>input_sequence_78214
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--------------------------------ACAACCCAGA-------GGCATCAGCCA--GCTCCTCACGAACGCACG
GTCGCAGAGACACCGCACGAGAGCAGCTCCACCACTTCCCTCCC----ACACGAGCCC---AAGAAGCAACCATGGCGGC
GGCGAAGGCCACCCTCGTCTGCTTCATGGTCATGGCTCTCGCGACGGCGCTGCTGGCAGTGCCGGGCGCGGTGGAGGCGG
CGACGTGCAGCCCGACGCAGCTGACCCCGTGCGCGCCGGCCATCATCGGGAACGCGGCGCCGAGCGCGGCGTGCTGCGGG
AAGCTCAAGGCGCACCCGGCGAGCTGCCTGTGCAAGTACAAGAAGGACCCCAACCTGCAGCGCTACGTCAACTCCCCCAG
CGGCAAGAAGGTCTTCACCGCGTGCAAGCTGCGCCTGCCAAGCTGCTGAACTAGCTATTGGTGC----------------
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-------------------------------------------CACGAGCTTCGTCCATGTCCCTCGCGCGTTGCACGTA
CACTACGTACGCTGGAGTACCGAGAGTGT---GTGAGGTA----------------------------------------
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---TAAT-------------------------------------------------------------------------
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-------AATAAA-------------------------------------------------------------------
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>chr1A_1_TraesCS1A01G374400
TGCTCTCTGATTTCCCTCCCAACTTCCTTGTCTTTGCTTCCAGGCCCCACCTCGGGCCCCGCTGCACCTCTTAATTCCTC
ATCGTAATTCTGCAAGAACTGCACGGAGCTACCAATCGACTCCCTCCCGTTATTCCGAAGGGCGTCTTCTCTCAGGTGCC
AGCTCCGCCATAGGAGCAGCAGGATTTTGGCTCGCCCTTCCTTGCTTTCCGCGTCCAGCAGATTCTGTTGGTAACTACAC
ATACAAATTTAGTGCTGGGCATTTGTCATTTGCAGATCTTGTAATGGTATGTACTGATTTGGGGATTAATCCATTTTTGA
TTCTTTACTTGATCTTAAGTGCAATCATATT----------------ATGCACACACCCAAAAACAAAGACACTTCTCTC
TTATTGTCATG----------------------TTTGAGTAGGTTGGACTCGATGAATTTTTTTTGTCGAAATTCCCAGC
AAGCACACCATAAGTTTTTTCTTTTTT-----GATCGAATGGTATGAAGGGAACAATGTTTATAAG-AAAATTTCTAAAA
TTTTCAATTATGTGCAATTCCTTGACCTAAAATCACTCAAAATGTGATGGTTTAATTGTGGAAATGATGACCCATGCTCA
CACT-AGCCATACAGTCTCAAGC-CCTCGACCCTCCATGAACGAGGAGGTTCGATCGATCTCTTCCTTAATC--------
---------------------------------------------------------------------TACGTGTAACT
CAGCTGCGCACACAAAACCGAGACTTTCCTTGAACGTTTCGGCACGCTCATGA-------TGGATTCCACACTTCCACCG
ACCCACTGAGATCATCAGGCTGCC-ATGTTCACATAGTA--AAAAAGCGCAACACGTCACCCCG----------GCCCGT
ACCGTCCGACGCGCCACGCGCCGTCTGGATCGGCCGCTAGTG--GAGCTCTGTGCCCACGCGCATGTCGGTAGCTAGTGC
ACCCATGCTTGATGCTTCCGCGTTGTACACTC------TGTCGCGCGCCACACCTACTACTACGTGCTGCATGCGGCCTA
TAAAACGCACCGTCGACCGCG-CCCATTCTCCACAACCCAGA-------GGCATCAGCCA--GCTCCTCACGAACGCACG
GTCGCAGAGACACCGCACGAGAGCAGCTCCACCACTTCCCTCCC----ACACGAGCCC---AAGAAGCAACCATGGCGGC
GGCGAAGGCCACCCTCGTCTGCTTCATGGTCATGGCTCTCGCGACGGCGCTGCTGGCAGTGCCGGGCGCGGTGGAGGCGG
CGACGTGCAGCCCGACGCAGCTGACCCCGTGCGCGCCGGCCATCATCGGGAACGCGGCGCCGAGCGCGGCGTGCTGCGGG
AAGCTCAAGGCGCACCCGGCGAGCTGCCTGTGCAAGTACAAGAAGGACCCCAACCTGCAGCGCTACGTCAACTCCCCCAG
CGGCAAGAAGGTCTTCACCGCGTGCAAGCTGCGCCTGCCAAGCTGCTGAACTAGCTATTGGTGC----------------
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-------------------------------------------CACGAGCTTCGTCCATGTCCCTCGCGCGTTGCACGTA
CACTACGTACGCTGGAGTACCGAGAGTGT---GTGAGGTA----------------------------------------
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---TAAT-------------------------------------------------------------------------
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-------AATAAAACGAGGCGAGTGCTGTATACTTTATAT-------ATTAAACAGAAATAAATT--GACAGCGCTGTAC
TACTTTGGTACGGTGCCC---GTTATGTCCATGTG-CATGTATACTCATGTCCTGTGTATGCCAGCATATACATGTCAGA
GTAATAAACATAAAT-TTTTGTTCTGTTCCCT---GCTTCGCTCCGAAAAGGAAGAAAATGTTTTTTGTTTGAAATGGAG
AAGAAAATACTAGTTAGTAGTTAGAATATATGAGAATAATACCCCTCCACATTCTTATGATATATCAATGGTAGCAACTT
GTGGCTACATGTTATAGCGTCTCACCTTCTAGGTTCGATAAAATGATTTGTGGCTAAAAAATTAAAAATAATAATGTGGA
TGACTTACATGTGCTTGATGATGTGAAGGATTTACATGTGTTGAGAAATGAAATGTGGAGTGCTTGTATCTGCTTAATAT
TATGGAGGACTTACATGTGCAAGAAAAAT-ATGTAGTGGGCTTCTACTTTTTGAAACAGAGAGGATGCAT-GCTTGCTTC
ATACATGTACTTTAGCAAAAGGGCGAGCCACAGAAAAACAACAATGAAATGGTCGGAAGGAAATGATGAGTCTATAAAAC
AGTGATACCAACTGTTAAGAACCTTGTTTAGTTTCTTGATCAAATTGTGAATTTGATCGCGGACACGAATTACATGGGAA
ATGTATAGCGTCTCGGGGTAGAAGTAGGGGGCAATTGTTGTGGACGAAGCTCTTGTCGATCAGGTCGGCCTGACCTCTTT
GGTCGTTCGATCG-GTTTGACCTTGGTAGTACATCGTCGGCGTGCACGGACCAGGGATACTGCCAGTTAACCTCTCCTAC
AAGACATTACCG-GGAATATACATAAAGTGATAAAGAGATTACCAAAGTACTAAAAATAACAAAGCATAAACTAAAAAGG
GAAAGAAAGGCGACGTGTACACTTTTTTTTGAAGGGAAGCAAAGTTTTATTGCTTACGTGTGCGTGGGCATATC
>chr1D_220
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-----------------------------------------------------------AGGTTCTGTTGGTATTTACAC
ATACAAATTTAGAGCTGGGCATTTGTCATTTGCAGATCTTGTAATGGTATGTACTGATGTGGGGATTAGTCTAATTTTGA
TTCTATACTTGAGCTTAAGTGCAATCATATT----------------A----------------CCAGGACACTTCTCTC
TCATTGTCATATTTGATTTTGAAACCAAGGAAATTTTAATAGGTTGGACTCGATGAATTGTTTTGGTTGAAATCGCCAGC
AAGCACACCTTAAGATTTTTTTGTTTGTTTTGGATCCCATGCTACAAAGGAAACAATATTTA--AGAAAAATTTCTAAAA
TTTTGAATTATGCACAATTCCTTGACCTAAAATCACTCAAAATGTGACGGTTTAATTGTGGAAATGATGACCCATGCTTA
CACTTACCCATACTGCCTCAAGC-CCTGGACACTCCATGAACCAGGAGGCTCGATCGATCTCTTCCTTAATCATCACAGT
CCAAAAACAATA----TGACCAGTGCACCGACGCG----------------------------CCCCTCTACGTGTAACT
CAGCAGCGCACACAG--CCGAGACTTTCCTTGATCGTTTCGGCACGCTCATGAATCATGATGGG--------TTCCACTG
ACCCACTGAGA-CATCAGTCTGGCCATGT---TCACATAGTAAAAAGCGCAACACGTCACATCAGTCTGGCCATGTCCGT
ACCGTCCGATGCGCCACGCGCCGTCTCGATCGGCTGCTAGTG--GAGCTCTGTGTCTGCGC-----------------GC
ACCCATGCTTGATGCTTCCGCGTTGCACACCTA--------------------CTACTACTACGTGCCGCAGACGGCCTA
TAAGACGCACCGTCGACCA-G-CCCATTCTCCACAACCC--A-------GGCACCAGCCA--GCTCCTCACCTACGCACA
GTCTCACAGACACTGCGCGAGAGCAGCTTCACTACTTCCCTCCC----ATCCGAGCCC---AAGAAGCAACAATGGTGGC
GTCGAAGGCCACCATCGTCTGCTTCATGGTCGTGACCCTCGCAGCGGCGCTGCTGGCGGCGCCGGGCGTGGTGGAGGCGG
TGACGTGCAGCCCGACGCAGCTGACCCCGTGCGCGCCGGCCATCATCGGGAACGCGGCGCCGAGCGCGGCGTGCTGCGGG
AAGCTGAAGGCGCACCCGGCGAGCTGCCTGTGCAAGTACAAGAAGGACCCCAACCTGCAGCGCTACGTCAACTCCCCCAA
CGGCAAGAAGGTCTTCGCCGCATGCAAGGTCCGCCTGCCAAGGTGCTGAACTAGCTATTGGTGC----------------
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-------------------------------------------CACGAGCTCCATCCAT---------------------
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>chr1B_223
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--------------------------------------------------------------TTCTGTTGGTATTTACAC
GTACAAATTTAGAGCTGGGCATTTGTCATTTGCAGATCTTGTAATGGTATGTACTGATGTGGGGATTAATCTAATTTTGA
TTCTATACTTGAGCTTAACTGCAATCATATTAAGCACAAACCTAAAAA----------------CAAAGACAGTTCTCTC
TTATTGTCATATTTGTTTCTGAAACCAAGGAAATTTTAATAGGTTG-----GATGAATTGTTTTGGTTGAAATCGCCAGC
AAGCACACCTTGAGATATATAT-----TTTTGGATCCCATGCTACAAATGGAACAATATTTATAAGAAAATTTTCTAAAA
CTTTGAAGTATGCACAATTGCTTGACCTAAAATCACTCAAAATGTGACAGTTCAATTGTGGAAATGATGACCCATGCTTA
CATTTAGCCATACTGCCTCAAGCCCCTCGACACTCCATG-----------------------------AATCATCGCCAT
CCCAAAAGGATA----CGACCTGTGCACCGACGCGCG----------AGCAGCTACCCGTGCACCCCTCTACGTGTAACC
CAGCAGCGCACAGAG--CCGAGACTTTCCTTGATCGTTTCGGCACGCCCATGA-------TGGG--------TTCCACTG
ACCCACTAAGATCATCAGGCTGGCCATGTTCATCACATAGTAAAAAGCGCAACACGTCACCCCG----------GTCAGT
ACCGTCCGATGCCCCACGCCCCGTCTCGATCGATCTAGTGGATCGAGCTCGGTGCCCGCGCGCATGTCGGTAG----TGC
ACCCGGGCTTGATGCTTCCGCGTAGCACCCTC------TGTCGCGCGCCACAC---CTACTACGTGCTGCATGCGGCCTA
TAAAAGGCGCA------------CCATTCTCCACAACGC--A-------GGCAGCAGCCA--ACTCCTCACCGACGCACA
GTCGCACAGACACAGCACGAGAACAGCTTCACCACTTCCCTCCCTCCCATCCGAGCCCAAGAAGCAGCAACAATGGCGGC
GTCGAAGGCCACCCT-GTCTGCTTCATGGTCGTGGCTCTCGTGACGGCGCTGCTGGCGGCGCCGGGCGCGGTGGAGGCGG
CCACGTGCAGCCCGACGCAGCTGCCCCCGTGCGCGCCGGCCACCATCGGGAACGCGGCGTCGAGCGCGGCGTGCTGCGGG
AAGCTGAAGGCGCACCCGGCGAGCTGCCTGTGCAAGTACAAGAAGGACCCCAACCTGCAGCGCTACGTCAACTCCCGCAA
CGGCAAGAAGGTCTTCGCCGCGTGCAAGCTGCACCTGCCAAGATGCTGAACTAGATATTGGTGCTGTTGGTGCCGCGCCT
CGCCTGCCGCGGCCCTCCTCTCCCTCACCCTCAGCTCACTGTCCCTCGCCGTCACCTGACTCACTGACGAAGAAGATGAA
GTTCAGAAAAGTTCAGAGAGGAGACAGTGGACACAGGGATTTTTCCGGCGCTTGTACGCCTTCTCCTTTTCTCGAGCACG
AACTCGACCGTGTCAACAAGATACAGGGGGGATCCGGGGCTTTATACCCGCGAGCACCGGCCTGCCAGGCCACGCCTCGC
ACCAACTCGCACACCCACTCCCCCACGTCCCGCGCGCTCTGGCCGCGCCCGAACGCGATCGCCACGGCCACCCCGCGCGC
CCGACGCGGTCTCCTCCCCGCGCTACTCGTCTACACGCAACGGCCCGAGCGCTCGCACGCAACGGACACACACGCACACA
CACCTGGTCACGCACGCACGCGACCCAGGCCGCCCTGGCTCGAGCCCGACGCGGCCACTGCACGCACGCACGCACGCGCA
CGCCACTCCCCGGGCCTCGCCACGGCTTATTCCCAACAGGTGCCACGAGCTTCGTCCATCTCTGTCTCGCGCGTGACAAT
GTGCCATGGCCGTTGGTGTACGTCACGTGTACGTGAGGTAATGGCCCGGTTTGGATACTCTAAC----------------
--TGAGTTAAAAGTTATAGTTAGATTCTAGCCCTAAACTAACCTTGAACTAACTTTAGCCGATGAGGTGTTTGGATGACA
GTGTTAGATGGAGCGCGGATACGGTGAGGCGCCTTCACGGGCGGTGCGAGAGTGAGGGGGGAGATGACAAGAAGCTTCAA
GGAAGTGAGGAAGGATCTCCTGCGGGAAGGGCGAGAGAAAAAAGTGCTTTTTAGTGATCCCGAGAAGAACTAAACCAAAT
AAACACCTTTTGGGTGGGTTAGATTTTTGGATATTTTTGGATTAGTTGAGTCCAAACTAACTCTAACCCATGGATCCAAG
CAGAGCCAATAAAACGAGGGGTGGGTTAGATACTTTATTATAAAAAAATTAAACAGAAATAAATT--GACAGCGCTGTAG
TACTTTGGTACGGTGCAC---GTCATG-----------------------------------------------------
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>chr1D_396
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---------------------------------TTTTAATAGGTTTGTCTCGATGAATATTTTTGGTTGAAACTGCCAGC
AAGCATAGCATAAGATTTTTATTTTTT-----TATCCATTGCCACAAATGGAACAGTATTTCTAAGAGAATTTTCTAAAA
TTTTGAATGATGCACAATTCCTTGACCTAAAATCACTCAAAATGTGACGGTTTAATTGTGGAAATGATGACCCGTGCTTA
------GCCATGCTGCCTCAAGC-GCTCGACACTCCATAAACCAGGAGGCTCGATCGATATCTTCCTTAATCATCGCCGT
CCCAAAAGGATATGGTCGACCTGTGCACCAACGCGCGTGCATGCGCAAGCAGCTACCTGAGCACCCATCTACGTGTAACT
CAGTAGTGCACAGAG--TCGATACTTTCCTTGAACGTTTCGCCACGCTCATGA-------TAGGTTCCACACTTCCACTG
ACCCACTGAGATCATCAGGCTGCCCATGTTCACATAGTA--AAAAAGCGCAAAACGTCACCCCG----------ATCCGT
ACCGTCCGATGCGCCACGCGCCGTCTCGATCGATCGCTAGTG--GAGCTCTGTGCCCGCGCGCATGTCGGTAG----TGC
ACGCACGCTTGACGCTTCCGTGTTGCACAGCATCACCGTGTCGCGCGCCACACCTACTACTACGTGCTGCAGACGGCCTA
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>chr1D_784
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----------------------------------TAGTA--ATAAAGCCCAACACGTCACCCGATCTGCAGCGT------
------CGATGCGCCACGCGCCGTGTCGATCGGTCCCTAGTG--GAGCTCTATGTCCACGCGCATGTCGGTAG----TGC
ACCCATGCTTGATGCTTCCGCGTTGTACACTC------TGTCGCGCGCCACACCTACTACCT-GTTGTGCATGCGGCCTA
TAAAACGCACCGTCGAACGCTCCCCATTCTCCACAACCC--AACCCATTGGCATCAGCCAACACTCCTCACCTACGCACA
GTCGCACAGACACCGCGCGAGAGCAGCTTCACCACTTCCCTCCC----ATCCGAGCCC---AAGGAGCAACCATGGCGGC
GTCGAAGGCCACCCTCGTCTGCTTCATGGCTGTGGCTCTCGCGGCGGCGCTGCTGGCGGTGCCGGGCGCGGTGGAGGCGG
CGACGTGCAGCCCGACGCAGCTGACCCCGTGCGCGCCGGCCATCATCGGGAACGCGGCGCCGAGCGCTGCGTGCTGCGGG
AAGCTCAAGGCGCACCCGGCGAGCTGCCTGTGCAAGTACAAGAAGGACCCCCACCTGCAGCGCTACGTCAACTCCCCCAA
CGGCAAGAAGGTCTTCGCCGCGTGCAAGCTGCGCCTGCCAAGGTGCTGAAGTAGCTA---GTGC----------------
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-------------------------------------------CACGAGCTTCGTCCATGTCCCTCGCACGTTGCACGTA
CGCTACGTACGTTGGAGTACCGAGAGTGT---GTGAGGTACTCCCTCCATCTTAAAATAAGTGTCTTGACTTTATATTAA
CTTTAGTATAAAGTTATATTAAGATTAAAACATTTATAGAGTAAGTGTAAAGTCGAGACACTTATTTTGAAAAGGAGGGA
GTATAAT-------------------------------------------------------------------------
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-------AATAAAACGAGGGGAGTGCTATATATACTTTACG---------AAACAGAAATAAATTTTGACAGTGTTGTAC
TACTGTGGTACGGTGCCAGCTGTTATGTTCATGTGTCACGTATACTCATGTCCTGTATATGGCAGCATGTATATGTCAGA
GTAATAAACATAAATATTTTGTTCTGTTCCGTTCCGCTCCGCTCCGGAAAGAAAGA------TTTTTTTTTGAATGGGAA
AAAAAATTAATAAATAAAATCAGA-----------------------------------ATATATGAACGGTAGCACCTG
C-GGTTACATGTTATATA---------------------AAAATGGTTTGTGGCTAAAAAAATTAATGAC-----GTGGA
AGGCTTACATGTGCTTGATGATGTGAAGGATTTGCATGTGTTGAGAAATTAAATGTGGAGTGCTTGTACGTGCTTAATAA
TATCGAGGACTTATATGTGCTAGAAAAAAAATGCAGTGGGCTTGTACTCTTTAAAAAATAGAGGATGACAAGCTTGCTTC
ATGCATGTACTTTAGGAAAAGGGCGAGCCACCG-AAAACAACAACGAGATGGTCGGAAAGAAATGATGAGTCAACAAAAT
GGCGATACCAAGTGTTAAGAACCTTGTTTAGACTCTCAATCGAATTTTGAATTTGATCATGGACATGAATTACTTGGG-A
ATGTGCAGTGTCTCGGGGTAGAAGC-GGGGGCAATTGTTGTGGACGAACCTCTTGTCGAAAT----GGCCTGACCTCTTC
GGTCGTTCGATGCAGTTGGACCCAAGCAGTACATCTTCGGCATGCATAGATCAGGGGTGTTCGCACTTAACCTTCCATGC
ATGACATTATGGAGGAATATACA---------------------------------------------------------
--------------------------------------------------------------------------
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--S-----------SS-----
------------S---------------------------------------------S------------S-S------
----S-------S-----------------------------------SSSSSSSSSSSSSSSS----------------
----------S-------------------------S-S-------------------------S--S------S-----
--------------S-----S---------------S----S--SS-----------S----------------------
----S-------SS---------------------------------S------------------------------S-
-------------S-S---------------S----------S------S------------------------------
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----S---------SSS----------------------------------------------S--------------S-
---------------------------------------------------------------------------S----
---------S----------------S----------------------------------------------SSSS---
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---------------------------------------SS------------------------------SS------S
------S---------------------S--------------------SS-----------------------------
-S-----------------------------S-------------------------S----------------------
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-------------------------------------------------------------------------------S
----------------S-------------------------S-------------------------------------
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-S---------S--------------------------------------------------------------------
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-------------------S-------S-----------S----------------------------------------
----------------------------S---------S-----------------S----S------S--S--------
------------------------------S-------S-------S----S----SSSSSS-----S------SS---S
--S---S--S--SS--SS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------S--S-------S--S
SS--S-----------SSSSSSSSSSSSSSSSSSSSSSS------S---------------S-S--SSSSSSSSS-----
S-S------------------------------S---------------S------------------SS---------S
---S---------S------S-------S----S---------S----S---S---S-S--------SSS----------
--S------------S---------------S-S----------S--S----------S-------------S-S----S
S-S--------S-------------------SS---SS---S----S-----------SS-----S-------S----S-
----SS--S---------------SS----------------------S----------SSSSSSS-------------S
-----------SS----S----SSS-S--------S-----S----SS--S-----S-SS-SS--S-------SS-S-S-
-S-------SS------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_123
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-----------------------CGGAGCTACCAATCGACTCC-------------------------------------
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>reverse_3136
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---------------CAAAAGGGCGAGCCACAGAA---------------------------------------------
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