Typing tool
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Typing tool
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Complete norovirus genomes
| KJ685406 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..5036
ORF2: 5017..6639
ORF3: 6639..7445
LOCUS KJ685406 7445 bp ss-RNA linear VRL 28-JAN-2015
DEFINITION Norovirus Hu/GII/BG1C0391/2012/BGD, partial genome.
ACCESSION KJ685406
VERSION KJ685406.1
DBLINK BioProject: PRJNA242747
KEYWORDS .
SOURCE Norovirus Hu/GII/BG1C0391/2012/BGD
ORGANISM Norovirus Hu/GII/BG1C0391/2012/BGD
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7445)
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 :: 122.4x
Sequencing Technology :: Ion Torrent
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7445
/organism="Norovirus Hu/GII/BG1C0391/2012/BGD"
/mol_type="genomic RNA"
/strain="Hu/GII/BG1C0391/2012/BGD"
/host="Homo sapiens; sex: F; age: 226D"
/db_xref="taxon:1486695"
/country="Bangladesh: Dhaka"
/collection_date="19-Apr-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..5036
/gene="POL"
/locus_tag="DC54_49796gpPOL"
CDS <1..5036
/gene="POL"
/locus_tag="DC54_49796gpPOL"
/note="genome polyprotein"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="AHX22027.1"
/translation="SSSDGVFSNMAVTFKRALGARPKQPPPKEIPPRPPRPPTPELVK
KIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPEETNTAFSVPPLNQRESRDAKEP
LTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVELTPLSLFWRPVYTPQYL
ISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNR
KPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLNILNILATCDWTFAGIVE
SLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPIVMGGIGLVLGFTKE
KIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLE
AIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINSLLARIAAAR
SLVHRAKEELSSRPRPVVVMISGKPGIGKTHLARELAKKIAASLTGDQRVGLIPRNGV
DHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDAII
ITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKDAFSPDFSH
IKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEYELQGPALTTFN
FDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLKQALKNIAIKKCQIVYNGG
TYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIA
GAAFVTTRIAKRMNIQNLWSKPQVEDTEEVANKDGCLKPKDDEEFVVSSDDIKTEGKK
GKNKSGRGKKHTAFSSKGLSDEEYDEYKRVREERNGKYSIEEYLQDRDRYYEEVAIAR
ATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPEDFKPKGKLWAD
DDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPI
KQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIKRPTGELMPLAARMG
THATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAA
ARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTTPLP
PGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPNVLEAAKKTIINVLE
QTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEE
GKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCV
TLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRDVLAAALEIMVKFSPEP
HLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNSIAHWLLTLCALSEVTDL
SPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDL
DGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPFETMIPHSQRPIQLMSL
LGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAP
SFVNEDGVE"
mat_peptide <1..926
/gene="POL"
/locus_tag="DC54_49796gpPOL"
/product="putative protein p48"
mat_peptide 927..2024
/gene="POL"
/locus_tag="DC54_49796gpPOL"
/product="NTPase"
/note="p41"
mat_peptide 2025..2561
/gene="POL"
/locus_tag="DC54_49796gpPOL"
/product="protein p22"
mat_peptide 2562..2960
/gene="POL"
/locus_tag="DC54_49796gpPOL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 2961..3503
/gene="POL"
/locus_tag="DC54_49796gpPOL"
/product="3C-like protease"
/note="3CLpro; calicivirin"
mat_peptide 3504..5033
/gene="POL"
/locus_tag="DC54_49796gpPOL"
/product="RNA-directed RNA polymerase"
gene 5017..6639
/gene="VP1"
/locus_tag="DC54_49796gpVP1"
CDS 5017..6639
/gene="VP1"
/locus_tag="DC54_49796gpVP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AHX22028.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6639..7445
/gene="VP2"
/locus_tag="DC54_49796gpVP2"
CDS 6639..7445
/gene="VP2"
/locus_tag="DC54_49796gpVP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AHX22029.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQVMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGVLPGRANLRDAVPARGSSSKSS
NSFTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNVSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 aatcttcaag tgacggtgtg ttttctaaca tggctgtcac ttttaagcgg gccctcgggg
61 cgcggcctaa acagccgccc ccgaaggaaa taccacccag acccccgcga ccacccacac
121 cagaattggt caaaaagatc cctcctcccc cacccaacgg ggaggatgaa ctagtggtct
181 cctacagcgc caaagatggc gtttccggac tgcctgagct cactactgtc agacaaccgg
241 aagaaaccaa cacggcgttt agtgtccccc cactcaacca aagggagagc agggacgcca
301 aggagccact aactggaaca attattgaaa tgtgggatgg agagatctac cattacggcc
361 tgtacgtgga acgaggtctt atacttggtg tgcacaagcc accggcagct atcagccttg
421 ccaaggtcga gctaacaccg ctctctttgt tctggagacc tgtatacacc ccccagtatc
481 tcatctctcc agacactctt aggagactac atggagagtc attcccctac actgcatttg
541 acaacaattg ctacgccttt tgttgttggg tattagacct aaacgactca tggctaagca
601 ggagaatgat tcagagaaca acaggtttct tcaggccgta ccaggattgg aacaggaagc
661 ccctccccac tatggatgat tccaaattaa agaaggtagc caacatattc ttgtgcactt
721 tgtcttcact attcaccaga cccattaagg acataatagg gaagttgaaa cctcttaaca
781 tccttaacat tctggctaca tgtgattgga ccttcgcagg catagtggaa tccttaatac
841 tcttggcaga actctttgga gttttctgga cacccccaga tgtgtctgcg atgatcgccc
901 ccttgctagg tgattatgaa ctgcaaggac ctgaggacct tgcagtggaa ctggtcccaa
961 tagtgatggg ggggataggt ttggtgctag gatttaccaa agagaaaatt ggaaagatgc
1021 tatcatccgc tgcatccact ttaagagctt gtaaagacct tggtgcatac ggactggaaa
1081 tcttaaaatt ggtcatgaag tggttcttcc caaagaaaga ggaagcaaac gaactggcta
1141 tggtgagatc catcgaggat gcagtgttag acctcgaggc aattgaaaac aaccacatga
1201 ccaccctact caaagacaaa gacagcttgg caacctacat gagaaccctt gaccttgagg
1261 aggagaaagc cagaaaactc tcaaccaaat ctgcttcacc cgatattgtg ggcacaatca
1321 actctcttct ggcaagaatc gctgctgcac gctccctagt gcatcgggcg aaagaagagc
1381 tctccagcag gccgagacct gtcgttgtga tgatatcggg aaaaccaggg atagggaaaa
1441 ctcaccttgc cagggagctg gccaagaaga tcgcggcctc cctcacaggg gaccagcgtg
1501 tgggtcttat cccgcgcaat ggtgtcgacc actgggacgc atataagggc gaaagagttg
1561 tcctatggga cgactatgga atgagcaacc ccatccatga tgccctcagg ttgcaggagc
1621 ttgctgacac ttgccccctc acgctaaatt gtgacagaat tgagaacaaa gggaaagtct
1681 ttgacagtga tgccataatt atcaccacca atctggccaa cccagcacca ctggattatg
1741 tcaactttga agcgtgctcg agacgcatcg acttccttgt gtacgcagaa gcccctgagg
1801 tggagaaggc aaagcgcgac ttcccaggtc aacctgacat gtggaaggac gctttcagtc
1861 ctgacttctc acacataaaa ttgtcattgg ctccacaggg tggttttgac aagaacggca
1921 acaccccgca tggaaaaggg gtcatgaaga ccctcactac tggctccctc atcgcccgag
1981 catcagggtt actccatgag aggctagatg aatatgaact gcaaggccca gccctcacca
2041 ctttcaactt tgaccgcaac aagatacttg cttttagaca gcttgctgct gaaaacaagt
2101 atgggctgat ggacacaatg agagttggaa aacagctcaa ggatgtcaag accatgtcag
2161 acctcaaaca agcactcaag aatatcgcga tcaagaagtg ccagatagtg tacaatggtg
2221 gcacctacac acttgaggcc gatggcaagg gtagtgtgaa agttgacaaa gtgcaaagtg
2281 ccactgtgca gaccaacaat gaactagccg gtgccctaca ccacctaagg tgcgctagaa
2341 tcagatacta tgttaagtgc gtccaggagg cactgtattc catcatccaa atcgctgggg
2401 ctgcattcgt caccacgcgc atcgctaagc gcatgaatat acagaatctc tggtccaagc
2461 cacaggtgga agacacagaa gaggtggcca acaaagatgg ttgcctaaaa cccaaagatg
2521 atgaagagtt tgtcgtctca tctgacgaca tcaaaactga gggcaagaaa gggaagaaca
2581 agtccggccg tggcaagaag cacacagcct tttcaagcaa agggctcagt gatgaggagt
2641 acgatgagta caagagagtc agagaagaaa ggaatggtaa gtactccata gaagagtacc
2701 ttcaggacag agacaggtac tacgaagagg tggccattgc cagggcaacc gaagaggact
2761 tctgtgaaga agaagaggcc aaaatccggc agagaatttt cagaccaaca aggaaacaac
2821 gcaaagaaga gagggcctct ctcggcttgg tcacaggctc tgaaatcagg aagagaaacc
2881 cagaagactt caaacccaag ggaaagctgt gggctgatga tgacagaagt gttgactaca
2941 atgagaaact caactttgag gccccaccaa gcatctggtc gcggatagtc aactttggtt
3001 caggttgggg cttctgggtc tcccccagtc tgtttataac atcaacccat gtcatacccc
3061 aaggtgcaaa agagttcttc ggagtcccta tcaagcaaat ccagatacac aaatcaggtg
3121 aattctgccg gttgagattc ccaaagccaa tcagaactga tgtgacgggc atgattctag
3181 aagaaggtgc gcccgagggg actgtggcca cactgctcat caagagacca actggagagc
3241 tcatgcctct ggcagccaga atggggaccc atgcaaccat gagaattcag gggcgcacag
3301 ttggagggca aatgggtatg ctcctgacag gatccaacgc caagagtatg gacctaggca
3361 caacaccagg cgactgcggc tgcccctaca tctacaagag ggggaatgac tacgtggtca
3421 taggagtcca tacggccgct gcccgtggag gaaacactgt catatgtgcc acccagggga
3481 gtgagggaga agccacactt gaaggaggtg acagtaaagg gacatactgt ggcgcaccaa
3541 tcttgggccc agggagcgct ccgaagctca gtaccaagac taagttttgg agatcatcca
3601 caacaccact cccacctggc acctacgaac cagcctacct cggtggcaaa gaccccagag
3661 tcaaaggtgg cccttcattg caacaagtta tgagggacca gctaaagcca ttcacagaac
3721 ccagaggcaa accaccaaga ccaaatgtgt tggaagctgc caagaaaacc atcatcaatg
3781 tccttgagca aacaattgat ccaccccaaa aatggtcatt tgcgcaagct tgcgcatccc
3841 ttgacaaaac cacctccagc ggccacccgc accatatgcg gaaaaacgat tgttggaatg
3901 gggagtcctt cacaggaaaa ttggctgatc aggcctccaa ggccaaccta atgtttgaag
3961 agggaaagaa catgactcca gtctacacag gtgcacttaa agatgagttg gtaaagaccg
4021 ataaagttta tggtaagatc aagaagaggc ttctgtgggg ttcagatctg gcgaccatga
4081 tacggtgcgc ccgcgctttt ggaggcctta tggatgaact caaggcacac tgtgtcacac
4141 ttcctgtcag agttggtatg aacatgaatg aggatggccc catcatcttt gagaagcact
4201 ccagatatag gtatcactat gatgctgatt attcccggtg ggactcaaca caacaaaggg
4261 atgtgctagc agcagcacta gaaatcatgg ttaagttctc tccagaacca cacctggccc
4321 agatagttgc agaagacctc ctttccccta gcgtaatgga tgtaggtgac tttcaaatat
4381 caataagtga gggtcttccc tctggggtac cttgcacctc ccagtggaat tccatcgccc
4441 actggctcct cactctttgt gcactctctg aagtcacgga cctgtcccct gacatcattc
4501 aggccaactc ccttttctcc ttctatggtg atgatgagat tgtaagcaca gacataaagt
4561 tggacccaga gaagctgaca gcaaaactca aggagtacgg gctgaaacca acccgccccg
4621 acaaaactga aggacccctt gttatctctg aagacctgga tggcctgaca ttcctccgga
4681 gaactgtgac ccgtgatcca gctggctggt ttggaaaatt ggaacaaagt tcaattctca
4741 ggcaaatgta ctggaccagg ggtcccaacc atgaagaccc atttgaaaca atgataccac
4801 actcccaaag acccatacaa ttgatgtcct tgctgggcga ggctgcactc cacggcccgg
4861 cattttatag caaaattagc aaattagtca ttgcagagtt gaaggaaggt ggcatggatt
4921 tttacgtgcc cagacaagag ccaatgttca gatggatgag attctcagat ctgagcacgt
4981 gggagggcga tcgcaatctg gctcccagtt ttgtgaatga agatggcgtc gagtgacgcc
5041 aacccatctg atgggtccgc agccaacctc gtcccagagg tcaacaatga ggttatggct
5101 ctggagcccg ttgttggtgc cgccattgcg gcacctgtag cgggccaaca aaatgtaatt
5161 gacccctgga ttagaaacaa ttttgtacaa gcccctggtg gagagtttac agtatcccct
5221 agaaacgctc caggtgaaat actatggagc gcgcccttgg gccctgatct aaatccctac
5281 ctatcccatt tggccagaat gtacaatggt tatgcaggtg gttttgaagt gcaggtaatt
5341 ctcgcgggga acgcgttcac cgccgggaag gtcatatttg cagcagtccc accaaatttt
5401 ccaactgaag gcttgagccc cagccaggtc actatgttcc cccatatagt agtagatgtt
5461 aggcaactag aacctgtgtt gattccctta cccgatgtta ggaacaattt ctatcattat
5521 aatcaatcaa atgaccccac cattaagttg atagcaatgt tgtatacacc acttagggct
5581 aataatgctg gggatgatgt ctttacagtt tcttgccgag ttctcacgag accatccccc
5641 gattttgatt tcatatttct agtgccaccc acagttgagt caagaactaa accattctct
5701 gtcccagttt taactgttga ggagatgacc aattcaagat tccccattcc tttggaaaag
5761 ttgttcacgg gtcccagcag tgcctttgtt gttcaaccac aaaacggcag gtgcacgact
5821 gatggcgtgc tcctaggcac cacccaactg tctcctgtca acatctgcac cttcagagga
5881 gatgtcaccc atatcactgg tagtcgtaac tacacaatga atttggcttc tcaaaattgg
5941 aacaattatg acccaacaga agaaatccca gcccctctag gaactccaga tttcgtgggg
6001 aagattcaag gcgtgctcac ccaaaccaca aggacagatg gctcaacacg cggccacaaa
6061 gctacagtgt acactgggag cgccgacttt gctccaaaac tgggtagagt tcaatttgaa
6121 actgacacag accatgattt tgaagctaac caaaacacaa agttcacccc agtcggtgtc
6181 atccaagatg gtggcaccac ccaccgaaat gaaccccaac agtgggtgct cccaagttac
6241 tcaggcagaa atactcataa tgtgcatctg gcccccgctg tagcccccac ttttccgggt
6301 gagcaacttc tcttcttcag atccaccatg cccggatgca gcgggtaccc caacatggat
6361 ttggactgtc tgctccccca ggaatgggtg cagtacttct accaagaggc agccccagca
6421 caatctgatg tggctctgct aagatttgtg aatccagaca caggtagggt tttgtttgag
6481 tgtaagcttc acaaatcagg ctatgttaca gtggctcata ctggccaaca tgatttggtt
6541 atccccccca atggttattt taggtttgat tcctgggtca accagttcta cacgcttgcc
6601 cccatgggaa atggaacggg gcgtagacgt gtggtataat ggctggagct ttctttgctg
6661 gattggcatc tgatgtcctt ggctctggac ttggttccct tatcaatgct ggggctgggg
6721 ccatcaacca aaaagttgag tttgaaaata acagaaaatt gcaacaagca tccttccaat
6781 ttagcagtaa tctacaacag gcttcctttc aacatgacaa agagatgctc caagcacaaa
6841 ttgaggccac caaaaagcta caacaggaaa tgatgaaagt taagcaggta atgctcctag
6901 agggtgggtt ctctgagaca gatgcagccc gcggggcaat caacgccccc atgacaaaag
6961 ctttggactg gagcgggaca agatactggg ctcccgatgc taggactaca acatacaatg
7021 caggccgctt ttccacccct caaccatcgg gggtactgcc aggaagagcc aaccttaggg
7081 atgctgtccc tgctcggggt tcctccagca aatcttctaa ctcttttact gctacttctg
7141 tgtactcaaa tcaaactact tcaacgagac ttggttctac agctggctct ggtaccagtg
7201 tctcgagcct cccgtcaact gcaaggacta ggagctgggt tgaggatcaa agtaggaatg
7261 tgtcaccttt catgaggggg gcccacaaca tatcgtttgt caccccacca tctagcagat
7321 cctccagcca aggcacagtc tcaaccgtgc ctaaagaggt tttggactcc tggactggtg
7381 ctttcaacac gcgcaggcag ccactcttcg ctcacattcg taagcgaggg gagtcacggg
7441 tgtaa
//