>input_sequence_63441
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----ATGGCCTCAACCTCACAGCCGCCCACAACGTATGAGTATGACCCCTCACGCCTTCTCTCTCTCTCTGGCTCTGTAG
A-------------------------------------------------------------------------------
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-TCTCTGTGTGAAGATATCTAACTTAATTTGTGTTGGAGTTTTTGGCTAAACCAATTCGGTTTTAGGGTTATCAACTTGA
TTATAC-----------ATGACTAGCCTAATTAATTTGTTGTCGTGGTCGATCGTTTACGGTTTCTCCAAACATATCCAC
AGGGGATATATAT--CT-CCTTCACCAAGCCGGCCGCCGAGCAAAACAAAAGAAGCGTCCCTTTCGTAGGAATCATTCGT
TCATGCATCCTCCCTTGATCTGCTCCAAATCCTTGT--GTGCTCTGAATCTGAT----------------TGTCTCGATC
GAGTTTTTATTTTAGCTAG----TAGCTAGCTAGATTCATGCATGTCCCTGTTTTCTTGGTCAGATTAGTTGCAAGTGCT
CTCGTTCATTCATGT----ACACGATGATCCATGAGAGTTATATTTCTATGTATCGTTGGTTAATTTGCAGAGGGAACGA
AGGAGGTGAGCGAGGTCATCATGGCGACGAGGAGGAGCAGCAGCAG---GGAGCTTGGGCGGAGG---CAGCCGGCGGCC
AGCCGCTGGTGATGCCGGAGGACGGGTACCAGTGGAAGAAGTACGGCCAGAAGTTCATCAAGAACATCCAGAAAATCAGG
TACGTAGACGGAAGTAAACGATGCATGTCGATCTGCCGGCCGGCCAACACCTTGTGGGAAATCCTAGTGCTGATAACGAA
GGGCGCG--CGGC-----GGTGCGGCGCATTG----TGCAGGAGCTACTTCCGGTGCCGCGACAAGCGGTGCGGCGCCAA
GAAGAAGGTGGAGTGGCAGCCGGGCGACCCCAACCTCCGCGTCGTCTACGACGGCGCCCACCAGCACGGCTCCCCGTCGT
CAAA---------CGGCGGTGGTCAGGACGCCGACGGCGCCGCCAACCGGTACGATCTCAGCACCCAGTACTTCGGCGGG
GCCGGCGCCCCCACGCCGCAGACGCAGTGA--------------------------------------------------
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>chr4D_1_TraesCS4D01G014100
CGGCCGACGTCAGGCCGCTGATCAGTACGGGCGTGCGCTAACGGAATTAAA-----GCCGCCGTCACGGCAGTGAATCGA
--TCCTCCATGTGATCCGTGGGTGAATTTGCATGCC-------ATGCATCCACGAGGCCCTATATATTTTATGTGAGCGG
ATCACATCACACAGTGGCACCACCTGCCAATTAAGCATATGGCTAGCTCTAGTTGCACCTTGCCTGGTTCAATGGATGCA
GCATTATCTATGT-TTTCTGGATCAATTCTTCTGGGTAATA-----TTTTTGGACTCCTTGCAAGCGAAGTAGACCCGTT
GATAGCGAGGCCACATCAAGATTTTTCATGTGCTGCAAGCCTGCAACTAAAAAAATCG--GTTTACTGCGTGCGTGCGCG
TGTGTAT----GTACTTTGTGCTCACTGCTTATAAAATGATCCTTTTCTATT-TTTTAGAAAAATTATTGAAAATTAAAC
TTGATCAGATGGCTGTGGATTTCGAATCGGCAATAACAAATTTTTT--TTGACATAGATTGATTTCACTAAGCTATATAT
TTTTGTCCGCGGGAATCACTAAGCTATATAGAATCACTAGTAGCGCACTTGAAACTAGGGCCCGAGATGTAAATTTGGTA
ATACTCATAGTAGTACGTGCACAACATCACGCTAGCTAATTTTGCTGAATCAGCTGGGTAGCTAGGGTAGGACAGAGCGT
GTGACCCAAAGTTTTCTTGGTCTCAGACGACGTTAACACGCGCGCGTTGCATCGTTGAAGCTTCCATTTGAACAAAAAAT
AACCTCGATTGATACCCCAAAGCT----TCTCATCCACTAGTAGCTAGTACTCCGATCCCTCGACACACACCCCCCACCC
CCACCCCACCCCTCTCTCTTGTGTATATATATACACTCTCTTCTGCAACTAGCCGAAGCTCACAGC-----------CCC
CCATCCGTTCATGTAGCTACTAGTAGTTAGCAACAGCGTGAGCATGGAAGCACTCCGGTGACCCGCTCCTCGTCGGTTTC
CGCCATGGCCTCAACCTCACAGCCGCCCACAACGTATGAGTATGACCCCTCACGCCTTCTCTCTCTCTCTGGCTCTGTAG
A-------------------------------------------------------------------------------
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-TCTCTGTGTGAAGATATCTAACTTAATTTGTGTTGGAGTTTTTGGCTAAACCAATTCGGTTTTAGGGTTATCAACTTGA
TTATAC-----------ATGACTAGCCTAATTAATTTGTTGTCGTGGTCGATCGTTTACGGTTTCTCCAAACATATCCAC
AGGGGATATATAT--CT-CCTTCACCAAGCCGGCCGCCGAGCAAAACAAAAGAAGCGTCCCTTTCGTAGGAATCATTCGT
TCATGCATCCTCCCTTGATCTGCTCCAAATCCTTGT--GTGCTCTGAATCTGAT----------------TGTCTCGATC
GAGTTTTTATTTTAGCTAG----TAGCTAGCTAGATTCATGCATGTCCCTGTTTTCTTGGTCAGATTAGTTGCAAGTGCT
CTCGTTCATTCATGT----ACACGATGATCCATGAGAGTTATATTTCTATGTATCGTTGGTTAATTTGCAGAGGGAACGA
AGGAGGTGAGCGAGGTCATCATGGCGACGAGGAGGAGCAGCAGCAG---GGAGCTTGGGCGGAGG---CAGCCGGCGGCC
AGCCGCTGGTGATGCCGGAGGACGGGTACCAGTGGAAGAAGTACGGCCAGAAGTTCATCAAGAACATCCAGAAAATCAGG
TACGTAGACGGAAGTAAACGATGCATGTCGATCTGCCGGCCGGCCAACACCTTGTGGGAAATCCTAGTGCTGATAACGAA
GGGCGCG--CGGC-----GGTGCGGCGCATTG----TGCAGGAGCTACTTCCGGTGCCGCGACAAGCGGTGCGGCGCCAA
GAAGAAGGTGGAGTGGCAGCCGGGCGACCCCAACCTCCGCGTCGTCTACGACGGCGCCCACCAGCACGGCTCCCCGTCGT
CAAA---------CGGCGGTGGTCAGGACGCCGACGGCGCCGCCAACCGGTACGATCTCAGCACCCAGTACTTCGGCGGG
GCCGGCGCCCCCACGCCGCAGACGCAGTGACCGGACCACCGGCGACGCACGGACGACGGGCGCCTTGCCTTGCCTTGCCG
GCCGACTGACT------------------------------------GGTGCCGCCGGCCGATGGCGCCATCAGGTGGAC
GCATGCATGGTAGCCGTTGAACGGCCGGCGGTGGCGGTGCCGGGGCGCCGCCGGTGCAGCGCTGTCGACGGTGTAGGTGG
CAGATTATCTGTGGTCAACGTGATTACAACACGTGCACTAGCTGGCTGGTTGAGCGGTCGCACTGCTACGACTAGTAGTA
TACTTGCACTGTAGTAGCTCCGTTTGTTTCCT------------------------------------------------
-----------------------------------------------------------GTATGTATGTA--------CG
ATTAGTTCAACTCCGGTACCTGAGGCCGCGAGTGCATCAGCATTCATTAGCAGTAACACCTGAGGCTGTCACGCCAAATG
TA-----GTGCAAGTGGATCGGATCGCTGAGTTGACTCTTCAAA-GCCTTCTTGCTATGCTTGCTTGCCCTCATCCTCAT
GGCGCCACAACACGGCCGACTATTAAAACCCAACACAAGGCTTTTTCTTCCGAAAAGAATAGGATCTCTACCATTATAAA
TTCATCGAAAAGTACAAAGCACGATAAAAATTACATCTAGGTGTCCAGACTAACGAACAACCACTGCGGCCGTCAGAATG
AGCCGCTGACTTGTCGCTATCCCCGCTCTCATACTGGGACCGGCTTGACCTTGTGCACGTGCCCGTAAGGATTAGCATCC
CGGAGCCGTAGTCGTTGTTGTTGGACCCTTGAATCGATCTGAAGAACCTGACACCAAATCTTGCCATCGCATACGCACGA
CGAAAAACTCTAACCTCGCCGCCTTGAGGAGCTGGCAGGAATCTACGCCGGAGCACCGTATAATCGGACCCGACGGATGA
ACTTGAGGAGGATCGGAGTGCAAAAGACTACTCAAAAAAGCGTCACCATCCATCCAAGCACTACCCCAGGGAGAACTAAA
ACCAAAACCTATCTACTAGCCGAAGCCGAGGCACCAAGACTCCCCTCCCCTCCACCGACCGTTGAAG
>chr4B_1
CGGCCGACGTCAGGCCGCTGATGAGTAGGGGCGTGCGCTAACGGAACTAAA-----GCCGCCGTCACGGCAGTGAATCAA
--TCCTCCATGTGATCCGTGGGTGAATTTGCATGCCGATTGCCATGCATCCACGAGTCCCTACATATTTTATGTGAGCGG
ATCACATCACGCAGTGTCATCACTTGCCAATTTCTTTT---------TAGTTG----CCATGCCTGGTTCAATGGATGCA
GCATTATCTATGTGTTTCTGGATCAATTCTTATGGGTAAATTATTTTTTTTGAACTCCTTGCAAGCGAAGTAGACCCGTT
GATAGCGAGGCCACATCAAGATTTTTCAAGTGCTGCAAGCCTGCAACCAATTTTTTTTTTGTTGACTGCGTGCGTGCGCG
TGTGTAT----GTACTTTGTGTTCACTGCTTATGAAGTGATTCTTTTCTATT-TTTTAG-AAAATTATTGAAAATTAAAC
TTGATCAGAC-GCTGGCGATTTCGAATAGGCAATAACAAAAAAAAAACTTGACCTTGATTGATTTCACTAAGCTGTATAT
AATCACTAG---------------------------CTAGTAGCGCACTTGAA---------------------------
----------TAGTACGTGCACAGCATCACGCTAGCTAATTGTGCTGAATCAGCTGGGTAGCTAGGGTAGGGCACAGCGT
T--ACCAAAAGTTTTCTTCGTCTC-GACGACGTTAACACGCGGACGTTGCATCGTTGAAGCTTCCATTTGAACAAAAAAT
AACCTTGATTGATACCCAAGAGCT----TCTCTTCCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NN------------------------------------------------------------------------------
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----------------------------------------------CTAAACAATTTTGGTTTTACGATTAGCAACTTAA
TTAGCATATGCATACATATGACTAACCTGATTAATCTGTTGTCGTGGTCGATCGTTTACGGTTTCTCCAAACATATCCAC
ATGAGATATATACTACT-CATTCACCAAGCCGGCCGCCGAGCAAAACAAAAGAAGCGTCCCTTTCGTAGGAATCATTCGT
TCATCCT-----------------CCAAATCCTTGTGCGTGCTCTGAATCTGAT----------------TGTCTCGATC
GAGTTTTTTTTTTCAGCTAG-------TAGCTAGATCCATGCATGCCCCTGTTTTCTTAGTCAGATTAAGTGCAAGTG--
CTCGTTCATTTATGT----ATCCAT----------GAGTTGTATTTCTATGTATTGG-------TTTGCAGAGGGAGCGG
AGGAGGTGAGAGGGGTCATCATGGCGACGAGGAGGAGCAGCAGCAGCAGGCAGCTTGGGCGGAGG---CAGCCGGCGTTC
AGCCGCTGGTGATGCCGGAGGACGGGTACCAGTGGAAGAAGTACGGCCAGAAGTTCATCAAGAACATCCAGAAAATCAGG
TGCGTAGACGGAAGTAAACGATGCATGTCGATCTGCCGGCCGGCCAACACCTTGGT-----------------TAACGAA
GGGCGCCGCCGGC-----GGCGCGGCGCATTGTGCGTGCAGGAGCTACTTCCGGTGCCGCGACAGGCGGTGCGGCGCCAA
GAAGAAGGTGGAGTGGCAGCCGGGCGACCCCAGCGTCCGCGTCGTCTACGACGGCGCGCACCTGCACGGCTCCCCGTCGT
CATCCAACGGCGGCGGCGGCGGCCAGGACGGCG------CCGCCAACCGGTACGATCTCAGCACCCAGTACTTCGGCGGC
GCG---GCTCCCACGCCGCAGACGCGGTGACCAGACGACGC---------------------------------------
-------GACG------------------------------------GGCGCCGCCGGCCGGTGGCGCCATCAGGAGGAC
GTG----TGGTAGCTGTTGAATGGCCGGCGGTGGCGGTGCCGGGGCGCCGCCGGTGCAGCGTTGTCGACGGTGTAGGTGG
CAGATTATCTGCGGTCAACGTGATTACAACAGGTGCACTAGCTAGCTGGTTGAGCGGTCGCACTGCTACGACTAGTAGTA
CTCCTACGTAC--GTAGCTCCGTTTGTTTCCT------------------------------------------------
-----------------------------------------------------------GTATGTATGTATGTATGTACG
ATTAGTTCAACTCTGGTACCTGAGGCCGCGAGTGCACCAGCATTAACTAGCAGTAACACCTGAGGCTGTCACGCTAAATG
CCAAAATGTACAAGTGGATCGGGTCGCTGGGTTGACTCTTCAAAAGCCTTCTTGC-------------------------
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>chr4A_1
CGGCCGACGTCAGGCCGCTGATGAGTACGGGCGTGCGCTAACGGGAAGCCCACACGGCCGCCTTCACGGCAACACTGTCA
CGTCCTCCGTGTGATCCATGGGTGAATTTGCATGCC-------ATGCATCCATGAGTC----TATATTTTATGTGAGAGG
ATCACATCACGCAGTGGCACCACTTGCCGATTAA-CATATGGCTAGCTAGTTG----CCTTGCCTGGTTCAATGGATGCA
GCATTATCTATGT-TTCCTGGATCAATTCTTCTGGGTAATA-----TTTCTGGGCTCCTTGCAGGCGAAGTAGACCCGTT
GATAGCGAGGCCACATCAAGATTTTTCATGTGCTGCAA--------CTACAAAATTCG--GTTGACTGCGTGCGTGCGCG
CGTGTACGTACGTACTTTGTGTTCCGTGTTTATAAAATGATATTTTTAATTTCTTTTAG-AGAACTATTGAAAAAGAAAC
TTGATCCGACGGCTGGGGATTTCGAATCGGCAATAAC--AAAAAAAACTTGACTTGGATTGATTTCACTAAGCTATATAT
AATCACTAG---------------------------CTAGTAGCGCACTTGAAACTAGGGCCCGA--TGTAAATTTGGTT
AATAGTGCTG--GTACGTGCACAGCATCACGCTAGCTAATTTTGCTGAATCAGCTGGGTAGCTAGGGTAGGACA----GT
GTGACCCAAAGTTTTCCTGGTCTCAGACGACGTTAACACGCGCGCGTTGCATCGTTGAAGCTTCCATTTGAACAAAA--T
AACCTCGATTGATACCCCCGAGAGCTTCTCTCATCCACTAGC----AGTACTCCGATCTCTCGACCCCCACCCCTCTCTC
--------------------GTGTATATATATACACTCTCTTCTGCAACTAGCCGAAGCTCACTGCAGCATCAATGTCCC
CCACCCGTTCATGTATCTA------GTTAGCAACAGCGTAAGTATGGAAGCACTCCGGTGACCCGCTAGCCNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTCTCTCGAT
CTCTATGTGTGAAGATATTCATTTTAATTTGTGTTGGA-TTTTTGGCTAAACCATTTTGGTTTTACGGTTAGCAACTTAA
TTAGCATATGCATACATATGACTGGCCTAATTAATCTGTTGTCGTGGTCGATCGTTTACGGTTTCTCCAAACATATCCAC
ATGGGATATATACTACTCCATTCACCAAGCCGGCCGCCGAGCAAAACAAAG---GCATCCCTTTCATAGGAATCATTCGT
TCATCCTT----CCTTGATCTGCTCCAAATCCTTGT--GTGCTCTGAATCTGATCTGGTTCGCCGAATGTTGTCTCGGTC
GAGTTTTCATTTTAGCTGGTTGCTAGCTAGCTAGATTCATGCATGCCCCTATTTTCTTAGTCGAATTA-----AAGTG--
CTCGTTCATCATTTATGTGATCGAT----------GAGTTATATTTGTATGTATTGG-------TTTGCAGAGGGAGCGG
AGAAGGTGAGCGCGGTCATCATGGCGACGAGGAGGAGCAGCAGCAG---GCAGCTTGGGCGGAGGAGGCAGCCGGCGTTC
AACCGCTGGTGATGCCGGAGGACGGGTACCAGTGGAAGAAGTACGGCCAGAAGTTCATCAAGAACATCCAGAAAATCAGG
TGCGCA----------------------------------CGGCCAACACCTCGTGAAAACCTTACTCCTAATCTGATTT
TAATGGATTGACGACGAAGGCACGGCGCATTGTGCATGCAGGAGCTACTTCCGGTGCCGCGACAAGCGGTGCGGCGCCAA
GAAGAAGGTGGAGTGGCAGCCGGGCGACCCCAGCCTTCGCATCGTCTACGACGGCGCGCACCAGCACGGCTCCCCAGCCT
CAAA---------CGGCGGTGGTCAGGACGGCGACGGCGCCGCCAACCGGTACGATCTCAGCACCCAGTACTTCGGCGGG
GCCGGCGCCCCCACGCCGCAGACGCGGTGACCAGACCACGC---------------------------------------
-------GACGCGACGGCCGCCTTGCCTTGCCGGCCGACTGACGACAGGTGCCGCCGGCCGGTGGCGCCATCAGGTGGAC
GCATGCATGGTAGCTGTTGAACGGCCGGCGGTGGCGATGCCGGTTCGCCGCCGGCGCAGCGCTGTCGACGGTTTAGGTGG
CAGATTATCTGTGGTCAACGTGATTACAAC--GTGCACTAGCTGGCTAGTTCAGCGGTCGCACTGCTACGACTAGTAGTA
CCT----------GTAGCTCCGTTTGTTCCCGATGTACTCCCTCCGTTCGGAATTACTTGTCTCGGAAATAGATGTATCT
ACAACTAAAATACGTCTAGATACATCCATTTCTGCGACAAGTAATTCCGAACGGAGGGAGTATGTATGTA--------CG
ATTAGTTCAACTCCGGTACCTGAGGCCGCGAGTGCATCAGCATTAATTAGCAGTAACACCTGAGGCTGTCACGCTAAATG
CCTAAATGTACAAGTGGATCGGATCGCTGAGTTGACTCTTCAAA-GCCTTCTTGCTTTGCTTGCTTGCCCTCATCCTCAT
GGCGCCACACCACAGCCCACTACTAAAA----------------------------------------------------
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>SNPs
----------------------S-----------------------S-------------------------------S-
--------------------------------------------------------S-----------------------
----------S------------S----------S-------------SSSSSSSSS-----------------------
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------------------------------------------------------S--------S----------------
---------------------S-------------------S-----------------S--------------------
---------S-----S------------------------SSSSSS-------S-S------------------------
SS-SSSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSS-----------------------------SS------------S
-SSSSSSSS--------------S--------------------------------------------------S-----
--------------------------------------------------------------------------------
-------------------S---------------------SSSSS------------S------S-S------S-S-S-
SSSSSSSSSSSSSSSSSSSS-------------------------------------------S----------------
---S-----------S---SSSSSS--------------S--S------------------------SSS-SSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
S-------------------------------------------------------------------------------
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----S-------------SS-SS---------------S---------------S--S-------S-----S------S-
---SSS-----------------------------S--------------------------------------------
-S----------S------S------------------------------------------------------------
----S-S-SSSS--------------------------------------------------------------------
-----------------S---------------------------S------------S---------SS--------SS
----------S---------SS-SSSSSSSSSSSS-------------------S-SSSSSSSS------------S--S
------------S-------------------------------------S--------------------------SS-
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-S------------------------------------------------------SS--SSSSSSSSSSSSS-------
------S-------------S-----------------------------------------------------------
--------------------------------S------------------------S----------------------
------------------------------S-------------------------------------------------
-------------------------S------S------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSS---S--------------------------------------------------S------------------
--------------S-----------------------------------------------------------------
-------------------------------S------------------------------------------------
SS-S-S-SSSSSS-------------------------------------------------------------------
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--------------------------------------------S-----------------------------S-----
SS-------S----------------------------------------------S-----------------------
---------S---S---S----S-----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_583
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---TGTCCGCGGGAATCACTAAG---------------------------------------------------------
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>reverse_2962
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-AGTGCAAGTGGATCGGATCG-----------------------------------------------------------
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