Typing tool
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Typing tool
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Complete norovirus genomes
| KC576909 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS KC576909 7509 bp ss-RNA linear VRL 23-OCT-2013
DEFINITION Norovirus Hu/GII.4/NIHIC4.2/2011/USA, complete genome.
ACCESSION KC576909
VERSION KC576909.1
DBLINK BioProject: PRJNA70471
KEYWORDS .
SOURCE Norovirus Hu/GII.4/NIHIC4.2/2011/USA
ORGANISM Norovirus Hu/GII.4/NIHIC4.2/2011/USA
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7509)
AUTHORS Madupu,R., Halpin,R.A., Ransier,A., Fedorova,N., Tsitrin,T.,
McLellan,M., Stockwell,T., Amedeo,P., Appalla,L., Bishop,B.,
Edworthy,P., Gupta,N., Hoover,J., Katzel,D., Li,K., Schobel,S.,
Shrivastava,S., Thovarai,V., Wang,S., Kim,M., Bok,K.,
Sosnovtsev,S.V., Wentworth,D.E. and Green,K.Y.
TITLE Direct Submission
JOURNAL Submitted (01-FEB-2013) 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 sequence lacks part of non-coding region.
##Genome-Assembly-Data-START##
Current Finishing Status :: Finished
Assembly Method :: clc_ref_assemble_long v. 3.22.55705
Genome Coverage :: 282.5x
Sequencing Technology :: Sanger; Illumina; 454
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7509
/organism="Norovirus Hu/GII.4/NIHIC4.2/2011/USA"
/mol_type="genomic RNA"
/strain="Hu/GII.4/NIHIC4.2/2011/USA"
/host="Homo sapiens"
/db_xref="taxon:1292143"
/geo_loc_name="USA: Maryland"
/collection_date="10-Mar-2011"
/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"
/PCR_primers="fwd_name: Ampl_7_Forward, fwd_seq:
gtgaatgawgatggcgt, rev_name: Ampl_7_Reverse, rev_seq:
ccagrctrtctttrtctt"
/note="genotype: GII.4"
gene 1..5100
/gene="POL"
CDS 1..5100
/gene="POL"
/note="genome polyprotein"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AGE99595.1"
/translation="MKMASNDASAAAVANSNNDTAKSSNDKMFSNMAVTLKRALGARP
KQPPPREIPQRPPRPPTPELIKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE
ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
HARVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGR
LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTM
PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATSKDGC
PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSRGTYCGAPILG
PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 1..990
/gene="POL"
/product="protein p48"
mat_peptide 991..2088
/gene="POL"
/product="NTPase"
/note="p41"
mat_peptide 2089..2625
/gene="POL"
/product="protein p22"
mat_peptide 2626..3024
/gene="POL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 3025..3567
/gene="POL"
/product="3C-like protease"
/note="3CLpro; calcivirin"
mat_peptide 3568..5097
/gene="POL"
/product="RNA-directed RNA polymerase"
gene 5081..6703
/gene="VP1"
CDS 5081..6703
/gene="VP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AGE99596.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRSNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQMILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSADFTPKLGSVQFGTDTDNDFETHQNTRFTPVGVIQDG
ATTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPNFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6703..7509
/gene="VP2"
CDS 6703..7509
/gene="VP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AGE99597.1"
/translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQELMKVKQTILLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRINPRTPIPARGSPSISS
NASTATSIHSNQTASTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKDVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc
61 gcaaaatctt caaatgacaa gatgttttct aacatggctg tcactcttaa aagagccctc
121 ggggcgcggc ctaaacagcc ccccccgagg gaaataccac aaagaccccc acgaccacct
181 actccagaac tgatcaaaaa gatccctcct cccccgccca acggagagga tgaagtagtg
241 gtttcttata gtgccaaaga tggcgtttcc ggtttgcctg agctttccac cgtcaggcaa
301 ccggaagaaa ccaatacggc cttcagtgtc cctccactca atcagaggga gaatagggac
361 gctaaggaac cactgactgg aacaattctg gaaatgtggg atggagaaat ctaccattat
421 ggcctgtatg ttgagcgagg tcttgtgctg ggtgtgcaca aaccaccagc tgccattagc
481 cacgccaggg tcgaattaac accactctcc ttgttctgga gacctgtgta cactcctcag
541 tacctcattt ctccagacac tctcaagaag ttacacggag aaacatttcc ctacacagcc
601 tttgacaaca actgctatgc cttttgttgt tgggtcctgg acctaaacga ctcgtggctg
661 agcaggagaa tgatccagag aacaactggc ttcttcagac cctaccaaga ttggaatagg
721 aaacccctcc ccactatgga tgattccaaa ttaaagaagg tagctaacat attcctgtgt
781 gccctgtctt cgctattcac caggcccata aaagacataa taggaaggtt aaggcctctc
841 aacatcatca acatcctggc ctcatgtgat tggactttcg cgggcatagt ggagtccttg
901 atactcttgg cagagctctt tggagttttc tggacacccc cagatgtgtc tgcgatgatt
961 gcccccttac tcggtgattt cgagttacaa ggacctgaag accttgtagt ggagctcgtc
1021 cctgtagtaa tgggggggat tggtctggtg ctaggattca ccaaagagaa gattggaaaa
1081 atgttgtcat ctgctgcatc caccttgaga gcttgtaaag accttggtgc atatgggcta
1141 gaaatcttaa agttagtcat gaagtggttc ttcccgaaga aagaggaagc taatgaactg
1201 gccatggtga gatccatcga ggatgcggta ctggaccttg aggcaattga aaacaaccat
1261 atgaccacct tgctcaaaga caaagatagc ctggcaacct acatgagaac ccttgacctc
1321 gaggaagaga aagccagaaa actctcaacc aagtctgctt cacctgacat cgtgggcaca
1381 atcaacgcgc ttctggcgag aatcgccgct gcacgctccc tggtgcaccg agcgaaggag
1441 gagctttcca gcagaccaag acctgtagtc ttgatgatat caggcaggcc aggaataggg
1501 aagacccacc ttgctaggga agtggctaag agaatcgcag cctccctcac aggagaccag
1561 cgtgtaggcc tcatcccacg caatggcgtc gatcactggg atgcgtacaa gggggagagg
1621 gtcgtcctat gggacgacta tggaatgagc aatcccatcc acgacgccct cagactgcaa
1681 gaactcgctg atacttgccc cctcacccta aattgtgaca ggattgagaa taaaggaaag
1741 gtctttgaca gcgatgtcat cattatcact actaatctgg ccaacccagc gccactggac
1801 tatgtcaact ttgaagcatg ctcgaggcgc atcgatttcc tcgtgtacgc agaagccccc
1861 gaggtcgaaa aggcgaagcg cgacttcccg ggccaacctg acatgtggaa aaacgctttt
1921 agttctgatt tctcacacat aaaactggca ctggctccgc aaggtggctt tgataagaac
1981 gggaacaccc cacacgggaa gggcgtcatg aagactctca ccactggctc cctcattgcc
2041 cgggcatcag ggctgctcca cgagagattg gatgagtttg aactacaggg cccagctctc
2101 accaccttca actttgaccg caacaaagtg cttgccttta gacagcttgc tgctgaaaac
2161 aaatatgggt tgatggacac aatgaaagtt gggaggcagc tcaaggatgt caaaaccatg
2221 ccagaactta aacaagcact caagaatatc tcaatcaaga agtgccagat tgtgtacagt
2281 ggttgcacct acacacttga gtctgatggc aaaggcaatg tgaaagttga cagagtccag
2341 agtacctccg ttcagactaa caatgagttg gctggcgccc tgcaccatct aaggtgcgcc
2401 agaatcaggt attatgttaa gtgtgttcag gaggccctgt attctatcat ccagattgct
2461 ggggctgcat ttgtcaccac gcgcatcatc aagcgtgtga acattcaaga cttatggtcc
2521 aagccacaag tggaaaacac agaggaggct accagcaaag acgggtgccc aaaacccaaa
2581 gatgatgagg agttcgtcat ttcatctgac gacattaaaa ctgagggtaa gaaggggaag
2641 aacaagactg gccgtggtaa aaagcataca gccttctcaa gtaaaggtct cagtgatgaa
2701 gagtatgatg agtacaagag aattagagag gaaagaaatg gcaagtactc catagaagag
2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gaccgaggaa
2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tcttcagacc aacaaggaaa
2881 caacgcaagg aagaaagggc ttctctcggt ttagtcacag gttctgaaat taggaaaaga
2941 aatccagaag acttcaagcc caaggggaaa ctatgggctg acgatgacag aagtgtggac
3001 tacaatgaaa aactcagttt tgaggcccca ccaagcatct ggtcaaggat agtcaacttt
3061 ggttcaggtt ggggcttctg ggtctccccc agcctgttca taacatcaac ccacgtcata
3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaattcaggt gcacaagtca
3181 ggcgaattct gtcgcttgag gttcccaaaa ccaatcagga ctgatgtgac tggcatgatc
3241 ttggaagaag gtgcgcccga aggcaccgtg gtcacactac tcatcaaaag gcctactgga
3301 gaactcatgc ccctagcagc tagaatggga acccacgcaa ccatgaaaat tcaagggcgc
3361 actgttggag gtcagatggg catgcttctg acagggtcca acgccaaaag catggatcta
3421 ggtaccacac caggtgattg cggctgtccc tacatctaca agagaggaaa cgactatgtg
3481 gtcattggag tccacacggc tgccgctcgt gggggaaaca ctgtcatatg tgccacccag
3541 gggggtgagg gggaagctac acttgaaggt ggtgacagta ggggaacata ctgtggtgca
3601 ccaatcctag gcccagggag tgccccaaaa ctcagcacca aaaccaaatt ctggagatca
3661 tccacagcac cacttccacc tggcacctat gaaccagcct accttggtgg taaagacccc
3721 agagtcaagg gtggcccctc gttgcagcaa gtcatgaggg accagctgaa accatttaca
3781 gagcctaggg gtaagccacc aaagccaagt gtgttagaag ctgccaagaa aaccatcatc
3841 aatgtccttg aacagacaat tgacccacct gagaagtggt cgttcgcaca agcttgcgcg
3901 tcccttgata agaccacttc tagcggccat ccgcaccaca tgcggaaaaa cgactgctgg
3961 aacggggagt ccttcacagg caagctggca gaccaggctt ccaaggccaa cctgatgttt
4021 gaagaaggga agaacatgac cccagtctac acaggtgcac ttaaggatga attagtcaaa
4081 actgacaaaa tttatggcaa gatcaagaag aggcttctct ggggctcgga tttggcaacc
4141 atgatccggt gtgctcgagc attcggaggt cttatggatg aactcaaagc acactgtgtc
4201 acacttcctg tcagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaag
4261 cattccaggt acagatacca ctatgatgct gattactctc ggtgggattc aacacaacag
4321 agagccgtgc tggcagctgc tctagaaatc atggttaaat tctcctcaga accacatttg
4381 gctcaggtag tagcagaaga ccttctttct cctagcgtag tggatgtggg tgacttcaca
4441 atatcaatca acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc
4501 gcccactggc ttctcactct ctgcgcactc tccgaagtca caaatttgtc tccagacatc
4561 atacaggcta attctctctt ctccttctat ggtgatgatg aaattgttag tacagacata
4621 aaattagacc cagagaagtt gacagcaaag cttaaggaat atgggttgaa accaacccgc
4681 cctgacaaaa ctgaagggcc tcttgttatt tctgaagact tagacggttt gacttttctg
4741 cggagaactg tgacccgcga ccctgctggt tggtttggaa aactggagca gagctcaata
4801 ctcaggcaaa tgtactggac taggggcccc aaccatgaag acccatctga atcaatgatc
4861 ccacactctc aaagacccat acaattgatg tccttactgg gagaggccgc actccacggc
4921 ccaacattct acagtaaaat cagcaagtta gtcattgcag agctaaaaga aggtggcatg
4981 gatttttacg tgcccaggca ggagccaatg ttcagatgga tgagattctc ggatctgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat
5161 ggctttggag cccgttgtcg gtgccgctat tgcggcgcct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa gtaactttgt acaagcccct ggtggagagt tcacagtatc
5281 ccctagaaac gctccaggtg aaatactttg gagcgcgccc ttaggccctg atctgaatcc
5341 ctacctatct catttggcca gaatgtataa tggttatgca ggtggttttg aagtgcagat
5401 gatcctcgcg gggaacgcgt tcaccgcggg aaaaattata tttgcagcag tcccaccaaa
5461 ttttccaact gaaggcttga gtcccagcca ggtcactatg ttcccccaca taatagtaga
5521 tgttaggcaa ttggaacctg tgttgatccc cttacctgat gttaggaata acttctatca
5581 ctataaccag tcaaatgatc ctaccattaa attgatagca atgctgtata caccactcag
5641 ggccaataat gccggggatg atgtcttcac agtctcttgt cgagtcctca cgaggccatc
5701 ccctgatttt gacttcatat ttctggtgcc acctacagtt gagtcaagaa ctaaaccatt
5761 tactgtccca gtcttgactg ttgaagaaat gaccaattca agattcccca ttcctttgga
5821 gaaattgttc acgggtccca gcagtgcctt tgttgttcaa ccacaaaacg gcagatgcac
5881 gactgatggc gtgctcttag gcaccaccca gctgtctcct gtcaacatct gcaccttcag
5941 aggggatgtc acccacattg cgggttcccg taattacaca atgaatttgg cctctctaaa
6001 ttggaacaat tatgacccaa cagaagagat tccagcccct ctgggaactc cagatttcgt
6061 gggaaagatc caaggtgtgc tcactcaaac cacaaaggga gatggctcga cccggggcca
6121 taaagctaca gtttacactg ggagtgccga cttcactcca aagctgggca gtgttcaatt
6181 tggtactgat acagataatg actttgaaac tcaccaaaac acaagattta ccccagtcgg
6241 tgtcatccag gatggtgcga ccacccaccg aaatgaaccc caacaatggg tgctcccaag
6301 ttattcagga agaaatgtcc ataatgtaca cctagcccct gctgtagccc ccaattttcc
6361 gggcgaacaa cttcttttct tcaggtccac tatgcccgga tgcagcgggt atcccaacat
6421 ggatttggat tgcctactcc cccaggagtg ggtgcaacac ttctaccaag aggcagctcc
6481 agcacaatcc gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcttgtt
6541 tgagtgcaaa ctccataaat caggctatgt cacagtggct cataccggcc aacatgattt
6601 ggtcatcccc cccaatggtt attttaggtt tgattcctgg gttaatcagt tctacacact
6661 tgcccccatg ggaaatggaa cggggcgcag acgtgcttta taatggctgg agctttcttt
6721 gctggattgg catctgatgt ccttagctct ggacttggtt ccctaatcaa tgctggggct
6781 ggggctatca accaaaagat tgattttgaa aataatagaa aattgcagca agcttccttt
6841 cagtttagca gcaatctaca acaagcttcc tttcaacatg ataaagagat gctccaagca
6901 caaattgagg ccactaaaaa gttgcaacag gaactgatga aagtcaaaca gacaatactc
6961 ttagaaggtg gattttctga aacagatgca gcccgtgggg caatcaacgc ccccatgaca
7021 aaggctttgg actggagtgg gacaaggtac tgggcccctg atgctaggac tacaacatac
7081 aatgcaggcc gcttttccac ccctcaacct tcgggggcac tgccaggaag aatcaatccc
7141 aggactccta tccccgcccg gggctccccc agcatatctt ccaatgcttc tactgctact
7201 tctatacatt caaatcaaac tgcttcaacg agacttggtt ctacagctgg ttctggcacc
7261 aatgtctcga gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga
7321 aatttgtcac ctttcatgag gggggctcac aacatatcgt ttgtcacccc accatctagc
7381 agatcctcca gccaaggcac agtctcaacc gtgcctaaag atgttttgga ctcctggact
7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaggcg aggggagtca
7501 cgggtgtaa
//