>input_sequence_68799
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------------------------------------------------------------ATGAGGCGTGAGGACCCAGA
ACTGC---------------------------------------------GCCAAGTTACCTCCCCAACCTTCCACGCTG
TACAGGGGGACACCGTCCTCATCACCGTCGCCGTCGACAACCCTCTCCTCGCCAGGAGCGTCGCCATCCAATGGCACGG-
--------------------------------------------------------------CACCGGCGAGGTGAGTA-
--CGCCAATCCCAAGCTTCTGCCGTGCGCGCGCTATA-----------GATGTTGATTTTGTCCGCAGATCGATTGATTC
ATTCCTGTGGTGGTGGTTGACGGGGGCTGCAGACTGGCACGCCGGCGACCGAC---GGCATCGACGGCCACACCTTGACG
TACAATTTCGTGGCGGACCGGCCGGGCACGTTCACCTTCCGCGCGCGCTACGGCCGCAACCGCCCCGCGACCTTCACCAA
GGCGCAGGGACGTGAGGCCTGGCCGTCCGCCGCCGGCGACCACGCACACACCG------------ATCGTGTCCGCGTGC
CACGCAGCCAAGAGGGGCCTTCCGCCTGCCGACGAACACGCACCCCTCCACGGACCGCCCACCAAGAGCTCGTCTACGTT
CGCGGCGGCCGGGGCCATGCGTGCGTCGAAGCGCAACTCATGGCCGGTAACACCACTATCTACCTCAATGACGAAGGCCC
GGTCGTGCGACTCCTCCGGTGGTCCGCTGTCGGATTGACGGCCGTGGCCTTGTGGGTCTCTGGTGTATGCGGCGAGCGGC
ATGACCCTGTTACACGCCGCCGAGCAGACGGCCCGTTGTTAGACGCAAGGTTTGTTGGTCGAGCAAACCCTCATGTTTCA
CGGGCTCCCAGCTTTCCACCGCCTTGA-----------------------------------------------------
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>chr1D_1_TraesCS1D01G035100
CGATCATATCCTCCTTGTTGATGCATTGCCTCTTCTAAGGGCTCGCGTATGAGTGCTTGAGGCCCTCGTCTGAACCGCCG
CAAAGCACACGTCACCACGACTCGCCTGAACTCTAGGGTTTGGAAGGAGGAAGTAGAGCGGCCGGGGATTCCACCAGAGG
CGTTCTTGTGTGGGTTTCTCCGTCCATTCTTTTCAATCGACCATCGTGCGATGTCAGAGAAAAACCACGAATGAGGTGGG
GACAGGTACACCAACGGACGAAGTCCGCGTGGAATAGGAGTGCGAAACAGAAACCTTATGTGTCTTCTAAGCAGTGTAAT
ATATATATAGGATATAGATATGTGTAGATGTGGATGTAGATTTTGGCTGGACTGTTCTTGTTTTTTTTATCACAATACAG
ACTCGGACGCTTATATATACGCACATACATTCACTCCTATGAACGCTCGCACGCACAACCTACCCTTATGAGCACCTTCA
AGACTTAGCCGGCACATCATTTTTGGATTGACGAAGTCATCACAAAGGCCTTCATAATCGACGGGAACGTCTGCTCCTAC
TAAATCGTCAGAAGACCTGAATAAATTCAGAAAAATGCGAGCACTAGTATCTAAGTTTAAGATGTGGACTTGCGATACTT
GGCATCTAGCATTGGACAGAA-AACGTGAAAATATCAAACGAACAATTAAAGGGTTGTTTCGGAAAGTGTCATGTTGGTT
GGCGGCTCGTGCTTAGCACCTCTAATTA-TTGATGATTAACGAGCATACTCTAGTTGACTGCACGTTGGCGTGTTTCTTG
TGATGATTGGACTGGACTAGAGTTTTGTATTACGGAGC------CAGCTACGGCTTGACGTCGACCCTAACGCGCCACGC
CGGCTGTGCGTCCGGGTCCGCTATGCTTCCTTCGTACGAAACCTAGCAAATGCATATACTTGCTACCCCATCGTCAGAGA
GAGAGAGAGAG----------GGAGAAGGTGGGGCAGCCACGGCCTA--GCTTCCAAGCCATGAGGCGTGAGGACCCAGA
ACTGC---------------------------------------------GCCAAGTTACCTCCCCAACCTTCCACGCTG
TACAGGGGGACACCGTCCTCATCACCGTCGCCGTCGACAACCCTCTCCTCGCCAGGAGCGTCGCCATCCAATGGCACGG-
--------------------------------------------------------------CACCGGCGAGGTGAGTA-
--CGCCAATCCCAAGCTTCTGCCGTGCGCGCGCTATA-----------GATGTTGATTTTGTCCGCAGATCGATTGATTC
ATTCCTGTGGTGGTGGTTGACGGGGGCTGCAGACTGGCACGCCGGCGACCGAC---GGCATCGACGGCCACACCTTGACG
TACAATTTCGTGGCGGACCGGCCGGGCACGTTCACCTTCCGCGCGCGCTACGGCCGCAACCGCCCCGCGACCTTCACCAA
GGCGCAGGGACGTGAGGCCTGGCCGTCCGCCGCCGGCGACCACGCACACACCG------------ATCGTGTCCGCGTGC
CACGCAGCCAAGAGGGGCCTTCCGCCTGCCGACGAACACGCACCCCTCCACGGACCGCCCACCAAGAGCTCGTCTACGTT
CGCGGCGGCCGGGGCCATGCGTGCGTCGAAGCGCAACTCATGGCCGGTAACACCACTATCTACCTCAATGACGAAGGCCC
GGTCGTGCGACTCCTCCGGTGGTCCGCTGTCGGATTGACGGCCGTGGCCTTGTGGGTCTCTGGTGTATGCGGCGAGCGGC
ATGACCCTGTTACACGCCGCCGAGCAGACGGCCCGTTGTTAGACGCAAGGTTTGTTGGTCGAGCAAACCCTCATGTTTCA
CGGGCTCCCAGCTTTCCACCGCCTTGAGTTAGTAGTGTCAATTTTCTTTCCCACTGGAAATATGATTATGTGGTTTCTAG
GAT---------AT-TTTGGTGTTTTCGCTTTCTTGATTCACGTATCGAGTTTGTACAAAAATCATAGTTGTTTGTCTTT
TTGTAATCTAGTGGAAATGAATTTGATTGCGG------AGTTGTCTAATTAATCTGTGTGTAAATGGTTGTATATATACT
TCAGATGTTTGGAACAATTATCTATTGTTATTGTAAATATACAAGTGCAAGAATGAATCAACCATTTTTTTTCATTGATG
AAGATCTACATTATATATCCCTAGAGGGGATGCATCCACAGGATGCATCGTTTCGAAAGGGAGGGGATAAAGAGGCACGG
CGGTTAGCGCATGCGAACCGCCTTTCAGTTACAATGTCTACCAGTTATCTGGCTAATCGACGATACGATGTCATGTTTTC
AAATAAAATGCCTGATAATTAGGTAGTAGACTTGAGTGAAAAAATAGAGGCAATCTTAAGAACGATTTTTAATTAGATTG
GCTGGGCATCTCCATCTTTGTATGACACATATATGTGGCTGGATCCAAAAGGTGCGCGGACACCACTTAAAACTGAAAGG
AGATATAATGTCACAACCAACTAAACATGTTTTGTGAATATTTTTCTCCCTCATTCCACCGTTCTAGGCAATTCATGAAG
TGATGAGTACAACCGAACTGTTGATTTAGGGGTTAAATTCTTCTTCCTACAACCGGAAGAACCTTTTTCTTTTCAACAGC
GGATCTAAGCCGTTCAACACGTAAAGAGAGGCAAAGGCTCAAAGAGTTGACGACAACCCTATGAATCAGTTTCCTAAACT
GTCGAGACCAAAGAGTATAGAGAAGGTTCTCATGCATGTGATCGGCATGGAAAAGGTCCCCGTGCTTCATTCACCGCGCG
GGGTCTTGAATGGCCGTGAAGGAGACATGACGATGATGACAATTTGTAGGCAATATTGATGGTGTTCCTCTTCCTGATGG
TGT
>chrUn_1
CGATCATATCCTCCTTGTTGGTGCATTGCCTCTTCCAAGGTCTCGCGTATCAGTGTTTGAGGC-----------------
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----------------------------------------------CCTCGTCTGAACCGCCGCAAGCACATGTCACTAC
TGCTCGCCTGAACTCTAGGGTTTGGAAGGTGGAGAAGAGTTGGGGATCTCCCCAGAGGCGTGCTTCCGTGGGTTTCTCCG
TCCATTCCTCCCAATCGAC---CATCGTGCGATGTTG-----------GAGAAAACCAACGAACAA--------------
------------------GATGGGGA------------------------------------------------------
-----------GGCGGACCGGCGGACGAA---------------------------------------------------
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-------------------------------------------------------GTCTCAGCGGAATAGGAGTGCGAAA
CAGAAACCTTACGT------------------------------------------------------------------
---------------------------------------------------------------------------GTTTT
CTTAGTAGTGTAATATATATAGAATATAGATATGTGTAGATGTGGA----------------------------------
----------------------------------------------------------TGTAGATTTTTGTCCG--AAGT
GCTCTTGTTTTTTACATCACAGT---------------------------------------------------------
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------------------------ACAGATGCAGACGCTCATAGACTCACTTCTATGAACGCACACACGCACAACTTACC
CCTGTGAGCACCTTCAAGACTGAGCCGACACATCATTTTGGGATTGATGAAGTCACCACATTCATAATAGACGGGAATGT
CGGCTCCAACTGAACGCACATCATCGGATGCCCTGTAATAAATCCAAAAAAATGCTAGCAGCAGTGTCAAGTCTAAGA--
---
>chr1B_618
TAAGGC--------------------------------------------------------------------------
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---------------------------------------------------------------GTGGACTTGCAATACTT
GCCTTCTAGCCTTGGACAAAAGAACGTGAAAATAGCAAACGGACAATTAAAGGGTTGTTTTGGAAAGTGTCCCGTTGG--
----------------CACCTCTAAAAA-TTGATGATTAACGAGCATACTCTAGTTGACTGCACGTTCGCGTGTTTCTTG
CGATGATTGGACTGGACTAGAGTTTTGTAATACTCCGGAAACAGCAGCTACGGCTTGACGTCGACCGTAACGCGCCACGC
CCGCTGCGCGTCCGGATCCACTCTGCTTCCTTCTTACGAAACCTAACAAATTCATATACTA-----CCCATCGTCAGAGA
GAGAGAGAGAC--ACACACACGGAGAAGGTGGGGCAGCCACGACCTA--GCTTCCAAGGCATGAGGCGT---GACCCAGA
ACTGC---------------------------------------------GTCAAGCTATCTCCCCAACCTTCCACGCTG
TACGGGGGGACACCGTCCTCCTCACCGTCGCCGTCGACAACCCTCTGCTCGCCAGGAGCGTCGCCATCCAATGGCACGG-
--------------------------------------------------------------CACCGGCGTGGTAACTAA
GCCAATAATCCCAATCTTCTCTCACGAGTCACGACCCCATGTTATACTGATGTTGATTTTGTCCACCGATCGACTAATTC
T--------GTGGTGGTTGATGGGTGCTGCAGACTGGCACGCCGGCGGCGGAC---GGCATCGAGGGCCACACCTTGACG
TACAATTTCGTGGCGGACCGGCCAGGCACGTTCACCTTCCGCGCACGCTACGGCCGCAGCCGCGCCGTGACCTTCACCGA
CGCGCAGGGACGCGAGGCCCGGCCGTCCGCCG---GTGACCGCGCACGCACGGACACCGCCGGACATCGCGTCCGCGTGC
CGCGCAGCCATGCGGGGCCTTCCGCCTGCCGACGAATGCACACTGCTCCACGGGCCACCGAGCCAGAACTCGTCTACGTC
CACGGCGGCCGGGGCCATGCGTGCGTCGAAGCGCAACTCATG--------------------------------------
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>chr1D_660
AAAAC---------------------------------------------------------------------------
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---------------------------GAAAATAGCAAACGAACATT--AAGGGTTGTTTTGGAAATTGTCACGTTGGAT
GGCGGCTCGTGCCTAGCACCTCTAACTATTTGATGATTAACGAGCTTAGTCTAGTTGACTGCACGTTGGCGTGTTTCTTG
TGATGATTGGCACGTTGGCGTGC--------------C------CAGCTACGGCTTGACGTCGACCGTGACGCGCCACGC
CCGCTGC-------------------TTCCTTCGCACGGAACCAATCACATGCATATGCTTACGACCCCATCGTCAGAGA
GAGAGAG--------------------GGTGGGGCAGCCACGACCTATAGCTTCCAAGCCATGAGAGGTGACCCCGAGCT
GCGGCAAGCAAAGGAGTTGGAGTCCCCGGGCCGCCAGCCAACCACCAACGGCCAAGCTACCTCCGCAACCTTCCACGCTG
TACGGGGGGACACCGTCCTCATCACCGTCGCCGTCGACAACCCTCTCCTCGCCAGGAGCGTCGCCATCCAATGGCACGG-
--------------------------------------------------------------CACCCGCGAGGTAACTAC
GCCGCCCATCCCAGGGGTCTGTCACCGAGTGATGTTA-----------GATGTTAATTTCATCCACCGATCGACTAATTG
T--------GTGGTGGTTGATGGGGGCTGCAGACCGGCACGCCGGCGGCCCAC---AGCATCGAGGGCCACACCTTGACG
TACAATTTCGTGGCGGACCGGCCGGGCACCTTCACCTACTGCGCGCGCTACGGCCGCAACCGCGCCGCGACCTTCACCGA
CGCGCAGGGACGCGAGGCCTGGCCGTCCGCCG---GCGACCGCGCACGCGCCGA---CGCCGGACATCGCGTCCGTGTGC
CACGCAGCTATGCGGGGCCTTCCGCCTGCCGACGAACACC------------GACGGGCGAGCAAGAACTCGTCTACGTC
CGCGGCGGCCGGAACCATGCGCGCGTTGAGGCGCAACTCATGGCTGGTAACACTACTATCTACCTCAATGACGAAGGCCC
GGTCGTGCGGTTCCTCCGGTGGTCCGCCGTCGGATTGACGGCCGCGGCCTTGTGGGTCTCAGCTGTATGCGGCGGGAGGT
GTGACCCTGTTATGCGCTGCCGAGGAGACGGCCCATT---AGACGTAAGGTTTATAGGTCGAGCAAATCCTCATGTTTCA
CGGGCTCCCAGCTTCCCGCCGCCTTGATTTATCATTGTCAAAAG-CTTTCCCACTGTAAATAAAATTATGTAGTTTCCAC
GAT---------ATTTTTGGTGTTGTCATTTCATTAATTGACGTGTCGAATCTGTAGAAAAATCACAGTTGTATTTC--T
TTGTAATCCAGTGAAAGGGAATTTGATCGTGC------AGTTGT------------------------------------
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>chr1A_841
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------------------------------------------------TACGGCTTGACGTCGACCGTAACGCGCCACGC
CCGCTGCACGTCCGGGTCCGCTCTGCTTCCTTCTTACGAAACCTAACAAATTCATATACTA-----CCCATCGTCAGAGA
GAGAGAGAGAGAGACACACAAGGAGAAGGTGGGGCAGCCACGACCTA--GCTTCCAAGCCATGAGGCGT---GACCCAGA
ACTGC---------------------------------------------GCCAAGCTACCTCCCCAACCTTCCACGCTG
TACGGGGGGACACCGTACTCATCACCGTCGCCGTCGACAAGCCTCTCCTCGCCCGGAGCGTCGCCATCCAATGGCACGG-
--------------------------------------------------------------CACCGGCGAGGTGAGTA-
--C-CCAATCCCAAGCTTCTGCCGCC--CGCGCTTTA-----------GATGTTGATTTTGACCGCAGATCGATTGATTC
ATTCCTGTGGTGGTGGTTGAC-GGGGCTGCAGACTGGCACGCCGGCGGCGGCCGATGGCATCAAGGGCCACACCTTGACG
TACAATTTCGTGGCAGACAGGCCGGGCACGTTCACCTTCCGCGCGCGCTACGGCCGCAACCGCGCGGCGACTTTCACCGA
CGCGCAGGGACGTGAGGCCTGGCCGTCCGCCGCCGGCGACCACGCACACACCG------------ATCGTGTCCGCGTGC
CACGCAGCCAAGAGGGGCCTTCCGCCTGCCGACGAACACGCACCCCTCCACGGACCGCCCACCAAGAGCTCGTCTACGTT
CGCGGTGGCCGGGGCCATGCGTGCGTCGAAGCGCAACTCATGGCAGGTAACACCACTATCTACCTTAATGACGAAGGCCC
GGTTGAGTGGCTCCTCCGATTGTCCGCCCTCGGATTGACGGCCGCGGCCTTGTGGGTCTGTGGTGTATGCGGCGGGCGGC
GTGCCCCTGTTATGCGCCGCAGAGGAGACGGCCCATT---GGACGTAAGGTTTGTAGGTCGAGCAAATCCTCACGTTTCA
TGGGCTCCCAGCTTCCCGCCGCCTTGAGTTAGTATTGTCAAAAA-AATTCCCACTGTAAATAAACATATGTGGTAGTTTT
CTTTCTATTGAAAT-TTTGGTGTTGTTGCTTCATTAATTTGCACATCGAGTTTGTAGAA-------------ATTTC--A
TTGTAATCTAGTGGAAATGAATTTGATTGTGTAATAGTAGTTGTCTAACTTA----TGTGTAAATGGTTGTGTG--TACT
CCAGATGTTTGTAACAATTATCTATTGTT---------------------------------------------------
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>chr1A_1026
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--------------------------------------------------GCCAAGCTACCTCCGCAACCTTCCACGCTT
CCC---------CCGTCCTCATCACCGTCGCCGTGAACAAGCCCCACTTCGCCAGGAGCGTCGCCATCCAATGGCACGC-
--------------------------------------------------------------CATCCGCGAGGTAACTAC
GCCGCTCATCCGAAGGGTCTGTCACCGAGCAATTTTA-----------GATGCTAATTCCGTTCACCGATCGACTAATTG
T--------ATGGTGGTTGATGGGGGCTGCAGACCGGCACGCCGGCGGCCCAC---GGCATCGAGGGCCACACCTTGACG
TACAATTTCGTGGCGGACCGGCTGGGCACCTTCACCTA---------------------CCGCGCCGCGACCTTCACCGA
CGCGCAGGGACGCGAGGCCGGGCCGTTCGCCG---GCGACTGCGCGCGCT--GA---CGCCGGACATCGCGTCCGCGTGC
CACGCAGCCATGCCGGGCCTTCCGCCTGCCGACGAACACC------------GACGGGCGAGCAAGAACTCATCTACGTC
CGCGGCGGCCGGGGCCATGCGTGCGTCGAGGCGCAACTCAAGGCTGGTAA------------------------------
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>SNPs
--------------------S--------------S----S---------S----S-------SSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----------S------
-S-S------S-------S---------------S-------------------------S-----------S-----S-
------------S------------S------------------------------------------------------
-----------------------------S---SSS------------------------------S-------------
-S----S---------------S----------------------S---------------S-S----------------
------------------------------------------S----------------------------S--------
--------------------------------------------------------S-----------------------
---S----------------------------------------------------------------------------
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--------------------------S-------S---------------------------------------------
-----------------------------------------------S----------------S---------------
---------------------------------------------------------------S--------------S-
S-------------------------------------------------------------------------------
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--------------------------------------------S-----------------------------------
---------S-----------------S----------------S-----------------------------S-----
S-----------SS----------S---------S--SSS-----S---------S-----------S------------
--------------S--S----------------S------SSSS-----------S-----SS---------------S
-------------------------------SS------S----------------S--------S------S-S--SS-
-----------------------------S-S----------------S-S-SSSS---------------S-SSS----
S----------S-----------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSS-S---S---S-S-----S---S-SSSSSSS-SSSSSSSSS-SSS-SSSSSSSS--S
SSS-S--S--SSSSSS-S-SS--SSSSS-S---SSS-S--SSSSSS---S-SSSSSSS-SSSSSSSSS-SS-SSSSSSSS
S--SSSSS-S--SS--SSS-SS-SSSSSSS-SS--SSSSS---SSSS-SSS-SSS-S-SS-SS--SS-SSS--SSSSSSS
SSS
>forward_178
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------------------------------------------------------------------------------GG
CGTTCTTGTGTGGGTTTC--------------------------------------------------------------
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>reverse_2300
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-----------------------------------------------------------GGAGGGGATAAAGAGGCACG-
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