>input_sequence_85579
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----------------------------------------------------------------ATGGACTGCGTGATCC
ATGTGGTGCTGGGGGTGGCCATGCGGAGGTGCATCTGCCGGCTGCACGAGGTCGTCGCCATGGCGATGGAGGTCGGCACG
GCGCTGCTCGTGGCCGTACGGTTCTCCGGCATGGCCTTCCGCCACACACCAGCGCCGACTCAGGCGGTCTCGGGGTCGAC
TCAGGCAGTCTCGGGGTCGACGCACTACTACTACTACGCCCCCGTGGCTGCCTCCATGGTTGGCATGTCCCGGCTCGACA
GGCACTAG------------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G513600
TCATATACAGTTGAATCATTCAAT--ACACTATGCGCAGTCATGATTCATTGTGTGCATAGTCTTTTTTGTCTACCCTAA
CAATGACAAGAGCTTCTTGC--------AAAAAAAATAAAAAAATTCACAGCAGATGTGCCTATTTGTTGAGAGAGGCCA
TTG------TGTACAGGTAGGCCATGGATGCACCTTGGCGTGC-TATAAAAATTCTTTAAACATACAACCATGATGTGGC
CATTGAGTAACTGAGATGACGACATGCACACATGGATTATTGCTGGTCGGATCTGATATTGAGAACCTAGCTCTTTTGTC
GGTAGAACATAGTACTATGCCTAGTTATAATAATCTAGTGCAACTGCGCAAGCTTAGGGATGTCCACATTTGATGATCTG
CCACAAATTGGTGTTCTGTAGTTAAGAAATTCTTCTAAAAATT-----------------------------AATT-TAA
GAAATCCATTCTGTCAAAATTTGATAATG---------------------------------------------------
-GGCATACACATATTGCAAATATGA------------------------------------AATATGTGAAACACAAATG
ACATCACTGAAAA-TACTTATGAATACAATTCCCATGAGC------ATATTATTTTTGTGTCATG---------------
-------ATTATTGGTCAAACATAATATTCTGTCTT-GTGTACGCCTTGCATTTTTTGGATGAGGAAGTAGCCATAACTA
CAAGTCATACTAACTAATTTAAAAAAAACTATTAAACAAATTTTTAAA--------------------------------
------------------------------------------------AAACTATTAAACAAATTCAGGCAAAT---TTT
AAAAATGGTAAGTTAGTAATTTTTCATGGATCTACACAACTTGCATCGGTCCATCAGACGGCCATCGGCATCACGTACAC
ACTAGGTACCAATTCTATATTGAAAGGTAGTAGATGACAAAAGCAACCTACCTGCCGTGTAAAACACACGCCGCGAGCTA
GCTAGTTCGATCGAACACACAACTAAATTAACGCCAGGCTTCCAAAGAAAAG---CTAGCTAGAGAGCAGCTAGGTCGTC
GACACCGGCGAGG-TCGATCTCGCCTTTGCCGCA------------GGCCGATCGATGTCCACCATGGACTGCGTGATCC
ATGTGGTGCTGGGGGTGGCCATGCGGAGGTGCATCTGCCGGCTGCACGAGGTCGTCGCCATGGCGATGGAGGTCGGCACG
GCGCTGCTCGTGGCCGTACGGTTCTCCGGCATGGCCTTCCGCCACACACCAGCGCCGACTCAGGCGGTCTCGGGGTCGAC
TCAGGCAGTCTCGGGGTCGACGCACTACTACTACTACGCCCCCGTGGCTGCCTCCATGGTTGGCATGTCCCGGCTCGACA
GGCACTAGCACTGGGGACCGGTGAGCTACACCCCTCTGGATTTGATGGCTAATCAATCGTGTA-TTTTTAT----TTAGT
GAGTAATAATGAAATTCAGTGCTTGATTAGCTACATACACACATGCGCACTGTATATTAAGCAATATATGTGTTCATCTT
GATATCGATATAGTAATTGATCAGTCTCGCATGC------------ATGGTGGTGATTAATTGGATCTT-GGTCAGGTGT
TCACTATTGTGAATTTGTGATGACTCCAGGGTTATACCCTCCTTTGGG--AAAAAACGGTGTCCATTTGTGTTTCTTTCT
TTGCTTGCTAGCTCGTTTTTGTTTTGGGGATTCATGATTCACTATTATGTAATCATGTGTGGACTAATTA----------
--AATCCTCCAGTGGTTTAGAATATAT----------------ATAGCACAAGAAGAATCGAGAGATAACAGACAAGAAT
TAGTTATTTCTGAATATATAGCACTAGACTGCATCCTGCATAGGTGAATCTTCTTCCTTGC--ATGTTCGTGTTTTATCG
CTGGGGTTGTCATTAATCGCTGCTTATGCATGTGATGTGCTATCAATTTGTGGATATTGTTC---GTAATAGTCCAACTA
ATGTAGTTCATTGAGAACTAATTACTGAATTCTTGCTATGTTGTTTCTGCATATTCTTAGCTGTACGTGTGGCTACTGAA
ATGTTTGATCTACTAGACTGTAATCAAAGATTAAAGTGCACTAGTTTGTTATAAGCAAATCATATATAAAACATCATAGC
TTTATTTGTTACTCCTATACATCTCTA------------------------------------TACATCTCTCCCAGGCG
AGGCTTCGTAAACTCGGTCATTTAATTGGTTTCTCTAAGTTGTATCAAAATACCTTTTTTTTCTAAGATTTGTTTCATTA
ATTACCTGACGTCCCATCTTATCTACTCCCAACAGCTCGCCATGCCTTGATTTTGAAATAACAAAATGTTCAAGTGTATT
TGTACCCGCCATATATTGAGTGTTCAGAAAAAGAAAAGGCACACTCAATTTATATCT
>chr3D_5
----ATACAGTTGAATCGTTCAGCCGACACTATGCACAGTTATGATTTGTTTTGTGCGTAGTCTTTTTTGTCTATCCTAA
CAGTGACAGGAGCTTCTCGC--------AAGAAAATAAAAAACAATGACAAGAGATGTGCCCATTTGTTGAGAGAGGAAT
ATTAATTGATGTACAAGTAGGACATGGATGCATCTCGGCGTGCATATAGAGATTCTCTAAACATACAACCATGATGAGGC
CATTGAGTAACTGAGATGACGACATGCACACATGGTA-----------GGATCTGATATACAGTACT-------------
--TAGATCATGGTACTATGCCTAGTTATAATAATCCAGTGCAACTGCGCAAGCTTAGGGATGTCCACATTTGAGGAGCTG
CCACAAATTGGTGTTATTTAATTAAGCAATTCTTTTTTTTTCCGGAGAATTAATTAAGCAAGTCAGCCAAAAAAAT-TAA
GAAATACATTCTGTCAAAAATTAATTATCAGCCAGTCCTTTCTCTGTGCTCGAAACTACTCCCACCCTTCCAAGAATCTA
AGGCATGCACATATTCCAAGATCTAAATTAACCTAACAATTAGACAAAATTG----------------------------
------------------------TATGAATCCAAGGATC------ATATCATTTTTGTGTCACTTGACTCGTACTTTTC
TAGTTAAATTGTTGGTAAAACATAATTTTCTGTTGCCGTGGACGCCTTGCATTTTTA-GATGACGGAGTAGCCACAACTA
CAAGTCGTACTACCTAAATGTTCTGGAAAGAAAGAGAGAAATTGAAAACAAAACTTTGTCCTGTTTCCATGCATTC--CT
CCTTGCCCCAACATGCTTAC--TGTGATTAATTTTTTTTCGGACAATGAAAACATTAACTAATTTCATTGTTTAAGGTTT
ACAAATAGTAAGTTGGTAAAAATTCATGGATCTACATAACCTGCATCGATCCATCAGACGGCCATCGGCATCACAT--AC
ACTAGCTACCAAATCTATATTGGAAGGTA---GATGACAAAAGCAACAGACCTGCCGTCTAAAACACACGCCACAAGCTA
GCTAGATCAATCGAACACACAAC---------GCTAGGCTTCCAAAGGAAACTAACTAGCTACAGAGAAGCTAGGTCGTC
GGCACCGGCGAGGGTCGATCTCACCTTTGACGCCGGCCGGCTGGCCGGCCAACCGATGCCGTCCATGGACTGCGCGATCC
ACGTGGTGCTGCGGGTGGTCATGCGGAGGAGCATCTGCCGGCTGCACGAGGTCGTCGCCATGGCCGTGGAGCTCGGCACG
GCGCTGCTCGTGGCCGTGCGGTTCTCCGGCATGGCCTTCCGCCGCACGCCAGCCCCGACTCAGGTG--------------
-------GTCTCCGGGTCGACTCACTATTACTACTACGCCCCCGTGGCGGCCTCCATGGTTGGCATGTCCAGGCTCGACA
GGCACTAGTC------ACCGGTGAGCTACATCCCGCTGGATTTGATGGCTAATCAATCGTGTTTTTTTTAT----TTTGT
GAGTAATAATGAAATTCAGTACTTGATTAGCTACATACACACATGTGCACTGTATATTAAGCAGTATATGTGTTCATCAT
GATATCGACATAGTAATTGATCACTCTCGCATCAATTTGGGAGCAAATGGTGGTGATTAATTGGATCTTTGGTCAGGTGT
CCACT--------TTTGTGATGACTCCAGGGTTATACCCCCCCTTGGG--AAAAA-TGGTGTCCATTTGTGTTTCTTTCT
TTGCTTGCTAGCTCATTTTTGTTTTGCGGATTCATGATTCACTATTATGTAATCATGTGCAAATGGTA---ACTAAGCCT
ATAATTCTCCAGTGGTTTATAGAATACATA--------------------------------------------------
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>chr3A_5
----ATACAGTTGAATCGTTCAGTCGACACTATGCACAGTCATAATTTGTTTTGTGAATAGTATTTTTTGTCTATACTAA
CAATGACAAGATCTTCTCGC--------AAA---------AAAAATGACAAGAGATGTGCCCATTTGTTGAGAGAGGAAT
AGTAA----TGTGCAAGTAGGCCATGGATGCACCACGGCGTGCATATAGAGATTCTCTAAACATACAACCATGATGTGGC
CATTGAGTAACTGAAATGACGACATGCACACATGGTA-----------GGATCTGATATACAGTACCTAGCTCTTTTGTC
AATAGAACATGGTACTATGCCTAGTTATAATAATCGAGTGCAACTGCGCAAGCTTACGGATGTCCACATTTGATGAGATG
CCACAAATTGGTGTTAATTAATTAAGCAATTCAGCCAA------------------------------AAAATAAT-AAA
GAAATCCATTCTGTCAAAAATTAATAATCAGCCAGTCCTTTCTCTGTGCTCGAAACTACTCCATCTTTTTCC-------A
AGACATGCACATATTCCAATATCTAAATTTACCTAACAATTAGACTTGCAAATGTGAAAAATATATGTGAAACACAAATG
GCATCAGTGAAAAATACTTATGAATATTAATCCAAAGATC------GTATCATTTTTGTGTCACTTGACT---ACTTTTC
TAGTTAAATTGTTGGCAAAACATATTTTTCTGTTGCCGTGTACACCTTGCATTTTTA-GATGACGGAGTAGCCACAACTA
CAAGTCGTACTACCTAAATGTTCTGGAAAGAAAGTGAGAAATTGAAAACAAAACTTTGTCCTGTTTTCATGCATTCCTCT
CCTTGCCCCAACACGCTTACTGTGTGATTAACTATTTTTTGGACAATGAAAACATTAACTAATTTCATTGTTTAAGGTTT
ACAAATAGTAAGTTGGTAAAAATTCATGAATCTACATAACCCGCATCGATCCATCAGAGGGCCATCGGCATCACAT--AC
ACTAGCTACCAAATCTATATTGGAAGGTA---GATGACAAAAGCAACAGACCTGCCGTCTAAAACACACGCCGCAAGCTA
GCTAGATCCATCGAACACACAAC---------GCCAGGCTTCCAAAGAAAACTAACTAGCTAGAAAGAAGCTAGGTCGTC
GGCACCGGCGAGGGTCGATCTCACATTTGACGCCGGCCGTCTGGCCGGCCGACCGATGTCGTCCATGGACTGCACGATCC
ATGTGGTGCTGGGGGTGGTCATGCGGAGGAGCATCTGCCGGCTGCACGAAGTCGTCGCCATGGCCGTGGAGCTCGGCACG
GCGCTGCTTGTGGCCGTGCGGTTCTCCGGCATGGCCTTCCGCCGCACGCGAGCCCCGACTCAGGTG--------------
-------GTATCGGGGTCGACTCACTATTACTACTACGCCCCCGTGGCGGCCTCCATGGTTGGCATGTCCAGGCTCGACA
GGCACTAGTC------ACCGGTGAGCTACACCCCTCTGGATTTGATGTCTAATCAATCGTG-----TTTTT----TTTGT
GAGTAATAATGAAATTCAGTGCTTGATTAGCTACA------CATGTGCACTGTATATTGAGCAATATATGTGTTCATCAT
GATATCGGCATAGTAATTGATCACTCTCACATCAATTTGGGAGCAAATGGTGGTGATTAATTGGATCTT-CGTCAGGTGC
CCACT--------TTTGTGATGACTCCAGGGTTATACCCCCCTTTGGGGAAAAAA-TGGTGTCCATTTGTGTTTCTTTCT
TCGCTTGCTAGCTCATTTTTGTTTTGAGGATTCATGATTCACTATTATGTCATTATGTGTAAATGGTA---ACTAAGCCT
ATAATTCTCCAGTGGTTTATAGAATGCATATAGCAGATATGAGATATCAGAAGCAGAATGGAGAGAGAACAGACAAGAAT
TAGTTACTCTGA---ATACAGCAATAGAGTGCATCCTATATAGGTGGATCTTCTTCCTTGCTAATGTCCATGTTTTATCG
TTCGGGTTCTTATTAATCGCTGGTTATGCATGTGATGTATTATCAATTTGCGGATATTGCTC---G---TAGTCCAACTA
ATTTTGTTCACTGAGAATTAATTACCGGATTCTTTGTGTGTTGTTTCTGTATATTGTTCACGGTACTTGTGATTTCTGAA
ATGTTTGATCTACTAGCTTGTAATCAAAGATAGTAATGCACTAGTTTGTTGTAAGAAAATTGAACATAAAGCCTCACAAT
TTTTGTTACTTGATTCAGTAATCATACCACTTAGGATTGTAAGCATTCATTAATTTCTTATACTACATCTCTCTAAGGCG
AGGCTTCCAAAACTAGGTCATTTAATTGGTTTCTCTAAGTTGTATCAAAGTACATTGTTTTTTT-AGATCTGTTTCATTA
ATTACCTGATGTGCCATGTAATCTATTTGCAACAGCTCGTGGTGCGTTGGTTGCGAAATAACAAACTGTTCAACTTTATT
T--------------------------------------------------------
>chr3B_5
----ATAAAGTTGAATCGTCCAGTCGACACTATGCACAGTCATGATTTGTTTTGTGCATAGTATCTTTTGTCTATACTAA
CAGTGACAAGAGCTTCTCGCAACAACAAAAA---------AACAATGACAAGAGATGTGCCCATTTGTTGACAGAGGAAT
AGTAA----TGTGCAAGTTGGCCATGGATGCACCACGGAGTGCATATAGAGATTCTCTGAACATACAACCATGATGTGGC
CATTGAGTAACTGAGATGACGACATGCACACATGGTA-----------GGATCTGATATACAATACCTAGCTCTTTTGTC
AATAGAACATGGTACTATGCCTAGTTATAATAATCGAGTGCAACTGCGCAAGCTTACGGATGTCCACATTTGATGAGATG
CCACAAATTGGTGTTAATTAATTAGGCAATTCAGCCAA------------------------------AAAATAAAAAAA
GATATCCATTCTTTAAAAAATTAATAATCAGCCAGTCCTTTCTCTGTGCTCGAAACTACTCCCTCCTTTCCAAGAATCTA
AGACATGCACATATTCCAAGATCTAAATTCACTTAGCAATTAGACTTGTAAATGTGAAAATAATATGTGAAACACAAATG
GCATCTGTGAAAAATACTTATGAATATGAATCCAAAGATCATAGGTGTACCATCTTTGTGTCACTTGACTTGTACTTTTC
TAGTTAAATTGTTGGTAAAACATAATTTTCTGTTGCCATGTACGCCTTGCATTTTTA-GATGACGGATTAGCCATAACTA
CAAGTCGTACTACCTAAATGTTCTGAAAAGAAAGAGAGAAATTGAAAACAAAACTTTGTCATGTTTTCATGCATTC--CT
ACTTGCTCCAACATGCTTAC--TGTGATTAACTATTTTTTGGACAATGAAA-CATTAACTAATTCCGTTGTTTAAGGCTT
ACAAATAGTAAGTTGGTAAAAATTCATGGATCTACACAACTCGCATAGATACATCAGACGGCCATCGGCATCACAT--AC
ACTAGCTACCAAATCTATATTGGAAGGTA---GATGACAGAAGCAACCTACCTGCCGTCTAAAACACACGCCGCGAGCTA
GCTAGATCGATCGAACACACAAC---------GCTAGGCTTCCAAAGAAAACTTACTAGCTGGAGAGAAGCTA-GTCGTC
GGCACCGGCGAGGGTCGATCTCACCTTTGACGCCGGCCGGCTGGCCGGCCAACCGATGTCGTCCATGGACTGTGCGATCC
ACGTGGTGCTGGGGGTGGTCATGCGGAGGAGCATCTGCCGGCTGCACGAAGTCGTCGCCATGGCTGTGGAGCTCGGCACG
GCGCTGCTAGTGGCCGTGCGGTTCTCCGGCATGGCCTTCCGCCGCACGCCAACCCCGACACAGGTG--------------
-------GTCTCGGGGTCGACTCACTACTACTACTATGCCCCCGTGGCCGCCTCCATGGTTGGCATGTCCAGGCTCGACA
GGCACTAGTC------ACCGGTGAGCTACACCCCTCTGGATTTGATGGCTAATCAATCGTG-----TTTTT----TTTGT
GAGTAATAATGAAATTCAGTGCTTGTTAGCT---A------CATGTGCACTGCA-------CAATATATGTGTTCATCAT
GATATCGACATAGTAATTGATCACTCTTGCATGTATTTGAGAGCAAATGGTGGTGATTAATTGGATCTT-GGTCAGGTGC
CCACT--------TTTGTGATGACTCCAGGGTTATACCCCCCTT--GGGAAAAAA-CGGTGTCCATTTGTGTTTCTTTCT
TCTCTTGATAGCTCGTTTTTGTTTTGAGGATTCATGATTCACTATTATGTAATTATGTGTAAACGGTAACTACTAAACCT
ATAATCCTCCAGTGGTTTATAGAATGCATATAACAGATATGAGATATCAAAAGTAGAATCGAGAGAGAACAGACACGAAT
TTGTAACTCTGA---ATATAGCAATAGAGTGCATCCTACATAGGTGGATCTTCTTCTTTGTTGATGTCCAGGTTTTATCA
TTCGGGTTGTTATTCATCGCTGCTTATGCATGTGAAGTATTATCAATTTGCGGATATTTCTCCTAG---TAGTCCAACTA
ATTTAGTTCACCGAGAACTAATTACCGGATTCTTGGTGTGTTGTTTCTGTATATTGTTCACTGTGCATGTGATTTCTGAA
GTGTTTGATCTACTAGCCTGTAATCAAAGATTATAATGCACTAGTTTGTTATAAGAAAATTGTACAGAAAACATCACAAC
TTTTGTTACTTGATTCAGTAATAATACCACTTAGGATTGTAAGCATTCATGAATTTCTTATACTACATCTCTCTAAGGCG
AGGCTTCCAAAACTAGGTC-TTTAATTGGTTTCTCTAAGTTGTATCAAAGTACCTTGTTT-TTT-AGATTTGTTTCATCA
ATTACCCGACGTGCCATGTAATCTA-TTGCAACAGCTTGTGATGCATTGGTTGTGAAATATCAAACTGTTCA--------
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>chr2A_710
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-----------------------------------------------------------------------------TTT
ACAAATAGTAAGTTGGTAAAAATTCATGAATCTACATAACCCGCATCGATCCATCAGACGGCCATCGGCATCACAT--AC
ACTAGCTACCAAATCTATATTGGAAGGTA---GATGACAAAAGCAACAGACCTGCCGTCTAAAACACACGCCGCAAGCTA
GCTAGCTAGACCGAACACACAAC---------GCCAGGCTTCCAAAGAAAACTAACTAGCTAGAAAGAAGCTAGGTCGTC
GGCACCGGCGAGGGTCGATCTCACATTTGACGCCGGCCGTCTGGCCGGCCGACCGATGTCGTCCATGGACTGCGCGATCC
ATGTGGTGCTGGGGGTGGTCATGCGGAGGAGCATCTGCCGGCTGCACGAAGTCGTCGCCATGGCCGTGGAGCTCGGCACG
GCGCTGCTTGTGGCCGTGCGGTTCTCCGGCATGGCCTTCCGCCGCACGCGAGCCCCGACTCAGGTG--------------
-------GTATCGGGGTCGACTCACTATTACTACTACGCCCCCGTGGCGGCCTCCATGGTTGGCATGTCCAGGCTCGACA
GGCACTAGTC------ACCGGTGAGCTACACCCCTCTGGATTTGATGTCTAATCAATCGTG-----TTTTTTTACTTTGT
GAGTAATAATGAAATTCAGTGGTTGATTAGCTACATACACACACGTGCACTGTATGTTAAGCAATATATGTGTTCATCAT
GATATCGACATAGTAATTGATCACTCTCGCATGC------------AT--------------------------------
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>SNPs
SSSS-------------S----S------------S-----------SS--S----------------------S-----
-----------------S-----------------SS-------S-S---SS---------S---------------SSS
S-S------------S-------------------S------------S-S-----S-----------------------
-----------------------------------SSSSSSSSSSSSS-----------SS--S----------------
SS--------S------------------------S----------------------------------------S---
---------------S-S--S-----S-----------SSSSS-------------------------------S-----
-------------------S--S-----S---------------------------------------------------
------S--------S---SSSSS--------------------------------------------------------
S-----S-------------------SS-S---S-S--S-----------S------------SS---------------
----------S-----S---------S------SSS--------------------SS-----S-S--------------
------S-----S----S-SSSSSS---SS-SSS-SSS--S--SS-----------------------------------
---------------------------------------------------SS-----SS--S----SSSSSSS------
-S----S-------S----SSS--------------------------S-------------------------S-SS--
-----S------S---------S------SSS--------------------------S---------------------
-----S-----------------SSSSSSSSS-------------------S---------------S------------
-S--------------------S------S---S------------------S-------SS------------S-----
------------------S----------S----------------------------------SS-----S--------
-----------------S-------------------------S---S-----S----------S-SSSSSSSSSSSSSS
SSSSSSS--------------S--------------------------S---------------------S---------
--------SSSSSSSS----------------------------------------------S--------------S--
---------------------------------------------S--------------------------------S-
--------S--------------S--------------------------------------------------------
S----SSSSSSSS--------------------------S---------------S------------------------
--------------------------S---------------------------------SS--SSSSSS----------
-------------------S-SS---S-------------------S--S---S------------S-------------
------S-SSSSSSS--------S----S--------S--------S--------------------S-S----------
S-S-------S---------------------------SS----------S--------S------SSS-----------
--S-------S--------------S-S-------S-S-----------S-----S--SS------S----SS-S-----
----------------S----------------S-S-------------------S----SS--S-----------S-S-
---SS--SS-SSSSSS-SSS---SSSS----------------------------------------------SS-----
-------SS-----S----------------------------------S------S-----S-S---------------
------------S----S-S-----S-SS----------SS----S---S--S------------S-------S-S----
-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_196
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----------------GTAGGCCATGGATGCACCTT--------------------------------------------
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>reverse_2220
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-----------------------------------------------------------GCTGTACGTGTGGCTACTGA-
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