>input_sequence_78218
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-----------------------------ATGGCGGCACTCAAGCTCAAGCTCATGGTGCCAC---CGGCAGGCTTTTGC
TTGTTTCTACTGCTCATGCCACCACTCCTACTTCCTCCTGGTAAGCATTTGCCTCCTTTCTCAGTCTTGCCTTCTTTCTT
TCTTACAAATATGACACTCTGCATCCTTCCTCCA----TGTTCTAATATTCTTTCTTTCCGAGACCAGTTTATTGCTGAT
CTGGTATGTGAGTGAAAGGATTATAAATTTATAATAAACTGCATGCCAAAATAGTTGAAAGGTTCATCGAACTAACACAA
GTTAATCACATTTTCTTTGTAGGATGTGCTGCCACTCGTCCTGATCCCACCCAAGGGCCATCTGAGGGCAACAACAGGAC
ATGCACGGAGCTGAGCAAGAGGAGCCCCATCCTCTACTGCGAGCACCACGCATGCGTCGACAACTGCCGCATCGAGGGCT
TCGCCGAGGGAGGGTTTTGCAACTGGCTGCGCTGCCTCTGCAAGAGGCCCTGCTGA------------------------
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>chr5A_1_TraesCS5A01G046300
TGGGGGTGTGCGCCCGCAAATTTGAAAGAAAGTTCATAAATACGAACAAGGCTTGACAAGACAGTCACTGGTTCCTTCTC
AAAAAGAAAAAAAAAAACAGTCACTGGTTGTGGCGTCGAACAAATTTTCAGGATTGCAGCAACAATGCTTGGTTTGCAAT
TATCTGTTGTGTTGTACACTGCTTTAGCCAGGGAAGTTTCTAGAGAAGATGCCCATGAAGAATGATGTGCGTAATAGTAC
GCCAC-----CATTCAC-ATTAGCACTTAGAGCATAATTGGTTTGATGCCAAAAATAAGCATGCCAATGTTTGACAGTGT
GCCAAATATTCGCTACTACTTGATTGATTCCCGAGTTGTCTTGTCTATCTCACATAAAGTTGCTAATATTTGGCAAGCCT
TGGTATTGCCAATATTTGGCAATTCCAACATTTGGCTAGCCAAATATTGGCAGCAAACCAATCATGCTTTTTGAGACCAA
GATAAGGATCATC---CACCCTGTGGAAATGGATCCCGTTGTTTTTC-TCTC-TTTTGCTGAACACACATCACATGCATG
CATCTATCCATC----TGCGTGTCATTGCTCAGGATCAGAGGAATAAAGTCTATCCATCTTGCTATCTATGGGTGCAAAG
TCCAACGGCCCGGCTCAAAACGCGCAC-----------TGGGACTGCACAAGAGCAAGAAGATAGCAGAGCATCGTAACC
GCAGCTGCCGCCACAATTTTGGTCAGTCGCCAGTTCTGGAAGACGCGCAGCCTCCCACCACATCTTCTTTCAGAGGGTTT
CCAAATGAGAGCACATTATCGCGTCTTGAAGATATAATAGTTGCATTATAATCCCACTCACATTTGTCTCTCTCTC-TTT
TTTCCTTCTCAGCCATCCATGGCTGCCTATAA-GAAGGGGAGGGGTTGATGGATGATGGCACTACCAA---CCTATCTGC
ATCTGCACCCTCTCCTCTGAATCTGATCTTCCTTACTCCCTTTCTTGGTTGAGCGGGAGACAGAG------A--------
------------------------GAGACATGGCGGCACTCAAGCTCAAGCTCATGGTGCCAC---CGGCAGGCTTTTGC
TTGTTTCTACTGCTCATGCCACCACTCCTACTTCCTCCTGGTAAGCATTTGCCTCCTTTCTCAGTCTTGCCTTCTTTCTT
TCTTACAAATATGACACTCTGCATCCTTCCTCCA----TGTTCTAATATTCTTTCTTTCCGAGACCAGTTTATTGCTGAT
CTGGTATGTGAGTGAAAGGATTATAAATTTATAATAAACTGCATGCCAAAATAGTTGAAAGGTTCATCGAACTAACACAA
GTTAATCACATTTTCTTTGTAGGATGTGCTGCCACTCGTCCTGATCCCACCCAAGGGCCATCTGAGGGCAACAACAGGAC
ATGCACGGAGCTGAGCAAGAGGAGCCCCATCCTCTACTGCGAGCACCACGCATGCGTCGACAACTGCCGCATCGAGGGCT
TCGCCGAGGGAGGGTTTTGCAACTGGCTGCGCTGCCTCTGCAAGAGGCCCTGCTGAATGTGACGATGCTGCTTCAGGATG
TTGCGAGCGATGCAACGAGTAATAACTAATAAGATGCATCAAAGTGTTGATGTGCATTTTCTCAAAAAAAAAAAGTGT--
TGATGCGCAAGTTGTAACCGCAACAAATTTCCTTCTCTAAAA--ATTTGTCAACTCCCAGTTGCAAGCTATATAA-TCTG
AGGAATCTAAATATTAGTTTAACAACCTGAGTTTAATTCCTAGAATTGATAGGTGATGCACAGGGGGTTTTCCCCATTTA
TTAAGGATCAAGTTTGGTGTGTA---------------------------------------------------------
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---------------------------------------------------------GTGGAACCACTCATCAAAAAATA
TCTTAATACTCATTTAAAAACA-ATCTGAGGACCATGTTTATCTTGATACTCATACTAAAAATGGCCATATGCATCTCTA
GTTGGTGCAGAGGCCGGA-GAAGT-AAAATTCTCCCCCATTTTTA---TGCAAAGAGAGCCTTGGCTCAGTGGTTGGGCA
TGCGGTTGTGCAGCCTAACAATCAGAGTTCAATTCCTAGAATTGACAGGTGATGCACAGGGGTTTTCCC-CATTTATTGA
GAATCAAGTTTGGTATGTGGTGAAACCACTCATCCCAAAATATCTTGATACTCATTTAAAAAAAGTAT-GAGGACCATAT
TTATCTTGGTACTCATACT-AAAATGGCCCTATGCATCCTTAGTCGGTGCAGTGGCCGGGGAAATTAAATTCTCCCCAAA
TTTTTAAGGTCCTGAACCTGAAGCCCCGTCCCCCGCGTCCCTCTCTGAGGCGACACGGGGGAACCCTAGCCGCCCCCGCT
GCCGGCCTCCCTCCACCCTCCCCCCCCCCCCTCGCCGCCGCCGAGAGCCACCGTTGCGCAAAGCCCAGGCAGTGCCGGCG
GCGGCGGGGCTTCTCCCCTGGCCCGACTTCCCTTCTTCCTCGCGGCGGCTTAGTCACTCCCGGTGGGCTTGGTGGCGCGA
CGCTTCGAAGCTCCGGCGGCGGCTCGCTTTGCGACAGGTTGGAGGGCTTGTCCCCGTCTGGTGG----------------
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>chr5B_19
------------------AATTTGAAAGAAAGTTCATAAATACGAACAAGGCTTGCCAAGACAGTCATTGGTTCCTTCTC
AAAAGGAAAAAAAAAGACAGTCGCTGGTTGTGGCGTCGAACAAATTTTG-GGATTGCAGCAACAATGCTTGGTTTACAAT
AATCTGTTGTGTTGTACACTGCTTTAGCCAGGGAAGTCTCTAGAGAAGATGTCCATGAAGAATGATGTGCGTAATAGTAC
GACAC-----CATTCACCATTAGCATTTAGAGA-----------------------------------------------
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----------------------------------------------------------------------------CCAT
GATAAGGATCATC---CAGCCTGTGGAAATGGATCGCGTTGTTTTCTTTCTC-TTTAGCTAAACACACATCACATGCATC
TATCTATCTATCTATATGTGTGTCATTGTTCAGGATTAGAGGAATAACGTCTATG--TCTTGCTATCTATGGGTGCAAAG
TCCAACGGTCCGGCTCAAAACGCACACTGAGAACATGGTGGGACTGCACAAGAGCCAGAAGATAGCTGAGCATCGTAACC
ATAGCTGCCGCCACAATTTTGGCCAGTCGCCAGTTTTGGAAGACGTGCAGCCTCCCACCACATCTTCTTTCAGAGTGTTT
CCAAATGAGAGCACATTATCACGTCTTGAAGATATAATAGTTGCATTATAATCCCACTTACATTTCTCT--CTCTC-TTT
TTTTCTTCTCATCCATCCATGGCTGCCTATAA-----GGGAGGGGTTGATGGATGATGGCACTACCAA---C-TATCTGC
ATCTGCATCCTCTCCTCTGAATCTGATCTTCCTTACTCCCTTTCTTTGTTGAGCGAGCGAGAGAGAGAGAGA--------
------------------------GAGACATGGCGGCACTGAAGCTCAAGCTCATGGTGCCACAGGCAGGCCTG---TGC
TTGCTGCTGCTGCTCATGCCACCATTCCTACTTCCTCCTGGTAAGCATTTGCCTCCTTCCTCAGTCCTGTATTATTTCTT
TCTGAAGAATATGACACTCTGCTTCCTTCCTTCCTCGGTGTTCTAATATTATTTCTCACT-AGACCAGTTTATTGCTGGT
CTGGTCTGTCAGTGAAAGGATTG--------TAATAAGCTGCATGCCCAAATAGTTGAAAGGTTCACCGAACTAACACCA
GTTAATCACATTCTCTTTGTAGGATGTGTTGCCACTCGTCCTGATCCCACCCAAGGGCCATATGAGGGCAACAAGAGGAC
CTGCACGGAGCTGAGCAAGAGGAGCCCCCTCCTCTACTGCGAGCACCACGCATGCGTCGTCAACTGCCGCATCGAGGGCT
TCGCCGAGGGAGGGTTTTGCAACTGGCTGCGCTGCCTCTGCAAGAGGCCTTGCTGAATGTGACGATGCTGCTTCAGGATG
TTGCCAGTGATGCAACTAGTAAATAAG--TAAGATGCATCAAAGTGTTGATGTGCATTTTCGCAAAAGAAAAATAAGTGG
TGATGCGCAAGTTGTAACCGCCACAAACTTCCTTCTCTAA---TATTTGTCAACTCCCAGTTGCAAGCTATATAAATCTG
AGGCATCTAAATATTAATT-------------------------------------------------------------
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>chr5D_99
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------------------AGTCACTGGTTGTGGCGTCGAACAAATTTTCAGGATCGCAGCAACAATGCTTGGTTTACATC
AATCTGTTGTGTTGTACACTGCTTTAGCCAGGGAAGTCTCTAGAGAAGATGTCCATGAAGAACGATGTGTTTAATTAGCA
CGCCACCATGCATCCACCATTACCATTTTAAG------------------------------------------------
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----------------------------------------------------------------------------CCAA
GATAAGGATCATCGGTCAGCCCGTGGAAATGGATCGCGTTGTTTTGC-TTCCTTTTTGCTGAACGCACATCACATGCATC
TATCTATCCATCT----GCGTGTCATTGCTCAGGATCAGAGGAATAAGGTCTATCTATCTTGCTATCTATGGGTGCAAAG
TCCAACGGCCCCGCTCAAAACGCGCACCGAGAACATGCTGGGACTGCACAAGAGCCAGAAGATAGCAGAGCATCGTAACC
GCAGCTGCCGCCACAATTTTGGTCAGTCGCCAGTTCTGGAAGACGTGCAGCCTCCCACCACATCTTCTTTCAGAGGGTTT
CCAAATGAGAGCACATTATCGCGTCTTGAAGATATAATAGTTGCATTATAATGCCACGTACATTTTTCT--CTTTTTTTT
TTCTCTTCTCAGCCATCCATGGCTGCCTATAAAGAAGGGGAGGGGTTGATGGATGATGGCACTACACCAGCC-TATCTGC
ATCTGCACCCTCTCCTCTGAATCTGATCTTCCTTACTCCCTTTCTTTGTTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA
GAGAGAGAGAGAGAGAGAGAGAGAGAGACATGGCGGAACTCAAGCTCAAGCTCATGGTGCCAC---CAGCCCTG---TGC
TTGCTGCTGCTGATCATGCCACCACTCCTACTTCCCCCTGGTAAGCATTTGCCTCCTTCCTCGGTCTCATCTTCTTTCTT
TCTGAAGAATATGACACTCTGCTTCTTTCC----TCGGCATTCTAATATTATTTCTTTCTGAGACCAGTTTATTGCTGGT
CTGGTATGTGAGTGAAAGGATTG--------TAATAAACTGCATGCCCAAATAGTTGTAAGGTTCATTGAACTAACACCA
ATTGATCACATTTTCTTTGTAGGATGTGCCGCCACTCGTCTTGATCCCACCCAAGGGCCATCTGAGGGCAACAACAAGAC
CTGCACGGAGCTGAGCAAGAGGAGCCCCATTCTCTACTGCGAGCACCACGCATGCGTCTACAACTGCCGTATCGAGGGCT
TCGCCGAGGGAGGGTTTTGCAACTGGCTGCGCTGCCTCTGCAAGAGGCCCTGCTGAATGTGACGATGCTGCTTCAGGATG
TTGCCAGTGATGCAGCTAGTAAATAAG--TAAGATGCATCAAAGTGTTGATGTGCATTTTCGCAAAAGAAAAATAAGTGG
TGATGCGCAAGTTGTAACCGCAACAAACTTCCTTCTCTAATACTATTTGTCAACTCCCAGTTGCAAGCTATATAAATCTG
AGGCATCTAAATATTAATT-------------------------------------------------------------
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>chr3A_1695
AGTC----------------------------------------------------------------------------
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-------------------TAACGACCTAAGTTCAATTCCTAGAATTGACAGGTGATGCATAGGGGTTTTCCCCCATTTA
TTGAGGATCAAGTTTGGTGTGT--TGTGAAACCACTCATCAAAAAATATCTTGATACTCATTT-AAAAAATTGGAGGACC
ATGTTTATTTTGGTACTCATACTAAAATGGTCGTATGCATCTTAGTTGGTGCAGAAGCCGGGGAAGTGAAATTCTTCCCC
ATTTTTAGCAAAGAGAGCCTTGGCTCAGTGGTTGGGCATGCGGTTGTGCAGTCTAACAACCCGAGTTCAATTCATAGAAT
TGACAGATGATGCACAGGGGCTTTCCTCCATTTATTGAGGATCAAGTTTGGTGTATGGTGGAACCACTCATCAAAAAATA
TCTTGATACTCATTTTAAAAAA-ATCTGAGGACCATGTATATCTTGGTACTCATCCT-AAAATGGCCGTATGCATTCCTA
GTTGGTGCAGAGGCCGG-GGAAGT-GAGATTCTCCCCTAATTTTA---AGCAAAGAGAGCCTTCGCTCAGTGGTTGGGCA
TGCGGTTGTGCAGCCTAACGACCTGAGTTCAATTTCTAGAATTGATAGGTGATGCACAGGGGTTTTCCCCCATTTATTGA
GAATCAAGTTTGGTGTGTGGTGGAACCACTCATCAAAAAAT-TCTTGATACTCATTTAAAAAAAATCT-GAGGACCATGT
ATATCTTGGTACTCATACT-AAAATGGCCGTATGCATCCCTAGTTGGTGTAGAGGCCGGGGAGGTGAAATTCTCCCCTAA
TTTTTA--------------------------------------------------------------------------
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>chr5A_1699
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-------------------TAACGACCCGAGTTCAAGTCCTAGAATTGAAGGGTGATGCACAGAGGTTTCCCCCCATTTG
TTAAGGATCAAGTTTGGTGTGT--GGTGAAACCACTCATCAAAAAATATCTTGATACTCATTT-AA--------------
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------------------AAAA-TTCTGAGGACCATGTTTATCTTGGTACTCATACTAAAA-TGGCCGTATGCATCCCTA
GTTGGTGCAGAGGCCGG-GGAAGT-GAAATTCTCCCCC-ATTTTA---AGCAAAGAGAGCCTTGGCTCAGTGGTTGGGCA
TGCGGTTGTGCAGCCTAACGACCCGAGTTCAATTCCTAGAATTGACAGGTGATGCACAGGGGTTTTCCCTCATTTATTGA
GGATCAAGTTTGGTGTGTGGTGAAACCATTCGTCGAAAAATATCTTGATACTCATTTAAAAAAAAATT-GAGGACCATGT
TTATCTTGGTACTCATACT-AAAATGGTCGTATGCATCCCTAGTTGGTGCAGAGGCCGGGGAAGTGAAATTCTCCCCCAT
TTTTTA--------------------------------------------------------------------------
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>chr6B_1699
ACCCG---------------------------------------------------------------------------
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-----------------------------AGTTCAATTCCTAGAATTGACAGGTGATGCACAGGGGTTTTCCTCCGTTTA
TTGAGGATCAAGCTTGGTGTGT--GGTGGAACCTATCATCAAGAAATATCTTGATACTCATTTAAA--------------
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------------------AAAA-TTCTGAGGACCATGTTTATCTTGGTACTCATACTAAAA-TGGCCGTATGCATCCCTA
GTTGGCGCAGAGGCCGG-GAAGTGAAAAACTCTCCCATTTTTTAA---TGCAAAGAGAGCCTTGGCTCAGTGGTTGGGCA
TGCGGTTGTGCAGCCTAACGACCCAAGTTCAATTCCTAGAATTGACAGGTGATGCACAGGGGTTTTCCCCCATTTATTGA
GGATCAAGTTTGGTGTGTGGTGAAACCACTCATCAAAAAATATCTTGATACTCATTTAAAAAAT-TAT-GAGGACCATGT
TTATCTTGGTACTCATACT-AAA-TGGCCGTATGCATCCCTAGTTGGTGCAGAGGCTGGGGAAGTGAAATTCTCCCCCAT
TTTACAGTGCAGAGAGAGCCTTGGCTCAGTGGTTGGGTATGTGGTTGTGCAACCCAAC----------------------
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-------------------GACCCGAGTTCAATTCTCAGAATTGACAGGTGATGCACAG---------------------
-------------------------------------------GGGTTTTTCCCCGTTTATTGAGGATCAAGTTTGATGT
GTGGTGGAACCACTCATCAATAAATATCTTGATACTCATTTAAAAAATTCTGAGGATCATGTTTATCTTGGTACTCATAC
TAAAATGGTCGTATGCATCCTTAGTTGGTGCAGAGGCCGGGAAGTGAAAATCTCCCCATTTTTAAGGTC
>chr7A_1700
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--------------------AACGACCCGAGTTCAATTCCTGGAATTGACAGGTGATGCACAGGGGTTTTTCCCCGTTTA
TTGAGGATCAAGCTTGATGTGT--GGTGGAACCAATCATCAAGAAATATCTTGATACTCATTTAAA--------------
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------------------AAAAAATCTGAGGACCATGTTTATCTTGGTACTCATACTAAAA-TGGCCGTATGCATCCTTA
GTTGGTGCAGAGGCCGG-GAAGTGAA--AATCTCCCCATTTTTTA---TGCAAAGAGAGCCTTGGCTCAGTGGTTGGGCA
TGCGGTTGTGCAGCCTAACGACCCGAGTTCAATTCCTAGAATTGACAGGTGATGCACGGGGGTTTTCCCCCGTTTATTGA
GGATCAAGTTTGGTGTGTGGTGAAACCACTCATCAAGAAATATCTTGATACTCATTTAAAAAT-ATCT-GAGGACCATGT
ATATCTTGGTACTCATACTAAAA-TGGCCGTATGCATCCCTAGTTGGTGCAGAGGCCGGG-AAGTGAAATTCTCTCCCAT
TTTAAGG-------------------------------------------------------------------------
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>chrUn_1704
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------------------------ACCCGAGTTCAATTCCTAGAATTGACAGGTGATGCACAGGGGTCTTTTCCCATTTA
TTGAGGATCAAGTTTGGTGTGTGTGGTGGAACCACTCATCAAAAAATATCTTGATACTCATTTAAA--------------
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------------------AAAAATTCTGAGGACCATGTTTATCTTAGTACTCCTACTAAAA-TGGTCGTATGCATCCCTA
GTTGGTGCAGAGGCCGGAGAAGTGAA--ATTCTCCCCCATTTTTAAGTTGCAATGAGAGCCTTGGCTCAGTGGTTGGGCA
TGCGGTTGTGCAGCCTAACGACCCGAGTTCAATTCCTAGAATTGACAGGTGATGCACAGGGGTTTTCCCTCATTTATTGA
GGATCAAGTTTGGTGTGTCGTGGAACCACTCATCAAAAAATATCTTGATACTCATTTTAAAAAT-TTCGGAGGACCATGT
-----TTGGTACTCATACTAAAA-TGGCCGTATGCATCCCTAGTTGGTGCAGAGGCCGGGGACGTGAAATTCTCCCCAAT
TTTTTAAGGT----------------------------------------------------------------------
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>SNPs
S-SS-SSSSSSSSSSSSS-------------------------------------S-----------S------------
----S----------S-----------------------------------------------------------S----
S------------------------------------S-------------S----------------------------
-S-----------------------S------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----
------------------S----------------S---------S---------------------------------S
S----------------------------------------------S-------S------------------------
-------------------------------------------------------S------------------------
---------------------------------------------S----------------------------------
----------------------------------------------------------S------S---SS---------
---S--------------------------------------------------------------------S-------
----------------------------------------------S--------S----S-------------------
-------------------------------------------------------------------S--SSSSSSS---
---S-S--S-------------------------------------------------S----------S----------
---S-SS---------------S--------S-S----------------S--------S------------------S-
----------------------SSSSSSSSS----------------S------------------------------S-
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S-------------------------------------------------------------------------------
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----S--S--------S-----SS-SSSS--------------------------------S-----S-----SSS----
---------------------------S------------S---------------------------------------
---S------------S------S---------S---------------S----------------S-------------
----------------------S---------------------------------------------------------
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----S----------S----S-------------------------S--------------------S--------S---
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-------------------S-S-S--------------------------------------------------------
--------------S-------------------SS----------------------------S-------------S-
-----------------------------S---------S----S-------S----------S-S--------------
----------SSS--SSSSSSS-S-S-SSSSSSS-S--SSS-SSS--S-SSSS-SSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSS-S-----S---SS----SSSSSSS-S-S-S-S-SS---SSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---S--S-------S-SS--S----------------
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>forward_1021
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-----------------------------------------TTCTTGGTTGAGCGGGAGAC-------------------
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>reverse_2833
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--------------------------------GACAGGTTGGAGGGCTTGTC----------------------------
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