>input_sequence_71647
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-----------------TCTATCCTTTCCTTATGCGCCCATATACAAGAAGAAAAGCAAACACAAGAGTCATGGAAGGCC
TGCTGCCGTTCCTGTACAGGGCCATCGTCCTCCACTATGCCGAAGGCGGCGGGTGGCGGACGGCCACCGGAGACAGCCCC
TTCCTCGGCAGCGACTCGCCATCTGCCTCTCGGCACTACTATGTCCGCCTCGCCGGCAGCGCCGACGACTCTGGCCGCCT
CCAGTTCGCCCCCT---CTTCTCTTGCCAGCCGCAACGCGCTCCTGTGATGGAATGAATGGATCATCATCTTCTCTCGTT
TGCTGG-TTTTTCTTTTC--------TCCTCTTCAATTAATTTTAGGCG-----------------------TGGGTGTC
GTATAGTACTCCTTCATTCTCAAGATATAAAAGCGCGCTTGACTTTGAACGGTTTTTGATGCATCACTCTGGTTACTAAT
ATATATCAAAGTACATGGACTGAACATGTATAAATGGCATATTGGCATAGTCATATTTGTCTTACAAAACAATTTTATTT
CCTATGTATGTATACTTCATAGACAGACAATACACTGAAGATCATAGTCAAAATTGTGCAACAAAGACCAAAAAAGTCTA
CGGGTGCCTTATATTTTGGGAAGTAGGGAGTGCGGTTTTGTGGTTTCAGACCGCAGGAAAGCATACTGGATCAATGATTT
ACAGTAATGATCAATGA---------------------------------------------------------------
-----------------------TTAAA----------------------------------------------------
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>chr3A_1_TraesCS3A01G059700
ATTATCTTTGCATGACCCTTCACTCTATCACGACTGATGTGTATGCGACCAAAATGTGATCCTCTCCTAGGCCGCTGAAT
ATCATCATTCAAAACCATGCCTAAAACGGTCTTAAATTCATCGTCGTCTTCTTCCTCTTCGGATGACCAATAGTCCTCGA
AGACTATCTCCCTCAACCTCTTCATCTACAATTCAAACGGCTACATGTTGCTAG-AAGATTCTTTATGGAGATTAAATTA
TGCGTTATTAAGGAAGCA----AGGCCAGACGACAGATATATATGCGAGAACTTTACTACACTGTTGTACTA-TGTGTTA
CATTATTGGGTGTCAAATGTAAACTCCTCCCAAGGGAGGCTGATTGTCACGTGTCATGTCCCTTTCTTGTGACTTGGATG
GGTGTCATTATCGTAATTTGGATGATGCTTGAGGCGGACCAGTTCCTTGGGTTCAGA-----------------------
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-------------TACTTGAGAAGGATGGTCTACCAGACATA----GGATT-------AGAGATA---CA----TATTTA
TCTTTGCAATAATA-----GGT----TCAGTCGATGTCCCAATTTTAAGCTTCGCTAGCGACAGTGGATAGGAAAACAGT
TAGGCATAACGAACCCAAT---TAGATTATGCCATGAGGT------------CCTTCGTTTTTAAACTGCATCTCTGCAT
TATTTATATTTTGTTCTTTGTATTGGTCTTCCTTGAACCAGAACCAACAGATTTGTTCTTTATTTGCCCTTGT----GAA
CATGCATATTCAC--ATTCCATACCTGTCGCATGCATAGAG-----------------------------AATTGCATCT
TGTCCTCTC-----GTGCAGACATCAACTT-----CCCCTCACAAAATTCATTTC--CACCAGAGGCTTGCAACCCG---
--TCGCCATCATCATCACCCATCTCTCCTCCTTCTCTCATTGACTAATTCTGTTTGCAAGCTAAGCAGGGCCTC-ATCAT
CCGATAACCTTTGATTAGCTTAGACTCAAAGCACATCTTGACACATATCTTATCATAGCTGCCTGTTTATAAACCCCCCG
TACAACAATCTTTTGCCTCTATCCTTTCCTTATGCGCCCATATACAAGAAGAAAAGCAAACACAAGAGTCATGGAAGGCC
TGCTGCCGTTCCTGTACAGGGCCATCGTCCTCCACTATGCCGAAGGCGGCGGGTGGCGGACGGCCACCGGAGACAGCCCC
TTCCTCGGCAGCGACTCGCCATCTGCCTCTCGGCACTACTATGTCCGCCTCGCCGGCAGCGCCGACGACTCTGGCCGCCT
CCAGTTCGCCCCCT---CTTCTCTTGCCAGCCGCAACGCGCTCCTGTGATGGAATGAATGGATCATCATCTTCTCTCGTT
TGCTGG-TTTTTCTTTTC--------TCCTCTTCAATTAATTTTAGGCG-----------------------TGGGTGTC
GTATAGTACTCCTTCATTCTCAAGATATAAAAGCGCGCTTGACTTTGAACGGTTTTTGATGCATCACTCTGGTTACTAAT
ATATATCAAAGTACATGGACTGAACATGTATAAATGGCATATTGGCATAGTCATATTTGTCTTACAAAACAATTTTATTT
CCTATGTATGTATACTTCATAGACAGACAATACACTGAAGATCATAGTCAAAATTGTGCAACAAAGACCAAAAAAGTCTA
CGGGTGCCTTATATTTTGGGAAGTAGGGAGTGCGGTTTTGTGGTTTCAGACCGCAGGAAAGCATACTGGATCAATGATTT
ACAGTAATGATCAATGA---------------------------------------------------------------
-----------------------TTAAATACAGTGATGATATCGCTGGTGTGGTCACCTCGAGATTTCAATGATTTGGCT
GGAATTAGGACCGTCAGCAGAAG------------ATTTCAATGATTCTCGTCAGTAGCCTGCATACTGTAGTGCTGTTG
TGTGCAGGATGGCTGCTACGAACACTCTCAATTTCATCATAATGTATGCTG-AAGCTTTCTACTTCCTCCGTTCCTAAAT
ATAAATCTTTCTAAAGATTCAGTAAGAACTACGTACGGATATATAGACATATTTTAGAGTGTAAATTCACTCATTTTACT
TTGTATGTAGTCCGCATTGGAATCTCTAAAAAGACTTATATTTAGGAACGGAGATAGTAGTTACTACTCCCTCCGTTCCC
AAATACTTGTCTTTCTAGGCATTTCAAATGGACTCAACATACGGATGTATGTAGACATATTTTAAAGTGTAGATTCATTC
ATTTTGCGCCGTATATAGTCACTTGTTGAAATCTCTAGAAAGACAAGTATTTAGGAACGAAGGGAGTACTTATTAAAGAA
ATATTAGTGTTACTAAATAATTACTATTAGTTTTTTAGAATAATAGTTTCAAACTCAAACAGCGAAACGTGTGACTTAAT
GCTCAAACTAAACTCCTGAGGGTTAATAGGATTGACATCTTACTATTGTCAGGAAAATAACAAATGCAGACTTGGAAACT
AGGGGGAATAGAACTCGAAAGTTAAGCGTGCTCAGGCTGAAATAGTGACAGAATGGGTGACCGGATGATTTGAAATGATG
ATGGGTGATTAGAGAATAGAGATTATAGATTAAATTAAGCAGTGACGAGGGGTGATTAGAGATTAAATTATAAAATAATT
TAAAAATTTAAAAATCAGAAAAAAAATAAAACAAAATTTAAAAAAAAAATTTAAAAAAAATAAAAAATTTGTAAAATTTC
CTTTAGTCACCGGAACTAAAGGTGGAGCTCCAGAGAGCGGCCACGTGAAGAGTCTTTAGTCCCGGTTCTAAAAAAATAAA
A
>chr3D_1
ATTATCTTTGCATGACCCTCCACTCTATCACGGTTGATGTGTATGCGACCAAAATGTGATCCTCTCCTAGGCCACCGAAT
ATCATCATTGAAAACCATGCCTAAAACGGTCTTAAATTCATCTTCGTCTTCTTCCTCTTCAGATGACGACTAGTCCTCGA
AGACTATCTCCCTCAACCTCTTCATCTACAATTCAAACGGCTACATGTTGCTAG-AAGATTCTTTATGGAGATTAGATTA
TGTGTTATTAAGGAAGCA----AGGCCAGACGATAGATATATATGCAAGAACTTT---ACACTGTTGTACTA-TGTGTTA
CATTATTGGGTGTCAAATGTAAACTCCT-CCAAGAGAGGCTGATTGTCATGTGTGGTGTCCCTTTCTCGTGACTTGGATG
GGTGTCATTACCGTAATTTGGACGATGCTTGAGGTGGACCGGTTCCTTGGGTTCAGA-----------------------
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-------------TGCTTGAGAAGGATGGTCTACCAGACATATATAGGGTT-------AGAGATG---CATATTTATTTA
TCTTTGCAATGATA-----GTTTAAGT-----GATGACCTAATTTTAAGCTCTGCTAACGACAGTGGATAGGAAAACTGT
TGGGCATGACGAACCCAATTAGTAGATTATGTCATGAGGT------------CCTTTGTTTTTGAACTGCATCTCTGCAT
TACTTATGTTTTGTTCTTTGTATTGGTCTTCCTTGAACCAGAACCAACAGATTTGTTCTTTATTTGCCCTTGTGAACGAA
CATGCATATTCAC--ATTCCATACCTGTCGCATGCGTAGAG-----------------------------AATTGCATCT
TGTCCTCTCTTGAAGTGCAGACATCAACTT-----CCCCTCACAAAATTCATTTC--CACCAGAGGCTTGCAACCCG---
--TCGCCATCATCATCACCCATCTCTCCTCCTTCTCTCATTGACTAATTCGGTTTGCAAGCTAAGCAAGGCCGTAATCAT
CCACTAACCTTTGATTAGCTAAGACTCAAAGCACATCTTGACACATATCTTGCCATAGCTGCCTGTCTATAAAACCTGTA
CGACA---------------ATCCTTTGCTTCTGCGCCCATATACAAGAAGAAAACAAAC----AGAGTCATGGAAGGCT
TGCTGCCGTTCCTGTACAAGGCCATCATCCTCCACTATGCCGAAGGCGG---GTGGCGGGCGGCCACCGGTGACAGCCCC
TTCCTCGGCAGTGACTCGCCATCGGCCTCTCGGTACCACTATGTCCTCCTCGTCGGCAGCGCCGACAACTCTGGCCGGCT
CCGGTTCGCCCCCGCTTCTCCTCCGGCCAGCCGCGACGCGCTCCTGTGATGGAATGAATGGATCA---TCTTCTCTCGTT
TCCGGG-TC---CTTCTT--------TCTTCTTCAGTAAATTTTAGGCC-----------------------TGGGT---
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>chr3A_206
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---------------------------------------------TGTTGCTAGAAAGATTCTTTCTGGAGATTAAATTA
TGTGTTATTATT-AAGCA----AGGCCAGAGGACAGATATATATGCGAGAACTTTACTACACTGTTGTACGA-TGTGTTA
CATTATTGGGTGTCAAATGTAAACTCCTCC-AAGAGAGGCTGATTGTCATGTGTCGTGTCTCTTTCTTGTTACTTGGATG
GGTGTCATTGTCGTAATTTTCTCAGTTTGGGT-----------------------GA-----------------------
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-------------TGCTTGAGAAGGATGGTCTACCAGACATA----GGATT-------AGAGATAGTACA----TATTTA
TCTTTGTAACGATA-----AGT----T-----GATGTCCTAATTTGAAGCTTTGCTAACAATTGCGTATAAG-AAACAGG
AAGGCATAACAAACCCCAT---TAGATTATGTCATGAGGT------------CCTTTGTTTTCAAACCACACCTCTGTA-
---TTATATTCTGTTCTTTGTATTGGTCTTCCTTGAACCAGAACCAACAGATTTGTTCTTTTTTTGTTCTTGTGAAC---
-ATGCATATTCAAATATTCCATACCTGTCGCATACATATGAAATTGCATCTGATTAAAAAAAACACATGAAATTGCATCT
TGTCCTCTCTTGAAGTGCAGACATCAACTT-----GCTCTCACAAAATTCATTTCGTCAACAGACGCATGCAACCCA---
--TCGCCATCATTATCATCACGAGTGTGTC---CTCTCGTTGACTAATCCAGTTCGCAAGCCGAGCAAGGCCGTAATCAT
CCACTAACCT------------------------------------------------------GTTTATAAACCCC-CA
TAAAACAATCTGTTGCCTCCATCCTTTCCTTCCGTGCCCCTATACAAT-----------ACACAAGGATCATGGAAGGCT
TGCTGCCGTTCCTGTACAGGGCCATCCTCCTCCACTACATCGACGGCGGCCGGACGC------CCACCGGCGACAGCCCC
TTCCCCCGCAGCGACTCGCCATCAACCTCACGGTCCTATTACGTCCGCCTCGCCGGCAGCGCCGACGACTTTGGCCGGCT
CCGGTTCGCCCCCA---CTTGTCCCGCCAGCAGCGACGCGCTCCTGTGATGGGAATAATGGATAATCATCTTCTCTCGTT
TCCGGGGTC---CTTCTT--------TCTTCTTCAGTAAATTTTAGGCG-----------------------TGGGT---
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>chr3D_206
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---------------------------------------------TGTTGCTAG-AAGATTCTTTCTGGAGATTAAATTA
TGTGTTATTATT-AAGCAAGCAAGGCCAGACGACAGATATATATGCGAGAACTTTACTACACTGTTGTACTA-TGTGTTA
CATTATTGGGTGTCAAATGTAAACTCCTCCCAAGGGAGGCTGACTGTCATGTGTCATGTCC----CTTGTTACTTGGATG
GGTGTCATTGTCGTAATTTTCTCAGTTTGGGT-----------------------GA-----------------------
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-------------TGCTTGAGAAGGATGGTCTACCAGACATA----GGATT-------AGAGATG---CATATTTATTTA
TCTTTGCAATGATA-----GTTTAAGT-----GATGCCCTAATTTTAAGCTTCCCTAACGACAGTGGATAGGCAAACAGT
TAGGCATAACGAACCCAAT---TAGATTATGTCATGAGGT------------CCTTCGTTTTTAAACTGCATCTCTGCAT
TATTTATATTTTGTTCTTTGTATTGGTCATGAG---------------------GTCCTTTATTTGTTCTTGTGAAG---
-ATGCATATTCAAATATTCCATACCTGTCGCATACATT-----------------------------TGAAATTGCATCT
TGTCCTCTCTTGAAGTGCAGACATCATCTTGCCGGCCCCTCGCAAAATTCATTTC--CTCCAGAGGCATGCAACCCAACC
CATCACCATCATCATCACCCATGTCTCCTCCT---CTCATTGACCATTTCAGTTTGCAAGCTAAGCAAGGCCATAATCAT
CCACTAACCTT-GATTAGCTAAGACTCAGAGCACATCTTAACACATATCT--------CTGCCTGTTTATAAAGCCG-CG
TACGACAATCCTTTGCCTCTATCCTTTGCTTCTGCGCCCATATACAAGAAGAAAAACAAACACAAGAGTCATGGAAGGCC
TGCTGCCGTTCCTGTACAGGGCCATCATCCTCCACTACGCCGAAGGCGGCGGGTGGCGGACGGCCACCGGCGACAGCCCC
TTCCTCCGCAGCGACTCGCCATCGGCCTCGCGGTACTACTATGTCCGCCTCGCCGGCAGCGCCGACGACTCTGGCCGGCT
CCGGTTCGCCCCCGCTTCTCCTCAGGCCAGCCGCGACGCGCTCCTGTGATGGAATGATTGG---ATCATCTTCTCTCGTT
TCTGGG-TCCTTCTTCTT--------TCTTCTTCTGTAAATTTTTGGCG-----------------------TGGGTGT-
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>chr3B_206
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---------------------------------------------TGTTGCTAGAAAGATTCTTTCTGGAGATTAAATTA
TGTGTTAT-ATT-AAGCAAGCAAGGTCAGACGACAGATATATATGCTAGAACTTTACTACACTGTTGTACTATTGTGTTA
CATTATTGGGTGTCAAATGTAAACTCCTCCCAAGGGAGGCTGATTGTCATGTGTCATGTCCCTTTCTTGTTACTTGGATG
GGTGTCATTATCGTAATTTGGATGATGCTTGAGGTGGACTAATTCAGATACTCCCTTTGTCCTAAAATTCTTGTCTTAGA
TTTGTCTAAATACGGATGTATCAAGTCACGTTTGAGTATTAGATACATCCATATCTAGGCAAATCTAAGACAAGAATTTT
GGGACGGAGGGAGTACTTGAGAAGGATGGTTTACCTGACATG----GGTTTTAAGCGTAGATATA---CT----CTAGTA
TGTTTGCAATGGCAGGTTTAGT----T-----GAGGTCCTAGTTTGAAGCTTCACTAACAACAGTGG-------------
-----ATAACCAACCCCAT---TATACTATGTCATGAGGTGAGGTAAGATGTCCTTAGTTTTCACGCCAAATATCTGTG-
---TTATATTTTGTTCTTTGGATTGGTCTTCCTTGAACCAGAACCAACAGATTTGTTCTTTGTTTGTTCTTGTGAGC---
-ATGCATATTCAAATATTCCATACCTGTCGCATACATT-----------------------------TGAAATTGCATCT
TGTCCTCTCTTGAAGTGCAGACATCATCTTGCCGGCCC-TCACAAAATTCATTTC--CTCCAGAGGCATGCAACCCAACC
CATCACCATCATCATCACCCATGTCTCCTCCT---CTCATTGACCATTTCCGTTTGCAAGCTAAGCAAGGCCATAATCAT
CCACTAACCTT-GATTAGCTAAGACTCAAAGCACATCTTAACACATATCT--------CTGCCTGTTTATAAAACCC-CG
TACGACAATCCTTTGCCTCTATCCTTTCCTTCTGCGCCCATATACGAGAAGAAAAACAAACACTAGAGTCATGGAAGGCT
TGCTGCCGTTCCTGTACAGGGCCATCATCCTCCACTACGCGGAA---GGCGGGTGGCGGACGGACACCGGAGACAACCCC
TTCCTCGACGGCGACTCGCCATCGGCCTCTCAGTACTACTACGTCCGCCTCACTGGCAGCCCTGACGACTCCAGTCAACT
AGGGTTTGCCGCCG---CTCCTCCGGCCAGCCACGGCGCGGTCCTGTGATGGAGTTAATAGATCATCATCGTCTCTCGTT
TCCGGG-TCTTTCTTCTTCTTCTTCTTCTTCTTCTTGACCTGGGTGTATGGTATGGATGACCTCTGGCCCTCTGGGTGTT
GTATAGTAC-----------------------------------------------------------------------
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---------------------------------GGTTCTGTGGTTTAGGACCACAGAGAAACATACTGGATCAATGATTT
ACAGTACTATAGTACTACCTATGTACCAAAATATAAAAGGTTTTTGCAGTTTAAATTGAACTGCAAAACGTCTTATATTT
TGGTATAGAGGGAGTACGTTTAGTTAAATAGAGCGATGATGTTGCTGGTGTGGTCACCTCGAGATTTCACTGATTTGGCA
TGAATTAGGAGCGTCAGCAGCAGCTAGCCAGCATTATTTCTTACATTTTCGTCAGTAGCATGTATGCTCTAGTGATGTTG
TGTGCAGGATGGCTGCTACGAACACTC--AATTTCGTCATAATGAATCCTTTAAGCTTTCTACTCCCTCCGT--------
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>SNPs
-------------------S------------SS---------------------------------------S-S----
---------S--------------------------------S-----------------S------S-S----------
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--S-----------------------------------------------------------------------------
-------------------------------------------------S------------------------------
----------------------------------S---------------------------------------------
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----------S----------------SSSSS-------S-----------------S----------------------
-------------------------------S------------------------------------------------
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--------------------------------------------------S----------------S----SS------
--SS----------------S------------------------------SS------------------------S--
-------------------------------S-----------------------S------------------------
--------------------------S-----------------------------------------------------
-----------------------S---------S-------------------------------------------S--
--S----------S---------SS---------S---------------------------------------------
-S-S----S------S-S----------S------S-S-----------------------------------------S
---------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----S--------SS----S---SS--S-------------------
------S-SSSSS-SS----------------------------------------------------------------
------------------------------S--S------S-S--------------------------S---------S
S---------S---------S-------------------SSSS---S-----------S--S--S--S-----S-----
---------------------------SS------S--------S--S--S-------------S-------SSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
S
>forward_74
------------------------------------------------------TGTGATCCTCTCCTAGGCCG------
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>reverse_1635
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----------------------------------GCGCTTGACTTTGAACGGTT--------------------------
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>forward_1465
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-----AGTTCGCCCCCTCTTCTCTT-------------------------------------------------------
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>reverse_2742
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---------------------TTAAGCGTGCTCAGGCTGAA---------------------------------------
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