGTCAGGCATTGAGAGCGACGCTCTGTTCATCTTGCTTGTGGAGAAAGATGCTGCTTTCATGCGC
CTCGCTGAGGACCGGTTCTACAACCGTTTTCCGTGCATCATATTGACAGCAAAGGGACAGCCGGATGTTGCCACCAGGTT
GTTCTTGCGCCGGCTTAAGGTAGAGCTGAAGCTGCCGGTACTCGCATTGGTGGACTCTGATCCATATGGGCTGAAGATCT
TGTCCGTGTATATGTGCGGCTCCAAGAACATGTCGTATGACAGTGCCAATCTGACAACGCCAGATATCAAGTGGCTTGGC
GTGCGGCCAAGTGATCTGGACAAGTACAGGGTACCGGAGCAGTGCCGGCTTCCCATGACTGATCACGATATCAAGGTAGG
AAAAGAGATGCTAGAGGAAGACTTCGTAAAGCAAAATGAAGGATGGGTCAAGGAGTTGGAGACGATGTTGCGAACAAAAC
AAAAGGCTGAGATTCAGGCTCTCAGCTCCTTTGGGTTCCAGTACCTGACTGAGGTATATCTACCCCTCAAGCTGCAGCAG
GAGGACTGGATTTGAGATCTCTTCTGATGGCAGGTGAATAGATGATCGTGTTGCTCTTTATCTTTGTGTTCATGTTGAGT
TTGGTTGGTTTCATTACTGATCCAATACATTCTCATCTTCTTGATGCATTTTACCAAGGACATAAGCCTTATGCAAGTT-
AGTATAAAAATGTTATCATCTGTGACTGGGAATTACTCCCTCTGTCCCGTAATATGCGAGTGTTTTTTACACTAATATAA
AAGTGTTTTTTACACTACACTAGTGTCAAAAACGTCTTATATTATGGGACGGAGAGAGTAGTATTCAGTGTACCTTGGCA
TTACATAAGGGCATCCTTCCTCATGATTAGTAGACTGACAAAAGCGTAGAATATTCAATCAGGATGCACGAGTTAACCAA
TATTGCTACTAAACGTGGTATCATGTTTCCAGCTGCAGATGATACAGAGAAAGAGCAGCTTGATCTAGGAGCATCAATTT
GACACCTGCGGGGGGCTAGCTTAAAAATACCTCATCTGTGCTGCATAACATTTGTGCGGCAGTCCCTTTGTATGATTTTA
TGTATTTGAAAAACTGTATGTTGTGTACTTGTGATATCTGCATTTAGAAGTATCTGCATCTGTGGAATTAGATATGACTT
ATGTGTATTTGAAAATTTGTATGTTGTGTTTTTCTTGTACTGCTGAAGATAGAATTTGGTGTAAGTTCTGATGCCTGTAT
TTAGAAGCTAGCATTCGCATCTGGAAAATCGGTTGCAAGAGATT--AGAGCTACTGCCATACTTTAG---TTTTTTTTGG
AAGGGATACTTATGTTTATCTGTATATCCTGCTAAAACAAAATGTAGTTTGTTTCAATATTTATCTGTGCAAACGCATGC
ACAGGTCAGATCACCTGAAAGCTTTGGCCTCTTTGGTTGAAACTAGCATAGCCCGTGCGATGGCACGCTGCGCCTGATGA
TGCATTATATTTATACGGATCGTAAAGGCCATTGTTATATTTTTAATGATAGAATTGCATA
>chr4D_675
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----------------------------------TTGAATTTATTGTC---GCCGGGTGTAGATGGACAGCGAGTAAAAA
AACTTCACGGAGACATCTTTTTTTTTTTTTTAACCTTCACGGAGACATCTGGCGCACAAGA------AAAAAAGACGTCA
GCGAGACGTGTTGCTGGGCCGAGCTTCTACGGGCTTCGTGGGCCGCGCGCTTGGCGCATAGGGTAGGTGCGGAGTGCGGA
-CCGTCTCCGTCCCTCCCATGCTCCCCAACCAAAGCCACAGCCACACTCCAGTTCGAATCCTGCCGCCGTCTCCGCCGTA
GTGTCCCCCACCCCTCGTCCCCGGTGATTCCGCCTTCAGATCTCTCCACATGTCGGAGAGGAAGCGCCGGGCTGGGGCAG
ATGCGGCCGCGGGGGGCTCGACCTCGAAGAAACCGCGCGGCGCCTCGGCCGCCGCATCCTACGCCCAATCCCTCCGCTCG
AAGCTCCGCCCGGACGCCTCCATCCTCGCCTCCCTCCGCGCCCTCGCCTCCGCCGCCTCCAAATCCAAGCCCGCGGCCGC
GTCCTCAGCCGGAGCGAAAGCCCTCTCCGAGGACGACCCGACCTCCGCCTCCTCCAACTACATCGTGGTCGCCGACCAGG
ACACCACCTCCGTCACCTCCCGCATCAACCGCCTCGTCCTCTCCGTCGCGCGGAGCATCCTGGCTGGCCGCGGCTTCTCC
TTCGCCGTCCCCTCCCGCGCCTCCTCGAACCAGGTATACCTCCCGGACCTCGACCGCATCGTGCTCCTCCGCCGCGAGTC
CGCGAGGCCCTTCGCCAACGTCGCCACCGCGCGCAAGGCCACCGTCACCGCGCGCGTCCTCTCCCTCGTCCACGCCGTCC
TGCGCAGGGGCATCCACGTCACCAAGAGGGATCTCTTCTACACCGACGTGAAGCTCTTCGGCGACCAGTCCCAGTCGGAT
GCCATCCTCGACGACGTCTCCTGCATGCTTGGGTGCACCCGCTCGTCGCTCCATGTCGTCGCCTCTGAGAAGGGCGTTGT
GGTTGGCCGCCTCATTTTTGCTGATGACGGCGACGTCATCGACTGCACGCGAATGGGCGTCGGCGGTAAGGCCATCCCGC
CCAACATCGACAGGGTGTCAGGCATCGAGAGCGACGCTCTGTTCATCTTGCTTGTGGAGAAAGATGCCGCTTTCATGCGC
CTCGCCGAGGACCGGTTCTACAACCGTTTTCCATGCATCATATTGACAGCAAAGGGGCAGCCGGATGTTGCCACCAGGTT
GTTCTTGCGCCGGCTTAAGGTAGAGCTGAAGCTGCCCGTTCTCGCATTGGTGGACTCTGATCCATATGGGCTGAAGATCT
TGTCAGTGTACATGTGTGGCTCCAAGAACATGTCGTATGACAGTGCCAATCTTACAACGCCGGATATCAAGTGGCTCGGC
GTGCGGCCAAGTGATCTGGACAAGTACAGGGTACCGGAGCAGTGCCGGCTTCCCATGACTGATCACGATATCAAGGTAGG
AAAAGAGATGCTAGAGGAAGACTTCGTGAAGCAAAATGAAGGGTGGGTGAAGGAGTTGGAGACGATGTTGCGAACAAAAC
AAAAGGCTGAGATTCAGGCTCTCAGCTCCTTTGGGTTCCAGTACCTGACTGAGGTATATCTACCCCTCAAGCTGCAGCAG
GAGGACTGGATTTGAGATCTCTTCTGATGGCAGGTGAATAGATGGTCGCGTTGCTCTTTATCTTTGTGTTCATGTTAAGT
TTGGTTGATTTCATTAGTGATCCAATACATTCTCATCTTCTTGATGCATTTTACCAAGGACATAAGCCTTATGCAAGTT-
AGTAGAAAAATGTTATGATCTGTGACTGAGAATTAC--------------------------------------------
---------------------------------------------------------GTAGTATTCAGTGTACCTTGGCA
TTACATAAGGGCATCCTTCCTCATGACTAGTCGACTGAC-AAAGCGTAGAATATTCAATCAGGATGCACGAGTTAACCAA
TATTGCTACTAAACCTGGTATCATGTTTCCAGCTGCAGATGATACAGAGAAAGAGCAGCTTGATCTAGGAGCATCAATTT
GACACCCGCGGGGGGCTAGCTTAAAAATACCTCATCTGTGCTGCATTACATTTGTGCGGCAGTCCCTTTGTATGATTTTA
TGTATTTGAAAAACCGTATGTTGTGTACTTGTGAGACCTGCATTTAGAAGTATCTGCATCTGTGGAATTAGATATGACTT
ATGTGTATTTGAAAATTTGTATGTTGCGTTTTTCTTGTACTGCTGAAGATAGAATTTGGTGTAAGTTCTGATGCCTGTAT
TTAGAAGCTAGCATTCGCATCTGGAAAATGGGTTGCAAGAGATTAGAGAGCTACTGCCATACTTTAG---TTTTTTTTGG
TGGGGATACTTATGTTTATCTGTATATCTTGTTAAAACAAAATGTAGTTCGTTTCAATATTTATCTTTG-----------
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>chr4B_711
TGAGG---------------------------------------------------------------------------
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----------------------------------------------------------------------------AAAA
AAAATCACAGAGGCATTTTTTTTAG------AACCTTCACGGAGACATCTGGCGCACAAGA------AAAAAAAACGTCA
GCGAGACGT--TGCTGGGCCAAGTTAGTACGGGCTTCGTGGGCCGCGCGCTTGGCGCATAGGGCA------GAGTGCGGA
CCCGTCTCCGTCCCTCCCATTCTCCCCAACCAAAACCACAGCCACACTACAGTTCGAATCCCGCCGCCGTCTCCGCCGTA
GTGCCCCCCACCCCTCCTCCCCGGTGATTCCGCCTCCAGATCTCTCCACATGTCGGAGAGGAAGCGCCGGGCGGGGGCAG
ATGCGGCCGCGGGGGGTTCGACCTCGAAGAAACCGCGCGGCGCCTCGGCTGCCGCATCCTACGCCCAATCCCTCCGCTCG
AAGCTCCGCCCGGACGCCTCCATCCTCGCCTCCCTCCGCGCCCTCGCCTCCGCCGCCTCCAAATCCAAGCCCGCGGCCGC
GTCCTCAGCCGGAGCGAAAGCCCTCTCCGAGGACGACCCGGCCTCCGCCTCCTCCAACTACATCGTGGTCGCCGACCAGG
ACACCACCTCCGTCACCTCCCGCATCAACCGCCTCGTCCTCTCCGTCGCGCGAAGCATCCTGGCTGGCCGCGGCTTCTCC
TTCGCCGTCCCCTCCCGCGCCTCCTCAAACCAGGTATACCTCCCGGATCTCGACCGCATCGTGCTCCTCCGCCGCGAGTC
CGCGAGGCCCTTCGCCAACGTCGCCACCGCGCGCAAGGCCACCGTCACCGCGCGCGTCCTCTCCCTTGTCCACGCCGTCC
TGCGCAGGGGCATCCACGTCACCAAGAGGGATCTCTTCTACACCGACGTGAAGCTCTTCGGCGACCAGTCCCAGTCGGAC
GCCATCCTCGATGACGTCTCCTGCATGCTTGGATGCACCCGCTCGTCACTCCATGTCGTCGCCTCTGAGAAGGGCGTTGT
GGTTGGCCGCCTCATTTTTGCTGATGACGGCGACGTCATCGACTGCACGCGAATGGGCGTCGGCGGTAAGGCCATCCCGC
CCAACATTGACAGGGTGTCAGGCATTGAGAGCGACGCTCTGTTCATCTTGCTTGTGGAGAAAGATGCTGCTTTCATGCGC
CTCGCCGAGGACCGGTTCTACAACCGTTTTCCGTGCATCATATTGACAGCAAAGGGCCAGCCGGATGTTGCCACCAGGTT
GTTCTTGCGCCGGCTTAAGGTAGAGCTGAAGCTGCCGGTGCTCGCATTGGTGGACTCTGATCCATATGGGCTCAAGATCT
TGTCCGTGTATATGTGCGGCTCCAAGAACATGTCATATGACAGTGCCAATCTTACAACGCCAGATATCAAGTGGCTCGGC
GTGCGGCCAAGTGATCTGGACAAGTACAGGGTACCGGAGCAGTGCCGGCTTCCCATGACTGATCACGATATCAAGGTAGG
AAAAGAGATGCTAGAGGAAGACTTCGTGAAGCAAAATGAAGGGTGGGTGAAGGAGTTGGAGACGATGTTGCGAACAAAAC
AAAAGGCTGAGATTCAGGCTCTCAGCTCCTTTGGGTTCCAGTACCTGACTGAGGTATATCTACCCCTCAAGCTGCAGCAG
GAGGACTGGATTTGAGATCTCTTCTGATGGCAGGTGAATAGATGATCGTGCTGCTCTTTATCTTTGTCTTCATGTTAAGT
TAGGTTGATTTCATTACTGATCCAATACATTCTCATCTTCTTGATGCATTTTACCAAGGACATAAGCCTTATGCGAGTTA
AGTAGAAAATTGTTATCATCTGTGGCTTAGAATTAGTATTTA--------------------------------------
--------------------------------------------------------------------TGTACCTTGGCA
TTGCATAAAGGCATCCTTCCTCATGACTAGTCGACTGAC-AAAGCGAAGAATATTCAATCAGGATGCATGAGTTAACCAG
TATTGCTACTAAACCTGGTGTCATGTTTCCAGCTGCAGATGATTTAGAGAAAGAGCAGCTTGATCGAGGAGCATCAATTT
AACACCTGCGGGGGGCTAGCTTAAAAATATCTCATCTGTGCCGCGTAACATTTGTGTGGCAGTCCCTTTGTATGATTTTA
TGTATTTGAAAAACCGTATGTTGAATACTTGTGAGACCTTTATTTAGAAGTATCTGCATCCGTGGAATTGGATATGCCTT
ATGTGTATTTGAAAAAAATTATGTTGCGTTTTTCTTGTACTGCTGAAGATATAATTTGGTGTAACTTCTGATGCCTGTAT
TTAGAAGCTAGCATTCGCATCTGGAAAATCAGTTGCAAGAGATTAGAG--CTACTGCGATACTTTATCTTTTTTCTTTTG
CGGGGATACTTATGTTTATCTGTA--------------------------------------------------------
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>SNPs
--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-------------SSSS------S------------S---------
---------------S--S-----------------------------------SSSSSSSSSSSSS-------------
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------------S-----------------------------S-------------------------------------
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--------------S------------------------S---------S------------------------------
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-----S--------------------------------------------------S-----------------------
---------------------------------------S----------------------------------------
----------------------------------------------------S-----------------------S---
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---------------------------S--------------S-----S-------------------------------
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----------------------------------------------------------------------------S---
-------S------------------------------------------------------------------------
----S-----------------------S--------SSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----------------------
--------------------------S----S-------S----------------------------------------
--------------S-----------------------------------------------------------------
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--------------S-------------------S-S-------------------------------------------
--------------------------S-----------------------------------------------------
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SS--------------------------S--S-----------------S----------------S--SSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_467
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-----------------------------------------------GCTGCTATGCACACGACATG-------------
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>reverse_1960
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---------------------------------------ACTCGCATTGGTGGACTCTG---------------------
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>forward_479
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-----------------------------------------------------------ACGACATGTTCCAGCCGATT-
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>reverse_2203
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------------------------------------------ATGGGTCAAGGAGTTGGAGAC-----------------
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>forward_578
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------------------------------------------------------------------------------AT
CGTCCAACAGCTATCGGC--------------------------------------------------------------
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>reverse_2518
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-------------------------------------CCCTCTGTCCCGTAATATGCG----------------------
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