Typing tool
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Typing tool
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Complete norovirus genomes
| KJ685411 | GII.4 Sydney | |
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| GII.P4 New Orleans |
ORF1: 1..5033
ORF2: 5014..6636
ORF3: 6636..7442
LOCUS KJ685411 7442 bp ss-RNA linear VRL 28-JAN-2015
DEFINITION Norovirus Hu/GII/BG1C0398/2012/BGD, partial genome.
ACCESSION KJ685411
VERSION KJ685411.1
DBLINK BioProject: PRJNA242747
KEYWORDS .
SOURCE Norovirus Hu/GII/BG1C0398/2012/BGD
ORGANISM Norovirus Hu/GII/BG1C0398/2012/BGD
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7442)
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 :: 178.9x
Sequencing Technology :: Ion Torrent
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7442
/organism="Norovirus Hu/GII/BG1C0398/2012/BGD"
/mol_type="genomic RNA"
/strain="Hu/GII/BG1C0398/2012/BGD"
/host="Homo sapiens; sex: F; age: 397D"
/db_xref="taxon:1486696"
/country="Bangladesh: Dhaka"
/collection_date="21-Oct-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..5033
/gene="POL"
/locus_tag="DC54_49797gpPOL"
CDS <1..5033
/gene="POL"
/locus_tag="DC54_49797gpPOL"
/note="genome polyprotein"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="AHX22037.1"
/translation="SSDGVLSSMAVTFKRALGARPKQPPPREKPQRPPRPPTPELVKN
IPPPPPNGEDEIVVSYSVKNGVSGLPDLSTVRQPEESNTAFSVPPLNQRENRDAKEPL
TGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELAPLSLYWRPVYTPQYLI
SPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRK
PLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNILNILASCDWTFAGIVES
LILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGFTKEK
IGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAIVRSIEDAVLDLEA
IENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARS
LVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVD
HWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIII
TTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHI
KLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNF
DRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTMPELKQALKNVSIKKCQIVYSGCT
YMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAG
AAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPKDDEEFVISSDDIKTEGKKG
KNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARA
TEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSEIRKRNPDDFKPKGKLWADD
DRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIK
QIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAVRMGT
HATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAA
RGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPTLSTKTKFWRSSTASLPP
GTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQ
TIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEG
KNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVT
LPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRAVLAAALEIMVKFSPEPH
LAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLS
PDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKPTRPDKTEGPLAISEDLN
GLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPSETMIPHSQRPIQLMSLL
GEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPS
FVNEDGVE"
mat_peptide <1..923
/gene="POL"
/locus_tag="DC54_49797gpPOL"
/product="putative protein p48"
mat_peptide 924..2021
/gene="POL"
/locus_tag="DC54_49797gpPOL"
/product="NTPase"
/note="p41"
mat_peptide 2022..2558
/gene="POL"
/locus_tag="DC54_49797gpPOL"
/product="protein p22"
mat_peptide 2559..2957
/gene="POL"
/locus_tag="DC54_49797gpPOL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 2958..3500
/gene="POL"
/locus_tag="DC54_49797gpPOL"
/product="3C-like protease"
/note="3CLpro; calicivirin"
mat_peptide 3501..5030
/gene="POL"
/locus_tag="DC54_49797gpPOL"
/product="RNA-directed RNA polymerase"
gene 5014..6636
/gene="VP1"
/locus_tag="DC54_49797gpVP1"
CDS 5014..6636
/gene="VP1"
/locus_tag="DC54_49797gpVP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AHX22038.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6636..7442
/gene="VP2"
/locus_tag="DC54_49797gpVP2"
CDS 6636..7442
/gene="VP2"
/locus_tag="DC54_49797gpVP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AHX22039.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 cttcaagtga cggagtgctt tctagcatgg ctgtcacttt taaacgagcc ctcggggcgc
61 ggcctaaaca gccccccccg agggaaaaac cacaaagacc cccacgacca cctactccag
121 aactggttaa gaatatcccc cctcccccac ccaacggaga ggatgaaata gtggtctctt
181 atagtgtcaa aaatggtgtt tccggcttgc ctgacctttc taccgtcagg caaccggaag
241 aatccaacac ggccttcagt gtccctccac tcaatcagag ggagaataga gatgctaagg
301 agccactcac tggaacaatt ctggaaatgt gggacgggga aatctaccat tatggcctgt
361 atgtggagcg aggtcttgta ctaggtgtgc acaaaccgcc agctgccatc agccttgcta
421 aggttgagct ggcaccactc tccttgtact ggagacctgt gtacactcct cagtacctca
481 tctctccaga cactctcaag aaattgtccg gagagacgtt cccctacaca gcctttgata
541 acaactgtta tgccttttgt tgctgggttc tggacctaaa tgactcgtgg ctgagtagaa
601 gaatgatcca gagaacaact ggtttcttca ggccctatca ggactggaat aggaaacccc
661 ttcctactat ggatgactcc aaaataaaga aggtagctaa catatttctg tgtgccctgt
721 cctcgctatt caccagaccc ataaaagata taatagggaa gataaggcct cttaatatcc
781 tcaacatctt agcctcatgt gattggacct ttgcgggtat agtggagtcc ctgatactct
841 tggcagaact ctttggagtt ttctggacac ccccagatgt gtctgcgatg attgccccct
901 tacttggtga ctacgagcta caaggacctg aggaccttgc agtggagctc gtccccgtgg
961 tgatgggggg aattggtttg gtgctaggat tcaccaaaga gaagattggg aaaatgttgt
1021 catctgctgc gtccactttg agagcttgca aagaccttgg tgcatatggg ctagagatcc
1081 taaagttagt catgaagtgg ttcttcccaa agaaggagga ggcaaatgag ctggctatag
1141 tgaggtccat cgaggatgca gtcctggatc tcgaggcaat tgaaaacaat catatgacca
1201 ccttgcttaa agataaagac agtctggcaa cctacatgag aacacttgac cttgaagagg
1261 agaaagccag gaaactctca accaagtctg cctcacccga catcgtgggt acaatcaacg
1321 ccctcctggc gagaatcgct gccgcacgtt ctctggtgca tcgagcgaag gaggagcttt
1381 ccagcagacc aagacctgtg gtgttgatga tatcaggcag gccaggaata gggaagaccc
1441 acctcgctag ggaagtggct aagagaatcg cagcctccct tacaggagat cagcgtgtgg
1501 gcctcatccc acgcaatggt gtcgaccatt gggatgcgta caagggggag agggtcgtcc
1561 tgtgggacga ttatggaatg agcaacccta ttcacgatgc cctcaggctg caagaactcg
1621 ctgacacttg tcccctcact ctgaactgtg acaggattga aaataaagga aaggtctttg
1681 acagcgatgt catcattatc accactaatc tggccaaccc agcaccactg gactatgtca
1741 actttgaagc atgctcgagg cgcattgact tcctcgtgta tgcagaagcc cctgaagtcg
1801 aaaaggcgaa gcgtgacttc ccaggccagc ctgacatgtg gaagaacgct ttcagttctg
1861 atttctcaca cataaaacta gcactggccc cacagggtgg tttcgataag aacgggaaca
1921 ccccacacgg aaagggcgtc atgaagaccc tcaccactgg ctcccttatt gcccgggcat
1981 cagggctact ccatgagagg ttggatgaat ttgaactgca gggcccagct ctcaccacct
2041 tcaacttcga tcgcaataaa gtgcttgcct ttagacagct tgctgctgaa aacaaatatg
2101 gattgatgga cacaatgagg gttgggaaac agctcaagga tgtcagaacc atgccagaac
2161 tcaaacaagc actcaagaat gtctcaatca agaagtgcca aatagtgtat agtggttgca
2221 cttacatgct tgagtctgat ggcaagggca atgtgaaagt tgacagaatc caaagcgccg
2281 ccgtgcagac caacaatgag ctggctggtg ccctgcacca cttgaggtgc gccagaatca
2341 gatactatgt caagtgtgtc caggaagccc tgtattccat catccaaatc gctggggctg
2401 catttgtcac cacgcgcatt gccaagcgca tgaacataca agacctatgg tccaagccac
2461 aagtggaaaa cacagaggag actaccagca aggacgggtg cccaaaacct aaggatgatg
2521 aggagttcgt catttcatcc gacgacatca aaactgaggg caagaaaggg aagaacaaga
2581 ctggccgtgg caagaagcac acagcatttt caagcaaagg cctcagtgat gaagagtatg
2641 atgaatacaa gaggattaga gaagaaagga atggcaagta ctctatagaa gagtaccttc
2701 aggacaggga caaatactat gaggaggtgg ccattgccag ggcgactgag gaagacttct
2761 gtgaagagga ggaggccaag atccggcaaa ggatctttag gccaacaagg aaacaacgca
2821 aggaggaaag agtctctctt ggtctggtca caggctctga aattaggaaa agaaacccag
2881 atgacttcaa acccaagggg aaattgtggg ctgacgatga caggagtgtg gactacaatg
2941 agaaactcag ctttgaggcc ccaccaagca tttggtcgag aatagtcaac tttggttcag
3001 gctggggatt ctgggtctcc cccagtctgt tcataacatc aacccatgtc ataccccagg
3061 gcgcaaagga gttctttgga gtccccatca aacaaataca ggtacacaag tcaggcgagt
3121 tctgtcgctt gagattccct aaaccaatca ggactgatgt gacgggcatg atcttggaag
3181 aaggcgcacc tgagggcacc gtggtcacac tactcatcaa aaggtccact ggggaactca
3241 tgcccctagc agttaggatg gggacccatg cgaccatgaa gatccaaggg cgcactgttg
3301 gaggccagat gggcatgctt ctgacaggat ccaacgccaa gagcatggac ctgggtacta
3361 caccaggtga ttgtggctgc ccctacatct acaagagagg taatgactat gtggtcattg
3421 gagtccacac ggctgccgca cgtgggggaa acactgtcat atgtgccacc caagggagtg
3481 aaggggaggc tacacttgag ggtggtgaca acaaggggac atactgtggt gcaccaatcc
3541 taggcccagg gagtgcccca acacttagca ccaagaccaa attctggaga tcgtccacag
3601 catcacttcc acctggcacc tatgaaccag cctatcttgg tggcaaggac cctagagtca
3661 agggtggccc ttcactgcag caagtcatga gggaacagtt gaagccattc acagagccca
3721 ggggcaagcc accaaaacca agtgtattag aagctgccaa gaagaccatc attaatgtcc
3781 ttgagcaaac aattgatcca cctgagaaat ggtcgttcgc acaagcttgc gcgtcccttg
3841 acaagaccac ttccagtggc catccgcacc acatgcggaa aaacgactgc tggaacgggg
3901 agtccttcac gggcaagctg gcagaccagg cttccaaggc caacctgatg tttgaagaag
3961 ggaagaacat gaccccagtc tacacagctg cgctcaagga tgagttagtt aaaactgaca
4021 aaatttatgg taagatcaag aagaggcttc tctggggctc ggatttggca accatgattc
4081 ggtgtgctcg agcattcgga ggcctaatgg atgaactcaa agcgcactgt gtcacactcc
4141 ccattagagt tggcatgaat atgaatgagg atggccccat catcttcgag aggcattcca
4201 ggtacacgta ccactatgat gctgactact ctcggtggga ttcaacacaa cagagagccg
4261 tgttggcagc agctctagaa atcatggtta aattctcccc agaaccacat ttggctcagg
4321 tagtcgcgga agaccttctt tcccccagcg tggtggacgt gggcgacttc acaatatcaa
4381 tcaatgaggg tcttccctct ggggtgccct gcacctccca atggaactcc atcgcccact
4441 ggcttctcac tctctgtgcg ctctctgaag tcacaaacct gtctcctgat accatacagg
4501 ctaattccct cttctctttt tatggtgatg atgaaattgt tagcacagac ataaaattgg
4561 acccagagaa attgacagca aaactcagag aatatgggtt aaaaccaacc cgccctgaca
4621 aaactgaagg accccttgcc atctctgaag acctgaatgg cctaactttc ctgcggagaa
4681 ctgtgacccg cgacccagct ggttggtttg gaaaactgga gcagagttca atactcaggc
4741 aaatgtactg gactaggggt cccaaccatg gagacccatc tgaaacaatg attccacact
4801 cccaaagacc catacaattg atgtccctac tgggggaggc cgctctccac ggcccagcat
4861 tttacagcaa aatcagcaaa ttggtcattg cagagctaaa agaaggtggt atggattttt
4921 acgtgcccag acaagagcca atgttcagat ggatgagatt ctcagatctg agcacgtggg
4981 agggcgatcg caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgccaac
5041 ccatctgatg ggtccgcagc caacctcgtc ccagaggtca acaatgaggt tatggctctg
5101 gagcccgttg ttggtgccgc cattgcggca cctgtagcgg gccaacaaaa tgtaattgac
5161 ccctggatta gaaacaattt tgtacaagcc cctggtggag agtttacagt atcccctaga
5221 aacgctccag gtgaaatact atggagcgcg cccttaggcc ctgatctaaa tccctaccta
5281 tcccatttgg ccagaatgta caatggttat gcaggtggtt ttgaagtgca ggtaattctc
5341 gcggggaacg cgttcaccgc cgggaaggtc atatttgcag cagtcccacc aaattttcca
5401 actgaaggct taagccccag ccaggtcact atgttccccc atatagtagt agatgttagg
5461 caactagaac ctgtgttgat tcccttaccc gatgttagga ataatttcta tcattacaac
5521 caatcaaatg accccaccat taagttgata gcaatgttgt atacaccact tagggctaat
5581 aatgctgggg acgatgtctt cacagtttct tgccgagttc tcacaagacc atcccccgat
5641 tttgatttca tatttttagt gccacccaca gttgagtcaa gaactaaacc attctctgtc
5701 ccagttttaa ctgttgagga gatgaccaat tcaagattcc ccattccctt ggagaagttg
5761 ttcacgggtc ccagcagtgc ctttgttgtt caaccacaaa acggcaggtg cacgactgat
5821 ggcgtgctcc taggcaccac ccaactgtct cctgtcaaca tctgcacctt cagaggggat
5881 gtcacccata tcacaggcag tcgcaactac acaatgaatt tggcttctct aaattggaac
5941 aattatgacc caacagaaga aatcccagcc cctctaggaa ctccagactt tgtggggaag
6001 attcaaggca tgctcaccca aaccacaagg acagatggct caacacgcgg ccacaaagct
6061 acagtgtaca ctgggagcgc cgactttgct ccaaaactgg gtagagttca atttgaaact
6121 gacacagacc atgattttga agctaaccaa aacacaaagt tcaccccagt cggtgtcatc
6181 caagatggta gcaccaccca ccgaaatgaa ccccaacagt gggtgctccc aagttactca
6241 ggcagaaata ctcataatgt gcatctggcc cccgctgtag cccccacttt tccgggtgag
6301 caacttctct tcttcagatc caccatgccc ggatgcagcg ggtaccccaa catggatttg
6361 gactgtctgc tcccccagga atgggtgcag tacttctacc aagaggcagc cccagcacaa
6421 tctgatgtgg ctctgctaag atttgtgaac ccagacacag gtagggtttt gtttgagtgt
6481 aagcttcata aatcaggcta tgttacagtg gctcacactg gccaacatga tttggttatc
6541 ccccccaatg gttattttag gtttgattct tgggtcaacc agttctacac gcttgccccc
6601 atgggaaatg gaacggggcg tagacgtgta gtataatggc tggagctttc tttgctggat
6661 tggcatctga tgtccttggc tctggacttg gttcccttat caatgctggg gctggggcca
6721 tcaaccaaaa agttgagttt gaaaataaca gaaaattgca acaagcatca ttccaattta
6781 gcagcaatct gcaacaggct tcctttcaac atgacaaaga gatgctccaa gcacaaattg
6841 aggccaccaa aaagctacaa caggaaatga tgaaagttaa gcaggcaatg ctcctagagg
6901 gtgggttctc tgagacagat gcagcccgcg gggcaattaa cgcccccatg acaaaagctt
6961 tggactggag cgggacaagg tactgggctc ccgatgctag gactacaaca tacaatgcag
7021 gccgcttttc cacccctcaa ccatcggggg cactgccagg aagagctaat cttagggatg
7081 ctgtccctgc tcggggttcc tccagcaaat cctctaactc ttctactgct acttctgtgt
7141 attcaaatca aactacttca acgagacttg gttctacagc tggttctggt accagtgtct
7201 cgagcctccc gtcaactgca aggactagga gctgggttga ggatcaaagt aggaatttgt
7261 cacctttcat gaggggggcc cacaacatat cgtttgtcac cccaccatct agcagatcct
7321 ctagccaagg cacagtctca accgtgccta aagaggtttt ggactcctgg actggcgctt
7381 tcaacacgcg caggcagcct ctcttcgctc acattcgtaa acgaggggag tcacgggtgt
7441 aa
//