>input_sequence_56116
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--------------------------------------------------------------ATGGCCGCCACCTTCGCC
GCCTCTCGCCTCCTCCTCCTGCTCATCCGCGTCGTGGCCACCGCCTCCTTCGCGTTCGGGCTCGCCGGCCGCGCGCAG--
-CTGGACCCGCAGCAGCTACTGGCGCTGCGCGCGCTCGGCCTCGGCGCGCACCGCGCCGGCGACCCCTGCGACGCGGACG
GCGCCGTGGCCGCGTCCTGCGACGCGGGGGCGCCGTTCCGGCGCGTGACGTCGCTCGCCCTCACCAACTGCTCCGACACC
ACCTCCGTCTCCGCCGCGGCGCTCGAGGCGCTCGCGCCGTCGCTCCGCGCGCTCGCCTTCTCGGACTGCCCCGCCGCGCC
GCCGCGGCTCCTCCCGCCGGAGCAGCTCGCCGTGGGTCTCCTGTCCTTCTCCTGCACCGCGTCTCTCGGCCGCCTCTCCG
CGGTGTGGCTCTCCCGCCTCGCCAACCTCACCGAGCTCACCGTCGCGGACACCCCTCTCGCCACCGGCTCCCCGTCCGAG
CTGGCCGTGGTCATCTCCCACATGGACCACCTCAACCGCCTCACCATTTCCAACGCCAACCTATCCGGCTTCCTCCCGCG
CCACTGGCACTGCCCCAACCTGACGCACCTCGACCTCTCCGGCAACCGCATCGCCGGCGCCATCCCCGACACCATCACCC
ACCTTGGCGGCATCACCCACCTGAACCTCAGCTCCAACGTTCTCAAAGGGCAGATCCCCACACACATCGGTGACCTCATT
TGGCTCACCACCGTGGACCTGTCCAACAACTCCCTCTCCGGCGGCATCCCGGAGACCGTCTCCACGCTGCCCGAGCTGGA
GGTGCTCAACCTGGGCTCCAACCGGCTCAACGGCAGCATTCCGCCGTTCTTGTCCAAGATGAGGGGCCTCAAGGAGCTCA
ACCTGGAGAACAACGACTTCGACGGCGTGGTGCCGTTCAGCGCCAGGTTCTTGTCGCGGCTGCGGGTGTTCAGGGCGGCC
GGGAACGGCAAGCTGTGCTACAACAGGTCGGAGCTCTCCGCCGAGGTGGCCGTGGGGGTGGCGCCGTGCGACAAGTACGG
GTTCCCGGTCACGGCTCCCCCGGCGACGGCGCAGTCGGAGAAGAGCACGGCGGACTACGACGACGGCGGCAGTGAAGGCG
ACGCGGACGGCGACGGCGACGCTCGTGGCGGCCCCAGCGCAGTGGTTCTCGGGCTCGCCATTGGTCTGTCCTGCTTGGCG
TTCGTGGTCATCTTGGTCGTCTGCCTCTGCAAGGTGTGCCGATGA-----------------------------------
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>chr3D_1_TraesCS3D01G289700
TTCAACCGGTATACTCGCATATGAAGTTTCACGAAGAAATCACATCCGTGGTAATCTGGGCAAAAATGACAAAATTAAAG
CTATATAAAAACACTATTTAATGAATAGTATGGTCGCATTTGTATTTCCTTCACTAAGAATACCATGGGTGTCAATACAT
CATGAAACTTCACACGTGAGTAGAATGATCGACTAAGTTTCATACTGCGAAATTGCAGATTTTTTTATTTTTTTAGTATT
TTTTATGAATTTACTATTTACGTGGGTGCGTGCGCACCATGTTCACCTTTGTATTTTCAACAAATTACAGCATTACTTGT
GAAGATGCCCCGGGCAGTTCAGAGTAAACGCTGACTTACACAAAATTCACTGCCCCTTGAAGATAAACAAAATTCACCGC
GCTACAGAACATCAAACTCTGACCCAGTGACCAGTGCGATGCCATCGCTGTTCTGTCACGAGCGAGCTTCGCACGTCCGA
CCACGCCGTTTCCTTGC---------AGAACTGCTCAGACACGCGATGGCCATCGTAGCGTAGCGTTGGAAGTTAGAGCA
GGCGGTCACATGAAGACTGGCAGGAAGCAGCAGCCGCTTTCTCATGGAAGCATTTGACAAGATGTTGCCCTCTCCCTCTG
TCTCTGCGCAGCCGAGAGAACGGCACGGATACGGATACCCCAGCCAGACAGCCACGAGCTGCTACCGCTGCTGCGCTCTC
TGCGCACCCGGACGAGGACGAGGACGAG-------------TGCCGAAAGCGACCGACCCCCGCTGCCCAAACAACGCAC
ACGCCCCCATCCGACCGTCCGCCCGCGTCCACCCAAGCATCCAACGGGCCGCGTCGAGCCGGGGGCGGGGGCCCCGCCAG
CGACGCGGGCAGGACAAAGCCTCGTAAACCGAGCGCGCGCACCACTCGCTCCACCTTCGAAACCTTTCCCGTGCTCCAAC
GCGCGCTCGTGCAGTGCGGGTGCGTGCTCTGCCTCCGCCTCTGCCTCTGCTCGTCCGTGGGCATGGCCGCCACCTTCGCC
GCCTCTCGCCTCCTCCTCCTGCTCATCCGCGTCGTGGCCACCGCCTCCTTCGCGTTCGGGCTCGCCGGCCGCGCGCAG--
-CTGGACCCGCAGCAGCTACTGGCGCTGCGCGCGCTCGGCCTCGGCGCGCACCGCGCCGGCGACCCCTGCGACGCGGACG
GCGCCGTGGCCGCGTCCTGCGACGCGGGGGCGCCGTTCCGGCGCGTGACGTCGCTCGCCCTCACCAACTGCTCCGACACC
ACCTCCGTCTCCGCCGCGGCGCTCGAGGCGCTCGCGCCGTCGCTCCGCGCGCTCGCCTTCTCGGACTGCCCCGCCGCGCC
GCCGCGGCTCCTCCCGCCGGAGCAGCTCGCCGTGGGTCTCCTGTCCTTCTCCTGCACCGCGTCTCTCGGCCGCCTCTCCG
CGGTGTGGCTCTCCCGCCTCGCCAACCTCACCGAGCTCACCGTCGCGGACACCCCTCTCGCCACCGGCTCCCCGTCCGAG
CTGGCCGTGGTCATCTCCCACATGGACCACCTCAACCGCCTCACCATTTCCAACGCCAACCTATCCGGCTTCCTCCCGCG
CCACTGGCACTGCCCCAACCTGACGCACCTCGACCTCTCCGGCAACCGCATCGCCGGCGCCATCCCCGACACCATCACCC
ACCTTGGCGGCATCACCCACCTGAACCTCAGCTCCAACGTTCTCAAAGGGCAGATCCCCACACACATCGGTGACCTCATT
TGGCTCACCACCGTGGACCTGTCCAACAACTCCCTCTCCGGCGGCATCCCGGAGACCGTCTCCACGCTGCCCGAGCTGGA
GGTGCTCAACCTGGGCTCCAACCGGCTCAACGGCAGCATTCCGCCGTTCTTGTCCAAGATGAGGGGCCTCAAGGAGCTCA
ACCTGGAGAACAACGACTTCGACGGCGTGGTGCCGTTCAGCGCCAGGTTCTTGTCGCGGCTGCGGGTGTTCAGGGCGGCC
GGGAACGGCAAGCTGTGCTACAACAGGTCGGAGCTCTCCGCCGAGGTGGCCGTGGGGGTGGCGCCGTGCGACAAGTACGG
GTTCCCGGTCACGGCTCCCCCGGCGACGGCGCAGTCGGAGAAGAGCACGGCGGACTACGACGACGGCGGCAGTGAAGGCG
ACGCGGACGGCGACGGCGACGCTCGTGGCGGCCCCAGCGCAGTGGTTCTCGGGCTCGCCATTGGTCTGTCCTGCTTGGCG
TTCGTGGTCATCTTGGTCGTCTGCCTCTGCAAGGTGTGCCGATGAGATGCCATGCGGGAGCGTCTCGTGAACTTTTTGTT
GCTTCTCTTGTGTTGACGAGGTTGGCTTACCA-----CTGCATGTTGAATAGTCGAATCCGAATTTTGCTGTC--GCTGT
GTGGTGTAACAGTGCATGTTGCACTCCTAAACCAGCATAGATCAACTGATCAGTCGAAAAAAATGGCGAAAAATACTACG
AAGAG-CCGCATTTGCAAAGCAGGGTA---------------TTTGCTGGCCAATGTCGTTGTTATTATTCAGTGTTGCC
TTTGTCCCGTAATCGCATTGTTCTACTAAC----TGTATGTATTCACTGCAGTATCACAAATTCATACGAGTAAAACAGC
TATGCATGTGGGCAAAGGGCATTCACGTGTGTGCTCAAAACAGCCAGAATCTTATGGACATCAGTTCAGTTTCGGGAAGA
AAAAAAAATCTCGTGTTCTAAAGGGATTACTGTACAAAGCATGCCCCGTCTGCCAGTTCTAAACCAGACGTGTAGATACC
GGACCCTGTCAGCCTGTCCGCACTGCATGTCACAAACTGATGTCCCTCCACTCTTCTATAAATATAAAACAAGAAAGAAA
CCGGTGAGGTTTCCTACGTGGCTGATGCAAATATGCATGATTGTCATTGTCTGGGTGGGTGTCTGTCTATGTAAACGAGG
GGAAGAAGGAGAAGTCGAGTGGAGAGAGTGATGGGGGCTGGACAAGAGTAGTGCTTCAATCTCCTTTGTTAGGCTTTTCC
GTGGACTGGCCGGCCTTATTTTCTCTTTAGTTTAGGCTTGAAGCGTACTCTGCCGCCAACCGGAGCCGCGCTCTTTCACG
GCCATCATGCATGCATGCAGAGCGCAGCTTGGCTGGCGGGCTAGGCCATGCCGGTCCCACACCATCCTCGGCTGCTCGCA
ACATGATGCACAGCTAGCCACGCTTTTGAGTTGCGCTGCCACTTCTGGCAAGGGCGCCGCAGTGATCTCTCTTTTCACAG
TACCTCGTTGACGGTAATCATACAACGCGATC
>chr3A_299
AACAAATTTAT---------------------------------------------------------------------
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--------------------------------------------------------------------AGCATTATCCAT
GAAGATGCCCCGGGCTGTTCTGATTAAA--------CGCTCAGAATTCACTGCCCCTTGAAGATAAACAGAATTCACCGC
GCTACAGGACATCAAACCCCGACCCAGTTACCAGTGCGATGCCGTCGCTGTTCTGTCACGAGCGAGCTTGGCAGGTCCGA
CCACGCCGTTTCGTTGCAGAGCTGCGAGAACTGCTCAGACACGCGATGGCCATCGTAGCGTGCGA----AGTTTCT-GCA
GGCCGTCACATGAAGACTCGCAGGAAGCAGCAGCCGCCCTCTCATGGAAGCATTTGACAAGATGTTGCCCTCTCCCTCTG
TCTCTGCGCAGCCGAGACAACGGCATCGGCACGGATACC----CCAGACAGCCACGAGCTGCTACCGCTGCTGCATCTGC
TGCGCTCTCTGCCGAGGCCGGGGACGAGCGTTGTGCGCTGATGCCGAAAGCCACCGACCCCTGCTGCCCAAACAACGCAC
ACGCCCGCATCCGACCGTCCGCCCGCGTCCATCCAAGCATCCAACGGGCCGCGTCGAGCCGGGGC--GGGGGCCCGCCAG
CGACGCGGGCAGGACAAAGCCTCGTAAACCGAGCGCGCGCACCACTCGCTCCACCTTTGAAACCTTTCCCGTGCTCCAAC
GCGCGCCGTGCTCT----------------------GCCTCTGCCTCTGCGCGTCCGTGGGCATGGCCGCCACCCTCGCC
GCCTCTCGCCTCCTCCTCCTGCTCATCAGCGTCGCGGCCACCGCCTCCTTCGCGCTCGGGCTCGCCGGCCGCGCGCAG--
-CTGGACCCGCAGCAGCTGCTGGCGCTGCGCGCGCTCGGCCTCGGCGCGCGCCGCGCCGGCGACCCCTGCGACGCGGGCG
GCGCCGTGGCCGCGTCCTGCGACGCGGGGGCGCCGTTCCGGCGCGTGACGTCGCTCGCCCTCACCAACTGCTCCGACACC
ACCTCCGTCTCCGCCGCGGCGCTCGAGGCGCTCGCGCCGTCGCTCCGCGCGCTCGCCTTCTCGGACTGCCCCGCCGCGCC
GCCGCGGCTCCTCCCGCCGGAGCAGCTCGCCGCGGGTCTACTATCCTTCTCCTGCACCGCGTCTCTCGGCCGCCTCTCCG
CGGTCTGGCTCTCCCGCCTCGCCAACCTCACCGAGCTCACCGTCGCGAACACCCCTCTCGCCACCGGCTCCCCGTCCGAG
CTGGCCGTGGTCATCTCGCACATGGACCACCTCAACCGCCTCACAATTTCCAATGCCAACCTATCCGGCTTCCTCCCGCA
CCACTGGCACTGCCCCAACCTGACGCACCTCGACCTCTCCGGCAACCGCATCTCCGGCGCCATCCCCGACACCATCACCC
ACCTTGGCGGCATCACCCACCTCAACCTCAGCTCCAACGCTCTCAAAGGGCAGATCCCCGCACACATCGGTGACCTCATT
TGGCTCACCACCGTGGACCTGTCCAACAACTCCCTCTCCGGCGGCATCCCGGAGACCGTCTCGACGCTGCCCGAGCTGGA
GGTGCTCAACCTGGGCTCCAACCGGCTCAACGGGAGCATACCGCCGTTCTTGTCCGAGATGAGGGGCCTCAAGGAGCTCA
ACCTGGAGAACAACGACTTCGACGGCGTGGTGCCGTTCAGCGCCAGGTTCTTGTCGAGGCTACAGGTGTTCAGGGCGGCC
GGGAACGGCAAGCTGTGCTACAACAGGTCGGAGCTCTCCGCCGAGGTGGCCGTGGGGGTGGCGCCGTGCGACAAGTACGG
GTTCCCGGTCACGGCTCCCCCGGCAACGGCGCAGTCCGAGAAGAGCACGGCGGGCTACGACGACGGCGGCAGTGACGGTG
ACGCGGACGGCGGCGACGACGCTCGTGGCGGCCCCAGCGCGGTGGTTCTCGGGCTCGCCATTGGCCTGTCCTGCCTGGCG
TTCGTGATCATCCTGGTCGTCTGCCTCTGCAAAGTGTGCAGATA------------------------------------
---------------ACGAGGTTGGTTTACCA-----CTGCATGTGGAATAGTCGGATCCGAAATTTGCTGTT--GCTGT
GTGGTGTAGCAGTGCATGTTGCACTCCTAAACCAGCATAGATCAATTGATCAATTGAGAAAAATGACGAAAAATACAACG
AAGAG-CCGCATTTGCAAAGCAGGGTATTCCTCTTGTTTTCGTTTGCTGGCCAATGTCGTTGTTATTATTAAGTGTTGCC
TTTGTGCCGTGGTCGCATTGTTCTACTGTATGTATGTATGTATCCACTGCAGTATCACAAATTCAGAAGAGTAAACCAGT
TAT-----------------------------------------------------------------------------
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>chr3B_349
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----------------------------CGCTGACTCGCTCAAAATTCACTGCCCGTTGAAGATAAACAAAATTCACCGC
GCTACAAAACATCAAACTCTGACCCAGTTACCAGTGCGATGCCATCGCTGTTCTGTCACGAGCGAGCTTCGCAGGTCCGA
CCACGCCGTTTCGTTGCAGAGCTGCGAGAACTGCTCAGACACGCGATGGCCATCGCAGCGCGCGA----AAGTTAGAGCA
GGCGGTCACATGAAGACTGGCAGGAAGCAGCAGCCGCTCTCCCATGGAAGCATTTGACAAGATGTTGCCCTCTCCCTCTG
TCTCTGCGCAGCCGAGACAACGGCA------CGGATACC----GGAGATAGCCACGAGCTGCTACCGCTGCTGCGCTCTC
TGCGCACCCCGACGAGGACGAGGACGAGCATTGCACACTGATGCCGAAAGCGACCGACCCCCGCTGCCCAAACCACGCAC
ACGCCCCCATCCGACCGTCCGCCCGCGTCCATCCAAGTATCCAACGGGGCGCGTCGAGCCGGGGGCGGGGGGCCCGCCAG
CGACGCGGGCAGGACAAAGCCTCGTAAACCGAGCGCGCGCACCACTCGCTCCACCTTCGAAACCTTTCCCGTGCTCCAAC
GCGCGCTCGTGCAGTGCGGGTGCGTG------------CTCTGCCTCTGCTCGTCCGTGGGCATGGCCGCCACCCTCGCC
GCCTCTCGCCTCCTCCTCCTGCTCATCCGCGTCGCGGCCACCGTCTCCTTCGCGCTCGGGCTCGCCGGCCGCGCGCAGCT
GCTGGACCCGCAGCAGCTGCTGGCGCTGCGCGCGCTCGGCCTCGGCGCGCACCGCGCCGGCGACCCCTGCGACGCGGACG
GCGCCGTGGCCGCGTCCTGCGACGCGGGGGCGCCGTTCCGACGCGTGACGTCGCTCGTCCTCACCAACTGCTCCGACACC
ACTTCCGTCTCGGCCGCGGCGCTCGAGGCGCTCGCTTCGTCGCTCCGCGCGCTCGCCTTCTCGGACTGCCCCGCCGCGCC
GCCACGGCTCCTCCCGCCGGAGCAGCTCGCCGCGGGTCTCCTGTCCTTCTCCTGCACCGCGTCTCTCGGCGGCCTCTCCG
CCGTTTGGCTCTCCCGCCTCGCCAACCTCACCGAGCTCACCGTCGCGAACACCCCTCTCGCCACCGGCTCCCCGTCCGAG
CTGGCCGTGGTCATCTCCCACATGGACCACCTGAACCGTCTCGCCATTTCCAATGCCAACCTATCCGGCTTCCTCCCGCA
CCACTGGCACTGCCCCAACCTGACGCACCTCGACCTCTCCGGCAACCGCATCGCCGGCGCCATTCCCGACACCATCACCC
ACCTTGGCAGCATCACCCACCTGAACCTCAGTTCCAACGTTCTCAAAGGGCAGATCCCCACACACATCGGTGACCTCATT
TGGCTCACCACCGTGGACCTGTCCAACAACTCCCTCTCCGGCGGCATCCCGGAGACCGTCTCCACGCTGCCCGAGCTGGA
GGTGCTCAACCTGGGCTCCAACCGGCTCAACGGGAGCATACCGCCGTTCTTGTCCGAGATGAGGGGCCTCAAGGAGCTCA
ACCTGGAGAACAACGACTTCGACGGCGTGGTGCCGTTCAGCGCCAGGTTCTTGTCGCGGCTGCGGGTGTTCAGGGCGGCC
GGCAATGGCAAGCTGTGCTACAACAGGTCGGTGCTCTCCGCCGAGGTCGCCGTGGGGGTGGCGCCGTGCGACAAGTACGG
GTTCCCGGTCACGGCTCCCCCGGCGACGGCGCAGTCGGAGAAGAGCGCGGCGGACTACGACGACGGCGGCAGTGATGGCG
ACGCGGACGGCGACGCCGACGCTCGTGGCGGCCCTAGCGCGGTGGTTCTCGGGCTCGCCATTGGCCTGTCCTGCTTGGCG
TTCGTGGTCATCTTGGTCGTCTGCCTCTGCAAGGTGTGCAGATGAGATGG---------------CGTGAACTTTTTGTT
GCTTCTCTTGTGTTGACGAGGTTGGTTTACAACATTGCTGCATGTTGAATAGTCGGATCCGCAATTTGCTGTTACGCTGT
GTAGTGTAGCACTGCATGTTGTACTCCTAAACCAGCATAGATCAATTGATCGGTTGAAACATTTGACGAAAAATACAACG
AAGAGGCCGTATTTGCAAAGCAG---------------------------------------------------------
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>SNPs
SS---SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-------SSSS-
---------------S----S--S------------SS-S----------------------------------------
----------------------------S--------------------------------------------S------
------------S------------------------------------------------SSSSSSSS-----------
--------------------------------------S-----------------------------------------
-----------------S-------SS-SS---------SSSS-------------------------------------
---------S----------------------------------------------------------------------
-------------------------------S---------------------------------------S--------
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--------------------------SSSSSSSSSS--------------------------------------S-----
----------------------------------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---------------
---------------------------------------S---------SSSSSSSSSSSSSSSS---------------
-------------------------S-----------------------------S-------S--------S-------
--------S------------------------------------S--------S----------S----------S---
----------------------------------------------------------------------S---------
-----S----SS---------------SSS-------------S---------------------S-S-------S---S
---SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_62
------------------------------------------CATCCGTGGTAATCTGGGCA------------------
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>reverse_1393
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--------------------------------TGGGTCTCCTGTCCTTCTCC----------------------------
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>forward_273
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-------------CTATTTACGTGGGTGCGTGC-----------------------------------------------
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>reverse_2296
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-------------------------------------------------------GGGAGCGTCTCGTGAACTTT-----
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