>input_sequence_63562
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--------------------------------------------------------------ATGAAGACGGGCGTGATC
ATCTTGTCCGTCGTGGTAGCGGTTTTTGGGGTGGCAAGCGCTGTGCTGGGGTTGATCGCCGAGGGCGCCAAGCTCACGGT
AAGTACA--------TTAGTAGTCTCGTAATCTAAGTACTCCGTCCGTCGGTTCGAAATTACTTGTCTCGAAAATAGATG
TATCTAAAACTAAAATACGTCTAGATACATCTATTTCTACGACAAGTAATTCTGAACGGAGAGAGTAGTACGTAGTAGTA
TGCATCTGAAGAAAACTAAAACGGACCGGCGACGCTTGTGGCGCGCAGCCGAATGACATCAAGATA---TCCAGAAACGA
GTGCGTGTACCCTGACAACCCGGCATACGCACTGGGGCTAGTGGCGGCCCTCCTGCTGCTGGTGGTCCAGATCACCGCCT
CCGCCGTCGGCGGCTGCTGCGGCTGCTGCAAGCCTCGGGGCGCCGGCTTCTCCGGGTCCAAGCGTT---CCAGGTCCAAG
AGGGTCATTGGCCTTGGCGCCCTCCTCTGCCTCGTCTCATGGTG----------AGCTTCCG---TGCTCATAGTCCATA
CATGATGCATGTGTGGCACAGTGGAAGCCACTGGTAGGCATGTCGAGGGTTCGTTCGATCGATGGAGGTGACGACGATCA
AATCAACGGGTGATGAATATGTTGTGTAT--GTGTGTGCAGGATAGCAGCGTTGATCGCGGAGTGGTTCTTCTTGCAAGG
TGCGTTCGGGAATGCCCCCATGACCCGCAGAACTCCACAGGGCCAGGGATGTACCTACCTCAAGGACGGCGTCTTCAGGA
TGGGCGCCATTCTGAGCATCCTCGCCACCGTGCTCGGGATCATATCTTACATCGTGCTTTACGTGGCGATGGCGGCGGCG
GCGGGTGCTGGTACTACCGC---TACCCTGGGCGCCGTGGCGGGGCCGTCGTCGGCGGGCGAGACCAAGCACGACGGCAT
CGCGATCGGCCAGCCTGCTGTCGCTCAACAGCAGTCGCAAGCGGTGTAG-------------------------------
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>chr1A_1_TraesCS1A01G271500
TGCATACATTTTACACTCACCCAACATGCCAAAAATACCCACAAAAGAAAAGAAAAAAAATCAAGTAATAAAGAAATATG
AAAATAAAAGCAAAAGGAGATAAAAACTGAAAAAAACAGAAAAAACAAATGAAGGAAAGGGATTAGCTGGGTCGCACCTG
GTAATGGGCTTTGTTTATTAACACAATCCAAGCACCTCATAGAACAAACCAGGGAAACAAAATAAGAATCGCAAAGCAAG
ATCAACGGCACACAAAATCGACTGAAGAAAGTAGTGGCTGCACCCACCTTCCGTGCACCCATGGTGCACCCACGTAAGAA
GACATAGCAAAAAATTCTGAAACTTTTCGGGAATGATAATCAACAAATGTTATGGGGGCGTGCAAAGTTTTGTGGTCAAA
TAAAATTCGAGGAGTTCTTTATAAAAAAGTCTTTTTTATAGAGAGCTCCTCGAATGTTATTTGAGCATCAAGTTTTGCAA
ACGCCCATAACATTTGTTGATAATCATTCGCACAAAATTTCAGAATGTTATAAAATGTCTTGATACATTTTCTTGCGTGG
GTGCACCGAGCCTGTGGGTAGAAAACTACTCTCGATCGACTGACCCGCAATAAAATTTCATGCCACTTACATACAGCTAA
ATGGCAATAA----AAGGGTCTCCTTTGCTTAAACCAGCAGCTGGGTCATCATTAGGCATTCCAGGCTTGTCGTTAGATG
ATCC-TTTCGGATACGACTATGCATGATCGTGAGCCTTAACCTCGCGGTCCTCGCCAGCCAGTGCGAGACAATGTTTGTT
CGTTTGCTTATGGACAAAAGAGTACGCGTGATTGCACCT-GTCGTGGAAAACTAATAGAGCATGCGACGTGCTCCG----
--------TATATAAAGCATCAGAACACGGCTTGTATCCATCCATCTCACACGGCGGCTTCCCGATCTTAGTAATCTG--
--GGACCAAAAGAGGAAGCAGCCAACGAGAGCGAGACATCAACTGAAACATCAGCGAGAGAAATGAAGACGGGCGTGATC
ATCTTGTCCGTCGTGGTAGCGGTTTTTGGGGTGGCAAGCGCTGTGCTGGGGTTGATCGCCGAGGGCGCCAAGCTCACGGT
AAGTACA--------TTAGTAGTCTCGTAATCTAAGTACTCCGTCCGTCGGTTCGAAATTACTTGTCTCGAAAATAGATG
TATCTAAAACTAAAATACGTCTAGATACATCTATTTCTACGACAAGTAATTCTGAACGGAGAGAGTAGTACGTAGTAGTA
TGCATCTGAAGAAAACTAAAACGGACCGGCGACGCTTGTGGCGCGCAGCCGAATGACATCAAGATA---TCCAGAAACGA
GTGCGTGTACCCTGACAACCCGGCATACGCACTGGGGCTAGTGGCGGCCCTCCTGCTGCTGGTGGTCCAGATCACCGCCT
CCGCCGTCGGCGGCTGCTGCGGCTGCTGCAAGCCTCGGGGCGCCGGCTTCTCCGGGTCCAAGCGTT---CCAGGTCCAAG
AGGGTCATTGGCCTTGGCGCCCTCCTCTGCCTCGTCTCATGGTG----------AGCTTCCG---TGCTCATAGTCCATA
CATGATGCATGTGTGGCACAGTGGAAGCCACTGGTAGGCATGTCGAGGGTTCGTTCGATCGATGGAGGTGACGACGATCA
AATCAACGGGTGATGAATATGTTGTGTAT--GTGTGTGCAGGATAGCAGCGTTGATCGCGGAGTGGTTCTTCTTGCAAGG
TGCGTTCGGGAATGCCCCCATGACCCGCAGAACTCCACAGGGCCAGGGATGTACCTACCTCAAGGACGGCGTCTTCAGGA
TGGGCGCCATTCTGAGCATCCTCGCCACCGTGCTCGGGATCATATCTTACATCGTGCTTTACGTGGCGATGGCGGCGGCG
GCGGGTGCTGGTACTACCGC---TACCCTGGGCGCCGTGGCGGGGCCGTCGTCGGCGGGCGAGACCAAGCACGACGGCAT
CGCGATCGGCCAGCCTGCTGTCGCTCAACAGCAGTCGCAAGCGGTGTAGAAGGCGTACTCTTGCTTCTACCGTCTCCTTT
---CGATGTACTCTTGGTTTAGTGTTGTCTTGCTTCCGTCACAACTGCCATGTCTTCCGGTTGTGGTAATTGATTCCGAT
TTGTGTCATTTCTGTTCCAGAGAGCTTTTGTTGTGCAAGTTTGGCGTGTTTGAGCTTTCAGATTGTGCAATGAGCGGTAC
CAACTCCACCATTTTAATTTATTTACTCGTGTTCGCCGTTCTTCGGTCATTTGATTCTTTTTTTGGTACAGTCGATTTTT
TTATCATTTTTGCTAAATATCATGTGCCTGAAATTTGTCGTGACCCCAGTCACTTTAGGCCGAAGGCAAGGACGATGTGA
GGAGCGCCGGCCACGGCGAGGCCAAGTCGTGTATGAGTGGGAACC----------GGCAGGAGCTAGCCCGTAACGTAAC
CAGGGGTGGAGGGCGGGAGGGGTGGGGTGGGGTGGGGTGGCGGAGTTGTTCATCTGGGCGCGACTTAGAGGAATAGCAGG
GGCGATGT-CAGCACGACGGCGGGGAGAGGGCGGGGCGGCGAGGTGGCACACGGTAGCGCCCGCCAGCCGCGGGTAATAG
GATGGTTGGGTCTGATTGCGCA-----------------AGGGCTGCTGGATTGGATCATGCGTTGAGGAAGATAGTGGG
AGGAGGAAGACGACCTTCGAACTGTTCGGGTAGGATTGAATGTGACTGATGCGAACTGTTTTTTAGGCACCTGAAGTATC
GGCGCTCTCTT----------TTTTTTGGCGGGCAACTAAGTCGAATTCATGGATGTGGGTTTGTTCGTATCATGATTCG
TGCGTGGGGAGGTTTGAACGTTCTTTTTTTAGTTTAATTTTCTAAGATTGATGGGCTGCTTTCATAGTTTCTTTTTAAAC
GCTTCAATTTGGATTGTTGGTTTTTAGGTTATTG---------TCAGTAGCACTATACTAGTGTGGATT-GGTGTCGTTT
CTGCTTCGCTTCCTCAGTTCTTCTCCCCTCTTGTTTCTCAGGTGGGTCAAGTTCTAGGGT
>chr1D_595
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----------------------------------ATTGACTGACCCAAAATAAAATTTCATGCAACTTACATGCAGCTAA
ATTGCAA-AA----AAGGGTCTCCTTTGCTTAAGCCAGCAGCTGAGTCATCATCAGGCAGTCCAGGCTTGTCGTTAGATG
ATCTTTTTCGGATACGACTATGCATGATGGTCAGCCTTAACCTCGCGGTCCTCGCCAGCCAGTGCGAAACAATGTTTGTT
CGTTTGCTTGTGGAC-AAAGAGTACGCGTGATTGCACCTCGTCGTGGAAAACTAGTAGCATGC-CGACGTGCACAGCGTG
CTCCATACTATATA-AGCATCAGAACACGGCTTCCATATCAATCCATCTCACGGCGGCTTCTCGATCTTAATCATCTCGA
TCGGACCAAAAGAGGAAGCAGCCAACGAGAGCGAGACATCAACTGAAACATCAGCCAGAGAAATGAAGACGGGCGTGATC
GTCTTGTCCGTCGTGGTAGCGGTTTTTGGGGTAGCAAGCGCTGTGCTGGGGTTCATCGCCGAGGGCACCAAGCTCACGGT
AAGTACA--------CTAGCAGTCTGGTAATCTAGTA-------------------------------------------
-----------------------------------------------------------------------GTCGTAGGA
TCCATCTGAAGAAAACTAAAACGGACCGGCGACGCTTGTGGCGCGCAGCCGAATGACATCAAGATA---TCCAGGAACGA
GTGCGTCTACCCTGACAACCCGGCATACGCACTGGGGCTAGTGGCGGCCCTCCTGCTGCTGGTGGCCCAGATCACCGCCT
CCGCCGTCGGCGGCTGCTGCGGCTGCTGCAAGCCTCGGGGCGCCGGCTTCTCCGGGTCCAAGAGCT---CCAGGTCCAAG
AAGATCATTGGCGTTGGCGCCCTCCTCTGCCTCGTCTCATGGTG----------AGCTTCCG---TGCTCATAGTCCATG
CATGAT-----------------------------------------------------------AGGTGACGACGATCA
AATCAACGGGCGAT--ATATGTTGTGTAT--GCGTGTGCAGGATAGCGGCGTTGATCGCGGAGTGGTTCTTCTTGCAAGG
TGCGTTCGGGAATGCCCCCATGACGCGCAGAACTACACAGGGCCGGGGATGTACCTACCTCAAGGACGGCGTCTTCAGGA
TGGGGGCCATTCTGAGCATCGTCGCCACCGTGCTCGGGATCATATCTTACATCGTGCTTTACGTGGCC---GCGGCGGCG
GCGGGTGCTGGTACTACCGC---TACCCTGGGGACCGTGGCGGGACCGTCGGCGGCGGGCGAGACCAAGCACGACGGCAT
CGCGATCGGCCAGCCTGCTGCCGCTCCACAACACTCAGAAGCTGTGT--AGGGCGTCCTCTTGCTTCTACCTC---TCCG
TCCCGATGTACTCTTGCTTTAGTGTTG-----CTTCCGTCGTAACTGCTATGTCTTCCG---------ATTG------AT
TCGTGTCATTTCTGTTCCAGAGAGTTTTTGTTGTGCAAGTTTGGCGTGTTTGAGCTTTCAGATTGTGCACTGTGCGGTAC
CAACACTATCAT----ATTAATTTACTCGTGTTCGCTATTCTTCAGTCATTTGATT-TTTCTTTTGTACAGTCGATTTTT
TTATTGGTTTTGCTAAACATTATGTGCCTTAAATTTTTCTTGACGCCGTTCACATTAG----------------------
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>chr1B_626
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-----------------------------------------------------------------CTTGCATACAGCTAA
ATGGCAA-AAAAAAAAGGGTCTCCTTTGCTTAAACCAGCAGCTGGGTCATCATTGGGCATTCTAGGCTTGTCGTTAGATG
ATCG-TTTCGGATACGACTATGCATGATCGTGAGCCTTAACCTCGCGGTCCTCGCCAGCCAGTGCGAGACAATGTTTGTT
CGTTTGCTTATGGAC-AAAGAGTACACGTGATTGCACCT-GCCGTGGAAAACTAATAGAGCATGCGACGTGCTCCG----
--------TATATA-AGGATCAGAACACGGCTTGTATCCATCCATCTCACACGGCGGCTTCCCGATCTTAGTAATCTG--
--GGACCAAAAGAGGAAGCAGCCAACGAGAGCGAGACATCAGCTGAAACATCAGCCAGAGAAATGAAAACTGGCGTGATC
GTCTTGTCCGTCGTGGTAGCGGTTTTTGGGGTGGCAAGCGCTGTGCTGGGGTTCATCGCCGAGGGCACCAAGCTCACGGT
AACTACACTAGTTAACTAGTAGTCTGGTAATCTA----------------------------------------------
-----------------------------------------------------------------------GTATTGGTA
TCCATCTGAAGAAAACTAAAACGAACCGGCGGTGTTTGTGGCGCGCAGCCGAATGACATCAAGATAATATCCAGGAACGA
GTGCGTGTACCCTGACAACCCGGCATACACACTGGGGTTAGTAGCGGCCCTCCTGCTGCTGGTGGCCCAGATCACCGCCT
CCGCCGTCGGCGGCTGCTGCGGCTGTTGCAAGCCTCGGGGCGCCGGCTACTCCGGGTCCAAGAGCT---CCAGGTCCAAG
AGGGTCATTGGCCTTGGCGCCGTCCTCTGCCTCGTCTCATGGTG----------AGCTTCCG---TGCTCATAGTCCATG
CATGAT-----------------------------------------------------------AGGTGACGACGATCA
AATCAACGGGCGAT--ATATGTTGTGTAT--GTGTGTGCAGGATAGCGGCGTTGATCGCGGAGTGGTTCTTCTTGCAAGG
TGCGTTCGGGAATGCCCCCATGACGCGCAGAATTCCACAGGGCCAGGGATGTACCTACCTCAAGGACGGCGTCTTCAGGA
TGGGGGCCATTCTGAGCATCCTCGCCACCGTGCTCGGGATCATATCTTACATCGTGCTTTACGTGGCGATGGCGGCGGCG
TCGGGTGCTGGTACTACCGC---TACCCTGGGGGCCGTGGCGGGGCCGTCGGCGGCGGGCGAGACCAAGCACGACGGGAT
CGCGATCGGCCAGCCTGCTGCCGCTCAACAACCCTCACAAGCTGTGTAGAGGGCGTACTCTTGCTTCTACCGTATATCAG
TCCCGTTGTACTCTTGCTTTAGTGTTG-----CTTCCGTCATAACTGCCATGTGTTCCGGTTGTGGTAATTG------AT
TCGTCTCATTTCTGTTCCAGAGAGTTTTTGTTGTGCAAGTTTGGCGTGTTTGAGCTTTCAGATTGTGCAATGTGCGGTAC
CAACACCATCGTTTTAATTTATTTACTCGTGTTCGATATTCTTCAGTCATTTGATTCTTTTG-TGGTACAGTC-ATTTTT
TTATCAGTTTTGTTAAACATCATGTGCGTGAAATTTGTCGTGACCCCAGTCACATTAGGTCGAAGGCAAGGACGGCGTGA
GGAGCGCCGGACATGGCGAGGCCAAGCCGTGTATCAGTGGGAGCTGGCAGTGGCTGGCAGGAGCTAGTCCGAAACGTAAC
CAAGGGTCACT------------------------------GGAGTTGTTCATCCGAGCGCGACTTAGAGGGATGGCAGG
GGTGATGTCCAGAACAACGGTGGGGGGAGGCCGGGGCGGCGAGGTG----------GCGCCCACCGGCCGCGGGTAATAG
AGGCCGGTGGTTAGGGATGGGTTTGAGGACGGTTGTGTGAGGGCTGCCGGGTTGGATCATGCGTTGAGGAAGATAGTGGG
AGGAGGAAGACGACCTTCGAACTGTTAGGATAGGATTGAATGTAGCCGATGAGAACTGTTTTTTAGGCACCTGAAGTATA
GGCGCTCTCTCTACATATATATTTTTTTGCGGGCAAGTAAGTCGTATTCATGGCCGTTGGTTTGTTCGTGTCATGATTCG
TGCGTGGGGAGGTTTGAACGTTCTTTTTTTGGTTTAATTTTCTACCGTTGTTAGGCTGCTTTCATAGTTTCTTTTTAAAC
ATTTCGATTTGGATTGTTGGTTTCTAGGTTATGACACCCGTTATCAGTAGCACTATACTAGTGCGGATTTGGTGTCGTTT
CTGCTTCTCTTCCTCGGTTCTTGTCCCCTCTTGTTTCTCAGGTGGGTCGAGTTCTAGGGT
>chr1B_1279
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----------------------------GCGATGCTCGTGGCGCGCAGCGGAATGACATTGAGGTGTA---CAGCAACGA
GTGCGTGTACCCTGACAACCCGGCGTACGCACTGGGGTTAGTGGCGGCCCTCCTGCTGCTGGTGGCCCAGATCACCGCCT
CGGCCGTCGGCGGTTGCTGCGGCCGCTGCATGCCTCGGGGCGCCGGCTTCTCCGGGTCCAAGCCCGTTGCCAAGTCCAAG
CGGGCCACC------GGCGCCGCCCTCTGCGTCCTCTCATGGTGAGCTAAGCTTCCGTGCTCAACTGCTCATAGCCCATC
CATTCCTGAC-------------------------ATGCATGTCGAGGGTTCGATCGA-----------GGTGACGGCCA
ATCCAATGGGCGATGAACATGCTGCCGTTGAGTGTGTGCAGGATAATGGCGTTGATCGCGGAGCGGTTCTTCTTGCTAGG
TGCGGCGAGGAACATCCCCATGACGCGCGAAACTAGCCAGGGCCGGGGCTGTCACCCCGTCAAGGACGGCGTCTTCATGA
TGGGGGCCGTTCTTAGCATCGTCGCCACCGTGCTCGGGATCATATCTTACATCATGCTTTA------C---GCGGCGGCG
GCAGGTGCTAATACTACTACTAGTACAATGAGGGCCGTGGCGGGCCCGTCGCCGGCAGGCGAGATCAACCATGACGGGAT
CGCGATCGGCCACCCTGTTGCCGCTCAACAACACGCACAAGCTGTGTAGAGGGCGTACTCTTGCTTCTACCATCT-----
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>chr1D_1284
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---------------------------------GCTCGTGGCGCGCAGCGGAATGACATTGAGGTGTA---CAGCAACGA
GTGCGTGTACCCTGACAACCCGGCATACGCGCTGGGGTTACTGGCGGCCCTCCTGCTACTGTTGGCCCAGATCACCGCCT
CGGCCGTCGGCGGTTGCTGCGGCCGCTGCATGCCTCGGGGCGCCGGCTTCTCCAGGTCCAAGGCCGTTGCCAAGTCCAAG
CGGGCCA------TTGGCGCCGCCCTCTGCGTCCTCTCATGGTGAGCTGAGCTAAGCTTCCG---TGCTCATAGTCCATC
CATTCCTGAC-------------------------AGGCATGTCGAGGGTTCGACCGA-----------GGTGACGGCCA
ATCCAACGGGCGATGAACATGCTGGCGTTGAGTGTGTGCAGGATAATGGCGTTGATCGCGGAGCGGTTCTTCTTGGTAGG
TGCGGCGGCGAACATCCCCATGACGCGCGAAACTAGCCAGGGCCGGGGGTGTCACGCCGTCAAGGACGGCGTCTTCATGA
TGGGGGCCATTCTCAGCATCGTCGCCACCGTGCTCGGGATCGTATCTTACATCATGCTTTA------C---GCGGCGGCG
GCTGGTGCTACTACTACC---------ATGGGGGCCGTGGCGGGGCCGTCGTCGGCAGGCGAGATCAGGCTTGACGGGAT
CGCGATCGGCCACCCTGTTGCTGCTCAACAACACGCACAAGCTGTGTAGAGGGCCTACTCTTGCTTCTAC----------
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>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--S---------SS---------------S----------------
-------S------------------------------------------------------------------------
---S----------------------------------------------------------------------------
---------------S----------------------------------------------------------------
--------------S-----------------------------------------------------------------
-------------------------------------------------------S------------------------
S----------------------------------------------------S------------S-------------
---------------S---------S--------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------
-S------------------------------------------------------------------------S-----
-----------------------------------------------------------------S--------------
----------------------------------------------------------------S---------------
-------------------------------------------------------------------------------S
------SS-SSSSSSSSSSSSSSSSSSSSSSSSSS------------------S----SSSSSSS---------------
----------S------------------------------------S--------------------------------
------------------------S-------------------------------------------------------
----S---------------------------------------------------------------------------
--------------------------------S-----------------------------------------------
--------------------S---------S--S--S-----S-------S------------------------SSSSS
----------------S----------SSSSS---------S------------------------------SSSSSS--
-S----------------------S-----------------------------------------------S-------
----S---S---------------------------SS------S-----------------------------------
------S----------S-----------------------------------S-----S--------------SS----
----------S--S------------S-------S-------S-S----------------------S---S--------
--S----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-------------S-S--------------S--S-----
--S---------S--S----S----S----S---------------SSSSSSSSSS------S--S--------------
SSSSSSSS---SS-SSSSS-SS-------------------------S--S-----------------------------
--------------------------S--S-------------SS-S----S---------------------------S
----------S----------------S--------S-------S--------SS--S-----------S----------
------------------------------S-------------SSS---S-S---------------------------
SS---S-----------------S--------SS-----------------------------S----------------
-------S-------S------S-------------------------S-----------
>forward_565
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-----------------------------------------------------------------CATTTTCTTGCGTGG
GTGCA---------------------------------------------------------------------------
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>reverse_2109
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----------------------------CTTGCTTCCGTCACAACTGC--------------------------------
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