>input_sequence_81419
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-----ATGGGGTTCCTTACACACATGGAAGCGTTCAATGCAGCATGCGAAGCAAAAAAGGCTGGGGCCAGGTGCGACGAG
AGGCTCGTCATTCATCGTGTGACCAACGGCGGGTGCTTTGACGACTTCAAGAAGGCGATGGACGAGTGCCGCGGCCATTA
CAGTCCCGAAACGTCCAAACGCGATATTGAGCGAGGCATCGGCGAGCTCGTGGTGGACGTGGAGGCGTGCGTCAAGGCCA
CGGCGGCCCTGCGCGAGTGCTTTGCTGGCAACCCCGCAAAGTTCAAGCACCAGTACCTTCGCCGCATGGACGAGGGCCTC
GACCAGGACACGAAGCCGTCGTGGGAGCAGATTCGGAAAGAGAAAGATGTAATGTTCAGGTGGTGGACTCACATGAGGAG
ACGTTAA-------------------------------------------------------------------------
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>chr1D_1_TraesCS1D01G447600
AAAAAATCCAGGGAAAAC-CATCTAAAAAGACGAAAACACTTGCAGAAAAATAAAATAAAATTCAAAGAAAGTGCCCAGA
GCACGACATGTGACGACCGCTGAGAGCGCGCCGTGCCAAGTGGCGCACTCCCAGCCCATCCC-AAGAGACCCTTGGAAGG
GTGGGAACGAGCGCTCCTCGGTTAGTTGCTCCCATTGTAAAGGAATTATTGTGACAGATATGAGCTCACTTGAATTTGTT
GTTTTGGGGGGTGCTCGCTTGAATTAGTGCTGGTTCCCGGCAAAAAGAAAAGAAAAGAAGAATTAGTATTT-AGGGGTAG
AAGAAGAATAATTAGTGTTGATTAATCCATAG-----------------------------------TAGCCCATCTTCT
AGCCTTT-AACTTCCTTATTAAGCGGTTCCTGCAAAAAAAAAACTTCCTTATTAAGCGTGTTCGTAAAAAAAGACTTCCT
TATTAATCTGCCAGTAGATTTTTTTTGAAGCTATAATCTGCCAGTAGATAGCCTTGGCACAAGTAACGGGATGGATAGAA
ACACAGTTGCAACGCATCGTACTACCGTGCATG------TATATGTTATTTATTTATTTTTGATTGAGAATCAGATACGT
ATTTTTTAGGATGATCGGATACGTTATTAACTTTTTTTTTGAAAGTGGATACGTTATTAACTTGGTTGATTGATTGACGG
TGCAATCGAGACCGAGCGTGATACGAACTGTGGCGGGTGTTCGGAGTGTCAGCAAAGAAACACTATGTATTTGCACGCCG
CATGTTTAAATCGAGTCCGCCTTGGAATACAAGTTGTGTCCGTGTAGTTCTAGGATAGGACCAAGGGTCGGCTGCTGATG
TATATTTATATGCATCACGGCTGCGCGAGATAGCACCGGCGAGGAGAAAGAGAAAAGAGATAAGAAGTAAAAGAAAGGGC
ACGACAAGGATCCCGGCTACGAGTTTCTTGTGTCTCGTGTTTGTCGGACAAGCGATTGATTTCGTTGTTAACCCTAGCTA
ACGCCATGGGGTTCCTTACACACATGGAAGCGTTCAATGCAGCATGCGAAGCAAAAAAGGCTGGGGCCAGGTGCGACGAG
AGGCTCGTCATTCATCGTGTGACCAACGGCGGGTGCTTTGACGACTTCAAGAAGGCGATGGACGAGTGCCGCGGCCATTA
CAGTCCCGAAACGTCCAAACGCGATATTGAGCGAGGCATCGGCGAGCTCGTGGTGGACGTGGAGGCGTGCGTCAAGGCCA
CGGCGGCCCTGCGCGAGTGCTTTGCTGGCAACCCCGCAAAGTTCAAGCACCAGTACCTTCGCCGCATGGACGAGGGCCTC
GACCAGGACACGAAGCCGTCGTGGGAGCAGATTCGGAAAGAGAAAGATGTAATGTTCAGGTGGTGGACTCACATGAGGAG
ACGTTAAGCTATGCTTGCATCCGCATCGAGCCTATATGTACTCGC-----ATTGATAAATGGGTTAGATCGATTATATTA
GCCTATACTAGTAGTGGATATTGGTAGGCACAAGCTATTTCGGTGTTGAATTATCCTTTTCCTTTTATTAGTTGTGAAGC
TTTTCGGTATAAGACGGATTAGATCGCGATTAGAATTCTTGATGTAATAGAAAAAGTTATGTCTATGTTGAATTATCTTT
AT-TTTTAGTTGCGTAGTTTCTCGGTATGTGCACGATACTTATATCTACTCCCTCCGTTTCTAAATATACTAAGTCTTTT
TAAAAATTTCATTATAGTGACTACATTCGGATGTATATAAACGTTTTTTAGAGTATAGGTTCATTCAGTTTGCTCTGTAT
GTAGTCTATAGTATGAAATCTCTCAAAAGACTCATATTTACAAACGAAAGGAGTAGTTCATTGTTCGCACTTGGTTGGTG
GTAGTATAGTTAACAAAAAAATTACCACGTGACATATGTGATAAGCAATTCAAACTAATCCAAATTAAAGGATTGATGGC
CATTCCTTGGTCGGAAAGTCTACCCTACCACCTGTACTAGAAATACGTACATAAACGTCTCATCGGCGGCACACGTCTTT
AGCAGAACGTTGGGTCGACCGCTTGCTACGTACGCACGTTAACCAGAAGAAGGCTTCAACGAGCCATCGCCGGAGCAGAA
GGCATGAGGATTGAGGGAGTAAATTGCATAAAAGTATTATAATTGGGGCATTGGAAGCAGATTGGTACCAAGATTGGTAA
TTTTTACGTGTCAGTACCAACTTTTGGGCGAGGCGTTGCAAAAGAGGCTAAAACAGCTGTTTATACGTATTGACACGGAA
ACTGACCAGTTGGGCCCGCCTGTCGGGTGCTGACATGGCATGTTTTTTCGCAAAAAACTCCCTGGAATCTCCTCTCTCTC
CCCCGAACGCTCTCCCCCTCCTCTGTCTCGATCTCCTCAGATCGGTTAAGGCA
>chr1B_1
AAAAAAACCAGGGAAAAAGCATCTAAAAAGATGAAAATGCTTGCGGAAAAAAAA--------TCAGATGAATTGCCCAGA
GCATGACACATGGCGACGGCTAAGAGCGCGCCGTGCCAAGTGGCTTACTCTCAGCCAATCCCCAAGTGACCCTTCGGGGG
CTGGGAATGAGCGCTCCTCAGTTAGTTGCTCCCATTGTAAAGGAATTAATGTGACAGATACGAGCTCACTTGAATTTGTT
GTTTTGGGGGCGTTCC-CTTGAATTAGTGCTGGTTCCCGGCAAAAAAAAAAGAAA-GAAGAAATAGTTTTTTAGGGGTAG
AAGAAGAAGAATTAATGCTGAGTAATTCATAGTTGGCTAGCCCATATTCTATTCGCGAAAAAAAAGTTAGCCCATCTTCT
AGCCTTTTAACTTCCTTATTTG--------------------------------------------AAAAAAAACTTCCT
TATTAATCTGCCAGCAGATAGCGTA-------------------------------GCACAAGTAACGCGATGGATAGAA
ACACGGTTGCAGCGCATTG---TACCGTGCATGTACTCCTATATGTTATTTATTTATTTTTGACTGAGAATCGGATACGT
TTTTTTTAGGGTGGTCGGATACGTTGTTAATTTGATTAATTG--------------------------------------
----ATTGAGACTGAGCGTGGTACGAACGGTGGCGGGGATTTGGAGTGTCAGCAACGAAACACTATGTATTTGCACGCCG
TG----------GAGTCCGGCTTGGAATACATGTTTTGTCCGTGTAGTTTTAGGAGAGGCCCAAGGC-------------
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---CCATGGGGTTCCTTGCACACATGGAAGCGGTCCATGCAGCAAGCGAAGCAAGCAAGGCTGGGGCCAGGTGCGACGAG
AGGCTCGTCATTCATCGTGTGACCAACGGCGGGTGCTTTGACGACTTCAACAAGGCCATGGACGAGTGCCGCGGCCACTA
CAGTCCCGAAACATCCAAACGTGATATTGAGCGAGGCACCGGCGAGCTCGTGGTGGACGTGGAGGCGTGCGTCAAGGCCA
CGGCGGCCCTGCGCGAGTGCTTTGCTGGCAACCCCGCAAAGTTCAAGCACCAGTACCTTCGCCGCATGGACGAGGGCCTC
GACCAAGACACGAAGCCGTCGTGGGAGCAGATTCGGGAAGATAAAAATGTCATGTTCAGGTGGTGGACTGACATGAGGAG
AAGCTAAGCTATGCTTGCATCTGCATCGAGCATATATGTACTCG-----TATTGATAAATGGGTTAGATCGATTATATTA
GC--ATACTGGTGGTGGATATAA-TAGGATCAAGCTATTTCGGTGTTAAATTAT-CTTTTCCTT----------------
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-T-TGTTAGTTGTGGAGCTTTTCGGTATAAGATGGATTAGATCGCGAT--------------------------------
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>chr1A_1043
GAAGCATCAAT---------------------------------------------------------------------
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----------------------------------------------------------GGCCGGCGCCAGGTGCGACGAG
AGGCTCGTCATACATCACGTGACCAACGGCGGGTGCTTCGACGACTTCAACAAGGCGATGGAAGAGTGCCGCGGCCGCTA
CAGTCCCGACACGTCACAACTCAACCTGATCCGAGGCGTGGCCAAGCGCGTCGTGGACGTGGAGGCGTGCGTCAAGGCCA
CGGCAGCGCTGCGTGAGTGCTTTGCCGACAACCCCGCCGTGTTCAAGCACCAGTACCTCCGCCGCATGGACGAAGGCCTC
GACCAGGACACCAACGCATCGCCGGACGATATTTGGAGGGATGAACGTGACATGTTCAGGTGGTGGACTGGCATGACGAG
AAGCTAAGCA------------------AGCATACACGTACATAAGATATATAGATAGATGGGCTAG-TCGATTATAGTG
AC--ATACTAGTACTGGATATAA-TAGGCACAAGCTATTTCGGTGTTGAATTTTTCTTTTCCTT---TTAGTTGTAGAGT
TTTTCGGATTAGATCGATTACGTTAGCGTTGATGAAGT---------TAGCAAAAGTTATTTCTGTGTTCAATTATCTTT
CTCTGTTAGTTGTGGAGTTTCTCGATATGTGCGCAATACTTATA------------------------------------
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>chr1A_1043
GAAGCATCAAT---------------------------------------------------------------------
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----------------------------------------------------------GGCCGGCGCCAGGTGCGACGAG
AGGCTCGTCATACATCACGTGACCAACGGCGGGTGCTTCGACGACTTCAACAAGGCGATGGAAGAGTGCCGCGGCCGCTA
CAGTCCCGACACGTCACAACTCAACCTGATCCGAGGCGTGGCCAAGCGCGTCGTGGACGTGGAGGCGTGCGTCAAGGCCA
CGGCAGCGCTGCGTGAGTGCTTTGCCGACAACCCCGCCGTGTTCAAGCACCAGTACCTCCGCCGCATGGACGAAGGCCTC
GACCAGGACACCAACGCATCGCCGGACGATATTTGGAGGGATGAACGTGACATGTTCAGGTGGTGGACTGGCATGACGAG
AAGCTAAGCA------------------AGCATACACGTACATAAGATATATAGATAGATGGGCTAG-TCGATTATAGTG
AC--ATACTAGTACTGGATATAA-TAGGCACAAGCTATTTCGGTGTTGAATTTTTCTTTTCCTT---TTAGTTGTAGAGT
TTTTCGGATTAGATCGATTACGTTAGCGTTGATGAAGT---------TAGCAAAAGTTATTTCTGTGTTCAATTATCTTT
CTCTGTTAGTTGTGGAGTTTCTCGATATGTGCGCAATACTTATA------------------------------------
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>chr1A_1043
GAAGCATCAAT---------------------------------------------------------------------
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----------------------------------------------------------GGCCGGCGCCAGGTGCGACGAG
AGGCTCGTCATACATCACGTGACCAACGGCGGGTGCTTCGACGACTTCAACAAGGCGATGGAAGAGTGCCGCGGCCGCTA
CAGTCCCGACACGTCACAACTCAACCTGATCCGAGGCGTGGCCAAGCGCGTCGTGGACGTGGAGGCGTGCGTCAAGGCCA
CGGCAGCGCTGCGTGAGTGCTTTGCCGACAACCCCGCCGTGTTCAAGCACCAGTACCTCCGCCGCATGGACGAAGGCCTC
GACCAGGACACCAACGCATCGCCGGACGATATTTGGAGGGATGAACGTGACATGTTCAGGTGGTGGACTGGCATGACGAG
AAGCTAAGCA------------------AGCATACACATATATAAGATATATAGATAGATGGGCTAG-TCGATTATAGTG
AC--ATACTAGTACTGGATATAA-TAGGCACAAGCTATTTCGGTGTTGAATTTTTCTTTTCCTT---TTAGTTGTAGAGT
TTTTCGGATTAGATCGATTACGTTAGCGTTGATGAAGT---------TAGCAAAAGTTATTTCTGTGTTCAATTATCTTT
CTCTGTTAGTTGTGGAGTTTCTGGATATGTGCGCAATACTTATA------------------------------------
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>chr1A_1043
GAAGCATCAAT---------------------------------------------------------------------
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----------------------------------------------------------GGCCGGCGCCAGGTGCGACGAG
AGGCTCGTCATACATCACGTGACCAACGGCGGGTGCTTCGACGACTTCAACAAGGCGATGGAAGAGTGCCGCGGCCGCTA
CAGTCCCGACACGTCACAACTCAACCTGATCCGAGGCGTGGCCAAGCGCGTCGTGGACGTGGAGGCGTGCGTCAAGGCCA
CGGCAGCGCTGCGTGAGTGCTTTGCCGACAACCCCGCCGTGTTCAAGCACCAGTACCTCCGCCGCATGGACGAAGGCCTC
GACCAGGACACCAACGCATCGCCGGACGATATTTGGAGGGATGAACGTGACATGTTCAGGTGGTGGACTGGCATGACGAG
AAGCTAAGCA------------------AGCATACACGTACATAAGATATATAGATAGATGGGCTAG-TCGATTATAGTG
AC--ATACTAGTACTGGATATAA-TAGGCACAAGCTATTTCGGTGTTGAATTTTTCTTTTCCTT---TTAGTTGTAGAGT
TTTTCGGATTAGATCGATTACGTTAGCGTTGATGAAGT---------TAGCAAAAGTTATTTCTGTGTTCAATTATCTTT
CTCTGTTAGTTGTGGAGTTTCTGGATATGTGCGCAATACTTATA------------------------------------
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>chrUn_1043
GAAGCATCAAT---------------------------------------------------------------------
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----------------------------------------------------------GGCCGGCGCCAGGTGCGACGAG
AGGCTCGTCATACATCACGTGACCAACGGCGGGTGCTTCGACGACTTCAACAAGGCGATGGAAGAGTGCCGCGGCCGCTA
CAGTCCCGACACGTCACAACTCAACCTGATCCGAGGCGTGGCCAAGCGCGTCGTGGACGTGGAGGCGTGCGTCAAGGCCA
CGGCAGCGCTGCGTGAGTGCTTTGCCGACAACCCCGCCGTGTTCAAGCACCAGTACCTCCGCCGCATGGACGAAGGCCTC
GACCAGGACACCAACGCATCGCCGGACGATATTTGGAGGGATGAACGTGACATGTTCAGGTGGTGGACTGGCATGACGAG
AAGCTAAGCA------------------AGCATACACGTACATAAGATATATAGATAGATGGGCTAG-TCGATTATAGTG
AC--ATACTAGTACTGGATATAA-TAGGCACAAGCTATTTCGGTGTTGAATTTTTCTTTTCCTT---TTAGTTGTAGAGT
TTTTCGGATTAGATCGATTACGTTAGCGTTGATGAAGT---------TAGCAAAAGTTATTTCTGTGTTCAATTATCTTT
CTCTGTTAGTTGTGGAGTTTCTGGATATGTGCGCAATACTTATA------------------------------------
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>chrUn_1043
GAAGCATCAAT---------------------------------------------------------------------
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----------------------------------------------------------GGCCGGCGCCAGGTGCGACGAG
AGGCTCGTCATACATCACGTGACCAACGGCGGGTGCTTCGACGACTTCAACAAGGCGATGGAAGAGTGCCGCGGCCGCTA
CAGTCCCGACACGTCACAACTCAACCTGATCCGAGGCGTGGCCAAGCGCGTCGTGGACGTGGAGGCGTGCGTCAAGGCCA
CGGCAGCGCTGCGTGAGTGCTTTGCCGACAACCCCGCCGTGTTCAAGCACCAGTACCTCCGCCGCATGGACGAAGGCCTC
GACCAGGACACCAACGCATCGCCGGACGATATTTGGAGGGATGAACGTGACATGTTCAGGTGGTGGACTGGCATGACGAG
AAGCTAAGCA------------------AGCATACACATATATAAGATATATAGATAGATGGGCTAG-TCGATTATAGTG
AC--ATACTAGTACTGGATATAA-TAGGCACAAGCTATTTCGGTGTTGAATTTTTCTTTTCCTT---TTAGTTGTAGAGT
TTTTCGGATTAGATCGATTACGTTAGCGTTGATGAAGT---------TAGCAAAAGTTATTTCTGTGTTCAATTATCTTT
CTCTGTTAGTTGTGGAGTTTCTGGATATGTGCGCAATACTTATA------------------------------------
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>chrUn_1043
GAAGCATCAAT---------------------------------------------------------------------
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----------------------------------------------------------GGCCGGCGCCAGGTGCGACGAG
AGGCTCGTCATACATCACGTGACCAACGGCGGGTGCTTCGACGACTTCAACAAGGCGATGGAAGAGTGCCGCGGCCGCTA
CAGTCCCGACACGTCACAACTCAACCTGATCCGAGGCGTGGCCAAGCGCGTCGTGGACGTGGAGGCGTGCGTCAAGGCCA
CGGCAGCGCTGCGTGAGTGCTTTGCCGACAACCCCGCCGTGTTCAAGCACCAGTACCTCCGCCGCATGGACGAAGGCCTC
GACCAGGACACCAACGCATCGCCGGACGATATTTGGAGGGATGAACGTGACATGTTCAGGTGGTGGACTGGCATGACGAG
AAGCTAAGCA------------------AGCATACACGTACATAAGATATATAGATAGATGGGCTAG-TCGATTATAGTG
AC--ATACTAGTACTGGATATAA-TAGGCACAAGCTATTTCGGTGTTGAATTTTTCTTTTCCTT---TTAGTTGTAGAGT
TTTTCGGATTAGATCGATTACGTTAGCGTTGATGAAGT---------TAGCAAAAGTTATTTCTGTGTTCAATTATCTTT
CTCTGTTAGTTGTGGAGTTTCT----------------------------------------------------------
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>SNPs
-----------------S-------------S-----SS-----S------S--SSSSSSSS---S-SS--S--------
---S----SS--S----S---S----------------------SS----S-----S---------S-------S-SS--
S------S-----------S----------------------------S-----------S-------------------
----------SSSSS-S-----------------------------S--------S------S----S------------
--------S-----S--S---S----S-----------------------------------------------------
--------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------S-------
--------------S----SSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------S-----------
----S------S-----S-SSS-----------------------------------------S--------S-------
S---------S--S-----------S----S--SS--SS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSS--S-----S-------S-------S--------SS--S-------------S------------------------
SSSSSSSSSSSS-------S-----------S---S-------------S-----S---S------SSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSS--------------S--------------S--S--------S---------SS------------------------
--------------------------------------------------S--------------------------S--
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-----------------------------------------S---S----S------------------S----------
-S-S-----------------S---------S------------S-----------------------------------
--SS-----------------SSS------------------------------S---------SSS--------SS--S
-------SS--SSS--SS-SS-S-S---S-S-SS-SSSSSSSSSSSS---S---------S---S----S----------
S---S-------S-S-----------------S-----------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_991
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-----------CCCGGCTACGAGTTTCTTGT-------------------------------------------------
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>reverse_2080
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-------------------------------------------------------------------------------T
AGCAGAACGTTGGGTCGAC-------------------------------------------------------------
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