>input_sequence_65528
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ATGCATACGCAGAGGGTGAGCGGCGAGCAGGCGGGGCCGGCGCTGCCGTGCGAGATCGCGGCGGACGACATGCCGGCGGC
GAGGAACGGGCACTACAGGCCGGGCAAGGCGGTGACGGCGTCGGTGTACCGGGCCAAGGTGGCGGGCCACTCGCGGGTGG
TGACGGTGTCATGGTCGCGGGACCTGCTGTCGCACGCCTTCGCGGTGGCCATCTCCGGCGCGGACGGCGCGTCGGCGGAG
TGCCGGGTGGACCTGCGGCCGTGGCAGTTCTGGCGGCGCGCGGGGTCCCGGCGCGTGGAGCTCGGCGGGGCCACGGTGCG
CGTGCTCTGGGACCTGCGCCGCGCGCGCTGGCACGGCGCCGGCGCGGGCCTCCCGGACCCGCGCGGCGGGTACTACGTCG
CCGTGGAGGCCGGCGGCGAGGTGGCGCTGGTGCTCGGCGACCTCCGCAAGGCGGCGCTCCGGCGCGCGTCGCC---CAGC
GCCCCGCCCGCGCTCGCGGCGGTCCCCGTGGCGCGCAGGGAGCACGTGTTCGGCCGGCGGCGGTTCGCGGCCAAGGCGCG
GTTCCACGACCAGGGCGCCGTCCACGACGTGGCCATCGACGTCGGCGGCGAGGACGACATGGAGATGGCCATCGCCATCG
ACGGCGAGGAGGCGGTCGCCGTCAAGCACCTGCAGTGGAAGTTCCGGGGCAACCAGTCGGTCACCTTCGGCCGGGCCAAG
GTGGAGGTGTACTGGGACGTGCACGACTGGCTCTTCGCGGGCGCCGCCGGCGGCGCCCGCCCGGCGCTCTTCATCTTCCG
GCCCATCGTGCTGTCCAGCGCGTCCGTGGGGGCCTCCACGCCGCTGCTCGCCGGCGTCGACGGCGCCGCGGGCGCCACCG
GGTTCTGCCTCTACCTCTACGCCTGGAAGCTCGACTGA------------------------------------------
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>chr1D_1_TraesCS1D01G026300
TTTCCCTTTCCCAAATTCCTCTCCTGCATCTGAATCTGTGTACTGGTGCTGGA-AACCTGAGGGCTCTCCAACCCAGCCG
GTTGATTAGTCAGTCAGTCAGCTGCACCCAGAATTCGGATCTGTGTTACAGTGGGCAGTGACACTGTCCACCCTCCAATG
TCACCCTGTCACCATGTTCAGGGGATGCATCCATGCAGCCATCATCACCAACACCAGCAGGATGATATTTTTGCTGGTCA
CTCTCAGAGGCAAATGTTGGTCACTTTCAGTCAGAGGAAGGAAATGCAGCACTTGA--GATCTTGAGATTGTTTTGTGGA
TCCAATGCATCATGGCTAAGAAACAAACC--CCCCAAGATGTCAAATGC-----------------CCCATTTTCACACA
GCAGCAGGAGAAACCCCCAAA----CCAGCT------------GCCAGAAGATACAAACAAGAGAGACAACACATCAGAT
TTGTCCCAAAGTACATAA---------------------------------------AATGGTC------------CATG
GATGCATGCATGAATGTATCCTAGCCAAGACAATTTTATTATCATTACTATGAGCTCT----------------------
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-----------------TTTTTTTGAGACAATATTATTACTA-TAAGCTGTATGTGCATGCATACACACACCAGTGTCCA
GCCCATGAATTATTATTATTATTATTAGTAGTAGTAGTATTATTAAGCTCTGT----ATGCATACACACACCAGTGTCCA
GCCCATGAATGAATTGAAA-----------TAAAATGGAAGGGATTGGTAGTCCACTCCAGCCATGGATGCCAATTATGT
ATGTATGCGTTCGTCTGTCTCCAGCCAGCTGAGCTGATCCCCCGGAAGACACGCACATTAGTCCCACCTCGCCCAGCGGG
GAGCTCATCACCCACCTTATCATCCGCAACCACCACGG-CGTCCTCCCCTCCCCCGCGCTATATATCCCTCTCTTCCTCC
ACCTGCGCCTCCTCTCCTCCGTTTCCTTTTCTTCCCCAGCTCCGGC---------------AGCAG-----------CGA
CCGAGCTACGGCGGTGAG--------GCGTGCATGACGGCGTAGTGGTTTCCATT---------------------GGCC
ATGCATACGCAGAGGGTGAGCGGCGAGCAGGCGGGGCCGGCGCTGCCGTGCGAGATCGCGGCGGACGACATGCCGGCGGC
GAGGAACGGGCACTACAGGCCGGGCAAGGCGGTGACGGCGTCGGTGTACCGGGCCAAGGTGGCGGGCCACTCGCGGGTGG
TGACGGTGTCATGGTCGCGGGACCTGCTGTCGCACGCCTTCGCGGTGGCCATCTCCGGCGCGGACGGCGCGTCGGCGGAG
TGCCGGGTGGACCTGCGGCCGTGGCAGTTCTGGCGGCGCGCGGGGTCCCGGCGCGTGGAGCTCGGCGGGGCCACGGTGCG
CGTGCTCTGGGACCTGCGCCGCGCGCGCTGGCACGGCGCCGGCGCGGGCCTCCCGGACCCGCGCGGCGGGTACTACGTCG
CCGTGGAGGCCGGCGGCGAGGTGGCGCTGGTGCTCGGCGACCTCCGCAAGGCGGCGCTCCGGCGCGCGTCGCC---CAGC
GCCCCGCCCGCGCTCGCGGCGGTCCCCGTGGCGCGCAGGGAGCACGTGTTCGGCCGGCGGCGGTTCGCGGCCAAGGCGCG
GTTCCACGACCAGGGCGCCGTCCACGACGTGGCCATCGACGTCGGCGGCGAGGACGACATGGAGATGGCCATCGCCATCG
ACGGCGAGGAGGCGGTCGCCGTCAAGCACCTGCAGTGGAAGTTCCGGGGCAACCAGTCGGTCACCTTCGGCCGGGCCAAG
GTGGAGGTGTACTGGGACGTGCACGACTGGCTCTTCGCGGGCGCCGCCGGCGGCGCCCGCCCGGCGCTCTTCATCTTCCG
GCCCATCGTGCTGTCCAGCGCGTCCGTGGGGGCCTCCACGCCGCTGCTCGCCGGCGTCGACGGCGCCGCGGGCGCCACCG
GGTTCTGCCTCTACCTCTACGCCTGGAAGCTCGACTGATCGATCGACAATTTCATTCGATCCATCATAGCCATTGTCCAT
CCTCATCATCAC-CATA-AAAACAAAAATGTGAAACCAAGATGAGCGCAACGTAGTAGCAACAATTTTCTCCGATTTTGT
ATTTCTTTTTTTCTTTCTCGCGAAAACGGCATAATTGAATATAATTCTTTCATAGACCACACAAACATAGTGGTTCACTT
TAC-TCATTCTCCTGAAATTTGCATTTGTTGAGCTCAAGCTCAGTGAGTGTGTGAGTTCACAATCTTGGCACTGTCCCAT
TCTA-CATGTGTGTAATTAATATGTGTGACACTGTAATTAGTAGCTTGATTAGTTAGGGATTAGGGAGACACTGTGGGGT
GGATGGCACATGCGGTGAGAGGGAGAGTGGGATCCAGTGGTGTGGTGTAGCAGCAGCTGTGCATGGACTGACTCATCAGA
CTGACCGATCAAGAGAGAGAGAGAGAAAAATATTGCCACCGCAAAAGGTGACAGGTTGGATCCACCACCCTAATCTGATC
ATGCTCATGGACCCAGATGAATTT-GA-TTAAGTCCATTGTTTTCTTGCCAAATTCACGCTATCATTGATCTGGGGTATC
CTATGTCTATGTGATGCCGTCTCACCTCTTTCTTCCCTTGACTTGTACTCCCTCCGTTCCAAATTACTCGTCGTGGTTTT
TGAACTGAATTCAAAAACCACGAGGAGTAATTTGGAACGGAGGAAGTACACGCAAAAGTAGTACTAGTGATATTAATGTT
TAATTATATATTTGTGCAAATATGAGTAATTTGGGAATGTTA-AAAAAAATGTGAGCTGGACCAGCATGTAGACCAGCTT
AAATATAGTTATTTGACAAAAAAAAACTATATGCTGGCTGATTTGT---ATTGCACAATGTTTTT-TGACAATTAATATG
ACTTTTTATGTCACGTAATCAACTTGTGTTTTATTGGTGCCTAACTGATGGTCAAATCTGGGCCTGGAAATGTGTGGGCG
CCTTTCATG
>chr1B_1
TTTCCCTTTCCCAAATTCCTCTCCTGCATCTGAATCTGTGTACTGGTGCTGGAGAACCTGAGG-------------GCCG
GTTGATTAGTCAGTCAGTCTGCTGCACACAGAATTCGGATCTGTGTTACAGTGGGCAGTGACACTGCCCACCCTCCAATG
TCACCCTGTCACCATGCTCAGGGGGTG----CATGCAACCATCATC----ACACCAGCAAGATGATATTTTT--------
--------------TGTTGGTCACTTTCAGTCAGAGGAA----ATGCAGAAC----TTGATCCTGAGATTGTTTTGTGGA
TCCAATGCATCAAGGCCGAGAAACAAACCCACCCCAAGATGTCAAATGCTCACCACACATCACTGCCCCATTTTCACACA
GCAGAAAGAGAAACCCCCAAACCAGCCAGCT------------GCCAGAAGATACAAACAGCAGAGACAACACATCAGAT
TTGTCCCAAGGTACATAA---------------------------------------AATGGCCCATGGATGCATGCATG
CATGCATGCATGAATGTATCCTAGCCAAGGCAATTA--------------------------------------------
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--------------------ATTATTATTACTATTATTATTATTAAGATGTGTATGCATGCATACACACACCAGTGTCCA
GCCCATGAAATGAAATGAAATGAAGTACTCTAAAATGGAATGGATTGGTAGTCCAG-CCAGCCATGGATGCCAATTATGT
A------------------------------AGCTGATCGCCCGCAGGACACGGAGATTAGTCCCACCTCGCCCAGCGGG
GAGCTCATCACCCACCTTATCATCCGCAACCACCACGGCCGTCCTCCCCTCCCCCGCGCTATATATCCCTCTCTCCCTCC
ACCTGCGCCTCCTCTCCTCCGCTTCCTTTTCTTCCCCAGCTCCGGC---------------AGCAGTATCCAGCGAGCGA
GCGAGCTCCGGCGGCAGGAGCAGTGTGCGTGCATGACGTGGCGTCTGCTGTAGTTTAGTTTACAGAGGTCTCGGCCGGCC
ATGCACACGCAGAGGGTGAGCGGCGAGCAGGCGGGCCCGGCGCTGCCGTGCGAGATCGCGGCGGACGACATGCCGGCGGC
GAGGAACGGGCACTACAGGCCGGGCAAGGCGGTGACGGCGTCGGTGTACCGGGCCAAGGTGGCGGGCCACTCGCGGGTGG
TGACGGTGTCGTGGTCGCGGGACCTGCTGTCGCACGCCTTCGCGGTGGCCATCTCGGGGGCCGACGGCGCGTCGGCGGAG
TGCCGCGTCGACCTGCGTCCCTGGCAGTTCTGGCGGCGCGCGGGGTCGCGGCGCGTGAACCTGGGCGGCGCCACGGTGCG
CGTGCTCTGGGACCTGCGCCGCGCGCGCTGGCACGGCGCCGGCGCGGGCCTCCCGGACCCGCGCGCCGGGTACTACGTCG
CCGTCGAGGCCGGCGGCGAGGTGGCGCTGGTGCTCGGCGACCTCCGCAAGGCCGCGCTCCGGCGCGCGTCCCCCAGCAGC
GCCCCGCCCGCGCTCGCGGCGGTCCCCGTGGCGCGCCGGGAGCACGTGTTCGGCCGGCGGCGGTTCGCGGCCAAGGCGCG
GTTCCACGACCAGGGCGCGGTGCACGACGTGGCCATCGACGTCGGCGGCGAGGACGACATGGAGATGGCCATCGCCATCG
ACGGCGAGGAGGCGGTCGCCGTCAAGCACCTGCAGTGGAAGTTCCGGGGCAACCAGTCCGTCACCTTCGGCCGGGCCAAG
GTGGAGGTGTACTGGGACGTGCACGACTGGCTCTTCGCGGGCGCCGCCGGCGGCGCCCGCCCCGCGCTCTTCATCTTCCG
CCCCATCGTGCTCTCCAGCGCCTCCGTGGGGGCCTCCACGCCGCTGCTCGCCGGCGTCGACGGCGCCGCCGGCGCCACCG
GGTTCTGCCTCTACCTCTACGCATGGAAGCTCGACTGATC---------------------CATCATAGCCATTGTCCAT
TCTCATCATCATTCATA-AAAACAAAAATGTGAAACCAAGATGAGCGCC---TAGTA---ACATTTTTCTCCGATTTTGT
AACCCTTTTTTTCTTTCTCGCGAAAACGGCATAAGTGAATATAATTCTTTCAAAAACCACACAAACACAGTGGTTCAATT
C-ATTCATTCTCCTGAAATTTGCATTTGTTCAGCCCAAGCTCAGTGGGTG----AGTTCACAATCTTGGCACTGTCCCAT
GCTACCATGTGTGTGATTAGTATGTGTGACACTGTAATTAGTGGCTTGATTAGTCAGGGATTAGGGAGACACTGTTGGGT
GGAAGGCACATGGGGTGAGAGGGAGGGTGGGATCCAGTGGTGTGGTGTGGCAGCAGCTGTGCATGGACTGACTCATCAGA
CTGACCGATCAAGAGAGAAAGAGAGAAAAATATTGCCACCGCAAAAGGTGACAGATTGGATCCACCACCCTAATCTGATC
ATGCTCATGGCCCCAGATGAATTT-GATTTAAGCTCATTGTTTTCTTGCCAAATTCACACCATCATTGATCTGGGGTATC
CTATGCCTATGTGATGCC-TCTCACCTCTTTCTTCCCTTGACTTGTAAAAGCAAA-------------------------
-----------------------------------------------------------AGTAGTAGTGGTAATAATGTT
TAA-------TTTGTGCAAATGTGAGTAGTTTGGGAATGTTTTAAAAAAATGTGAGCTGGACCAGCATGTAGACCAGCTT
AAATATAGTTATTTGACAC--AAAGATGATATGTTGCCTGATTTGTGCTATTGAACAATGTTTTT-TAACAATTAATATA
ACTTTTGTGTGACATGATTG-ACTTACGTTTTATTGGTGCCTAACTTATGATCGAATCTGAATCTGGAAATGTGCGGGCG
TCTCACATG
>chr1A_1
TTTCCCTTTCCCAAATTCCTCTCCTGCATCTGAATCTGTGTACTGGTGCTGCA-AACCTGAGGGCTCTCCAACCCAGCTG
GTTAACT--------AGTCAGCTGCACACAGAATTCGGATCTGTGTTACAGTGGGCAGTGACACTGTCCACCCTCCAATG
TCACCCTGTCACCATGTTCAGGGGATGCATCCATGCAGCCATCATCACCAACACCAGCAAGATGATATTTCTGTTGGTCA
CTTTCAGAGGCAAATGCTGGTCACTTTCAGTCAGAGGAA----ATGCAGCACCATTTTGATCTTGAGATTGTTTTGTGGA
TCCAATGCATCA-GGCTAAGAAACAAAT-----CCAAGATGTCAAATGCTCCCCACCCATCACTGCCCCATTTTCACACA
GC------AGAAACCCCCAAACCAGCTGCATGGATCGGTGCCAGCCAGAAGATACAAACAACACAGACAACACATCAGAT
TTGTCCCAAAGTACACTAATATTAATTGGAACTTTGGAAGATACTGCACTAGTACATAATGGTCCATAGATGCA-----G
CATGCATGCACGCATGTATCCTACTCCCTCCATTCCTAAATATAAGTTTTTTTAGAGATTTCAATATGGACTACTCCATA
CGAAGTAAAATGAGTGAATCTACAGTTTAAAATACATATGTATACATCCATATGTACTCCCTCCGTTCCGAATTACTTGT
CTTAGATTTGTCTAGATACGGAGATATCTAGCACTAAAATGAGTCTAGATCCGTATCTAGACAAATTCAAGACAAGCAAT
TCGGAACGGAGGGAATAGTTCATATTGAAATCTCTAAAATGACTTGTACTCCCTCCGTTCTAAATTACTCGTCGCAGAAA
TGGATGTATCTAAAACTAAAATACATCTAGATACATTCATACCTGCGACAAGTAACTCGGAACGGAGAGACTATTTAGAA
ACGGAGGGAGTAGCAAATTTTTTTTGAGCAAAATTATTATTAGTAAGCTGTATGTGCATACACACACAC-----------
---------------------------------------------------------------ACACACACCAGTGTCCA
GCCCATGAATGAATTGAAA-----------TAAAATGGAAGGGATTGGTAGT-----CCAGCCATGGATGCCAATTATGT
ACT----CGTTGGTCTGTCTCCAGCCAGCTGAGCTGATCCCCCGGAAGACACGCACATTAGTCCCACCTCGCCCAGCGGG
GAGCTCATCACCCACCTTATCACCCGCAACCACCACGT-CGTCCGT-CCTCCCCTGCGCTATATATCCCTCTCCCCCTCC
ACCTGCGCCTCCTCTCCTCCGTTCCCTTTTCTTCCTCAGCTCCGGCGGCAGCGAGCGTAAGAGCGG-----------CGT
GCGAGCTCCGGCGGCAGTAGCAGTGTGCGTGCATGACGCGGCCGCTGCTGTAGTTTAGTTTACAGAGGTTTCTGCCGGCC
ATGCATGCGCAGAGGGTGAGCGGCGAGCAGGCGGGCCCGGCGATGCCGTGCGAGATCGCGGCGGACGACATGCCGGCGGC
GAGGAACGGGCACTACAGGCCGGGCAAGGCGGTGACGGCGTCGGTGTACCGCGCCAAGGTGGCCGGCCACTCGCGGGTGG
TGACGGTGTCGTGGTCGCGGGACCTGCTGTCGCACGCCTTCGCCGTCGCCATCTCCGGCGCGGACGGCGCGTCGGCGGAG
TGCCGTGTCGACCTGCGGCCGTGGCAGTTCTGGCGGCGCGCGGGGTCCCGGCGCGTGGACCTGGGCGGCGCCACGGTGCG
CGTGCTCTGGGACCTGCGCCGCGCGCGCTGGCACGGCGCCGGCGCGGGCCTCCCGGACCCGCGCGCCGGGTACTACGTCG
CCGTGGAGGCCGGCGGCGAGGTGGCGCTGGTGCTCGGCGACCTCCGCAAGGCGGCGCTCCGGCGCGCGTCGCC---CAGC
GCCCCGCCCGCGCTCGCCGCCGTCCCCGTCGCGCGCAGGGAGCACGTGTTCGGCCGGCGGAGGTTCGCGGCCAAGGCGCG
GTTCCACGACCAGGGCGCCGTCCACGACGTGGCCATCGACGTCGGCGGCGAGGACGACATGGAGATGGCCATCGCCATCG
ACGGCGAGGAGGCGGTCGCCGTCAAGCACCTGCAGTGGAAGTTCCGGGGCAACCAGTCCGTCACCTTCGGCCGGGCCAAG
GTGGAGGTGTACTGGGACGTGCACGACTGGCTCTTCGCGGGCGCCGCCGGCGGCGCCCGCCCGGCGCTCTTCATCTTCCG
CCCCATCGTGTTGTCCAGCGCGTCCGTGGGGGCCTCCACGCCGCTCCTCGCCGGCGTCGACGGCGCCGCGGGCGCCACCG
GGTTCTGCCTCTACCTCTACGCCTGGAAGCTCGACTGATCGATCCACAA-TTCGTTCGATCCATCATAGACATTGTCCAT
CCTCCTCCTTATCATCATAAAACAAAAATGTGAAACCAAGATGAGTGCAACGTAGTA---ACAATTTTCTCCGATTTTGT
AACTCTTTCTTGTTCCGG-----AAACGGCATAATTGAATATAATTCTTTCAAAAACCACACAAACATAGTGGTTCACTT
CAATTCATTCCCCTGAAATTTGCATTGC-TCAGCTCAAGTTCACTGAGTG----AGCTCACAATTTTGGATGTA------
--TA-CATGTGTGTAATTAGTATGTGTGACACTGTAATTAGTAGATTGATTAGTTAGGGATTAGAGAGACACTGTGGGGT
GGAAGGCACATGGGGTGAGAGGGAGAGTGGGTTCCAGTGGTGTGGTGTAGCAGCAGCTGTGCATGGACTGACTCATCAGA
CTGACCGATCAAGAGTGAGAGAGAGAAAAATATTGCCACCGCAAAAGGTGACAGATTGGATCCACCACCCTAATCTGATC
ATGCTCATGGCCCCAGATGAATTTTGA-TTAGGTTTATTGTTTCCTTGCCAAATTCACACTATCATTGATCTGGGGTATC
CTATGTCTATGTGATGCCCTCTCACCTCTTCCTCCCCTTGACTTCTAAAAGCAAA-------------------------
-----------------------------------------------------------AGTAGTAGTTATAGTAATGTT
TAA-------TTTGTGCGAATGTGAGTACTTTGGACATGTTT-TGAAAAATGTGAGCTGGACCAGCATGTGGACCAGCTT
CAATATAGTTATTTGACAC--AAAAATTATATGTTGCCTGATTTGT---ATTGAATAATGTTTTTCTAACAATTGATATA
ACTT-------------------TTGTGTTTTATTGGTGCCTAACTGATGGTCAAATTTGAGTCTGGAAATGTGCGGGCG
CCTTTCATG
>SNPs
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---------------------------S----------------------------------------------------
-----------------------------------------------------------S-------------S------
--S------------------------------------SSSS---------SSSS------------------------
------------S-------------------------------------------------------------------
----S-S------------------------------------------------------S------------------
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S----------------------------S-----S--SSSSS-SSSS-S-SSSSSSS----------------------
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------------------------SSSS---S-------S-------------------S--S------SSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSS-------S--S--S--S----------S-S------------------------------
-------------------------------------------------------SS-----------------------
-SSSSSS----S--------------------------------------------------------------------
--------------------------------------------------------------------------S-----
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S------S------SSS---------------------SS-SS-SS-S-SSSS---------------------------
-----------------------------------S--------------------------------------------
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----------S---------------------------------------------------------------------
-----S--S--------------------------------------------------S--S-----S-----------
-----------------------------------------------------------------S--------------
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----------------------------------------------------------S---------------------
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S-------------------------------------------------------------------------------
--------------------------------------------S----S---S--------------------------
-----------S---------------------------------------------SSS--------------------
-SS-------------------------------------------------S-S-------------------------
S-S---------------------------S-------------------SSSS--------------------------
S------------------S------------------------------------------------------------
---S--------S-------------------------------------------------------------------
------------------------------------------------------S-------------------------
----------S-----------------------S-----------------------S---------------------
------------------S----------------------------SSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----S--------S-------
---SSSSSSS-----------S------S------------S--------------------------------------
------------------SSS-----S------S--S----------------S-------------S-----------S
------SSSSSSSSSS-S-SS---------------------------------------S-S-----------S-----
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>forward_1050
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----------------------------------------------------------------------CCAGTGTCCA
GCCCATGAAT----------------------------------------------------------------------
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>reverse_3093
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----------------------------------------------------TCCGTTCCAAATTACTCGTCGT------
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