Typing tool
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Typing tool
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Complete norovirus genomes
| KJ685402 | GII.4 Sydney | |
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| GII.P4 New Orleans |
ORF1: 1..5041
ORF2: 5022..6644
ORF3: 6644..7450
LOCUS KJ685402 7450 bp ss-RNA linear VRL 28-JAN-2015
DEFINITION Norovirus Hu/GII/BG1C0434/2012/BGD, partial genome.
ACCESSION KJ685402
VERSION KJ685402.1
DBLINK BioProject: PRJNA242747
KEYWORDS .
SOURCE Norovirus Hu/GII/BG1C0434/2012/BGD
ORGANISM Norovirus Hu/GII/BG1C0434/2012/BGD
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7450)
AUTHORS Das,S.R., Halpin,R.A., Mohan,M., Fedorova,N., Tsitrin,T., Puri,V.,
Stockwell,T., Amedeo,P., Bishop,B., Gupta,N., Hoover,J., Katzel,D.,
Schobel,S., Shrivastava,S., Ahmed,T., Haque,R., Knobler,S.,
Miller,M., Wentworth,D.E. and Nelson,M.
TITLE Direct Submission
JOURNAL Submitted (03-APR-2014) J. Craig Venter Institute, 9704 Medical
Center Drive, Rockville, MD 20850, USA
COMMENT This work was supported by the National Institute of Allergy and
Infectious Diseases (NIAID), Genome Sequencing Centers for
Infectious Diseases (GSCID) program.
The genome sequence was generated using overlapping PCR amplicons
spanning the genome. The amplicons were pooled by sample and then
barcoded and sequenced using Next Generation Sequencing platforms.
The consensus sequences of the internal PCR primer hybridization
sites were manually verified using reads from amplicons that
spanned across the sites.
##Genome-Assembly-Data-START##
Current Finishing Status :: Finished
Assembly Method :: clc_ref_assemble_long v. 3.22.55705
Genome Coverage :: 192.0x
Sequencing Technology :: Ion Torrent
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7450
/organism="Norovirus Hu/GII/BG1C0434/2012/BGD"
/mol_type="genomic RNA"
/strain="Hu/GII/BG1C0434/2012/BGD"
/host="Homo sapiens; sex: F; age: 302D"
/db_xref="taxon:1486698"
/country="Bangladesh: Dhaka"
/collection_date="04-Sep-2012"
/PCR_primers="fwd_name: Ampl_1_Forward, fwd_seq:
gtgaatgawgatggcgt, rev_name: Ampl_1_Reverse, rev_seq:
ttggttgagagyttyctg"
/PCR_primers="fwd_name: Ampl_2_Forward, fwd_seq:
ccgcaaaatcttcaagtg, rev_name: Ampl_2_Reverse, rev_seq:
cwacaggtcttggtctgctrga"
/PCR_primers="fwd_name: Ampl_3_Forward, fwd_seq:
tcaaccaartctgcttcacctg, rev_name: Ampl_3_Reverse, rev_seq:
ratcctttgccggatcttgg"
/PCR_primers="fwd_name: Ampl_4_Forward, fwd_seq:
ggcaagaagcacacagcctt, rev_name: Ampl_4_Reverse, rev_seq:
crrctctytgttgtgttgaatccc"
/PCR_primers="fwd_name: Ampl_5_Forward, fwd_seq:
tggyaagatcaagaagaggc, rev_name: Ampl_5_Reverse, rev_seq:
acaacaaargcacygctrgg"
/PCR_primers="fwd_name: Ampl_6_Forward, fwd_seq:
gagrccrtccccygattttg, rev_name: Ampl_6_Reverse, rev_seq:
atcaatyttgtcttttcaca"
/note="genotype: GII"
gene <1..5041
/gene="POL"
/locus_tag="DC54_49804gpPOL"
CDS <1..5041
/gene="POL"
/locus_tag="DC54_49804gpPOL"
/note="genome polyprotein"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="AHX22017.1"
/translation="AKSSSDGVLSSMAVTFKRALGARPKQPPPREKPQRPPRPPTPEL
VKNIPPPPPNGEDEIVVSYSVKNGVSGLPDLSTVRQPEESNTAFSVPPLNQRENRDAK
EPLTGAILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELAPLSLYWRPVYTPQ
YLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDW
NRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNILNILASCDWTFAGI
VESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGFT
KEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAIVRSIEDAVLD
LEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAA
ARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRN
GVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDV
IIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDF
SHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTT
FNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTMPELKQALKNVSIKKCQIVYS
GCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQ
IAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPKDDVEFVISSDDIKTEG
KKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAI
ARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSEIRKRNPDDFKPKGKLW
ADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGV
PIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAVR
MGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHT
AAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPTLSTKTKFWRSSTAS
LPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPKPSVLEAAKKTIINV
LEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMF
EEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAH
CVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRAVLAAALEIMVKFSP
EPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVT
NLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKPTRPDKTEGPLVVSE
DLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPSETMIPHSQRPIQLM
SLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNL
APSFVNEDGVE"
mat_peptide <1..931
/gene="POL"
/locus_tag="DC54_49804gpPOL"
/product="putative protein p48"
mat_peptide 932..2029
/gene="POL"
/locus_tag="DC54_49804gpPOL"
/product="NTPase"
/note="p41"
mat_peptide 2030..2566
/gene="POL"
/locus_tag="DC54_49804gpPOL"
/product="protein p22"
mat_peptide 2567..2965
/gene="POL"
/locus_tag="DC54_49804gpPOL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 2966..3508
/gene="POL"
/locus_tag="DC54_49804gpPOL"
/product="3C-like protease"
/note="3CLpro; calicivirin"
mat_peptide 3509..5038
/gene="POL"
/locus_tag="DC54_49804gpPOL"
/product="RNA-directed RNA polymerase"
gene 5022..6644
/gene="VP1"
/locus_tag="DC54_49804gpVP1"
CDS 5022..6644
/gene="VP1"
/locus_tag="DC54_49804gpVP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AHX22018.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6644..7450
/gene="VP2"
/locus_tag="DC54_49804gpVP2"
CDS 6644..7450
/gene="VP2"
/locus_tag="DC54_49804gpVP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AHX22019.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 cgcaaaatct tcaagtgacg gagtgctttc tagcatggct gtcactttta aacgagccct
61 cggggcgcgg cctaaacagc ctcccccgag ggaaaaacca caaagacccc cacgaccacc
121 tactccagaa ctggttaaga atattccccc tcccccaccc aacggagagg atgaaatagt
181 ggtttcttat agtgtcaaaa atggtgtttc cggcttgcct gacctttcta ccgtcaggca
241 accggaagaa tccaacacgg ccttcagtgt ccctccactc aatcagaggg agaatagaga
301 tgctaaggag ccactcactg gagcaattct ggaaatgtgg gacggggaaa tctaccatta
361 tggcctgtat gtggagcgag gtcttgtact aggtgtgcac aaaccgccag ctgccatcag
421 ccttgctaag gttgagctgg caccactctc cttgtactgg agacctgtgt acactcctca
481 gtacctcatc tctccagaca ctctcaagaa attgtccgga gagacgttcc cctacacagc
541 ctttgataac aactgttatg ccttttgttg ctgggttctg gacctaaatg actcgtggct
601 gagtagaaga atgatccaga gaacaactgg tttcttcagg ccctaccagg actggaatag
661 gaaacccctt cccactatgg atgactccaa aataaagaag gtagctaaca tatttctgtg
721 tgccctgtcc tcgctattca ccagacccat aaaagatata atagggaaga taaggcctct
781 taatatcctc aacatcttag cctcatgtga ttggaccttt gcgggtatag tggagtccct
841 gatactcttg gcagaactct ttggagtttt ctggacaccc ccagatgtgt ctgcgatgat
901 tgccccctta cttggtgact acgagctaca aggacctgag gaccttgcag tggagctcgt
961 ccccgtggtg atggggggaa ttggtttggt gctaggattc accaaagaga agattgggaa
1021 aatgttgtca tctgctgcgt ccactttgag agcttgcaaa gaccttggtg catatgggct
1081 agagatccta aagttagtca tgaagtggtt cttcccaaag aaggaggagg caaatgagct
1141 ggctatagtg aggtccatcg aggatgcagt cctggatctc gaggcaattg aaaacaatca
1201 tatgaccacc ttgcttaaag ataaagacag tctggcaacc tacatgagaa cacttgacct
1261 tgaagaggag aaagccagga aactctcaac caagtctgcc tcacccgaca tcgtgggtac
1321 aatcaacgcc ctcctggcga gaatcgctgc cgcacgttct ctggtgcatc gagcgaagga
1381 ggagctttcc agcagaccaa gacctgtggt gttgatgata tcaggcaggc caggaatagg
1441 gaagacccac ctcgctaggg aagtggctaa gagaatcgca gcctccctta caggagatca
1501 gcgtgtgggc ctcatcccac gcaatggtgt cgaccattgg gatgcgtaca agggggagag
1561 agtcgtcctg tgggacgatt atggaatgag caaccctatt cacgatgccc tcaggctgca
1621 agaactcgct gacacttgtc ccctcactct gaactgtgac aggattgaaa ataaaggaaa
1681 ggtctttgac agcgatgtca tcattatcac cactaatctg gccaacccag caccactgga
1741 ctatgtcaac tttgaagcat gctcgaggcg cattgacttc ctcgtgtatg cagaagcccc
1801 tgaagtcgaa aaggcgaagc gtgacttccc aggccagcct gacatgtgga agaacgcttt
1861 cagttctgat ttctcacaca taaaactagc actggcccca cagggtggtt tcgataagaa
1921 cgggaacacc ccacacggaa agggcgtcat gaagaccctc accactggct cccttattgc
1981 ccgggcatca gggctactcc atgagaggtt ggatgaattt gaactgcagg gcccagctct
2041 caccaccttc aatttcgatc gcaataaagt gcttgccttt agacagcttg ctgctgaaaa
2101 caaatatgga ttgatggaca caatgagggt tgggaaacag ctcaaggatg tcagaaccat
2161 gccagaactc aaacaagcac tcaagaatgt ctcaatcaag aagtgccaaa tagtgtatag
2221 tggttgcact tacatgcttg agtctgatgg caagggcaat gtgaaagttg acagaatcca
2281 aagcgccgcc gtgcagacca acaatgagct ggctggtgcc ctgcaccact tgaggtgcgc
2341 cagaattaga tactatgtca agtgtgtcca ggaagccctg tattccatca tccaaatcgc
2401 tggggctgca tttgtcacca cgcgcattgc caagcgcatg aacatacaag acctatggtc
2461 caagccacaa gtggaaaaca cagaggagac taccagcaag gacgggtgcc caaaacctaa
2521 ggatgatgtg gagttcgtca tttcatccga cgacatcaaa actgagggca agaaagggaa
2581 gaacaagact ggccgtggca agaagcacac agcattttca agcaaaggcc tcagtgatga
2641 agagtatgat gaatacaaga ggattagaga agaaaggaat ggcaagtact ctatagaaga
2701 gtaccttcag gacagggaca aatactatga ggaggtggcc attgccaggg cgactgagga
2761 agacttctgt gaagaggagg aggccaagat ccggcaaagg atctttaggc caacaaggaa
2821 acaacgcaag gaggaaagag tctctcttgg tctggttaca ggctctgaaa ttaggaaaag
2881 aaacccagat gacttcaaac ccaaggggaa attgtgggct gacgatgaca ggagtgtgga
2941 ctacaatgag aaactcagct ttgaggcccc accaagcatt tggtcgagaa tagtcaactt
3001 tggttcaggc tggggattct gggtctcccc cagtctgttc ataacatcaa cccatgtcat
3061 accccagggc gcaaaggagt tctttggagt ccccatcaaa caaatacagg tacacaagtc
3121 aggcgagttc tgtcgcttga gattccctaa accaatcagg actgatgtga cgggcatgat
3181 cttggaagaa ggcgcacctg agggcaccgt ggtcacacta ctcatcaaaa ggtccactgg
3241 ggaactcatg cccctagcag ttaggatggg gacccatgcg accatgaaga tccaagggcg
3301 cactgttgga ggccagatgg gcatgcttct gacaggatcc aacgccaaga gcatggacct
3361 gggtactaca ccaggtgatt gtggctgccc ctacatttac aagagaggta atgactatgt
3421 ggtcattgga gtccacacgg ctgccgcacg tgggggaaac actgtcatat gtgccaccca
3481 agggagtgaa ggggaggcta cacttgaggg tggtgacaac aaggggacat actgtggtgc
3541 accaatccta ggcccaggga gtgccccaac acttagcacc aagaccaaat tctggagatc
3601 gtccacagca tcacttccac ctggcaccta tgaaccagcc tatcttggtg gcaaggaccc
3661 tagagtcaag ggtggccctt cactgcagca agtcatgagg gaacagttga agccattcac
3721 agagcccagg ggcaagccac caaaaccaag tgtattagaa gctgccaaga agaccatcat
3781 taatgtcctt gagcaaacaa ttgatccacc tgagaaatgg tcgttcgcac aagcttgcgc
3841 gtcccttgac aagaccactt ccagtggcca tccgcaccac atgcggaaaa acgactgctg
3901 gaacggggag tccttcacgg gcaagctggc agaccaggct tccaaggcca acctgatgtt
3961 tgaagaaggg aagaacatga ccccagtcta cacagctgcg ctcaaggatg agttagttaa
4021 aactgacaaa atttatggta agatcaagaa gaggcttctc tggggctcgg atttggcaac
4081 catgatccgg tgtgctcgag cattcggagg cctaatggat gaactcaaag cgcactgtgt
4141 cacactcccc attagagttg gcatgaatat gaatgaggat ggccccatca tcttcgagag
4201 gcattccagg tacacgtacc actatgatgc tgactactct cggtgggatt caacacaaca
4261 gagagccgtg ttggcagcag ctctagaaat catggttaaa ttctccccag aaccacattt
4321 ggctcaggta gttgcggaag accttctttc ccccagcgtg gtggacgtgg gcgacttcac
4381 aatatcaatc aatgagggtc ttccctctgg ggtgccctgc acctcccaat ggaactccat
4441 cgcccactgg cttctcactc tctgtgcgct ctctgaagtc acaaacctgt ctcctgatac
4501 catacaggct aattccctct tctcttttta tggtgatgat gaaattgtta gcacagacat
4561 aaaattggac ccagagaaat tgacagcaaa actcagagaa tatgggttaa aaccaacccg
4621 ccctgacaaa actgaaggac cccttgtcgt ctctgaagac ctgaatggcc taactttcct
4681 gcggagaact gtgacccgcg acccagctgg ttggtttgga aaactggagc agagttcaat
4741 actcaggcaa atgtactgga ctaggggtcc caaccatgga gacccatctg aaacaatgat
4801 tccacactcc caaagaccca tacaattgat gtccctactg ggggaggccg ctctccacgg
4861 cccagcattt tacagcaaaa tcagcaaatt ggtcattgca gagctaaaag aaggtggtat
4921 ggatttttac gtgcccagac aagagccaat gttcagatgg atgagattct cagatctgag
4981 cacgtgggag ggcgatcgca atctggctcc cagttttgtg aatgaagatg gcgtcgagtg
5041 acgccaaccc atctgatggg tccgcagcca acctcgtccc agaggtcaac aatgaggtta
5101 tggctctgga gcccgttgtt ggtgccgcca tcgcggcacc tgtagcgggc caacaaaatg
5161 taattgaccc ctggattaga aacaattttg tacaagcccc tggtggagag tttacagtat
5221 cccctagaaa cgctccaggt gaaatactat ggagcgcgcc cttaggccct gatctaaatc
5281 cctacctatc ccatttggcc agaatgtaca atggttatgc aggtggtttt gaagtgcagg
5341 taattctcgc ggggaacgcg ttcaccgccg ggaaggtcat atttgcagca gtcccaccaa
5401 attttccaac tgaaggctta agccccagcc aggtcactat gttcccccat atagtagtag
5461 atgttaggca actagaacct gtgttgatcc ccttacccga tgttaggaat aatttctatc
5521 attacaatca atcaaatgac cccaccatta agttgatagc aatgttgtat acaccactta
5581 gggctaataa tgctggggac gatgtcttca cagtttcttg ccgagttctc acaagaccat
5641 cccccgattt tgatttcata tttttagtgc cacccacagt tgagtcaaga actaaaccat
5701 tctctgtccc agttttaact gttgaggaga tgaccaattc aagattcccc attcctctgg
5761 aaaagttgtt cacgggtccc agcggtgcct ttgttgttca accacaaaac ggcaggtgca
5821 cgactgatgg cgtgctctta ggcaccaccc aactgtctcc tgtcaacatc tgcaccttca
5881 gaggggatgt cacccatatc acaggcagtc gcaattacac aatgaatttg gcttctcaaa
5941 attggaacaa ttatgaccca acagaggaaa tcccagcccc tctaggaact ccagactttg
6001 tggggaagat tcaaggcatg ctcacccaaa ccacaaggac agatggctca acacgcggcc
6061 acaaggctac agtgtacact gggagcgccg actttgctcc aaaactgggt agagttcaat
6121 ttgaaactga cacagaccat gattttgaag ctaaccaaaa cacaaagttc accccagtcg
6181 gtgtcatcca agatggtagc accacccacc gaaatgaacc ccaacagtgg gtgctcccaa
6241 gttactcagg cagaaatact cataatgtgc atctggcccc cgctgtagcc cccacttttc
6301 cgggtgagca acttctcttc ttcagatcca ccatgcccgg atgcagcggg taccccaaca
6361 tggatttgga ctgtctgctc ccccaggaat gggtgcagta cttctaccaa gaggcagccc
6421 cagcacaatc tgatgtggct ctgctaagat ttgtgaatcc agacacaggt agggttttgt
6481 ttgagtgtaa gcttcataaa tcaggctatg ttacagtggc tcacactggt caacatgatt
6541 tggttatccc ccccaatggt tattttaggt ttgattcttg ggtcaaccag ttctacacgc
6601 ttgcccccat gggaaatgga acggggcgta gacgtgtagt ataatggctg gagctttctt
6661 tgctggattg gcatctgatg tccttggctc tggacttggt tcccttatca atgctggggc
6721 tggggccatc aaccaaaaag ttgagtttga aaataacaga aaattgcaac aagcatcctt
6781 ccaatttagc agcaatctgc aacaggcttc ctttcaacat gacaaagaga tgctccaagc
6841 acaaattgag gccaccaaaa agctacaaca ggaaatgatg aaagttaagc aggcaatgct
6901 cctagagggt gggttctctg agacagatgc agcccgcggg gcaattaacg cccccatgac
6961 aaaagctttg gactggagcg ggacaaggta ctgggctccc gatgctagga ctacaacata
7021 caatgcaggc cgcttttcca cccctcaacc atcgggggca ctgccaggaa gagctaatct
7081 tagggatgct gtccctgctc ggggttcctc cagcaaatcc tctaactctt ctactgctac
7141 ttctgtgtac tcaaatcaaa ctacttcaac gagacttggt tctacagctg gttctggtac
7201 cagtgtctcg agcctcccgt caactgcaag gactaggagc tgggttgagg atcaaagtag
7261 gaatttgtca cctttcatga ggggggccca caacatatcg tttgtcaccc caccatctag
7321 cagatcctct agccaaggca cagtctcaac cgtacccaaa gaggttttgg actcctggac
7381 tggcgctttc aacacgcgca ggcagcctct cttcgctcac attcgtaaac gaggggagtc
7441 acgggtgtaa
//