>input_sequence_57574
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--------------------------------------------------ATGAATCGACGCTCGCGCCGCAGAGGCAAG
CGCGGGCGCACGAGCCCGGACCCCCCAGCGAAGCGCCGCCGCGGCCCGCTGGAGTCGATGCCCGGCGAGCTGGAGGCCGC
TCCAGCTCCAGC------------------------------GCCGTCCGTAGTGATGGTCGCCGGGCTGCCGCCCGGGT
GCGGGGTGATAGAGCTAAAGTCGCGCCTGGAGGCGTACGGC-CCCGTCGCGCGCACTCGCATAGACGCAGCCGCGGCCAC
CGGGCACGTCTCCTTCCGCTCCGCTGCCGCTGCCACGGCCGCCATTGCCGCTTCCCTCGACCCCGAGTGCGGCATCACCA
TCGGATCCAAGAAGGTAAAGATCTAC-----GTTTGCTGAAGCGTGATGTCGCAGTTGCTGGATTCAGCATCAGGGGAGC
CAATTTTTTGCTAGATTCGGGCCAATGCTAACTTGCTGTACATCTAGCAAGATCCGGTTAAGGTTCCAGCCTTCTTT---
---------TACTTGTAGTGCCAAAACAGCTGGATTTGTTGAGGTGCAAACCAGCTAGTTGATGGTGAATGCGTGAATTT
CCCTGATGCCTCTAACA-----AGGCTAGACCAGGCATTGGTAGTCCATTACCCCTTTTAGGTTCATATTATGTTGGTAG
GTTTTAGCTCAGTTCAGACATGTCAAACCCAATCTGGTTGTTCACTTTTGTCATTCACTTGGTAGTTTAA---TTTTTAT
TTACCCAAGCATTCTAGATTTTCGTAATCTAATCAATTTGCATACTCAT-TATCTCTGCAAAGTT-GATTGACTATTTGA
TATGTTGTGCTTCATA--GCAGTAACAATAACTGATTAAAATGGCAGGACTTGCAAAATTGAATACAGACCAGAATTAAG
CATTTATATCTGTGATATACTGCTTGACATCACCCAATAGACTCTGTTGATCTCTGTGAGATT------------CTTGC
TCAATTCATATGAAGCGTATGGGTGTGGGTTTCAGATGTATACTGTGTCTTGCTTTCACTTTATTCGCCAACCTTTGGTA
CTCAGATTGGTGTTTCTTTCGTTTGATACAGGTTTTAGTTGTACAGGCAAGTGAGGCGCCAAACAATTCGACAAGCGTAG
TTCAATCAGACCCAGCGGATGCGAGTAACAATTTTGTGAGTGATGCTTTGGCCATCCCAAGCTCCAGAATAGCTCCAGAA
GCAATCCACAAAGCGCGAGAAATAGTCGCTTATGATGATCTGTTCTGA--------------------------------
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>chr3A_1_TraesCS3A01G319200
GTTATTTATGAAAATCGCTCAGAAAAAATGTGTAGATTCCAAAAATGCTATTATCTTACATGTTAATCATTTAAGAAAAA
TAGTACTTTTTCTTATATGTGGTAATTCGAAAATGTCAATTATATATGTTTTCCACTCATTTAAATTGACTAGATAAGAT
AGTTAGATGCTCTCACAAAATATATTATTTGGTGCCTAGCTTTCGCTCCTTTTTTTTAAAAAAAAACTACTAGCTAGCTT
TTGTTCTTTTTCAAAGAAAAACTACTAGCTAGCTTAGTGATATATATGTACGTGTAGAAATATATGTCTACATGTCGTTG
TGT--------------------------------------ATGTAAAGCAGTTGATGGTCGGCTACAAATGACATGGAC
TAAAAAGGAATAATGTCCGATTCGCGCGCGCGCGGGGGGGAGGGGGCGCAAGGGAGGTAGGGCCTGGAGTTTGCACAAGC
CGTGACATCAGACGGTGATTGGAAGGGCAGGAGGTCTCGACCAGATATCAATCATGATCTTGCCTAACACAAACAAACAT
GTTTTGCTTGCTCCCACCGTTACTCCAGATTAATCTACTTGATGTTATTGTTACTATTAAATTTGTTCATAATATTATTT
ATTT---------------------------TTAATAAGCTGAAGTAAGTTGACTCGGGACCAAATCTCATGTTTCAAAT
TGACATCCTGAGAAATCCTACCCTCAGTTGATTCATTGTTCGACATGTTGTTCATTGTTTTGGAAGCTCACTGCGCCGAA
TGACCACTGGTTGTGATGTTAAAACAGAGGGCATGGACTTGTGAAGAGTGGTGAGAATGCTTATGATATTAGAGACGTGT
GTTATTGTTTGATCTCCCG--------------CACATTTACAGGTAGTATAAATCTAAGTTCTTCTCCAAAGAAATTAT
AAATCAAGTAGCACAACCATATATCAGAAAAACAACGCCGCAGA--GTCTCAAAAGGCGACCAGCCACGAAACCAACTGA
AGTCTGAGCTCTGG---------CACCCTCAATCTGTACGGACTAGAGTCATGAATCGACGCTCGCGCCGCAGAGGCAAG
CGCGGGCGCACGAGCCCGGACCCCCCAGCGAAGCGCCGCCGCGGCCCGCTGGAGTCGATGCCCGGCGAGCTGGAGGCCGC
TCCAGCTCCAGC------------------------------GCCGTCCGTAGTGATGGTCGCCGGGCTGCCGCCCGGGT
GCGGGGTGATAGAGCTAAAGTCGCGCCTGGAGGCGTACGGC-CCCGTCGCGCGCACTCGCATAGACGCAGCCGCGGCCAC
CGGGCACGTCTCCTTCCGCTCCGCTGCCGCTGCCACGGCCGCCATTGCCGCTTCCCTCGACCCCGAGTGCGGCATCACCA
TCGGATCCAAGAAGGTAAAGATCTAC-----GTTTGCTGAAGCGTGATGTCGCAGTTGCTGGATTCAGCATCAGGGGAGC
CAATTTTTTGCTAGATTCGGGCCAATGCTAACTTGCTGTACATCTAGCAAGATCCGGTTAAGGTTCCAGCCTTCTTT---
---------TACTTGTAGTGCCAAAACAGCTGGATTTGTTGAGGTGCAAACCAGCTAGTTGATGGTGAATGCGTGAATTT
CCCTGATGCCTCTAACA-----AGGCTAGACCAGGCATTGGTAGTCCATTACCCCTTTTAGGTTCATATTATGTTGGTAG
GTTTTAGCTCAGTTCAGACATGTCAAACCCAATCTGGTTGTTCACTTTTGTCATTCACTTGGTAGTTTAA---TTTTTAT
TTACCCAAGCATTCTAGATTTTCGTAATCTAATCAATTTGCATACTCAT-TATCTCTGCAAAGTT-GATTGACTATTTGA
TATGTTGTGCTTCATA--GCAGTAACAATAACTGATTAAAATGGCAGGACTTGCAAAATTGAATACAGACCAGAATTAAG
CATTTATATCTGTGATATACTGCTTGACATCACCCAATAGACTCTGTTGATCTCTGTGAGATT------------CTTGC
TCAATTCATATGAAGCGTATGGGTGTGGGTTTCAGATGTATACTGTGTCTTGCTTTCACTTTATTCGCCAACCTTTGGTA
CTCAGATTGGTGTTTCTTTCGTTTGATACAGGTTTTAGTTGTACAGGCAAGTGAGGCGCCAAACAATTCGACAAGCGTAG
TTCAATCAGACCCAGCGGATGCGAGTAACAATTTTGTGAGTGATGCTTTGGCCATCCCAAGCTCCAGAATAGCTCCAGAA
GCAATCCACAAAGCGCGAGAAATAGTCGCTTATGATGATCTGTTCTGATAGGCGTTCTTCCTCTAGATAAGGGAGAAATC
AGTGTGCTGTTGTGCAATATTAGGGTCTTTAGGTGTCTAACTGTAACCGAG----GTATCTCCTATCTTGTGATGTTGCA
CTGTAGGCTGCAACTAATTGCTTGTCTTCATCATTGAACCTATGTGTAGATCAAGCAGTGTCGTACTATGTGAGTTTTCA
CTGAATTAATTTACTACCATGCAAATCAGGCATTATACATGATTACATTCGTACTAGAAACAAAGTGATGTAGGCAAAAA
AGAAACCAGAAAGCAACTCCTGGTTAACCAAAATTGTGTTCTCGACCAGCATAAAAAGTAGCAACAATAAAATTTAAAGG
GCACATCATCTGTACTCCATGTATATCCTGGAAGAAATGGTATCAAATAGTTAGCCTATACACACAAGCTATTATTTACA
CATTAGTATCTGGGAAATGAGCAAGTTCCTTTCTCAGTGTGGGCGAGATTCTTTCTGCAGCATGATGTCATTGGACCTTG
CCAGCATTTTCACTGAATGGCTTGCCTCATCTTGGTGATAGTTGGGTGCTTTATCAACTTCAGTCTGTTGGTACACCACT
TACTTGAGCTCTTTCA--AATGGTGACTTTACTGACTCAGAACACATTGCAGCTGAACTGAGCAATTATGTGCTATTCTT
GAAGCTTCTTGCCTTCCTTTTGGGGTACCACTCAGCATGTCTCACTAATGTTGCTACAAATTTTTAAAATAAAGAAAGTT
AAGGAGAATCCCAAGTAGT-------------------AATCTGTGTGCTGGTAAGATAAACGAAGACGTAAATTCTAGG
CCAATGTCACAACAGGTTAAATACAAGGTATAGCCAAAATGCATCATTTGTTGAAAGAGGAGAATAGCCTTGTAATAATA
TCTGCCTGCCCAATTATTCA--------TAGGATAGTGTTGATATGACTGGTTGATTACTGTCAGAAGTAACCAACGTTC
TACACAGATAGATTGGTCAAAAAAAGCAGACATAATTCTAA
>chr3D_1
GTTATTTATGAAAATCGCTCAGAAAAAATGTGTAGATTCCAAAAATGCTATTATCTTACATGTTAATCGTTCAAGAAAAA
TAGTACTTTTTCTTATATGTGATATTTTGAAAATGTCCATTACATATGTTTTCCATCCATTTAAATTGACTAGATAGGAT
AGTTTGATGCTCCCACAAAATATATTA-TTGGTGCCTAGCTTTCGTTCCTTTTTAAAGAAG--AAACTACTAGCTAGCTT
TTGTTCTTTTCCAAAGAAAAACTACTAGCTAGCTTAGTGATATATATGTACGTGTAGAAACATATGTCTACATGTCATTG
TGTACAGTGGGGCCGCCGCCATTGCATGTCAACGCTCATCAATGTGAAGCAGTTGATGGTCGGCTACAAATGACATGGAC
TGGAAAGGAGCAATGTCAGATTCA-------------------GGGGGCAAGGGAGCTAGGGTCTGAAGTTTGCACGAGC
CGCAACATCAGACGGCGATTGGAAGGGGAGGAGGTCTCGACCAGATATCAATCATGATCTCGCCTAACACAAACAAGCAT
GTTTTGCTTGCTCCCACCGTTACTCCAGATTTTAAATTTAGCTCATGACATCATGTCCAAATTTATTAATAATGTTATTA
CTTCAAATTTTAATTTTAATTTCAAAATGAATTAATAAGCTGAACTAAGTTGACTCGGGACCAAATCTCATGTCTCAAAT
TGACATCCTGAGAAATCCTACCCTCATTTGATTCATTATTCCACATGTTGTTCATTGTTTTGGAAGCTCACTGTGCCGAA
TGACCATTGGTCGTGATGTTAAAATAGAGGGCATGGACTTGTGAAGAGTCATGAGAATGCTTATCATATTAGAGACGTGT
GTTATTGTTTGATCTCCCGTTGCAACGCATGGACACATTTACAG---GTATAAATCTAAGTTCTTCTCCGAAGAAATTAT
AAATCAAGTAGCACAACCGTATGTCAGAAAAACAACGCCGCAGAAAGTCTCAAAAGGCGCCCAGCCACAAAACCAACTGA
AGTCTGAGCTCTGAAGCGGCGGCCACCCTCAATCTGTACGGACTAGAGTCATGAATCGACGCTCGCGCCGCAGAGGCAAG
CGCGGGCGCACGAGCCCGGACCCCCAGGCGAAGCGCCGCCGCGGCCCGCTGGAGTCGATGCCCGGCGAGCTGGAGGCCGC
TCCAGCTCCAGTGCCGGCGCCGGCGCCGGCTGCGGCTGCGCAGCCGTCCGTAGTCATGGTCGCCGGGCTGCCGCCCGGGT
GCGGAGTGATAGAGCTAAAGTCGCGCCTGGAGGCGTACGGCACCA-TCGCGCGCACTCGCATAGACGCCGCCGCGGCCAC
CGGGCACGTCACCTTCCGCTCCGCTGCCGCTGCCACGGCCGCCATTGCCGCTTCCCTCGACCCCGAGTGCGGCATCACCA
TCGGATCCAAGAAGGTAAAGATCTAC-----GTTTGCTGAAGCGTGATGTCGGAGTTACTGGATTCAGCATCAGGGGAGC
CAATTCTTTTACTAGATACGGCCAATGGTAACTTGCTGTACATCTAGCAAGATCCGGTGAAGGTTCCAGCCTTTTTTTAT
TAGGTTTATTACTTATAGTGCCAAAACAGATGGATTTGTTGAAGTGCAAAGCAGTTATTTGATGGTGAATGCGCGAATGG
CACCGATGCTTCTTCCAAACCTAGGCCAGACCAGGCATTGGTAGTCCATTACCCCTTTTAGGTTCATATTATGTTGGTAG
GTTTTAGCTCAGTTCAGACATGTGAAACCCAATCTGGCTGTTCACTTTTGTCATTCACTTGGTAGTTTAATTTTTTTTAT
TTACCCAAGCATTCTAGATTTTCTTAATATAATCAATGTGCATGCTCATCTAGCTCTGCAAAGTTGGATTGACTATTTGA
TATGCTGTGCTTCATATAGCAGTAACAATAACTGATTAAAATGCGAGGACTTGCAAAATTGAATACAGACCAGAATTAAG
CATTTATATCTGTGATATACTGCTTGACATCACCCAATAGACTCTGTTGATCTCTCTGAGATT------------GTTGC
TCAATTCATATGAAGCGTACGGTTGTGGGTTTCAGATGTATACTGTGTCTTGCTTGCACTTTATTTGCCAACCTTTGGTA
CTCAGATTGGTGTTTCTTTCGTTTGATACAGGTTTTAGTTGTACAGGCAAGTGAGGCGCCAAATAATTCGACAAGCGTAG
TTCAATCAGACCCAGCAGATGCGAGTAACAATATTGCTAGTGATGCTTTGGCCATCCCAAGCTCCAGAATAGCTCCAGAG
GCGATCCACAAAGCGCGAGAAATAGTCGCTTATGATGATCTGTTCTGATAGGCATTCTTCCTCTAGATAAGGGAGAAATC
AGTGTGCTGTTGTGCAATATTAGGGTCTTTAGCTGTCTAACTGTAACTGAGAGGGGTATCTCCTATCTCGTGATGTTGCG
CTGTAGGCCACAACTAATTGCTTGTCTTCATCATTGAACCTATGTGTAGATCAAGCAGTGTCGTACTATGTGACTTTTCA
CTGAATTAATTTATTACCATGCAAATCAGGCATTATACATGATTACATTTGTACTAGAAACAAAGTGGTGTAAGCAAAA-
-------AGAAAGCAACTCCTGGTTAAACTTTCTGTAATGTTG------------------------TAAAATTTAAAGG
GCACATCATCTGTACTCCATGTATATCATGGAAGAAATGGTATCAAATAGTTGGCCTATACACACAAGCTATTATTTACA
CATTAGTATCTGGGAAATGAGCAAGTTTCTTTCTCAGTGTGGGCGAGATTCTTTCTGCAGCATGATGTCATTGGACCTTG
CCAGCATTT-CACTGAATGGTTTGCCTCATCTTGGTGATAGTTGGGTGCTTTATCAACTTCAGTCTGTTGGTACACCACT
TACTTGAGCTCTTTCATTAATGGTGACTTTACTGACTCAGAACACATTGCAGCTGAACTGAGCAATTATGTGCTATTCTT
GCAGCTTCTTGCCTTCCTTCTGGGGTACCACTCAGCATGTCTCACTAATGTTGCTACAAAATTTTAAAATAAAGAAAGTT
AAGGAGAATCCCAAGTGTCACAACAGGTCACCCTCCAAAATCTGTGTGCTGGTAAGATAAACGAAGACGTAAATTCTAAG
CCAATGTCACAACAGGTTAAATACAAGGAATAGCCAAAATGCATCATTTGTTGAAAGAGGAAAAGAGCCTTGTAATAATA
TCTGCCTGCCCAATTATTCA--------TA--------TTGATATGACTGGTTGATTACTGTCAGAAGTAACCAACGTTC
TACACAGATAGATTGGTCAAAAAAAGCAGACATAATTCTAA
>chr3B_937
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---------------------------------------------------------CGACCAGCCACAAAACCAACTGA
AGTCTGAGCTCTGAAGCGGCGGCTACCCTCAATCTGTACGGACTAGAGTCATGAATCGACGCTCGCGCCGTAGAGGCAAG
CGCGGGCGCACGAGCCCGGACCCCCCGGCGAAGCGCCGCCGCGGCCCGCTGGAGTCGATGCCCGGCGAGCTGGAGGCCGC
TACAGCTCCAGTGCCGGCGCCGGCTGCGGCTC------CGCAGCCGTCCGTAGTGATGTTCGCCGGGCTGCCGCCCGGGT
GCGGAGTGATAGAGCTAAAGTCGCGCCTGGAGGCGTACGGC-CCA-TCGCGCGCACTCGCATAGACGCCGCCGCGGCAAC
CGGGCACGTCACCTTCCGCTCCGCTTCCGCTGCCACGGCCGCCATTGCCGCTTCCCTCGACCCCGAGTGCGGCATCACCA
TCGGATCCAAGAAGGTAAAGATCTACAGTACGTTTACTGAAGCGTGATGTCGGAGTTGCTGGATTCAGCATCAGGGGAGC
CAAAATTCTGCTAGATTCGTT-CAATGCTAACTTGCTTTACATCTAGCAAGATCCGGTAAAGGTTCGAGCCTTCTTTACT
AGGT----TTACTTGTAGTGCCAGAACAGTTGCATTTGTTAAAGTGCAAGCCAGCCATTTGATGGTGAATGCGCGAATTT
CACTGATGCTTCTTACA-----AACCTAGGCCATTCCCTAT--------------TTTTAGGCCCATATTATGTTGGTAT
GT---------------------GAAACCCAATCTGGTTTTTCAGTTTTGTCATTCATTTGGTTATTTATT---------
------------------TTTTCTTAATCCAATCAATTTGCATGCTCATCTAGCTCTGCAAAGTTGGATTGACTATTTGA
TATGTTGTGCTTCATA--GCAGTAACAATAACTGATTAAAATGCCAGGACCTGTAAAAATTAATGGAGACCAGAATTAAG
CATTTATATCTGTGATATACTGTTTGACATCACCCAATAGGCTCTGTTGATCTCGGTGAGATTGTTGCTAACTTTGTTGC
TCAATTCGTATGAAGCATACTGTTGTGGGTTTCAGATGTATACTGTGTCTTGCTTGCACTTTATTTGCCAACTTTTGGTA
CTCAGATTGGTGTTTCTTTCGTTCGATACAGGTTTTAGTTGTACAGGCAAATGAGGCGCCAAATAATTCGACGAGCGTAA
TTCAATCAGAGCCGGCGGATGCGAGTAACAATATTGCAAGTGATACTTTGGCTATCCCAAGCTCCAGAATAGCTCCAGAA
GCGATCCACAAAGCGCGAGAAATAGTCGCTTATGATGACCTGTTCTGATACGCACTCTTCCTCTAGACAAGGGAGAAATC
AGTGTGCTGTTGTGCAAAATTAGGGTCTTTAGCTGCCTAACTGTAACCA--AGGGGTATCTCCTATCTCATGATGTTGCG
CTGTAGGCCGTGACGAATTGCTTGTCTTCATCATTGAACCTATGTCGTACTGTGTAGCAGAAATTTGCTTCTAACATCGT
TCAAAAGATG----------------------------------------------------------------------
-----------------------------------------------------------------AAAAAAAATTAAAGG
GCACATCATTTGTACTCCATG--TATCATGGAAGAAATGGTATCAAATAGTTGGCCTATACACACAAGCTATTATTTACA
CATTATTATCTGGGAAATGAGCAGGTTTCTTTC-CAGTGTGGGCGAGATTCTTTGTGCAGCATGATGTCATTGGACCTTG
ACAGCATTT-CACTGAATGGCTTGCCTCATCTTGGTAATAGTTGGGTGCTTTATCAACTTCAATCTGTTGGTACACCACT
TACTTGAGCTTTTCCATTAATGGTGACTTTACTGACTCAGAACACATTGCAGCTGAACTGAGCAATTATGTGCTATTCTT
GAAGCTTCTTGACTTCCTTTTGGGGTACCACTCAGCATGTCTCACTAATGTTGCTACAAAATTTTAAAATAAAGAAAGTT
AAGAAGAATCCCAAGTAGT-------------------AATCTGTGTGTTGGTAAGATAAACGAAGACGTAAATTCTAGG
CCAATGTCACAACAGGTTAAATACAAGGTATAGCCAAAATGCATCATTTGTTGAAAGAGGAAAAGAGCCTTGTACTAATA
TCTGTCTGCCCAATTATTCATAGGATAGTA--------TTGATATGACTGGTTGACTACTGTCAGAAGTAATCACTGTTC
TACACAGATAGACTGGTCAAAAAAATCAGGCATCGTTCTAA
>SNPs
--------------------------------------------------------------------S--S--------
---------------------S--S--S---------S----S------------SS-------------------S---
----S-------S--------------S-----------------S--------SSSS--SSS-----------------
----------S-------------------------------------------------S---------------S---
---------------------------------------------S----------------------------------
-SS------SS------S-----SSSSSSSSSSSSSSSSSSSS---S---------S-----S---S---------S---
--SS-----------S-----------S--------------------------------S---------------S---
-------------------------------SSSSSSS-S-S-SS-SSSS-S-SSSSS------S--S-----S-----S
S--S----------------------------------------S----------------------------S------
--------------------------S----------S---S-------------------------------S------
------S----S------------S------------------------SS-------------S---------------
--------------------------------------------SSS----------------------S----------
------------------S---S---------------------------------------------S-----------
-------------S------------------------------------------------------------------
--------------------------S-----------------------------------------------------
-----------S--------------------------------------------------------------------
----S---------------------------------------SS----------------------S-----------
----------S---------------------------------------------------------------------
----------------------------------------------------S---------------------------
----------------------------------------------------------S---------------------
-----------------------------S------------S--------------S---------------S------
-S-------S---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
SSSSSSS--------------------S-SSSS-SSSS-SS-SSSSSSSSSSSSSSSSSSSSSSS---------------
---------------------------S------------------------S---------------------------
---------------------------S----------------------------------------------------
---------S----------------------------------------------------------------------
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------------------------------------------------------------S-------------------
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-------------------------------------------------------------S--S---------------
------------------------------SSSSSSSS------------------------------------------
-----------------------------------------
>forward_428
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--------AATAATGTCCGATTCGCGCG----------------------------------------------------
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>reverse_2278
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-------------------------------------GAGTGATGCTTTGGCCATCC-----------------------
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>forward_1690
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----------------------------------------------------------------------GCGTGAATTT
CCCTGATGCC----------------------------------------------------------------------
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>reverse_2890
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---------TCACTGAATGGCTTGCCTCA---------------------------------------------------
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