>input_sequence_59578
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------ATGGCTTCCTCTTTGCTCCACTGCTCCGACAAGCTCCCGTTCATGGACGTGGAGACCATCCTCCACATGAAAGA
AGGCCTCGACGAGAGCAGCTACGCGCAGAACTCCTCGCTCCAGAAAAGGGGCATGGACACCCTCAAGAGCCTCATCATCA
ACTCGGCGACGGACGTGTACATCTCCCAGATGCCGGAGAGGTTCACGGTGGCCGACCTCGGCTGCTCCTCGGGCCCCAAC
GCGCTCTGCCTGGTGGAGGACATCATCGGGGGCATCGGCAAGGTCTGCTGCCGGTCGTCGCAGCCGCCGCCCGAGTTCTC
GGTGCTCCTCAACGACCTCCCCACCAACGACTTCAACACCATCTTCTTCAGCCTGCCGGAGTTCACCCACAGGCTCAAGT
CCGCCGCCAAGTCCGACGAGTGGGGCCGGCCGATGGTGTTCCTGTCCGGCGTGCCCGGGTCCTTCTACGGGAGGCTGTTC
CCGAGGACCAGCGTGCACTTCATCTGCTCCTGCTCCAGCCTGCACTGGCTCTCCCAGGTCCCGCCGGGCCTCTTCGACGA
GGCCAAGGCGCCGATCAACAAGGGGAAGATGTACATATCGAGCACGAGCCCGCCCGCCGTGTCAGTGGCCTACCGGAGGC
AGTTCCAGAGGGACTTCAGCCTGTTCCTCAAGTCGCGCGCCGCCGAGGTCTTCCCCGGCGGGCGGATGGTTCTGGCCATG
CTCGGCCGGCAGACCGACGAGTGCGTCGACAGGAGGACGACCTTCCTGTGGGAGCTCCTCTCCGAGTCCTTCGCCGCGCT
CGTGTCACAGGGGCTCGTGGAGCAGGACAAGGTGGACGCCTACAACGTGCCCTTCTACGCGCCGTCGCTGCAGGAGATCG
AGGTGGAGGTGCGGCTGGAGGGGTCCTTCAGCCTCGACTACGTGCAGACGTACGAGATCAACCTCAGCAGCAGCGGCGAC
GCCAAGGAGGACGGCAGGACGGTGTCCATGGCGATCAGGGCCATCCAGGAGTCCATGCTCAGCCACCACTTCGGCCCGGA
CATCGTCGACGCGCTGTTCCACGAGTACACGCAGCTCGTCACCGAGTCCATGGAGAGGGAAGAGGTCAAGAGCGTCCAGA
TAGGGGTAGTCCTCACCAGGTTGTGA------------------------------------------------------
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>chr3D_1_TraesCS3D01G256000
CAAAGGTAAGTTCTTGGCAATCTGCT----TGGTCTGGCTCTGAAATGGGTGGTGTGCGTGT---TACTAGGTCTGCAAA
TAGCATTGTCTGCCCCTGTCCCAATGGGCGGCGACGCTAGGCAGCTAGA-----GGATGGCTTTGTC----CTCTGCATT
CGTTCAGTTAGTCCGTGTTTATCCACTTCTCCCGTGTGTGTTCAATCAAGAACCTTCCATTTCTGAAACGAAGCGCTGAA
AAGAGAGGCTTTTTGCACATGGAAATGCCTGTTAGCAAAGTGGGCATGCTTTCAGGAATTGCAC----CCATTTCCCTTT
GTCCATTCAGGCATGGGAATGTCGTCCTTTCCTAATAGCAAGAACAAAATCTTGCTTAGAAAAAGCTTGGATATGTCTCT
GAGTTGCGACCATGCCTGCATGCATAG----GAGTCCTAGTAGAGACAGGGTACCAATTGAGCACCAAAGGTGTCGGTTG
ACTCAGGTTTTCAGCCACTTGCTGGCGAGGGAACATGGCGCATAAATTTATTTCTACCATTCTTTCTTTTTATATGTTCC
AAAAGGAAAAAAGTTTTCACCAG-----TTGTTTTGCTGCTTGCAGCACCTTTTCTTTTTCTTCCATGTACTGTTTTCGC
CACACTTTCACTTGGTTTCACCTGGG---GGTCAAATCTAGCACCATGCATGATATGATAGCAGCGAATCACAGAC-CAT
GTACTGAAAGCTTGACAGTATTGTAC-TTTTATCTGAACCTGGCTTCTCAATCAGTCACACCAAACCCAGCCAAAAAGGA
GATCTCAGTTAGACATATCACGCTCTGTTTGCGCAAAGCGGCCTAAACAGATGCCTCGAGAATATTTGTTTACACCT---
---ACCGTGGGCAGGGGCAGGGT--ATAATTTGTGCAAAATGAGGATGTACTGCACAATTAACCAGAGTTCTGACCCTGT
ATATTACATGACCGCAGGAAGAAGGCCA-ATCAACTCCCGAGACTTGAGATCGAGCTAGTCCACTACCAC---ACAGTAG
CCGGCAATGGCTTCCTCTTTGCTCCACTGCTCCGACAAGCTCCCGTTCATGGACGTGGAGACCATCCTCCACATGAAAGA
AGGCCTCGACGAGAGCAGCTACGCGCAGAACTCCTCGCTCCAGAAAAGGGGCATGGACACCCTCAAGAGCCTCATCATCA
ACTCGGCGACGGACGTGTACATCTCCCAGATGCCGGAGAGGTTCACGGTGGCCGACCTCGGCTGCTCCTCGGGCCCCAAC
GCGCTCTGCCTGGTGGAGGACATCATCGGGGGCATCGGCAAGGTCTGCTGCCGGTCGTCGCAGCCGCCGCCCGAGTTCTC
GGTGCTCCTCAACGACCTCCCCACCAACGACTTCAACACCATCTTCTTCAGCCTGCCGGAGTTCACCCACAGGCTCAAGT
CCGCCGCCAAGTCCGACGAGTGGGGCCGGCCGATGGTGTTCCTGTCCGGCGTGCCCGGGTCCTTCTACGGGAGGCTGTTC
CCGAGGACCAGCGTGCACTTCATCTGCTCCTGCTCCAGCCTGCACTGGCTCTCCCAGGTCCCGCCGGGCCTCTTCGACGA
GGCCAAGGCGCCGATCAACAAGGGGAAGATGTACATATCGAGCACGAGCCCGCCCGCCGTGTCAGTGGCCTACCGGAGGC
AGTTCCAGAGGGACTTCAGCCTGTTCCTCAAGTCGCGCGCCGCCGAGGTCTTCCCCGGCGGGCGGATGGTTCTGGCCATG
CTCGGCCGGCAGACCGACGAGTGCGTCGACAGGAGGACGACCTTCCTGTGGGAGCTCCTCTCCGAGTCCTTCGCCGCGCT
CGTGTCACAGGGGCTCGTGGAGCAGGACAAGGTGGACGCCTACAACGTGCCCTTCTACGCGCCGTCGCTGCAGGAGATCG
AGGTGGAGGTGCGGCTGGAGGGGTCCTTCAGCCTCGACTACGTGCAGACGTACGAGATCAACCTCAGCAGCAGCGGCGAC
GCCAAGGAGGACGGCAGGACGGTGTCCATGGCGATCAGGGCCATCCAGGAGTCCATGCTCAGCCACCACTTCGGCCCGGA
CATCGTCGACGCGCTGTTCCACGAGTACACGCAGCTCGTCACCGAGTCCATGGAGAGGGAAGAGGTCAAGAGCGTCCAGA
TAGGGGTAGTCCTCACCAGGTTGTGACTCGAGTCTGTCTACTGACTCTATTTTTCTTTAGCAAGTTTAGGTTTGACTCTG
TTCTATTGTCATATTCAAGGCCTGTTTGGTTGGAGATTTAATTTGCCACGCCTAAGGTAAGGTATCAGCCACACCTGTGG
CGCGCCGTAGAAGTGTGGCGAGCAAAACAAACGCCACACCTTTTGGCGAAAATCCTACTGGAGAAACAACTACGCACTGT
GGCAAGCCAAACATTAGTATAGAACCAAACGCATGCCTAGAAAGTTGTGGCTCGCCGCACCTTTGGCTTGGCAAGCTAAG
GCTGGAACCAAACAGCCCCAGTATTGTTTAGTAGTACTCCGGTCCGGTCCATAAGG------------------------
-----------------------------------------------------------AGTAATTGGCAGCAA--GTCA
CATTTATCATTGGAAAATGTTTAAAATCGGCCGACCGGCAGAGACTGACGCCGGTCACCTCCATGTGTGTATCCTTTGTC
TCTTCAGCTTTACGCCATGTAGCAAGTTTAGCTTAGAATCTCGAATA------TCATTTCTAAACCCTGGCTTGTCTCCG
CCCGGTTAAAAATAATTCAC------ACAAAATACAAAAAAATTCCAATTTTTGCTCTAAATTCTAGATCATTTAAACAT
ATGAGTAGCTCTCAGAGAAAAGACAAATTGGGTTA-------------GAACAGTAAACGTTTTACATATCCTAAATTTG
TGTTTTTTGCCGAGAACTACTCAGATATCCAAATGATCTGGAACTTGGAGCACACCGCACGCACCAAATTATCTACCATG
TGATGTGGTCACCTATTATAGGTAGGGTCAAGGACCATGCCAGCATTCGGATGAATACATCAGGAGGATCACTGGAGGGC
TCTACAACACTCGGGCAACCACACGTCACTCGGCGTCAGGAACAACCACTCGGATGTACAGGACAAGGAGGCGTCGTGGA
GCTGCAACGGTCGAGGCATCCTAAGTCATCCAGTAAATAGAGTTATGGCTACCGTTACTTGTAACTGCTGTAGTATAGGC
TCATTAGACTAGTAAA
>chr3B_1
CAAAGGTAAGTTCTTGGCAATCTGCT----TGGTCTGGCTCTGAAATGGGTGGCGTGCATATCAGTACTAGGCTTGCAAA
CAGCATTGCCTGCCCCTGTCCCCATGGGTGGTGTTGCTAGGCAGCTAGA-----GGATGGCTTAATTTGTGCTCTGCGTT
CGTTCAATTAGTCCGTGTTTATCCACTTCTCCCGCTTGTGTTCAATCAAGAACCTTCCATTTCTGAAACGAAGCGCTGAA
AAGAGAGGCTTTTTGCACATGGAAATGCATGTTAGCAAAGTGGGCATGCTTTCAGGAATTGCAC----CCATT------T
GTCCATTCAGGCATGGGAATGTTGTCCTTTCCTAATTGCAAGAACAAAATCTTGCTTAGAAAAGGCATGGATATGTCTCT
GAGTTGCGACCATGCCTGCATAGGAGTCATAGACTCATAGTAGAGACAGGGCACCAATTGAGCACCAAAGGTGTCGGTTG
ACTCAGGTTTTCAGCCACTTGCTGGCGAGGGAACATGGCGCATAAATTTATTTCTCCCATTCTTTCTTTTTATATATTCC
AAAAGGAAAAG-GTTTTCACCAG-----TTGTTTTGCTGCTTGCAGCACCTTTTCTCTCTCTCTC-----------TCGC
CACACTTTCACTTGGTTTCACCTGAG---GGTCAAATCTAGCACCATGCATGATATGATAACAGCGAATCACAGAC-CAT
GTACTTAAAGCTTGACAGTATTGTAC-TTT-ATCTGAACCTGGCTTCTCAATCAGTCACACCAAACCCAGCCAAAAAGGA
TATCTCAGTTGGACATATCACGCTCTCATTGGGCAAAGCGGCCTAGACAGATGCCTCGAGAATATTTGTTTACACCT---
---ACCGTGGGCA-GGGCAGGGT--ATAATTTGTGCGAAATGATGATGTACTACACAATTAACCAGAGTTCTGACCGTGT
ATATATGCACTGCATTACAGGTAGAAGGCATTAATTCTTGAAACTTGAGAGACG----GTCCACTACCAC---ACAGTAG
CCGGCAATGGCTTCCTCTTTGCTCCACTGCTCCGACAAGCTCCCGTTCATGGACGTGGAGACCATCCTCCACATGAAAGA
AGGCCTGGACGAGACCAGCTACGCGCAGAACTCTTCGCTCCAGAAAAGGGGCATGGACACCCTCAAGAGCCTCATCATCA
ACTCGGCAACGGACGTGTACATCTCCCAGATGCCGGAGAGGTTCACGGTGGCCGACCTCGGGTGCTCCTCGGGCCCCAAC
GCGCTCTGCCTGGTGGAGGACATCATCGGAGGCGTCGGCAAGGTCTGCTGCCGGTCATCGCAGCCGCCGCCGGAGTTCTC
GGTGCTCCTCAACGACCTCCCGACCAACGACTTCAACACCATCTTCTTCAGCCTGCCGGAGTTCACCCACAGGCTTAAGT
CCGCCGCCAAGTCCGACGAGTGGGGCCGGCCGATGGTGTTCCTCTCCGGCGTGCCCGGGTCCTTCTACGGGAGGCTGTTC
CCGAGGACCAGCGTGCACTTCATCTGCTCCTGCTCCAGCCTGCACTGGCTCTCTCAGGTCCCGCCGGGCCTCTTCGACGA
GGCCAAGACGCCGATCAACAAGGGGAAGATGTACATATCGAGCACGAGCCCTCCCGCCGTGTCCGTGGCCTACCGGAGGC
AGTTCCAGAGGGACTTCAGCCTGTTCCTCAAGTCGCGCGCCGCCGAGGTCTTCCCCGGCGGCCGGATGGTTCTGGCCATG
CTCGGCAGGCAGACCAACGACTGCGTCGACCGGAGGACGACCTTCCTGTGGGAGCTCCTCTCCGAGTCCTTCGCAGCGCT
CGTGTCGCAGGGGCTGGTGGAGCAGGACAAGGTGGACGCCTACAACGTGCCGTTCTACGCGCCGTCGCTGCAGGAGATCG
AGGTGGAGGTGCGGCTCGAGGGGTCCTTCAGCCTCGACTACGTGCAGACGTACGAGATCAACCTCAGCAGCAGCGGCGAC
GCCAAGGAGGACGGCAGGACGGTGTCCATGGCGATCAGGGCCATCCAGGAGTCCATGCTCAGCCACCACTTCGGCCCCAA
CATCGTCGACGCGCTGTTCCACAAGTACACACAGCTCGTCACCGAGTCCATGGAGAGGGAAGAGGTCAAGAGTGTCCAGA
TAGGGGTAGTCCTCACCAGGTTGTGACTCGAGTCTGCCTACTGACTGTATTTTTCTTTAGCAAGTTTAGGTTTGACTCTG
TTCTATTGTCATATTC----------------------------------------------------------------
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-------------------TGTATTGTTTAGTACTCCCTCTGTAAACTAATATAAGAGCATTTAGATTACTAAAGTAGTG
ATCTAAACGCTCTTATATTTGTTTACGGAGGGAGTAGCAGTTTGTCAAAAAAAAATAGCAGTAATTGGCAGCAA--GTCA
CATTTATCATGGGAAAATGTTTAAAATCGGCCAACCGGGAGCG--------------CCTCCATGTGTGCATCTTTTGTC
TCTTCAGCTTTACGCCA---------------------------------------------------------------
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>chr3A_1
CAAAGGTAAGTTCATCACAATCTGCTTGCATGGTTTGGCTCTGAAATGGGTGGTGTGCGTG---------------CAAA
TAGCATTGTCTGCA------CCCATGGGTGGTGATGCCAGACAGCTAGACTAGAGGATGGCTTTCCG----CTCCGCATT
CGTTCAGTTACTCAGTGTTTATCCACTTCTCCCGCATGTGTTCAATCAAGAACCTTCCATTTCTGAAACGAAGAGCTGAA
AAGAGAGGCTTTTTGCACATGGAAATGCCTGTTAGCAAAGTGGGCATGCTTTCAGGAACTACCCATTTCCATT------T
GTCCATTCAGGCATGGGAATGTCGTCCTTTCCTAATAGCAAGAACAAAATCTTGCTTAGAAAAAGCATGGATATGTCTCT
GAGTTGCGACCATGCCTGCATAGGAGTCGGTCATGGT------AGACAGGGTACCAGTTGAGCACCAAAGGTGTCGGTTG
ACTCAGGTTTTCGGCCACTTGTTGGCGAGGGAACATGGCGCACAAATTTATTTCTCCCATTTTTTCTTTTTATATATTCC
AAAAGGAAAAG-GTTTTCACCAGTACTCTTGTTTTGCTGCTTGCAGCACCTTTTCTCTCTG---------------TCGC
CACACTTTCACTTGGTTTCACCTGATGATGGTCAAATCTAGGGCCATGCATGATATGATAACAGCGAATCGCAGACTCAT
GTACTGAAAGCTTGACAGTATTGTACTTTT-ATCTGAACCTGGCTTCTCAATCAGTCACACCAAACCAAGCCAAAAAGGA
TATCTCAGTTAGACATATCACGCTCTCTTTGGGCAAAGCGGCCTAAACAGATGCCTCGAGAATATTTGTTTGTTTACACC
TACACCGTGGGCA-GGGGCAGGGTAATAATTTGTGCAAAATGAGGATGTACTACACAATTAACCAGAGTTCTGACCGTGT
ATATTACATGACCGCAGGAAAGAAGGCA-ACCAATTCTCGAGACTTGAGATCGAGCTTGTCCACTATACCACAACAGTAG
CCGGCAATGGCTTCCTCTTTGCTCCACTGCTCCGACAAGCTCCCGTTCATGGACGTGGAGACCATCCTCCACATGAAAGA
AGGCCTCGACGAGAGCAGCTACGCGCAGAACTCCTCGCTCCAGAAGAGGGGCATGGACACCCTTAAGAGCCTCATCGTCA
ACTCGGCGACGGACGTGTACATCTCCCAGATGCCGGAGAGGTTCACAGTGGCCGACCTCGGGTGCTCCTCGGGCCCCAAC
GCGCTCTGCCTGGTGGAGGACATCATCGGGGGCGTCGGCAAGGTCTGCTGCCGGTCGTCGCAGCCGCCGCCCGAGTTCTC
GGTGCTCCTCAACGACCTCCCCACCAACGACTTCAACACCATCTTCTTCAGCCTGCCGGAGTTCACCCACAGGCTCAAGT
CCGCCGCCAAGTCCGACGAGTGGGGCCGGCCGATGGTGTTCCTGTCCGGCGTGCCCGGGTCCTTCTACGGGAGGCTGTTC
CCGAGGACCAGCGTGCACTTCATCTGCTCCTGCTCCAGCCTGCACTGGCTCTCCCAGGTCCCGCCGGGCCTCTTCGACGA
GGCCAAGGCACCGATCAACAAGGGCAAAATGTACATATCGAGCACGAGCCCGCCCGCCGTGTCCGTGGCCTACCGGAGGC
AGTTCCAGAGGGACTTCAGCCTGTTCCTCAAGTCGCGCGCCGCCGAGGTCTTCCCCGGCGGGCGGATGGTGCTGGCCATG
CTCGGCAGGCAGAGCGACGAGTGCGTGGACAGGAGGACGACCTTCCTGTGGGAGCTCCTCTCGGAGTCCTTCGCGGCGCT
CGTGTCGCAGGGGCTGGTGGAGCAGGACAAGGTGGACGCGTACAACGTGCCGTTCTACGCGCCGTCGCTGCAGGAGATGG
AGGTGGAGGTGCGGCTGGAGGGGTCCTTCAGCCTCGACTACGTGCAGACGTACGAGATCAACCTGAGCAGCAGCGGCGAC
GCCAAGGAGGACGGCAGGACGGTGTCCATGGCGATCAGGGCCATCCAGGAGTCCATGCTCAGCCACCACTTCGGCCCGGA
CATCGTCGACGCGCTCTTCCACAAGTACACGCAGCTGGTCACCGAGTCCATGGAGAGGGAAGAGGTCAAGAGTGTCCAGA
TAGGGGTAGTCCTCACCAGGTTGTGACTCGAGTCTGTCTACTGACTGTATTTTTCTTTAGCAAGTTTAGGTTTGACTCTG
TTCTATTGTCATATTC----------------------------------------------------------------
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-------------------AGTATTGTTTAGTAGT---------------------------------------------
-----------------------------------------------------------AGTAATTGGCAGCAAAAGTCA
CATTTATCATGGGA------------------------------------------------ATGTGTGCATCCTTTGTC
TCTTCAGCTTTACGCCATGTATCAAGTTTAGCTTAGAATCTCGAATAGGAGTATCATTTCTAAACCCAGGCTTAGCTCCA
CACGGTTAAAAAAAATCACACAAAATACAAAAGAAAAAAAAAATCCAATTTTTGCTCTGAATTTCAGATCATTTGGACAT
ATGAGTAGCTCTCAGAAAAAAAGACAAATTTGGGTTAAAACAGTACATGAACAGTAAACGTTTTACATATCCTAAATTTG
TGTTTTT-GCCGAGAGTTACTCAGATGTCCAAATGATCTAGAACTTGGAGCGCACCTCACGCATCAAATTATCTACCAT-
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>SNPs
------------------------------------------------------------------------SS------
----------------------S-----S--S--S-----------------------------S-S-------------
----------------------------------SS--------------------------------------------
-------------------------------------------------------------------------SSSSSS-
------------------------------------------------------------------S-------------
---------------------SSSSSS------S--S-------------------------------------------
-------------------------------------------------------S-------------------S----
----------SS--------------------------------------------S-S---SS-SSSSSSSSSSS----
------------------------S-----------------------------------S-------------------
------------------------------S-------------------------------------------------
S-------------------------S----S------------------------------------------------
-------------S--------------------------------------S-----------------------S---
---------------------S---S--------S--S-------------------S----------------------
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-------------------------------------------------------------S------------------
---------------------------------S----------------------------------------------
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---------------------------------------------------------------S----------------
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------S-------------------------------------------------------------------S-----
------S--------S-----------------------------------S----------------------------
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----------------------S-------------------------------------------------S-------
----------------------------------------------S---------------------------------
----------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSS----------------S-SS-S--SSSS-SSSSS-S-------------------------
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----------S---------------------S-----S--S-SSSSSSSSSSSSSS------------S----------
---------------------S---------------------------------------------S-----SS----S
-S----------S---SSSS------------S-S-------S---------------S----SS---------SS----
----------------S----SSSS--S-SS-SSS---------------------------------------------
-------S-------SS---------S------------S-----------S----S------S---------------S
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSS
>forward_437
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-----------------GCCTGCATGCATAGGAGTCC-------------------------------------------
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>reverse_2283
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------------------------------------------TTGCCACGCCTAAGGTAAGG------------------
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