>input_sequence_58439
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------------------------------------------------------------------ATGAATGCAGGTGT
TCTTCCCACTCTCGGTCTTCTTGTATCAGCTTCCACACAC-TTGGCT------------GTAACAGGGC--AATCAATGG
CGCTCCTACGTCCGCGCCTAGCCGCC---CTGCTCGCTCTGTGCGCGTGCGCCATGGCTGCGCCGGCGGCCGCCGCCAAC
GTGTCGATCACGACGTGCCGATCCTTCTGCGGCAACATCACGGTGGACTACCCGTTCGCGCTCCACGCCGGGTGCGGCCA
CGCGGGGTTCCGCGACCTGCTCTACTGCATCGACCGCACGCTCATGCTGCACCTCCCCTCGGGCTCCTACCGCGTCCTCG
ACGTCGACTACGCCTACCGCGGCCTCACCCTGCACGACCCGGCCATGTCCGACTGCCGCGCCATCGACCGCTCCCCGGGC
GGCCGGGGCAACGGGTTCGTCGTCGAGCCGTGGCGCGCGCCGTTCCTGGCCCCGGACCCGGACAACGTGTTCCTCCTCCT
CGGCTGCCGCGCCAGCTCGCCGCTCTTCCAGGGCTTCCCCGACCGCCACCTGCCGTGCCGGAACGTGTCCGGGATGGGGT
GCGGCGACTACTACGGCTGCCCCGCGTGGGACGACTACGGGCGCCGGCCGTCCGGCGCGGCGTACGGGTCGGCCGTGCCG
CCCGAGTGCTGCGCGGTGTCGTGGGGCGCCATCCGGGCGGTGAACGTGAGCCGTCTCCAGTGCGAGGGGTACAGCAGCGC
GTACAGCCTCGCGCCGGTGCGCGCCGAGGGGGCCGGCGGGTGGGCGTACGGCATCCGGGTGGCGTGGGCGCTGCCGGAGG
CGAACCGGGGGTTCTGCGGCGCGTGCCGCGCCACGGGCGGGGTGTGCGGCCACGACGTGGAGAGCCGCGGCGACCTGTGC
CTCTGCGGTGACTGGAACTCGACCTCCAACTGCGACTCCTCGGCGGACGCCGCGCCGTCAAGCGCCGCGGCGCCTGGCGC
CGCCATTGCCGCCCTTCTCTTGGCCCTTCTCGCCTCAGGTACCGTAACATATTGACGTAGTACATTTCAGTAGTCTCTTG
CTTCTTAGCTGCGATGCATCATTCCATAA---------------------------------------------------
---------GATCTGAATTTGGATGTTGTTTCGAGTTCTCTGCGCCTCTCATTTCATTTGCTGATAGAGGTGTCGCTACG
TCTGATGCAGGATTGTCGTCCGGATCAATAGCCAACATTTGA--------------------------------------
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>chr1D_1_TraesCS1D01G255300
GGATTGAATACCAATATCACAGGATCTTGATATTCAGATTGAATGCCAACATTTCTGTTTGGATGTTTACGTATTCGGAA
CATGGACTTGATATTGAGGTTGAATGCCAAAATGATGTTTACAATTTACATGTTTCAAACTGAAGTATCCATGACATGCC
CATTTATTGGAATGATCCATCATCCAATTTCTTCTTACGAGTA--------ATATCTTGAGCGAGAAAGATGGAAGCATG
TGCGTGA-GGAAGCATCTATACTATCTTGGACCAGAAAGAATACAACTACTCTTTGCTATTGCTTGCAACAAACTCAGCT
TCGTGCACCTGCAATTAAAGTAGAGGATGCACACAGAGAGCACACAGGCACATAGGAACAAACTCCGAAATATTACAAAA
TAAAAATCATAAAGTATACGTAGGTAAGTAAATCGCGAGCCGTATTTGATAAATATTTATTTACAC----AATCACATTA
ATACGATCAATTAAATCAC-AGCTAATGTATTAAAATATTTATACTCAGTTGCAATGCACGAACAATTATCTAGTGTATT
AAAGACAAAGTATTATACCTTCATAGTTGACATGTAGTAGTTTGATTTGTAAGTTTAGCATTTTTGTCCATGCAAAAAAA
AAAGGTTTAGCATTTTTGTTTGTTTATA---TATGTTAATTTTGAATGCCCATCCTTAAAATCCGGGACCCACTGCACGC
CTGCCTTGCAGAATTCTCAAATGTGAAATGTAAACAGTTTCAAAAGTTTAGGGTGTGTATATTTTTG--------GTCCT
GGACCTGAAGGGTGCAATCTACAATTTTGTTGCGACTTTCACTTTTTACAAGATGTAAGAGAGAGCAAGAATTCCAAAGC
AGTGGACATGAAGACTAATTACATAATAATAATTCAAAAGAAA-GCTAAAGCAAAAGCCCCGAAAAAGAAAAGCAAATGA
TGCCTCCCAGCTCTTCGCCAAAAGCAAGCAAGGAATCGATCCGTGCTGCTTTGTTGCTTAACTAGAATGAATGCAGGTGT
TCTTCCCACTCTCGGTCTTCTTGTATCAGCTTCCACACAC-TTGGCT------------GTAACAGGGC--AATCAATGG
CGCTCCTACGTCCGCGCCTAGCCGCC---CTGCTCGCTCTGTGCGCGTGCGCCATGGCTGCGCCGGCGGCCGCCGCCAAC
GTGTCGATCACGACGTGCCGATCCTTCTGCGGCAACATCACGGTGGACTACCCGTTCGCGCTCCACGCCGGGTGCGGCCA
CGCGGGGTTCCGCGACCTGCTCTACTGCATCGACCGCACGCTCATGCTGCACCTCCCCTCGGGCTCCTACCGCGTCCTCG
ACGTCGACTACGCCTACCGCGGCCTCACCCTGCACGACCCGGCCATGTCCGACTGCCGCGCCATCGACCGCTCCCCGGGC
GGCCGGGGCAACGGGTTCGTCGTCGAGCCGTGGCGCGCGCCGTTCCTGGCCCCGGACCCGGACAACGTGTTCCTCCTCCT
CGGCTGCCGCGCCAGCTCGCCGCTCTTCCAGGGCTTCCCCGACCGCCACCTGCCGTGCCGGAACGTGTCCGGGATGGGGT
GCGGCGACTACTACGGCTGCCCCGCGTGGGACGACTACGGGCGCCGGCCGTCCGGCGCGGCGTACGGGTCGGCCGTGCCG
CCCGAGTGCTGCGCGGTGTCGTGGGGCGCCATCCGGGCGGTGAACGTGAGCCGTCTCCAGTGCGAGGGGTACAGCAGCGC
GTACAGCCTCGCGCCGGTGCGCGCCGAGGGGGCCGGCGGGTGGGCGTACGGCATCCGGGTGGCGTGGGCGCTGCCGGAGG
CGAACCGGGGGTTCTGCGGCGCGTGCCGCGCCACGGGCGGGGTGTGCGGCCACGACGTGGAGAGCCGCGGCGACCTGTGC
CTCTGCGGTGACTGGAACTCGACCTCCAACTGCGACTCCTCGGCGGACGCCGCGCCGTCAAGCGCCGCGGCGCCTGGCGC
CGCCATTGCCGCCCTTCTCTTGGCCCTTCTCGCCTCAGGTACCGTAACATATTGACGTAGTACATTTCAGTAGTCTCTTG
CTTCTTAGCTGCGATGCATCATTCCATAA---------------------------------------------------
---------GATCTGAATTTGGATGTTGTTTCGAGTTCTCTGCGCCTCTCATTTCATTTGCTGATAGAGGTGTCGCTACG
TCTGATGCAGGATTGTCGTCCGGATCAATAGCCAACATTTGACGGCGTCATGTGTTCATCCAACAGTGACGACTGACGAG
CAGTTCCTGCCGCCATGATTACCTCCGCCGTCTGGTGTACCGCCATAGTACTTTTGTGTAGACAAAAACTAGTGCGACTG
AAATGTTTATCTGCGACATAAATCTTTGATTAGGAAATCAGTGCCATATTACATTCGAAGTATATCTACAAAACATATGC
GAGTTAGAATTGGTGTGCTTTGTGAGCTTGCTCGATTCATCATGCTTATTCGATTTGATGTGGCTCCGTTT-GCATCTGT
GACTTGTGAGTGAGACGAGAGCACTATTTCTCACAGGAAGAGAAAGAAAAAAGAGCGTCGCTTCCGGGAGGTTTCGAACC
TGGGTCGCCTACTTGATCGTGAGGGCAGTTAGCCCACGCTAGACTGCAGTCGCCTAAATAGTAGGTCGGGCCTTCTTAAG
TTGAAACGAACCGTGTTTCCATTGTTTCTTTTCCAGGATTTTTCAGTTTTTTTCCACTATTTTCATTGATTTTTCTTTCT
CCTTTTTTGTTTTTTCATTTTCTTTTAATTTTTTTGGTTTATTTTGTTTTTTGGTCTTCTTCTCCATTTTTTGTTTGGTT
TTCTTTTTTCTTCTCCATTTTTTCTTTGGGTTTTTTCTTATTTTTTTCGTTTTCACTCTACATTTTCGTATATGTCAAAA
ATATTTTCTTAATAAGTGATCAACATTTTTTGTACACACGTTCATCATTGTGCGAACGCTTATTCAACATTTTTCAAATA
CTTGTTCAATATTTTAATACTTATTAAATATTTTTTCAATAATTTCCAAATACTCGTTCAACATTTTTCAAAATACTTGT
TCAACATTTTAAATACTTATTCAACATTTTTCAAATACTCATTCAACATTTTTTAATACTTATTCAACATTTTTCAAATA
CTTGTTCAACATTTTTAATATTTATTCAATATTTTTAGATACTTGTTCAATTTTTTTAATATGCAATCATCAATTTTCAA
ATA
>chr1B_3
--ATTGAATACCAATATCACATGATATTGATATTTAGATTGAATGCCAATATTTCTATTTGGATGTTTAGGTATTCGGAA
CACGAACTTGATATTGAGGTTGAATGCCAAAATGATGTTTACAATTTACATGTTTCAAACTGAAGTATCCATGACATGTT
CATGTATTGGAATGATCCATCATCTAATTTCTTCTTACGAGTACTTCTATAATATCTTGAGCCAGAAAGAGGGAAGCATG
TGCGTGTGGGAAGCATCTATAATATCTTGGACCATAAAGAATACAACTACTCTTTGCTATTGCTTGCAACAAACTCAGCT
TCGTGCACCTGCAGTTAAAGTAGAGGATGGACAGAGAGAGCACACATGCACATAGGAACAGACTCCGAATTATTACAAAA
TAAAAATCATAAAGTATAAGTAGGTAAGTAAATCACGAGCAGTATTTAATAAACATTTATTTACAC----AATCACATTA
ATATGGCCAATTAAATCAT-AGCTAACATATTAAAATATTTATACTGAATTGCAACACAA-GACAATTATCTAGTTTATT
AAAGACAA------------------------------------------------------------------------
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>chr1A_436
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--------------------------------------------TTTTATAAACACTTAATTTAAATAATAAACACATTA
ATATGAGCTATTAAATCACGAGCTAACATACTTAAATATTTGTACCCCTGCAAAC-GCACGGACAATTATCTAGTCTACT
AAAGACAAACTATTACACCTTCATAGTTGATATGTAGTAGTTTGATCTGTAAGTTTAGCAAAAAAAAATTGCGAATATAA
----GTTTAGCATTTTTGTTTGTTTATAGTATATGTTAATTTTGAATGCCCATCCTTAAAATCCAGGACT-----CACGC
CTGCCTTGCAGAATTCTCAAATGTGAAATGTAAACAATTTCAAGAGTTTAGGGTGTTTAGATTTTATTTTATTTTGTCCT
GGACCTGAAGGGTGCGATCTACTATTTTGTTGCAACTTTCACTTTTTACAAGATGTAAGAGAGAGCAAGAATTCGAAAGC
AGCGGACATGAAGACTAATGAGATAATAATAATTCAAAAGAAAAGCAAAAGCAAAAGCCCCGAAAAAGAAAAGCAAATGA
TGCCTCCCAGCTCTTCACCAAAAGCAAGCAAGGAATTGATCCGTGTTGCTTTGTTGCTTAACTA----GAATGCCGGTGT
TCTAGCCACTCTCGATCTTCTTGTATCAGCCTCCACACACATTGGCCATCTCGCAAGCCGTGACATGGCAAAATCAATGG
CGCTCCTCCGTCCGCGCCTAGCCGCCGCCCTGCTCGCTCTGTGCGCGTGCGCCATGGCTGCGCCGGCGGCCGGCGCCAAC
GTGTCGATCACGACGTGCCGGTCCTTCTGCGGCAACATCACGGTGGACTACCCGTTCGCGCTCCACGCCGGGTGCGGCCA
CGCGGGGTTCCGCGACCTGCTCTACTGCATCGACCGCACGCTCATGCTGCACCTCCCCTCGGGCTCCTACCGCGTCCTCG
ACGTCGACTACGCCTACCGCGGCCTCACTCTGCACGACCCGGCCATGTCCGACTGCCGCGCCATCGACCGCTCCCCGGGC
GGCCGGGGCAACGGGTTCGTCGTCGAGCCGTGGCGCGCGCCGTTCCTGGCCCCTGACCCGGACAACGTGTTCCTCCTCCT
CGGCTGCCGCGCCAGCTCGCCGCTCTTCCAGGGCTTCCCCGACCGCCACCTGCCGTGCCGGAACGTGTCCGGGATGGGGT
GCGGCGACTACTACGGCTGCCCCGCGTGGGACGACTACGGGCGCCGGCCATCGGGGGCGGCGTACGGGTCGGCCGTGCCG
CCCGAGTGCTGCGCCGTGTCGTGGGGCGCCATCCGGGCGGTGAACGTGAGCCGGCTCCAGTGCGAGGGGTACAGCAGCGC
GTACAGCCTCGCGCCGGTGCGCGCGGAGGGGGCCGGCGGCTGGGCGTACGGCATCCGGGTGGCGTGGGCGCTGCCGGAGG
CGAACCGGGGGTTCTGCGGCGCGTGCCGCGCCACGGGCGGGGTGTGCGGCCACGACGTGGAGAGCCGCGGCGACCTCTGC
CTCTGCGGTGACTGGAACTCGACCTCCAACTGCGACTCCTCGGCGGACGCCGCGCCGTCAAGCGCCGCGGCGCCTGGCGC
CGCCATTGCCACTCTTCTCTTGGCCCTTCTCGCCTCAGGTA----AACATATTGACGTAGCACATTTCAGCAGTCTCTTG
CATCATCTCATATATTTTTCACCATGCATTTCGCAACCTCGATCACCTCACGATTGTGGGATTAACTGACTAACTAAACG
CAGCAGGTCGATCTGAATTTGGACGTTGTTTCTAGTTCTTTGTGCCTCTCATTTCATTTGCTGATGCAGATGTCGCTACC
TCTGGTGCAGGATTGTCGTCCGGATCAATGGCGAACATGTGACGGGGTCATGTGTTCATCCAACAGTGACCACTGACGAG
CTGTTCGTGCCGCCATGATTACCTCCGCCGTCTGGTGTACCGCCGTAATACTTTTGTGTAGACAAAAACTAGTGCGGCTG
AAATGTTTATCTGCGGCATAAATCTTTGATTAGGAAATCAGTGTCATATTACATTCGAAGTATACCTACAAAACATATGC
GAGTCACCATTTGTGTGCTTTCTGAGCTTGCTCGATTCATCATGCTTATTCGATTTTATGTGTCTCCGTTTTGCATTTGT
GA------------------------------------------------------------------------------
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>chr1B_547
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AAAGACAAAGTAGTATACCTTCATAGTTGATATGTATTAGTTTGATTTGTAAGTTTAGCATTTTTGTCCATGCAAAA--A
AAAGGTTTAGCATTTTTGTTTGTTTATA---TATGTTAATTTTGAATGCCCATCCTAAAAATCCGGGACCCACTGCACGC
CTGCCTTGCAGAATTCTCAAATGTGAAATGTAAACAGTTTCAAGAGTTTAGGGTGTTTAGATTTTTG--------GTCCT
GGACCTGAAGGGTGCAATCTACAATTTTGTTGCAGCTTTCACTTTTTACAAGATGTAAGAGAGAGCGAGAATTCGAAAGA
AGTGGACATGAAGACTATTGACATAATAATAATTCAAAAGAAA-GCAAAAGCAAAAGCCCCTAAAAAGAAAAGCAAATGA
TGCCTCCCAGCTCTTCGCCAAAAGCAAGCAAGGAATCGATCCGTGCTGCTTTGTTGCTTAACTA----GAATGCAGGTGT
TCTTCCCACTCTCGATCTTCTTGTTTCAGCCTCCACACAC-TTGGCCATCTCGCAAGCCGTGACAGGGC--GATCAATGG
CGCCCCTACGTCCGCGCCTG---GCCGCCCTGCTCGCTCTGTGCGCGTGCGCCATGGCTCCGCCGGCGGCCGCCGCCAAC
GTGTCGATCACGACGTGCCGGTCCTTCTGCGGCAACATCACGGTGGACTACCCGTTCGCGCTCCACGCCGGGTGCGGCCA
CGCGGGGTTCCGCGACCTGCTCTACTGCATCGACCGCACGCTCATGCTGCACCTCCCCTCGGGCTCCTACCGCGTCCTCG
ACATCGACTACGCCTACCGCGGCCTCACCCTGCACGACCCGGCCATGTCCGACTGCCGCGCCATCGACCGCTCCCCGGGC
GGCCGCGGCAACGGGTTCGTCGTCGAGCCGTGGCGCGCGCCGTTCCTGGCCCCGGACCCGGACAACGTGTTCCTCCTCCT
CGGCTGCCGCGCCAGCTCGCCGCTCTTCCAGGGCTTCCCCGACCGCCACCTGCCGTGCCGGAACGTGTCCGGGATGGGGT
GCGGCGACTACTACGGCTGCCCCGCGTGGGACGACTACGGGCGCCGGCCGTCGGGGGCGGCGTACGGGTCGGCCGTGCCG
CCCGAGTGCTGCGCGGTCTCGTGGGGCGCCATCCGGGCCGTGAACGTGAGCCGGCTCCAGTGCGAGGGGTACAGCAGCGC
GTACAGCCTCGCGCCGGTGCGCGCGGAGGGGGCCGGCGGCTGGGCGTACGGCATCCGGGTGGCGTGGGCGCTGCCGGAGG
CGAACCGGGGGTTCTGCGGCGCGTGCCGCGCCACGGGCGGGGTGTGCGGCCACGACGTGGAGAGCCGCGGCGACCTGTGC
CTCTGCGGTGACTGGAACTCGACTTCCAACTGCGACTCCTCGGCGGACGCCGCGCCGTCAAGCACCGCCACGCCTGGCAT
CGCCATTGCCGCTCTTCTCTTGGCCCTTCTCGCCTCAGGT-----AACATATTGACGTAGTACATTTCAGTAGTCTCTTC
CAGCATCTCATATATTTTTCACCATGCATTTCGCAACCTCGATCACCTCACGGTTGTGGGATTAATTGACTAACTCAACG
CAGCAGGCTGATCTGAA-TTTGATGTTGTTTCGAGTTCTTTGTCCTTCCCATTTCATTTGCTGATACAGATGTCACTGCC
TCTGGTGCAGGATGAGGGACAGAGGGAGTGTGCC---TGTGAAGGCGTCATGT-TTCATCCAACAGTGGCCACTGACGAG
CTGTTCGTGCCGCCATGATTACCTCCGCCGTCTGGTGTACCGCTGCAATACTTTTGTGTAGACAAAAACTAGTGCGACTG
AAATGTTTGTCTGCGGCATAAATCTTTGATTAGGAAATCAGTGTCATATTACATTCGAAGTATACCTACAAAACATATGC
GAGTCAGAACTGGGGTATATTGTGAGCTTGCTCGATTCATCATGCTTATTCGATTTGATGTGGCTCCGTTT-GCATTTGT
GA------------------------------------------------------------------------------
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>SNPs
SS-------------------S---S--------S--------------S------S------------S----------
--S-S-------------------------------------------------------------------------SS
---S--------------------S-------------------------------------S-------S---------
------S--------------S------------S---------------------------------------------
-------------S---------------S---S------------S-------------S--------S----------
------------------S---------------S-----S------S-----S--------------------------
---S--S-------------------SS--------------------S------S-----S-------------S----
------------------------------S----------------------------------------------S--
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-------------------------------------------S------------S--S--------------------
---------------------------------S----------------------------------------S-----
-------------------S--------------------------S---------------------------------
----------------------------------------------------------------SSSS------------
--------------S---------------S---------------S--------------S------------------
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--------------------S-----------------------------------------------------------
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----------------------------------------------------S--S------------------------
-----------------------------------------------------S--------------------------
------------------------S--------------S----------------------------------------
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------------S----------------------------SSSS-----------------------------------
-S--S-SS-SSSS--SSS---SSSSSS-S---------------------------------------------------
---------------------------------------S--S-----------------------S--S---------S
----S------------------------S--------S-------------------------------S---------
-S----S-------------------------------------S--S--------------------------------
---------------S---------------------------S--------------------S---------------
----S-----------------------------------------------------------------------S---
--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSS
>forward_367
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---------------------------TGCACACAGAGAGCACACAG---------------------------------
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>reverse_1221
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--------------------ATCCTTCTGCGGCAACATCA----------------------------------------
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>forward_1055
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---------------------------------------------------------------------------GGTGT
TCTTCCCACTCTCGG-----------------------------------------------------------------
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>reverse_2639
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------------------------------------------------------------------------------CC
TGGGTCGCCTACTTGATC--------------------------------------------------------------
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