>input_sequence_87459
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-------------------------------ATGAACAAGGT---GAAGAGCCATGGCGGCAAGCACAAGGGGTC---A-
--GGA---------AGAGGAGGGATCAGCAGGATGCTAAGGCAACACAAGGCCAGGCTCTACATCATCCGGCGATGCGTC
GTCATGCTCCTCTGCTACCATGACTGA-----------------------------------------------------
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>chr3D_1_TraesCS3D01G058600
TGCTTTAATATAGTGTGCATCAGTTGGCGTAGAAGTCAAGTTTCACAATGTTGGGCCAACTTTATATAGAAAAATATATA
TATCCACAAAACCATATATATATATACACCATATGAAAATGTATTTCATGATGAATCTAACCCCATTGATTTAGTACTCC
AAATGTTCACAGTTTTTTCTATAAATTTGGCCAAAATTGACGAAGTTCTTGACTTTAAAAGATTCTAATAAGCACTATAT
GTCTATACTTTTGGACAGAGAGTGTACCTATATTATGTTCACAGTTTTTTCTACTCCCTCCGTCCGGAAATACTTGTCGA
AAAAATGCATAAAATGAATGTATCTAGAACTAAAATACATCTAGATACATTCATTCCTCCGACAAGTATTTCCGGACGGA
GGGAGTATAAATTTGGCCAAAATGACGAAGTTTTTGACTTTAAAAGATTCTAATAAGCACTATATGTCTATATTTTTGGA
CAGAGAGTGTGCCTGTATTATGTTCACAGTTTTTTCTATAAATTTGGCTAAAATGACGAAGTTTTTGACTTTAAAAGATT
CTAATAAGCACTATGTGTCTATATTTTTGGACAGAGGGGGTAACTACCATGTGTGGATTATTTC---GATGACTTTG-CA
AGAGGATCTGCCTACTTGTCCCTGGTCTTGAACTGCAGTGAAGCCAACTTCCCGGCTTTCTAGGCAATTGTCCCCGGGAG
TGTCATCGGAATCCGCTGCACCTCGAGAGAGTCTGGTG-------------------CATACAACAAGGGGCATAT----
---GGCCCCAACTCTT--TACCCAACGTCT-CGTCCTAGTT-GCAAAGATGTGAGGATCATGTGAGAGAGTAGCCTGTCG
TTTTGT-------GCCATTTGGCCA----------TTCCTATATAAGCA----TGGCAATGCCACAGCAGAGACAG----
ATCCATCCATCCAG--TAGCAGCAGTGGAAGAGCAGAGCAGGGAGCCTTCCTTCCAGCTCACCACCTA--CA----CCTA
GCTCAACCACCACCCTACTGCTCAGCC----ATGAACAAGGT---GAAGAGCCATGGCGGCAAGCACAAGGGGTC---A-
--GGA---------AGAGGAGGGATCAGCAGGATGCTAAGGCAACACAAGGCCAGGCTCTACATCATCCGGCGATGCGTC
GTCATGCTCCTCTGCTACCATGACTGAC-------CTTACATTGGTGTCCTGTTCTTCGTTTGGT----TCTCGT----T
TGTAGCTAGGCTAGTTAGGCTTAGACAGATTCTC--TGGTGTGTGTGTGTGTGTG------------TGTGTGTGTGTGT
TCATAGGGTAGTGTATGCTTAGATAGGTTCCGCTCACGGTTAGTTTGG-ATGTTGAAGTTTTGTGTGGTGACATGGTTCT
CCTAAGTCCTGCAACGGCAAGGATGTGCATATA---TCTGAGATGTTTGGTCT---------------------------
-----AAAGGAATG-TCTCGGAGAAACGAAAAAGATTTTTT--TTATTATGGAAGTGCTGAGCAAAAGATTATCTCTTGG
CATCATCCAATTGT---------CTGTTCTGTTGAAGCATAACTGTGAATTGCGAGCCTCTAACTGCTAACG--------
TTTAGGCCCTGTTTGGATTAGTGTTTTCTTTAGAATACACCTGTAAAAGAAATACACGTCTCCACCGGCCGGTTTCATTT
CCAGTCGGAAAACCCTCATGCCCAGTAAAATACACTTGTAAATCTTACACCTCTGTATTGAATTACACCTATACCAAGCG
CGCCCTTATATGTGTCCTTTCGGGGTGTTCTTATTTCGTTCGATTGGG------------------------------TC
AGTTAATGGGACGATTTTTCATACAAGGCCATCTTAACGGAGTGCATTTTGGGACTGAATTTGCAAAGATATTCAGAAAA
ATTGCAGCATTGTCCTT--GTTTTACCTCAAAATTTCAGCGAAACTTTACTTTGTGAGTTCAACATTTCAGGGGAAACTT
CAAACATATTTTTTTCTGCAAAAAAGGTTCTATTTCTGATGATAACCTCACACTTAGAAATTGAAAGACTCATTTTAACT
TCTGCCCAGTTTGCAGACACACTGAGCGACTATCTACACACAACTCCTTGCTCATGGTCAAGGACTAGTGGCTTTCTGGC
AGTATTATTATCATATAAATCAGTTTATCTAGGAAATATTTGTGGTAAACCGAGCAGCACTGGGCACAGAAACGAGAAGC
TTCAAGGTACGTACAGTCCTCGCA
>chr3A_1
TGCTTTAATATAGTGTGCATCAGTTGGCGTAGAAGTCAAGTTTCACAGTGTTTGGCCATGATTATATAGAAA---ATAAA
TATCTACAAAACCAAATATATATATAC--CATATGAAAATGTTTTTCATGATGAATCTAACTCCATTGA-TTAGTATTCT
AAATGCTCACAATTGTTTCTATGAATTTGGCCAAAATTGACGAAGTTCTTGACTTTAAAAGATTCTAATAAGCACTATAT
GTCTACATTTTTCGACAA--AGTGTACCTATATTATGT------------------------------------------
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----------------------------------------------------GTGGATTATTCC---AATAACTTTG-CA
AGAGGATCTGTCTACTTGTCCCTGGTCTTGCACTGCAGTGAAGCCAACTTCCTGACTTCCTAGGCGGTTGTCCCCTGGAG
TGTCATCGGAATCCGCTGCACCTCGAG--AGTCTGCTG-------------------CATACTACAAGGGGCATAT----
---GGCCTCAACTCTCTCTACCCAGCGTCT-TTTCCTAGTAGGCAAAGATGTGAGGATCATGTGAGAGAGTAGCCTGTCA
TTTTGT-------ACCATTTGGCCACGACGTACCCTTCCTATATATGCA----TGGCAATGCCACAGCAGAGGCCGATCC
ATCCATCCATCCAG--TAGCAGCAGTGGAAGAGCAGAGCGGGTAGCCTTCCTACCAGCTCACCACCTAGGCA----CCTA
GCTCAACCACCACCGTACTGCTCAGCC----ATGAACAAGGT---GAAGAGCAATGGCGGCAAGCACAAGGGGTC---A-
--GGA---------GGAGGAGGGATCAGCAGGATGCTGAGGCAACACAAGGCCAGGCTCTACATCATCCGGCGATGCATC
GTCATGCTCCTATGCTACCATGACTGAC-------CCTACATTGGTGTCCTGTCCTCCGTTTGGT----TCTCGT----T
TGTAGCTAGGCTAGTTAGGCTTAGACAGATTCTC--TGGTGTGTGTGTGTGTGTG------------TGT----------
------------------TTAGATAGACTTCGCTGGCGTAT------G-ATGTTGAAGTTTTGTGTGGTGTCATGGTTCT
C-TAAGTCCTGCAACGGCAAGGATGTGCATGTA---TCTGAGATGTTTGGTCT---------------------------
-----AATGGAAGG-TCTCGGAAAAATGAAAAAGAAAAAAAA--TATTATGGAAGTGCTGAGCAAAAGATTATCTCTTGG
CATCATCCAATTGT---------TTGTTCTGTTGAAGCATAACTGTGAATTGTGAACCTCTAACTGCTAAGG--------
TTTA----------------------------------------------------------------------------
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--------TATGTGTCCTTTTGGGGTGTTCTTATTTCGTTCGATTGGGTCATTTTTTTTTGCAGGAAATTCGATTGGGTC
AGTTAATGGGACGATTTTGCACACAAGGCCATCTTAACGGAGTGCATTTTGGGACTGAATTTGCAAAGATATTCAGAAAA
AATGCAGCATTGTCCTT--GTTTTACCTCAAAATTTCAGCGAAATTTTACTTTGTGAGTTCAACGTTTCAGGAGAAAATT
CAAACATAATTTTTTTCTAAAAAAAGGTTCTATTTCTGATGATAACCTCACACTTAGAAATTGAAAGACTCATTTTAACT
TCTGCCCAGTTTGCAGACACACTGAGAGACTATCTACACACAACACCTTGCTCATGGTCAAGGACTAGTGGCTTTCTGGC
AGTATTATTATCATATAAATCAGTTTATCTAGGAAATATTTGTGGTAAACCGAGCAGCACTGGCCACAGAAACGAGAAGC
------------------------
>chr3B_127
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----------------------------------------------CATGATGAATCTAACTCCATTGA-TTAGTATTAT
AAATGTTAACAGTTTTTTCTATAAATTTGGCCAAAATTGACGAAGTTTTGGACTTTAAAAGATTCTAATAAGCACCATAT
GTCTAT--TTTTGGACAGAGAGTGTACCTATATTATGT------------------------------------------
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----------------------------------------------------GTGGATTATTCCGATGATGACTTTG-CA
AGAGGATCTGTCTACTTGTCCCTGGTCTTGCACTGCAGTGACGCCAACCTCCCGGCTTTCTAGGCGATTGTCCCCTGGAG
TGTCATCGGCATATGTTGCACCTCGAG--AGAGTCTGCTGCATACTACAA------------------GGGCATAT----
---GGCCCCAACTCTCTGTACCCAACGTCT-CTTCCTAGTGGGCAAAGATGTGAGGATCATGTGAGAGAGTAGTCTGTCG
TATTGT-------GCCATTTGGTCATGGCCTACCCTTCCTATAT----A----TGGCAATGCCACCGCAGAGGCCGATCC
ATCCATCT----AG--TAGCAGCAGTGGAAGAGCAGATCAGGGAGCCTTCCTTCAAACTCGCCACCTAGGCA----CCTA
GCTCAACCACCACCCTACTGCTCAGCC----ATGAACAAGGT---GAAGAGCCATGGCGGCAAGCACAAGGGGTC---A-
--GGAGGAGGAGGGGGAGGAGGGATCAGCAGGATGCTGAGGCAACACAAGGACAGGCTCTACATCATCCGGCGATGCGTC
GTCATGCTCCTCTGCTACCATGACTGAC-------CCTACATTGGT-----------------------TCTCGT----T
TGTAGTTAGGCTAGTTAGGCTTAGACCGATTCTCTGTGATGTGTGTGTGTGTGTG------------TGTGTGTGTGTGT
TCATAGGGTAGTGTATGTTTAGATAGATTTCGCTGACGGTCAGTTTGG-ATGTTGAAGTTTTGTGTGGTGTCATGGTTCT
CCTAAGTCCTGCAACGGCAAGGATGTGCAT-------CTGAGATGTATATGGTC--------------------------
----TAATGGAAGG-CCTCGGAAAAATGAAAAAGAAAAAAAA--TATTATGGAAGTGCTGAGCAAAAGATTATCTCTTGG
CATCATCCAATTGTCCGTATTGTCTGTTCTGTTGAAGCATAACTGTGAATTGTGAGCCTCTAACTGCTAGCGGAGTGCAC
TTTA----------------------------------------------------------------------------
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--------TATGCTTCATTTTGGGGTGTTCTTATTTTGCTTGATTGGG------------------------------TC
AGTTAATGGGACAATTTTGCACACATGGCCATCTTAACGGAGTGCATTTTGGGACTGAATTTGCAAAGATATTCAGAAAA
ATTGCAGCATTGCTCCTTCGTTTTACCTCAAAATTTCAGCGAAATTTT----TGTGAGTTCAACGTTTCAGGGGAAAATT
CAAACATA-TTTTTTTCTGCAAAAAGGTTCTATTTCTGATGATAACTTCACACTTAGAAATTGAAAGACTCATTTTAACT
TCTGCCCAGTTTGCAGACACACTGAGCGACTATCTACACACAACTCCTTGCTCATGGTCAAGGACTAGTGGCTTTCTGGC
AGTATTATTATCATATAAATCAGTTTATCTAGGAAATATTTGTGGTAAACCGAGCAGCACTGGCCACAGAAACGAGAAGC
TTCAAGGTACGTACAGTCCTCGCA
>chr3B_611
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--------------------------------------------------GTGTGGATTATTTT---CATAAAATGTACA
AGAGGAGCTGTCTACTTGTCCTTGGTCTTGAACTGCAGTGAAGCCAACTTCCCAGTTTTCTAGGCGATTGTCCCCTAAAG
TGTCATCGGTATCCGCCGCACCTTGAG--AGAGGCTGCTGCATGTGCCTCCACACTTCCTGCTACAGG-------TGGTT
TATGCCCCCAACATCTCATAAGCTTTTTATACTTGCAAGTAGGAAAAGATGTGAGGATGACGCCAGAGTAGTTTGTC---
TTTTGT-------GCCATTTGGCCATGCCGTACCCTTCCTATAT----AAGCATGGCAATGCTAAAGCAGAGGCAGACCA
ATCCAGTA--------TAGCAGCAGTGGAAGAGCGGAGCAGTGAGCCTTTCTTCCAGCTCAC--------CA----CCTA
GCTCAACCATCACCTTTTTGTTCAGCCA-GGATGAACAAGGT---GAAGAGCCATGGCGGCAAGCACACGGGGTCAGCA-
--GGA---------GGAGGAGGGATCAGCAGGATGCTGAGGCAACACAAGGCCAGGCTCTACATCATCCGGCGATGCGTC
GTCATGCTCCTCTGCTACCATGACTGAC-------CCTACATTGCTGTCCTGTTCTTCGTTTGATCCTCTCTCGT----T
TGTAGCTAGGCTAGCTAGGCTTAGACAGATTCTC--TGTTGTGTGTATGTGTTCATAGGGTAGTGTAG------------
----------------GCTTAGATAGATTTCGCTGCCGGTTAGTTAGGAATCTTGAAGTTTTGTGTGGTGATATGGTTCT
CCTAAGTCCTGCAACGGCAAGGATGTGCATGTAGTATCTGACATGTTTGGTCT---------------------------
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>chr3D_613
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----------------------------------------------------GTGGATTATTTT---CATAAAATGTACA
AGAGGAGCTGTCTACTTGTCCTTGGTCTTGAACTGCAGTGAAGCCAACTTCCCAGTTTTCCAGGCGATTGTCCCCTAAAG
TGTCATCGGAATCTGCCGCACCTTGAG--AGAGGCTGCTGCATGTGCCTCCACACTTCCTGCTACAGG-------T----
---GCCCCCAACATCTCGTAAGCTTTTTATACTTGCAAGTAGGAAAAGATGTGAGGATGATGCCAGAGTAGTTTGTC---
TTTTGTGCCATTTGCCATTTGGCCATGCCGTACCCTTCCTATAT----AAGCATGGCAATGCCAAAGCAGAGGCAGAGCA
ATCCAGTA--------TAGCAGCAGTGGAAGAGCGGAGCAGGGAGCCTTTCTTCCAGCTCAC--------CA----GCTA
GCTCAACCACCACCTTCTTGTTCAGCCA-GGATGAACAAGGT---GAAGAGCCATGGCGGCAAGCACACGGGGTCAGCA-
--GGA---------GGAGGAGGGATCAGCAGGATGCTGAGGCAACACAAGGCCAGGCTCTACATCATCCGGCGATGCGTT
GTCATGCTCCTCTGCTGCCATGACTGAC-------CCTACATTGGTGTCCTGTTCTTCGTTTGATCCTCTCTCGT----T
TGTAGCTAGGCTAGCTAGGCTTAGACAGATTCTC--TGTTGTGTGTATGTGTGCATAGGGTAGTTTATGT----------
------------------TTAGATAGATTTCGCTGACGGTTAGTTCGG-ATGTTGAAGTTTTGTGTGGTGCCATGGTTAT
ACTAAGTCCTGCAACGGCAAGGATGTGCATGTAGTATCTGAGATGTTTGGTCTTGCCATCTTTGTTCTGAATTTGCTCCA
TCAGTAATGGAAGGTTCTCAGAAAAGAGAAAAAGAAAAAACAATTATTATGAAAGTGCTGAGCAAAAGATTATCTCTTGG
CATCGTCCAATTGTAC---------------------CATAATTGTGACCTGTGAGTCTCTGATTGCTAACGCCA-----
--TA----------------------------------------------------------------------------
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--------CATGCGTCCTTTTGGGGTGTTCTTATTTCGCTCGATTAGG------------------------------TC
AGTTGTTGGGACGATTTCACACACAAGGCCATCTCAAAGGAGTGCATTTTCGGAATGAATTTGCAAAGTTACTCAGGAAA
TTGGCACCTAATT----------------AATATTTCAGGGAAAGGC-------------CACCATTTCAGGGCAAAATT
TGAACATG-TTTTTTTCCGCAGAAAATTTCTATTTCTGATGGTAACCTCACACTTAGACATTGAAAGACTCATTTTATCT
TCTGCCCAGTATGCAGACACACTGAGCGACTATCTACACACAGCTCCTTGCCAT--------------------------
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>chr3A_663
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--------------------------CTTGAACTGCAGTGAAGCCAACTTCCCAGTTTTCTAGGCGATTGTCCCCTAAAG
TGTCATCGGAATCCGCCGCACCTTGAG--AGAGGCTGCTGCATGTGCCTCCACACTTCCTGCTACAGGTGGTTTAT----
---GCCCCCAACATCTCATAAGCTTTTTATACTTGCAAGTAGGAAAAGATGTGAGGATGATGTCAGAGTAGTTTGTC---
TTTTGT-------GCGATTTGGCCATGCCGTACCCTTCCTATAT----AAGCATGGCAACGCCAAAGCAGAGGCAGACCC
ATCCAGTATAGCACTATAGCAGCAGTGGAAAAGCAGAGCAGGGAGCCTTTCTTCCAGCTCAC--------CA----CCTA
GCTCAATCACCACCTTCTTGTTCAGCCAGGGATGAACAAGGT---GAAGAGCCATGGCGGCAAGCACACGGGGTCAGCA-
--GGA---------GGAGGAGGGATCAGCAGGATGCTGAGGCAACACAAGGCCAGGCTCTACATCATCCGGCGATGCGTC
GTCATGCTCCTCTGCTACCATGACTGAC-------CCTACAAAGGTGTCCTGTTCTTCGTTTGGT----CCTCGT----T
TGTAGCTAGGCTAGCTAGGCTTAGACAGATTCTC--TGTTGTGTGTATGTGTTCGTAGGGTAGTGTATGT----------
------------------TTAGATAGATTTAGCTGACGGATAGTTTGG-ATGTAGAAGTTTTGTGTGGTGCCATGGTTCT
CCTAAGTCCTGCAACGGCAAGGATGTGCATGTAGTATCTGAGATGTTTGGTCTTGCCATCTTTGTTGTGAATTTGCTCCA
TCAGTAATGGAAGG-TCTCAGAAAAAAGAAAAAGAAAAAACAATTATTATGAAAGTGCTGAGCAAAAGATTATCTCTTGG
CATCATCCAATTGT------------------------------------------------------------------
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>chr3D_809
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------------------------------------------GCAAAGATGTAAGGATCATGTGAGAGAGTAATCTGTCG
TTTTGT-------GCCATTTGGCCATGACGT--CCTTCCTATAT----GAGCATGGCAATGCCATAGCAGAGGCAGATCC
ACGTAG--------TATAGCAGCAGTGGATGTGCAGCGCAGG-AGACCTCCTTCCTTCTCACCGCCTAGCTAGCTGCCTA
GCTCAACCATCACCGTCCTGCTCAGCAA-GGATGAACAAGGTTAAGAAGAGCCATGGCGGCAAGCACAAGGGGGCAGAAT
CGGGA---------GGAGGAGGGATCAGCAGGATGCTGAGGCGACATACGGCCAGGCTCTGCATCATCCGGCAATGCGTC
GCCATGCTCCTCTGCTACCATGACTGACGTGTGACCCTACATGGGTGTTCTGTTATTCCTTTGTTCTACTAGTTTGTAGT
TGTAGCTAGGCTAGG-----TTTGACAGGTCCTT--TGGTGTGTACTTATATGTTGGATGGAG-----------------
----------------------------------------------GG-CTGTTGAAGTTTTGTGTGGTT---TGGTTCT
CCTAAGTCCTGCAACGGCAAGGATGTGCATGTA---TCTGAGATGTT---------------------------------
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>SNPs
-----------------------------------------------S----S-----SSS-----------SSS---S-
----S---------S------------SS-------------S------------------S-------S------S--S
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-------S------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------------------------
----------S------------------------------------------------------S---------S----
---------------------------SS------S--------------------------S-----------------
--------------------------------S-------S---------------------------------------
---------------------------------------------S--------------------------S-------
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--------------S----------------------S------------------------------------------
------------------------------------S-------------------------------------------
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--------------------------S--S----S---------------------------------------------
------------------------------S-------------------------------------------------
-------S----S---------S---S--------SSSSSS---------------------------------------
----------------------------------------------------S---------------------------
----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSS------------S-----------------------------------------------------------
------------------S--S----------------------------------------------------------
--------------------------------------------S--------------------------------S--
--------S------SSSS-------------------------------------------------------------
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---------------------------------------------------------------S----------------
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>forward_311
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---------------------------------------------------TACTCCCTCCGTCCGGAAAT---------
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>reverse_1829
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--------------------------------------------------------------------CTATACCAAGCG
CGCCCTTA------------------------------------------------------------------------
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