>input_sequence_68488
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--------------------------------------ATGGCCGGCACCGTTGAGGACAGCGGGAACACGGCGCCGTCG
TCGCCGGCCGGGCTCCGCGGCGCCGACCTGGCCCTGAGGGTGCTTCTGTTCGCCGTCTCGTTGTCGGGGCTCGTCGTGCT
GGTCACCGCCAAGCAGACGGAGATGGTGCCCCTGGTCCTGACGCCGCCGTTCAGATTCGGGCCGGTGCCCGCCCAGTTCA
AAGACTCGCCAGCGCTCATGTACGTGAGTTGATCGTC---ATGTCATACGTCTCTCCTCTCCTACGGGAATTGATAACTT
CCGCGTA-GGAAC----GGTGCGTATAATAACATGGATTGCTGATGCTTATTGTGTG-CCCTGTCTACGTGTGGTTTGCA
GTTATCTTCTTGTGGCGCTGTGCATGACGAGCTTGTATAGCCTTCTGACGGCCGCCACCTCGGTCAAGTCCATGTCAAGC
TCGGCTTCCTGTGCCAAGGGGATCTTCGTCCTCATTCTGCTTGATGTGGTCAGTATCTT------------CTGCCTTGA
ATGATTTGTTCTCACATGTACTGTAGTTGCACGCAGGGCACAGCTTGATGTAACAATCCTATCTATAACC-------ATG
GCAGGTTTACGCGGGCATCATGGCGTCGGCGACGGGCACGGCGGGGGCCGTGGCCTGGGTGGGGCTGAAGGGCAACTCGC
ACACGCGGTGGAACAAGATCTGCAACATCTACGGCAAGTTCTGCCGGCACATCGGCAGCGCCACCTGCCTCGGCCTCATC
GCCTCCATCATCCTCGTCCTCCTCGTCGTCCTCAACGCCTACTCCCTCTACCGGAGAAGCCGCTGA--------------
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>chr1A_1_TraesCS1A01G248700
GCCGAATTGGGCCTGAAATTGTTTTTACAAGTATAATGGAATAATCCTTTGTTTCACGCTCGATCAAAGCTCACCGAAGT
TGATTTTCATTTTTATCAGAGGGAAGGTTGCTCTAGGCGCTCTCCAGTG---------------------------TCAC
GTTGCTGAGGATT-----TACTAAACGAGCAACTAAGGTGATGCTTTGATGGATTACCTCGCAATCTTACCGTGCTAACA
TGCTGACATTGTGTGTCTGTGGGAGGTTAGGATAATATATGTATGCGAATTAACATATTGTAGCATGACCAGTTGTGTTC
ACGATTTGATCCCCACGATCTGTCGTAATCTTGTACACGATCAAGCGTCGTCGTATTGGTAGTATTAGTAATACCAATAC
GGCCCGATGAGATAGGCTTCTCGAAACATAAACATACAATCCGTACTATCAGATAGAGCACGTTGACTAACACAAACTAG
ATAAGCAACCCCTAACGAGAATCATGGATGCGATCGGCGCGTGAAAGCGATGGATGCATTTGGAGAACAGCTAGCCACGT
CAACATTACCATTGCTTGTCTGACTGAC------CAACTGGTGTACAACTTCCATTTTATTAGGG---------------
--------------------------------------TCGGTATATGGATGTCACCTTCCCTACCGGTATCACACACAA
TGTAG-------AA------------------------------------------------------------------
-----------------------------------------------------------------GCACAAGTGCTGAAT
TCCAATTA------------------------------------------------------------------------
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------------------------------------------------------------ACGGAGAGCACGTGAACACA
CCCAAACCCAAACATATTCACGGTGTGGATGAGGCTGTCAACA---------CGATCATACTAAGTTG-CGTACAAAGCG
GGC-TACTTGCAAGTCAAAGTCAGAAGTGCA-TG---CGTACTTGCAGCAGCCTGCGTGTAAACAATGGCAATGAC----
----------ATTGTGCATTCTCACGTACGTGCCCCACCCCACCCCACCCCGGCGGCGGCTACAAGCCTATAAAACCACG
CACTGCCGTGCCTGGGCGTCCCGGCGATCAATCCATTGAA---TCTCTTCTAGTGCTCGGAAACCGCAGACTC-----CC
CGCCCAGCTATAGACAAGCGCGCGCCCCGATCGAAGGGATGGCCGGCACCGTTGAGGACAGCGGGAACACGGCGCCGTCG
TCGCCGGCCGGGCTCCGCGGCGCCGACCTGGCCCTGAGGGTGCTTCTGTTCGCCGTCTCGTTGTCGGGGCTCGTCGTGCT
GGTCACCGCCAAGCAGACGGAGATGGTGCCCCTGGTCCTGACGCCGCCGTTCAGATTCGGGCCGGTGCCCGCCCAGTTCA
AAGACTCGCCAGCGCTCATGTACGTGAGTTGATCGTC---ATGTCATACGTCTCTCCTCTCCTACGGGAATTGATAACTT
CCGCGTA-GGAAC----GGTGCGTATAATAACATGGATTGCTGATGCTTATTGTGTG-CCCTGTCTACGTGTGGTTTGCA
GTTATCTTCTTGTGGCGCTGTGCATGACGAGCTTGTATAGCCTTCTGACGGCCGCCACCTCGGTCAAGTCCATGTCAAGC
TCGGCTTCCTGTGCCAAGGGGATCTTCGTCCTCATTCTGCTTGATGTGGTCAGTATCTT------------CTGCCTTGA
ATGATTTGTTCTCACATGTACTGTAGTTGCACGCAGGGCACAGCTTGATGTAACAATCCTATCTATAACC-------ATG
GCAGGTTTACGCGGGCATCATGGCGTCGGCGACGGGCACGGCGGGGGCCGTGGCCTGGGTGGGGCTGAAGGGCAACTCGC
ACACGCGGTGGAACAAGATCTGCAACATCTACGGCAAGTTCTGCCGGCACATCGGCAGCGCCACCTGCCTCGGCCTCATC
GCCTCCATCATCCTCGTCCTCCTCGTCGTCCTCAACGCCTACTCCCTCTACCGGAGAAGCCGCTGATCGAACTAGGCGTC
CAGCCCCGCTCCCTCCTCCGGCTGGCGGGACAAATTTCATGTGCCGTGCATGTCATCCGTCGGCTTTGGTGAGCTCTGCC
GGCCGGCGGTCAGTTGTATAAAAGATGCTACGTGTTCCTGTGGCTGTGGAGTGCTCTACGACATGCGTGTGTGCGTGCGT
GTACATGTGCGTTGACGTTTATC-CTTGTTTGTTTCTACAACACGTTGCTTTGTGACAGTAAGCACGACTTTTATCGGCC
AAAATCACTGTTGTAACCTTTGTGGCATAGTTTAGCATGATTTAATTAACCCTGTTTTGAGAAAAATGGATTTAACCTTT
TTGCTATCGCCAACGGT------GGTAGGATTTAACGTAC---CACCAGGGTCTATGGCACCAGAAACCTAGTCGTCGTC
ACGCTCATGC-------GGGCAAGTGGTTAGCACATTAAACCCTAGGCCGGCAT-----ACGGTAGGCACCTAGAGGGGG
TAAGTGAATGGGGAATG-GGTGGGCGGTAGGGCA----ACCCTACCACCAAGGTCCTCA-CGGTACGGTAGTAAATTTAG
CCCAAAATGGTACTGAAAGTTTCCGTACGTTTCTGCAGGCGGAAGGACATGTAACCCTGCCACCAAGAACCTTGATGATG
GGCCCATGTAGTCACTCCAGAGCTCATTTACCATTTTGTCTAGCACACAATT----------------------------
---------------------------AACATTCAAATTTCACCACACAACAATTGTCCATCACACAACAATTTGATCAC
AAATAGTTCAACATACCAAGTTCAA----------------------------CATAGCGTGTTCAACATACAAAGTTGG
ACACGACCAAATAGAAGGTTCTCAAATACTACATAGCAAGCAAGTGTCCATATTACTTTCTTTCCCTCTTGCTTAGACAA
TCCTCAACTCTCTTTGTGCAACCCTCATTTGGTTTTAGGCCGCCTCGAGCACGCTCTCTCTGGAAAGGCGATGGACTCTT
AAGGATCCTCTACATGCCC----------CCTCGTTTGGGATGGTTGAGTGAGTGAAGGTCCATCTG
>chr1D_42
-----------------------------------------TAATCCTCTGTTTCACGCTCGAACAAAGCTCACCGAAGT
TGATTTTCATTTTTATCAGAGAGAAGGTTGCTCTAGGCGCTCTCGGTCGAGATGTTCTCTTTGTGTCTTCCGCTGATCAA
GTTACTAAGGATTTACTGTACTGAACGAGCAACTAAGGTGATGCTTCGATGGATGATACTGTATTGCC------------
-----------------------------------------------AATTAACATATTGTAGCATGACCAGTTGTGATC
ACGATTTGATCCCCACGATCTGTCGTAATCCTGTATACGATCAAGCATCGCT---------GTATTAGTAATACCAATAT
GGCCGGATGGGATAGGCTGCTCGAAACATAAACATA-------TACTATCAGATAGAGCACGTTGACTACCACAAACTAG
ATAAGCAACCCCTAACGAGAATCATGAATGCGATAGGCAAGTGAAAGCGATGGTTGCATTTGGAGAACAGCTAGCCACGT
CAACATTACCATTGCTTGTCTGACTGACCAACCGCAACTGGTGTACAACTTCCATTTTATTATGG---------------
--------------------------------------T------GTGGATGTCAGCTTCCCTGCCGATATCACACACAA
TGTACTCCCTCCGTTTGGAATTACTTGTCATAAAAATGAATGTATCTAACTTGTCATAAAAATGAATGTATCTACAACTA
AAATACATCTAGATACATTTATTTTTTGATGAGTAATTCCGAACGGAGGGAGTAGAAGCACAACTGCACAAGCGCTGAAT
CCCAATCA------------------------------------------------------------------------
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------------------------------------------------------------ACGGAGAGCACGTGAACACA
CGCAAACCCAAACATATTCGCGGTGTGGATGAGACTGTCAATGCAGCGGACGCGATCGTACTAGGTTG-CGTACAAACCG
GGC-TACTTACAAGTCAAAGTCAGACATGCATGCGTACGTACTTACAGCAGCCTGCATGTAAACAAAGGCAGTAAC----
----------AGCGTGCATTCT----CACGTGCCCCACCCCACCCCA-----GCGGCGGCTACAAGCCTATAAAACCACG
CACTGCCGTGCCACGACGTCCCGGCGATAGATCCATTAATAACTCTGTGCTAGAGCTCATAAACCGCAGACTCCCCCGCC
CGCCCAGCTATAGACAAGCGCGCGGCCCGACCGAAGGCATGGCCGGCACGGTGGAGGACAGCGGGAAGACGGCGCCGTCG
TCTCCGGCCGGGCTCCGCGGCGCCGACCTGGGCCTGAGGGTGCTGCTGTTCGCCGTCTCGCTGTCGGGGCTCGTCGTGCT
GGTCACCGCCAAGCAGACGGAGATGGTGCCCCTGGTCCTGACGCCGCCGTTCAGATTCGGGCCGGTCCCCGCCCAGTTCA
AAGACTCGCCAGCGCTCATGTACGTGAGTCGATCGTCGTCATGTCATACCTACCTCCTCTCCTACGGGCATTAATAAGCT
TCCACGTTGGTACGTACGGTGGATATAGTAACATGGACTGTTGATGCTTA-TGGTGTGCCCTATCTACGTGTGGTTTGCA
GTTATCTTCTTGTGGCGCTGTGCATGACGAGCTTGTATAGCCTTGTGACGGCCGCCAGCTCCGTCAAGTCCATGTCAAGC
TCGGCTTCCTGTGCCAAGGGGATCTTCGTCCTCATTCTGCTTGATGTGGTGAGTATCTTGTACATGAACTACTACCTTGA
ATGAATTGTTCTCACATGTGT---AGTCAC--------------------TAACAATCCTATATATAACCATTAACTATG
GCAGGTTTACGCGGGCATCATGGCGTCGGCGACGGGCACGGCGGGGGCCGTGGCCTGGGTGGGGCTGAAGGGCAACTCGC
ACACGCGGTGGAACAAGATCTGCAACATCTACGACAAGTTCTGCCGCCACATCGGCAGCGCCACCTGCCTCGGCCTCATC
GCTTCCATCCTCCTCGTCCTCCTCGTCGTCCTCAACGCCTACTCCCTCTACCGGAGAAGCCGCTGATCGAACCAGGCGTC
CAGCCCCACTCCTTCGTCCGGCTGGCGGGACATATTTCATGTGCCCTGCATGCCATCCGTCGGCTTTGGTGAGCTTTGCC
AGCGGGCGGTCAGTTGTATAAAAGATGCTACGTGTTCCTGTGGCTGTGGAGTGCTCTCCGATA----------------T
GTTCATGTGCGTTGATGTTTTAAACTTGTTTGTTTCTACAACACGTTGCTTTGTGACAGTAAGCACGACTTTTATCGGTC
AAAATCACGGTTCTGACCTTTGTGGCATAGTTTGGAACGATTGGACCCGTTCT------AAAAAAACCGAATTTGACCAT
TTGCTATCGCCATCGTCCGCGACGGTAGGATTTAACGTACTGCCACCAGGATCTATGGCGGTAGAAATCTGGTCGCTGTC
ACAGCACTCGTTGACGTGGACAAGTGGCTAGCACATTAAAACCTACGCCAGCGTCCTTGGCGGTAGACACCTGAAGCGGG
TAAGAGATTGGGGGCTTTGGTGGGCGGTAGGGCATGTAACCCTATTGCCAACGTCTATGGCGGTAGGGTACTAAATTTAG
CTCAAAACGGTACTGAAAGTTCTCGTGCGTTTCTTTAGGCAGTAGGGCATGTAACCCTATCGCCAGGAAAGTGGCGGTA-
GGCCCATGTAACCACTCCAGAGCTCATTTACCATTCTGACTAGCACACAATTGACATCAAATAACAATATAATTCAGTAT
AACAACAATATAATTGCGTATAACCATAACATTTAAATTCCACCACACAACAATTGTCCATCACTAAATAATTTGATCAT
AGATAGTTCA------------------------------------------ACATAGAGTGTTCAACATACCAAGTTCA
ACGCAACCAAATAGAAGGTTCTCAAATACTACATAGCAAGCAAGTGTCCATATTACTTTCCTCCCCTCTTGCTTAGACGA
TCCTCGGCTCTCTTTGTGCGGTCCTCATTTGGTTTGAGACCGCCTCGAGCACGCTCTCTCTGGAACGGCGATGGACTA-T
AAGGATCCTCTATAGGCCCCC-------TCCTCATTTGGGATGGCAGAGTGAGTGGAGGTCCATCTG
>chr1B_417
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------------------------------------------------TCAGATAGGGCACGTTGACTAACACAAACTAG
ATAAGCAACCCCTAACCAGAATCGGGAATTCTATCAGCGAGTGAAAGCGATGGATACATTTG-AGAACAGGTAGCCACGT
CAATATTAGCATTGCTTATCTGACTGACCAATC------GGTGTAGAACTTTCATTTCACTATGATAATATACTATAGAC
CAATGACCATGCATGCTAGTAAGTGGGGTCAGTGTGGAT------ATGGATGTCACCTCCCGTGCCGGTAGGAGACATAC
CATCACACAATAAA------------------------------------------------------------------
-----------------------------------------------------------------GCACAAGGGCGCATT
TGGTTACTTTCTCAGTGAAGCTTGGTTTAGCGGAGCCTATTTAAGTGTATACAGACTCTTGCTATGTTCTGTATGTCGTT
TGGTTTGCTGCATCAAGCCTAACTCGTATTCTCAACCCGCGTGGAAAACGGTTGATCTGAGCGTTTCTCGAGAGCCAGGC
TGGAAGCACTTTAAGTTTCGTGCAGCCCAGTTTCTACATACAAGCTAGACAACCAATCAACTCACTATTTAACCCATGAG
AGACTGGTTGGGCTTGATGCAGCCTACCAAACGCGTCCAGCGCTTGCTTGAATTCTAAAGAAAGAGAGCACGTGAACGCG
CCAAAACGTAAG--TATTTGCGGTGTGGATGAGACTG-CAACATAGTGGACGCGATCGTGGTAAGTTGGCGTACAACGCG
GGCTTACTTACAAGTCAAAGTCAGACATGCATTG---CGTACCTGCAGCAGCCTGTGTGTAAACAAGGGCAAGGGCAGTG
ACTGGCTGATAGCGTGCATTCTCATGCACGTGCCCCACCCTGGGCCA-----GCGGCGGCTACAAGCCTATAAAACCACG
CACTGCCGTGCCACGACGCCTCGGCGATCAATCCGTTGAA---TCTCTGCTAGTGCTCAGAAACCGCAGACTC-----CC
CGCCCAGCTATAGACAAGTGCGCGCCCCGACCGAAGGCATGGCCGGCACGGTGGAGGACAGCGGGAAGACGGCGCCGTCC
TCTCCGGCCTGGCTCCACGGCGCCGACCTGGGCCTGAGGGTGCTGCTGTTCGCCGTCTCGCTGTCGGGGCTCGTCGTGCT
GGTCACCGCCAAGCAGACGGAGATCGTGCCCTTG--------------------------------------------CA
AAGACTCGCCAGCGCTCATGTACGTGAGTCGATCGTCG---TGACATACGTCTCTCCTCTCCTACGGGAATTAATAAACT
TCCACGTTGGTAC----GGTGCATATAAAAACATGGACTGCTGATGCTTA-TGTGTA-CCCTGTCTACGTATGGTTCGCA
GTTATCTTCTCGTGGCGCTGTGCATGACGAGCTTGTATAGCCTTCTGACGGCCGCCAGCTCCGTCAAGTCCATGTCAAGC
TCGGCTTCCTGTGCCAAGGGGATCTTCGTCCTCATTCTGCTTGATGTGGTGAGTATCTT------------CTACCTTGA
ACGAATTGTTCTCACATGTGC---AGTTGCACGCAGGCCACTGGTTGATGTAACGATCCTATGTGTAACC-------ATG
GCAGGTTTACGCGGGCATCATGGCGTCGGCGACGGGCACGGCGGGGGCCGTGGCCTGGGTGGGGCTGAAGGGGAACTCGC
ACACGCGGTGGAACAAGATCTGCAACATCTACGACAAGTTCTGCCGCCACATCGGCAGCGCCACCTGCCTCGGCCTCGTC
GCCTCCATCATCCTCGTCCTCCTCGTCGTCCTCAACGCCTACTCCCTCTACCGGAGAAGCCGCTGATCGAACCAGGCGTC
CAGCCCTGCTCCCTCGTCCGGCTGGCGG-ACAAATTTCATTTGCCCTGCATGTCATCCGTCGGCTTTGGTGAGCTTTGCG
GGCCGGCGGTCAGTTGTATAAAAGATGCTACGTGTTCCTGTGGCTGTGGAGTGCTCTCCGATA----------------T
GTTCATGTACGTTGATGTTTTAAACTTGTTTGTTTCTACAACACATTGCTTTGTGACAGTAAGCACGACTTTTATCGGTC
AAAATCACGGTTCTGATCTTTGTGGCATAGTTTGGAACGATTGGACCCATTCT------AAAAAAAACGAATTTGACCAT
TTGCTATCGCCATCATCCTCAGCGGTAGGATTTAACGTACTACCACCAGGATCTATGGCGGTAGAAATATGGTCGTTGTC
GCAGCACTCGTTGACGTGGACAAGTAGCTAGCACATTAAAACTTATGCCAGCGTCCTTGACGGTAGACATCTTGAGCGGG
TAAGAGATTGGGGGCTTTTGTGGGCGGTAGGGCATGTAACCCTATTACCAAGGTCTATGGCGGTAGGGTACTAAATTTAG
CCT-AAACGATACTAAAAGTTCTCGGATGTTTCTTTAGGCGGTAGGGCATGTAACCCTATCGCCAGGAAAGTGGCGGTA-
GGCCCATGTAACCACTCCAGAGCTCATTTACCATTCTGACTAGCACACCGTTGACATCAAATAACAATATAATTCAGTAT
AACAACAATATAATTGCGTATAACCATAACATTCAAATTCCACCATACAACAATTGTCCATCACAAAATAATTTGATCAC
AAATAGTTCAACATACCAAGTTCAATATAGAGTGTTCAACATACCAAGTTCAACATAGAGTGTTCAACATACCAAGTTCA
ATGCAACCAAATACAAGGTTCTAAAATACTACATAGCAAGCAAGTGTCCATATTACTTTCTTCCCCTCTTGTTTAGACGA
TCCTCGGCTCTCTTTGCGTGGTCTTCATTTGGTTTGAGACCGCCTCGAGCACGCTCTCTCTGGAACGGCGATGGACTA-T
AAGGATCCTCTATCCTCTATAGCCCCCTTCCTCATTTGGGACGACTGAGTGAGTGGAGGTCCATCTG
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-------S--------------S----------------
---------------------S----------------------SSSS-------------------------------S
---S--S---------------S-----------------------S-------S-SSSS-S-S-SSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------------------------S--
------------------------------S----S----------S---SSSSSSSSSSS------------------S
----S----S--------S-----------------SSSSSSS-------------------------------------
--------------------------S------------S----------------------------------------
--------------------------------------------------------------S-----------------
---------------------------------------SSSSSS------------------S----------------
----S---------------------------------------------------------------------------
------------------------------------------------------------------------S-------
------S-------------------------------------------------------------------------
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-------------------S-------------S-----------------------S----------------------
---------S---------------SS---------------------------------------S-------------
-----------SS-----------S-S--------------------SSSSS----------------------------
------------SS-S--------------------------------S---------S---------------------
------------------------------S------S-----------S--S--------------S------------
--S----------------------------S------------S---------------S-------------------
------------------------------------------------------------------S-------------
-----------------------------S------------------------------------------S----SS-
S-SSSSS---S-----------S--------------S------------S-----S-----------------------
---------------------------------------------------------S---S------------------
--------------------------------------------------S----------------------S------
----S--------------S-SSS-------------S---S-S------------------S-----------------
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---------------------------------S------------S---------------------------------
------------------------------------------------------------------------S-------
---------------S-----------------------------S-----------------------------S----
---------------------------------------------------------S---S-SSSSSSSSSSSSSSSS-
--S------------S----SSS-------------------------------------------------------S-
--------S---S-S------------------S-S-S----SS-SSS-SS--SSSSSS-S-----SS--S--SSS-SS-
------------S--SS---------------------------------S--------SSS-----S--S-----S---
--SSSSS-SS---------S-------S------------S----S---S--S-------------S-----S---S---
----S--S-----SS-S---------------------------SS---------SSSS------S----S---------
-------S-------------SS-----------SS------S---S-----------SS-S---S---SS-S-SS-SSS
----------SS-----------------------S--S-----------------------------------------
---------------------------------------S-------------------------S--S-----------
----------------------------------------------------------S-------------S-----SS
--S-S---------------------------------------------------------S---------------S-
-----SS------------SSS-------------S--S--------------------------S-----------SS-
------------S-S------------------S----------S----------S-----------
>forward_248
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--------------------------------------------------------------------ACCGTGCTAACA
TGCTGACA------------------------------------------------------------------------
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>reverse_1843
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--GCGTAGGAACGGTGCGTATA----------------------------------------------------------
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>forward_1347
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-----------------------------------------------GCAGCCTGCGTGTAAACAAT-------------
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>reverse_3030
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---------------------------------------------------------------------CCTTGATGATG
GGCCCATGT-----------------------------------------------------------------------
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