>input_sequence_60050
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---------------------------------------------------------------------------ATGAA
GCTGATCGCAGCCTACCTTCTCGCCTATCTGGGCGGGAACTCTTCCCCAAGTGCCGCTGACGTCAAGAACATCCTTGACT
CAGGTAATTCTTCTTTGTTGGTTTTAAGTTATACTGGCTCAGATACTCTCTACTTGGGTAA-------TGCCTCTAGCTT
CCCTTATGGTTTGACCTATTTAGCATGGTATAAAAGATAAAATATTTGCTGCACTACTTGCTGTTTGCTGAAT----ATA
ACATAAATCCAATCTTTTCACTTCCAGTCAGGTCATTGAGTACTATTATATTCTGAGGTTTCAAATATGCAATAACTTAT
TGCTTGTTATGATTATGGTCGCATATCAAAACTTGTCAATTTGGGTCCTTCATGAGAGGATGTGAGACCAAAAAAAATGC
TTATTGTATTTGTTATTCATGTGAGAATCTAGTTATGATATTGTGCATATCATCTGACTTGGAAATTGCTTGTTACAGTT
GGTGCTGAGGCTGATGAAGAAAAGCTTGAGTTCCTTCTTGCTGAACTCAAAGGCAAGGACATCACAGAAGTGATTGCATC
TGGAAGGGAGAAGTTTGCCGCTGTGCCTTCAGGTGGGGGTGCCATTGCTGTGGGAGCTCCAGCTGCTGCATCTGGTGGTG
CCGCAGCACCTGCTGCTGAGTCAAAGAAGGAGGAGAAGGTTGAAGAGAAGGAAGAATCTGATGAAGTAAGTATTTTTCCA
CCTTGCAATGGTTTCTCAGTCACTTTAGTTCTGTGG-CCTTAAGTTATTCTAGCTGGACTTACATTGTAGCAAGCAACCC
ACATTCAACTTTGTTCAGCTGTTGTTGTTGCAAGTAGTGACTTTTTAGTTTTGGCATGACAAGTG-CCATTTCAAATTCA
CTGCCTAGTTGCAAGTAGAAGCTAGAATTCCTCCCGCAGCATGCAAATTGTTAAACCTGATCACATACTCCCTCCGTTCG
GAATTAGTTGTCTCGAAAATGGATGTATCTAGAACTAAAATACGTCTAGATACATCCATTTCTGCGACAAGTAATTCTGA
ACAGAGGGAGTACTTGTATGTGAATTATTGTGAACTTGCTGACATTCTCGTTTTCTTTATGCAGGACATGGGTTTCAGTC
TGTTCGACTAA---------------------------------------------------------------------
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>chr1A_1_TraesCS1A01G277500
TCTGGGCCTACAAAGAGGCACCAGAAAATGGAATACCATGGACTGTTTATGAGCTGATTTTTTTTT---AGAA--TTAAA
TACGGGCCAAGTGGGCACTGTGGTTCTGGATCCG--GGAGATTGTGGCCTTTGGGCTTGCGTTTCGGAGCCCGGAGAAGT
CGCTCCACTGATCCAGAACCTTCTGAGAGATCGAGTGGCCTCTGATTCGGCCCGATTGCCCGTATATAAAAGCGAAATGG
TTCGGCTCATTTGGCTAGAACCCTAGCTCACGCACGAAGCCCC-TCCGCCGCCGTCCTCGCGTCTTCTCCTGCGCATCTC
GGAGGT-AGGCTTCCCCC-----AATCCCGTCCTTTTCGCACTCAATTCTGCGCCAGGCAAGGGCCCTGCTGCAGCGATC
CCGTTGGAAATCCGTCTTGTTCTGCGGTAGGGGAATT-TTTGTTGGATGCGGAGATGAGTGTTCCTGTTTGTTCGTTTTC
GTAGATCTGTGCGGTATAGGTTGCTTAATTGTCGCGTG--TATCTTGCTTAGTTGTTGCGCCGCTAGATCTCTAGCTTGC
GCCTGCGCGCCGGGTTTCAGGAGATCTGATTTCCCCATATAGAAACACGGCAGGCCATTACTGTGT-GATTCTTGTTTAC
CCAGTGAAGATGCAGAAACCCCCGGGTCTTCGAAGGCTCGAATCTAAGATGCACGGGGG----ATGTTTATTATTGTTCT
TTTCGTGCACAACTTCAATTTACGTGCATAACTCCATTCATTCATTCAGATCCTCCGATGTTCATCTCT----GATTTCC
GAGTGGAAAATAATTGCTATGGTATTTAGTGATTTCATATCGTAGCCACTTGCTTTCATTTGGCCTTGAACCCTAGTAAT
TTTGGCATTCTGTGTTTTTGA-TTTTCCATGCGTCTTGCTGTCGATCTATTTGGATCTGACAGTACTCCCA--------T
CTTGAGCATATACTTAGCCTTCCATGCCGTTTAACTTTAATTCTGTTTGTTTTCAGGTGCTTCCTAGTTTCCACGATGAA
GCTGATCGCAGCCTACCTTCTCGCCTATCTGGGCGGGAACTCTTCCCCAAGTGCCGCTGACGTCAAGAACATCCTTGACT
CAGGTAATTCTTCTTTGTTGGTTTTAAGTTATACTGGCTCAGATACTCTCTACTTGGGTAA-------TGCCTCTAGCTT
CCCTTATGGTTTGACCTATTTAGCATGGTATAAAAGATAAAATATTTGCTGCACTACTTGCTGTTTGCTGAAT----ATA
ACATAAATCCAATCTTTTCACTTCCAGTCAGGTCATTGAGTACTATTATATTCTGAGGTTTCAAATATGCAATAACTTAT
TGCTTGTTATGATTATGGTCGCATATCAAAACTTGTCAATTTGGGTCCTTCATGAGAGGATGTGAGACCAAAAAAAATGC
TTATTGTATTTGTTATTCATGTGAGAATCTAGTTATGATATTGTGCATATCATCTGACTTGGAAATTGCTTGTTACAGTT
GGTGCTGAGGCTGATGAAGAAAAGCTTGAGTTCCTTCTTGCTGAACTCAAAGGCAAGGACATCACAGAAGTGATTGCATC
TGGAAGGGAGAAGTTTGCCGCTGTGCCTTCAGGTGGGGGTGCCATTGCTGTGGGAGCTCCAGCTGCTGCATCTGGTGGTG
CCGCAGCACCTGCTGCTGAGTCAAAGAAGGAGGAGAAGGTTGAAGAGAAGGAAGAATCTGATGAAGTAAGTATTTTTCCA
CCTTGCAATGGTTTCTCAGTCACTTTAGTTCTGTGG-CCTTAAGTTATTCTAGCTGGACTTACATTGTAGCAAGCAACCC
ACATTCAACTTTGTTCAGCTGTTGTTGTTGCAAGTAGTGACTTTTTAGTTTTGGCATGACAAGTG-CCATTTCAAATTCA
CTGCCTAGTTGCAAGTAGAAGCTAGAATTCCTCCCGCAGCATGCAAATTGTTAAACCTGATCACATACTCCCTCCGTTCG
GAATTAGTTGTCTCGAAAATGGATGTATCTAGAACTAAAATACGTCTAGATACATCCATTTCTGCGACAAGTAATTCTGA
ACAGAGGGAGTACTTGTATGTGAATTATTGTGAACTTGCTGACATTCTCGTTTTCTTTATGCAGGACATGGGTTTCAGTC
TGTTCGACTAAGCGCTTCAGTTCCTCCCCCCTACCCTCTGTTTACCCTAGTATCTGTCGTGTGTGGCCTGCCACAACAGC
GCCTGCATAATAT--CTAGAGACCTGAAGTTCGTGCTATTTTGCTTGGGACAATGTATATGTTTAGTACCTTCGTATGTG
AGTGTGTTACTGCTTCTGCAGCCTTGAGCAGTTGATTGATAAATTGGTGTTATGTTTC-TCGCATATGTCT----TGATG
TTTGTGGTCGATGAAAGTGCACATGATCTTTTGATGTTCTGAATGGTTTATCTGGTGAAAGGATCTTGATTTTCTCTGTG
ACTGAATGGGTTTTCTCTGGGATGGAATGCCCTTTCCTCACACTGGTGACTATA--TGACCATTTTTCACAGTGAGATCT
CACACTCGCTTCTCTGAACAGATAAAGGAGAATGGAGATGCAAACATAGATTTGAATAAATTGGTGGACACTTTTTGACA
AATATTTCATTCATATCATTCATTATTCATTGGATCTTCATACAACTGGGGTATTGTGAGCTTTGACGAGAGGCACCAGA
AACAGCAGACATCACCTGCGATACTTGAGCAAAGAGGAAGGGCGATGCTAGGTGCCGGCGCACCGGCTGAAAGTTTTGGC
CGGTCCTGCCCCAGCCCTTGGAAAAATGATTTGTCCTGGATGCGGAAAAAAGTTGCCAACGTTGACATAAAAAGTTTCAA
CCGTATATGAGAAAAGCTTCAAACGGCTATCAGCGACAAAAAAGTTTTGGTTGCAGTCCGCGCGCGGTCACCTTGGTCAT
CGTCGTCGCGCACCCCGACCGCCACGGGGTTGAAGCACATGGACATCGCCCCGGCCGCTGCGGGGTTGCAGCACATGGAC
ATCGCCGTGGTAGCAACCCGTCGTCCTCGGTTGCAGCATCTCCCATGGTCACCCCGGTCGCCCTACATGGATGTAGCAAA
AAACTTCACCGGTAGAAGCAAAATTCTACTATGGTTGTAGCAAAAATCAAACACTGTCGC
>chr1D_2
-CTGGGCCTACGAAGAGGTACCAGAAAATGGAATACCTTGGACTGTTTATGACCTGAGTTTTTTTTTTGAGAA--TTAAA
TATGGGCTGAGTGGGTACTCTGGTTCTGGAGAGCCCGGAGATTGTGGCCTTTGGGCTTGCGTT-CGGAGGCCAGAGAAGT
TTCCCCACTGATCCAGAACCA-----------GAGTGGTCGCTGATTCGGCCCGACTGCCCGTATATAAAAGCGAAATGG
TTCGGCTCATTTGGCTAGAACCCTAG-TCGCGCACGAACCCCCCTCCGCCGCCGACCTCGCGTCTTCTCCTGTGCATCTC
GGAGGTAAGGCTTCCCCCAATCCAATCCCGTCCTTTTCGCACTCAATTCTGCGCCAGGCAAGGCCCCTGCTGCAGCGATC
TCGTTGGAAATCCGTGTTGTTCTGCGGTAGGGGAATTATTTGTTGGATGCCGAGACGAGTGTCCCTGATTGT---TTTTC
GTAGATCTGTGCGGTATAGGTTGCTTGGTTGTCGCGTATATATGTTGCTTAATTGTTGCTCCGCTAGATCTCTAGCTTGC
ACCTGCGCGCCAGGTTTCAGGAGATCTGATTTCCCCATTTAGAAACACGGCAGGTCATTCCTGCGTGGATTCTTGTTTAC
CTAGTGAAGAAACC---ACCTCCGGGGCTTCAAAGGCCCGACTCTAAGATGCACGGGAGGGTCCTGTTTATTATTGTTCT
TTTCATCCATAACTG-AATTTACATGCATAACTCCATTCATTCACTCAAATCCTCCGATGTTCATCTCT----CATTTCC
GAGTGGGAAATAATTGCTATGGTATTTAGTGATTTCATGTCGTAGCTACGTGCTCTCTTTTGGCCTTGAACCCTAGTAAT
TTTGGCACTCTGTATTTTTGA-TTTTCCATGTTTCTTGCTGTTGATCTTGTTGGATCTGACAGTACGCCCACTCCCATCT
TTTCACCATATAGTTAGCCCGCCATGGCATTTAACTGTAATTCTGTTTGTTTTCAGGTGCTTCTTGGTTTCCACGATGAA
GCTGATCGCTGCCTACCTCCTCGCCTATCTTGGTGGGAACTCTTCCCCAAGTGCCGCTGATGTCAAGAACATCCTGGACT
CAGGTAATTCTTCTTTGTTGGGTGCAAGTTATACTGGTTCAGATACACTTTACTAGGGCAA-------TGCCTCTAGCTT
TTCTTATGGTTGACG--ATTTAGCATGGTATAAAAGATAAAATATTTGCTGCACTCTTTTCTGTTGCTGAATATAACATA
A-----ATCAAATCTTTTCACTTTCAGTCAGGTTATTGAG--------------------------------TAACTTAT
TGCTAGTTATGATTATGGTCGCATATTGAAACTTTTCAATTTGGGTCCTTCATGAGAGGATGTGAGACC-AAAAAAATGC
TTATTGCCTTTGTTATTCATGTGAGAATCTAGTTATGATATTGTGCATATCATTTGACTTGGAAATTGCTTGTTACAGTT
GGTGCTGAGGCTGATGAAGAAAAGCTTGAGTTCCTTCTTGCTGAACTGAAAGGCAAGGACATCACAGAAGTGATTGCATC
TGGAAGGGAGAAGTTTGCCGCTGTGCCTTCAGGTGGGGGTGCCATTGCTGTGGGAGCTCCAGCTGCTGCATCTGGTGGTG
GCGCAGCACCTGCTGCTGAGTCAAAGGAGG---AGAAGGTTGAAGAGAAGGAAGAATCTGATGAAGTAAGTATTTTTCCA
CCTTGCAATGGTTTCTCAGTTACTTTAGTTCTGCGCTCCATAAGTTATTCTAGCTGGACTTACATTATAGCAAGAATCCA
ACATTCAACTTTGTTCAACTGTTGTTGTTGCAAGTAGCGACTTGTTAGTTTTGGCACAACAATTG-CCATTTTGAATTCA
CTGCCTAGTCGCAAGTAGAAGCTGGCATTCCTTCCGTAGCATGCAAATTGTTAAGACCTGATAACTT-------------
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-------------TTGTGTGTGAATTACTGTGACCTTGCTGACATTCTCGTTTTCTTTATGCAGGACATGGGTTTCAGTC
TGTTCGACTAAGCACTTCAGTCACTCCCCCCTACCCTCTCTTTACCCTAGTATCTGTCGCCTGTGGCCTGCTACAACGGC
GCCTGCATA--AT--CTAGAGACCTAAAGTTCATGCTATTTTGCTTGGGACAATGTATATGTCTAGTACCTTCGTATGCG
AGTGTGTGACTGCTTCTGCAGCCTTGAGAAGTTGATTGATAATTCGCTGGTGTTATGTTTCTTGCATATATCTCGTGATG
TTTGTG--------------------------------------------------------------------------
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>chr1B_42
-----------------------------------------ACTGTTTATGGGCTGAGTTTTGTTTGAGAAACATTTAAA
TATGGGCTGAGTGGGTACTGTGCTTATG--GAGCCCGGAGATTGTGGCCTTTGGGCTTGCGTT-CGGAGCCCAGAGAAGT
CTCTCCACTGGTCCAGAACCTTCTGAGAGATCGAGTGGTCTCTGATTCGGCCCGATCGCCCGTATATAAAAGCGAAATGG
TTCGACTCATTTGGCTAGAACCCTAGCTCGCGCACGAACCCCC-TCCGCCGCCGACCTCGCGTCTTCTCCTGCGCATCTC
GGAGGT-AGGTTTCCCCC-----AGTCCCATCCTTTCCGCACTCAATTCTGCACCAGGCAAGGTCCCTGCTGCGGCGATC
TCGTTTGAAATCCGTCTTGTTCCGCAGTAGGGGAATTATTTGTTGGATGCGAAGACGAGTGTTCCTGTTTGTTCGTTTTC
GTAGATCTGTGCGGTATAGGTTGCTTAATCGTC-CGTG--TGTGTTGCTTAATTGTTGCTCCGCTAGATCTCTAGCTTGC
GCCTGCGCGCCAGGTTTCAGGAGATCTGATTTCCCCATTTAGAAACACGGCAGGTCATTCCTGCGTGGATTCTTGTTTAC
CTAGTGAAAGAAT-----CCTCCGGGGCTTCGAAGGCTAGGATCTAAGATGCACGGGAGGGTCATGTTTGTCATTGTTCT
TTTCATGCAGAAGTGTAATTTACATGCATAACTCCATTCATTCACTCAAATACTCCGATGTTCATCTCTCTAAGATTTCC
GAGTGGGAAATAATTGCTATGGTATTT-------TCGTATCGTAGCCACATGCTTTCTGTTGGCCTTGAGCCCTATTAAT
TTTGGCCTTCTGTATTTTTTTGTTTTCCATGTGTCTTGCTGTCGATCTATTTGGATATGACAGTACTCCCA--------T
CTTCAGCATATACTTAGCCTGCCATGCCGTTTAACTGTAATTCCGTTTGTTTTCAGGTGCTTCCTAGTTTCCACGATGAA
GCTGATCGCTGCCTACCTCCTCGCCTATCTGGGTGGGAACTCTTCCCCAAGTGCCGCTGACGTCAAGAACATCCTGGACT
CAGGTAATTCTTCTTTGCTTGGTGCAAGTTATACTGGTTCAGATACTCTTCACTTAGGGATTAGGGATTGCCTCCAGCTT
TTCTTATGGATTGATGTATTTAGCATGATATAAAAGATAAAAT--TTGCTGCACTCTGTTCTGTTGCTGAACATAACATA
ACATAAATCCAATCTTTGTACTTTCAGTCAGGTCATTGAGTTCTATTATATTTTGAGGTTTCAAATGTACAATAACTTAT
TGCTAGTTATGATTATGGTCGCATATCAAAACTTGTCAATTTGGCTACTTCATCAGAGGATGTGAGAGCGAAAAAAATTC
TTATTGTCTTTGTTATTCATGTGAGAATCTAGTTATGATATTGTTCATATCGTTTGACTTGGAGATTGCTTGTTACAGTT
GGTGCCGAGGCTGATGAAGAAAAGCTTGAGTTCCTTCTGGCTGAACTCAAAGGCAAGGACATCACAGAAGTGATTGCATC
TGGAAGGGAGAAGTTTGCCGCTGTGCCTTCAGGTGGGGGTGCCATTGCTGTGGGAGCTCCAGCTGCTGCATCTGGTGGTG
CCGCCGCACCTGCTGCTGAGTCAAAGGAGG---AGAAGGTTGAAGAGAAGGAAGAATCTGATGAAGTAAGTATTTTTCCA
CCTTGCAATGGTTTCTCAGTTACTTTAGTTCTGTGG-CCATAAGTTATTCTAGCTGGACTTACATTATAGCAAGCAACCC
ACATTCAACTTTGTTCAGCTGTTGTTGTTGCAAGTAGTGACTTGTTAGTTTTGGCACGACAATTTACCATTTCAAATTCA
CTGCCTAGTTGCAAGTAGAAGCTAGAATTCCTTCCGCAGCATGCAAATTGTTAAACCTGATCACAT--------------
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-----------ACTTATATTTGATTTACTGTGAACTTGCTGACATTCTCGTTTTCTTTATGCAGGACATGGGTTTCAGTC
TGTTCGACTAAGCGCTTCAGTTCCTCCCCCCTACCCTCTGTTTACCCTAGTATCTGTCGTGTGTGGCCTGCCACAACAGC
GCCTGCATA--ATATCTAGAGACCTAAAGTTCGTGCTATTTTGCTTGGGACAATGTATATGTTTAGTACCTTAGTATGTG
AGTGTGTTACTGCTTCCGCAGCGTTGAGAAGTTGATTGATAATTTGCTGGAGTTATGTTTCTCTCATGCCT----TGGTG
TTTGCGGTCG-TGATAGTGCACATGGACTTTTGATGTTCTTAATGGTTTATCTGGTGAAAGGATCTTGATTTTCTCTATG
ATTGAATGGGTTTTCTCTGGGATCGAATGCTCTTTCTTCACACTGGTGTGACCATCTGACCATTTTTCACAGTGAGATCT
CACACTCACTTCTCTGAACAG--AAAGGAGAATGGAGAAGCACACATAGTTTTGACTAAATTGGTGTACATTTTTTGACT
AATATTTCATGCATATCGTTCATCTTTCATTGGATCTTCATAAAACTGGGGTATTGTGAGCTTTGACAAGAGGCATCAGA
AACAGCAGACATCATCTGCGATACTTCAGGAAAGAGGAAG----------------------------------------
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>SNPs
S----------S------S------------------S-------------------S----------------------
--S----SS------S--------------SSSS-----------------------------S--------S-------
-S------------------------------------S-----------------------------------------
-----------------------------S--------S---------------S-------------------------
---------------------------------------------------------------S----------------
S------------------------------------------------------S------------------------
-------------------------------------------S-------S-------S--------------------
-----------S--------------------------S---------------S----S---S----------------
-S--------SS-SSSS---S-----S------------------------------S----------------------
----S----S----SS-------S--------------------S---S-------------------------------
------S------------------------------------------S-------S----------------------
-------------S-----------------S------------------------------------------------
---S----------------S---------------S-------------------------------------------
---------S--------S--------------S-----------------------------------------S----
---------------------S-SS------------S-----------S--------S---------------------
SS------------SS---------------------------------------SS--S-----SSSSS-SS-------
-----------------------S-----------------S----------S-------------S-S-----------
----S----------------------------------------------------------------S----------
-------S---------------------------------------------S--------------------------
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--------------------------S---SSS-----------------------------------------------
--------------------S------------------S--------------------------S-------------
-------------------------------------------S------------S-----S-----------------
--------------------------------S---------------------------------SSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSS----------------S----------------------------------------------------
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---------SS--------------S------------------------------------------------------
----------------------------S-------------S---S--S-S-SS-SS---S-SS---------------
----------S---S----------SS-------------S------------------------------------S--
-S---------------------S------S-----S-----------SSSSS---------------------------
-------S-------------SS---------------S---S------S-----S----------S---S--------S
----------S------S-----SS-----------------S------------------------S-------S----
--------------S-----------S--S----------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_620
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----------------------------------------AGAAACACGGCAGGCCATTA--------------------
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>reverse_1987
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------------------------------------------------------------------ACTCCCTCCGTTCG
GAATTAG-------------------------------------------------------------------------
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>forward_1707
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-------ACCTGCTGCTGAGTCAAAGA-----------------------------------------------------
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>reverse_2896
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---------------GCTTCAAACGGCTATCAGCG---------------------------------------------
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