>input_sequence_83952
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------------------------------------------------------------------------ATGAGTTA
CAAGCCGTTGCCCCGAAGGACGGA--GTGGCCAGATAGCGTTATCAAAAAGTGCCCAGAGCTGGCCGCATGCTATTATGC
CACTAGGGCCAACACGGATGAGGTCGCGGAGGACATGCAACGGAGGATGCTCGAGACACAGAAAGACTACAGGCAACAGC
TGAAAACCAAGGGCATAGTCAC--CTACGAGGAGGAGGTTGATGAGGACTACGACGAAGACGAAGACTACGCTCCATTGC
ATCCACCGGGTCGGTGGAGGCACCGACCTGGCGTCATGAAAAATCGCCAAGGAGAGACTAGGAGGCTGAATTAA------
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>chr1B_1_TraesCS1B01G048600
TGCCAACCTACCGCCAGGGAACTCGGCGGTAGGTTTGTGTGGGCTACCGCCGTGGTCTTTGGCGGTAGGTACGTCACCAG
CCGTTAACGGATTGACGGCCGTCAGGCACACCTACCGTCGGAACCTGTGGCGGTAGGTTGTGCAACCCTACCGCCTGAGG
TTTTGGCGGTAGCAAAAGGGTCAGATTTCAAAATGTTTTCAGACTGGGGTCAAATCTCGATTTTGTTTCACAAAAGGGAC
AAAACATGAAATTTTGCCTAACAACGTCTAGCATGAACAATTGCGCCATGTCATGATTTGCGGGGCCCACCTGCCACAGT
CGTCATCAAAACGACCAAAGCCGTAGTG------TTTTTTTAAAAGATTAGCCTTGGAA---------------------
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----------------------------------------TTAGTGATTTTGGGTACAAAACTGTAGACTTGTGGTTTCC
GCAACCCTAGCCTTTAATATCGATGTTTTGTGCAATTCACTCCCTGTCAGTTGCCCACGAA---GAAACAAGTAAATGCT
TTGTATTCATGTTTGATTTAGTTATGTCCCTGGTTTTTGCTTCGTATTCGGGTACCCGATTCCAATCCTAATAAGAATAC
TAGTTCCAGATCTGTGGAGCTGTGATCCGGATGATCTTCTGCTGACTGCGGCTGCGAATCGGATAGATACTCTTTTGATT
TTCAGTTTTCTTATTAAGTGTATCGCATTTAGGACTTGGACTCCGACAAAGACAAGGAGTCGAGCAGACTTCCGATGGGA
TTCGAATCGAATCGCTCGCGCTCGCCCCTGTATAAATATGCGTCGAGAGGCGCCTGGTTTCTCACCCGAACAATTTCTCG
CAG-----------------------------------------------------------------------------
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--------------------------------------TGCAGATCCCAATGGCAAGTTCATCTTCAAGTTCCGTCGAGG
AGAAGGAGGTGGTGGATTTGCAGGATCAGAAAATCAAGGTGGGTGGTGACAAGCCGTCGATCGAGTCGGCAGGCAGCCCT
GCAGATCCAGCACCAAAGAAGAAGAAAAAGAAGATCCTGCGTGTGGTGC-------CGATGTGAAATATGTCATGAGTTA
CAAGCCGTTGCCCCGAAGGACGGA--GTGGCCAGATAGCGTTATCAAAAAGTGCCCAGAGCTGGCCGCATGCTATTATGC
CACTAGGGCCAACACGGATGAGGTCGCGGAGGACATGCAACGGAGGATGCTCGAGACACAGAAAGACTACAGGCAACAGC
TGAAAACCAAGGGCATAGTCAC--CTACGAGGAGGAGGTTGATGAGGACTACGACGAAGACGAAGACTACGCTCCATTGC
ATCCACCGGGTCGGTGGAGGCACCGACCTGGCGTCATGAAAAATCGCCAAGGAGAGACTAGGAGGCTGAATTAAATAAAA
AAATCAAGCAACTCTATCTAGCTATATCATCATGCTTCCAGCTCTTCGGGTTTTTTTTTCTTAATTACTTTGTTTGTGAA
CCTGGTTCAGTTATGTCTTCCGTATGATCATCTAAGCGCCATGAAGGATTTGGTTTTGTCTTGTTTTCTTACTGGGTTAT
GAGTCCCATGCCAATTGTGCTTTATACAAATAAGGAATATTTGTTCCTTGCGGTTTTGTTCATTTACTGTATTCTCTGAT
TGTTAGAGCCTGACAACACCGGAATTGCAAATTCAATATGTGAGTATTTCTAAAGAACATCAATATGT----GACACCTT
GGAAGCCACAGGATAATTGTGTGCTATGCAAATCATATAACAAAGTTGGCATTGTTTCTTGTGTTTTTGTTCATTTATTT
TC--TATATACCGCCCCTTTATGTCTCCTTTGCATCCACCCTGGCGTCATGAAAAATCACCAAGGAGAGACGAGGAATTT
TAGTTAAATTAGATCCAAACAAATCTATCTAGTTTTCTTTTTTGTTTGAGAAATCTATCTAGC--TATATTGATATAAAG
TCGTGGTTCTTTCAGATCATCAGTTGTGTCTTTCCTATGAACATATAAGGCGCC--------------------------
TTGCCTGTTTCGACTGGACTTATGTCCCATGCTAATTGTTCTATGAAAATACCAAGAA---TTATATGTTCCTTGTGGAT
TATGGTTTTGTTCACTTTATTCTTTGATTGTCATGTGTCATAAGTAAGCCCAGTAATACTAGAAC---------------
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------TAGAACATCATTATGTGATCTCTGAAAATCCCAAGATCCCAGTTTTCTATCCAAAGCAAATACCAGGAAGATTT
TTTCTTTCTTTCTTGTGGTTTCATTCAGTTATCTATAGTGCTATTAGACTTGTGGGAGTTGTAAGCACCATAGCAAGAAC
AAGATTGCAAAATCATTGTGAATATCAGTTTAAATGAAAATCACCTATGGATTTAGTGTATTCCTGCTCATATGTTTACC
CACATGTTGATT
>chr1D_259
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------------------TAACGACGTCCAGCGTGCACAGTTGCACCACATCATCATTTACGGGGCCCACCTGCCATAAT
CGTCATCAAAACAAGCAAAGCCGTCAATTAATGTTTTTTGCAAAAAAATAGCCTCGGAT---------------------
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----------------------------------------TTAGTTGGTTTGTGCATAAAACTGTAGAATTGTGGTTTCC
GCAACCCCATTCTTCAATGTCGATGTTTTCTGCAATTCACTCCCTATCAGTTGCCCACG---AAGAAACAAGTAAATGC-
---------------------TTATGTCCCTGATTTCTGCTTCGTATTCGTGTACCGGATTCCAATCCTAATAAGATTAC
TAGTTCCAGATCTGTGGAGCTGTGATCCGGATGATCTTCTGCCGACTGCGGCGGCGAATCCGCAGTGCAGATCTTCTGCC
GATTA---------------------------------------------------------------------------
-----------------------------------------------------CTAGTTTCTCACTCGAACAATTTATCG
CAGTGTGTTGAGTAAATAGGCAATTTTTCGATTAAATTAATCCATGAGTAAATCACTAGGGCGTGGTTTCAGAAACGCGG
ACGTACGGGATGGAGTCACCGGCGGCAGCAGCAGCAAGGGAACGACGGTGGGCGTGTGCGTAGGTGTGAGCTCGGCTCGG
CTCAATCCCGCAACCCGCGGCGTGGCGACGTACGGGATGGAGTCACCGGCGGCAGCAGCAGCAAGGGAACGACGGTGGGC
GTGCACGTAGGTGTGAGCTCGGCTCGGCTCAATCCCGCAATCCGCGGCGCGGCGCGGCGCGGCGGCGGAGGAGGAGGAGT
GCGCGAGGGCCTCTTCTCTTCTCAAGCTCCAATAGCATGTAGAAGAGAAACCCTTATAAGGAGGTCCAACTCCTCTTCCA
TTTTCGGGGTGGGCCTAAACTTCCCACTACACCTAGTGCCATATAACCCACATGGGCCCTTAAAGATTTTTCAGAAATTG
CTACATGGGCCTAGAGCCCATCTCAAATTTCAGCACAGTGCAGATCCCAATGGCAACTTCATCTTCAAGTTCCGTCGAGG
AGAAGGAGGGGGTGGATTTGCAGGATCAGAAAATCAAGATGAGTAGTGACAAGCCGTCGGTCGAGTCGGCAGGCAGCCCT
GCAGATCCAGCACCAAAGAA---GAAAAAGAAGATCCTGCGTGTGGTGCCTGAGAGCGACGTGAAATATGTCATGAGTTA
CAAGGCGTTGCCCCAAAGGACGGA--GTGGCCAGATAGCGTTGTCAAAAAGTGCCCAGAGCTGGCCGCATGCTATTATGC
CACCAGCGTTGTCAAACGAAAGAGCTGGCC--------------------------------------------------
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---------------------------GCAGATCATATAACAAGGTTGGCGTCGTTTCTTGCGTTTTTGTTCATTTATTT
TCTATATATACCGCCCCTTTATGTCTCCTTTGCATCCACCCTGGCGTCATGAAAAATCACCAAAGAGAGACGAGGGAGTT
TAATTAAATTAGATCCAAACAAATCTAACTAG--TTCTTTTTTATTTGAGAAATCTATCCAGC--TATATTGACATAAAG
TCGTGGTTCTTTCAGCTCATCAGTCATGTCTTTCCTATGAACTTCTAAGGCGCCAGGAAGGTTTTTATTCACATCTTATT
TTGCCTGTTTCGACTGGACTTATGTCCCCTGCTAATTGTGCTATGAAAATACCAAGAAGAATTATATGTACCTTGTGGAT
TATAGTTTTGTTCACCGTATTCTTTGATTGTCAAGTATCATAAGTAAGCACAGTAACACTAGAATTAGGCCAACTCCACC
GTGCGACCCTATCCTGTCCGCCCCCGTCCGTTTGGGGTAAAAGGGACAAACGAGACGGCCCAGCGCGCGGGCGCAAACGG
ACTTTTGTCCACTTTGTGTCCGCTTTCGACCCATCCCCGGCCCAAGTTTGCGCCGGTTTTGGGGTGAAACGGACAGCGCG
CGGACAGGCGGGACGCGAGCGCTTGTCCTCCCCTGGCCCGCCTGTCGGTGGGAGAAACCAACCCCCCCTCCCCACGCCCA
TTTGGCGCCATTTCCCCCAAACCCTCTCACGTCCCTACCGCCGCCCCCTCTCTCCCCCGTCCATGGCCGACGCCCCGCCG
AGTTCCGGCGGCCTGGCCGTCGACCCGCCCGCAAAGGTGAAGAAGAAGGCGCCAAGGAAGCCGCGGTCGGAGTGCACGCC
GGAGGAGATCGCCAAGTTGGACGCGGAATCGGCGAAGAGGAGGGAATGGAGAGCGGTCGTCAAGGTCAATGCCGCCGCGG
CCAAGTTCGCCGCCCAGCGCGATGAGCTGGAGGCCACGCAGCGCAAGGCCGCTGCCGACGAGAAGGAGGACCTCGTCAAC
AAAGCGCACGCCATCCTCATGCTTGGCATGGGCCGTTCGGCCGGGTTCCCTGCAGCGGCCGTCGGCCCGGCGAGCACAGG
CTCGTCAGTCGCCCGGCCTACGCACTGCCAATCGCCGATGTCGCGCACCGCGCCCATGTCGCCCGGCTTTCCTCCGCCAT
GGCACGACGGCCAGACCCGTTTCTCGGGGTCGCCGGACGTGGGCTTGTTCGCGCCGTCCACACTGCGCCCCGCGGCCGTC
ATCGACCTCAACGTCACGCCTGGGTCCAGCAGCGGCGGCCGGCCGTCCGTCGAGATGCAAAGAAAGCAGGCACGGGCACC
GTTCACGGGCACCATGCCGGCCCCCCGCGTCTTGTTTGACGGAATGCCAACCCCAACGCCAACGGTCAGCGACCCCTTCT
ACAACCAGTACATGGAGGACGTGATCTTCGAGGGTGGGCATGGCCGTGCCTACGACCCCGAGGAGACCCAAAGTCAGGAT
GGCCGCGCCCAGTACGTCCCCGATGAAGAGGCCGACGACCGTGCTGACTACGACCATGGTGACTCGTGGCATGAAGACGA
TGACATCTATGTCGAAGGTGATGGTGATGAAGAAGAAGAAGAAGGCAATGACGTTGATATTAGTGGCGCGCCATTGTTCA
TCGACGAGCTCACCCAAAGAGCGGAAGCACGAAAGAAGAGGAAGAGCATTCGCACGGGTTCATATACACAAGATGAGGAC
AAGTTGATTTGCCAAGCTTGGATGGAGATTAGCCAAGATCCGAGGACCGGCACGCAACAAAAGGGCATTGTTTTTTGGAC
GAGAGTCCACAAAACATTCCATGAAAGGAAGATGTTTGAGCCCTACCAAATTACAGGCAACCGTGACATCGGCTCGATTC
AAAAGAGATGGTTGTTCATCCAACAAGAATGCAAAAAGTATTGCGCCGCATTTAAGAGCGTTGAAGCACGGCCCGTGAGT
GGTCTCGGTGTTGGGGACATGGTATGCTCTCCTCTTCCTAGCCATTTCCTTGCTACGGCCATGAGACTTCGGCCGTGTAT
ATGTTTGCATGTTCACTTGTTCTTGATCATGTGGTGTAGGCATTTCAATCTTTGGAGGCATTCAAGGCCCGGCACAATGA
CAAGCCATTCACTCTTACGCATTGTTGGACGATCATCAACAATTGCCCTAAGTTCAAGGACCAATACCGTGAACTACAAA
GGAAGAGAGGCAAGATGGCCAAGTTCGCCGGAGGTGGAGATGGCGAGGCGTTGAAGAGGCCGAGGGGCAAGACCAACTCC
AAGGTTGACGATATACGTGATGCCTCATCCATGGCCTTGCATGAGACTTTGCATGGCATGATGTCCCAAAAGGATGTGAG
GGACGAGAAGAAGCGGCAAAGCAAGGACGAGCAAATGAAGCAATACCTAGACCTTCAAAGACAGAAGCTTGAGATGGAGG
AGGCGGCCAATCGGAGGAAGATCGACATGGAGGAGACGGCCCGGCAAAGGCAGCTCGACATGGAGGAGGCGGCCCGGCAA
AGGCAGCTCGACATCGAGGCCGACAACGTCAAGGCCAGGCAGAGGCAGCTCGACATCGAGGCCACCAATGCCGCCACCAA
AGCGAAGGAGGTGGCCCTTGCGATCATGAGTGTGGACTTGTCGAAGATGAGCGAGAAGACGAGGGCCTGGTTCGAGGCCA
GGCAGAAGGAGATGCTCGACGCCGAAGGCCTGAAGTAGGTCGTCCGATCGGCGTCGGCCGTTCTTTTTTGGAGGCTGGCA
TGGGTGCCGCCCGCCCGCTGGGCCGCTGGCAGTGTGCCGGCGAGAAAAACATTCATTCTGGAGGCCGGCTGTGTTGCCGG
CCGCTGGCTGTGTTGCCGCGAGGACAACTATTCATTTTGGAGGCTGGCTGTGTTGCCGGCCGCTGGCTGATGCCGGCGAT
GGACGTGTAGGCCGCTGGCTCTGTTGCCGGCGTGATGAACCGGGGCCGCTGGACTAGGGCTTGGCATCTGAAACATTGCT
TTTAGTTTTTTAAATAGACGCGGACAGGATGGGGCAAATGAATGCGGCCGGGCGCACGGCCACCGCATCCCAGGACATGC
CCGGACACGACCGCAAATTCCTATCCAAACGGACAGAATCCGGACAAAACGGACGTCCGTTTGGGGTCGCACAATGGAGT
TGGCCTTAGAACATCATTATGTGATCTCTGGAAACCCCAAGATCCCTGTGTTCTATGAAAAGCAAATACCAAGAAGATAT
TTT-----TTTCTTGTGGTTTCATTCAGTTATCTATAGTGCTATTAGACTTGTGGAAGTTGTAAGCACGATA-CAAGAAC
AAGATTGCAAAATCATTGTGAATATCAGTTTAAATGAAAATCACATATGGATTTAGTGTATTCCTGGTCATATGTTTACC
CGCATGTTGATT
>chr1A_369
GCACCGCCCCGGCGTCATGAAGAATCACCAAGGAGAGACGAGGAAACTAAATTAAGTTAGATCCAAACAAATCAATCTAG
GTTTTTTTTTGTTTGAGAAATCTATCTAGCTATATTGACATAAAGTCGTGGTTCTTTCAGCTATCAGCCGTGCCTTTCCG
AGTTTATTTTGCCTATTTCGACTGGACTTATGTCCCATGCTAATTGTGCTATGCAAATACCAAGAAAAATTATATGTTCC
TTGTGGTTTTTTTATTTACTGTATTCTTTAGTTGTTAAGAGTCGTAAGTAAGCGCAGTAACACGAATTACAACATCATCA
TCATGTGATCTCTGGAAACCCCGTTCCTTGTGTTCTATGCAAATCAAATACCAAGAAGATATAATTTTTTTCTTGTGGTT
TCATTCAGTTATCTATAATGCTATTAGACTTGTGGAGTTGTAAGCACGACCAAGAACAAGATTGCAAAATCATTGTGAAA
ATCACCTATGGATTTAGTGTATTCCTGCTGATTTTGAACTCTCTTTCAGCCCTCTTATTTCTGTGATTAGAAACTACTCC
CTCCCTCCCATATAATGTACTCTACGAATACTATATCTGCATCAGAGCACAGAGAGACAGGTCATCTGCATCAGAGCAGG
AAAACCAAACGACTCTGCAATTTTTATTCCATTACATGTCAGACTGAAATTTTGTAAACAGAAAGCTGAAGCAAAATAAA
AATTCAGAATAGAAAGCTGAAGCAAAATAAAAATTCAGAGAAGGTTTTGCATCGTGTTAATGTAACTAGCACAACTACGA
AGGCACCACACAGTCCAGATATTTTGTAGGCACATTCTTTTACTTTCTGATCTGCAATCTACTGGCCCTCGCACCATCTT
TGATTTCTTGATGCATCGTGTCCTCAACGGCTCAGCCCCACACCGTAATGGCAATGGCATGCGAACGATAGATTCTTTGC
ACGATAGATTAAATTCCGTGTGCCTCCACCAGACCATTTGATCTCAAAAATGGAACCGGTACATTTATCACTCGCGGGAG
CGACGAAGGAAGGGGGGCTGGTTTTTGCAATGAGATGGAATTAGTGGTTTTGGGTACAAAACTGTAGAATTGTGGTTTCT
GCAACCCTAGTCTTCAATGTTTATGTTTTCTGCAATTCACTCCCTATCAGTTGCCCACAAAAAAAAAACAAGTAAATGCT
TCGTATTCATGTTTGATTTAGTTATGTCCCTGATTTCTGCTTCGTATTCGTGTACCCGATTCCAATCCTAATAAGAATAC
TAGTTCCAGATCTGTGGAGCTGTGATCCGGATGATCATCTGCTGACTGCGGCGGCGAATCGGATAGATACTCTTTTGTTT
TGAAGTATATA---------TATCGATTTTAGGACTTGGACTCC------GACAAGGAGTCGAGCAGACTTCCGATGGGA
TTCGAATCGAATCGCTCGCGCTCGCCCCTGTATAAATATGCGTCCAGAGGCGCCTGGTTTCTCACCCGAACAATTTATCG
CAGTG---------------------------------------------------------------------------
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----------------------------------------CAGATCCCAATGGCAACTTCATCTTCAAGTTCCGTCGAGG
AGGAGGAGGTGGTGGATTTGCAGGATCAAGAAATCAAGGTGGGTGGTGACAAGCCGTCGGTCGAGTCGGCAGGCAGCCCT
GCAGATCCAGCACAAAAGAA---GAAAAAGAAGATCCTGCGTGTGGTGCCTGAGAGCGATGTGAAATATGTCATGAGTTA
CAAGCCGTTGCCCCAAAGGACGGAGTGTGGCCAGATAGCGTTATCAAAAAGTGCCCAGAGCTGGCCGCATGCTATTATGC
CACCAGGGCCAATACGGATGAGGTCGTGGAGGACATGCAACGGAGGATGCTCGAGACACAGAAAGACTACAGGCAACAGC
TGAAAAACAAGGGCATAGTCACACCTACGAGGAGGAGGTTGATGAGGACTACGACGAAGACGAAGACTACGCTCCACTGC
ATCCACCGGGTCGGAGGAGGCACCGACCTGGCGTCATGAAAAATCGCCAAGGAGAGATTAGGAGGCTGAATTAAATTAAA
AT-TCAAGCAACTCTATCTAGCTATATCATCATGCTTCCAGCTCTTCGT-TTTTTTCTTCTTAAATACTTTGTTTGTGAA
CCTGGTTCAGTTATGTCTTCCGTATGATCATCTAGGCGCCATGAAGGATTTTATTTTGTCTTGTTTTCTTACTGGATTAT
GAGTCACATGCCAGTTGTGCTATATACAGACAAGGAATATTTGTTCTTTGTGGTTTTGTCCATTTACTGTATTCTCTGAT
TGTTAGAGCCTGACAACACCGGGATTGCAAATTCAACATGCGAGTATTTCTAAAGAACATCAATATGCGACAGACACCTT
GGAAGCCACAGGATAATTGTGTGCTATGCAAATCATATAACAAGGTTGGTGTCGTTTCTTGTGTTTTTGTTCATTTATTT
TC--TATATACCGCCCCTTTATGTCTCCTTTGCATCCACCCTGGTGTCATGAAAAATCACCAAGGAGAGACGAGGAAGTT
TAATTAAATTAGATCCAAACAGATCTATCTAG--TTTTTTTTTGTTTGAGAAATCTATCTAACTATATATTGACATAAAG
CCGTGGTTCTTTCAGCACATCAGTCGTGTCTTTCCTATGAACACCTAAGGCGCC--------------------------
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>SNPs
SSS-SS--SSSSSSSSSS---SSSSSSSSS---SSS-SSSS--SS--SSSSS-SSSS-SSSS-SSS-SSS-SSSSS-S--
SSS--SSSSSS--SSS-SSSSSS-SSS-SSSS--SS-S-SS--SS-SSS-SSSSSSSSS-SSSSSSS-SSSSS-S-SSS-
SS--SSSSS-SS-S-SSSS-S-S-SSS-S-SSSSSSS-S-SS-S--S-S-SSSSSSSSSSSSSSSSSSSSS-S-S-SSS-
SSSSSS-SSSS--S-SSS--------------S--S--------S----S----S----S----------------S-S-
------------S-S---------SSSS-----------SS----S-S------S-------------------------
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----------------------------------------------S---------------------S-----------
----------S---S---S----------S---------------S----------------------------------
-S------------------------------S---S-------------S-----------------------------
----------------------------------------------------S------------------------S--
-SS---S-SSSSSSSSSSSS-----SS-----------------SSSSSS------------------------------
--------------------------------------------S-------------------------------S---
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--------------------------------------------------------S-----------------------
-----------------------------------------------------------S--------------------
--------------------SSS---------------------------------------------------------
--------------S-----------------------------------------------------------------
---S----------------------S-----------------------------------------------------
------S---------------------------------------------------------------------S---
--------------S------------------------------------------S------------------S---
-SS---------------------------------------------SS------S-------S---------------
----------------------------------S----------------SS----------------------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-----------SS----------------S--S------------S------S-------S---------------
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------------------------------S---S-----------S--S------SS-------------S------S-
---SSSSS-----------------------------------------------S------------S---S-------
--------------------------------------------S---------------------S-------------
-S----------
>forward_1135
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---------------------------------------------------------------------------TTTCC
GCAACCCTAGCCTTT-----------------------------------------------------------------
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>reverse_2868
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-------------------------------------------------------------------TGACACCTTGGAA
GCCACAG-------------------------------------------------------------------------
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