>input_sequence_75807
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------------------------------------------------------------------------------AT
GTCGAGCGCCAGCCAGAAGCAGCAGCAGCAGCAGCAG---GCGAAGAAGCCGGCGGCGGCGGAGGACGTCGAGATCAAGA
AGGTCTTCTCCCGCTTCGACACGGACGGCGACGGCCGGATCTCGCCGTCCGAGCTGGCGGCCGTGTCGCGCGCCATCGCG
CCGCCG---GCCACCGAG---TCCGCGCAGGGCCGCGAGGTGGCGTCCATGATGGACGAGCTCGACACCGACCGCGACGG
CTACGTGGACCTCGGCGAGTTCGCCGCCTTCCACGGCCGCGGCCGCGAGGAGCGCGAGCTCGACGCCGAGCTGCGCGACG
CCTTCGACGTCTACGACATCAACGGCGACGGCCGCATCTCCGTCGCCGAGCTCAGCAAGGTCCTGAGCCGCATCGGCGAG
GGATGCAGCACCGAGGAGTGCGAGAAGATGATCGCCTCCGTCGACGTCGACGGCGACGGCTGCGTCGGATTCGAGGAGTT
CAAGAAGATGATGACCGCCGGTGACGCCGGCGCACCACCTCAACCCGAAGCGA---TCGCCGTGCCTGACAGCAACAAAC
CCAAGAAGGAGTGA------------------------------------------------------------------
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>chr3B_1_TraesCS3B01G045500
TGCCAAATATCGTACCATGACATTTGTATTATGCAGATGTTTTTTGAGTGTACACACCCTTCATGCCATGGGAGTCGAAC
GGAGCATTTCTGCCAGGAGTCAGCTGATAGCGAACGACTTTAGCAATCCTATGTGGCCAGAGGGCCGCGCCAAGATCCGT
GCAACGGTGAAGAGAGCGCTCGCCAGGGTTGGAAGCTCAGCGAACGTTCGCCAGATAGTATTTCCATAAATTAACCTATA
CGTACCCCCACACTAGTAAAAATCACCGGCGCAGTGAAAAAGGGAGTGGCGGCCATGATATCCTGCACGAACCTTTGTTG
TGAAAAGAGAACCTTTATTCTGAAAAGTTGCACGCCAAGAAGGCA-AGGATGGGACGCCACGAGCAACGACGACCTCACA
TGGGTGGGGATACTTCGCTCCGTCCACGCCCGCCGCGTCATGTGTCC----ATCCCTCCGCCACGCACACCCACTACACC
GTAGCCGCTCACGGCGACAAGTTCCACGAACCATGCCGGCAAAGGAATAAATAAACCGGTCCGCGACAGACGCAGACGTG
GCCGGTGATTCACGCGAGCTGCTGACTTCTCTCGAGCACCGAGGAACCTGCC-GCTCGGCGGGACGCGGAAAGGTCCGTC
CATACA-CCGAGATCCGCATCGCGCGCATCCGGCCGTACGCTTGCCCATCGCCGCGAAGCCACGCCTGGCCGGCCGACGC
GCCGCCCCACGCAACCGGGAGAAGAGAAGACAACGCGCTCGCCGCTCC--------------CCTCCCCGCGTCGGAGTT
ACTCC---ACTTCTTTATCCGGAAGGAGGGAGGGTGGTCGGTGCG------CGTCCGTAGCGCGTGCTCGCCGGTATTAA
TACCCC----AGAGCCCACTGCAACCTCCACCCATCCCACCA-CATTCAAGTCGAAGAAGCTCCTCGATCTCCATCACTG
CAACCAGCCACTTGAGCTC-TGAATCTTTGAAGCTCAGCCAGTTCGCCGCGACCACCGAGAGCCTCAAGTTTC--GCCAT
GTCGAGCGCCAGCCAGAAGCAGCAGCAGCAGCAGCAG---GCGAAGAAGCCGGCGGCGGCGGAGGACGTCGAGATCAAGA
AGGTCTTCTCCCGCTTCGACACGGACGGCGACGGCCGGATCTCGCCGTCCGAGCTGGCGGCCGTGTCGCGCGCCATCGCG
CCGCCG---GCCACCGAG---TCCGCGCAGGGCCGCGAGGTGGCGTCCATGATGGACGAGCTCGACACCGACCGCGACGG
CTACGTGGACCTCGGCGAGTTCGCCGCCTTCCACGGCCGCGGCCGCGAGGAGCGCGAGCTCGACGCCGAGCTGCGCGACG
CCTTCGACGTCTACGACATCAACGGCGACGGCCGCATCTCCGTCGCCGAGCTCAGCAAGGTCCTGAGCCGCATCGGCGAG
GGATGCAGCACCGAGGAGTGCGAGAAGATGATCGCCTCCGTCGACGTCGACGGCGACGGCTGCGTCGGATTCGAGGAGTT
CAAGAAGATGATGACCGCCGGTGACGCCGGCGCACCACCTCAACCCGAAGCGA---TCGCCGTGCCTGACAGCAACAAAC
CCAAGAAGGAGTGATACATG-TGCTTTTGCTTGTAAA-AAAATTGTAATCCGAGGGAGCGAA------------------
TTAGTTGTCAG------TCCCTGTTGGCCATAGTCTTCT---GGTCTGAA------------AAAAAATGGGAATAAGGA
TCAATGTGCAATTGCCATTGTCGTGCTGTACCTCTACGATAACGGTTGTGTGTGCACGGTAGCAGTACTAGTACTAGATA
TTTTCTCCGAGTATGGTCATCTTGCTACTTCATTTTCACATGAAAATGAAGTGCCATGTTGATGTTGAAGGGTGATAAGC
ATCCATTATCAATGTTACTTGTAATCGCATTCGGCAATAAATGTGTTGTCATCTTATGATGTTTCCTATTCTGAGAGATA
CTCCCTCTGTAAACAGATATAATGCTTTAAAACATGGTGATGATAATCAATAAAACAAGCCAGTAACCCAATATTGGAAG
CCAATATCAAATTTATGTGGAGTATATCAGCAATATTTTCTTTAAAACATACTGCATCCATTCCAAAATAACTAGCCTAC
CAAAATGTCTTATATTTTGAAATGGAGGTAGTATTTGCAAATATCCGAAACTCTATGAGCAGATTGAGAAAACCAAGATA
AAACAATTTTCTCTTGAACTATGAAAGTGAACTCCAGTATATTGTAATATAAAATATGTTTGACAGTTTTCATTGTGAAG
ACATAAATAGTGAATACTTGTTGGAAATTAATAAAATGTGTTAAAAGGCCACAAAAATGACGGGCCCACTCCAACAGATC
TTCAGGCCAATCAGCATCGCGTTCTTTTGGTCATAAGATGGTAAAATTGGGAATAAGGGTCAATGTGTGATTGTCACTAT
TTGTGTTGTACCTCTACGGT---GACGGTTGTGTGTGCACGGTACTCGTG-------GTACTACTAGATATTTTCTCCGA
GTGTAGGCATCTTGCTA--TACTTCATTTTCACATGAGAATGGATTTATCAGTTCGGT----GCGATGTTGATGTTGAAG
GGTGAT---AGCCAATGCGTCGTCAACATTATTT----------------------------------------------
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>chr3A_92
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-----------GCCAGGGGTCAGCTGATAGCGAACGACTTTAGCAATCCTATAGGACCAGGGGGCGCGT-CAAGATCCGT
GCAACGGCGGAGAGAGCGTTCGCCAGGGTTGGGTCC-CAGCGAACGTTCGCCAGACAGTATTTCCGTAAATTAACCTATA
TGTACCCCCACACTAAT-AAAATCACGAGCGCAGTGAAAAAGCGAGTGGTGGCCATGATACCCTGCACGAACCTTTGTTG
TGAAAAGTGAAGCTTTATTCTGAAAAGTTACACGCCAAGAAGGCAAAGGATGGGACGCCGCGAGCAACGACGACCTCACA
TGGGTGGGGATACTTCGCTCCGTCCACGCCCGCCGCGTCATGTGTCC----ATCCCTCGGCCAC-----------ACACC
GTAGCCGCTCACGGCGACAAGTTCCACGAACCAGGCCGGCAAAGGAATAAATAAACCGGCCCGCGACAGACGCAGACGTG
GCCGGTGATTCACGCGAGCTGCTGACTTCTCTCGAGCACCGAGGAAGCTGCCCGCCCGGCGGGACGCGGAAAAGTCCTCC
CTCAGCCCCGAGATTCGCATCGCGCGCATCCGGCCGTACGCTTGCCCATCGCCGCGAAGCCACGCCTGGCCG----ACGC
GCCGCCCCACGCAACCGGGAGAAGAGAAGACAACGCGCTCGCCGCGTACTGATATGACTCCGCCTCCCCGCGGCGGAGTT
ACTCCTCCACTTCTTTATCCCGAAGGAGGGAGGATGGTCGGTGCGCTCCGTCGTCCGTAGCGCGTGCCCGCCGGTATTAA
TACCCCAGAGAGAGCCCACTGCAACCTCCACCCATCGG---AACATTCAAGTT---CAAGCTCCCCCATCTCCATCACTA
CAACCAGCCACCTC--------AAGCTTTGAAGCTCAGCTAGCTCGCCGCGACCGTCGAG--TCTCAAGTCTTGGGCCAT
GTCGAGCGGCGGCGGGAAGCAGCAGCAGCAGCAGCAG---GCGAAGAAGCCGGCGGCGGCGGAGGACATCGAGATCAAGA
AGGTCTTCTCCCGCTTCGACACGGACGGCGACGGCCGGATCTCGCCGTCGGAGCTGGCGGCCGTCTCCCGCGCCATCGCG
CCGCCG---GCCACCGAG---TCCGCGCAGGGGCGGGAGGTGGCGTCCATGATGGACGAGCTCGACACCGACCGCGACGG
CTACGTGGACCTCGGCGAGTTCGCCGCCTTCCACGGCCGCGGCCGCGGGGAGCGCGAGCTGGACGCCGAGCTGCGCGACG
CCTTCGACATCTACGACATCAACGGCGACGGCCGCATCTCCGTCGCCGAGCTCAGCAAGGTCCTCAGCCGCATCGGCGAG
GGGTGCAGCACCGAGGACTGCGAGAAGATGATCGCCTCCGTCGACGTCGACGGCGACGGCTGCGTCGGCTTCGACGAGTT
CAAGAAGATGATGACCGGCGACGTCGCCGGCGCACCACCTCAACCCGAAGCGA---CCGCCGCCCCTGACAGCAACAAAC
CCAAA---GAGTGATACATGC-----TTGCTTGTAAA-TTCGTAGTAATGTGAGGGGGGCGAAGGGA----AGGTGTATG
TTAATTGTCAG------TACCTGTTGGGCATAGTGTTCT---GGTCTGAAGATG------GTAAAAATTGGGAATAAGGA
TCAATGTGCAATTGCCACTC------------------------------------------------------------
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TTGTGCTGTACCTCTAAGGT---AACGGCTGTGTGTGCACGCTACTCGTAGTAGTACGTACTACTAGATATTTTCTCCTA
GTGTGGGCATCTTGCC----ACTTCATTTTCACATGAGAATGGATTTATCAGTTCGGTCAGTGCGATGTTGATGTTGAAG
GGTGATGATACCCAATGCATCGTCAACAATATTT----------------------------------------------
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>chr3D_255
AGTAA---------------------------------------------------------------------------
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--------------------AATCACGAGTGCAGTGAAAAAGGGAGTGGCGGCCATGATATCCTGCACGAATCTTTTG--
-----------------TTCTGAAAGGTCGCACGCCAAGGCC----AGGATGGGACGCCACGAGCAACGACGACCTCACA
TGGGGATGCAT--TTTGCTCCGTCCACGCCCGCCGCGCCATGTGTCTGCCTATCCCGCGGCCACG--CACCCACTCCACC
GTAGCCGCTCACGGCGACAAGTTCCACGAACCAGGCCAGCAAAGGAATAAATAAACCAGTCCGCGGCAGACGCAGACGTG
GCCGGTGATCCAC----GCTGCTGACTTCTCCCGAGCACCGAGGAAGCTG-----CCGGCGGGACGCGGAAAAGTCCTCC
CCTACA-CCGAGATTCGCATCGCGCGCATCCGGCCGTACGCTTGCCCATCGCCGCGAACCGACGCCTGGCCG----ACGC
GCCGCCCCACGCAACCGGGAGAAGACAAGAGAACGCGCTCGCCGCTCC--------------CCTCCCCGCGTCGGAGTT
ACTCC---ACTTCTTTATCCGGAAGGAGGGAGGGTGGTCGGTGCG------CGTCCGTAGCGCGTGCTCGCCGGTATTAA
TACCCA----AGAGCCCACTGCAACCACCACCCATCAG---A-CATTCAAGTG---GAAGCTCCCCGATCTCCATCACTA
CAACCAGCCACTTGAGCTC-TGAATCTTTGAAGCTCAGCCAGCTCGCCGCGACCGTCGAG--CCTCAAGTTTC--GCCAT
GTCGAGCGGCGGCCGGAA------GCAGCAGCAGCAG---GCGGAGAAGCCGGCGGCGGCGGAGGACATGGAGATCAAGA
AGGTCTTCTCCCGCTTCGACACGGACGGCGACGGCCGGATCTCGCCGTCGGAGCTGGCCGCCGTGTCCCGGGCCATCGCG
CCGCCG---GCCACCGAG---TCCGCGCAGGGCCGCGAGGTGGCGTCCATGATGGACGAGCTCGACACCGACCGCGACGG
CTACGTCGACCTGGGCGAGTTCGCCGCCTTCCACGGCCGCGGCCGCGGGGAGCGCGAGCTGGACGCCGAGCTGCGCGACG
CCTTCGACATCTACGACATCAACGGCGACGGCCGCATCTCCGTCGCCGAGCTCAGCAAGGTCCTCAGCCGCATCGGCGAG
GGATGCAGCACCGAGGACTGCGAGAAGATGATCGCCTCCGTCGACGTCGACGGCGACGGCTGCGTCGGCTTCGACGAGTT
CAAGAAGATGATGACCGGCGACGTCG---GAGCCCGACCCGAAGCCGAAGCCGAGGCCGGCGTCCCCGACAGCAACAAAG
CCAAGAAGGAGTGATCCGTTC-----TTGCTTGTAAA-TT-GTAGTAATGTGAGGGGGGCAAGTGAGAAGGAGGTGTATG
TTAATTGTCAAGTACTCTACCTATTGGGCATAGTGTTCTTCTGGTCTGAACAGG------GTAAAAATTGGGAATAAGGA
TCAATGTGCAATTGACACTG------------------------------------------------------------
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TTGTGCTGTACCTGTACGGTAACAACGGCTGTGTGTGCACGGTACTCGTAGTA-------CTAGTAGATATTTTCTCCGA
GTGTGCGCATCTTGCTA--TACTTCATTTTCACATGAGAATGGATTTATCAGTTCGGTCAGTGCGAGGTTGATGTT----
------------CAATGCATTGTCAACATTATTTATATTGGCACTTGACAATGGATGTATTGTTATTTTCAAGATGTTGA
ATATTTTTAAGCATATGCTTTAAACTGATTTCACAGGGACTCCGGCGAAAATTAATTGTATTTCCTTGGCTATAAATTTT
GATATACGTTATCCGCCGAACCAGGGGACCCGGGCGGAGATTGTGCCACCACGGCTGCGGGGGGCAGCGTGGGGGTGGCC
GGATGTGTTTGGGTGGTGCTGGCGGTGGTCGGGGTCGGCACTGTTCGACGGTTGGCGGGCGTGGCGGTGGGATTCTGGTA
GGCTGCTGCTTGCTGTGGATCTCGGATGCCAGTGCGGCGGCCCGATGGGTCTTTGCCTCGGTGGGGCGAGGACGGCCAGG
TGTGGTCGTCGTTGGTGGCGGGAGGCCGGCGGTGTCAGGTGTTACCTCTCTGCATCGTTGATGAGCAAGTCTTTCCTTCC
TGCAGAGGGAGGGGGGGTTCACCCGGCGACCTGCTCCATTGTCTTGTCTTCAATGGTTTGGATTCCAGTCATGGTCCGGG
AGGAATCTCCGCACAGCTTGCCTATGCTGGCAGCGTCGATGCCTGCAAGTGTCGTATCCCTCTTGGGGGCGCTGCCATGA
TCTTGATCATGTCCTACCTCGAGCGCCGGGAAAAATCCTTGTTCTGGTTCTCCGAAACAGGCAGGGACGGAGACGCGACG
TCGTTTTCTGCATGAAGGCGATGCCTTGGCGGTTCGCAGAGTCCTCAGAGCTGGAGTTTAGGACGTCTCGTTCTTGGTGT
GGGTTGCCCCTCTGGACATGGCCCCCAGGGGCGCTATGTATTTCATCGGCGGCGCATCCTGGCGTCATCTTCTTCTGGTC
CGGTTAGGTCCTACCTCCCACTTGCCGAGTCCTCTAGGCGCTTCTTCTGGTCCGGTTAGGTCCTACCTCCCACTTGCCGA
GTCCTCTAGGCGCTATGTGGTGTAATCTGAGGGGAGCGCATTAGTTTTCAGTACATGTTGGGTATAATGTTCTTCTGGTC
TGAAGATGGTAAAAATTGAGAATAAGGATCAATGTGCAATTGCCATTGTTGTGCTGTACGGCTACGGTAACGGCTGCGTG
TGCACGGTACTCGTAGTACTAGTAGATATTTTCTCCGAGTGTGCGCATCTTGCTATACTTCATCACATGAGAATGGATTT
ATCAGTTCGGTCAGTGCGATGTTGATGTTGAAGTGTGATACCCAATGC
>chr3D_830
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-----------------------------------------------------------GCGCGTGCTCGCCGGTATTAA
TACCCC----AGAGCCCACTGCAACCTCCACCCATCCGACCA-CATTCAAGTG---GATGCTCCTCGATCTCCATCACTA
CAGCC---CACTTGAGTTCTTGAAGCTTCGAAGCTCACCTAGCTCGCCGCG-----------------------GGCCAT
GTCGAGCGCCGGCAAGAA------GCAGCAGCAGCAGCAGGCGAAGAAGCCGGCGGCGGCGGAGGACATCGAGATCAAGA
AGGTCTTCTCCCGCTTCGACACGGACGGCGACGGCCGGATCTCGCCGTCGGAGCTGGCCGCGGTGTCACGCGCCATCGCG
CCCCCCGCCGCCACCGACTCCTCCGCGCAGGGCCGCGAGGTGGCCTCCATGATGGACGAGCTCGACACCGACCGCGACGG
CTACGTCGACCTCGGCGAGTTCGCGGCCTTCCACGGCCGCGGCCGCGGGGAGCGCGAGCTGGACGCCGAGCTGCGCGACG
CCTTCGACATCTACGACATCAACGGCGACGGCCGCATCTCCGTCGCCGAGCTCAGCAAGGTCCTCAGCCGCATCGGCGAG
GGATGCAGCACCGAGGACTGCGAGAAGATGATCGCCTCCGTCGACGTCGACGGCGACGGCTGCGTCGGGTTCGAGGAGTT
CAAGAAGATGATGACCGCCGGTGACGCCAGCGCCCGACCCGAAGC---AGCGA---CCGGCGCCGCTGACAACAACAAAG
CCAAGAAGGAGTAGTGATCCATGCTTTTGCTTGTAAAGAAGATTGTAATCTGAGGGGAGCGAAATGG----AGGTGTTC-
----------------------------------CTTCT---GGTCTCAAAATGGTACTAGTAAAAATTTGGAATAAGGA
TC------------------------------------------------------------------------------
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------------TCTACGGT---AACGGTTGTGTGTGCACGGTACTAGTACTAGA-------ACTAGATATTTTCTCCGA
GCGTGGGCATCTTGCTACCTACTTCATTTTCACATGAAAATGGATTTATCAGTTCGGTCGGTGCGATGTTGATGTTGAAG
GGTGAT---ACCCAATGCATTGCCAACATTATTTGTAATCGGGTTCGGCAATACATGTGTTGTCATTTTGGTAACGTTGA
ATACTTTTAAGCATATGCTTTAAAATGAATGATTTCATTAATAGTAGTTGTAAACAATTTTACACGCAACAAATATTAGA
AGGTAATATCTATATCTATACCTACGTAATATCTCTATCTATACCTACAGAAAAATATTATCTATACATATACCTAATTA
TTTGGCTTGTATGAACAGATTGAGAAAACCAAGATAAAACAATTTTCTCTTGAACTATGAAAGTGAACTCAAATATATTG
TAATACAAAATATTTTTGACAATTTTCATTGCGAAGATATAA--------------------------------------
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>SNPs
S-SS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSS------S----------------------------------SS-S----S----SSSSS----------
-------S-S--------S-------------SSS-S------------------S---------S--------------
S--------------S-S--------SS----------------------------------------------------
-------S---S--------------------------------------------------------------------
----------------------------------------------------------S------SS-------------
---------------------------------S----------------------------------------------
----------------------------------------------S--------S----------------S----SS-
-S------------S---------------------------------------------------------SSSS----
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-------------------------------------S--------------SSSS-----------------------S
------------------------------------------S-----------SS----SS------------------
----------S--------------------------------------------------------S------------
-------------------------------------------------S-----------------S------------
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-----------------------------------------------S------------S-------------------
--------S-------------------------------------------------------S---------------
-----------------S--------------------------------------------------S-----------
--------------------------------------------------------S------S----------------
----------------------------------------S---------S-----S-SS--------------------
---S--------------S--------S---------------------------------------S------------
-----------------S--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
-----S-----------------S-------------------------S------------------------------
----S---------------------------------------------------------------------------
----------S-------S-------------------------------------------------------------
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>forward_80
------------------------------------------------------------TCATGCCATGGGAGTCGAAC
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>reverse_1810
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-------------------------------------------------GTGTGCACGGTAGCAGTACT-----------
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