>input_sequence_59258
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------------------------------------------------------ATGTCCACGGAGAGGTAAGA----GT
CCCTCAAGAAACCATGCTTCTTCGATGCTTGTACTTGATTTGTTTTTAAATAAAAGGCTCCCTTTGTTTGTTTGG-----
ATTATCCTTTCTGGTCAGAAGAATCTAATTTAGATGTGTTTTTTCTATCTATATATGACGTTTGCCTAAAAGGTTTATCG
AGAGATCTATGATAGCAGTGCCTTTTCCTGTTCTTGCGGCCACAATTTTAGCACTTCGGTCTGCATCGCGCGCTTTGAGA
TCCCCGCTACTTAATTCCATCCAAAATAAACCCTAAT---CTTTCGGGCTTCCACCAGGGAGAGACTCGACGAGATCGGT
AAGAAGATCAAGCGAGAGCCGGACCCCGCCGCCGC------CATCGCGGGCGTAGTAGTCGCCGTCTCACCGACCGAGCA
CCACGGCCCTCGCCGCCTAGGCCTCGTTGGCCCAGGCATCGGCGGCGCCGCGAACATAGCGACCCCGTGCGCCGCGTGCA
AGCTCCTCCGCCGGCGCTGCGCGCACGAGTGCCCCTTCGCCCCCTACTTCTCCCCGCACGAGCCCCACAAGTTCGCCGCC
GTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGGTACCATCAAACTATTTTAATGGTTTCCTTTTTTT
T-GGTTAATTCCACCGTCCGTGTTTTGTGTTAATTAATGGCGTACGTCGGTGCATGTCACGCGCTGTTTCAGGAGGTGCC
CGAAGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAGGCGAACCTGCGGCTGCGCGACCCGGTGTACGGCTGCA
TGGGCGCGATCTCCATGCTGCAGCAGCAGGTGAACGCGCTGGAGGCCGAGCTGCAGGCCGTCAGAGCCGAGATCTTCAAG
CACAGGTACCGGCAGGCCGGCGTCGGCGTCGGCGT------GGCAAACCTCATTGTCGACGACGACGTTAGTGCCGCTGC
AGCCGGCGGCTTCATGGCTCCTGCCACGTCGCTGGTGCACACCGCTGACGTGGTGTCCGTGGCGGAGGCCGGCCAAGAAG
TGGCCGTAATGCCGTCGACGGCCACGGCCACGGCGTACGCTGCCGGACAGCCGTCGAGCACTGACTACAGCTCCCTCGAC
ACAAGTGAGCATGATGCATACTTTGGTTGA--------------------------------------------------
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>chr3D_1_TraesCS3D01G340000
GCCTCGCGGGCCCCACTACCCACCAGGGCGCGCCAGATGGGGGTGGCGCGCCCTGGTGCCTAGTGGGCAGC-TGGCCCCC
CCTCCAGTGGGTCTTGCTTCAAGTAATTTTTACATATTCCAAAATAATTCCCCAAAAAGTTTCTCCAATTCCGAGAACTT
TTATTTCTGCACAAAAACAACACCATGGTAGTTTTGCTAAAAACATCGTTAGTTCAGGTTAATTTCATTCAAATTATGCA
AATTAGAGTCCAAAACAAGAGTAAAAGCGTTAGAAAAAGTAGAGACGATGAAGACGTATTAGACACGGCCGGCCCGGCGC
CTGCAGCGAACCCGCAACCTCCTCATCCTCCGACTCGGTGTCATCCGAATCGAGGGCCCAGAAGCGGTTGACAGGAAGCA
CCGCAGACGACGGAAGCGGCAAGGCAGATGGGGAGGGGGAGGCCGGACCGATGGACCCAGGGGGCCGCGGGGAGGGAGAA
GAGGAGGTGGGGAAGGGCACACCGCCGGCCACCGCCGCGGGGAG-AGAGGGGAGGGAGAGAGGAGAGCCATCTGCCGACT
CCCCTTATTTTTATTTATTTACTCGCATTTTATGTTAGAACCATCGAAGTACGAATTGTAACCGAGGTAAAATGGTCAAG
TGGGATCT----CCAGGCAGCTTCTTGTTTTCAACAGCATTTCTTTCATTCCCTTGACATGAGCAGAAGCACCAGGGCGC
AGGGGCACGAGGGA----GGGAGGGCCGGCCAACTAATCGAGTCAATGTTCCTTGGCTTGGCTTGCCAACATTTCTTCCT
CCTCCCTCGCCCATTTACTTACTA-CCAATTGTGTGCATGCTTTACGCCCATCCCCCTCATTAATGCCTTGCCTTTTAAG
CACTCTTTCCTTCCTCGCAATTCCAAACTTTACACTTCTCTACTACCTGTCCGTCTCCCTCCCCCTCGCTCTCAATTGTT
CCTCTGTCATTCTCCGTCTCTCCGTCTCCCAAGC---AAGGGGAGCATGCCTCTATGTCCACGGAGAGGTAAGA----GT
CCCTCAAGAAACCATGCTTCTTCGATGCTTGTACTTGATTTGTTTTTAAATAAAAGGCTCCCTTTGTTTGTTTGG-----
ATTATCCTTTCTGGTCAGAAGAATCTAATTTAGATGTGTTTTTTCTATCTATATATGACGTTTGCCTAAAAGGTTTATCG
AGAGATCTATGATAGCAGTGCCTTTTCCTGTTCTTGCGGCCACAATTTTAGCACTTCGGTCTGCATCGCGCGCTTTGAGA
TCCCCGCTACTTAATTCCATCCAAAATAAACCCTAAT---CTTTCGGGCTTCCACCAGGGAGAGACTCGACGAGATCGGT
AAGAAGATCAAGCGAGAGCCGGACCCCGCCGCCGC------CATCGCGGGCGTAGTAGTCGCCGTCTCACCGACCGAGCA
CCACGGCCCTCGCCGCCTAGGCCTCGTTGGCCCAGGCATCGGCGGCGCCGCGAACATAGCGACCCCGTGCGCCGCGTGCA
AGCTCCTCCGCCGGCGCTGCGCGCACGAGTGCCCCTTCGCCCCCTACTTCTCCCCGCACGAGCCCCACAAGTTCGCCGCC
GTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGGTACCATCAAACTATTTTAATGGTTTCCTTTTTTT
T-GGTTAATTCCACCGTCCGTGTTTTGTGTTAATTAATGGCGTACGTCGGTGCATGTCACGCGCTGTTTCAGGAGGTGCC
CGAAGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAGGCGAACCTGCGGCTGCGCGACCCGGTGTACGGCTGCA
TGGGCGCGATCTCCATGCTGCAGCAGCAGGTGAACGCGCTGGAGGCCGAGCTGCAGGCCGTCAGAGCCGAGATCTTCAAG
CACAGGTACCGGCAGGCCGGCGTCGGCGTCGGCGT------GGCAAACCTCATTGTCGACGACGACGTTAGTGCCGCTGC
AGCCGGCGGCTTCATGGCTCCTGCCACGTCGCTGGTGCACACCGCTGACGTGGTGTCCGTGGCGGAGGCCGGCCAAGAAG
TGGCCGTAATGCCGTCGACGGCCACGGCCACGGCGTACGCTGCCGGACAGCCGTCGAGCACTGACTACAGCTCCCTCGAC
ACAAGTGAGCATGATGCATACTTTGGTTGACATGCATGGATTTACTTGCGGTTCTGGTGATTGATGGAGAACACAATCGA
TTAATTAACTCGCCAAATAAACTTTATGTGCAAGTATAA--CTCTCTCTATACATGTATCTTCTCTAGAACTAGATATAG
CTGCTGTGGATATCTTGGGTGAGAAAAATATTGTCCAGTGATCGAGATGTATCTGCCCTCATAAATTTCTTGTGTGTGTC
CACTCATCCAGTGTGATTGCTTGGTTGATTTAAT--TAATTGATTGATTTGTAAAATAAAAA-CTTAGAGCTCACACTTT
AACTGACACTAGTT------------------------------------------------------------------
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--------------------------------------------------------------------GCCAGGCTTAGA
ATTAGTTGGAAATAGAATAATCGACAGTATTTGTTTTCTTTGTTCTTTTATGATGAGTGTTTAGCACTGCATCTGCAAGC
GTGTATATATTTCAACGTGGTTATTTTTGCTAAGCAGTGCGCTAG-TTTTATGTTGTGCTAGCTTGCACTCAATAGGATC
CGTCGTTTTCTCCTTAGCTATTTGATTCCATGAATTTCTCAATGATTGATATGAATTTGCGTGTAAGCTAGCATTTTCAG
CATGTTCATGAGTCATAACAGATTAACAGTACTACAGCACTACAGATTTTCAGCACCTTCTCCTCTGTACATAGGTCAAT
TAACATCGAAAGTTTGGGGATCTCACATTAGGTGAGTATGTGTCTTCATTTTCCCTCCAACCTTTTAAATCTGGAGCAAA
TTTTTCTGAATATA---TTCTTTAAGCTGAAAAGGGTTTACAATCGTACTGGGGCCAAAATCAAGTATTTTTTTTACTGA
TTAGCTCGGAAATGACACATATGAGCCTGACACGGTGTCGATATGGCATGCATTTGTGAATGCATGCATGTCAATTCTGA
TAGTTAAGTCACATCTTTTT-TTAAAGCTAGTTAAGTCACATCTTTATCATTGTTCACTAGCTAACCGATTTGTTTTGGC
AATTCGTTATTTTTGCTCAAGAAT-ACTGTACATTGATATGACAAATTGAAATTA
>chr3B_1
GCCTCGTGGGCCCCACTACCCACCAGGGCGCGCCAGATGGGGGTGTCGCGCCCTGGTGCCTAGTGAGCAGCTTGGGCCCC
CCTCCAGTGGGTCTTGGTTCAAGTAATTTTTATATATTTCAAAATAATTCTTCAAAAAGTTTCTCCAATTTTGAGAACTT
TTATTTCTGCACAAAAACAGCACCATGGTAGTTCTGCTAAAAACCTCGTTAGTTCGGATTAGTTTCATTCAAATTATACA
AATTAGAGTTCAAAATAAGAGCAAAAACGTTAGGAAAAGTAGATACGGTGAAGACGTATTAGGCACGACTGGCCCGGCGC
CTGCAACGAACCCGCAAGCTCCTCATCCTCCGACTCGGTGCCATCCGAATCGAGGGCACAGAAGCGGTTGACAGGAAGCA
CCGCAGACGACGGAAGCGACAAGGCAGAGAGGGA-GGGGAGGCCGGACCGATGGACCCAGGGGGGCACGGGGAGGGAGAA
GAGGAGGTGGGGGAGGGCACACCACCGGCCACCGCCGCGGGGAGCAGAGGGGAGGGAGAGAGGAGAGCCATCTGCCGGCT
CCCCTTATTTTTGTTTATTTACTCGCATTTTATGTTAGAACCATCGAACTATGAATTGTAACGGAGGTAAAATGGTCAAG
TGG-----------AGGCAGCTTCTTGTTTTCAACAGCATTCCTTTCATTCCCTTGACATGAGCAGAAGCACCAGGGCGC
AGGGGCACGAGGGA----GGGAGGGCCGGCCAACTAATCGAGTCAACGTTCCTTGGCTTGGCTTGCCAACATTTCTTCCT
CCTCCCTCGCCCATTTACTTACTA-CCAATTGTGTGCATGCTTTACGCCCACCCCCCTCATTAATGCCTTGCCTTTTAAG
CACTCTTTCCTTCCTCGCAATTCCAAACTTTACACTTCTCTACT----------------CCCCCTCGCTCTCAATCGTT
CCTGTGTC---CTCCGTCTCTCCGTCTCCCAGGCGAGGAGGAGAGCATGCCTCTATGTCCACGGAGAGGTAATGAAGTGA
CCCTCAAG-AACCATGCTGCTTCGATGCTTGTACTTGATTTTTTTTAAAAT-AAAGGTTCCCTTTGTTTGTTTTG-----
ATTATCCTTTCCGGTCAGAATAATCTAATTTAGATGTGTTTTTTCTATCTATATATGACTTTTGCCTAAAAGGTTTATCG
AGAGATCTATGATAGCAGTTCCTTTTCCTGTTCTTGCGGCCACAATTTTGGCACTTTGGTCTGCATCGCGCGCTTTGAGA
TCCCCGCTACTTAATTCCATCCAAAATAAACCCTAATGATCTTCTGGACTTCCACCAGGGAGAGACTCGACGAGATCGGT
AAGAAGATCAAGCGAGAGCCGGACCCCGCCTCCGC------CATCGCGGGCGTCGTAGTCGCCGTCTCACAGACCGAGCA
CCACGTCCCTCGCCGCCTAGGCCTCGTTGGCCCAGGCATCGGCGGCGCCGCGAACATAGCGACCCCGTGCGCCGCGTGCA
AGCTCCTCCGCCGGCGCTGCGCGCACGAGTGCCCCTTCGCCCCCTACTTCTCCCCGCACGAGCCCCACAAGTTCGCCGCC
GTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGGTACCATCAAACTATTTTAATGGTTTCCTTTTTTT
T-G-TTAATTCCACCGCCCGTGTTTTGTGTTAATTAATGGCGTACGTCGGTGCATGTCACGCGCTGTTTCAGGAGGTGCC
CGAGCCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAGGCGAACCTGCGGCTGGGCGACCCGGTGTACGGCTGCA
TGGGCGCGATCTCCATGCTGCAGCAGCAGGTGAACGCGCTGGAGGCCGAGCTGCAGGCCGTCAGGGCCGAGATATTCAAG
CACAGGTACCGGCAGACCGGCGTCGGCGTCGGCGTCGGCGCGGCAAACCTCATTGTCGACGACGACGTCAGTGCCGCCGC
AGCCGGCGGCTTCATGGCTCCTGCCACGTCGCTGGTGCACACCGCTGGCGTGGTGTCCGTGGCGGAGGCCGGCCAAGAAG
TGGACACAATGCCGTCGACGGCCACGGC------GTACGCTGCCGGACAGCCATCGAGCACCGACTACAGCTCCCTCGAC
ACAAGTGAGCATGATGCATACTTTGGTTGACATGCATGGATTTACTCGCGGTTCTGGTGATCGATGGAGATCACAATTGA
TTAATTAACTCGCCAAATAAACTTTATGTGCAAGTATAA--CTCTCTCTATACATGTATCTTCTCTAGAACTAGATATAG
CTGTTGTGGATATCTTGGGTGAGAAAAAGATTGTCCAGTGATC--GATGTATCTGCCCTCATAAATTTCTTGTGCGTGTC
CACTCATCCAATGTGATTGCTTGGTTGATTTAATTATAATTGATTGATTTGTAAAATAAAAAGCTTAGAGCTAACACTTT
AACTGACACTACTTCCTCCGTCTAGGTGAGTAAGTCATCTTAAGCTGTGCACCGTGACCAAGGAGGATAAGAAAACGAGA
GACCTTAATGTTTATTTGCTAATTAATAGCATTGCATGCAATGAACTAACCATTGCATGTCGTGTTTAGTAGTCTCAAGT
CATTAAAAGCATGCACACCCATCATCTCTTATTGGTTGATATGTCAATAAACAAGAAACGAAGTACAAATTAATGCACCG
TGCCTAAGTGTTTTGGGATTATTTGGTTTTCGTAAGATGACTTACACACCTAGACGAAGGAAGTAGTTGCTAGGCTTGGA
---AGTTGGAAATAGAATAATCGACAGTATTTGTTTTCTTTGTTCTTTTGTGATGAGTGTTTAGCACTGCATCTGCATGC
GTGTATATATTTCAACATGGTTATTTTTGTTAAGCAGTACGCGAG-TTTATTGTTGTGCTAGCTTGCACTCAATAAAATC
CGTCGTTTTCTCCTTAGCTATTTGATTCCATGAATTTCTCAATGATTGATATGAATTTGCGTGTAAGCTAGCATTTTCAG
CATGTTCATGAGTCATACCTGATTAACAGTACTACAGCACTACAGATCTTCATCATCTTCTCCTCTGTACATAGGTCAAT
TAACATCGAAAGTTTGGGGATCTCACATTATGTGAGTATGTGTCTTCATTTTCCCTCCAACCTTTTGAATCTGGAGCAAG
TTGTTCTGAATCAA---TTCTTTAAGCTGAAAAGGGTTTACAATCATATTGGGGCCAAAATAAAGTTTTT--GTAACTGA
TTAGCTCGGAAATGACACATATGAGCCTGGCACGGTGTCGATATGGCATGCATTTGTGCAAGCGTGCATGTCAATTCTGA
TAGTTAAGTCACATCTTTTT-TTAAAGCTAGTTAAGTCACGTCTTTATCATTGTTCACTAGTTAACTGATTTGTTTTGGC
AATTGGTTATTTTGCT-CAAGTAGAACTGTACATTGATATGACAAATTGAAATTA
>chr3A_614
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-------------------------------------------------------TTGTAACCGAGGTAAAATGGTCAAG
TCAAGTGGATCCCCAGGCAGCTTCTTGTTTTCAACAGCATTTCTTTCATTCCCTTGACATGAGCAGAAGCACCAGGGCGC
AGGGGCACGAGGGAGAGAGGGAGGGCCGGCCAACTAATCGAGTCAACGTTCCTTGGCTTGGCTTGCCAACATTTCTTCCT
CCTCCCTCGCCCATTTACTTACTACCCAATTGTGTGCATGCTTTACGCCCATCCCCCTCATTAATGCCTTGCCTTTTAAG
CACTCTTTCCTTCCTCGCAATTCCAAACTTTACACTTCTCTACTACCTGTCCGTCTCCCTCCCCCTCGCTCTCAATTGTT
CCTGTGTCGTTCTCCGTCTCTCCGTCTCCCAAAC---GAGGAGAGCATGCCTCTATGTCCACGGAGAGGTAAGA----GA
CCCTCAAGAAACCATGCTGCTTCGATGCTTGTACTTGATTTGTATTTAAATAAAAGGCTCCCTTTGTTTGTTTTGATTTC
ATTATCCTTTCTGGTCAGAAGAATCTAATTTAGATGTGTTTTTTCTATCTATATATGACTTTTGCCTAAAAGGTTTATCG
AGAGATCTATGATAGCAGTGCCTTTTCCTGTTCTTGCGGCCACAATTTTAGCACTTGGGTCTGCATCGCCCGCTTTGAGA
TCCCCGCTACTTAATTCCATCCAAAATAAACCCTAAT---CTTCGGGGCTTCCACCAGGGAGAGACTCGACGAGATCGGT
AAGAAGATCAAGCGAGAGCCTGACCCCACCGCCGCCGCTGCCATCGCGGGCGTCGTAGTCGCCGTCTCACCGACCGAGCA
CCACGTCCCGCGCCGCCTAGGCCTCGTTGGCCCGGGCATCGTCGGCGCCCCGAACATAGCGACCCCGTGCGCCGCGTGCA
AGCTCCTCCGCCGGCGCTGCGCGCACGAGTGCCCCTTCGCCCCCTACTTCTCCCCGCACGAGCCCCACAAGTTCGCCGCC
GTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGGTACCATCAAACTATTTTAATGGTTTCCTTTTTTG
GGG-TTAATTCCACCGTCCGTGTTTTGTGTTAATTAATGGCGTACGTCGGTGCATGTCACGCGCTGTTTCAGGAGGTGCC
GGAAGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAGGCGAACCTGCGGCTGCGCGACCCGGTGTACGGCTGCA
TGGGCGCGATCTCGATGCTGCAGCAGCAGGTGAACGCGCTGGAGGCCGAGCTGCAGGCCGTCAGGGCCGAGATCTTCAAG
CACAGATACCGGCAGGCCGGCGTCGGCGTCGGT------GCGGCACACCTCATTGTCGACGACGACGTCAGTGCTGCCGC
AGCTGGCGGCTTCAGGGCTCCTGCCACGTCGCTGGTGCACACCGCTGACGTGGTGTCCGTCGCTGAGGCCGGCCAAGAAG
TGGCCACAATGCCGTCGACGGCCACGGCCACGGCGTACGCTGCCGGACAGCCGTCGAGCACTGACTACAGCTCCCTCGAC
ACAAGTGAGCATGATGCATACTTTGGTTGACATGCATGGATTTATTTGCTGTTCTGGTGATTGATGGAGATCACAATCGA
TTAATTAACTCGCCAAATAAACTTTATGTGCAAGTATAACTCTCTCTCTATACATGTATCTTCTCTAGAACTAGATATAG
CTGCTGTGGATACCTTGGGTGAGAAAAAGATTGTCCAGTGATC--GATGTATCTGCCCTCATAAATTTCTTGTGTGTGTC
CACTCATCCAGTGTGATTGCTTGGTTGATTTGTA------------------AAATAAAAAAACCTAGAGTTCACACTTT
AACTGACACTAGTT------------------------------------------------------------------
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--------------------------------------------------------------------GCTAGGCTTAGA
---AGTTAGAAATAGAATAATCGACAGTATTTGTTTTCTTTGT-CTTTTATGATGAGTGTTTAGCACTGCATCTGCATGC
GTGTATATATTTCAACATGGTTATTTTTGTTAAGCAGTACGCTAGTTTTTTTGTTGTGCTAGCTTGCACTCAATAGGATC
CGTCGTTTTCTCCTTAGCTATTTGATTCCATGAATTTCTCAATGATTGATACGAATTTGCGTGA-----AGCATTTTCAG
CATGTTCATGAGTCATAACAGATTAACAGTACTACAGCACTACAGATTTTCAGCACCTTCTCCTCTGTACATAGGTCAAT
TAACATCGAAAGTTTGGGGATCTCACATTATGTGAGTATGTGTCTTCATTTTCCCTCCAACCTTTTGAATCTGGAGCAAA
TTTTTCTGAATCTATTCTTCTTTAAGCTGAAAAGGGTTTACAATCATACTGGGGCCAAAATCAAGTTTTT--TTAACTAA
TTAGCTCTGAAATGACACATATGAGCTTGACACGGTGTCGATATGGCATGCATTTGTGAATGCATGCATGTCAATTCTGA
TAGCTAAGTCACATCTTTTTTTTAAAGCTAGTTAAGTCACATCTTTATCATTGTTCACTAGCTAACCGATTTGTTTTGGC
AATTCGTTATTTTTGCCCAAGTAGAACTGTACATTGATATGACAAATTGAAATTA
>SNPs
------S--------------------------------------S-------------------S---------S----
----------------S---------------S-----S-----------SS------------------SS--------
-------------------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----------------------------
---SS-SS------------------------------------------------------------------------
----------------------------------------------S---------------------------------
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---S----S----------------------------S---S-------------------------------------S
------------------S------------------------------------------------------S------
-----------------------------------------------------------S--------------------
--------------------------------------------------------S-----------------------
-------------------------------------------SS-----------------------------------
-----------------------------------------------------S--------------------------
-----S--------------------------------------------------------------------------
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---S----------------------------------------------------------------------------
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----------------------------------------------------------------S---------------
--------------------------------------------------------------------S--------S--
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-----SS-------------------------------------------------------------------------
----------------------------------------------------------------------S---------
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----------------------------S--------------SS-----------------------------------
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----------------------------------------------------------------------S---------
SSS--------------------------------------------------------------------------S--
----------------S------------S--------S-----------S-----------------------------
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------------------------------S-----------------------------------S-------------
-----------S---------------------------------S--------------------S---SS--S-----
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----------------S----S-S-------------------------------
>forward_998
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-------------------TCTCTCCGTCTCCCAAGCA------------------------------------------
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>reverse_1905
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----------------------------------------------------------------AGCCGAGATCTTCAAG
CACA----------------------------------------------------------------------------
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>forward_1040
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-----------------------------------------------------------TGTCCACGGAGAGGTAAGAGT
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>reverse_3246
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---------------------------------------------GTACTGGGGCCAAAATCAAGT--------------
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