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Partial 2015 Bahia Brazil Zika Sequences


niman

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LOCUS       KX101060               10331 bp    RNA     linear   VRL 26-APR-2016
DEFINITION  Zika virus isolate Bahia02, partial genome.
ACCESSION   KX101060
VERSION     KX101060.1  GI:1022831289
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10331)
  AUTHORS   Naccache,S.N., Theze,J., Sardi,S.I., Somasekar,S., Greninger,A.L.,
            Bandeira,A.C., Campos,G.S., Tauro,L.B., Faria,N.R., Pybus,O.G. and
            Chiu,C.Y.
  TITLE     Discovery of a persistent Zika virus lineage in Bahia, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10331)
  AUTHORS   Naccache,S.N., Somasekar,S., Sardi,S.I., Bandeira,A.C., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-APR-2016) Laboratory Medicine, University of
            California, San Francisco, 185 Berry Street, #0134, San Francisco,
            CA 94107, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SURP+ v. 1.0 2016; Geneious v. 6.1.8
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10331
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="Bahia02"
                     /isolation_source="serum"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="May-2015"
     CDS             <1..10032
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ANA85187.1"
                     /db_xref="GI:1022831290"
                     /translation="IKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTAMAAE
                     VTRRGSAYYMYLDRNDAGEAISFPTTLGMNKCYIQIMDLGHXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXVVYGTCHHKKGEARRSRRAVTLPSHSTRKLQTRSQTXLESREY
                     TKHLIRVENWIFRNPGFALAAAAIAWLLGSSTSQKVIYLVMILLIAPAYSIRCIGVSN
                     RDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASIS
                     DMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKK
                     MTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGG
                     FGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
                     ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKL
                     RLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVG
                     RLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEAT
                     VRGAKRMAVLGDTAWXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXGICGISSVSRMENIMWRSVEGELNAILEENGV
                     QLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGKSYFVRAAKTNNSFVXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     GYRTQMKGPWHSEELEIRFEECPGTKVHVEETCGTRGPSLRSTTASGRVIEEWCCXXX
                     XXXPLSFRAKDGCWYGMEIRPRKEPESNLVRSMVTAGSTDHMDHFSLGVLVILLMVQE
                     GLKKRMTTKIIISTSMAVLVAMILGGFSMSDLAKLAILMGATFAEMNTGGDVAHLALI
                     AAFKVRPALLVSFIFRANWXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXLGLTAVRLVDPINVVGLLLLTRSGKRXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     VEDDGPPMREIILKVVLMTICGMNPIAIPFAAGAWYVYVKTGKRSGALWDVPAPKEVK
                     KGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGSALRSGEGRLDPYWGDV
                     KQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGERARNIQTLPGIFKTKDGDIGAVALDY
                     PAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGRREEETPVECFEPSMLKKKQ
                     LTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAPTRVVAAEMEEALRGLPVRYMTT
                     AVNVTHSGTEIVDLMCHAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXNGNEIAACLTKAGKRVIQLSRKTFETEFQKTKHQEWDFVVTTDISXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXVILAGPMPVTHASAAQRRGRIGRNPNKPGDEYLYGGGCA
                     ETDEDHAHWXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     KRGDLPVWLAYQVASAGITYTDRRWCFDSTTNNTIMEDSVPAEVWTRHGEKRVLKPRW
                     MDARVCSDHAALKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAVLMRAE
                     TGSRPYKAAAAQMPETLETIMLLGLLGTVSLGIFFVLMRNKGIGKMGFGMVTLXASAW
                     LMWLSEIEPARIACVLIVVFLLLVVLIPEPEKQRSPQDNQMAIIIMVAVGLLGLITAN
                     ELGWLERTKSDLSHLMGRREEGATIGFSMDIDLRPASAWAIYAALTTFITPAVQHAVT
                     TSYNNYSLMAMATQAGVLFGMGKGMPFYAWDFGVPLLMIGCYSQLTPLTLIVAIILLV
                     AHYMYLIPGLQAAAARAAQKRTAAGXXXXXXXXXXXXTDIDTMTIDPQVEKKMGQVLL
                     IAVAVSSAXLSRTAWGWGEAGALITAATSTLWEGSPNKYWNSSTATSLXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCREEA
                     RRALKDGVATGGHAVSRGSAKLRWLVERGYLQPHGKVIDLGCGRGGWSYYAATIRKVQ
                     EVXXXXXXXXGHEEPVLVQSYGWNIVRLKSGVDVFHMAAEPCDTLLCDIGESSSSPEV
                     EEARTLRVLSMVGDWLEKRPGAFCIKVLCPYTSTMMETLERLQRRYGGGLVRVPLSRN
                     STHEMYWVSGAKSNTIKSVSTTSQLLLGRMDGPRRPVKYEEDVNLGSGTRAVVSCAEA
                     PNMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHGSYEAPTQGSASSLINGVVRLLS
                     KPWDVVTGVTGIAMTDTTPYGQQRVFKEKVDTRVPDPQEGTRQVMSMVSSWLWKELGK
                     HKRPRVCTKEEFINKVRSNAALGAIFEEEKEWKTAVEAVNDPRFWALVDKEREHHLRG
                     ECQSXXXNMMGKREKKQGEFGKAKGSRAIWYMWLGARFLEFEALGFLNEDHWMGRENS
                     GGGVEGLGLQRLGYVLEEMSRIPGGRMYADDTAGWDTRISRFDLENEALITNQMEKGH
                     RALALAIIKYTYQNKVVKVLRPAEKGKTVMDIISRQDQRGSGQVVTYALNTFTNLXXX
                     XXXXXXXXXXXEMQDLWLLRRPEKVTNWLQSNGWDRLXXXXXXXXXXXXXXXXXXFAH
                     ALRFLNDMGKVRKDTQEWKPSTGWDNWEEVPFCSHHFNKLHLKDGRSIVVPCRHQDEL
                     IGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRRDLRLMANAICSSVPVDWVPTGR
                     TTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKTPVTKWTDIPYLGKREDLWCGSL
                     IGHRPRTTWAENIKNTVNMVRRIIGDEEKYMDYLSTQVRYLGEEGSTPGVL"
     mat_peptide     1..135
                     /product="capsid peptide"
     mat_peptide     136..405
                     /product="propeptide"
     mat_peptide     406..630
                     /product="membane protein peptide"
     mat_peptide     631..2145
                     /product="envelope protein peptide"
     mat_peptide     2146..3231
                     /product="NS1 peptide"
     mat_peptide     3232..3885
                     /product="NS2A peptide"
     mat_peptide     3886..4317
                     /product="NS2B peptide"
     mat_peptide     4318..6126
                     /product="NS3 peptide"
     mat_peptide     6127..6567
                     /product="NS4A peptide"
     mat_peptide     6568..8073
                     /product="NS4B peptide"
     mat_peptide     8074..10029
                     /product="NS5 peptide"
     gap             1919..2298
                     /estimated_length=380
     gap             2546..2915
                     /estimated_length=370
     gap             3496..3796
                     /estimated_length=301
     gap             3877..4134
                     /estimated_length=258
     gap             5059..5366
                     /estimated_length=308
     gap             5728..5873
                     /estimated_length=146
     gap             6088..6200
                     /estimated_length=113
     gap             7238..7424
                     /estimated_length=187
     3'UTR           10033..10331
ORIGIN      
        1 ataaagaagt tcaagaaaga tctggctgcc atgctgagaa taatcaatgc taggaaggag
       61 aagaagagac gaggcgcaga tactagtgtc ggaattgttg gcctcctgct gaccacagct
      121 atggcagcgg aggtcactag acgtgggagt gcatactata tgtacttgga cagaaacgat
      181 gctggggagg ccatatcttt tccaaccaca ttggggatga ataagtgtta tatacagatc
      241 atggatcttg gacacannnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
      301 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn ngttgtgtac
      361 ggaacctgcc atcacaaaaa aggtgaagca cggagatcta gaagagctgt gacgctcccc
      421 tcccattcca ctaggaagct gcaaacgcgg tcgcaaacct gkttggaatc aagagaatac
      481 acaaagcact tgattagagt cgaaaattgg atattcagga accctggctt cgcgttagca
      541 gcagctgcca tcgcttggct tttgggaagc tcaacgagcc aaaaagtcat atacttggtc
      601 atgatactgc tgattgcccc ggcatacagc atcaggtgca taggagtcag caatagggac
      661 tttgtggaag gtatgtcagg tgggacttgg gttgatgttg tcttggaaca tggaggttgt
      721 gtcaccgtaa tggcacagga caaaccgact gtcgacatag agctggttac aacaacagtc
      781 agcaacatgg cggaggtaag atcctactgc tatgaggcat caatatcaga catggcttcg
      841 gacagccgct gcccaacaca aggtgaagcc taccttgaca agcaatcaga cactcaatat
      901 gtctgcaaaa gaacgttagt ggacagaggc tggggaaatg gatgtggact ttttggcaaa
      961 gggagtctgg tgacatgcgc taagtttgca tgctccaaga aaatgaccgg gaagagcatc
     1021 cagccagaga atctggagta ccggataatg ctgtcagttc atggctccca gcacagtggg
     1081 atgatcgtta atgacacagg acatgaaact gatgagaata gagcgaaggt tgagataacg
     1141 cccaattcac caagagccga agccaccctg gggggttttg gaagcctagg acttgattgt
     1201 gaaccgagga caggccttga cttttcagat ttgtattact tgactatgaa taacaagcac
     1261 tggttggttc acaaggagtg gttccacgac attccattac cttggcacgc tggggcagac
     1321 accggaactc cacactggaa caacaaagaa gcactggtag agttcaagga cgcacatgcc
     1381 aaaaggcaaa ctgtcgtggt tctagggagt caagaaggag cagttcacac ggcccttgct
     1441 ggagctctag aggctgagat ggatggtgca aagggaaggc tgtcctctgg ccacttgaaa
     1501 tgtcgcctga aaatggataa acttagattg aagggcgtgt catactcctt gtgtaccgca
     1561 gcgttcacat tcaccaagat cccggctgaa acactgcacg ggacagtcac agtggaggta
     1621 cagtacgcag ggactgatgg accttgcaag gttccagctc agatggcggt ggacatgcaa
     1681 actctgaccc cagttgggag gttgataacc gctaaccccg taatcactga aagcactgag
     1741 aactctaaga tgatgctgga acttgatcca ccatttgggg actcctacat tgtcatagga
     1801 gtcggggaga agaagatcac ccaccactgg cacaggagtg gcagcaccat tggaaaagca
     1861 tttgaagcca ctgtgagagg tgccaagaga atggcagtct tgggagacac agcctggg 
          [gap 380 bp]    Expand Ns
     2299                    gg tatctgcggg atctcctctg tttcaagaat ggaaaacatc
     2341 atgtggagat cagtagaagg ggagctcaac gcaatcctgg aagagaatgg agttcaactg
     2401 acggtcgttg tgggatctgt aaaaaacccc atgtggagag gtccacagag attgcccgtg
     2461 cctgtgaacg agctgcccca cggctggaag gcttggggga aatcgtactt cgtcagagca
     2521 gcaaagacaa ataacagctt tgtcg                                     
          [gap 370 bp]    Expand Ns
     2916                                       gggct acaggaccca aatgaaaggg
     2941 ccatggcaca gtgaagagct tgaaattcgg tttgaggaat gcccaggcac taaggtccac
     3001 gtggaggaaa catgtggaac aagaggacca tctctgagat caaccactgc aagcggaagg
     3061 gtgatcgagg aatggtgctg cagnnnnnnn nnnnnnnccc cactgtcgtt ccgggctaaa
     3121 gatggctgtt ggtatggaat ggagataagg cccaggaaag aaccagaaag caacttagta
     3181 aggtcaatgg tgactgcagg atcaactgat cacatggatc acttctccct tggagtgctt
     3241 gtgattctgc tcatggtgca ggaagggctg aagaagagaa tgaccacaaa gatcatcata
     3301 agcacatcaa tggcagtgct ggtagctatg atcctgggag gattttcaat gagtgacctg
     3361 gctaagcttg caattttgat gggtgccacc ttcgcggaaa tgaacactgg aggagatgta
     3421 gctcatctgg cgctgatagc ggcattcaaa gtcagaccag cgttgctggt atctttcatc
     3481 ttcagagcta attgg                                                
          [gap 301 bp]    Expand Ns
     3797                  ccct gggactaacc gctgtgaggc tggtcgaccc catcaacgtg
     3841 gtgggactgc tgttgctcac aaggagtggg aagcgg                         
          [gap 258 bp]    Expand Ns
     4135                                                            gtggag
     4141 gatgacggtc cccccatgag agagatcata ctcaaggtgg tcctgatgac catctgtggc
     4201 atgaacccaa tagccatacc ctttgcagct ggagcgtggt acgtatacgt gaagactgga
     4261 aaaaggagtg gtgctctatg ggatgtgcct gctcccaagg aagtaaaaaa gggggagacc
     4321 acagatggag tgtacagagt aatgactcgt agactgctag gttcaacaca agttggagtg
     4381 ggagttatgc aagagggggt ctttcacact atgtggcacg tcacaaaagg atccgcgctg
     4441 agaagcggtg aagggagact tgatccatac tggggagatg tcaagcagga tctggtgtca
     4501 tactgtggtc catggaagct agatgccgcc tgggacgggc acagcgaggt gcagctcttg
     4561 gccgtgcccc ccggagagag agcgaggaac atccagactc tgcccggaat atttaagaca
     4621 aaggatgggg acattggagc ggttgcgctg gattacccag caggaacttc aggatctcca
     4681 atcctagaca agtgtgggag agtgatagga ctttatggca atggggtcgt gatcaaaaat
     4741 gggagttatg ttagtgccat cacccaaggg aggagggagg aagagactcc tgttgagtgc
     4801 ttcgagcctt cgatgctgaa gaagaagcag ctaactgtct tagacttgca tcctggagct
     4861 gggaaaacca ggagagttct tcctgaaata gtccgtgaag ccataaaaac aagactccgt
     4921 actgtgatct tagctccaac cagggttgtc gctgctgaaa tggaggaagc ccttagaggg
     4981 cttccagtgc gttatatgac aacagcagtc aatgtcaccc actctggaac agaaatcgtc
     5041 gacttaatgt gccatgcc                                             
          [gap 308 bp]    Expand Ns
     5367                             gaac ggcaatgaga tcgcagcttg tctgacaaag
     5401 gctggaaaac gggtcataca gctcagcaga aagacttttg agacagagtt ccagaaaaca
     5461 aaacatcaag agtgggactt tgtcgtgaca actgacattt cagnnnnnnn nnnnnnnnnn
     5521 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     5581 nnagtcattc tggctggacc catgcctgtc acacatgcca gcgctgccca gaggaggggg
     5641 cgcataggca ggaatcccaa caaacctgga gatgagtatc tgtatggagg tgggtgcgca
     5701 gagactgacg aagaccatgc acactgg                                   
          [gap 146 bp]    Expand Ns
     5874                                                           gaaaaga
     5881 ggagatcttc ctgtttggct ggcctatcag gttgcatctg ccggaataac ctacacagat
     5941 agaagatggt gctttgatag cacgaccaac aacaccataa tggaagacag tgtgccggca
     6001 gaggtgtgga ccagacacgg agagaaaaga gtgctcaaac cgaggtggat ggatgccaga
     6061 gtttgttcag atcatgcggc cctgaag                                   
          [gap 113 bp]    Expand Ns
     6201                       cgctgtgctc atgcgggcag agactggaag caggccttac
     6241 aaagccgcgg cggcccaaat gccggagacc ctagagacca ttatgctttt ggggttgcta
     6301 ggaacagtct cgctgggaat ctttttcgtc ttgatgagga acaagggcat agggaagatg
     6361 ggctttggaa tggtgactct trgggccagc gcatggctca tgtggctctc ggaaattgag
     6421 ccagccagaa ttgcatgtgt cctcattgtt gtgttcctat tgctggtggt gctcatacct
     6481 gagccagaaa agcaaagatc tccccaggac aaccaaatgg caatcatcat catggtagca
     6541 gtaggtcttc tgggcttgat taccgccaat gaactcggat ggttggagag aacaaagagt
     6601 gacctaagcc atctaatggg aaggagagag gagggggcaa ccataggatt ctcaatggac
     6661 attgacctac ggccagcctc agcttgggcc atctatgctg ccttgacaac tttcattacc
     6721 ccagccgtcc aacatgcagt gaccacttca tacaacaact actccttaat ggcgatggcc
     6781 acgcaagctg gagtgttgtt tggtatgggc aaagggatgc cattctacgc atgggacttt
     6841 ggagtcccgc tgctaatgat aggttgctac tcacaattaa cacccctgac cctaatagtg
     6901 gccatcattt tgctcgtggc gcactacatg tacttgatcc cagggctgca ggcagcagct
     6961 gcgcgtgctg cccagaagag aacggcagct ggcannnnnn nnnnnnnnnn nnnnnnnnnn
     7021 nnnnnnnnga ctgacattga cacaatgaca attgaccccc aagtggagaa aaagatggga
     7081 caggtgctac tcatagcagt agccgtctcc agcgccntac tgtcgcggac cgcctggggg
     7141 tggggggagg ctggggccct gatcacagcc gcaacttcca ctttgtggga aggctctccg
     7201 aacaagtact ggaactcctc tacagccact tcactgt                        
          [gap 187 bp]    Expand Ns
     7425                                                 gtgcag agaagaggcc
     7441 cgccgcgccc tcaaggacgg tgtggcaacg ggaggccatg ctgtgtcccg aggaagtgca
     7501 aagctgagat ggttggtgga gcggggatac ctgcagcccc atggaaaggt cattgatctt
     7561 ggatgtggca gagggggctg gagttactac gccgccacca tccgcaaagt tcaagaagtg
     7621 aannnnnnnn nnnnnnnnnn nnnnggtcat gaagaacccg tgttggtgca aagctatggg
     7681 tggaacatag tccgtcttaa gagtggggtg gacgtctttc atatggcggc tgagccgtgt
     7741 gacacgttgc tgtgtgacat aggtgagtca tcatctagtc ctgaagtgga agaagcacgg
     7801 acgctcagag ttctctccat ggtgggggat tggcttgaaa aaagaccagg agccttttgt
     7861 ataaaagtgt tgtgcccata caccagcact atgatggaaa ccctggagcg actgcagcgt
     7921 aggtatgggg gaggactggt cagagtgcca ctctcccgca actctacaca tgagatgtac
     7981 tgggtctctg gagcgaaaag caacaccata aaaagtgtgt ccaccacgag ccagctcctc
     8041 ttggggcgca tggacgggcc taggaggcca gtgaaatatg aggaggatgt gaatctcggc
     8101 tctggcacgc gggctgtggt aagctgcgct gaagctccca acatgaagat cattggtaac
     8161 cgcattgaaa ggatccgcag tgagcacgcg gaaacgtggt tctttgacga gaaccaccca
     8221 tataggacat gggcttacca tggaagctat gaggccccca cacaagggtc agcgtcctct
     8281 ctaataaacg gggttgtcag gctcctgtca aaaccctggg atgtggtgac tggagtcaca
     8341 ggaatagcca tgaccgacac cacaccgtat ggtcagcaaa gagttttcaa ggaaaaagtg
     8401 gacactaggg tgccagaccc ccaagaaggc actcgtcagg ttatgagcat ggtctcttcc
     8461 tggttgtgga aagagctagg caaacacaaa cggccacgag tctgtaccaa agaagagttc
     8521 atcaacaagg ttcgtagcaa tgcagcatta ggggcaatat ttgaagagga aaaagagtgg
     8581 aagactgcag tggaagctgt gaacgatcca aggttctggg ctctagtgga caaggaaaga
     8641 gagcaccacc tgagaggaga gtgccagagt tgnnnnnnca acatgatggg aaaaagagaa
     8701 aagaaacaag gggaatttgg aaaggccaag ggcagccgcg ccatctggta tatgtggcta
     8761 ggggctagat ttctagagtt cgaagccctt ggattcttga acgaggatca ctggatgggg
     8821 agagagaact caggaggtgg tgttgaaggg ctgggattac aaagactcgg atatgtccta
     8881 gaagagatga gtcgcatacc aggaggaagg atgtatgcag atgacactgc tggctgggac
     8941 acccgcatca gcaggtttga tctggagaat gaagctctaa tcaccaacca aatggagaaa
     9001 gggcacaggg ccttggcatt ggccataatc aagtacacat accaaaacaa agtggtaaag
     9061 gtccttagac cagctgaaaa agggaaaaca gttatggaca ttatttcgag acaagaccaa
     9121 agggggagcg gacaagttgt cacttacgct ctcaacacat ttaccaacct agnnnnnnnn
     9181 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nncgagatgc aagacttgtg gctgctgcgg
     9241 aggccagaga aagtgaccaa ctggttgcag agcaacggat gggataggct nnnnnnnnnn
     9301 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnggtttgc acatgccctc
     9361 aggttcttga atgatatggg aaaagttagg aaggacacac aagagtggaa accctcaact
     9421 ggatgggaca actgggaaga agttccgttt tgctcccacc acttcaacaa gctccatctc
     9481 aaggacggga ggtccattgt ggttccctgc cgccaccaag atgaactgat tggccgggcc
     9541 cgcgtctctc caggggcggg atggagcatc cgggagactg cttgcctagc aaaatcatat
     9601 gcgcaaatgt ggcagctcct ttatttccac agaagggacc tccgactgat ggccaatgcc
     9661 atttgctcat ctgtgccagt tgactgggtt ccaactggga gaactacctg gtcaatccat
     9721 ggaaagggag aatggatgac cactgaagac atgcttgtgg tgtggaacag agtgtggatt
     9781 gaggagaacg accacatgga agacaagacc ccagttacga aatggacaga cattccctat
     9841 ttgggaaaaa gggaagactt gtggtgtgga tctctcatag ggcacagacc gcgcaccacc
     9901 tgggctgaga acattaaaaa cacagtcaac atggtgcgca ggatcatagg tgatgaagaa
     9961 aagtacatgg actacctatc cacccaagtt cgctacttgg gtgaagaagg gtctacacct
    10021 ggagtgctgt aagcaccaat cttaatgttg tcaggcctgc tagtcagcca cagcttgggg
    10081 aaagctgtgc agcctgtgac ccccccagga gaagctggga aaccaagcct atagtcaggc
    10141 cgagaacgcc atggcacgga agaagccatg ctgcctgtga gcccctcaga ggacactgag
    10201 tcaaaaaacc ccacgcgctt ggaggcgcag gatgggaaaa gaaggtggcg accttcccca
    10261 cccttcaatc tggggcctga actggagatc agctgtggat ctccagaaga gggactagtg
    10321 gttagaggag a
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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
48071399078%0.0100%KX101060.1
47891394878%0.096%KU940228.1
47891394178%0.096%KU940224.1
47741389878%0.096%KU509998.3
47741388778%0.096%KU321639.1
47731386478%0.096%KU647676.1
47691386578%0.096%KX051563.1
47651384578%0.096%KX087102.1
47651385678%0.096%KU926309.1
47651384578%0.096%KU820897.1
47621383378%0.095%KU870645.1
47621383378%0.095%KU926310.1
47621388578%0.095%KU729218.1
47621386478%0.095%KU527068.1
47601387478%0.095%KU991811.1
47601384578%0.095%KU922960.1
47601384278%0.095%KU922923.1
47601387478%0.095%KJ776791.1
47561381778%0.095%KX087101.1
47531381878%0.095%KU501215.1
47511384978%0.095%KU729217.2
47451385178%0.095%KU707826.1
47441380678%0.095%KX117076.1
47441384978%0.095%KU497555.1
47421383578%0.095%KU365780.1
47381384478%0.095%KU365779.1
47351379378%0.095%KU820899.2
47351381778%0.095%KU365778.1
47331382678%0.095%KU365777.1
47291378878%0.095%KU963796.1
47201375078%0.095%KU744693.1
46811363478%0.095%KU681081.3
46721374877%0.095%KU853013.1
46701374877%0.095%KU853012.1
46621372177%0.095%KU955589.1
46551373777%0.095%KU955590.1
46371371277%0.095%KU740184.2
46081340778%0.094%KU955593.1
45451318478%0.094%KU681082.3
43511342576%0.095%KU761564.1
43381342276%0.095%KU312312.1
42221331275%0.095%KU501217.1
42221331275%0.095%KU501216.1
42131328375%0.095%KU820898.1
42041328375%0.095%KX056898.1
41451316975%0.094%KU866423.1
41181299275%0.094%KF993678.1
40801288175%0.094%JN860885.1
40781281975%0.094%EU545988.1
37071188275%0.091%HQ234499.1
34581002478%0.086%KU720415.1
34581000878%0.086%LC002520.1
3454998678%0.086%KU955594.1
3449998678%0.085%KU963573.1
3445996878%0.085%AY632535.2
3440998178%0.085%KU955595.1
3431996878%0.085%KU955592.1
3422994578%0.085%KU955591.1
3391993078%0.085%KF268949.1
3353993078%0.085%KF268950.1
3353993878%0.085%KF268948.1
3012958476%0.084%KU963574.1
3007944375%0.085%DQ859059.1
2978945175%0.084%KF383116.1
2964953775%0.084%KF383119.1
2964953075%0.084%HQ234498.1
2942927575%0.084%KF383118.1
2919944775%0.084%HQ234501.1
2913937775%0.084%HQ234500.1
2892946175%0.084%KF383115.1
2879938075%0.084%KF383117.1
2792369119%0.099%KU312314.1
2778367119%0.099%KU312313.1
2562913572%0.083%KF383121.1
2315275014%0.099%KU312315.1
2300326217%0.099%KU646828.1
2287324917%0.099%KU646827.1
2287228712%0.099%KJ634273.1
19501142569%0.092%KU940227.1
1804766570%0.083%KF383120.1
16631159465%0.099%KX101061.1
16581059859%0.099%KX101066.1
1654165411%0.090%KU179098.1
164917959%0.099%KU740199.1
1577909552%0.096%KX101064.1
148914899%0.090%KX059014.1
148914899%0.090%KX059013.1
140214029%0.090%KM078936.1
140214029%0.090%KM078930.1
140014009%0.090%KM078971.1
140014009%0.090%KM078970.1
140014009%0.090%KM078961.1
139813989%0.090%KM078929.1
139513959%0.090%KM078933.1
125212528%0.089%KJ873160.1
122312236%0.098%KT200609.1
107610767%0.088%KJ873161.1
107210728%0.088%KF270886.1
103410347%0.087%KM851039.1
1032621534%0.096%KX101062.1
102910299%0.080%AF013415.1
102010207%0.086%KM851038.1
101410148%0.086%AF372422.1
100910097%0.087%KU985087.1
100210027%0.087%KU556802.1
99614548%0.098%KU686218.1
9719717%0.089%KF383022.1
9669667%0.088%KF383026.1
9609607%0.088%KF383037.1
9579577%0.088%KF383036.1
9579577%0.088%KF383032.1
9539537%0.088%KF383034.1
9539537%0.088%KF383029.1
9489487%0.088%KF383033.1
9469467%0.087%EU303241.1
931670739%0.092%KX101067.1
9309307%0.087%KF383039.1
9309307%0.087%KF383038.1
9309307%0.087%KF383028.1
9269267%0.087%KF383031.1
9219217%0.087%KF383046.1
9019017%0.086%KF383035.1
8978977%0.087%KF383045.1
8958956%0.086%KU232300.1
8938937%0.086%KF383043.1
890594234%0.090%KX101063.1
8888887%0.086%KF383041.1
8868866%0.086%KU232290.1
8848846%0.086%KU232297.1
8848847%0.086%KF383042.1
8778776%0.086%KU232292.1
8758756%0.086%KU232294.1
8708706%0.086%KU232298.1
8668666%0.086%KU232296.1
8668666%0.086%KU232293.1
8618616%0.086%KU232295.1
8578577%0.085%KF383040.1
8508506%0.086%KU232288.1
8478476%0.086%KU232289.1
8438436%0.085%KU232299.1
8418416%0.085%KU232291.1
8368364%0.099%AB908162.1
8298295%0.095%KF383083.1
8298295%0.095%KF383052.1
8258255%0.094%KF383064.1
8258255%0.094%KF383049.1
8258255%0.094%KF383048.1
8218215%0.094%KF383047.1
8208205%0.094%KF383066.1
8208205%0.094%KF383065.1
8188185%0.094%KF383072.1
8188185%0.094%KF383054.1
8168165%0.094%KF383069.1
8148145%0.094%KF383073.1
8148145%0.094%KF383071.1
8098095%0.094%KF383074.1
8078075%0.094%KF383068.1
8018015%0.093%KF383050.1
8008005%0.093%KF383070.1
7987985%0.093%KF383079.1
7927925%0.093%KF383076.1
7927925%0.093%KF383063.1
7897895%0.093%KF383081.1
7837835%0.090%KU867812.1
7837835%0.093%KF383080.1
7837835%0.093%KF383075.1
7627625%0.092%KF383051.1
7087087%0.081%KF383017.1
7047047%0.081%KF383016.1
7047047%0.081%KF383015.1
6996997%0.081%KF383020.1
6976977%0.081%KF383021.1
695283865%0.069%DQ859064.1
6816817%0.080%KF383019.1
6776773%0.097%KF258813.1
6456453%8e-18099%KU985088.1
6216213%9e-17399%KX062045.1
6166163%4e-17199%KX062044.1
6166166%4e-17177%KF383103.1
6166166%4e-17177%KF383086.1
5925926%4e-16476%KF383104.1
5805806%3e-16076%KF383085.1
5785783%9e-16099%KR815989.1
5715716%1e-15775%KF383114.1
5715716%1e-15775%KF383088.1
5655656%6e-15675%KF383106.1
5655656%6e-15675%KF383087.1
5625626%7e-15575%KF383107.1
5535536%4e-15275%KF383089.1
5535535%4e-15283%KF383062.1
549131837%5e-15168%EU082199.2
5475476%2e-15075%KF383101.1
5475476%2e-15075%KF383097.1
5445446%2e-14974%KF383099.1
5445445%2e-14983%KF383082.1
5385386%8e-14874%KF383098.1
5385385%8e-14883%KF383056.1
5365362%3e-14799%KR816334.1
5365365%3e-14783%KF383057.1
5355352%1e-14699%KR816333.1
5355352%1e-146100%KM212966.1
5355355%1e-14683%KF383061.1
535145839%1e-14667%EF158064.1
5315312%1e-14598%KR816335.1
5295292%4e-14599%KM212965.1
5295292%4e-14599%KM212964.1
5295292%4e-14599%KM212963.1
529137138%4e-14567%EF158060.1
5115116%1e-13973%KF383084.1
5085082%1e-138100%KJ579441.1
5085086%1e-13873%KF383113.1
506605534%5e-13898%KX101065.1
504133137%2e-13767%GQ851604.1
5025022%6e-13799%KJ680134.1
502137538%6e-13767%EF158062.1
497138338%2e-13567%JX041632.1
493123435%3e-13467%DQ256376.1
486134238%5e-13266%EF158058.1
486134238%5e-13266%DQ525916.1
477143136%2e-12967%FJ753286.2
468142536%1e-12666%KT823415.1
462139139%5e-12566%FJ753287.2
443120637%5e-11966%KJ501495.1
4395393%6e-11898%KU758878.1
4254252%1e-11399%KU954085.1
425116937%1e-11366%KR348977.1
425116937%1e-11366%KR348976.1
4255864%1e-11388%KF270887.1
4174172%2e-111100%KU926326.1
4174172%2e-111100%KU926325.1
4174172%2e-111100%KU926324.1
4174172%2e-111100%KU926323.1
4164162%7e-11199%KT381874.1
4084082%1e-108100%KM212961.1
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LOCUS       KX101061               10564 bp    RNA     linear   VRL 26-APR-2016
DEFINITION  Zika virus isolate Bahia03, partial genome.
ACCESSION   KX101061
VERSION     KX101061.1  GI:1022831291
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10564)
  AUTHORS   Naccache,S.N., Theze,J., Sardi,S.I., Somasekar,S., Greninger,A.L.,
            Bandeira,A.C., Campos,G.S., Tauro,L.B., Faria,N.R., Pybus,O.G. and
            Chiu,C.Y.
  TITLE     Discovery of a persistent Zika virus lineage in Bahia, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10564)
  AUTHORS   Naccache,S.N., Somasekar,S., Sardi,S.I., Bandeira,A.C., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-APR-2016) Laboratory Medicine, University of
            California, San Francisco, 185 Berry Street, #0134, San Francisco,
            CA 94107, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SURP+ v. 1.0 2016; Geneious v. 6.1.8
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10564
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="Bahia03"
                     /isolation_source="serum"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="May-2015"
     CDS             <1..10209
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ANA85188.1"
                     /db_xref="GI:1022831292"
                     /translation="ARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIKPSLGL
                     INRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTAMAA
                     EVTRRGSAYYMYLDRNDAGEAISFPTTLGMNKCYIQIMDLGHMCDATMSYECPMLDEG
                     VEPDDVDCWCNTTSTWVVYGTCHHKKGEAXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXFRNPGFALAAAAIAWLLGSSTSQKVIYXXXXXXXXXXXXXXXXXXX
                     XXXXXXGMSGGTWVDIVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASI
                     SDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLG
                     GFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNK
                     EALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDK
                     LRLKGVSYSLCNAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPV
                     GRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEA
                     TVRGAKRMAVLGDTAWXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTGVFVYNDV
                     EAWRDRYKYHPDSPRRLAAAVKQAWEDGICGISSVSRMENIMWRSVEGELNAILEENG
                     VQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGKSXFVRAAKTNXSFVXDGDTLK
                     ECPLKHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLECDPAVIGTAVKXXXXXXXXXG
                     YWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGIEESDLIIPKSXXXXXXXXXXX
                     XGYRTQMKGPWHSEELEIRFEECPGTKVHVEETCGTRGPSLRSTTASGRXXXXXXXXX
                     XXXXPLSFRAKDGCWYGMEIRPRKEPESNLVRSMVTAGSTDHMDHFSLGVLVILLMVQ
                     EXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXNTGGDVAHLAL
                     IAAFKVRPALLVSFIFXXXXXPRESMLLALASCLLQTAISALEGDLMVLINGFALAWL
                     AIRAMVVPXXXXXXXXXXXXXXXXXXXXXXXXWRAGLATCGGFMLLSLKGKGSVKKNL
                     PFVMALGLTAVRLVDPINVVGLLLLTRSGKRSWPPSEVLTAVGLICALAGGFAKADIE
                     MAGPMAAVGLLIVSYVVSGKSVDMYIERAGDITWEKDAEVTGNXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAGAWYVYVKTGKRSGALWDVPAPKEV
                     KKXXXXXXXXXXXXXXXXGSTQVGVGVMQEGVFHTMWHVTKGSALRSGEGRLDPYWGD
                     VKQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGERARNIQTLPGIFKTKDGDIGAVALD
                     YPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGRREEETPVECFEPSMLKKK
                     QLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAPTRVVAAEMEEALRGLPVRYMT
                     TAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLYIMDEAHFTXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKTKHQEWDFVVTTDISXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXMPVTHASAAQRRGRIGRNPNKPGDEYLYGGXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XKRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIMEDSVPAEVWTRHGEKRVLKPR
                     WMDARVCSDHAALKSFKEFAAGKRGAALGVMEALGTLPGHMTERFQEAIDNLAVLMRA
                     ETGSRPYKAAAAQMPETLETIMLLGLLGTVSLGIFFVLMRNKGIGKMGFGMVTLGASA
                     WLMWLSEIEPARIACVLIVVFLLLVVLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXGWLERTKSDLSHLMGRREEGATIGFSMDIDLRPASAWAIYAALTTFITPAVQHAV
                     TTSYNNYSLMAMATQAGVLFGMGKGMPFYAWDFGVPLLMIGCYSQLTPLTLIVAIILL
                     VAHYMYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSLCNIFRGSYL
                     AGASLIYTVTRNAGLVKRRGGGTGETLGEKWKARLNQMSALEFYSYKKSGITEVCREE
                     ARRALKDGVATGGHAVSRGSAKLRWLVERGYLQPYGKVIDLGCGRGGWSYYAATIRKV
                     QEVKGYTKGGPGHEEPVLVQSYGWNIVRLKSGVDVFHMAAEPCDTLLCDIGESSSSPE
                     VEEARTLRVLSMVGDWLEKRPGAFCIKVLCPYTSTMMETLERLQRRYGGGLVRVPLSR
                     NSTHEMYWVSGAKSNTIKSVSTTSQLLLGRMDGPRRPVKYEEDVNLGSGTRAVVSCAE
                     APNMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHGSYXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXTTPYGQQRVFKEKVDTRVPDPQEGTRQVMSMVSSWLWKELG
                     KHKRPRVCTKEEFINKVRSNAALGAIFEEEKEWKTAVEAVNDPRFWALVDKEREHHLR
                     GECQSXXXXXXXXXXXXXXXXXXXXXXXXXXXMWLGARFLEFEALGFLNEDHWMGREN
                     SGGGVEGLGLQXXXXXXXXXXXXXXXXXXXXXXXXXDTRISRFDLENEALITNQMEKG
                     HRALALAIIKYTYQNKVVKVLRPAEKGKTVMDIISRQDQRGSGQVVTYALNTFTNLVV
                     QLIRNMEAEEVLEMQDLWLLRRPEKVTNWLQSNGWDRLKRMAVSGDDCVVKPIXXXXX
                     XXXXXXXXXXXXXXXXXXWKPSTGWDNWEEVPFCSHHFNKLHLKDGRSIVVPCRHQDE
                     LIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRRDLRLMANAICSSVPVDWVPTG
                     RTTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKTPVTKWTDIPYLGKREDLWCGS
                     LIGHRPRTTWAENIKNTVNMVRRIIGDEEKYMDYLSTQVRYLGEEGSTPGVL"
     mat_peptide     1..312
                     /product="capsid peptide"
     mat_peptide     313..582
                     /product="propeptide"
     mat_peptide     583..807
                     /product="membane protein peptide"
     mat_peptide     808..2322
                     /product="envelope protein peptide"
     mat_peptide     2323..3408
                     /product="NS1 peptide"
     mat_peptide     3409..4062
                     /product="NS2A peptide"
     mat_peptide     4063..4494
                     /product="NS2B peptide"
     mat_peptide     4495..6303
                     /product="NS3 peptide"
     mat_peptide     6304..6744
                     /product="NS4A peptide"
     mat_peptide     6745..8250
                     /product="NS4B peptide"
     mat_peptide     8251..10206
                     /product="NS5 peptide"
     gap             568..690
                     /estimated_length=123
     gap             2096..2365
                     /estimated_length=270
     gap             3442..3578
                     /estimated_length=137
     gap             4264..4402
                     /estimated_length=139
     gap             5316..5529
                     /estimated_length=214
     gap             5868..6050
                     /estimated_length=183
     gap             6652..6752
                     /estimated_length=101
     gap             7111..7405
                     /estimated_length=295
     gap             8429..8534
                     /estimated_length=106
     3'UTR           10210..10564
ORIGIN      
        1 gcccgtgtga gcccctttgg gggcttgaag aggctgccag ccggacttct gctgggtcat
       61 gggcccatca ggatggtctt ggcgattcta gcctttttga gattcacggc aatcaagcca
      121 tcactgggtc tcatcaatag atggggttca gtggggaaaa aagaggctat ggaaataata
      181 aagaagttca agaaagatct ggctgccatg ctgagaataa tcaatgctag gaaggagaag
      241 aagagacgag gcgcagatac tagtgtcgga attgttggcc tcctgctgac cacagctatg
      301 gcagcggagg tcactagacg tgggagtgca tactatatgt acttggacag aaacgatgct
      361 ggggaggcca tatcttttcc aaccacattg gggatgaata agtgttatat acagatcatg
      421 gatcttggac acatgtgtga tgccaccatg agctatgaat gccctatgct ggatgagggg
      481 gtggaaccag atgacgtcga ttgttggtgc aacacgacgt caacttgggt tgtgtacgga
      541 acctgccatc acaaaaaagg tgaagca                                   
          [gap 123 bp]    Expand Ns
      691                                  ttcaggaacc ctggcttcgc gttagcagca
      721 gctgccatcg cttggctttt gggaagctca acgagccaaa aagtcatata cnnnnnnnnn
      781 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
      841 nnnnnnggta tgtcaggtgg gacttgggtt gatattgtct tggaacatgg aggttgtgtc
      901 accgtaatgg cacaggacaa accgactgtc gacatagagc tggttacaac aacagtcagc
      961 aacatggcgg aggtaagatc ctactgctat gaggcatcaa tatcagacat ggcttcggac
     1021 agccgctgcc caacacaagg tgaagcctac cttgacaagc aatcagacac tcaatatgtc
     1081 tgcaaaagaa cgttagtgga cagaggctgg ggaaatggat gtnnnnnnnn nnnnnnnnnn
     1141 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     1201 nnnnnnnnnc tggagtaccg gataatgctg tcagttcatg gctcccagca cagtgggatg
     1261 atcgttaatg acacaggaca tgaaactgat gagaatagag cgaaggttga gataacgccc
     1321 aattcaccaa gagccgaagc caccctgggg ggttttggaa gcctaggact tgattgtgaa
     1381 ccgaggacag gccttgactt ttcagatttg tattacttga ctatgaataa caagcactgg
     1441 ttggttcaca aggagtggtt ccacgacatt ccattacctt ggcacgctgg ggcagacacc
     1501 ggaactccac actggaacaa caaagaagca ctggtagagt tcaaggacgc acatgccaaa
     1561 aggcaaactg tcgtggttct agggagtcaa gaaggagcag ttcacacggc ccttgctgga
     1621 gctctagagg ctgagatgga tggtgcaaag ggaaggctgt cctctggcca cttgaaatgt
     1681 cgcctgaaaa tggataaact tagattgaag ggcgtgtcat actccttgtg taacgcagcg
     1741 ttcacattca ccaagatccc ggctgaaaca ctgcacggga cagtcacagt ggaggtacag
     1801 tacgcaggga ctgatggacc ttgcaaggtt ccagctcaga tggcggtgga catgcaaact
     1861 ctgaccccag ttgggaggtt gataaccgct aaccccgtaa tcactgaaag cactgagaac
     1921 tctaagatga tgctggaact tgatccacca tttggggact cctacattgt cataggagtc
     1981 ggggagaaga agatcaccca ccactggcac aggagtggca gcaccattgg aaaagcattt
     2041 gaagccactg tgagaggtgc caagagaatg gcagtcttgg gagacacagc ctggg    
          [gap 270 bp]    Expand Ns
     2366                            gtaca ggggtgttcg tctataacga cgttgaagcc
     2401 tggagggaca ggtacaagta ccatcctgac tccccccgta gattggcagc agcagtcaag
     2461 caagcctggg aagatggtat ctgcgggatc tcctctgttt caagaatgga aaacatcatg
     2521 tggagatcag tagaagggga gctcaacgca atcctggaag agaatggagt tcaactgacg
     2581 gtcgttgtgg gatctgtaaa aaaccccatg tggagaggtc cacagagatt gcccgtgcct
     2641 gtgaacgagc tgccccacgg ctggaaggct tgggggaaat cgtmcttcgt cagagcagca
     2701 aagacaaatm acagctttgt cgnggatggt gacacactga aggaatgccc actcaaacat
     2761 agagcatgga acagctttct tgtggaggat catgggttcg gggtatttca cactagtgtc
     2821 tggctcaagg ttagagaaga ttattcatta gagtgtgatc cagccgttat tggaacagct
     2881 gttaagnnnn nnnnnnnnnn nnnnnnnnnn nnnggctact ggattgagag tgagaagaat
     2941 gacacatgga ggctgaagag ggcccatctg atcgagatga aaacatgtga atggccaaag
     3001 tcccacacat tgtggacaga tggaatagaa gagagtgatc tgatcatacc caagtcttnn
     3061 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nngggctaca ggacccaaat gaaagggcca
     3121 tggcacagtg aagagcttga aattcggttt gaggaatgcc caggcactaa ggtccacgtg
     3181 gaggaaacat gtggaacaag aggaccatct ctgagatcaa ccactgcaag cggaagggnn
     3241 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnccccac tgtcgttccg ggctaaagat
     3301 ggctgttggt atggaatgga gataaggccc aggaaagaac cagaaagcaa cttagtaagg
     3361 tcaatggtga ctgcaggatc aactgatcac atggatcact tctcccttgg agtgcttgtg
     3421 attctgctca tggtgcagga a                                         
          [gap 137 bp]    Expand Ns
     3579                                          ga acactggagg agatgtagct
     3601 catctggcgc tgatagcggc attcaaagtc agaccagcgt tgctggtatc tttcatcttc
     3661 nnnnnnnnnn nnnnnccccg tgaaagcatg ctgctggcct tggcctcgtg tcttttgcaa
     3721 actgcgatct ccgccttgga aggcgacctg atggttctca tcaatggttt tgctttggcc
     3781 tggttggcaa tacgagcgat ggttgttcca nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     3841 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn ngtggagagc aggccttgct
     3901 acttgcgggg ggtttatgct cctctctctg aagggaaaag gcagtgtgaa gaagaactta
     3961 ccatttgtca tggccctggg actaaccgct gtgaggctgg tcgaccccat caacgtggtg
     4021 ggactgctgt tgctcacaag gagtgggaag cggagctggc cccccagcga agtactcaca
     4081 gctgttggcc tgatatgcgc attggctgga gggttcgcca aggcagatat agagatggct
     4141 gggcccatgg ccgcggtcgg tctgctaatt gtcagttacg tggtctcagg aaagagtgtg
     4201 gacatgtaca ttgaaagagc aggtgacatc acatgggaaa aagatgcgga agtcactgga
     4261 aac                                                             
          [gap 139 bp]    Expand Ns
     4403                         cagctgga gcgtggtacg tatacgtgaa gactggaaaa
     4441 aggagtggtg ctctatggga tgtgcctgct cccaaggaag taaaaaagnn nnnnnnnnnn
     4501 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnggtt caacacaagt tggagtggga
     4561 gttatgcaag agggggtctt tcacactatg tggcacgtca caaaaggatc cgcgctgaga
     4621 agcggtgaag ggagacttga tccatactgg ggagatgtca agcaggatct ggtgtcatac
     4681 tgtggtccat ggaagctaga tgccgcctgg gacgggcaca gcgaggtgca gctcttggcc
     4741 gtgccccccg gagagagagc gaggaacatc cagactctgc ccggaatatt taagacaaag
     4801 gatggggaca ttggagcggt tgcgctggat tacccagcag gaacttcagg atctccaatc
     4861 ctagacaagt gtgggagagt gataggactt tatggcaatg gggtcgtgat caaaaatggg
     4921 agttatgtta gtgccatcac ccaagggagg agggaggaag agactcctgt tgagtgcttc
     4981 gagccttcga tgctgaagaa gaagcagcta actgtcttag acttgcatcc tggagctggg
     5041 aaaaccagga gagttcttcc tgaaatagtc cgtgaagcca taaaaacaag actccgtact
     5101 gtgatcttag ctccaaccag ggttgtcgct gctgaaatgg aggaagccct tagagggctt
     5161 ccagtgcgtt atatgacaac agcagtcaat gtcacccact ctggaacaga aatcgtcgac
     5221 ttaatgtgcc atgccacctt cacttcacgt ctactacagc caatcagagt ccccaattat
     5281 aatctgtata ttatggatga ggcccacttc acaga                          
          [gap 214 bp]    Expand Ns
     5530          g ttccaagcgt gaggaacggc aatgagatcg cagcttgtct gacaaaggct
     5581 ggaaaacggg tcatacagct cagcagaaag acttttgaga cagagttcca gaaaacaaaa
     5641 catcaagagt gggactttgt cgtgacaact gacatttcag nnnnnnnnnn nnnnnnnnnn
     5701 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     5761 nnnnnnnnnn nnnnnnccat gcctgtcaca catgccagcg ctgcccagag gagggggcgc
     5821 ataggcagga atcccaacaa acctggagat gagtatctgt atggagg             
          [gap 183 bp]    Expand Ns
     6051                                                        gaaaagagga
     6061 gatcttcctg tttggctggc ctatcaggtt gcatctgccg gaataaccta cacagataga
     6121 agatggtgct ttgatggcac gaccaacaac accataatgg aagacagtgt gccggcagag
     6181 gtgtggacca gacacggaga gaaaagagtg ctcaaaccga ggtggatgga tgccagagtt
     6241 tgttcagatc atgcggccct gaagtcattc aaggagtttg ccgctgggaa aagaggagcg
     6301 gctcttggag tgatggaagc cctgggaaca ctgccaggac acatgacaga gagattccag
     6361 gaagccattg acaacctcgc tgtgctcatg cgggcagaga ctggaagcag gccttacaaa
     6421 gccgcggcgg cccaaatgcc ggagacccta gagaccatta tgcttttggg gttgctagga
     6481 acagtctcgc tgggaatctt tttcgtcttg atgaggaaca agggcatagg gaagatgggc
     6541 tttggaatgg tgactcttgg ggccagcgca tggctcatgt ggctctcgga aattgagcca
     6601 gccagaattg catgtgtcct cattgttgtg ttcctattgc tggtggtgct c        
          [gap 101 bp]    Expand Ns
     6753                                    cggatggt tggagagaac aaagagtgac
     6781 ctaagccatc taatgggaag gagagaggag ggggcaacca taggattctc aatggacatt
     6841 gacctgcggc cagcctcagc ttgggccatc tatgctgcct tgacaacttt cattacccca
     6901 gccgtccaac atgcagtgac cacttcatac aacaactact ccttaatggc gatggccacg
     6961 caagctggag tgttgtttgg tatgggcaaa gggatgccat tctacgcatg ggactttgga
     7021 gtcccgctgc taatgatagg ttgctactca caattaacac ccctgaccct aatagtggcc
     7081 atcattttgc tcgtggcgca ctacatgtac                                
          [gap 295 bp]    Expand Ns
     7406                            cttca ctgtgtaaca tttttagggg aagttacttg
     7441 gctggagctt ctctaatcta cacagtaaca agaaacgctg gcttggtcaa gagacgtggg
     7501 ggtggaacag gagagaccct gggagagaaa tggaaggccc gcttgaacca gatgtcggcc
     7561 ctggagttct actcctacaa aaagtcaggc atcaccgagg tgtgcagaga agaggcccgc
     7621 cgcgccctca aggacggtgt ggcaacggga ggccatgctg tgtcccgagg aagtgcaaag
     7681 ctgagatggt tggtggagcg gggatacctg cagccctatg gaaaggtcat tgatcttgga
     7741 tgtggcagag ggggctggag ttactacgcc gccaccatcc gcaaagttca agaagtgaaa
     7801 ggatacacaa aaggaggccc tggtcatgaa gaacccgtgt tggtgcaaag ctatgggtgg
     7861 aacatagtcc gtcttaagag tggggtggac gtctttcata tggcggctga gccgtgtgac
     7921 acgttgctgt gtgacatagg tgagtcatca tctagtcctg aagtggaaga agcacggacg
     7981 ctcagagtcc tctccatggt gggggattgg cttgaaaaaa gaccaggagc cttttgtata
     8041 aaagtgttgt gcccatacac cagcactatg atggaaaccc tggagcgact gcagcgtagg
     8101 tatgggggag gactggtcag agtgccactc tcccgcaact ctacacatga gatgtactgg
     8161 gtctctggag cgaaaagcaa caccataaaa agtgtgtcca ccacgagcca gctcctcttg
     8221 gggcgcatgg acgggcctag gaggccagtg aaatatgagg aggatgtgaa tctcggctct
     8281 ggcacgcggg ctgtggtaag ctgcgctgaa gctcccaaca tgaagatcat tggtaaccgc
     8341 attgaaagga tccgcagtga gcacgcggaa acgtggttct ttgacgagaa ccacccatat
     8401 aggacatggg cttaccatgg aagctatg                                  
          [gap 106 bp]    Expand Ns
     8535                caccac accgtatggt cagcaaagag ttttcaagga aaaagtggac
     8581 actagggtgc cagaccccca agaaggcact cgtcaggtta tgagcatggt ctcttcctgg
     8641 ttgtggaaag agctaggcaa acacaaacgg ccacgagtct gtaccaaaga agagttcatc
     8701 aacaaggttc gtagcaatgc agcactaggg gcaatatttg aagaggaaaa agagtggaag
     8761 actgcagtgg aagctgtgaa cgatccaagg ttctgggctc tagtggacaa ggaaagagag
     8821 caccacctga gaggagagtg ccagagttgn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     8881 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnatat gtggctaggg
     8941 gctagatttc tagagttcga agcccttgga ttcttgaacg aggatcactg gatggggaga
     9001 gagaactcag gaggtggtgt tgaagggctg ggattacaan nnnnnnnnnn nnnnnnnnnn
     9061 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nngggacacc
     9121 cgcatcagca ggtttgatct ggagaatgaa gctctaatca ccaaccaaat ggagaaaggg
     9181 cacagggcct tggcattggc cataatcaag tacacatacc aaaacaaagt ggtaaaggtc
     9241 cttagaccag ctgaaaaagg gaaaacagtt atggacatta tttcgagaca agaccaaagg
     9301 gggagcggac aagttgtcac ttacgctctt aacacattta ccaacctagt ggtgcaactc
     9361 attcggaata tggaggctga ggaagttctc gagatgcaag acttgtggct gctgcggagg
     9421 ccagagaaag tgaccaactg gttgcagagc aacggatggg ataggctcaa acgaatggca
     9481 gtcagtggag atgattgcgt tgtgaagcca attgannnnn nnnnnnnnnn nnnnnnnnnn
     9541 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn ngtggaaacc ctcaactgga
     9601 tgggacaact gggaagaagt tccgttttgc tcccaccact tcaacaagct ccatctcaag
     9661 gacgggaggt ccattgtggt tccctgccgc caccaagatg aactgattgg ccgggcccgc
     9721 gtctctccag gggcgggatg gagcatccgg gagactgctt gcctagcaaa atcatatgcg
     9781 caaatgtggc agctccttta tttccacaga agggacctcc gactgatggc caatgccatt
     9841 tgttcatctg tgccagttga ctgggttcca actgggagaa ctacctggtc aatccatgga
     9901 aagggagaat ggatgaccac tgaagacatg cttgtggtgt ggaacagagt gtggattgag
     9961 gagaacgacc acatggaaga caagacccca gttacgaaat ggacagacat tccctatttg
    10021 ggaaaaaggg aagacttgtg gtgtggatct ctcatagggc acagaccgcg caccacctgg
    10081 gctgagaaca ttaaaaacac agtcaacatg gtgcgcagga tcataggtga tgaagaaaag
    10141 tacatggact acctatccac ccaagttcgc tacttgggtg aagaagggtc tacacctgga
    10201 gtgctgtaag caccagtctt aatgttgtca ggcctgctag tcagccacag cttggggaaa
    10261 gctgtgcagc ctgtgacccc cccaggagaa gctgggaaac caagcctata gtcaggccga
    10321 gaacgccatg gcacggaaga agccatgctg cctgtgagcc cctcagagga cactgagtca
    10381 aaaaacccca cgcgcttgga ggcgcaggat gggaaaagaa ggtggcgacc ttccccaccc
    10441 ttcaatctgg ggcctgaact ggagatcagc tgtggatctc cagaagaggg actagtggtt
    10501 agaggagacc ccccggaaaa cgcaaaacag catattgacg ctgggaaaga ccagagactc
    10561 catg
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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
18461467693%0.0100%KX101061.1
18461442892%0.0100%KX087102.1
18461455593%0.0100%KX051563.1
18461457693%0.0100%KU509998.3
18461452993%0.0100%KU820897.1
18461443792%0.0100%KU647676.1
18461400589%0.0100%KU312312.1
18461447492%0.0100%KU321639.1
18401450893%0.099%KX087101.1
18401446192%0.099%KU991811.1
18401455193%0.099%KU926309.1
18401442192%0.099%KU922960.1
18401442192%0.099%KU922923.1
18401433792%0.099%KU853013.1
18401433892%0.099%KU853012.1
18401440792%0.099%KU501215.1
18401451393%0.099%KU365778.1
18371454092%0.099%KU940228.1
18371453892%0.099%KU940224.1
18371451593%0.099%KU870645.1
18371452993%0.099%KU497555.1
18371444892%0.099%KU707826.1
18371453193%0.099%KU527068.1
18371444192%0.099%KU365779.1
18371446692%0.099%KJ776791.1
18311448493%0.099%KX117076.1
18311386889%0.099%KX056898.1
18311447593%0.099%KU963796.1
18311432092%0.099%KU955590.1
18311431392%0.099%KU955589.1
18311451393%0.099%KU926310.1
18311386489%0.099%KU820898.1
18311428291%0.099%KU740184.2
18311456493%0.099%KU729218.1
18311399690%0.099%KU761564.1
18311389589%0.099%KU501217.1
18311442192%0.099%KU365780.1
18311442192%0.099%KU365777.1
18281448193%0.099%KU820899.2
18281442792%0.099%KU729217.2
18281430993%0.099%KU681081.3
18281389189%0.099%KU501216.1
18241431892%0.099%KU744693.1
18221374989%0.099%KU866423.1
18191347188%0.099%KF993678.1
17841405793%0.099%KU955593.1
17841343389%0.099%JN860885.1
17831333489%0.099%EU545988.1
17681383093%0.098%KU681082.3
17591158675%0.099%KX101066.1
16631159674%0.099%KX101060.1
16441235589%0.096%HQ234499.1
1627901660%0.096%KX101064.1
15841165283%0.091%KU940227.1
1575358324%0.099%KU646828.1
1566357424%0.099%KU646827.1
1566268916%0.099%KU312315.1
1566386023%0.099%KU312314.1
1566205612%0.099%KJ634273.1
1557384223%0.099%KU312313.1
14691049293%0.093%KU955595.1
14691048693%0.093%KU955592.1
14671054293%0.093%LC002520.1
14651045993%0.093%KU955591.1
14621051793%0.093%KU955594.1
14621055193%0.093%KU720415.1
14581048893%0.093%AY632535.2
1451233715%0.094%KU740199.1
14111041493%0.092%KF268949.1
13971045093%0.092%KF268950.1
13971045293%0.092%KF268948.1
13751043692%0.093%KU963573.1
1310993689%0.089%KF383115.1
1297988289%0.088%KF383116.1
1292986489%0.088%HQ234501.1
1283980889%0.088%KF383117.1
1283991689%0.088%DQ859059.1
1274997989%0.088%KU963574.1
1274978189%0.088%HQ234500.1
1256956785%0.087%KF383121.1
1256997189%0.087%KF383119.1
1256996589%0.087%HQ234498.1
1252969189%0.087%KF383118.1
1099800384%0.084%KF383120.1
1038747250%0.093%KX101067.1
1018159010%0.099%KU686218.1
101210128%0.088%KF270886.1
9879876%0.099%KU758878.1
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LOCUS       KX101062               10323 bp    RNA     linear   VRL 26-APR-2016
DEFINITION  Zika virus isolate Bahia04, partial genome.
ACCESSION   KX101062
VERSION     KX101062.1  GI:1022831293
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10323)
  AUTHORS   Naccache,S.N., Theze,J., Sardi,S.I., Somasekar,S., Greninger,A.L.,
            Bandeira,A.C., Campos,G.S., Tauro,L.B., Faria,N.R., Pybus,O.G. and
            Chiu,C.Y.
  TITLE     Discovery of a persistent Zika virus lineage in Bahia, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10323)
  AUTHORS   Naccache,S.N., Somasekar,S., Sardi,S.I., Bandeira,A.C., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-APR-2016) Laboratory Medicine, University of
            California, San Francisco, 185 Berry Street, #0134, San Francisco,
            CA 94107, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SURP+ v. 1.0 2016; Geneious v. 6.1.8
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10323
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="Bahia04"
                     /isolation_source="serum"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="Jun-2015"
     CDS             1..9999
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ANA85189.1"
                     /db_xref="GI:1022831294"
                     /translation="MRIINARKEKKRRGADTSVGIVGLLLTTAMAAEVTRRGXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTMSYECPMLDEGVEPDDVDCWCNT
                     TSTWVVYGTCHHKKGEARRSRRAVTLPSHSNXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIQPENL
                     EYRIMLSVHGSQHSGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAQMAVDMQTLTPVGRLITANPVITE
                     STXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSQILIGTLLMWLGLNTKNGS
                     ISLMCLALGGVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEGELNAILEENGVQLTVVVGSVKN
                     PMWRGPQRLPVPVNELPHGWKAWGKSYFVRAAKTNNSFVVDGDTLKXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXNDTWR
                     LKRAHLIEMKTCEWPKSHTLWTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXWCCRECTMPPLSFRAKD
                     GCWYGMEXXXXKEPESNLVRSMVTAGLTDHMDHFSLGVLVILLMVQEGLKKRMTTKII
                     ISTSMAVLVAMILGGFSMSDLAKLAILMGATFAEMNTGGDVAHLALIAAFKVRPALLV
                     SFIFRANWTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAWLAIRAMVVPRTDN
                     ITLAILAALTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXALAGGFAKADIXMAGPMAAVGLLI
                     VSYVVSGKSVDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSXXXXXXXPMREI
                     ILKVVLMTICGMNPIAIPFAAGAWYVYVKTGKRSGALWDVPAPKEVKKGETTDGVYRV
                     MTRRLLGSTQVGVGVMQEGVFHTMWXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXTVILAPTRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEI
                     VDLMCHATFTSRLLQPIRVPNYNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXGKRVIQLSRKTFETEFQKTKHQEWDXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTDEDHAHWLE
                     ARMLLDNIYLQDGLIASLYRPEADKVAAIEGXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXDRRWCFDGTTNNTIMEDSVPAEVWTRHGEKRVLKPRWMDARVCSDXXX
                     XXXXXXXXXXXXXXALGVMEALGTLPGHMTERFQEAIDNLAVLMRAETGSRPYKAAAA
                     QMPETLETIMLLGLLGTVSLGIFFVLMRNKGIGKMGFGMVTLGASAWLMWLSEIEPAR
                     IACVLIVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTFITPAVQHAVTTSYNNYSLMAM
                     ATQAGVLFGMGKGMPFYAWDFGVPLLMIGCYSQLTPLTLIXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXGEAGALITAATSTLWEGSPNKYWNSSXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXGGTGETLGEKWKARLNQMSALEFYSYKKSGITEVCREEARRALKDGVATG
                     GHAVSRGSAKLRWLVERGYLQPHGKVIDLGCGRGXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXTMMETLERLQRRYGGGLVRVPLSRNSTHEMYXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXVVSCAEAPNMKIIGNRIE
                     RIRSEHAETWFFDENHPYRTXXXXXSYEAPTQGSASSLVNGVVRLLSKPWDVVTGVTG
                     IAMTDTTPYGQQRVFKEKVDTRVPDPQEGTRQVMSMVSSWLWKELGKHKRPRVCTKEE
                     FINKVRSNAALGAIFEEEKEWKTAVEAVNDPRFWALVDKEREHHLRGECQSCVYNMMG
                     KREKKQGEFGKAKGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXLLYFHRRDLRLMANAICSSVPVDWVPTGRTTXXXXXXXXX
                     XXXXXXXXXXXXXWIEENDHMEDKTPVTKWTDIPYLGKREDLWCGSLIGHRPRTTWAE
                     NIKNTVNMVRRIIGDEEKYMDYLSTQVRYLGEEGSTPGVL"
     mat_peptide     1..102
                     /product="capsid peptide"
     mat_peptide     103..372
                     /product="propeptide"
     mat_peptide     373..597
                     /product="membane protein peptide"
     mat_peptide     598..2112
                     /product="envelope protein peptide"
     mat_peptide     2113..3198
                     /product="NS1 peptide"
     mat_peptide     3199..3852
                     /product="NS2A peptide"
     mat_peptide     3853..4284
                     /product="NS2B peptide"
     mat_peptide     4285..6093
                     /product="NS3 peptide"
     mat_peptide     6094..6534
                     /product="NS4A peptide"
     mat_peptide     6535..8040
                     /product="NS4B peptide"
     mat_peptide     8041..9996
                     /product="NS5 peptide"
     gap             117..234
                     /estimated_length=118
     gap             401..983
                     /estimated_length=583
     gap             1048..1621
                     /estimated_length=574
     gap             1704..1986
                     /estimated_length=283
     gap             2080..2320
                     /estimated_length=241
     gap             2534..2726
                     /estimated_length=193
     gap             2809..3038
                     /estimated_length=230
     gap             3465..3566
                     /estimated_length=102
     gap             3644..3886
                     /estimated_length=243
     gap             4385..4885
                     /estimated_length=501
     gap             5075..5370
                     /estimated_length=296
     gap             5446..5668
                     /estimated_length=223
     gap             5793..5904
                     /estimated_length=112
     gap             6417..6675
                     /estimated_length=259
     gap             6866..7110
                     /estimated_length=245
     gap             7188..7290
                     /estimated_length=103
     gap             7543..7852
                     /estimated_length=310
     gap             7948..8082
                     /estimated_length=135
     gap             8700..9582
                     /estimated_length=883
     3'UTR           10000..10323
ORIGIN      
        1 ctgagaataa tcaatgctag gaaggagaag aagagacgag gcgcagatac tagtgtcgga
       61 attgttggcc tcctgctgac cacagctatg gcagcggagg tcactagacg tgggag   
          [gap 118 bp]    Expand Ns
      235                                                            accatg
      241 agctatgaat gccctatgct ggatgagggg gtggaaccag atgacgtcga ttgttggtgc
      301 aacacgacgt caacttgggt tgtgtacgga acctgccatc acaaaaaagg tgaagcacgg
      361 agatctagaa gagctgtgac gctcccctcc cattccaacc                     
          [gap 583 bp]    Expand Ns
      984                          catccag ccagagaatc tggagtaccg gataatgctg
     1021 tcagttcatg gctcccagca cagtggg                                   
          [gap 574 bp]    Expand Ns
     1622  cagctcaga tggcggtgga catgcaaact ctgaccccag ttgggaggtt gataaccgct
     1681 aaccccgtaa tcactgaaag cac                                       
          [gap 283 bp]    Expand Ns
     1987       tcac aaattctcat tggaacgttg ctgatgtggt tgggtctgaa cacaaagaat
     2041 ggatctattt cccttatgtg cttggcctta gggggagtg                      
          [gap 241 bp]    Expand Ns
     2321                                             tagaagggga gctcaacgca
     2341 atcctggaag agaatggagt tcaactgacg gtcgttgtgg gatctgtaaa aaaccccatg
     2401 tggagaggtc cacagagatt gcccgtgcct gtgaacgagc tgccccacgg ctggaaggct
     2461 tgggggaaat cgtacttcgt cagagcagca aagacaaata acagctttgt cgtggatggt
     2521 gacacactga agg                                                  
          [gap 193 bp]    Expand Ns
     2727                             gaat gacacatgga ggctgaagag ggcccatctg
     2761 atcgagatga aaacatgtga atggccaaag tcccacacat tgtggaca            
          [gap 230 bp]    Expand Ns
     3039                                          at ggtgctgcag ggagtgcaca
     3061 atgcccccac tgtcgttccg ggctaaagat ggctgttggt atggaatgga gannnnnnnn
     3121 nggaaagaac cagaaagcaa cttagtaagg tcaatggtga ctgcaggatt aactgatcac
     3181 atggatcact tctcccttgg agtgcttgtg attctgctca tggtgcagga agggctgaag
     3241 aagagaatga ccacaaagat catcataagc acatcaatgg cagtgctggt agctatgatc
     3301 ctgggaggat tttcaatgag tgacctggct aagcttgcaa ttttgatggg tgccaccttc
     3361 gcggaaatga acactggagg agatgtagct catctggcgc tgatagcggc attcaaagtc
     3421 agaccagcgt tgctggtatc tttcatcttc agagctaatt ggac                
          [gap 102 bp]    Expand Ns
     3567                             ggcc tggttggcaa tacgagcgat ggttgttcca
     3601 cgcactgata acatcacctt ggcaatcttg gctgctctga cac                 
          [gap 243 bp]    Expand Ns
     3887                                                   gcgc attggctgga
     3901 gggttcgcca aggcagatat agrgatggct gggcccatgg ccgcggtcgg tctgctaatt
     3961 gtcagttacg tggtctcagg aaagagtgtg gacatgtaca ttgaaagagc aggtgacatc
     4021 acatgggaaa aagatgcgga agtcactgga aacagtcccc ggctcgatgt ggcgctagat
     4081 gagagtggtg atttctccnn nnnnnnnnnn nnnnnnnncc ccatgagaga gatcatactc
     4141 aaggtggtcc tgatgaccat ctgtggcatg aacccaatag ccataccctt tgcagctgga
     4201 gcgtggtacg tatacgtgaa gactggaaaa aggagtggtg ctctatggga tgtgcctgct
     4261 cccaaggaag taaaaaaggg ggagaccaca gatggagtgt acagagtaat gactcgtaga
     4321 ctgctaggtt caacacaagt tggagtggga gttatgcaag agggggtctt tcacactatg
     4381 tggc                                                            
          [gap 501 bp]    Expand Ns
     4886                            gtact gtgatcttag ctccaaccag ggttgtcgct
     4921 gctgaaatgg aggaagccct tagagggctt ccagtgcgtt atatgacaac agcagtcaat
     4981 gtcacccact ctggaacaga aatcgtcgac ttaatgtgcc atgccacctt cacttcacgt
     5041 ctactacagc caatcagagt ccccaattat aatc                           
          [gap 296 bp]    Expand Ns
     5371                                  ggaaaacggg tcatacagct cagcagaaag
     5401 acttttgaga cagagttcca gaaaacaaaa catcaagagt gggac               
          [gap 223 bp]    Expand Ns
     5669                               ag actgacgaag accatgcaca ctggcttgaa
     5701 gcaagaatgc tccttgacaa tatttacctc caagatggcc tcatagcctc gctctatcga
     5761 cctgaggccg acaaagtagc agccattgag gg                             
          [gap 112 bp]    Expand Ns
     5905                           gataga agatggtgct ttgatggcac gaccaacaac
     5941 accataatgg aagacagtgt gccggcagag gtgtggacca gacacggaga gaaaagagtg
     6001 ctcaaaccga ggtggatgga tgccagagtt tgttcagatn nnnnnnnnnn nnnnnnnnnn
     6061 nnnnnnnnnn nnnnnnnnnn nnnnnnnnng gctcttggag tgatggaagc cctgggaaca
     6121 ctgccaggac acatgacaga gagattccag gaagccattg acaacctcgc tgtgctcatg
     6181 cgggcagaga ctggaagcag gccttacaaa gccgcggcgg cccaaatgcc ggagacccta
     6241 gagaccatta tgcttttggg gttgctagga acagtctcgc tgggaatctt tttcgtcttg
     6301 atgaggaaca agggcatagg gaagatgggc tttggaatgg tgactcttgg ggccagcgca
     6361 tggctcatgt ggctctcgga aattgagcca gccagaattg catgtgtcct cattgt   
          [gap 259 bp]    Expand Ns
     6676                 acttt cattacccca gccgtccaac atgcagtgac macttcatac
     6721 aacaactact ccttaatggc gatggccacg caagctggag tgttgtttgg tatgggcaaa
     6781 gggatgccat tctacgcatg ggactttgga gtcccgctgc taatgatagg ttgctactca
     6841 caattaacac ccctgaccct aatag                                     
          [gap 245 bp]    Expand Ns
     7111                                  ggggaggctg gggctctgat cacagccgca
     7141 acttccactt tgtgggaagg ctctccgaac aagtactgga actcctc             
          [gap 103 bp]    Expand Ns
     7291                                  ggtggaacag gagagaccct gggagagaaa
     7321 tggaaggccc gcttgaacca gatgtcggcc ctggagttct actcctacaa aaagtcaggc
     7381 atcaccgagg tgtgcagaga agaggcccgc cgcgccctca aggacggtgt ggcaacggga
     7441 ggccatgctg tgtcccgagg aagtgcaaag ctgagatggt tggtggagcg gggatacctg
     7501 cagccccatg gaaaggtcat tgatcttgga tgtggcagag gg                  
          [gap 310 bp]    Expand Ns
     7853                                                          gcactatg
     7861 atggaaaccc tggagcgact gcagcgtagg tatgggggag gactggtcag agtgccactc
     7921 tcccgcaact ctacacatga gatgtac                                   
          [gap 135 bp]    Expand Ns
     8083                                               gtggtaag ctgcgctgaa
     8101 gctcccaaca tgaagatcat tggtaaccgc attgaaagga tccgcagtga gcacgcggaa
     8161 acgtggttct ttgacgagaa ccacccatat aggacnnnnn nnnnnnnnng aagctatgag
     8221 gcccccacac aagggtcagc gtcctctcta gtaaacgggg ttgtcaggct cctgtcaaaa
     8281 ccctgggatg tggtgactgg agtcacagga atagccatga ccgacaccac accgtatggt
     8341 cagcaaagag ttttcaagga aaaagtggac actagggtgc cagaccccca agaaggcact
     8401 cgtcaggtta tgagcatggt ctcttcctgg ttgtggaaag agctaggcaa acacaaacgg
     8461 ccacgagtct gtaccaaaga agagttcatc aacaaggttc gtagcaatgc agcactaggg
     8521 gcaatatttg aagaggaaaa agagtggaag actgcagtgg aagctgtgaa cgatccaagg
     8581 ttctgggctc tagtggacaa ggaaagagag caccacctga gaggagagtg ccagagttgt
     8641 gtgtacaaca tgatgggaaa aagagaaaag aaacaagggg aatttggaaa ggccaaggg
          [gap 883 bp]    Expand Ns
     9583                                               ctccttta tttccacaga
     9601 agggacctcc gactgatggc caatgccatt tgctcatctg tgccagttga ctgggttcca
     9661 actgggagaa ctacctnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     9721 nnnnnnnnnn nnnnnnnnnn gtggattgag gagaacgacc acatggaaga caagacccca
     9781 gttacgaaat ggacagacat tccctatttg ggaaaaaggg aagacttgtg gtgtggatct
     9841 ctcatagggc acagaccgcg caccacctgg gctgagaaca ttaaaaacac agtcaacatg
     9901 gtgcgcagga tcataggtga tgaagaaaag tacatggact acctatccac ccaagttcgc
     9961 tacttgggtg aagaagggtc tacacctgga gtgctgtaag caccagnnnn nnnnnnnnnn
    10021 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nntgtgcagc ctgtgacccc cccaggagaa
    10081 gctgggaaac caagcctata gtcaggccga gaacgccatg gcacggaaga agccatgctg
    10141 cctgtgagcc cctcagagga cactgagtca aaaaacccca cgcgcttgga ggcgcaggat
    10201 gggaaaagaa ggtggcgacc ttccccaccc ttcaatctgg ggcctgaact ggagatcagc
    10261 tgtggatctc cagaagaggg actagtggtt agaggagacc ccccggaaaa cgcaaaacag
    10321 cat
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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
1063785944%0.0100%KX101062.1
1063780344%0.098%KU940228.1
1063780344%0.098%KU940224.1
1054775944%0.097%KX051563.1
1054777944%0.097%KU509998.3
1054773244%0.097%KU926310.1
1054762444%0.097%KU853013.1
1054761944%0.097%KU853012.1
1054775244%0.097%KU527068.1
1054768744%0.097%KU647676.1
1054734141%0.097%KU501217.1
1054734141%0.097%KU501216.1
1054735041%0.097%KU312312.1
1054772944%0.097%KJ776791.1
1049773844%0.097%KX117076.1
1049768444%0.097%KX087102.1
1049730741%0.097%KX056898.1
1049773244%0.097%KU963796.1
1049772544%0.097%KU991811.1
1049759944%0.097%KU955590.1
1049773244%0.097%KU870645.1
1049774344%0.097%KU926309.1
1049768244%0.097%KU922960.1
1049768244%0.097%KU922923.1
1049724741%0.097%KU866423.1
1049731041%0.097%KU820898.1
1049757443%0.097%KU740184.2
1049772744%0.097%KU820899.2
1049772944%0.097%KU820897.1
1049776344%0.097%KU729218.1
1049737341%0.097%KU761564.1
1049772144%0.097%KU707826.1
1049770544%0.097%KU365780.1
1049771444%0.097%KU365779.1
1049772744%0.097%KU365778.1
1049770544%0.097%KU365777.1
1049772344%0.097%KU321639.1
1045774944%0.097%KX087101.1
1045761344%0.097%KU955589.1
1045769844%0.097%KU729217.2
1045770044%0.097%KU501215.1
1040773444%0.097%KU497555.1
1036761544%0.097%KU681081.3
1036713441%0.097%KF993678.1
1032621534%0.096%KX101060.1
1031747444%0.097%KU955593.1
1031706941%0.097%JN860885.1
1031702041%0.097%EU545988.1
1012734344%0.096%KU681082.3
1012763944%0.096%KU744693.1
9809805%0.096%KT200609.1
940748842%0.092%KU940227.1
904653141%0.092%HQ234499.1
886710842%0.092%KX101064.1
886615836%0.092%KX101061.1
872608635%0.092%KX101066.1
82012697%0.096%KU740199.1
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LOCUS       KX101063               10440 bp    RNA     linear   VRL 26-APR-2016
DEFINITION  Zika virus isolate Bahia05, partial genome.
ACCESSION   KX101063
VERSION     KX101063.1  GI:1022831295
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10440)
  AUTHORS   Naccache,S.N., Theze,J., Sardi,S.I., Somasekar,S., Greninger,A.L.,
            Bandeira,A.C., Campos,G.S., Tauro,L.B., Faria,N.R., Pybus,O.G. and
            Chiu,C.Y.
  TITLE     Discovery of a persistent Zika virus lineage in Bahia, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10440)
  AUTHORS   Naccache,S.N., Somasekar,S., Sardi,S.I., Bandeira,A.C., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-APR-2016) Laboratory Medicine, University of
            California, San Francisco, 185 Berry Street, #0134, San Francisco,
            CA 94107, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SURP+ v. 1.0 2016; Geneious v. 6.1.8
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10440
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="Bahia05"
                     /isolation_source="serum"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="Dec-2015"
     CDS             <1..>10103
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ANA85190.1"
                     /db_xref="GI:1022831296"
                     /translation="FLRFTAIKPSLGLINRWGSVGKKEAMEIIKXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXTMSYECPMLDEGVEPDDVDCWCNTTSTWVVYGTCHHKKGEARR
                     SXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXLKCRLKMDKLRLKGVSYSLCNAAFTFTKIPAETLHGTVTV
                     EVQYXXXXXXXXXXAQMAVDMQTLTPVGRLITAXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXQILIGTLLMWLGLNTKNGSISLMCLALGGVXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXRGPQRLPVPVNELPHG
                     WKAWGKSYFVRAAKTNNSFVVDGDTLKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPWHSEELEIRFEECPGTKXXXX
                     XXXXXXXXXXXXXXXXXXXXXXWCCRECTMPPLSFRAKDGCWYGMEXXXXKEPESNLV
                     RSMVTAGSTDHMDHFSLGVLVILLMVQEGLKKRMTTKIIISTSMAVLVXXXXXXXXXX
                     XXXXXXXXXXATFAEMNTGGDVAHLALIAAFKVRPALLVSFIFRANWTXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXLINGFALAWLAIRAMVVPRTDNITLAILAALTPLARGTLLM
                     AWRAGLATCGGFMLLSLKGKGSVKKNLPFVMALGLTAVRLVDPINVVGLLLLTRSGKR
                     SWPPSEVLTAVGLICALAGGFAKADIEMAGPMAAVGLLIVSYVVSGKSVDMYIERAGD
                     ITWEKDAEVTGNSPRLDVALDESGDFSLVEDDGPPMREIILKVVLMTICGMNPIAIPF
                     AAGAWXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXVGVMQEG
                     VFHTMWHVTKGSALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGHSEVQLXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXMLKKKQLTVLDLHPGAGKTXXXXXXXVREAIKTRLR
                     TVILAPTRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRV
                     PNYNLYIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXVWFVPSVRNGNEIAACLTKAGXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXTDEDHAHWLEARMLLDNIYLQDGLIASLY
                     RPEADKVAAIEGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGITYTDRRWCFDGT
                     TNNTIMEDSVPAEVWTRHGEKRVLKPRWMDARVCSDXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXNKGIGKMGFGMVTLGASAWLMWLSEIEPARIACVLIVVFLLLVVLIPEP
                     EKQRSPQDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXTFITPAVQHAVTTSYNNYSLMAMATQAGVLFGMGKGMPFYAW
                     DFGVPLLMIGCYSQLTPLTLIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGEAGALITAATST
                     LWEGSPNKYWNSSTATSLCNIFRGSYLAGASLIYTVTRNAGLVKRRGGGTGETLGEKW
                     KXXXXXXXXXXXXXXXXXXXXXVCREEARRALKDGVATGGHAVSRGSAKLRWLVERGY
                     LQPHGKVIDLGCGRGGWSYYAATIRKVQEVKGXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXCDIGESSSSPEVEEARTLRVXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXPLSRNSTHEMYWVSGAKSNTIKSVSTXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXVVSCAEAPNMKIIGNRIERIRSEHAETWFFDENHPYR
                     TXXXXXSYEAPTQGSASSLVNGVVRLLSKPWDVVTGVTGIAMTDTTPYGXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXAVNDPRFWALVDKEREHHLRGECQSCVYNMMGKREKKQGEFGKAKGXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXRMYAD
                     DTAGWDTRISXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTQEWKPSTGWDNWEEV
                     PFCSHHFNKLHLKDGRSIVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIHGKGEWMTTEDMLVVWNRVWIEEND
                     HMEDKTPVTKWTDIPYLGKREDLWCGSLIGHRPRTTWAXXXXXXXXXXXXIIGDEEKY
                     MDYLSTQVRYLGEEGSTP"
     mat_peptide     1..219
                     /product="capsid peptide"
     mat_peptide     220..489
                     /product="propeptide"
     mat_peptide     490..714
                     /product="membane protein peptide"
     mat_peptide     715..2229
                     /product="envelope protein peptide"
     mat_peptide     2230..3315
                     /product="NS1 peptide"
     mat_peptide     3316..3969
                     /product="NS2A peptide"
     mat_peptide     3970..4401
                     /product="NS2B peptide"
     mat_peptide     4402..6210
                     /product="NS3 peptide"
     mat_peptide     6211..6651
                     /product="NS4A peptide"
     mat_peptide     6652..8157
                     /product="NS4B peptide"
     mat_peptide     8158..10103
                     /product="NS5 peptide"
     gap             93..351
                     /estimated_length=259
     gap             486..1577
                     /estimated_length=1092
     gap             1798..2104
                     /estimated_length=307
     gap             2197..2518
                     /estimated_length=322
     gap             2651..3024
                     /estimated_length=374
     gap             4326..4459
                     /estimated_length=134
     gap             4642..4894
                     /estimated_length=253
     gap             5202..5426
                     /estimated_length=225
     gap             5493..5785
                     /estimated_length=293
     gap             6157..6422
                     /estimated_length=266
     gap             6595..6792
                     /estimated_length=198
     gap             6983..7227
                     /estimated_length=245
     gap             7711..7835
                     /estimated_length=125
     gap             7896..8031
                     /estimated_length=136
     gap             8458..8679
                     /estimated_length=222
     gap             8817..8991
                     /estimated_length=175
     gap             9039..9478
                     /estimated_length=440
     gap             9585..9798
                     /estimated_length=214
     3'UTR           <10131..10440
ORIGIN      
        1 tttttgagat tcacggcaat caagccatca ctgggtctca tcaatagatg gggttcagtg
       61 gggaaaaaag aggctatgga aataataaag aa                             
          [gap 259 bp]    Expand Ns
      352                                                         accatgagc
      361 tatgaatgcc ctatgctgga tgagggggtg gaaccagatg acgtcgattg ttggtgcaac
      421 acgacgtcaa cttgggttgt gtacggaacc tgccatcaca aaaaaggtga agcacggaga
      481 tctag                                                           
          [gap 1092 bp]    Expand Ns
     1578                   ctt gaaatgtcgc ctgaaaatgg ataaacttag attgaagggc
     1621 gtgtcatact ccttgtgtaa cgcagcgttc acattcacca agatcccggc tgaaacactg
     1681 cacgggacag tcacagtgga ggtacagtac nnnnnnnnnn nnnnnnnnnn nnnnnnnnca
     1741 gctcagatgg cggtggacat gcaaactctg accccagttg ggaggttgat aaccgct  
          [gap 307 bp]    Expand Ns
     2105     cacaaa ttctcattgg aacgttgctg atgtggttgg gtctgaacac aaagaatgga
     2161 tctatttccc ttatgtgctt ggccttaggg ggagtg                         
          [gap 322 bp]    Expand Ns
     2519                                                                gg
     2521 agaggtccac agagattgcc cgtgcctgtg aacgagctgc cccacggctg gaaggcttgg
     2581 gggaaatcgt acttcgtcag agcagcaaag acaaataaca gctttgtcgt ggatggtgac
     2641 acactgaagg                                                      
          [gap 374 bp]    Expand Ns
     3025                           ccatgg cacagtgaag agcttgaaat tcggtttgag
     3061 gaatgcccag gcactaaggn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     3121 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnatggt gctgcaggga gtgcacaatg
     3181 cccccactgt cgttccgggc taaagatggc tgttggtatg gaatggagan nnnnnnnngg
     3241 aaagaaccag aaagcaactt agtaaggtca atggtgactg caggatcaac tgatcacatg
     3301 gatcacttct cccttggagt gcttgtgatt ctgctcatgg tgcaggaagg gctgaagaag
     3361 agaatgacca caaagatcat cataagcaca tcaatggcag tgctggtann nnnnnnnnnn
     3421 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnngtgc caccttcgcg
     3481 gaaatgaaca ctggaggaga tgtagctcat ctggcgctga tagcggcatt caaagtcaga
     3541 ccagcgttgc tggtatcttt catcttcaga gctaattgga cnnnnnnnnn nnnnnnnnnn
     3601 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     3661 nnnctcatca atggttttgc tttggcctgg ttggcaatac gagcgatggt tgttccacgc
     3721 actgataaca tcaccttggc aatcttggct gctctgacac cactggcccg gggcacactg
     3781 cttatggcgt ggagagcagg ccttgctact tgcggggggt ttatgctcct ctctctgaag
     3841 ggaaaaggca gtgtgaagaa gaacttacca tttgtcatgg ccctgggact aaccgctgtg
     3901 aggctggtcg accccatcaa cgtggtggga ctgctgttgc tcacaaggag tgggaagcgg
     3961 agctggcccc ctagcgaagt actcacagct gttggcctga tatgcgcatt ggctggaggg
     4021 ttcgccaagg cagatataga gatggctggg cccatggccg cggtcggtct gctaattgtc
     4081 agttacgtgg tctcaggaaa gagtgtggac atgtacattg aaagagcagg tgacatcaca
     4141 tgggaaaaag atgcggaagt cactggaaac agtccccggc tcgatgtggc gctagatgag
     4201 agtggtgatt tctccctggt ggaggatgac ggtcccccca tgagagagat catactcaag
     4261 gtggtcctga tgaccatctg tggcatgaac ccaatagcca taccctttgc agctggagcg
     4321 tggta                                                           
          [gap 134 bp]    Expand Ns
     4460                     g agtgggagtt atgcaagagg gggtctttca cactatgtgg
     4501 cacgtcacaa aaggatccgc gctgagaagc ggtgaaggga gacttgatcc atactgggga
     4561 gatgtcaagc aggatctggt gtcatactgt ggtccatgga agctagatgc cgcctgggac
     4621 gggcacagcg aggtgcagct c                                         
          [gap 253 bp]    Expand Ns
     4895                                      cgatgc tgaagaagaa gcagctaact
     4921 gtcttagact tgcatcctgg agctgggaaa accnnnnnnn nnnnnnnnnn nntagtccgt
     4981 gaagccataa aaacaagact ccgtactgtg atcttagctc caaccagggt tgtcgctgct
     5041 gaaatggagg aagcccttag agggcttcca gtgcgttata tgacaacagc agtcaatgtc
     5101 acccactctg gaacagaaat cgtcgactta atgtgccatg ccaccttcac ttcacgtcta
     5161 ctacagccaa tcagagtccc caattataat ctgtatatta t                   
          [gap 225 bp]    Expand Ns
     5427                             agtt tggtttgttc caagcgtgag gaacggcaat
     5461 gagatcgcag cttgtctgac aaaggctgga aa                             
          [gap 293 bp]    Expand Ns
     5786                            agact gacgaagacc atgcacactg gcttgaagca
     5821 agaatgctcc ttgacaatat ttacctccaa gatggcctca tagcctcgct ctatcgacct
     5881 gaggccgaca aagtagcagc cattgagggn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     5941 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     6001 nnnnnnggaa taacctacac agatagaaga tggtgctttg atggcacgac caacaacacc
     6061 ataatggaag acagtgtgcc ggcagaggtg tggaccagac acggagagaa aagagtgctc
     6121 aaaccgaggt ggatggatgc cagagtttgt tcagat                         
          [gap 266 bp]    Expand Ns
     6423   gaacaagg gcatagggaa gatgggcttt ggaatggtga ctcttggggc cagcgcatgg
     6481 ctcatgtggc tctcggaaat tgagccagcc agaattgcat gtgtcctcat tgttgtgttc
     6541 ctattgctgg tggtgctcat acctgagcca gaaaagcaaa gatctcccca ggac     
          [gap 198 bp]    Expand Ns
     6793              actttcat taccccagcc gtccaacatg cagtgaccac ttcatacaac
     6841 aactactcct taatggcgat ggccacgcaa gctggagtgt tgtttggtat gggcaaaggg
     6901 atgccattct acgcatggga ctttggagtc ccgctgctaa tgataggttg ctactcacaa
     6961 ttaacacccc tgaccctaat ag                                        
          [gap 245 bp]    Expand Ns
     7228                              ggg gaggctgggg ctctgatcac agccgcaact
     7261 tccactttgt gggaaggctc tccgaacaag tactggaact cctctacagc cacttcactg
     7321 tgtaacattt ttaggggaag ttacttggct ggagcttctc taatctacac agtaacaaga
     7381 aacgctggct tggtcaagag acgtgggggt ggaacaggag agaccctggg agagaaatgg
     7441 aaggnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     7501 nnnnnggtgt gcagagaaga ggcccgccgc gccctcaagg acggtgtggc aacgggaggc
     7561 catgctgtgt cccgaggaag tgcaaagctg agatggttgg tggagcgggg atacctgcag
     7621 ccccatggaa aggtcattga tcttggatgt ggcagagggg gctggagtta ctacgccgcc
     7681 accatccgca aagttcaaga agtgaaagga                                
          [gap 125 bp]    Expand Ns
     7836                                       gtgtg acataggtga gtcatcatct
     7861 agtcctgaag tggaagaagc acggacgctc agagt                          
          [gap 136 bp]    Expand Ns
     8032                                                         ccactctcc
     8041 cgcaactcta cacatgagat gtactgggtc tctggagcga aaagcaacac cataaaaagt
     8101 gtgtccaccn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     8161 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnng tggtaagctg cgctgaagct
     8221 cccaacatga agatcattgg taaccgcatt gaaaggatcc gcagtgagca cgcggaaacg
     8281 tggttctttg acgagaacca cccatatagg acnnnnnnnn nnnnnngaag ctatgaggcc
     8341 cccacacaag ggtcagcgtc ctctctagta aacggggttg tcaggctcct gtcaaaaccc
     8401 tgggatgtgg tgactggagt cacaggaata gccatgaccg acaccacacc gtatggt  
          [gap 222 bp]    Expand Ns
     8680                                           g ctgtgaacga tccaaggttc
     8701 tgggctctag tggacaagga aagagagcac cacctgagag gagagtgcca gagttgtgtg
     8761 tacaacatga tgggaaaaag agaaaagaaa caaggggaat ttggaaaggc caaggg   
          [gap 175 bp]    Expand Ns
     8992                                                         aggatgtat
     9001 gcagatgaca ctgctggctg ggacacccgc atcagcag                       
          [gap 440 bp]    Expand Ns
     9479                                                                ac
     9481 acacaagagt ggaaaccctc aactggatgg gacaactggg aagaagttcc gttttgctcc
     9541 caccacttca acaagctcca tctcaaggac gggaggtcca ttgt                
          [gap 214 bp]    Expand Ns
     9799                    at ccatggaaag ggagaatgga tgaccactga agacatgctt
     9841 gtggtgtgga acagagtgtg gattgaggag aacgaccaca tggaagacaa gaccccagtt
     9901 acgaaatgga cagacattcc ctatttggga aaaagggaag acttgtggtg tggatctctc
     9961 atagggcaca gaccgcgcac cacctgggcn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
    10021 nnnnggatca taggtgatga agaaaagtac atggactacc tatccaccca agttcgctac
    10081 ttgggtgaag aagggtctac accnnnnnnn nnnnnnnnnn nnnnnnnnnn gttgtcaggc
    10141 ctgctagtca gccacagctt ggggaaagct gtgcagcctg tgaccccccc aggagaagct
    10201 gggaaaccaa gcctatagtc aggccgagaa cgccatggca cggaagaagc catgctgcct
    10261 gtgagcccct cagaggacac tgagtcaaaa aaccccacgc gcttggaggc gcaggatggg
    10321 aaaagaaggt ggcgaccttc cccacccttc aatctggggc ctgaactgga gatcagctgt
    10381 ggatctccag aagagggact agtggttaga ggagaccccc cggaaaacgc aaaacagcat
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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
1195802444%0.0100%KX101063.1
1189796844%0.099%KU940228.1
1186792744%0.099%KX087101.1
1186796544%0.099%KU940224.1
1186795244%0.099%KU926310.1
1186796544%0.099%KU729218.1
1186790244%0.099%KU707826.1
1186795044%0.099%KU527068.1
1186742941%0.099%KU501217.1
1186742541%0.099%KU501216.1
1186788444%0.099%KU501215.1
1186788944%0.099%KU365780.1
1186789444%0.099%KU365779.1
1186788544%0.099%KU365777.1
1186746942%0.099%KU312312.1
1186792344%0.099%KJ776791.1
1180793044%0.099%KX117076.1
1180794544%0.099%KX051563.1
1180796644%0.099%KU509998.3
1180793044%0.099%KU963796.1
1180791144%0.099%KU991811.1
1180781044%0.099%KU955589.1
1180791244%0.099%KU870645.1
1180739341%0.099%KU866423.1
1180779944%0.099%KU853013.1
1180779744%0.099%KU853012.1
1180793044%0.099%KU820899.2
1180790944%0.099%KU729217.2
1180780144%0.099%KU744693.1
1180792144%0.099%KU321639.1
1177790344%0.099%KX087102.1
1177795644%0.099%KU926309.1
1177740741%0.099%KU820898.1
1177775544%0.099%KU740184.2
1177794844%0.099%KU820897.1
1177746942%0.099%KU761564.1
1177197411%0.099%KU740199.1
1177795644%0.099%KU497555.1
1177790944%0.099%KU365778.1
1171740241%0.099%KX056898.1
1171778444%0.099%KU955590.1
1171789344%0.099%KU922960.1
1171789344%0.099%KU922923.1
1171789644%0.099%KU647676.1
1153782444%0.099%KU681081.3
1135723641%0.098%KF993678.1
1133718641%0.098%JN860885.1
1131768544%0.098%KU955593.1
1130774343%0.097%KU940227.1
1117753244%0.097%KU681082.3
1090712841%0.097%EU545988.1
1072661841%0.096%HQ234499.1
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LOCUS       KX101064               10735 bp    RNA     linear   VRL 26-APR-2016
DEFINITION  Zika virus isolate Bahia11, partial genome.
ACCESSION   KX101064
VERSION     KX101064.1  GI:1022831297
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10735)
  AUTHORS   Naccache,S.N., Theze,J., Sardi,S.I., Somasekar,S., Greninger,A.L.,
            Bandeira,A.C., Campos,G.S., Tauro,L.B., Faria,N.R., Pybus,O.G. and
            Chiu,C.Y.
  TITLE     Discovery of a persistent Zika virus lineage in Bahia, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10735)
  AUTHORS   Naccache,S.N., Somasekar,S., Sardi,S.I., Bandeira,A.C., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-APR-2016) Laboratory Medicine, University of
            California, San Francisco, 185 Berry Street, #0134, San Francisco,
            CA 94107, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SURP+ v. 1.0 2016; Geneious v. 6.1.8
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10735
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="Bahia11"
                     /isolation_source="serum"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="Apr-2015"
     5'UTR           1..>79
     gap             80..378
                     /estimated_length=299
     CDS             <379..10378
                     /codon_start=2
                     /product="polyprotein"
                     /protein_id="ANA85191.1"
                     /db_xref="GI:1022831298"
                     /translation="LRIINARKEKKRRGADTSVGIVGLLLTTAMAAEVTRRGSAYYMY
                     LDRNDAGEAISFPTTLGMNKCYIXXXXXXXXXXXTMSYECPMLDEGVEPDDVDCWCNT
                     TSTWVVYGTCHHKKGEARRSRRAVTLPSHSXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXILLIAPAYSIRCIGVSNRDFVEGMSGGT
                     WVDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXVNDTGHETDENRAKVEITXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLKCRLKMDKLRLKGVSYSLCN
                     AAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITE
                     STENSKMMLELDPPFGDSYIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXQILIGTLLMWLGLNTKNGS
                     VSLMCLALGGVLIFLSTAVSADVGCSVDFSKKETRCGTGVFVYNDVEAWRDRYKYHPD
                     SPRRLAAAVKQAWEDGICGISSVSRMENIMWRSVEGELNAILEENGVQLTVVVGSVKN
                     PMWRGPQRLPVPVNELPHGWKAWGKSYFVRAAKTNNSFVVDGDTLKXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAVKGKEAVHSDLGYWIESEKNDTWR
                     LKRAHLIEMKTCEWPKSHTLWTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXWCCRECTMPPLSFRAKD
                     GCWYGMEXXXXKEPESNLVRSMVTAGSTDHMDHFSLGVLVILLMVQEGLKKRMTTKII
                     ISTSMAVLVAMILGGFSMSDLAKLAILMGATFAEMNTGGDVAHLALIAAFKVRPALLV
                     SFIFRANWTXXXSMLLALASCLLQTAISALEGDLMVLINGFALAWLAIRAMVVPRTDN
                     ITLAILAALTPLARGTLLVAWRAGLATCGGFMLLSLKGKGSVKKNLPFVXXXXXXXXX
                     XXXXXXVVGLLLLTRSGKRSWPPSEVLTAVGLICALAGGFAKADIEMAGPMAAVGLLI
                     VSYVVSGKSVDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSXXXXXXXPMREI
                     ILKVVLMTICGMNPIAIPFAAGAWXXXXXXXXXXXXXXDVPAPKEVKKGETTDGVYRV
                     MTRRLLGSTQVGVGVMQEGVFHTMWHVTKGSALRSGEGRLDPYWGDVKQDLVSYCGPW
                     KLDAAWDGHSEVQLLAVPPGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXVREAIKTRLRTVILAPTRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEI
                     VDLMCHATFTSRLLQPIRVPNYNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXGKRVIQLSRKTFETEFQKTKHQEWDXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLYGGGCAETDEDHAHWLE
                     ARMLLDNIYLQDGLIASLYRPEADKVAAIEGXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXDRRWCFDGTTNNTIMEDSVPAEVWTRHGEKRVLKPRWMDARVCSDHAA
                     LKSFKEFAAGKRGAAFGVMEALGTXXXXXXXXXXXXXXXXXVLMRAETGSRPYKAAAA
                     QMPETLETIMLLGLLGTVSLGIFFVLMRNKGIGKMGFGMVTLGASAWLMWLSEIEPAR
                     IACVLIVVFLLLVVLIPEPEKQRSPQDNQMAIIIMVAVGLLGLITAXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTFITPAVQHAVTTSYNNYSLMAM
                     ATQAGVLFGMGKGMPFYAWDFGVPLLMIGCYSQLTPLTLIVAIILLVAHYMYLXXXXX
                     AAAARAAQKRTAAGIMKNPVVDGIVVTDIDTMTIDPQVEKKMGQVLLIAXXXXXXXXX
                     XXXXXXGEAGALITAATSTLWEGSPNKYWNSSXXXXXXXXXXXXXXXXXXXIYTVTRN
                     AGLVKRRGGGTGETLGEKWKARLNXXXXXXXXXXXXXXXXXVCREEARRALKDGVATG
                     GHAVSRGSAKLRWLVERGYLQPHGKVIDLGCGRGGWSYYAATIRKVQEVKGXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXTMMETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGA
                     KSNTIKSVSTTSQLLLGRMDGPRRPVKYEEDVNLGSGXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXTWAYHGSYEAPTQGSASSLVNGVVRLLSKPWDVVTGVTG
                     IAMTDTTPYGQQRVFXXKVDTRVPDPQEGTRQVMSMVSSWLWKELGKHKRPRVCTKEE
                     FINKVRSNAALGAIFEEEKEWKTAVEAVNDPRFWALVDKEREHHLRGECQSCVYNMMG
                     KREKKQGEFGKAKGSRAIWYMWLGARFLEFEALGFLNEDHWMGRENSGGGVEGLGLQR
                     LGYVLEEMSRIPGGRMYADDTAGWDTRISRFDLENEALITNQMEKGHRALALAIIKYT
                     YQNKVVKVLRPAEKGKTVMDIISRQDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGKV
                     RKDTQEWKPSTGWDNWEEVPFCSHHFNXXXXXXXXXXXXXXRHQDELIGRARVSPGAG
                     WSIRETACLAKSYAQMWQLLYFHRRDLRLMANAICSSVPVDWVPTGRTTWSIHGKGEW
                     MTTEDMLVVWNRVWIEENDHMEDKTPVTKWTDIPYLGKREDLWCGSLIGHRPRTTWAE
                     NIKNTVNMVRRIIGDEEKYMDYLSTQVRYLGEEGSTPGVL"
     mat_peptide     380..481
                     /product="capsid peptide"
     mat_peptide     482..751
                     /product="propeptide"
     mat_peptide     752..976
                     /product="membane protein peptide"
     mat_peptide     977..2491
                     /product="envelope protein peptide"
     mat_peptide     2492..3577
                     /product="NS1 peptide"
     mat_peptide     3578..4231
                     /product="NS2A peptide"
     mat_peptide     4232..4663
                     /product="NS2B peptide"
     mat_peptide     4664..6472
                     /product="NS3 peptide"
     mat_peptide     6473..6913
                     /product="NS4A peptide"
     mat_peptide     6914..8419
                     /product="NS4B peptide"
     mat_peptide     8420..10375
                     /product="NS5 peptide"
     gap             777..947
                     /estimated_length=171
     gap             1044..1430
                     /estimated_length=387
     gap             1486..1839
                     /estimated_length=354
     gap             2139..2366
                     /estimated_length=228
     gap             2913..3046
                     /estimated_length=134
     gap             3188..3417
                     /estimated_length=230
     gap             4923..5234
                     /estimated_length=312
     gap             5454..5749
                     /estimated_length=296
     gap             5825..6025
                     /estimated_length=201
     gap             6172..6283
                     /estimated_length=112
     gap             6915..7054
                     /estimated_length=140
     gap             7973..8231
                     /estimated_length=259
     gap             8454..8570
                     /estimated_length=117
     gap             9465..9722
                     /estimated_length=258
     3'UTR           10379..10735
ORIGIN      
        1 gttgttgatc tgtgtgaatc agactgcgac agttcgagtt tgaagcgaaa gctagcaaca
       61 gtatcaacag gttttattt                                            
          [gap 299 bp]    Expand Ns
      379                    gc tgagaataat caatgctagg aaggagaaga agagacgagg
      421 cgcagatact agtgtcggaa ttgttggcct cctgctgacc acagctatgg cagcggaggt
      481 cactagacgt gggagtgcat actatatgta cttggacaga aacgatgctg gggaggccat
      541 atcttttcca accacattgg ggatgaataa gtgttatata cnnnnnnnnn nnnnnnnnnn
      601 nnnnnnnnnn nncaccatga gctatgaatg ccctatgctg gatgaggggg tggaaccaga
      661 tgacgtcgat tgttggtgca acacgacgtc aacttgggtt gtgtacggaa cctgccatca
      721 caaaaaaggt gaagcacgga gatctagaag agctgtgacg ctcccctccc attcca   
          [gap 171 bp]    Expand Ns
      948                                                    tga tactgctgat
      961 tgccccggca tacagcatca ggtgcatagg agtcagcaat agggactttg tggaaggtat
     1021 gtcaggtggg acttgggttg atg                                       
          [gap 387 bp]    Expand Ns
     1431                                                        tcgttaatga
     1441 cacaggacat gaaactgatg agaatagagc gaaggttgag ataac               
          [gap 354 bp]    Expand Ns
     1840                                           c ttgaaatgtc gcctgaaaat
     1861 ggataaactt agattgaagg gcgtgtcata ctccttgtgt aacgcagcgt tcacattcac
     1921 caagatcccg gctgaaacac tgcacgggac agtcacagtg gaggtacagt acgcagggac
     1981 tgatggacct tgcaaggttc cagctcagat ggcggtggac atgcaaactc tgaccccagt
     2041 tgggaggttg ataaccgcta accccgtaat cactgaaagc actgagaact ctaagatgat
     2101 gctggaactt gatccaccat ttggggactc ctacattg                       
          [gap 228 bp]    Expand Ns
     2367                             caca aattctcatt ggaacgttgc tgatgtggtt
     2401 gggtctgaac acaaagaatg gatctgtttc ccttatgtgc ttggccttag ggggagtgtt
     2461 gatcttctta tccacagccg tctctgctga tgtggggtgc tcggtggact tctcaaagaa
     2521 ggagacgaga tgcggtacag gggtgttcgt ctataacgac gttgaagcct ggagggacag
     2581 gtacaagtac catcctgact ccccccgtag attggcagca gcagtcaagc aagcctggga
     2641 agatggtatc tgcgggatct cctctgtttc aagaatggaa aacatcatgt ggagatcagt
     2701 agaaggggag ctcaacgcaa tcctggaaga gaatggagtt caactgacgg tcgttgtggg
     2761 atctgtaaaa aaccccatgt ggagaggtcc acagagattg cccgtgcctg tgaacgagct
     2821 gccccacggc tggaaggctt gggggaaatc gtacttcgtc agagcagcaa agacaaataa
     2881 cagctttgtc gtggatggtg acacactgaa gg                             
          [gap 134 bp]    Expand Ns
     3047                                                   gctg ttaagggaaa
     3061 ggaggctgta cacagtgatc taggctactg gattgagagt gagaagaatg acacatggag
     3121 gctgaagagg gcccatctga tcgagatgaa aacatgtgaa tggccaaagt cccacacatt
     3181 gtggaca                                                         
          [gap 230 bp]    Expand Ns
     3418                                                               atg
     3421 gtgctgcagg gagtgcacaa tgcccccact gtcgttccgg gctaaagatg gctgttggta
     3481 tggaatggag annnnnnnnn ggaaagaacc agaaagcaac ttagtaaggt caatggtgac
     3541 tgcaggatca actgatcaca tggatcactt ctcccttgga gtgcttgtga ttctgctcat
     3601 ggtgcaggaa gggctgaaga agagaatgac cacaaagatc atcataagca catcaatggc
     3661 agtgctggta gctatgatcc tgggaggatt ttcaatgagt gacctggcta agcttgcaat
     3721 tttgatgggt gccaccttcg cggaaatgaa cactggagga gatgtagctc atctggcgct
     3781 gatagcggca ttcaaagtca gaccagcgtt gctggtatct ttcatcttca gagctaattg
     3841 gacnnnnnnn naaagcatgc tgctggcctt ggcctcgtgt cttttgcaaa ctgcgatctc
     3901 cgccttggaa ggcgacctga tggttctcat caatggtttt gctttggcct ggttggcaat
     3961 acgagcgatg gttgttccac gcactgataa catcaccttg gcaatcttgg ctgctctgac
     4021 accactggcc cggggcacac tgcttgtggc gtggagagca ggccttgcta cttgcggggg
     4081 gtttatgctc ctctctctga agggaaaagg cagtgtgaag aagaacttac catttgtcnn
     4141 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nacgtggtgg gactgctgtt
     4201 gctcacaagg agtgggaagc ggagctggcc ccctagcgaa gtactcacag ctgttggcct
     4261 gatatgcgca ttggctggag ggttcgccaa ggcagatata gagatggctg ggcccatggc
     4321 cgcggtcggt ctgctaattg tcagttacgt ggtctcagga aagagtgtgg acatgtacat
     4381 tgaaagagca ggtgacatca catgggaaaa agatgcggaa gtcactggaa acagtccccg
     4441 gctcgatgtg gcgctagatg agagtggtga tttctccnnn nnnnnnnnnn nnnnnnnccc
     4501 catgagagag atcatactca aggtggtcct gatgaccatc tgtggcatga acccaatagc
     4561 catacccttt gcagctggag cgtggtannn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     4621 nnnnnnggat gtgcctgctc ccaaggaagt aaaaaagggg gagaccacag atggagtgta
     4681 cagagtaatg actcgtagac tgctaggttc aacacaagtt ggagtgggag ttatgcaaga
     4741 gggggtcttt cacactatgt ggcacgtcac aaaaggatcc gcgctgagaa gcggtgaagg
     4801 gagacttgat ccatactggg gagatgtcaa gcaggatctg gtgtcatact gtggtccatg
     4861 gaagctagat gccgcctggg acgggcacag cgaggtgcag ctcttggccg tgccccccgg
     4921 ag                                                              
          [gap 312 bp]    Expand Ns
     5235                tagtcc gtgaagccat aaaaacaaga ctccgtactg tgatcttagc
     5281 tccaaccagg gttgtcgctg ctgaaatgga ggaagccctt agagggcttc cagtgcgtta
     5341 tatgacaaca gcagtcaatg tcacccactc tggaacagaa atcgtcgact taatgtgcca
     5401 tgccaccttc acttcacgtc tactacagcc aatcagagtc cccaattata atc      
          [gap 296 bp]    Expand Ns
     5750                                                      g gaaaacgggt
     5761 catacagctc agcagaaaga cttttgagac agagttccag aaaacaaaac atcaagagtg
     5821 ggac                                                            
          [gap 201 bp]    Expand Ns
     6026                            ctgta tggaggtggg tgcgcagaga ctgacgaaga
     6061 ccatgcacac tggcttgaag caagaatgct ccttgacaat atttacctcc aagatggcct
     6121 catagcctcg ctctatcgac ctgaggccga caaagtagca gccattgagg g        
          [gap 112 bp]    Expand Ns
     6284                                                gatagaa gatggtgctt
     6301 tgatggcacg accaacaaca ccataatgga agacagtgtg ccggcagagg tgtggaccag
     6361 acacggagag aaaagagtgc tcaaaccgag gtggatggat gccagagttt gttcagatca
     6421 tgcggccctg aagtcattca aggagtttgc cgctgggaaa agaggagcgg cttttggagt
     6481 gatggaagcc ctgggaacac nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     6541 nnnnnnnnnn gtgctcatgc gggcagagac tggaagcagg ccttacaaag ccgcggcggc
     6601 ccaaatgccg gagaccctag agaccattat gcttttgggg ttgctaggaa cagtctcgct
     6661 gggaatcttt ttcgtcttga tgaggaacaa gggcataggg aagatgggct ttggaatggt
     6721 gactcttggg gccagcgcat ggctcatgtg gctctcggaa attgagccag ccagaattgc
     6781 atgtgtcctc attgttgtgt tcctattgct ggtggtgctc atacctgagc cagaaaagca
     6841 aagatctccc caggacaacc aaatggcaat catcatcatg gtagcagtag gtcttctggg
     6901 cttgattacc gcca                                                 
          [gap 140 bp]    Expand Ns
     7055                                      actttc attaccccag ccgtccaaca
     7081 tgcagtgacc acttcataca acaactactc cttaatggcg atggccacgc aagctggagt
     7141 gttgtttggt atgggcaaag ggatgccatt ctacgcatgg gactttggag tcccgctgct
     7201 aatgataggt tgctactcac aattaacacc cctgacccta atagtggcca tcattttgct
     7261 cgtggcgcac tacatgtact tgnnnnnnnn nnnnnnggca gcagctgcgc gtgctgccca
     7321 gaagagaacg gcagctggca tcatgaagaa ccctgttgtg gatggaatag tggtgactga
     7381 cattgacaca atgacaattg acccccaagt ggagaaaaag atgggacagg tgctactcat
     7441 agcnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnng gggaggctgg
     7501 ggctctgatc acagccgcaa cttccacttt gtgggaaggc tctccgaaca agtactggaa
     7561 ctcctcnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     7621 nnnaatctac acagtaacaa gaaacgctgg cttggtcaag agacgtgggg gtggaacagg
     7681 agagaccctg ggagagaaat ggaaggcccg cttgaaccnn nnnnnnnnnn nnnnnnnnnn
     7741 nnnnnnnnnn nnnnnnnnnn nnnnnnnggt gtgcagagaa gaggcccgcc gcgccctcaa
     7801 ggacggtgtg gcaacgggag gccatgctgt gtcccgagga agtgcaaagc tgagatggtt
     7861 ggtggagcgg ggatacctgc agccccatgg aaaggtcatt gatcttggat gtggcagagg
     7921 gggctggagt tactacgccg ccaccatccg caaagttcaa gaagtgaaag ga       
          [gap 259 bp]    Expand Ns
     8232             gcactatga tggaaaccct ggagcgactg cagcgtaggt atgggggagg
     8281 actggtcaga gtgccactct cccgcaactc tacacatgag atgtactggg tctctggagc
     8341 gaaaagcaac accataaaaa gtgtgtccac cacgagccag ctcctcttgg ggcgcatgga
     8401 cgggcctagg aggccagtga aatatgagga ggatgtgaat ctcggctctg gca      
          [gap 117 bp]    Expand Ns
     8571                                                        ggacatgggc
     8581 ttaccatgga agctatgagg cccccacaca agggtcagcg tcctctctag taaacggggt
     8641 tgtcaggctc ctgtcaaaac cctgggatgt ggtgactgga gtcacaggaa tagccatgac
     8701 cgacaccaca ccgtatggtc agcaaagagt tttcannnnn aaagtggaca ctagggtgcc
     8761 agacccccaa gaaggcactc gtcaggttat gagcatggtc tcttcctggt tgtggaaaga
     8821 gctaggcaaa cacaaacggc cacgagtctg taccaaagaa gagttcatca acaaggttcg
     8881 tagcaatgca gcattagggg caatatttga agaggaaaaa gagtggaaga ctgcagtgga
     8941 agctgtgaac gatccaaggt tctgggctct agtggacaag gaaagagagc accacctgag
     9001 aggagagtgc cagagttgtg tgtacaacat gatgggaaaa agagaaaaga aacaagggga
     9061 atttggaaag gccaagggca gccgcgccat ctggtatatg tggctagggg ctagatttct
     9121 agagttcgaa gcccttggat tcttgaacga ggatcactgg atggggagag agaactcagg
     9181 aggtggtgtt gaagggctgg gattacaaag actcggatat gtcctagaag agatgagtcg
     9241 cataccagga ggaaggatgt atgcagatga cactgctggc tgggacaccc gcatcagcag
     9301 gtttgatctg gagaatgaag ctctaatcac caaccaaatg gagaaagggc acagggcctt
     9361 ggcattggcc ataatcaagt acacatacca aaacaaagtg gtaaaggtcc ttagaccagc
     9421 tgaaaaaggg aaaacagtta tggacattat ttcgagacaa gacc                
          [gap 258 bp]    Expand Ns
     9723   tgggaaaa gttaggaagg acacacaaga gtggaaaccc tcaactggat gggacaactg
     9781 ggaagaagtt ccgttttgct cccaccactt caacaannnn nnnnnnnnnn nnnnnnnnnn
     9841 nnnnnnnnnn nnnngccgcc accaagatga actgattggc cgggcccgcg tatctccagg
     9901 ggcgggatgg agcatccggg agactgcttg cctagcaaaa tcatatgcgc aaatgtggca
     9961 gctcctttat ttccacagaa gggacctccg actgatggcc aatgccattt gctcatctgt
    10021 gccagttgac tgggttccaa ctgggagaac tacctggtca atccatggaa agggagaatg
    10081 gatgaccact gaagacatgc ttgtggtgtg gaacagagtg tggattgagg agaacgacca
    10141 catggaagac aagaccccag ttacgaaatg gacagacatt ccctatttgg gaaaaaggga
    10201 agacttgtgg tgtggatctc tcatagggca cagaccgcgc accacctggg ctgagaacat
    10261 taaaaacaca gtcaacatgg tgcgcaggat cataggtgat gaagaaaagt acatggacta
    10321 cctatccacc caagttcgct acttgggtga agaagggtct acacctggag tgctgtaagc
    10381 accagtctta atgttgtcag gcctgctagt cagccacagc ttggggaaag ctgtgcagcc
    10441 tgtgaccccc ccaggagaag ctgggaaacc aagcctatag tcaggccgag aacgccatgg
    10501 cacggaagaa gccatgctgc ctgtgagccc ctcagaggac actgagtcaa aaaaccccac
    10561 gcgcttggag gcgcaggatg ggaaaagaag gtggcgacct tccccaccct tcaatctggg
    10621 gcctgaactg gagatcagct gtggatctcc agaagaggga ctagtggtta gaggagaccc
    10681 cccggaaaac gcaaaacagc atattgacgc tgggaaagac cagagactcc atgag
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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
22861170066%0.0100%KX101064.1
22861156866%0.092%KU940228.1
22801119162%0.094%KU940227.1
22801141965%0.092%KU940224.1
22801157766%0.092%KU729218.1
22771157466%0.092%KU509998.3
22771155466%0.092%KU926310.1
22771141766%0.092%KU707826.1
22771142266%0.092%KU365780.1
22771143566%0.092%KU365779.1
22771142266%0.092%KU365777.1
22771146266%0.092%KU321639.1
22711155066%0.092%KX051563.1
22711136665%0.092%KU853013.1
22711141366%0.092%KU729217.2
22711156766%0.092%KU527068.1
22711089663%0.092%KU312312.1
22711133465%0.092%KJ776791.1
22691136365%0.092%KU853012.1
22681149466%0.092%KX087101.1
22681142066%0.092%KU991811.1
22681154166%0.092%KU497555.1
22681079562%0.092%KU501217.1
22681079562%0.092%KU501216.1
22681145366%0.092%KU501215.1
22621153066%0.092%KX117076.1
22621119265%0.092%KU955590.1
22621152966%0.092%KU870645.1
22621156366%0.092%KU926309.1
22621151466%0.092%KU365778.1
22591074162%0.092%KX056898.1
22591144066%0.092%KU963796.1
22591121265%0.092%KU955589.1
22591067162%0.092%KU866423.1
22591075262%0.092%KU820898.1
22591124065%0.092%KU740184.2
22591152066%0.092%KU820899.2
22591088963%0.092%KU761564.1
22591133866%0.092%KU744693.1
22531143166%0.092%KX087102.1
22531130965%0.092%KU922960.1
22531130465%0.092%KU922923.1
22531154566%0.092%KU820897.1
22531131865%0.092%KU647676.1
22231134366%0.091%KU681081.3
22081047262%0.091%KF993678.1
21861114866%0.091%KU955593.1
21861037562%0.091%JN860885.1
21631099766%0.090%KU681082.3
21361027962%0.090%EU545988.1
2048957362%0.089%HQ234499.1
1627901451%0.096%KX101061.1
1617888949%0.096%KX101066.1
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LOCUS       KX101065               10348 bp    RNA     linear   VRL 26-APR-2016
DEFINITION  Zika virus isolate Bahia15, partial genome.
ACCESSION   KX101065
VERSION     KX101065.1  GI:1022831299
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10348)
  AUTHORS   Naccache,S.N., Theze,J., Sardi,S.I., Somasekar,S., Greninger,A.L.,
            Bandeira,A.C., Campos,G.S., Tauro,L.B., Faria,N.R., Pybus,O.G. and
            Chiu,C.Y.
  TITLE     Discovery of a persistent Zika virus lineage in Bahia, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10348)
  AUTHORS   Naccache,S.N., Somasekar,S., Sardi,S.I., Bandeira,A.C., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-APR-2016) Laboratory Medicine, University of
            California, San Francisco, 185 Berry Street, #0134, San Francisco,
            CA 94107, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SURP+ v. 1.0 2016; Geneious v. 6.1.8
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10348
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="Bahia15"
                     /isolation_source="serum"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="Jan-2016"
     CDS             1..>9872
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ANA85192.1"
                     /db_xref="GI:1022831300"
                     /translation="MRIINARKEKKRRGADTSVGIVGLLLTTAMAAEVTRRGXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTMSYECPMLDEGVEPDDVDCWCNT
                     TSTWVVYGTCHHKKGEARRSRRAVTLPSHSXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLKCRLKMDKLRLKGVSYSLCN
                     AAFTFTKIPAETLHGTVTVEVQYXXXXXXXXXXAQMAVDMQTLTPVGRLITANPVITE
                     STXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXQILIGTLLMWLGLNTKNGS
                     ISLMCLALGGVXXXXXXXXXXXXGCSVDFSKKETRXGTGVFVYNDVEAWRDRYKYHPD
                     SPRRLAXXXXXXXXXXXXXXXXXXXXXXXXXXXVEGELNAILEENGVQLTVVVGSVKN
                     PMWRGPQRLPVPVNELPHGWKAWGKSYFVRAAKTNNSFVVDGDTLKXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPWH
                     SEELEIRFEECPGTKXXXXXXXXXXXXXXXXXXXXXXXXXXWCCRECTMPPLSFRAKD
                     GCWYGMEXXXXXXXXXXXXXXXXXXXXXXXXDHFSLGVLVILLMVQEGLKKRMTTKXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXATFAEMNTGGDVAHLALIAAFKVRPAXXX
                     XXXXXXXXXXXXSMLLALASCLLQTAISALEGDLMVLINGFALAWLAIRAMVVPRTDN
                     ITLAILAALTXXXXXXXLVAWRAGLATCGGFMLLSLKGKGSVKKNLPFVXXXXXXXXX
                     XXXXXXVVGLLLLTRSGKRSWPPSEVLTAVGLICALAGGFAKADIEMAGPMAAVGLLI
                     VSYVVSGKSVDMYIERAGDITWEKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMREI
                     ILKVVLMTICGMNPIAIPFAAGAWXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXRV
                     MTRRLLGSTQVGVGVMQEGVFHTMWHVTKGSALRSGEGRLDPYWGDVKQDLVSYCGPW
                     KLDAAWDGHSEVQLLAVPPGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXPEIVREAIKTRLRTVILAPTRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEI
                     VDLMCHATFTSRLLQPIRVPNYNLYIMDEAHFTDPSSIAARGYISTRVEMGEAAAIFM
                     TATPPGTRDAFPDSNSPIMDTEVEVPERAWSSGFDWVTDHSGKTVWFVPSVRNGNEIA
                     ACLTKAGKRVIQLSRKTFETEFQKTKHQEWDFVVTTDISEMGANFKADRVIXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLYGGGCAETDEDHAHWLE
                     ARMLLDNIYLQDGLIASLYRPEADKVAAIEGXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXDRRWCFDGTTNNTIMEDSVPAEVWTRHGEKRVLKPRWMDARVCSDHAA
                     LKSFKEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXNKGIGKMGFGMVTLGASAWLMWLSEIEPAR
                     IACVLIVVFLLLVVLIPEPEKQRSPQDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTFITPAVQHAVTTSYNNYSLMAM
                     ATQAGVLFGMGKGMPFYAWDFGVPLLMIGCYSQLTXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIYTVTRN
                     AGLVKRRGGGTGETLGEKWKXXXXXXXXXXXXXXXXXXXXXVCREEARRALKDGVATG
                     GHAVSRGSAKLRWLVERGYLQPHGKVIDLGCGRGGWSYYAATIRKVQEVKGXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPLSRNSTHEMYWVSGA
                     KSNTIKSVSTTSQLLLGRMDGPRRPVKYEEDXXXXXXXXXXXXXXXXXXMKIIGNRIE
                     RIRSEHAETWFFDENHPYXXXXXXXXXXXXXXXXXXXXXXXXVRLLSKPWDVVTGVTG
                     IAMTDTTPYGQQRVFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXTAVEAVNDPRFWALVDKEREHHLRGECQSCVYNMMG
                     KREKKQGEFGKAKGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     LGYVLEEMSRIPGGRMYADDTAGWDTRISRFDLENEALITNQMEKGHRALALAIXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXLLYFHRRDLRLMANAICSSVPVDWVPTGRTTXXIHGKGEW
                     MTTEDMLVVWNRVWIEENDHMEDKTPVTKWTDIPYLGKREDLWCGSLIGHRPRTTWA"
     mat_peptide     1..102
                     /product="capsid peptide"
     mat_peptide     103..372
                     /product="propeptide"
     mat_peptide     373..597
                     /product="membane protein peptide"
     mat_peptide     598..2112
                     /product="envelope protein peptide"
     mat_peptide     2113..3198
                     /product="NS1 peptide"
     mat_peptide     3199..3852
                     /product="NS2A peptide"
     mat_peptide     3853..4284
                     /product="NS2B peptide"
     mat_peptide     4285..6093
                     /product="NS3 peptide"
     mat_peptide     6094..6534
                     /product="NS4A peptide"
     mat_peptide     6535..8040
                     /product="NS4B peptide"
     mat_peptide     8041..9872
                     /product="NS5 peptide"
     gap             117..234
                     /estimated_length=118
     gap             398..1460
                     /estimated_length=1063
     gap             1704..1987
                     /estimated_length=284
     gap             2534..2907
                     /estimated_length=374
     gap             4544..4847
                     /estimated_length=304
     gap             5507..5646
                     /estimated_length=140
     gap             5793..5904
                     /estimated_length=112
     gap             6067..6305
                     /estimated_length=239
     gap             6478..6675
                     /estimated_length=198
     gap             6851..7244
                     /estimated_length=394
     gap             7594..7914
                     /estimated_length=321
     gap             8357..8548
                     /estimated_length=192
     gap             8701..8832
                     /estimated_length=132
     gap             8997..9582
                     /estimated_length=586
     gap             9873..10067
                     /estimated_length=195
     3'UTR           <10068..10348
ORIGIN      
        1 ctgagaataa tcaatgctag gaaggagaag aagagacgag gcgcagatac tagtgtcgga
       61 attgttggcc tcctgctgac cacagctatg gcagcggagg tcactagacg tgggag   
          [gap 118 bp]    Expand Ns
      235                                                            accatg
      241 agctatgaat gccctatgct ggatgagggg gtggaaccag atgacgtcga ttgttggtgc
      301 aacacgacgt caacttgggt tgtgtacgga acctgccatc acaaaaaagg tgaagcacgg
      361 agatctagaa gagctgtgac gctcccctcc cattcca                        
          [gap 1063 bp]    Expand Ns
     1461                       cttgaaatgt cgcctgaaaa tggataaact tagattgaag
     1501 ggcgtgtcat actccttgtg taacgcagcg ttcacattca ccaagatccc ggctgaaaca
     1561 ctgcacggga cagtcacagt ggaggtacag tacnnnnnnn nnnnnnnnnn nnnnnnnnnn
     1621 ncagctcaga tggcggtgga catgcaaact ctgaccccag ttgggaggtt gataaccgct
     1681 aaccccgtaa tcactgaaag cac                                       
          [gap 284 bp]    Expand Ns
     1988        cac aaattctcat tggaacgttg ctgatgtggt tgggtctgaa cacaaagaat
     2041 ggatctattt cccttatgtg cttggcctta gggggagtgn nnnnnnnnnn nnnnnnnnnn
     2101 nnnnnnnnnn nnnnggggtg ctcggtggac ttctcaaaga aggagacgag atgmggtaca
     2161 ggggtgttcg tctataacga cgttgaagcc tggagggaca ggtacaagta ccatcctgac
     2221 tccccccgta gattggcagn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     2281 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnng tagaagggga gctcaacgca
     2341 atcctggaag agaatggagt tcaactgacg gtcgttgtgg gatctgtaaa aaaccccatg
     2401 tggagaggtc cacagagatt gcccgtgcct gtgaacgagc tgccccacgg ctggaaggct
     2461 tgggggaaat cgtacttcgt cagagcagca aagacaaata acagctttgt cgtggatggt
     2521 gacacactga agg                                                  
          [gap 374 bp]    Expand Ns
     2908                              cca tggcacagtg aagagcttga aattcggttt
     2941 gaggaatgcc caggcactaa ggnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     3001 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnat ggtgctgcag ggagtgcaca
     3061 atgcccccac tgtcgttccg ggctaaagat ggctgttggt atggaatgga gannnnnnnn
     3121 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     3181 nnngatcact tctcccttgg agtgcttgtg attctgctca tggtgcagga agggctgaag
     3241 aagagaatga ccacaaagan nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     3301 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnng tgccaccttc
     3361 gcggaaatga acactggagg agatgtagct catctggcgc tgatagcggc attcaaagtc
     3421 agaccagcgt nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnaaagcatg
     3481 ctgctggcct tggcctcgtg tcttttgcaa actgcgatct ccgccttgga aggcgacctg
     3541 atggttctca tcaatggttt tgctttggcc tggttggcaa tacgagcgat ggttgttcca
     3601 cgcactgata acatcacctt ggcaatcttg gctgctctga cacnnnnnnn nnnnnnnnnn
     3661 nngcttgtgg cgtggagagc aggccttgct acttgcgggg ggtttatgct cctctctctg
     3721 aagggaaaag gcagtgtgaa gaagaactta ccatttgtcn nnnnnnnnnn nnnnnnnnnn
     3781 nnnnnnnnnn nnnnnnnnnn nnacgtggtg ggactgctgt tgctcacaag gagtgggaag
     3841 cggagctggc cccctagcga agtactcaca gctgttggcc tgatatgcgc attggctgga
     3901 gggttcgcca aggcagatat agagatggct gggcccatgg ccgcggtcgg tctgctaatt
     3961 gtcagttacg tggtctcagg aaagagtgtg gacatgtaca ttgaaagagc aggtgacatc
     4021 acatgggaaa aagannnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     4081 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn ccatgagaga gatcatactc
     4141 aaggtggtcc tgatgaccat ctgtggcatg aacccaatag ccataccctt tgcagctgga
     4201 gcgtggtann nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     4261 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn acagagtaat gactcgtaga
     4321 ctgctaggtt caacacaagt tggagtggga gttatgcaag agggggtctt tcacactatg
     4381 tggcacgtca caaaaggatc cgcgctgaga agcggtgaag ggagacttga tccatactgg
     4441 ggagatgtca agcaggatct ggtgtcatac tgtggtccat ggaagctaga tgccgcctgg
     4501 gacgggcaca gcgaggtgca gctcttggcc gtgccccccg gag                 
          [gap 304 bp]    Expand Ns
     4848                                                    tcc tgaaatagtc
     4861 cgtgaagcca taaaaacaag actccgtact gtgatcttag ctccaaccag ggttgtcgct
     4921 gctgaaatgg aggaagccct tagagggctt ccagtgcgtt atatgacaac agcagtcaat
     4981 gtcacccact ctggaacaga aatcgtcgac ttaatgtgcc atgccacctt cacttcacgt
     5041 ctactacagc caatcagagt ccccaattat aatctgtata ttatggatga ggcccacttc
     5101 acagatccct caagtatagc agcaagagga tacatttcaa caagggttga gatgggcgag
     5161 gcggctgcca tcttcatgac cgccacgcca ccaggaaccc gtgacgcatt tccggactcc
     5221 aactcaccaa ttatggacac cgaagtggaa gtcccagaga gagcctggag ctcaggcttt
     5281 gattgggtga cggatcattc tggaaaaaca gtttggtttg ttccaagcgt gaggaacggc
     5341 aatgagatcg cagcttgtct gacaaaggct ggaaaacggg tcatacagct cagcagaaag
     5401 acttttgaga cagagttcca gaaaacaaaa catcaagagt gggactttgt cgtgacaact
     5461 gacatttcag agatgggcgc caactttaaa gctgaccgtg tcatag              
          [gap 140 bp]    Expand Ns
     5647       ctgt atggaggtgg gtgcgcagag actgacgaag accatgcaca ctggcttgaa
     5701 gcaagaatgc tccttgacaa tatttacctc caagatggcc tcatagcctc gctctatcga
     5761 cctgaggccg acaaagtagc agccattgag gg                             
          [gap 112 bp]    Expand Ns
     5905                           gataga agatggtgct ttgatggcac gaccaacaac
     5941 accataatgg aagacagtgt gccggcagag gtgtggacca gacacggaga gaaaagagtg
     6001 ctcaaaccga ggtggatgga tgccagagtt tgttcagatc atgcggccct gaagtcattc
     6061 aaggag                                                          
          [gap 239 bp]    Expand Ns
     6306      gaaca agggcatagg gaagatgggc tttggaatgg tgactcttgg ggccagcgca
     6361 tggctcatgt ggctctcgga aattgagcca gccagaattg catgtgtcct cattgttgtg
     6421 ttcctattgc tggtggtgct catacctgag ccagaaaagc aaagatctcc ccaggac  
          [gap 198 bp]    Expand Ns
     6676                 acttt cattacccca gccgtccaac atgcagtgac cacttcatac
     6721 aacaactact ccttaatggc gatggccacg caagctggag tgttgtttgg tatgggcaaa
     6781 gggatgccat tctacgcatg ggactttgga gtcccgctgc taatgatagg ttgctactca
     6841 caattaacac                                                      
          [gap 394 bp]    Expand Ns
     7245                                                 aatcta cacagtaaca
     7261 agaaacgctg gcttggtcaa gagacgtggg ggtggaacag gagagaccct gggagagaaa
     7321 tggaaggnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     7381 nnnnnnnngg tgtgcagaga agaggcccgc cgcgccctca aggacggtgt ggcaacggga
     7441 ggccatgctg tgtcccgagg aagtgcaaag ctgagatggt tggtggagcg gggatacctg
     7501 cagccccatg gaaaggtcat tgatcttgga tgtggcagag ggggctggag ttactacgcc
     7561 gccaccatcc gcaaagttca agaagtgaaa gga                            
          [gap 321 bp]    Expand Ns
     7915                                                            ccactc
     7921 tcccgcaact ctacacatga gatgtactgg gtctctggag cgaaaagcaa caccataaaa
     7981 agtgtgtcca ccacgagcca gctcctcttg gggcgcatgg acgggcctag gaggccagtg
     8041 aaatatgagg aggatgnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     8101 nnnnnnnnca tgaagatcat tggtaaccgc attgaaagga tccgcagtga gcacgcggaa
     8161 acgtggttct ttgacgagaa ccacccatat agnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     8221 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn ntgtcaggct cctgtcaaaa
     8281 ccctgggatg tggtgactgg agtcacagga atagccatga ccgacaccac accgtatggt
     8341 cagcaaagag ttttca                                               
          [gap 192 bp]    Expand Ns
     8549                               ag actgcagtgg aagctgtgaa cgatccaagg
     8581 ttctgggctc tagtggacaa ggaaagagag caccacctga gaggagagtg ccagagttgt
     8641 gtgtacaaca tgatgggaaa aagagaaaag aaacaagggg aatttggaaa ggccaagggc
          [gap 132 bp]    Expand Ns
     8833              ctcggata tgtcctagaa gagatgagtc gcataccagg aggaaggatg
     8881 tatgcagatg acactgctgg ctgggacacc cgcatcagca ggtttgatct ggagaatgaa
     8941 gctctaatca ccaaccaaat ggagaaaggg cacagggcct tggcattggc cataat   
          [gap 586 bp]    Expand Ns
     9583                                               ctccttta tttccacaga
     9601 agggacctcc gactgatggc caatgccatt tgctcatctg tgccagttga ctgggttcca
     9661 actgggagaa ctacctnnnn natccatgga aagggagaat ggatgaccac tgaagacatg
     9721 cttgtggtgt ggaacagagt gtggattgag gagaacgacc acatggaaga caagacccca
     9781 gttacgaaat ggacagacat tccctatttg ggaaaaaggg aagacttgtg gtgtggatct
     9841 ctcatagggc acagaccgcg caccacctgg gc                             
          [gap 195 bp]    Expand Ns
    10068                                                    ccc cccaggagaa
    10081 gctgggaaac caagcctata gtcaggccga gaacgccatg gcacggaaga agccatgctg
    10141 cctgtgagcc cctcagagga cactgagtca aaaaacccca cgcgcttgga ggcgcaggat
    10201 gggaaaagaa ggtggcgacc ttccccaccc ttcaatctgg ggcctgaact ggagatcagc
    10261 tgtggatctc cagaagaggg actagtggtt agaggagacc ccccggaaaa cgcaaaacag
    10321 catattgacg ctgggaaaga ccagagac
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Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
1189836449%0.0100%KX101065.1
1189826848%0.0100%KU940228.1
1189826348%0.0100%KU940224.1
1184819848%0.099%KX087102.1
1184820548%0.099%KU991811.1
1184818548%0.099%KU922960.1
1184818548%0.099%KU922923.1
1184828848%0.099%KU820897.1
1184829948%0.099%KU729218.1
1184829048%0.099%KU527068.1
1184819148%0.099%KU647676.1
1184823448%0.099%KJ776791.1
1180827249%0.099%KX087101.1
1180829048%0.099%KX051563.1
1180831548%0.099%KU509998.3
1180825948%0.099%KU870645.1
1180829549%0.099%KU926310.1
1180829349%0.099%KU926309.1
1180820348%0.099%KU729217.2
1180828449%0.099%KU497555.1
1180819848%0.099%KU707826.1
1180778246%0.099%KU501217.1
1180778246%0.099%KU501216.1
1180818348%0.099%KU501215.1
1180819848%0.099%KU365779.1
1180827049%0.099%KU365778.1
1180821948%0.099%KU321639.1
1175828849%0.099%KX117076.1
1175828449%0.099%KU963796.1
1175811748%0.099%KU955589.1
1175776246%0.099%KU866423.1
1175774446%0.099%KU820898.1
1175806147%0.099%KU740184.2
1175828449%0.099%KU820899.2
1175774946%0.099%KU761564.1
1171775346%0.099%KX056898.1
1171808848%0.099%KU955590.1
1171819248%0.099%KU365780.1
1171818948%0.099%KU365777.1
1171777646%0.099%KU312312.1
1166810448%0.099%KU853013.1
1166810448%0.099%KU853012.1
1157811148%0.099%KU744693.1
1153756046%0.099%KF993678.1
1148803448%0.099%KU955593.1
1148816249%0.099%KU681081.3
1148753546%0.099%JN860885.1
1130744646%0.098%EU545988.1
1103787349%0.097%KU681082.3
1045693646%0.095%HQ234499.1
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LOCUS       KX101066               10632 bp    RNA     linear   VRL 26-APR-2016
DEFINITION  Zika virus isolate Bahia01, partial genome.
ACCESSION   KX101066
VERSION     KX101066.1  GI:1022831301
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10632)
  AUTHORS   Naccache,S.N., Theze,J., Sardi,S.I., Somasekar,S., Greninger,A.L.,
            Bandeira,A.C., Campos,G.S., Tauro,L.B., Faria,N.R., Pybus,O.G. and
            Chiu,C.Y.
  TITLE     Discovery of a persistent Zika virus lineage in Bahia, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10632)
  AUTHORS   Naccache,S.N., Somasekar,S., Sardi,S.I., Bandeira,A.C., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-APR-2016) Laboratory Medicine, University of
            California, San Francisco, 185 Berry Street, #0134, San Francisco,
            CA 94107, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SURP+ v. 1.0 2016; Geneious v. 6.1.8
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10632
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="Bahia01"
                     /isolation_source="serum"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="May-2015"
     5'UTR           1..3
     CDS             4..10275
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ANA85193.1"
                     /db_xref="GI:1022831302"
                     /translation="MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPI
                     RMVLAILAFLRFTAIKPSLGLINXXXXXXKKEAMEIIKKFKKDLAAMLRIINARXXXX
                     XXXXXXXXXXXXLLLTTAMAAEVTRRGSAYYMYLDRNDAGXXXXXXXXXXMNKCYIQI
                     MDLGHMCDATMSYECPMLDEGVEPDDVDCWCNTTXXXXXXXTCHHKKGEARRSRRAVT
                     LPSHSTRKLQTRSQTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXSGGTWVDVVLEHGGCVTVMAQDKPTVDIE
                     LVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWG
                     NGCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEYRIMLSVHGSQHSGMIVNDTGHET
                     DENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWF
                     HDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAE
                     MDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCNAAFTFTKIPAETLHGTVTVEVQYAG
                     TDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVG
                     EKKITHHWHRSGSTIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFG
                     AAFKSLFGGMSWFSQILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTAVSADVGC
                     SVDFSKKETRCGTGVFVYNDVEAWRDRYKYHPDSPRRLAAAVKQAWEDGICGISSVSR
                     MENIXWRSVEGELXAILEENGVQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGK
                     SYFVRAAKTNNSFVVDGDTLKECPLKHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLE
                     CDPAVIGTAVKGREAVHSDLGYWIESEKNDTWRLKRAXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEELEIRFEECPGTKXHVEETCGTR
                     GPSLRSTTASGRVIEEWCCXXXXXXPLSFRAKDGCWYGMEIRPRKEPESNLVRSMVTA
                     GSTDHMDHFSLGVLVILLMVQEGLKKRMTTKIIISTSMAVLVAMILGGFSMSDLAKLA
                     ILMGATFAEMNTGGDVAHLALIAAFKVRPALLVSFIFRAXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLAILAALTPLARGTLLVAWRAGL
                     ATCGGFMLLSLKGKGSVKKNLPFVMALGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXAGGFAKADIEMAGPMAAVGLLIVSYVVSGKSVDMYIERAGDITWEKD
                     AEVTGNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXKEVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMW
                     HVTKGSALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGERARN
                     IQTLPGIFKTKGGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAIT
                     QGRREEETPVECFEPSMLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAP
                     TRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLY
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKT
                     KHQEWDFVVTTDISEMGANFKADRVXXXXXXXXXXXXXXXXXXXXXPMPVTHASAAQR
                     RGRIGRNPNKXGDEYLYGGGCAETDEDHAHWLEARMLLDNIYLQDGLIASLYRPEADK
                     VAAIEGEFKLRTEQRKTFVELMKRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIM
                     EDSVPAEVWTRHGEKRVLKPRWMDARVCSDHAALKSFKEFAAGKRGAAFGVMEALGTL
                     PGHMTERFQEAIXXXAVLMRAETGSRPYKAAAAQMPETLETIMLLGLLGTVSLGIFFV
                     LMRNKGIGKMGFGMVTLGASAWLMWLSEIEPARIACVLIVVFLLLVVLIXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXGWLERTKSDLSHLMGRREEGATIGFSMDIDLRPA
                     SAWAIYAALTTFITPXXXHAVTTSYNNYSLMAMATQAGVLFGMGKGMPFYAWDFGVPL
                     LMIGCYSQLTPLTLIVAIILLVAHYMYLIPGLQAAAARAAQKRTAAGIMKNPVVDGIV
                     VTDIDTMTIDPQVEKKMGQVLLIAVAVSSAXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKRRGGGTGETLGEKWKARLNQ
                     MSALEFYSYKKTGITEVCREEARRALKDXXXXXXXXXXXXXXXXXXXXXXXXLQPHGK
                     VIDLGCGRGGWSYYAATIRKVQEVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXIGESSSSPEVEEARTLRVLSMVGDXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLLLGRMDGPRRP
                     VKYEEDVNLGSGTRAVVSCAEAPNMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHG
                     SYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGIAMTDTTPYGQQRVFKEKVDTRVPD
                     PQEGTRQVMSMVSSWLWKELGKHKRPRVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXREKKQGEFGKAKGSRAIWYMWLGA
                     RFLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTYQNKVVKVLRPAEKGKTVMDIISRQ
                     DQRGSGQVVTYALNTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXWKPSTGWDNWEEVPFCSHH
                     FNKLHLKDGRSIVVPCRHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRR
                     DLRLMANAICSSVPVDWVPTGRTTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKT
                     PVMKWTDIPYLGKREDLWCGSLIGHRPRTTWAENIKNTVNMVRRIIGDEEKYMDYLST
                     QVRYLGEEGSTPGVL"
     mat_peptide     4..378
                     /product="capsid peptide"
     mat_peptide     379..648
                     /product="propeptide"
     mat_peptide     649..873
                     /product="membane protein peptide"
     mat_peptide     874..2388
                     /product="envelope protein peptide"
     mat_peptide     2389..3474
                     /product="NS1 peptide"
     mat_peptide     3475..4128
                     /product="NS2A peptide"
     mat_peptide     4129..4560
                     /product="NS2B peptide"
     mat_peptide     4561..6369
                     /product="NS3 peptide"
     mat_peptide     6370..6810
                     /product="NS4A peptide"
     mat_peptide     6811..8316
                     /product="NS4B peptide"
     mat_peptide     8317..10272
                     /product="NS5 peptide"
     gap             703..916
                     /estimated_length=214
     gap             3030..3193
                     /estimated_length=164
     gap             3732..3892
                     /estimated_length=161
     gap             4049..4169
                     /estimated_length=121
     gap             4330..4539
                     /estimated_length=210
     gap             5356..5595
                     /estimated_length=240
     gap             7360..7553
                     /estimated_length=194
     gap             7866..7999
                     /estimated_length=134
     gap             8074..8187
                     /estimated_length=114
     gap             8745..8937
                     /estimated_length=193
     gap             9020..9277
                     /estimated_length=258
     gap             9403..9647
                     /estimated_length=245
     3'UTR           10276..10632
ORIGIN      
        1 gtcatgaaaa acccaaaaaa gaaatccgga ggattccgga ttgtcaatat gctaaaacgc
       61 ggagtagccc gtgtgagccc ctttgggggc ttgaagaggc tgccagccgg acttctgctg
      121 ggtcatgggc ccatcaggat ggtcttggcg attctagcct ttttgagatt cacggcaatc
      181 aagccatcac tgggtctcat caatagnnnn nnnnnnnnnn ngaaaaaaga ggctatggaa
      241 ataataaaga agttcaagaa agatctggct gccatgctga gaataatcaa tgctaggaan
      301 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnctcct gctgaccaca
      361 gctatggcag cggaggtcac tagacgtggg agtgcatact atatgtactt ggacagaaac
      421 gatgctgggg nnnnnnnnnn nnnnnnnnnn nnnnnnnnna tgaataagtg ttatatacag
      481 atcatggatc ttggacacat gtgtgatgcc accatgagct atgaatgccc tatgctggat
      541 gagggggtgg aaccagatga cgtcgattgt tggtgcaaca cgacgtnnnn nnnnnnnnnn
      601 nnnngaacct gccatcacaa aaaaggtgaa gcacggagat ctagaagagc tgtgacgctc
      661 ccctcccatt ccactaggaa gctgcaaacg cggtcgcaaa cc                  
          [gap 214 bp]    Expand Ns
      917                  tgtc aggtgggact tgggttgatg ttgtcttgga acatggaggt
      961 tgtgtcaccg taatggcaca ggacaaaccg actgtcgaca tagagctggt tacaacaaca
     1021 gtcagcaaca tggcggaggt aagatcctac tgctatgagg catcaatatc agacatggct
     1081 tcggacagcc gctgcccaac acaaggtgaa gcctaccttg acaagcaatc agacactcaa
     1141 tatgtctgca aaagaacgtt agtggacaga ggctggggaa atggatgtnn nnnnnnnnnn
     1201 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     1261 nnnnnnnnnn nnnnnnngga gtaccggata atgctgtcag ttcatggctc ccagcacagt
     1321 gggatgatcg ttaatgacac aggacatgaa actgatgaga atagagcgaa ggttgagata
     1381 acgcccaatt caccaagagc cgaagccacc ctggggggtt ttggaagcct aggacttgat
     1441 tgtgaaccga ggacaggcct tgacttttca gatttgtatt acttgactat gaataacaag
     1501 cactggttgg ttcacaagga gtggttccac gacattccat taccttggca cgctggggca
     1561 gacaccggaa ctccacactg gaacaacaaa gaagcactgg tagagttcaa ggacgcacat
     1621 gccaaaaggc aaactgtcgt ggttctaggg agtcaagaag gagcagttca cacggccctt
     1681 gctggagctc tagaggctga gatggatggt gcaaagggaa ggctgtcctc tggccacttg
     1741 aaatgtcgcc tgaaaatgga taaacttaga ttgaagggcg tgtcatactc cttgtgtaac
     1801 gcagcgttca cattcaccaa gatcccggct gaaacactgc acgggacagt cacagtggag
     1861 gtacagtacg cagggactga tggaccttgc aaggttccag ctcagatggc ggtggacatg
     1921 caaactctga ccccagttgg gaggttgata accgctaacc ccgtaatcac tgaaagcact
     1981 gagaactcta agatgatgct ggaacttgat ccaccatttg gggactccta cattgtcata
     2041 ggagtcgggg agaagaagat cacccaccac tggcacagga gtggcagcac cattggaaaa
     2101 gcatttgaag ccactgtgag aggtgccaag agaatggcag tcttgggaga cacagcctgg
     2161 gactttggat cagttggagg cgctctcaac tcattgggca agggcatcca tcaaattttt
     2221 ggagcagctt tcaaatcatt gtttggagga atgtcctggt tctcacaaat tctcattgga
     2281 acgttgctga tgtggttggg tctgaacaca aagaatggat ctatttccct tatgtgcttg
     2341 gccttagggg gagtgttgat cttcttatcc acagccgtct ctgctgatgt ggggtgctcg
     2401 gtggacttct caaagaagga gacgagatgc ggtacagggg tgttcgtcta taacgacgtt
     2461 gaagcctgga gggacaggta caagtaccat cctgactccc cccgtagatt ggcagcagca
     2521 gtcaagcaag cctgggaaga tggtatctgc gggatctcct ctgtttcaag aatggaaaac
     2581 atcawgtgga gatcagtaga aggggagctc aamgcaatcc tggaagagaa tggagttcaa
     2641 ctgacggtcg ttgtgggatc tgtaaaaaac cccatgtgga gaggtccaca gagattgccc
     2701 gtgcctgtga acgagctgcc ccacggctgg aaggcttggg ggaaatcgta cttcgtcaga
     2761 gcagcaaaga caaataacag ctttgtcgtg gatggtgaca cactgaagga atgcccactc
     2821 aaacatagag catggaacag ctttcttgtg gaggatcatg ggttcggggt atttcacact
     2881 agtgtctggc tcaaggttag agaagattat tcattagagt gtgatccagc cgttattgga
     2941 acagctgtta agggaaggga ggctgtacac agtgatctag gctactggat tgagagtgag
     3001 aagaatgaca catggaggct gaagagggc                                 
          [gap 164 bp]    Expand Ns
     3194               gtgaaga gcttgaaatt cggtttgagg aatgcccagg cactaagrtc
     3241 cacgtggagg aaacatgtgg aacaagagga ccatctctga gatcaaccac tgcaagcgga
     3301 agggtgatcg aggaatggtg ctgcagnnnn nnnnnnnnnn ccccactgtc gttccgggct
     3361 aaagatggct gttggtatgg aatggagata aggcccagga aagaaccaga aagcaactta
     3421 gtaaggtcaa tggtgactgc aggatcaact gatcacatgg atcacttctc ccttggagtg
     3481 cttgtgatyc tgctcatggt gcaggaaggg ctgaagaaga gaatgaccac aaagatcatc
     3541 ataagcacat caatggcagt gctggtagct atgatcctgg gaggattttc aatgagtgac
     3601 ctggctaagc ttgcaatttt gatgggtgcc accttcgcgg aaatgaacac tggaggagat
     3661 gtagctcatc tggcgctgat agcggcattc aaagtcagac cagcgttgct ggtatctttc
     3721 atcttcagag c                                                    
          [gap 161 bp]    Expand Ns
     3893                                                          ccttggca
     3901 atcttggctg ctctgacacc actggcccgg ggcacactgc ttgtggcgtg gagagcaggc
     3961 cttgctactt gcggggggtt tatgctcctc tctctgaagg gaaaaggcag tgtgaagaag
     4021 aacttaccat ttgtcatggc cctgggac                                  
          [gap 121 bp]    Expand Ns
     4170                                g gctggagggt tcgccaaggc agatatagag
     4201 atggctgggc ccatggccgc ggtcggtctg ctaattgtca gttacgtggt ctcaggaaag
     4261 agcgtggaca tgtacattga aagagcaggt gacatcacat gggaaaaaga tgcggaagtc
     4321 actggaaac                                                       
          [gap 210 bp]    Expand Ns
     4540                                           a aggaagtaaa aaagggggag
     4561 accacagatg gagtgtacag agtaatgact cgtagactgc taggttcaac acaagttgga
     4621 gtgggagtta tgcaagaggg ggtctttcac actatgtggc acgtcacaaa aggatccgcg
     4681 ctgagaagcg gtgaagggag acttgatcca tactggggag atgtcaagca ggatctggtg
     4741 tcatactgtg gtccatggaa gctagatgcc gcctgggacg ggcacagcga ggtgcagctc
     4801 ttggccgtgc cccccggaga gagagcgagg aacatccaga ctctgcccgg aatatttaag
     4861 acaaagggtg gggacattgg agcggttgcg ctggattacc cagcaggaac ttcaggatct
     4921 ccaatcctag acaagtgtgg gagagtgata ggactttatg gcaatggggt cgtgatcaaa
     4981 aatgggagtt atgttagtgc catcacccaa gggaggaggg aggaagagac tcctgttgag
     5041 tgcttcgagc cttcgatgct gaagaagaag cagctaactg tcttagactt gcatcctgga
     5101 gctgggaaaa ccaggagagt tcttcctgaa atagtccgtg aagccataaa aacaagactc
     5161 cgtactgtga tcttagctcc aaccagggtt gtcgctgctg aaatggagga agcccttaga
     5221 gggcttccag tgcgttatat gacaacagca gtcaatgtca cccactctgg aacagaaatc
     5281 gtcgacttaa tgtgccatgc caccttcact tcacgtctac tacagccaat cagagtcccc
     5341 aattataatc tgtat                                                
          [gap 240 bp]    Expand Ns
     5596                 gttcc aagcgtgagg aacggcaatg agatcgcagc ttgtctgaca
     5641 aaggctggaa aacgggtcat acagctcagc agaaagactt ttgagacaga gttccagaaa
     5701 acaaaacatc aagagtggga ctttgtcgtg acaactgaca tttcagagat gggcgccaac
     5761 tttaaagctg accgtgtcat nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     5821 nnnnnnnnnn nnnnnnnnnn acccatgcct gtcacacatg ccagcgctgc ccagaggagg
     5881 gggcgcatag gcaggaatcc caacaaamct ggagatgagt atctgtatgg aggtgggtgc
     5941 gcagagactg acgaagacca tgcacactgg cttgaagcaa gaatgctcct tgacaatatt
     6001 tacctccaag atggcctcat agcctcgctc tatcgacctg aggccgacaa agtagcagcc
     6061 attgagggag agttcaagct taggacggag caaaggaaga cctttgtgga actcatgaaa
     6121 agaggagatc ttcctgtttg gctggcctat caggttgcat ctgccggaat aacctacaca
     6181 gatagaagat ggtgctttga tggcacgacc aacaacacca taatggaaga cagtgtgccg
     6241 gcagaggtgt ggaccagaca cggagagaaa agagtgctca aaccgaggtg gatggacgcc
     6301 agagtttgtt cagatcatgc ggccctgaag tcattcaagg agtttgccgc tgggaaaaga
     6361 ggggcggctt ttggagtgat ggaagccctg ggaacactgc caggacacat gacagagaga
     6421 ttccaggaag ccattgannn nnncgctgtg ctcatgcggg cagagactgg aagcaggcct
     6481 tacaaagccg cggcggccca aatgccggag accctagaga ccattatgct tttggggttg
     6541 ctaggaacag tctcgctggg aatctttttc gtcttgatga ggaacaaggg catagggaag
     6601 atgggctttg gaatggtgac tcttggggcc agcgcatggc tcatgtggct ctcggaaatt
     6661 gagccagcca gaattgcatg tgtcctcatt gttgtgttcc tattgctggt ggtgctcata
     6721 cnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     6781 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnncg gatggttgga gagaacaaag
     6841 agtgacctaa gccatctaat gggaaggaga gaggaggggg caaccatagg attctcaatg
     6901 gacattgacc tacggccagc ctcagcttgg gccatctatg ctgccttgac aactttcatt
     6961 accccnnnnn nnnnncatgc agtgaccact tcatacaaca actactcctt aatggcgatg
     7021 gccacgcaag ctggagtgtt gtttggtatg ggcaaaggga tgccattcta cgcatgggac
     7081 tttggagtcc cgctgctaat gataggttgc tactcacaat taacacccct gaccctaata
     7141 gtggccatca ttttgctcgt ggcgcactac atgtacttga tcccagggct gcaggcagca
     7201 gctgcgcgtg ctgcccagaa gagaacggca gctggcatca tgaagaaccc tgttgtggat
     7261 ggaatagtgg tgactgacat tgacacaatg acaattgacc cccaagtgga gaaaaagatg
     7321 ggacaggtgc tactcatagc agtagccgtc tccagcgcc                      
          [gap 194 bp]    Expand Ns
     7554                                                           caagaga
     7561 cgtgggggtg gaacaggaga gaccctggga gagaaatgga aggcccgctt gaaccagatg
     7621 tcggccctgg agttctactc ctacaaaaag acaggcatca ccgaggtgtg cagagaagag
     7681 gcccgccgcg ccctcaagga cnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     7741 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nncctgcagc cccatggaaa ggtcattgat
     7801 cttggatgtg gcagaggggg ctggagttac tacgccgcca ccatccgcaa agttcaagaa
     7861 gtgaa                                                           
          [gap 134 bp]    Expand Ns
     8000                     a cataggtgag tcatcatcta gtcctgaagt ggaagaagca
     8041 cggacgctca gagttctctc catggtgggg gat                            
          [gap 114 bp]    Expand Ns
     8188                              gtg ccactctccc gcaactctac acatgagatg
     8221 tactgggtct ctggagcgaa aagcaacacc ataaaaagtg tgtccaccac gagccagctc
     8281 ctcttggggc gcatggacgg gcctaggagg ccagtgaaat atgaggagga tgtgaatctc
     8341 ggctctggca cgcgggctgt ggtaagctgc gctgaagctc ccaacatgaa gatcattggt
     8401 aaccgcattg aaaggatccg cagtgagcac gcggaaacgt ggttctttga cgagaaccac
     8461 ccatatagga catgggctta ccatggaagc tatgnnnnnn nnnnnnnnnn nnnnnnnnnn
     8521 ncnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     8581 nnaggaatag ccatgaccga caccacaccg tatggtcagc aaagagtttt caaggaaaaa
     8641 gtggacacta gggtgccaga cccccaagaa ggcactcgtc aggttatgag catggtctct
     8701 tcctggttgt ggaaagagct aggcaaacac aaacggccac gagt                
          [gap 193 bp]    Expand Ns
     8938                                                               aga
     8941 gaaaagaaac aaggggaatt tggaaaggcc aagggcagcc gcgccatctg gtatatgtgg
     9001 ctaggggcta gatttctag                                            
          [gap 258 bp]    Expand Ns
     9278                                         aca cataccaaaa caaagtggta
     9301 aaggtcctta gaccagctga aaaagggaaa acagttatgg acattatttc gagacaagac
     9361 caaaggggga gcggacaagt tgtcacttac gctcttaaca ca                  
          [gap 245 bp]    Expand Ns
     9648                                                    gtg gaaaccctca
     9661 actggatggg acaactggga agaagttccg ttttgctccc accacttcaa caagctccat
     9721 ctcaaggacg ggaggtccat tgtggttccc tgccgccacc aagatgaact gattggccgg
     9781 gcccgcgtct ctccaggggc gggatggagc atccgggaga ctgcttgcct agcaaaatca
     9841 tatgcgcaaa tgtggcagct cctttatttc cacagaaggg acctccgact gatggccaat
     9901 gccatttgtt catctgtgcc agttgactgg gttccaactg ggagaactac ctggtcaatc
     9961 catggaaagg gagaatggat gaccactgaa gacatgcttg tggtgtggaa cagagtgtgg
    10021 attgaggaga acgaccacat ggaagacaag accccagtta tgaaatggac agacattccc
    10081 tatttgggaa aaagggaaga cttgtggtgt ggatctctca tagggcacag accgcgcacc
    10141 acctgggctg agaacattaa aaacacagtc aacatggtgc gcaggatcat aggtgatgaa
    10201 gaaaagtaca tggactacct atccacccaa gttcgctact tgggtgaaga agggtctaca
    10261 cctggagtac tgtaagcacc aatcttaatg ttgtcaggcc tgctagtcag ccacagcttg
    10321 gggaaagctg tgcagcctgt gaccccccca ggagaagctg ggaaaccaag cctatagtca
    10381 ggccgagaac gccatggcac ggaagaagcc atgctgcctg tgagcccctc agaggacact
    10441 gagtcaaaaa accccacgcg cttggaggcg caggatggga aaagaaggtg gcgaccttcc
    10501 ccacccttca atctggggcc tgaactggag atcagctgtg gatctccaga agagggacta
    10561 gtggttagag gagacccccc ggaaaacgca aaacagcata ttgacgctgg gaaagaccag
    10621 agactccatg ag
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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
31551390075%0.0100%KX101066.1
31461373974%0.099%KU940228.1
31391364374%0.099%KU940224.1
31281378675%0.099%KU509998.3
31281367674%0.099%KU321639.1
31221379075%0.099%KU729218.1
31221366274%0.099%KJ776791.1
31191366074%0.099%KU991811.1
31191372875%0.099%KU870645.1
31191375475%0.099%KU926309.1
31191365474%0.099%KU922960.1
31191365474%0.099%KU922923.1
31191365474%0.099%KU707826.1
3119406121%0.099%KU646828.1
31191366574%0.099%KU647676.1
31191309271%0.099%KU501217.1
31191309271%0.099%KU501216.1
31191364274%0.099%KU365780.1
31191364574%0.099%KU365779.1
31191374175%0.099%KU365778.1
31191363374%0.099%KU365777.1
31131371275%0.099%KX117076.1
31131364774%0.099%KX087102.1
31131375575%0.099%KX051563.1
31131369875%0.099%KU963796.1
31131353074%0.099%KU955589.1
31131296471%0.099%KU866423.1
31131370775%0.099%KU820899.2
31131374875%0.099%KU820897.1
3113405021%0.099%KU646827.1
31131362774%0.099%KU501215.1
31121364574%0.099%KU729217.2
31101373275%0.099%KX087101.1
31101307071%0.099%KX056898.1
31101352674%0.099%KU955590.1
31101307771%0.099%KU820898.1
31101350373%0.099%KU740184.2
31101321672%0.099%KU761564.1
31101374175%0.099%KU497555.1
31081355274%0.099%KU853013.1
31081355274%0.099%KU853012.1
31041375075%0.099%KU527068.1
31041320272%0.099%KU312312.1
31011372575%0.099%KU926310.1
30651352175%0.099%KU681081.3
30501348574%0.099%KU744693.1
30381257670%0.098%KF993678.1
30251255471%0.098%EU545988.1
30201329975%0.098%KU955593.1
30201266271%0.098%JN860885.1
29871309775%0.098%KU681082.3
27871173071%0.095%HQ234499.1
2677316916%0.099%KU312315.1
2677404723%0.099%KU312314.1
2664401923%0.099%KU312313.1
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LOCUS       KX101067               10566 bp    RNA     linear   VRL 26-APR-2016
DEFINITION  Zika virus isolate Bahia12, partial genome.
ACCESSION   KX101067
VERSION     KX101067.1  GI:1022831303
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10566)
  AUTHORS   Naccache,S.N., Somasekar,S., Sardi,S.I., Bandeira,A.C., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-APR-2016) Laboratory Medicine, University of
            California, San Francisco, 185 Berry Street, #0134, San Francisco,
            CA 94107, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SURP+ v. 1.0 2016; Geneious v. 6.1.8
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10566
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="Bahia12"
                     /isolation_source="serum"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="May-2015"
     CDS             <1..10209
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ANA85194.1"
                     /db_xref="GI:1022831304"
                     /translation="ARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIKPSLGL
                     INRWGSVGKKEAMEIIKXXXXXXXXXLRIINARKEKKRRGADTSVGIVGLLLTTAMAA
                     EVTRRGSAYYMYLDRNDAGEAISFPTTLGMNKCYIXXXXXXXXXXXXXSYECPMLDEG
                     VEPDDVDCWCNTTSTWVVYGTCHHKKGEARRSRRAVTLPSHSXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHETDENRAKVEITPNSPRAEATLG
                     GXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAQMAVDMQTLTPV
                     GRLITANPVITESTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXQILIGTL
                     LMWLGLNTKNGSISLMCLALGGVXXXXXXXXXXXXXXXXXFSKKETRCGTGVFVYNDV
                     EAWRDRYKYHPDSPRRLAAAVKQAWEDGICGISSVSRMENIMWRSVEGELNAILEENG
                     VQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGKSYFVRAAKTNNSFVVDGDTLK
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXECDPAVIGTAVKGKEAVHSDLG
                     YWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGIXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXPWHSEELEIRFEECPGTKXXXXXXXXXXXXXXXXXXXXXXXXXXWCCRE
                     CTMPPLSFRAKDGCWYGMEXXXXXXXESNLVRSMVTAGSTDHMDHFSLGVLVILLMVQ
                     EGLKKRMTTKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXATFAEMNTGGDVAHLAL
                     IAAFKVRPALLVSFIFRANWTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAWL
                     AIRAMVVPRTDNITLAILAALTPLARGTLLVAWRAGLATCGXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXVVGLLLLTRSGKRSWPPSEVLTAVGLICALAGGFAKADIE
                     MAGPMAAVGLLIVSYVVSGKSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     LVEDDGPPMREIILKVVLMTICGMNPIAIPFAAGAWXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXVGVMQEGVFHTMWHVTKGSALRSGEGRLDPYWGD
                     VKQDLVSYCGPWKLDAAWDGHSEVQLLAVPXXXXXXXXXXXXXXXXXKGGDIGAVALD
                     YPAGTSGSPILDKCGRVIGLYGNGVVIKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXPEIVREAIKTRLRTVILAPTRVVAAEMEEALRGXXXXXXT
                     TAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLYIXXXXXXXXXXXXXXXXXXXX
                     RVEMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEVPERAWSSGFDWVTDHSGKTVW
                     FVPSVRNGNEIAACLTKAGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXVLMRA
                     ETGSRPYKAAAAQMPETLETIMLLGLLGTVSLGIFFVLMRNKGIGKMGFGMVTLGASA
                     WLMWLSEIEPARIACVLIVVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXGMGKGMPFYAWDFGVPLLMIGCYSQLTXXXXXXXXXXX
                     XXXXXXXXXXXXAAAARAAQKRTAAGIMKNPVVDGIVVTDIDTMTIDPQVXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXYWNSSTATSLCNIFRGSYL
                     AGASLIYTVTRNAGLVKRRGGGTGETLGXXXXXXXXXXXXXXXXXXXXXXXXXVCREE
                     ARRALKDGVATGGHAVSRGSAKLRWLVERGYLQPHGKVIDLGXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXLKSGVDVFHMAAEPCDTLLCDIGESSSSPE
                     VEEARTLRVLSMVXXXXXXXXXXXXXXXXXXXXSTMMETLERLQRRYGGGLVRVPLSR
                     NSTHEMYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXNLGSGTRAVVSCAE
                     APNMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHGSYEAPTQGSASSLVNGVVRLL
                     SKPWDVVTGVTGIAMTDTTPYGQQRVFKEKVDTRVPDPQEGTRQVMSMVSSWLWKELG
                     KHKRPRVCTKEEFINKVRSXXXXXXXXXXXXXXXXXXXAVNDPRFWALVDKEREHHLR
                     GECQSCVYNMMGKREKKQGEFGKAKGXXXXXXXXLGARFLEFEALGFLNEDHWMGREN
                     SGGGVEGLGLQRLGYVLEEMSRIPGGRMYADDTAGWDTRISRFDLENEALITNQMEKG
                     HRALAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKTPVTKWTDIPYLGKREDLWCGS
                     LIGHRPXXXXXXXXXXXXXXXXXIIGDEEKYMDYLSTQVRYLGEEGSTPGVL"
     mat_peptide     1..312
                     /product="capsid peptide"
     mat_peptide     313..582
                     /product="propeptide"
     mat_peptide     583..807
                     /product="membane protein peptide"
     mat_peptide     808..2322
                     /product="envelope protein peptide"
     mat_peptide     2323..3408
                     /product="NS1 peptide"
     mat_peptide     3409..4062
                     /product="NS2A peptide"
     mat_peptide     4063..4494
                     /product="NS2B peptide"
     mat_peptide     4495..6303
                     /product="NS3 peptide"
     mat_peptide     6304..6744
                     /product="NS4A peptide"
     mat_peptide     6745..8250
                     /product="NS4B peptide"
     mat_peptide     8251..10206
                     /product="NS5 peptide"
     gap             608..1276
                     /estimated_length=669
     gap             1353..1831
                     /estimated_length=479
     gap             1914..2197
                     /estimated_length=284
     gap             2744..2850
                     /estimated_length=107
     gap             3675..3776
                     /estimated_length=102
     gap             3910..4012
                     /estimated_length=103
     gap             4199..4308
                     /estimated_length=110
     gap             4419..4552
                     /estimated_length=134
     gap             4917..5057
                     /estimated_length=141
     gap             5586..6381
                     /estimated_length=796
     gap             6631..6978
                     /estimated_length=348
     gap             7244..7382
                     /estimated_length=139
     gap             7741..7870
                     /estimated_length=130
     gap             8158..8268
                     /estimated_length=111
     gap             9196..9891
                     /estimated_length=696
     3'UTR           10210..10566
ORIGIN      
        1 gcccgtgtga gcccctttgg gggcttgaag aggctgccag ccggacttct gctgggtcat
       61 gggcccatca ggatggtctt ggcgattcta gcctttttga gattcacggc aatcaagcca
      121 tcactgggtc tcatcaatag atggggttca gtggggaaaa aagaggctat ggaaataata
      181 aagannnnnn nnnnnnnnnn nnnnnnnnng ctgagaataa tcaatgctag gaaggagaag
      241 aagagacgag gcgcagatac tagtgtcgga attgttggcc tcctgctgac cacagctatg
      301 gcagcggagg tcactagacg tgggagtgca tactatatgt acttggacag aaacgatgct
      361 ggggaggcca tatcttttcc aaccacattg gggatgaata agtgttatat acnnnnnnnn
      421 nnnnnnnnnn nnnnnnnnnn nnnnnnnnng agctatgaat gccctatgct ggatgagggg
      481 gtggaaccag atgacgtcga ttgttggtgc aacacgacgt caacttgggt tgtgtacgga
      541 acctgccatc acaaaaaagg tgaagcacgg agatctagaa gagctgtgac gctcccctcc
      601 cattcca                                                         
          [gap 669 bp]    Expand Ns
     1277                  gaca tgaaactgat gagaatagag cgaaggttga gataacgccc
     1321 aattcaccaa gagccgaagc caccctgggg gg                             
          [gap 479 bp]    Expand Ns
     1832                                   cagctcaga tggcggtgga catgcaaact
     1861 ctgaccccag ttgggaggtt gataaccgct aaccccgtaa tcactgaaag cac      
          [gap 284 bp]    Expand Ns
     2198                                         cac aaattctcat tggaacgttg
     2221 ctgatgtggt tgggtctgaa cacaaagaat ggatctattt cccttatgtg cttggcctta
     2281 gggggagtgn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnac
     2341 ttctcaaaga aggagacgag atgcggtaca ggggtgttcg tctataacga cgttgaagcc
     2401 tggagggaca ggtacaagta ccatcctgac tccccccgta gattggcagc agcagtcaag
     2461 caagcctggg aagatggtat ctgcgggatc tcctctgttt caagaatgga aaacatcatg
     2521 tggagatcag tagaagggga gctcaacgca atcctggaag agaatggagt tcaactgacg
     2581 gtcgttgtgg gatctgtaaa aaaccccatg tggagaggtc cacagagatt gcccgtgcct
     2641 gtgaacgagc tgccccacgg ctggaaggct tgggggaaat cgtacttcgt cagagcagca
     2701 aagacaaata acagctttgt cgtggatggt gacacactga agg                 
          [gap 107 bp]    Expand Ns
     2851                                  gagtgtgatc cagccgttat tggaacagct
     2881 gttaagggaa aggaggctgt acacagtgat ctaggctact ggattgagag tgagaagaat
     2941 gacacatgga ggctgaagag ggcccatctg atcgagatga aaacatgtga atggccaaag
     3001 tcccacacat tgtggacaga tggaatagnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     3061 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnncca
     3121 tggcacagtg aagagcttga aattcggttt gaggaatgcc caggcactaa ggnnnnnnnn
     3181 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     3241 nnnnnnnnat ggtgctgcag ggagtgcaca atgcccccac tgtcgttccg ggctaaagat
     3301 ggctgttggt atggaatgga gannnnnnnn nnnnnnnnnn nagaaagcaa cttagtaagg
     3361 tcaatggtga ctgcaggatc aactgatcac atggatcact tctcccttgg agtgcttgtg
     3421 attctgctca tggtgcagga agggctgaag aagagaatga ccacaaagan nnnnnnnnnn
     3481 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     3541 nnnnnnnnnn nnnnnnnnng tgccaccttc gcggaaatga acactggagg agatgtagct
     3601 catctggcgc tgatagcggc attcaaagtc agaccagcgt tgctggtatc tttcatcttc
     3661 agagctaatt ggac                                                 
          [gap 102 bp]    Expand Ns
     3777                                                              ggcc
     3781 tggttggcaa tacgagcgat ggttgttcca cgcactgata acatcacctt ggcaatcttg
     3841 gctgctctga caccactggc ccggggcaca ctgcttgtgg cgtggagagc aggccttgct
     3901 acttgcggg                                                       
          [gap 103 bp]    Expand Ns
     4013                                                          acgtggtg
     4021 ggactgctgt tgctcacaag gagtgggaag cggagctggc cccctagcga agtactcaca
     4081 gctgttggcc tgatatgcgc attggctgga gggttcgcca aggcagatat agagatggct
     4141 gggcccatgg ccgcggtcgg tctgctaatt gtcagttacg tggtctcagg aaagagtg 
          [gap 110 bp]    Expand Ns
     4309                                                     ct ggtggaggat
     4321 gacggtcccc ccatgagaga gatcatactc aaggtggtcc tgatgaccat ctgtggcatg
     4381 aacccaatag ccataccctt tgcagctgga gcgtggta                       
          [gap 134 bp]    Expand Ns
     4553                                                          gagtggga
     4561 gttatgcaag agggggtctt tcacactatg tggcacgtca caaaaggatc cgcgctgaga
     4621 agcggtgaag ggagacttga tccatactgg ggagatgtca agcaggatct ggtgtcatac
     4681 tgtggtccat ggaagctaga tgccgcctgg gacgggcaca gcgaggtgca gctcttggcc
     4741 gtgcccnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnncaaag
     4801 ggtggggaca ttggagcggt tgcgctggat tacccagcag gaacttcagg atctccaatc
     4861 ctagacaagt gtgggagagt gataggactt tatggcaatg gggtcgtgat caaaaa   
          [gap 141 bp]    Expand Ns
     5058                   tcc tgaaatagtc cgtgaagcca taaaaacaag actccgtact
     5101 gtgatcttag ctccaaccag ggttgtcgct gctgaaatgg aggaagccct tagaggnnnn
     5161 nnnnnnnnnn nnnngacaac agcagtcaat gtcacccact ctggaacaga aatcgtcgac
     5221 ttaatgtgcc atgccacctt cacttcacgt ctactacagc caatcagagt ccccaattat
     5281 aatctgtata ttatnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     5341 nnnnnnnnnn nnagggttga gatgggcgag gcggctgcca tcttcatgac cgccacgcca
     5401 ccaggaaccc gtgacgcatt tccggactcc aactcaccaa ttatggacac cgaagtggaa
     5461 gtcccagaga gagcctggag ctcaggcttt gattgggtga cggatcattc tggaaaaaca
     5521 gtttggtttg ttccaagcgt gaggaacggc aatgagatcg cagcttgtct gacaaaggct
     5581 ggaaa                                                           
          [gap 796 bp]    Expand Ns
     6382                        gtgctcatg cgggcagaga ctggaagcag gccttacaaa
     6421 gccgcggcgg cccaaatgcc ggagacccta gagaccatta tgcttttggg gttgctagga
     6481 acagtctcgc tgggaatctt tttcgtcttg atgaggaaca agggcatagg gaagatgggc
     6541 tttggaatgg tgactcttgg ggccagcgca tggctcatgt ggctctcgga aattgagcca
     6601 gccagaattg catgtgtcct cattgttgtg                                
          [gap 348 bp]    Expand Ns
     6979                    gg tatgggcaaa gggatgccat tctacgcatg ggactttgga
     7021 gtcccgctgc taatgatagg ttgctactca caattaacac nnnnnnnnnn nnnnnnnnnn
     7081 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnggc agcagctgcg
     7141 cgtgctgccc agaagagaac ggcagctggc atcatgaaga accctgttgt ggatggaata
     7201 gtggtgactg acattgacac aatgacaatt gacccccaag tgg                 
          [gap 139 bp]    Expand Ns
     7383   gtactgga actcctctac agccacttca ctgtgtaaca tttttagggg aagttacttg
     7441 gctggagctt ctctaatcta cacagtaaca agaaacgctg gcttggtcaa gagacgtggg
     7501 ggtggaacag gagagaccct gggagnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     7561 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnngg tgtgcagaga agaggcccgc
     7621 cgcgccctca aggacggtgt ggcaacggga ggccatgctg tgtcccgagg aagtgcaaag
     7681 ctgagatggt tggtggagcg gggatacctg cagccccatg gaaaggtcat tgatcttgga
          [gap 130 bp]    Expand Ns
     7871            gtcttaagag tggggtggac gtctttcata tggcggctga gccgtgtgac
     7921 acgttgctgt gtgacatagg tgagtcatca tctagtcctg aagtggaaga agcacggacg
     7981 ctcagagttc tctccatggt nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     8041 nnnnnnnnnn nnnnnnnnnn nagcactatg atggaaaccc tggagcgact gcagcgtagg
     8101 tatgggggag gactggtcag agtgccactc tcccgcaact ctacacatga gatgtac  
          [gap 111 bp]    Expand Ns
     8269                                                     aa tctcggctct
     8281 ggcacgcggg ctgtggtaag ctgcgctgaa gctcccaaca tgaagatcat tggtaaccgc
     8341 attgaaagga tccgcagtga gcacgcggaa acgtggttct ttgacgagaa ccacccatat
     8401 aggacatggg cttaccatgg aagctatgag gcccccacac aagggtcagc gtcctctcta
     8461 gtaaacgggg ttgtcaggct cctgtcaaaa ccctgggatg tggtgactgg agtcacagga
     8521 atagccatga ccgacaccac accgtatggt cagcaaagag ttttcaagga aaaagtggac
     8581 actagggtgc cagaccccca agaaggcact cgtcaggtta tgagcatggt ctcttcctgg
     8641 ttgtggaaag agctaggcaa acacaaacgg ccacgagtct gtaccaaaga agagttcatc
     8701 aacaaggttc gtagcnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     8761 nnnnnnnnnn nagctgtgaa cgatccaagg ttctgggctc tagtggacaa ggaaagagag
     8821 caccacctga gaggagagtg ccagagttgt gtgtacaaca tgatgggaaa aagagaaaag
     8881 aaacaagggg aatttggaaa ggccaagggn nnnnnnnnnn nnnnnnnnnn nnnnctaggg
     8941 gctagatttc tagagttcga agcccttgga ttcttgaacg aggatcactg gatggggaga
     9001 gagaactcag gaggtggtgt tgaagggctg ggattacaaa gactcggata tgtcctagaa
     9061 gagatgagtc gcataccagg aggaaggatg tatgcagatg acactgctgg ctgggacacc
     9121 cgcatcagca ggtttgatct ggagaatgaa gctctaatca ccaaccaaat ggagaaaggg
     9181 cacagggcct tggca                                                
          [gap 696 bp]    Expand Ns
     9892                                                         atccatgga
     9901 aagggagaat ggatgaccac tgaagacatg cttgtggtgt ggaacagagt gtggattgag
     9961 gagaacgacc acatggaaga caagacccca gttacgaaat ggacagacat tccctatttg
    10021 ggaaaaaggg aagacttgtg gtgtggatct ctcatagggc acagaccgnn nnnnnnnnnn
    10081 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnngga tcataggtga tgaagaaaag
    10141 tacatggact acctatccac ccaagttcgc tacttgggtg aagaagggtc tacacctgga
    10201 gtgctgtaag caccagtctt aatgttgtca ggcctgctag tcagccacag cttggggaaa
    10261 gctgtgcagc ctgtgacccc cccaggagaa gctgggaaac caagcctata gtcaggccga
    10321 gaacgccatg gcacggaaga agccatgctg cctgtgagcc cctcagagga cactgagtca
    10381 aaaaacccca cgcgcttgga ggcgcaggat gggaaaagaa ggtggcgacc ttccccaccc
    10441 ttcaatctgg ggcctgaact ggagatcagc tgtggatctc cagaagaggg actagtggtt
    10501 agaggagacc ccccggaaaa cgcaaaacag catattgacg ctgggaaaga ccagagactc
    10561 catgag
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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
1041923753%0.0100%KX101067.1
1041746742%0.093%KX101064.1
1038747043%0.093%KX101061.1
1036912153%0.093%KX087101.1
1036916453%0.093%KU509998.3
1036912753%0.093%KU870645.1
1036913453%0.093%KU926310.1
1036914553%0.093%KU926309.1
1036915953%0.093%KU729218.1
1032913253%0.092%KX117076.1
1032912753%0.092%KU820899.2
1032911953%0.092%KU527068.1
1029913053%0.092%KU820897.1
1027646440%0.092%KX101066.1
1023913953%0.092%KX051563.1
1023912353%0.092%KU963796.1
1023913453%0.092%KU497555.1
1020910753%0.092%KU365778.1
1014895553%0.092%KU681081.3
1005869253%0.092%KU681082.3
1000880953%0.091%KU955593.1
937913252%0.092%KU940228.1
937863549%0.092%KU940227.1
937912752%0.092%KU940224.1
931670738%0.092%KX101060.1
931905352%0.092%KU321639.1
930903552%0.092%KU729217.2
930904752%0.092%KU707826.1
928902952%0.092%KX087102.1
928901352%0.092%KU501215.1
926905452%0.092%KU991811.1
926901752%0.092%KU922960.1
926901752%0.092%KU922923.1
926902952%0.092%KU647676.1
926906352%0.092%KJ776791.1
922893752%0.092%KU744693.1
922902952%0.092%KU365780.1
922904052%0.092%KU365779.1
922902952%0.092%KU365777.1
884580532%0.094%KX101063.1
883654253%0.088%KU955595.1
883654653%0.088%KU955592.1
883656653%0.088%LC002520.1
879656653%0.087%KU955594.1
879653053%0.087%KU955591.1
879656653%0.087%KU720415.1
875653253%0.087%AY632535.2
872851550%0.090%KU501217.1
872851050%0.090%KU501216.1
872191312%0.090%KU312314.1
872860550%0.090%KU312312.1
866846850%0.090%KX056898.1
866891952%0.090%KU955590.1
866893552%0.090%KU853013.1
866893452%0.090%KU853012.1
866190412%0.090%KU312313.1
863895052%0.089%KU955589.1
863844750%0.089%KU866423.1
863847250%0.089%KU820898.1
863889052%0.089%KU740184.2
863860450%0.089%KU761564.1
8638635%0.089%KU686218.1
847657753%0.086%KF268949.1
838662353%0.086%KF268950.1
838663153%0.086%KF268948.1
836818250%0.088%JN860885.1
818810650%0.088%EU545988.1
803172910%0.091%KU646827.1
8018015%0.088%KU758878.1
800172610%0.091%KU646828.1
789818049%0.099%KF993678.1
787647452%0.086%KU963573.1
7809835%0.099%KT200609.1
764753649%0.086%HQ234499.1
76010426%0.091%KU312315.1
713541731%0.097%KX101062.1
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