>input_sequence_65011
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----------------------------------------------------------------ATGGCGATAGCGCTAG
CGCAAACAAGCCGCGCGAATCTGGGCCTCCGCCTCAATCATGGCGCTGTAGTGGCCTCACCTTCTTGGAAGCTTTACCAC
AACCCTCACTACTTCTCACCTCGCGGCGACTCCTCCGGCCCCTCTCGCAGATCCCCTTCTTGCCCAGAGCACCGCAGACC
TATGATCGTGGCGAATTTCGACGAAGACGACGGCGGCG---GCGGCATGGAGCGGCAGCTGGGGTACGGCGACGGGGGCG
CGACGTCGGTGCCGGAGCTCCTGGCGCGGGTCGAGGAGCTCGCGGCGGAGCTCGAGTTCGAGAGGCGCATGCGACGCAAG
GTTGAGGCGCTCAACGAGGCGCTCGCCGCCGAGCTCGCCG----------------------------------------
--------------AGGAGCGGCGCCGGGTCGAGGCGGAGCGCGCGAGGATGCGGGAGGAGCTCGACGAGGAGCGGCGGA
TGCTGCGCGTCGCGGAGCTGTGGCGGGAGGAGAGGGTGCGGATGAAGCTCGCCGACGCCCGGGCCGCCGTCGAGGAGAAG
CTGCGGGAGGTCGCCGACGCCGGGCAGCGTGCTGCCGATGCCACCGCCGCTGCCGAAGGCTGCAGCTGCAGGAGCGGCAG
CCCGATCGGCGGCAAGGCAAGCCCGGCCAGTGTTGGGCAGCAAAGCCCAGCGAGCAGTCGGCACGGCCAACAAAGCCCGG
CGAGCGGTCAGCACTCCCAATCGCACCGGCGAGAAGTCACTGGCGGCGAGAACCCTCACATCAGGAGGGGGATCAAGGGG
TCCGTGGAGTTCCCGAGGGCCGTCCGTGTGCGGCCGCGCGGCGAGGAGCGCGTGGATCTGGTGTCCAACATCGAGTGCCA
ACGGGCGCAGCTGCGCGTCCTCATGCGGCACCGGAGTCCCGCCACCGCCGGCATGCCGGGCCTCGTCGGCGCGGCGCCGG
ACAACCTCGTCGTGTAA---------------------------------------------------------------
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>chr1A_1_TraesCS1A01G218300
GGCCGCGGCCCGTGGTAGTGGTGGAGGGAGAGGCGGCAGAGCTCTGGTGAAGACGAAAACATAGTTGCGGTGGCAAACCT
TGAACTGCTCGAGGATGATCTCAGCGATGCGTGGAGATGCAACGTGAAAGCGGAAAATGAGTGGTGAGCGCATAGCAACG
AAGAAGTCGGCGGCACAGCCACCAAGAGCAGCCTGGAGTAGAGCAGCGACGACAATGGTGTCGAGCTGGCGGTTGGAGAA
GTCGAAGACGACGTAGAGAGACGACGCGAGGTGGAGCTCAGGGGTGGTGATGTCGAGGCGAAAGTAGCGGCTGCAGTCGT
CCTTGAACTCGAGCCCCATGGCGTTTCCGCAGCCAAGGAAGTATC-GGAGAGCGACTTGACCGGCCCTGGCATAGGGCAA
GTCGAGGAAGATGGATGGAGGTGGCGCAACCGTGGGCGTGAGCACGTCGTTGGGGTGGATGGTGAGGGTGGCGGGTGGTG
GAGGTGAAGGTGAAGGG------------GGGAGGAGGTGCTCGGCCACCGTGGTGGCCGCCGGAGCAGTCGGAGGTGGT
GGAGAAGGGAGGGGAGGGAGCGAGAGCGAAAGCGAGAGCGGTCGAGGCATCGTTGCCCATGAAGATGGGAGTGATATCCC
AATTTGTTTTAGCAAACTTCACGTTCCACTTAAGAAATGAGAAAAAAAAAAGGTTGAGCATGAAGTGAAGTGGCCAGCTC
ATGCACACACATGCTCCCTCCCGGTCTGCCATAAGGCAGCAGCATGCCAGAC-GACGGAAAGAAGTTAAAATCTTACTGC
AGTGTCTGCTGAAGAGAAGACGATGGAGCATG-ATCGCCATGATGGCAGCTCAGAGAATTGAGATCGTGCATGTGAGACG
TGTGACCTTCCTTCTCCTCATCGCC-----TCCCTCCCCTTTTACAGCTCACAAAGGCAGCGTCGACAAGAAGTA----G
TAAAATATTCGATCTCGTGCTCGGAAAGATGGCGTAGGTGACCCGGCGCGCGAAAGCGGAGGCCATGGCGATAGCGCTAG
CGCAAACAAGCCGCGCGAATCTGGGCCTCCGCCTCAATCATGGCGCTGTAGTGGCCTCACCTTCTTGGAAGCTTTACCAC
AACCCTCACTACTTCTCACCTCGCGGCGACTCCTCCGGCCCCTCTCGCAGATCCCCTTCTTGCCCAGAGCACCGCAGACC
TATGATCGTGGCGAATTTCGACGAAGACGACGGCGGCG---GCGGCATGGAGCGGCAGCTGGGGTACGGCGACGGGGGCG
CGACGTCGGTGCCGGAGCTCCTGGCGCGGGTCGAGGAGCTCGCGGCGGAGCTCGAGTTCGAGAGGCGCATGCGACGCAAG
GTTGAGGCGCTCAACGAGGCGCTCGCCGCCGAGCTCGCCG----------------------------------------
--------------AGGAGCGGCGCCGGGTCGAGGCGGAGCGCGCGAGGATGCGGGAGGAGCTCGACGAGGAGCGGCGGA
TGCTGCGCGTCGCGGAGCTGTGGCGGGAGGAGAGGGTGCGGATGAAGCTCGCCGACGCCCGGGCCGCCGTCGAGGAGAAG
CTGCGGGAGGTCGCCGACGCCGGGCAGCGTGCTGCCGATGCCACCGCCGCTGCCGAAGGCTGCAGCTGCAGGAGCGGCAG
CCCGATCGGCGGCAAGGCAAGCCCGGCCAGTGTTGGGCAGCAAAGCCCAGCGAGCAGTCGGCACGGCCAACAAAGCCCGG
CGAGCGGTCAGCACTCCCAATCGCACCGGCGAGAAGTCACTGGCGGCGAGAACCCTCACATCAGGAGGGGGATCAAGGGG
TCCGTGGAGTTCCCGAGGGCCGTCCGTGTGCGGCCGCGCGGCGAGGAGCGCGTGGATCTGGTGTCCAACATCGAGTGCCA
ACGGGCGCAGCTGCGCGTCCTCATGCGGCACCGGAGTCCCGCCACCGCCGGCATGCCGGGCCTCGTCGGCGCGGCGCCGG
ACAACCTCGTCGTGTAACAATGTACTCCTACTCACTGCTTAGTTACTCTAATCATATGTAACTTTCACCAGGATA----A
TG-AAAAAACAAGCAACTTGTGCGCTGCAGTCGTTTGCTTC-AGAAGCTTTGAGGTGCTCTAGTCTCATCTTGCTTAACG
TTTCTCC-AATTGGCGGGGGCT---TGGTTTTCCTTCGAGTGTTTGTGCCGCTGAAGCTGGTCTCAGTGGTGGAATGGAG
CTCGGAGTGGCCATTTTGATTCAGCGGCATGACGCGTTGAGATTTTGGGACACACTTGTTTGGTTGGCGTCCGTCCGTCT
GATGTCACCCGCAGGACTCCCAGTTCCTGCCATCTTTCCTGGAGTCCAGTGCTCGAGTGGACTAGGGATCAG------TG
TGAGGGTGCCTTGCTTAGTAGAGGGACAAATCACTGATTTAACCCTTTAGGGTAACTTTAGCACACAAAAAAACCTTTTT
TTTAAATAAAACGATTTGACCTCTTCTTGCAATGGCCCAGCCCTTCCGCGTTGCAGCACTAAGTGGTTGTTTGGATACCA
AATACAGTTTTGCTAGAACTCATCTAGATGAGATTTAATTTGGTCTCATTCATCTTTTATAGCCATTGGATGTGATGCTA
TAAGATGCGTATGTGCTGACGTGGGTTGTATCCGTTCTTGTTTTCCAGATGAATGAGACCAAATTACGTCTCATCTAGAT
GAGTTCTAGGTACTCCCTACCAAATATAATCCACGAAGATAGGGAAAACCAGTTTTTAGCTGCGTTTTAGCAAAATCCGT
TTTAGTAAGTAATTGGTGAACAACCGGTTTATAGAAATATATGTTTGGCCTTTTTGAACACAGTACAGAGGCAAGCAAAG
TGTATAGCTGACTTAATTGGATATCTACTCGTCCGTGACCTTCTTCTCTCTCACACACATCTCGCAAATTGGCCATTGGA
GACCTGCCAAGCTCCATCCTCAAGCCCTGATCGTTGTCACAGTCCCATGACACCGCTGCTCCACTAGGGTCGG
>chr4D_1
GGCCGCAGCCGGTGGTGGTGATGGAGGGAGAGGTGGCAGAGCTCTGATGAAGGAGATAGCGAAGTTGCGGTGGCAAACCT
TGGACTGATCGAGGATGATCTCAGCGATGCGTGGAGATGCAACGTGAAAGCGGAAAATGAGTGGTGAGCACATAGCAACG
AAGAAGTCAGCGGCACAGCCACCAAGAGCAGCCTGGAGTAGAGCAGCGACGACGATGGTGTCGAGGTGGCGGTTGGAGAA
GTCGAAGACGATGTAGAGAGGCGACGCGAGGTGGAGCTCAGGGGTGGTGATGTCGAGGCGAAGGTAGCGGCTGCAGTCGT
CCTCGAACTCGAGACCCATGGCGTTGCCGCAGCCAAGGAAGCATCGGGAGAGCTACTTGACCGGCCTTGACGTAGGGCAA
GTCGAGGAAGATGGATGGAGGTGGCACAACCATGGGTGTGAGCGCGTCGTTGGGGTGGATGATGAGGGTGGCGGGTGGTG
GAGG------TGAAGGG------------GGCAGGAGGTGCGCAGCCGCCATGGTGGCCGCCAGAGCAGTCGGAGGTGGT
GGAGAAGGGAGGGG------------------------------------------------------------------
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>chr1B_13
------------TGGTGGTGGTGGTGGGAGGGGTGGCAGGGCTCTGGCGAAGGCGAAAGCATAGTGATGGTGGTGGACCT
TGGACTATTCAAGGATGATCTCAGCGATGCATGGAGATGCAACGTGGAAGCGGAAAATGAGTGGGGAGCACATAGCAACG
AAGAAGTCGGCGGCACAGCCACCAAGAGCAGCCTGGAGTAGAGCAGCGACGACGATGGTGTCAAGGTGGTGGACGGAGAA
GTCAAAGACAACATAGAGAGGCGACGCGAGGTGGAGCTCGGGGGTGGTGATGTCGAGACGAAGGTAGCGGTTGCAGTCAT
CCTCGAACTCGAGCCCCATGGCATTTCTGCAGGCGAGGAAGCATC-GAAGAGCCACCTGACTGGCCTTGACGTAGGGCAA
GTCGAAGAAGATGGATGGAGGTGGCGCTACCGAGGGGGTGAGCTCGTCGTTGGGGTGGGTGGTGAGGGTGGGGGGAGGTA
GAGGCGTGTCAGGGGCATGTGGTGGAGCAGGGAGGAGGTGCTCGGCAGCCGGGGTGGCCGCCGGAGCAAA----------
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-----------------------------------------------CGGGGGAGGAGGAGGCGGGAGCGGGAGCGGGAG
CG------------------------------------------------------------------------------
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>chr5A_40
---------------------------------------AGCTCTGGTGAAGGTGAAGGCGAAGCTGCGGTGGCAAACCT
TGGACTGCTCGAGGATGATCTCAGCGATGCGTGGAGATGCAACGTGAAAGCGGAAAATGAGTGGTGAGCACATAGCAACG
AAGAAATCGGCGGCCCAGCCACCAAGA---------------GCAGCGACGATGATGGTGTCGAGTTGGCGGTTGGAGAA
GTTGAAGACGACGTAGAGAGGCAGCGCGAGGTGGAGCTCAGGGGTGGTGATGTCGAGGCGAAGGTAGCGGCTGCAGTCGT
CCTCGGACTCGAACCCCATGGTGTTTCCATGGCCAAGGAAGCATT-GGAGAGCAACTTGACCGGCCCTGGCGTAGGGCAA
GTCGAGGAAGATGAATGGAGGTGGTGCAACCGTGGGCATGAGCGCGTCGTTGGGGTGGATGGTGAGGATGGCAGGTGCTG
GAGG------TGAAGGG------------GGGAGGAGGTGCTCGGCCGGCGTGGTGGCCGCCGGAGCAGTCGGAGGTGGT
GGAGAAGGGAGGGGAGGGAGCGAGAGCGAGAGCG----------------------------------------------
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>chr1B_619
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-----------------------------------------------------------------------TGATATCCC
AATTTGTTTTAGCAAACTTCACGTTCCACTTGAGAAATGAGAAAAAAAAAAGGTTGAACATGAAGTGAAGTGGCCAGCTC
ATGCACGCACATGTTCTCTCCTGGCCTGCCATAAGGCAGCAGCATGCCGGTC-GACGGAAAGAAGTT-AAATCTTACTGC
AGTGTCCGCTGAAGAGAAGACGATGGAGCATG-ATCGCCATGATGGCAGCGCAGAGAATTGAGATCGTGCATGTGAGACG
TGTGACCTTCCTTCTCTTCGTCGCC-----T-----CCCTTTTACAGCTCACAAAGGCAGCGCGCGACAAGTATAGTACG
TAAAATATTGGATCTCGTGCTCGGAAAGATGGCGTAGGTGACCGGGCGCGCCAAAGTGGAGGCCATGGCGATAGCGCTAG
CGCAAACAAGCCGCGCGAATCTGGGCCTCGGCCTCAATCATGGCGCTGTAGTGGCCTCACCTTCTTGGAAGCTTTACCAC
AACCCTCACTACTTGTCACCTCGCGGCGACTCTTCCGGCCCCTCTCGCAGATCCCCTTCTCGCCCAGAGCACCGCAGACC
TATGATCGTGGCGAATTTCGACGAAGACG---GCGGCG---GCGGCATGGAGCAGCAGCTGGGGTACGGCGACGGTGGCC
TGACGTCGGTGTCGGATCTCCTGGCGCGGGTCGAGGAGCTCGCGGCGGAGCTTGAGTTCGAGAGGCGCATGCGGCGCAAG
GTTGAGGCGCTCAACGAGGTGCTCGCCGCGGAGCTCGCCG----------------------------------------
--------------AGGAGCGGCGCCGGGTCGAGGCGGAGCGCGCGAGGATGCGTGAGGAGCTCGACGAGGAGCGGCGGA
TGCTGCGCGTCGCGGAGCTGTGGCGGGAGGAGAGGGTGCGGATGAAGCTCGCCGACGCCCGGGCCGCCGTCGAGGAGAAG
CTGCGGGAGGTCGCCAACGCCGGGCACCGTGCTGCCGATGCCACCGCCGCTGCCGAAGGCTGCAGCTGCAGGAGCGGCAG
CCCGATCGGCGGCAAGGTAAGCCTGGCGAGTGTTGGGCAGCAAAGCCCAGCGAGCAGTCAGCACGGCCAACAAAGCCCGG
CGAGCGGTCAGCACTCCCAATCGCACCGGCGAGAAGTCACTGGCGGCGAGAACCCTCACATCAGGAGGGGGATCAAGGGG
TCCGTGGAGTTCCCGAGGGCTGTCCGTGTGCGGCCGCGCGGCGAGGAGCGCGTGGATCTGGTGTCCAACATCGAGTGCCA
ACGGGCGCAGCTGCGCGTCCTCATGCGGCACAGGAATCCGGCCGCCGCCGGCATGCCGGGCCTCGTCGGCGCGGCGCCAG
ACAACTTCGTCGTGTAACAATGTACTCACTA------CTTAGTTACTCTAATCATATGTAACTTTCACCAGGATA----A
TGAAAAAAAAAAGCAACTTGTGCGCTGCAGTCGTTTGGTTC-AGAAGCTTTCAGGTGCTCTAGTCTTG---------ACG
TTTCTCGAAATTGGCGGGGGCTGGATGGTTTTCCT---------------------------------------------
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>chr1D_624
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----------------------------------------------------------------------------TCCC
AATTTGTT-TAGCAAACTTCACGTTCCACTTGAGAAATGAGAAAAAAAAG-GGTTGAACGTGAAGTGAGGTGGCCAGCTC
ATGCACGCACATGCTCCCTCCCGGCCTGCCATAAGGCAGCAGCATGCCGGTCTGACGGAAATAAGTT-AAATCTTACTGC
AGTGTCTGCTGAAGAGAACGCGATGGAGCATGAATCGCCATGATGGCAGCTCAGAGAATTGAGATCGTGCATGTGAGACG
TGTGACCTTCCTTCTCCTCGTCGCCTCCCTT-----CCCTTTTACAGCTCACAAAGGCAGCGTCGACAAGAAGTAA----
TAAAATATTCGATCTCGTGCTCGGAAAGATGGCGTAGGTGAGCGGGCGCGCGAAAGTGGAAGCCATGGCGATAGCGCTAG
CGCAAACAAGCCGCGCGAATCTTGGCCTCGGCCTCAATCATGGCGCTGTAGTGGCCTCACCTTCTTGGAAGCTTTACCAC
AACCCTCACTACTTGTCACCTCGCGGCGACTCCTCCGGCCCCTCTCGCAGATCCCCTTCTCGCCCAGAGCACCGCAGACC
TATGATCGTGGCGAATTTCGACGAAGACG---GCGGCGGCCGCGGCATGGAGCAGCAGCTTGGGTACGGCGACGGGGGCG
TGGCGTCGGTGTCGGAGCTCCTAGCGCGGGTGGAGGAGCTCGTGGCGGAGCTCGAGTTCGAAAGGCGCATGCGGCGAAAG
GTTGAGGCGCTCAACGAGGCGCTCGCCGCGGAGCTCGCCGAGGAGCGGCGCCGGGTCGAGGCCGAGCGAGCGAGGATGCG
GGAGGAGCTCGACGAGGAGCGGCGCCGGGTCGAGGCCGAGCGCGCGAGGATGCGGGAGGAGCTCGACGAGGAGCGGCGGA
TGCTGCGCGTCGCGGAGCTGTGGCGGGAGGAGCGGGTGCGGATGAAGCTTGCCGACGCTCGGGCCGCCGTCGAGGAGAAG
CTGCGGGAGGTCGCCGACGCCGGGCAGCGTGCTGCCGATGCCACCGCCGCTGCCGAAGGCTGCAGCTGCAGGAGCGGCAG
CCCGATCGGCGGCAAGGCAAGCCCGGCGAGTGTTGGGCAGCAAAGCCCAGCGAGCAGTCAGCACGGCCAACAAAGCCCGG
CGAGCGGTCAGCACTCCCAATCGCACCGGCGAGAAGTCACCGGCGGCGAGAACCCTCACATCAGGAGGGGGATCAAGGGG
TCCGTGGAGTTCCCGAGGGCTATCCGTGTGCGGCCGCGCGGCGAGGAGCGCGTGGATCTGGTATCCAACATCGAGTGCCA
ACGGGCGCAGCTGCGCGTCCTCATGCGGCACCGGAGTGCGGCCGCCGCCGGCATGACGGGCCTCGTCGGCGCGGCGCCGG
ACAACCTCGTCGTGTAACAATGTACTCACCA------CTTAGTTACTCTAATCATATGTAACTTTCACCAGGATATATAA
TG-AAAAAACAAGCAACTTGTGCGCTGCAGTCGTTTGCTTTGAGAAGCTTCCAGGTGCTCTAGTCTCATCTTGCTTAACG
TTTACCGAAACTGGCGGGGGCTGGATGGTTTTCCTCCGGGTGTCTGTGCCGCTGAAGCTGGTCTCTGGGGTGGAATCGAG
CTCGGAGTGGCCATTCTGATTCAGCGGCATGACGCGTTGAGATTTTTGGACACACTTGCTTCGGTTGG---CGTCCGTCT
GATGTCACCCGCACGACTCCCAGTTCGTGCCATCTTTCGTGGAGTCCAGTGCTCCAGTGGATTCAGGTTCAGTGTGACTG
TGAGGGTGCCTTGCTTAG--------------------------------------------------------------
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>SNPs
------S---S-----S----------------S------------------S-----S---------------------
--S------------------------------------------------------------------S----------
-----------------------------------------------------S-----------S--------------
--------------------S-----------------------------------------S-----------------
---S-------------------------------------S-----------S-----------------S--------
-------------------------------------------S------------------------------------
----S-SSSS-------------------------------------S--------------------------------
-----------------------------S----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------
-------------------------------S-------------------------S----------------------
------S-----------------S-----------------------S-S----------------S------------
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-------------------S-----------SSSSS--------------------------------------------
-------------------------------------------S------------S-----------------------
-----------------------------S--------------------------------------------------
--------------S---------------------------------------------S-------------------
-----------------------------SSS---------------------S--------------------------
S----------S-------------------------------------------------------------S------
-----------------------------S--------------------------------------------------
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---------------------------S-------------------------------S--------------------
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--------------------S-----------------------------------------------------------
---------------------------------------S---S------------------------------------
---------------------------SSSSSSSSSS-------------------------------------------
---------------------------------------------------S----------------------------
------S----------------------------S--S----S---------------------S-S--------S---
---------------S------------------------------S-----------S--S-S-S-SSSS---------
-------------S------------S-----------S---------------S------S-SS--S------------
------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_1004
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------------------------AAAGATGGCGTAGGTGACCC------------------------------------
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>reverse_2955
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--------------------------------------------------------------------------ATTGGA
GACCTGCCAAGCTC-----------------------------------------------------------
