>input_sequence_61699
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-----------------------------------------------------ATGGGTGCGTCTGCCTCAGCCCCC-TG
CGCCGGGTTGGAGGATTTCGCCGACGACATGTGCCTTGCTTTCGACCCCACTGTGTCGCCCCATTACGAGGTACTTCTTC
TTCCCGAAGTTCCTCACAAGCTGGGTTCCATGACAGTATTCACGGAGGAATCAGAGTGGCCGCCTTCTTCGTATACAATA
AGAGCCTTCTCTTCAAGGACATGGACATGGGAGGAGAGGGTGTTGGTCCGGAGAGGGGAGGCCGCAGGGGCCATTGCTGA
GATGCACTCACCTAGGGCTAGGGAACCAGAGCATCGCTATGCCGTCTACTGGAAAGGAGAGCTTTATGTGCACTGCCAAA
ATGACTCCATTATGCGGTACTCATTCACCCCTTAAGCAAACAATGACATTTGTTATTGGGTTTTGATTTTGCCCATTTTC
-TAAGCTGAAACTCATCGTCCTATCAATTAACATGCGTTTTCTCTCAATTGACTTCACATTTGCAGCATAACCTTGTCGA
ATGGCGAGTATGAAGTTATTAAACCGCCTACAAGCATGGATGAGTTTACAGATTTTTATATAGGGAAATCGAAGAGGGGG
CTGTACTGTGCTTTAATTTATAAAGATAGATCATACCGACTTCAGGTTTGGTTACTTAGTGAATTGAGGGGTAAAATGGA
GTGGGGGTTGAAGATTGACACCAGCCTTGTGCCAGTGGTGGCAATGTTTTCTTGGTTGTCTCATGAAGAAAATTCCGGTC
CGTGGATCTTACATGGTGGTAATTATGATGGAGATGGTAAAAAAGTGATCGTGGATGATAAATGTGAATGGGACTTCAAC
AATGGTATTATCCTTGAGGCAAGAGATGGGGATGAATGTGACTTTGTGTCTGATAGTATTTATTTCCTTGGATTTCATCC
GTATTATGAGATTGCCTTCTTGTGGGTATCAAGAGCAAGAGTAGTTGCCTATCATTTGAGTAGCTCGAAAGTTCAAGACT
TGGGCATGTTACACGTACAATGTGTAGGAGATTCCTTTCCATACACACCATATTGGACAGGAGAGTTATTTGAAAAGCAT
TAA-----------------------------------------------------------------------------
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>chr3B_1_TraesCS3B01G278800
TCACCACATCCAATCACCACACCAGTCTCATGGCCACGGCCGGCCGCCGCCAACGCAGATCGCACCAGGATTGCCACCC-
---ATCTTCCTAATCTTGGTCGTACGC---GGAAACGGCCAAATGACCCCCGTCCCTTTGGGAGCGGGCTGGCCACCACC
GTGGCCGAAGCCGGCGACGGCG--GCAGCAGCAAGGCCGATTTGTAGAGGGTTGGCGGCCGGGGTAGGTTTTCAGCCCCT
TGGCCGCCACAAGAGGGACGACATGGTGGAAGTGAACGCTCTGACATCAAGTACAGTTACTGGAACCATCAATTTCTGTA
TGTAAAGCGACCAAAGTGACTATCGTCAACAAGT-TTTTTTTTCACTAA-TTTTTTTTAATCCTAAAAGAGCAAGTTTAA
TGACGCATAATGCATTTTACTAAATTAA-AAAAAAACACTAAACGTCCTTATGCATGCGGAGATCCTAACGATTTACGGC
AGGCACGGTCAGTCAGCCGCACACCGCGCAACTAGAGTCGATTGCAAAACCTAATCGAATCCCGTCTCAGCTACACACAT
CCCACCAAGAGCCAGCCCCTCGATCGATCCGTCACCATCAGCTAGCGCCCTCTCTGTTTTCGAAATGAATTAGTTCATCG
GCATCCATGGACCATGGCCCTGGTGGCGGCACAGCTGCTACCTGATGGCGTCCTCGCCAGCGTCCTCCGGCATCTCGCGC
CGCGCAGCCTCGCCGCATCTCGCTGTGTCTGCAAAAGCTGGCGTGCCGTCGTCGACGACTGGCGCCTGCTGCGGACGGAT
CTCCTACCGCTATCCCTCTCCGGGATCTTCTTCATGGAGGAGATCTTTCCGGCCCTCCCGAAATTCTTCGCGAGCCCGTC
GATAGATGGCAAGATCGCAGCCAGGCTCGACTACCTGGACACCAAATTTGAGGGTTATTTGCA-TATTATGGATCATTGC
AATGGCCTTCTCTTGCTTTGGGATCAACTGGTGGTCAATCCAGCAACTCGACAATGGGTGCGTCTGCCTCAGCCCCC-TG
CGCCGGGTTGGAGGATTTCGCCGACGACATGTGCCTTGCTTTCGACCCCACTGTGTCGCCCCATTACGAGGTACTTCTTC
TTCCCGAAGTTCCTCACAAGCTGGGTTCCATGACAGTATTCACGGAGGAATCAGAGTGGCCGCCTTCTTCGTATACAATA
AGAGCCTTCTCTTCAAGGACATGGACATGGGAGGAGAGGGTGTTGGTCCGGAGAGGGGAGGCCGCAGGGGCCATTGCTGA
GATGCACTCACCTAGGGCTAGGGAACCAGAGCATCGCTATGCCGTCTACTGGAAAGGAGAGCTTTATGTGCACTGCCAAA
ATGACTCCATTATGCGGTACTCATTCACCCCTTAAGCAAACAATGACATTTGTTATTGGGTTTTGATTTTGCCCATTTTC
-TAAGCTGAAACTCATCGTCCTATCAATTAACATGCGTTTTCTCTCAATTGACTTCACATTTGCAGCATAACCTTGTCGA
ATGGCGAGTATGAAGTTATTAAACCGCCTACAAGCATGGATGAGTTTACAGATTTTTATATAGGGAAATCGAAGAGGGGG
CTGTACTGTGCTTTAATTTATAAAGATAGATCATACCGACTTCAGGTTTGGTTACTTAGTGAATTGAGGGGTAAAATGGA
GTGGGGGTTGAAGATTGACACCAGCCTTGTGCCAGTGGTGGCAATGTTTTCTTGGTTGTCTCATGAAGAAAATTCCGGTC
CGTGGATCTTACATGGTGGTAATTATGATGGAGATGGTAAAAAAGTGATCGTGGATGATAAATGTGAATGGGACTTCAAC
AATGGTATTATCCTTGAGGCAAGAGATGGGGATGAATGTGACTTTGTGTCTGATAGTATTTATTTCCTTGGATTTCATCC
GTATTATGAGATTGCCTTCTTGTGGGTATCAAGAGCAAGAGTAGTTGCCTATCATTTGAGTAGCTCGAAAGTTCAAGACT
TGGGCATGTTACACGTACAATGTGTAGGAGATTCCTTTCCATACACACCATATTGGACAGGAGAGTTATTTGAAAAGCAT
TAATTTATGTTCCCAGGGGTTTGCTTTCGGTGCCATATGACTTGTAACTTACATTGGTGAGTATGATTTTTTTACAAGAA
ATGCAGTTAACAGTTGAGTCTGGTGTTATTACTTTTCTGAAATTGGAGTCCTGTCTTAATTTTAATTC--TTTTTTACCC
ACCTATTTAGGATATGGCTCCGTT--GTTAATCCCTTCCCCGCCAGGATTCTGGACAAAACGCCGTCGATTAGCTGGGAT
CACTCTGGCAGAGGATTCTTCCCCGCACACCTTGTTTGGTGCATCCGGTTGCACATTCTTCCTCTGCATACTCTGTTTAT
ATACATTGACTTTTATATATGAAAGCACAAGGAGCTGCAGTAGCAACTTGGTAATACAAATAAACTTTGTGCAAGGAGTT
AGCAAAATTACGAGCATACTTGACATTTTTCTGAAAACCTTTTGGTGGCACAGTCACAGGTT---GCTTGGGCTGTTTTG
TTCTGGGAACAATCACATTATTTTAAGTGGCCGAAGAAAATTAATTACAGAAAACACTACATCCCTTTCTA---ATGATT
AATTATTTTCTGCACAATACTTCTCAGCTTTATCATGTTTTTCTATAGTCAAGCGTATCTAATGGTGTTCCTACAATATC
AAGTGTTTGACCAGCTCGCTTTTATGGACTGAAGTTGACAAGGAGAGGTTTAGGACAGTCACTACTTACTAGAGGAGCTC
ATGTTCTCTCTTAAAATTGTA--CTCCTTGCTATTCTGATACCATTAAATTTTAGGTTACAATTTTTCTTACAAACTGTG
TGCATGCTCAGCTGTGG-------------------TGTCTTAAACAGGTGTCTTTTTAACGTTCATGTAAATCGGGCAG
GATACCATTCTCAATAGTGACTTCTGAACAATCTAGTGACTTCTCAAGTTCCTGAACAATCATCTTGTGCTGTATTTGGG
GAGCGGAAACTTTTGTTGAGATTTGTGATGCTGAAACACAAGGGGGGGCATGGATTCTTATGGCATGCAACCAA
>chr3B_1
TCACCACATCCAACCACCACGCCAGTCTCATGGCCACGGCTGGCCGCCGCCAACGCAGATTGCACCAGGACCGCCACCCA
TATATCTTCCTAATCTCGGTCGTACGCGCTGGAAACGGCCAGATGACCCCCGTCCCTTTGGGAGCGGGTCGGCCACCACC
GTGGCCGAAGCCGGCGACGGCGCGGCAGCAGCAAGGCCGATGAGTAGAGGGTTGGCGGCGGGG-TAGGGTTTCAGCCCCC
GGGCCGACACAGGAGGGACGACACTGTGGAAGTGAACGCTCTGACATCAAGTACAATTACTGGAACCATCAATTTCTGTA
TGTACAGTGACCAAAGTGACTATCATCAACAAGTAT-TTTTTTCACTAAATTTTTTT--ATCCTAAAAGAGCAAGTTTAA
TGACGCATAATGCATTTTACTATAAATTTAAAAAAACACTAAACGTCCAGATGCATGCGGAGATCCTAACAATTTACGGC
AGGCACGGTCAGTCAGCCGCACTCCGTGGAACTAGAGTCGATTGCAAAACCTA---------------------------
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>chr3D_1
TCACCACATCCAATCACCGCGCCAGTCTCATGGCCACGACCGGCCGCCGCCAACGCAAATCGCACCAGGATCGCCACCCA
T----CTTCCTAATCTTGGCCGTACACGCTGGAAATGGCCAGATAA-CCCCGTCCCTTTAAGAGCGGGCCGGCCACCACC
ATGGCCGAAGCCGGCGATGGC--GGCAGCAGCGAGGCCGATGAGTAGAGGGTTGGCGGCGGGG-TAGGTTTTCGGCCCCC
GGGCCGCCACAGGAGGGACGACATGGTGGAAGTGAACGCTCTGACATCAAGTGCAATTA----------------CTGTA
TGTACAGTGACCAAAGTGACTATCATCAACAAGT-T-TTTTTTCACTAATTTTTTTTTAATCCTAAAAGAGCAAGTTTAA
TGACGCATAATGCATTTTACTAAATTAA-AAAAAAACACTAAAC-TCCAGATGCATGCGGAGATCCTAACGATTTACGGC
AGGCACGGTCAGTCAGCCGCACTCCGCGGAACTAGAGTCGATTGCAAATCCTAATCGAATCCCGTCTCAGCTACACACAT
CCCACCAAGAGCCAGCCCCTCGATCGATCCGTCACCATCAGCTAGCGCCCTCTCTGTTTTCAAGACGAATTAGTTCATCG
GCATCCATGGACCATGGCCCTGGTGGCGGCACAGCTACTACCTGATGGCGTCCTCGCCAGCGTCCTCCGGCGCCTGGCGC
CGCGCAGCCTCGCCGCATCTCGCTGTGTCTGCAAAAGCTGGTGCGACGTCGTCGACGACTGGCGCCTGCTGCGGACGGAT
CTCCTCCCGCTATCCCTCTCCGGGATCTTCTTCATGGAGGAGATTTTTCCGGCCCTCCCGAAATTCTTCGCGAGCCCGTC
GATAGATGGCAAGATCGCAGCCAGGCTCGACTACCTGGACACCAAATTTGAGGGCTATCTGCA-TATTATGGATCATTGC
AATGGACTTCTCTTGCTTTGGGATCAACTGGTGGTCAATCCAGCAACTCGACAATGGGTGCGTCTGCCTCATCCCCCCTG
CGCCGGGTTGGAGGACTTCGCCGACGACATGTGCCTTGCTTTCGACCCCACTGTGTCGCCCCATTACGAGGTACTTCTTC
TTCCCAAAGTTCCTCACAAGTTGGGTTCCATGACTGTATTCACGGAGGAATCAGAGTGGCCGCCTTCTTGGTATACAATA
CGTGTCTTCTCTTCAAGGACATGGACATGGGAGGAGAGGGTGTTGGTCCGGAGAGGGGAGGCTGCAGGGGCCATTGCTGA
CATGCAGTCACCTAGGGCTAGGGAACCAGAGCATCGCTATACCGTCTACTGGAAAGGAGAACTTTATGTGCACTGCCAAA
ATGACTCCATTATGCGGTACTCATTCACCCCTTAAGCAAACGATGATATTTATTATTGGGTTTTGGTTTTCCTCATCTTT
TTAAGCTGAAACTGATTGTCCTATCTATTAACATGCGTTTTCTCTTCATTGACTTCACATTTGCAGCATAACCTTGTCGA
ATGGTGAGTATGAAGTGATTAAACCGCCTACAAGCATGGATGAGTTTACAGAATTTTATATTGGGAAATCGAAGAAGGGG
CTGTACTGTGCTTTAATTTATAAAGATAGATCATACCGACTTCAGGTTTGGTTGCTTAGTGAATTGAGGGGTAAAATGGA
GTGGGGGTTGAAGATTGACACCAGCCTTGTGCCAGTGGTGGCAATGTTTTCTTGGTTGTCTCACGAAGAAAATTCCGGTC
CGTGGATCTTACATGGTGGTAATTATGATGGAGATGGTAAAAAAGTGATCGTGGAAGATAAATGTGAATGGGACTTCAAC
AATGGTATTCTCCTTGAGGCAAGAGATGGGGATGAATGCGACTTTGTCTCTGGTAGTATTTATTTCCTTGGATTTCATCC
GTATGATGAGATTGCCTTCTTGTGGGTGTCAAGAGCAAGAGTAGTTGCCTATCATTTGAGTAGCTCGAAAGTTCAAGACT
TGGGCATGTTACACGTACAATGTGTAGGAGATTCCTTTCCATATACACCATATTGGACAGGAGAGTTATTTGAAAAGCAT
TAATTTATGTTCCCAGGGGTTTGCTTTCGATGCCATATGACTTGTAACTTACAGTGGTGAGTATGATTTTTTTACAAGAA
ATGCAGTTAACAGTTGAGTCTGGTCTTGTTACTTTTCTGAAATTGGAGTCCTGTCTTAATTTTAAATTCTTTTTTAGCCA
CCTTATTTAGGACATGGCTCCATTCGGTTAATCCCTTCCCCGCCAGGATTCTGGACAAAACCCGGTGGATCAGCTGGGAT
CACTCTGGCAGAGCTTCCTTCCCCGCACACTTTGTTTAGTGCATCCGGTTGCACATTCTTCCTCTGCATACTCTGTGTAT
ATACATCGACTTTTGTATATGAAAGCACAAGGAGCTGCAGTACCAACTTTGTAATACAAATCAACTTTGTGCAAGGAGTT
AGCAAAATTACGAGCCTACTTGTCATTTTTCTGAAAACCATTTTGTGGCCCAATCACAGGTTATTGCTTGGGTTGTTTTG
CCCTAGGAACAATCACATTATTTTAAGTGGACAAAGAAAATTAATTACGGAAAATACTACATTCCTTTCTACTAATGATT
AATGATTTTCCCCACAATACTTCTCAGCTTTATCATGTTTTTCCAGAGTCAAGCGTATCTAATGGTGTTCCTACAATATC
AAGTGTTTGACCAACTCGCTTTTATTAGATGAAGTTGGCAAGGAGAGGTTTAGGACAGTCACTACT-ACTAGAGGAGCTC
ATGTTCTCTCCTAAAATTGCACTCTCCTTCCTATTCTGATACCACTAAATTTTAGGTTACATTTTTTCTTACAAACTCTG
TGCATGCTCAACTGTGGTGCCAC------TGTTAATTGTCTTAAACAGGTGTCTTAAT---GTTCATGTAAATCAGGCAG
GGTACCATTCTCAATAGTGACTTG-------------------TCAAGTTCCTGGACAATCATTTTGTGCTGTATTTGGG
GAGTGGAAACTTTTGTTGAGATCTGTGATGCTGAAACACAAGCA-GGGCATGGATTCTTATGGTATGCAACCAA
>chr3A_369
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-----------------------------------------------------------ATCCTAAAAGAGCAAGTTTAA
TGACGCAAACTGCATTTTACTT----------AAAAAACTAAACGTCCAGATGCATGCGGATATTCTAACGATTAACGCT
AGGCACGGTTAGTCAGCCGCACACCGCGGAACTAGAGTCGATTGCAAATCCTAATCGAATCCCACCTCAGCTACACACAT
CCCACCGAGAGCCAGACCCTCGATCGATCCGTCACCATCAGCTAGCGCCCTCTCTGTTTTTGAAACAAAATAGTTCATCG
GCATCCATGGACCATGGCCCTAGTGGCGGCACAGCTGCTACCTGATGGCGTCCTTGCTAGCGTCCTCCGGCACCTGGCGC
CGCGCAGCCTCGCCGCATCTCGCTGTGTCTGCAAAAGCTGGTGTGTCGTCGTCGACGACTGGCGCCTGCTGTGGACGGAT
CTCCTCCCGCTATCCCTCTCCGGGATCTTCTTCATGGAGGAGATCTTTCCGGCCCTCCCGAAATTCTTTGCGAGCCCGTC
GATAGATGGCAAGATCGCAGCCAGGCTCCGCTACCTGGACAGCAAATTTGAGGGTTATCTGCATTATTATGGATCATTGC
AATGGACTGCTCCTGCTTTGGGATCAACTGGTGGTCAATCCAGCAACTCGACAATGGGTGCGTC----------------
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>chr3A_1007
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-----------------------------------------------------------GCGTCTGCCTCAGCCCCCCTG
TGCCGGGTTGGATGACTTCGCCGACGACATGTACCTTGCTTTCGAACCCACTGTGTCGCCCCATTACAAGGTACTTCTTC
TTCCCAAAGTTCCTCACATGCTGGGTCCTGAGACAATATTCAGGGAGGAATCAGAATGGCCGCCTTCTTGGTATACAATA
CGAGTCTTCACTTCAAGGACATGGACATGGGAGGAGAGG-TGCTGGTCCGGAGAGGGGAGGCCGCAGGGGCCATTGCTGA
CATGCACTCACCTAGGGCTAGGGAACCAGAGCATCGCTATGCCGTCTATTGGAAAGGAGCGCTTTATGTGCACTGCCAAA
ACGAATCCATTATGCGGTACTCATTCACCCCTTAAGCAAACAATGACATTTATTATTGGGTTTTGATTTTCCCCATTTTG
---AGTTGAAACTCATCGCCCTATCAATTAACATGCATTTTCTCTCAATTGACTTCACATTTGCAGCATAACCTTGTCGA
ATGGCGAGTATGAAGTTATTAAATCGCCTACAAGCATGGATGAGTTTACAGATTTTTATATATGGAAATCGAAGAGGGGG
CTGTACTGTGCTTTAATTTATAAAGATAGATCATACCGACTTCAGGTTTGGTTACTTAGTGAATTGAGGGGTAAAATGGA
GTGGGGGTTGAAGATTGACACCAGCCTTGTGCTAGTGGTGGCAATGTTTTCTTGGTTGTCTCACGAAGAAAATTCCGTTC
CGTGGATCTTACATGGTGGTAATTATGATGGAGATGGTAAAAAAGTGATCGTGGAAGAGCAATGTGAATGGGACTTCAAC
AATGGTAGTATCCTTGAGACAAGAGATGGGGATGAATATGACTTTGTGTCTGGTAGTATTTATTTCCTTGGATTTCATCC
GTATTATGAGATTGCCTTCTTGTGGGTATCAAGAGCAAGAGTAGTTGCCTATCATTTGAGTAGCTTGAAAGTTCAAGACT
TGGGCATGTTACACGTACAATGTGTAGGAGATTCCTTTCCATACACACCATATTGGACAGGGGAGTTATTTGGAAAGCAT
TGATTTATGTTCCGAGGGGTTTACTTTCGATGCCATAAGA----TAACTTACATTGGTGAGTATGATC-TTTTACAAGAA
ATGCGGTTAACAGTTTAGTCTGGTGTTATTACTTTTCTGAAATTAAAGTCCCGTCTTATTTTTAATTC--TTTTTAGCCA
CCTTATTTAGGATATGGCTCCATACGGTTATTATCTCCCCCGCCGGGATTCTCGACAAAACCCTGTCGATCAACCGGGAT
GACTCTCGCAGAGCATTCTTCCCCGTACACTTTGTTTAGTGCGGCTGGTTCCACATTCTTCCTCTGCATGCTCTGTTTAC
ATACATCGACTTTTGTATATGAAAGCACAAGCAGCTGTAGTACAAACTTTGTAATACAAATCAACTTAGTATAAGGAGTT
AGCAAAATTACGAGCCTACTTGTCATTTTTCTGAAAACCATTTTGTGGCCCAATCACAGGTTATTGCTTGGGCTGTTTTG
TCCTAGGAACAATCACATTATTTTAAGTGGACAAAGAAAATTAATTACAGAAAACACTACATCCCTTTCTA---ATGATT
AATGATTTTTCGCACAATTCTTCTAAGCTTTATCATGCTTTTCTATAGTCAAGCGTATCTAATGGTGTTCCTACAATA-C
AAGTGTTTGACCAACTCGCTTTTATTGGATGAAGTTGACAAGGAGAGGTTTAGAACAGTCACTACTTACTAGAGGAGCTC
ATGTTGTCTCTTAAAATTGCACTCTCCTTGCTATTCTGAAACCATTAAATTTTTTGTTACAATTTTTCTTACAAACTCTG
TGCATGCTCAACTGTGGTGCCACTGTTAGTGTTAATTGTCTTAAACAGGTGTCTTAAT---GTTCATGTAAATCAGGCAG
GATACCATTCTCAATAGTGACTTG-------------------TCAAGTTCGTGAACAATCATTTTGTGCTGTATTTGGG
GAGTGGAAACTTTTGTTGAGATTTGTGATGCTGAAACACAAGC-GGGGCATGGATTCTTATGGTATGCAACCAA
>SNPs
--------------------S--------------------------------------------------S--------
-----------------------------------------S---------------------------S----------
-----------------------------------------SS----------------S---S---------------S
S----------S-------------------------------------------S------------------------
----S--S----------------S-----------S-------------------------------------------
------------------------------------------------SS------------------------------
----------------------------S---------------------------------------------------
-----------------------------------------------------------------S--------------
------------------------------------------------------------------------S--S----
-----------------------------------------S---S----------------------------------
-----S--------------------------------------------------------------------------
----------------------------------------------------------S---------------------
-----S--------------------------------------------------------------------------
---------------S----------------------------------------------------------------
-----S---------------------------------------------------------------S----------
S---S---------------------------------------------------------------------------
S-------------------------------------------------------------------------------
---------------------------------------------------S------------------S--------S
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---------------------------------------------------------------S----------------
-------------------------------------------------------S------------------------
----------------------------------------------------S---------------------------
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-----------------------------S--------------------------------------------------
---------------------------------------------------------------------------SS--S
S-S------------------S---------------------------------------S-S------S---------
-------------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--------------------------------------------SS-SSS-------------S-----
-----------------------SSSSSSSSSSSSSSSSSSSS--------------------S----------------
---S--------------------------------------SS-------------------S----------
>forward_762
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----------------------CTGTGTCTGCAAAAGCTGGC--------------------------------------
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>reverse_2334
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-------------GATTCTTCCCCGCACACCTT-----------------------------------------------
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