>input_sequence_81566
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----------ACACACAAGCATCTA-CACACGATCTGATTATTATCTTGCTTAGAGAGGAAGGTAGC-----TAGC----
CTGCATCTTTCAGCTGCGCCTGGTCAAACATGGCTTCCATGGGGTTCAGCTATGCGCAGATACATGTGCGGCAGGAGAAG
GTCAGGCAGAGGATCAACCAACAAGAAGCCGCCAACAAGACGGCCGTG------------AAGAACAAGAACATCGGTGA
AGAAGACAAGATCAACAAGAAAAACTGTGATTCGTGGACCACCGCCGGCAGGGTGCATCCGTGCGCATCTTCCACGGCAG
CGGCGGCGGCTACGGCTAGGCCAGTGCCAGAGAGGTGAGGCTGGCTGGCGATGCGTCTTCTCTTCTCTG-----------
------------------------------------AGTAGTTTTAGCTTGTCTCAAGATTTCCTCAAGGAAATAAA---
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>chr1D_1_TraesCS1D01G066200
GACAAAATAATGTCTCATGAAAAACCTTTTTTAACTTTCGGGGTTTTAAGATCAAAT---CAAATACACAAGAACATTGA
GGTGTATACTACATATCTATAAAGTTTCAAGATCAAATACGCTTTGGTGTGATCCGTATAAAAAGGCAAAATCATAGACT
------------------TGTGTTAGAGTGACATTATTTTATTTTGTGTGTGACCAAGAATAGAAAAA----TCATAATG
AAAATTTATGGAGATGTTGTATACATCCCTAGGTTCATTTGTATCTTCTTTCAGGAAATTTGGAACTTCAAAAATAAGTT
TTCCGCC-TTTTAAAAAATAAGGGCTCTGATCAAAAAAATAAG----CGCCCACCGTGGGGCTCGAACCCACGACCACAA
GGTTAAGAGCCTTGCGCTCTACCAACTGAGCTAGACGGGCTTTGTGTCAGTAGCTTCATTCGCATGTATATATCAGGTAT
ATCAAGCAAAAAGTCTGAGCTA----------------AAGGTTTGCTCAATTATCAGCGTGCAAGCAAGTAATTAGTTT
TTTTTTAAGCTGGAAACGTCCTTCCATTACTTAACCTCGCTCA----TCATCAGAATCACCAAAGCATACATGGAGTCAG
GGACT----TGTTCCTTTCCACCAGGATATCATGAGTTGGATGGAATCATCCATTCATGCATTATTATACTACTCCGTAG
ACAAATATAGACGCC-------TCAGTGGAAAGTCGCAAAGGCAACATCGAAACTTGTCGCATGGAGGCACAAACGGCGA
AAGGTAGGCGGCCGG-----CAGCCCACCAGGAACACAAAACCGTTTGCTTGTGCCCACAGGTAGTGC---CAATAATTC
CACAACCGT-------------------CTGCGATTGCAAA---------------------CGCTGTTTATGATTGCTT
CCGAATCC-TCTCC--CTGGTGACACCTACCGCCTACCACCACCAGATG-------------AGGAGATAAGTCCACACC
GGATATCATCAAGAAACTCGGTGCCCCG-CCCCCAATAATTGCAGCCCGAGCATATAAATACAC----CCGGCTGTATCC
ATATGTATGCACACACAAGCATCTA-CACACGATCTGATTATTATCTTGCTTAGAGAGGAAGGTAGC-----TAGC----
CTGCATCTTTCAGCTGCGCCTGGTCAAACATGGCTTCCATGGGGTTCAGCTATGCGCAGATACATGTGCGGCAGGAGAAG
GTCAGGCAGAGGATCAACCAACAAGAAGCCGCCAACAAGACGGCCGTG------------AAGAACAAGAACATCGGTGA
AGAAGACAAGATCAACAAGAAAAACTGTGATTCGTGGACCACCGCCGGCAGGGTGCATCCGTGCGCATCTTCCACGGCAG
CGGCGGCGGCTACGGCTAGGCCAGTGCCAGAGAGGTGAGGCTGGCTGGCGATGCGTCTTCTCTTCTCTG-----------
------------------------------------AGTAGTTTTAGCTTGTCTCAAGATTTCCTCAAGGAAATAAAGAT
GTGTGCTCATATATGTGTTTTTTCCACAAACTTGGGGATATCAATCAACGCCAAACAATCAAATATGC--TCCAGCCACA
--------------------------------------------------------------------------------
---------------------------GAT-----------------------CTAAAATTGTTTCTGACAGGCCTGCCT
GTCGACTAACAAAGAGACTCACTAGAAGATGCAGGAACAGAGTA------TTTTTTACATGGCCATAGAGC---------
-----CATGGTATTGGTACTCTCCTATCTTGAGACTGGAATCTTAATATTGCCAAGAACCTAGCTACTGACTAAAAGTGC
TTGATCCTGAACTTCCACTCCCCCTTCACGGCATCAAACGCCACGAATTCAGCGCCATTCTTCTCGGTCCATTGCGCCAG
AATCTCCTTATACCTGTCGACTTCTGCCCCCTCCGTCAACTGCAACCCGGTCTTCTTATCGACGCACTTCACATTCAGGA
GTGTGATCTCTGCAGGCTTGTTGAGCTCCTGCCCCACAGGAGGTCTCTTGCTCTCATCTGTGTAGACCAGGATCTCGCGG
TCCTTGAACTCCACTATGGAAGCGATGTCAAGCTTCCTCACATCGGTTTCTCCATCAAACTTGATGCTGCCGTAGCCATG
CCTGCCGACCGTGAA-GTCCTTCACATGTGAGCAACAACCTGGCTCATTGCTTTCTCGTGCAGCAAGCTCTGCGATCGAC
GGCAAGGTGTAATAGTCTGCCTTATAGAGCCGAGGTAGCACACTCTCACTCACAGGGGCACCACCAAATGGAGTTATCAC
AGGATCAAATGGATT---------------ACTCCTAGCCAGGACAGCACCGTTGATATACCCTTTCTGTTCCCCACCGG
ATCCTGATGATGGTGAACAAGATGTCAGTAACTCAAT-GCATATATCGTATGGCAACACACAAAGCATGAAGT-AGCTTC
GGTTCTGAGATATCAAATATTTTGACATTTGGGTTCCACAAGTGCTAATGGAGAACTTGGGTTTGCTACTAGGATTCTTC
A--------TTGCAACGTGCC-----------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------------------AGTGAAGAATTGCTTGAATAAAGTATCGCTAGAA------------------------
-------------------
>chr1A_31
CAAAT------------------------------------------------------------ACACAAGAACATTGA
GGTGTATAGTACATATCTATAAAGTTTCAAGATCAAATAAGCTTTGGTGTGATCCGTATAAAAAG-CAAAATCATGGACT
TTTATAGTGAATAGTACATGTGTTAGAGTATCATTAATTTATTTTGTGTGTGTACCTTAACCAAAACATATTTCATAATG
AAAATTTATGTAGATGTTATATACATCCCTAGGCTCATTTGTATTTTCTTTCAGAAAATTTGGAACTTCAAAATATA-TT
TTCTGCC-TTTTAAAAAATATGGGCTTTGATGCAATGCT-----------------------------------------
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-------------------------------------------C-----------------------------------T
TTTTGTAA------------------------------------------------------------------------
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-------------------------------------------------------ATCTGTGTATATTTTGTTCAT----
---------------------------TCAATCATCTTTGAGGTATTTTCTTGATGAAAATT-ACATGCTTCCAAGCATG
TTCAAGAAAAAAAAAACA--------------------------------------------------------------
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-------------------------------------------------------------------------ATTCTTC
A--------TTGGACCAAACTCTTACGTATGAAGTAATTTGGCTTTGTAACATAACATTAATTTTCGGGAGTTTTATCCA
ATATGCAATACACAAGAACATTGAGGTGTATAGTACATATCTATGAAGTTTCAAGATCAAATACGCTTTGGTGTGATCCG
TATAAAAAGCAAAATCATGGACTTTTATAGTGAATAGTACATGTGTTAGAGTGATATTATTATTTTTGTGTGTGTGTACC
TTGAACCAAAACATATTTTCATAATGAAAATTTACGGAGATGTTGTATACGTCCCTAGGTTCATTTGTATTCTCTTTCAG
AGAATTTGGAACTTGAAAA
>chr1B_31
------------------------------TTAACTTTCAGAGTTTTAAGGTCAAATACGCAAATACACAAGAACATTGA
GGTGTATAGTACATATCTATAAAGTTTCAAGATCAAATACGCA-------------------------------------
---------AATAGTACATGTGTTAGAGTGACATTATTTTATTTTGTGTGTGTG--------------------------
---------------------TACATATCTAGGCTCGTTTGTATTTTCTTTCAAGGAAAAAGT-----------------
--------------------------------------------AATCGCCCACCGTGGGGCTCGAACCCACGACCACAA
GGTTAAGAGCCTTGCACTCTACCAACTGAGCTAGACGGGCTTTGTGTCACTTGCTTCATTCACGGCTATATATGTGATAC
ACCAAACAAAAGCCTTCCTCTGCCTACCTACCGAGCTCAAGGTTTGCTCAATTATCAGCGTGCAAGCGAGTGATTAGTTT
C-TTTTAACCTGGAAATATCCTTCCATTACTTAACCTCGCC-------CAGCAGAATCACCAAAGCATACATGGAGTCAG
GGACTCAGTTGTTCCTTTCCACCAGGATATCATTAGTCGGATGGAATCATCCATTCATGCATTATTATACTACTCCATAG
ACAAATATAGACGC-------GTCAGTGGGAAGTCGCAAAGGCAACATCGAAACTTGTCGCGTAGAGGCACAAGCGGCGA
AAGTTGGGCAGCCGG-----CAGCCCACCAGGAACACAAAACCGTTTGCTTGTGCCCACAGGTAGTGCTGCTAATAATTC
CGCAACCGTTTCCCGCAGCCAGCAGCGCCTGCGACTGCAACCCTGCAAGCAGAAAAGGCAGCCGCTGTTTGTGATTGCTT
CCGAATTCCTCTCCCTCTGGCGACACCTACCGCCTACCACCACCAGAGG-------------AG---ATAAGTCCACACC
GGATATCATCAAGAAACTCGGTGCCCCGCCCCCCAATAATTGCAGCCCGCGCATATAAATACAC----CC----GTATCC
ATATGTATGCACACACAAGCATCTA-CACACGATCCGATTAT-ATCTTGCTTTAAGAGGAAGGTAGCTGGAGTAGC----
CTGCATCTTTCAGCTGCGCCTGGTCAAACATGGCTTCCATGGGGTTCAGCTATGCGCAGATACATGTGCGGCAGGAGAAG
ATCCGGCAGAGGATCAACCAACAAGAAGCCGCCAAGAAGACGACCGTG------------AAGAGT------ATCGGTGA
AGGAGATAAGATCAAGAAGAAAAACTGCGACTCATGGACCGCCGCCGGCAGGGTGCATCCGTGCGCGTCTTCCACGGCCG
CGGCGGCGGCTACGGCTAGGCCGGTGCCAGAGAGGTGAGGCTGGCTGGCTGTGCGTCTTCTCTTCTCTGTAGGCCACAAG
AGGCTTGATTTGAGAGTTTAGTTTGTGTCTCTGATGAGTAGTTTTAGCTTGTCTCAAGATTTCCTCGAGGAAATAAAGAT
GTGTGCTCATATGTC--------CCACAAGCTTGTGGATATCAT------ACGAACAATCAAATATATAGTCCAGCCACA
CATTTAAAACTGTTTTTCTTTTGACGAAAAAGCAGCAGATTGCTGATTTTCATTGATAAAGTGGTAGAAGTAAACAGTTA
CAGGCCACTGAAAGGAAAAGAAAAAGTGAT-----------------------CTAAAATTGTTTCTGACAGGCCTGCCT
GTCGACTAACAAAGAGACTCACTAGAAGATGCAGGAACAGAGTTTTTTTTTTTTTTACATAGCCACAGAGC---------
-----CATGGTATTGGTTGC------------GACTGGAATCTTAATATTGCCAAGAACCTAGCTACTGACTAAAAGTGC
TTGATCCTGAACTTCCACTCCCCATTCACGGCATCAAACGCCACGAATTCAGCGCCATTCTTCTTGGTCCATTGCGCCAG
AATCTCCGTATACCTGTCAACTTCTGCCCCCTCCGTCAACTGCAACCCGGTCTTCTTATCGACGCACTTCACATTCAGGA
GTGTGATCTCTGCAGGCTTGTTGAGCTCCTGCCCCACAGGAGGTCTCTTGCTCTCATCTGTGTAGACCAGGATCTCGCGG
TCCTTGAACTCCACGATGGAAGCGATGTCGAGCTTCCTCACATCGGTTTCTCCATCAAACTTGATGCTGCCGTAGCCATG
CCTGCCGACCGTTAA-GTCCTTCACATGTGAGCAACAACCTGGCTCGTTGCTTTCTCGTGCAGCAAGCTCTGCGATCGAC
GGCGAAGTGTAATAGTCTGCCTTATAGAGCCGAGGTAGGACACTCTCACTCACAGAGGCGCCACCAAATGGAGTTATCAC
AGGATCAAATGGATT---------------A---------------GCACCGTTGATATACCCTTTCTGTTCCCCAGCGG
ATTCTGATGATGGTGAACAAGATGTCAGTAACTCAATTGCATATATCATATGGCAACACAAATAGGATGAAGT-AGCTTC
GGTTCTGAGATATCAAATATTTTGACATTTGGGCTCCACAAGTGCTAATGGAGAACTTTGGTTTGCTCCTAGGATTCTTC
ATTGTAAATTTGTAACGTGCC-----------------------------------------------------------
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----------------------AGTGAAGAATTGCTTG------------------------------------------
-------------------
>chr1A_251
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-----------------------------------CATTTGTATTCTCTTTCAGAGAATTTGGAACTTCAAAATACA--T
TTCTGCCTTTTCCAAAAACATGGGCTCTGATAAAAAAAAAAGCAAATCGCCCACCGTGGGGCTCGAACCCACGACCACAA
GGTTAAGAGCCTTGCGCTCTACCAACTGAGCTAGACGGGCTTTGTGCCACTTGCTTCATTCGTCTGTATATATCCAAAAT
AG--AACAAAAGCCCTCCTCCACCTACTCAGCAGAATGATTACC-----------------------------------T
TTTTTTAAGCTGGAAATATCTTTCCATTCCTTGACCTCGCTCAGCGCTCAGCAGAATCACCAAAGCATACATGGAGTCAG
GGACTC----GTTCCTTTCCATCAGGATATCATTAGCTCGACGGAAT----CATTCATGCATTATTATGC-------TAG
ACACATATAGACGCCTCAGTGGTCAGTGGGAAGTCGCAAAGGCAACATCGAAACTTGTCGCGCAGAGGCACAAACGGCGA
AAGGTGGGCAGCCTTGCCGCCAGCCCACCAGGAACACAAAACCGTATGCTTGTGCCCACAGGTAG---TGCCAATAATTC
CACAACCGTTTCCCGCAGCCAGCAGCGTCTGCGATTGCAACCCTATGA----AAAAGGCAGGCGCTGTTTGTGATTGCTT
CCGAATCA-TCTCCCTCTGGTGACACCTACCGCCTACCACCACCAGAGGAGATACTCCTAACAG---ATAAGTCCACACC
GGATATCATCAAGAAACTCGGTGCCCCG-CCCCCAATAATTGCAGCCCTCGCATATAAATACGCCCGGCC----GTATCC
ATATGTATGCACACACACAGACATCTCACACGATCCAATTAT-ATCCTGCTTAAAGAGGAAGGTAGC-----TAGCTAGG
CTGCATCTTTCAGCTGCGCCTGGTCAAACATGGCTTCCATGGGGTTTAGCTATGCGCAGGTACATGTGCGGCAGGAGAAG
GTCCGGCAGAGGATCAGCCAACAAGGAGCCGCCAACAACTCGACCGTGAAGAACAAGAACAAGAGT------ATCGGTGA
AGAAGACAAGATCAGCAAGAAAAACTGCGACTCATGGGCCGCCGCCGGCAGGGTGCATCCGTGCGCATCTTCCACGGCGG
CGGCGGCGGCTG------GGCCGGTGCCGGAGAGGTGAGGCTGGCTGGCGATGAGTTTTCTCTTC-----AGGCCACAAG
AGGCTTGATTCGAGAGTTTAGTTTGTGTTTGTGAC---TAGTCTTAGCTTCTCTCAATATTTCCTCAAGGGAATAAAGAT
GTATGCTAGTATGTTTGCTTGTCTCAA----TAGTGCCAATATTTCAACGACCAACAATCAAATATAC--TTCAGCCACA
--------------------------------------------------------------------------------
---------------------------GTTATCTGATAGCTCGAAATCCCCACCTAAAATTGTTTCTGACAGGCCTGCCT
GTCGACTAACAAAGAGACTCACTAGAAGATGCAGGACAGAGTA--------TTTTTACATAGCCAGAGCCATGGTATCAC
CCTGTC----------TTCC------------AACTGGAATCTTACTACTGCGAAGAACCTAGCTACTGACTAAAAGTGC
TTGATCCTGAACTTCCACTCCCCCTTCACGGCATCAAACGCCACGAATTCAGCGCCATTCTTCTCGGTCCATTGCGCCAG
AATCTCCTTATACCTGTCGACTTCTGGACCTTCCGTCAACTGCAACCCGGTCTTCTTATCGACGCATTTCACATTCAGGA
GGGTGATCTCTGCAGGCTTGTTGAGCTCCTGCCCCACAGGAGGTCTCTTGCTCTCATCTGTGTAGACCAGGATCTCGCGG
TCCTTGAACTCTACGATGGAAGCGATGTCGAGCTTCCTCACATCAGTTTCTCCATCAAACTTGATGCTGCCATAGCCATG
CCTGCCGACCGTGAA-GTCCTTCACATGTGAGCAACAACCTGGCTCGTTGCTTTCTCGTGCAGCAAGCTCTGCGATAGAC
GGCGAGGTGTAATAGTCTGCCTTATAGAGCCGAGGAAGCACACTTTCACTCACAGGGGCACCACCAAATGGAGTTATCAC
AGGATCAAATGGATTACTCCTAGCCAGGACA---------------GCACCGTTGATATACCCTTTCTGTTCCCCAGCGG
ATCCTGATGATGGTGAACAAGATGTCAGTAACTCAAT-GCATATATCGTATGGCAACACACAAAGCATGAAGT-AGCTTT
GGTTCTGAGATATCAAATATTTTGACATTTGGGCTCCACAAGTGCTAATGGAGAACTTGGGTTTGCTCCTAGGATTCTTC
C--------TTGTAACGTGCC-----------------------------------------------------------
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----------------------AGTGAAGAATTTCTTGAATAAAGTATTGCTAGAA------------------------
-------------------
>chr5A_1301
CGGCTAC-------------------------------------------------------------------------
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------------------GGCCAGTGCCAGAGAGGTGAGGCTGGCTGGCGATGCATCTTATCTCTGAG------------
-------------------------------------------TTAGCTTGTCTCAA------CTCAAGGAAATAAAGAT
GTGTGCTCAGATGTGTC---TTTCCACAAACTTGTGGATATCATTCAACGACGAACAAAATTGTTGTTT-----------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------CTGACT
GTCGACTAACAAAGA-------TAGAAGATGCAGGAACAGAGTA------TTTTTTACAGAGCCATAGAGC---------
-----C----------TTGC------------AACTGGAATCTTAATATT-----GAACCTAACTACCGATTAAAAGTGC
TTGATCCTGAAC--------------------------------------------------------------------
-----------------------------CCTCCGTCAAATGCAACCCGGTCTTCTTATCGACGCACTTCACATTCAGGA
GTGTGATCTCTGCAGGCTTGTTGAGCTCCTGCACCACAGGTGGTCTCTTGCTCCCATCTGTGTAGACAAGGATCTCACGG
TGCTT-AACTCCATGATGGATGCGATGTCGAGCTTCCTCACATCGGTTTCTCCATCAAACTT-ACGCTGCCGTAGCCATG
CCTGCCGACCCTGAAAGTCCTTCACATGTGAGCAATAATCTGGCTCGTTGCTTTCTCCTGCAGCAAGCTCTGC-------
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>chr5D_1535
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-------------------------AAGATGCAGGAACAGAGTA------TTTTTTACATAGCCATAGAGC---------
-----CTTG----------------------------------------------------------CGACTAAAAGTGC
TTGACCCTGAAC--------------------------------------------------------------------
-----------------------------CCTCCGTCAACTGCAACCCGGTCTTCTTATCGACGCACTTCACATTCAGGA
GTGTGATCTCTGCAGGCTTGTTGAGCTCCTGCGCCACAGGTGGTCTCTTGATCTCATCTGTGTAGACAAGGACCTCACGG
TGCTTGAACTCCACGATGGATGCGATGTCGAGCTTCCTCACATCGGTTTCTCCATCAAACTTGACGCTGCCGTAGCCATA
CCTGCCGACCCTGAA-GTCCTTCACATCTGAGCAACAATCTGGCTCGTTGCTTTCTCCTGCAGCAAGCTCTGC-------
---AAGGTGTAATAGTCTGCCTTATAGAGCCGAGGTAGCGCACACTCACTCACAGGGGCACCACCAAATGGAGTTATCAC
AGGATCAAATGGATTCCTCCTAGCCAGGACT---------------GCACCATTGATATACCCTTTTTGTTCCCCAGCAG
AT---------------CAAGATGTCAGTAACTCAAT-GCATATATCGCATGGCAACACACACAGCATGAAGTTAGCTTC
GGTTCTGAGAT-TCAAATATTTTGACATTTGGGCTCCACAAGTGCTAATGGAGAACTTGGGTTTACTCCTAGGATTCTCC
A--------TTGTAACGTGCC-----------------------------------------------------------
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----------------------AGTGAAGAATTGCTTGAATAAAGTATTCGCTGGAA-----------------------
-------------------
>SNPs
S-S-S-SSSSSSSSSSSSSSSSSSSSSSSS---------S-S--------S-----------------------------
--------S--------------------------------------------------------S---------S----
----------------------------------------------------SS-SSS--SSS---S-------------
----------S-------S--------------S----------S----------------------------SSS-S--
---S----------------S----------S-------S-SS-------------------------------------
-------------------------------------------------S-S-----------S----------S-S---
-S---S-----SSS--SSS------------------------------------------------S---S--------
----------------SS--------------------------------S-----------------------------
---------------------------------S------------------------------------------S---
-----------------------------S-------------------------------S-S----------------
-----S---S----------------------------------------------------------------------
----------------------------------------S-----------------------------S---------
-----------------------------------------------S----------------SSS-------------
-------------------------------------------------S--------------------SSSS------
-----------------------------------S------S----------S--------------------------
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---S--------------------------------------S---------------------SSSSSSSS--------
---------------------------S--S--S------S-------------------------------------S-
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------------S----S----------------S--------S------S-S-------------S-------------
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------------------------------------------------------------S-------------------
-----------------S-SSSSSSSSSSSSS------------------------------------------------
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--------------S-----------------------------------------------------------------
----------------------------------------------S---------------------------------
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-------------------------------SSSSSSSSSSSSSSS------------------------------S---
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---------------------------------S---------------------------------S------------
------------S-------------------------------------------------------------------
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------------------------------------------------S-------------------------------
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>forward_1090
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------------------------------CCCCAATAATTGCAGCCCGA------------------------------
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>reverse_2519
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--------------------------------------CCAGGACAGCACCGTTGATA----------------------
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