cov pid 1 [ . . . . : . . . 80 1 7300690/20-253 100.0% 100.0% QKLPAKVKKCHFGD----GKCLVESANALLR-DFPKGIPEVD--LKPFNVLSVRDWLLVNDSQVGGAWYYFNLINQINYG 2 7300689/20-252 99.6% 54.5% QILPKEIKKCRFGD----SKCIVNSMNAIIK-NYPKGIPAIG--LKPIDVVDIRDSKFWNDAMVGAFWLNFDLFNQVNYG 3 7301542/40-274 97.8% 23.6% SEKPAFLPSCRIYEP-GFTKCSTNSIQKLLD-QLNIGIPEVLERFGPFDPMRVRDIVFKQDN-NEVATIRANLTDLVVKG 4 7301544/17-251 97.8% 19.8% TEKPSYIESCKIYEP-EFTKCSTRSIQAFMN-QLVKGVPEIEESFGPIDPMRQEQLVFKQDN-SDVATLSANLTDMLIRG 5 7301541/26-258 97.8% 20.8% AEKPDFLIPCIVGDP-NFNVCLTKNFQSFFR-QWKDGIPGYN-AVGSFDPFYIKRVKFTQDA-SRSIAINADLKEVYVAG 6 7300097/32-259 97.4% 23.9% DQLPSFLKVCHRNAP-DLDTCVRESYEELRP-RLMEGIPELY--IPAMEPLVVPQVKMDQDS--GAIYLHSVYRNVKVTG 7 7300096/42-270 97.0% 20.4% QERPSWLQTCKRSNP-NEDKCFRQLFEGCFP-ALAAGIPEIG--VKSFEPLNIDQVSVSKGS--GNLVLSGGFQDLVIRG 8 7296800/20-249 97.0% 22.5% QEQPYYLQQCPRDEA-QINECLRESGNKLVH-YLQKGVPELD--IYEIEPVMIDEIGIVLGS--GPDGYRALFRNIQAYG 9 7296799/19-246 96.5% 17.8% AETPPYIKQCHRNDP-KLVDCFIGAIEHLKP-YLANGIPDIQ--LPSVEPFKMDTLALQLTE--GPQGYKITLKNMEAFG 10 7301295/18-249 98.7% 21.5% AKFPEDPKPCKYGD----GECIMKLCNTLFSENSAEGDPGLN--LMQLDPLKVDRMVISQGESSSPVGITLTFTDNLLYG 11 3261846/27-260 99.1% 20.0% EGFPSPLKRCKLQD----ESCLLAQAQTFFQ-AFKNGIPERQ--VAALEPIALGTMFIESGGHSESIKFKLTMSDAKLYN 12 7301297/21-250 98.3% 22.2% SDFPSGIERCAIMD----EQCLEDRVNFVLRNYAKSGIKELG--LIPLDPLHVKKFKIGRNP-HSPVNIDLSFHEMDILG 13 7301176/12-238 97.0% 23.1% DFSAEGFPKCKRDAN--FDKCLVDAVNVAIQ-QLKAGNREFG--IPPLEPLTVKKLVIDAGN--APINLRQALKNVKVHD 14 6560645/18-239 94.8% 20.1% KTAVLPVEKCHLED----SKCMIPAIQKALP-VFLDGLPDLG--INVMDVLEMDDIKFDI------SGLQFSLTEGKLKG 15 5052546/33-262 97.4% 17.0% REIPGDIPTCREGDI-NISECIKQGLQQITP-RMKYGISELN--IPPLDPFEMGKSSYSYTS--GLLQGRISMKNVVIHG 16 7298030/22-250 97.4% 18.3% KNYFADLPKCSTEED-QLGECVKQLFNTLTP-RLKDGNPELR--IEPYEPLHLNRTSFQYSS--GTVNGRITVRNAKIYG 17 7298031/93-323 97.0% 14.3% SSGSNEVTPCSLNSP-DLNECIRGLIQSFAPKLRYQGVPEFN--MDSIDPYFYKRGIFRYTN--DGIQGGLLIKNMEIYG 18 7300762/37-260 95.2% 17.0% TDLKHLLGRCHWSDE-DFNECMRQVFNDLRA-YFTTGVPDYN--IKPFDPHHCSYVELRRGESQGLGSFRLILRNVSEYG 19 505621 95.7% 14.1% ASYAVHQKKCNSKD----SECLKNYFQEVVWEAAKNGLPEVG--IPILDPVEIKDYHVSV------PGWVSFDFDGVGQE 20 7287790 96.5% 12.3% ASAASMGQPIETQS---ISSTIVDVIEGIKE-QMPCGFTSVG--LPPLAPLRIDHQDINIDS--SVLKAQGTIDHFRLNG 21 7287791 97.0% 15.5% ARNPAKPDTQGLIL----NGSVKKAINGLLN-QMPCGWPQYG--IPPLDPYTNADLRIHLAE--SVVDTLLQFLRFRFDG 22 7287789 96.1% 10.3% CQGAEVAEPLSGRS---FSSVIVDGLEAFRV-VLQNGSPRFG--IPVMAPMKAAQRSFEINS--GEFSGTFGVENFELQG 23 7287793 97.4% 11.0% CVIFVALLCCSLGSAKLFDDELRELTEFLRL-QMRCGYPARG--VPILAPAQMAYKEIGIRT--ENFGCNGNFTDLIIEG 24 7295803 92.6% 11.1% QEASESDDALKIKE---SQASIAAQVEAMLV-HFQQEDPQGLPGVPVPDPLEVPNVKKSM------GMANLDMKQVKAYG 25 6625564 95.7% 15.0% SDGDALLKPCKLGD----MQCLSSATEQFLE-KTSKGIPQYD--IWPIDPLVVTSLDVIAPS---DAGIVIRFKNLNITG 26 726332 95.2% 11.9% SEGGVFFNPCYKSD----IKCLSNATETFLE-KTCNGYPNTE--IKAIDPLVIPELKVVVDE---SMGLVFDFKNINIVG 27 Q26300 95.7% 11.9% SDQGALFEPCSTQD----IACLSRATQQFLE-KACRGVPEYD--IRPIDPLIIPSLDVAAYD---DIGLIFHFKNLNVTG 28 Q9V3P4 94.8% 13.1% -QEGVEVAPQFIV-----SWQARRFIRKLQK-QMECGWPQYG--IPVLAPLRINEFDLDYKK--GIFETLNHVFRLKIAG consensus/100% .........................hp.h.......t..th...h...tsh......h..........h.....p....t consensus/90% t........h.h.t.....tsh.t.hp.hh...h.tG.sth...h..htsh.h.p..h..........h...h.p....s consensus/80% tphs..h..Cthtp....tpshhp.hpthh...h.pGhPpht..l.sh-Ph.htph.ht.tt....hth.hthpph.hhG consensus/70% pphss.hp.Cphts....spClhp.hpthh..thtpGhPphs..l.sh-Phphtphthphsp..tshthphshpsh.lhG cov pid 81 . 1 . . . . : . 160 1 7300690/20-253 100.0% 100.0% FENTTITE-IRGFDKD-PTTTKIEIHGKIPRLVYK-GDYVAKGR-------MLWFVDIHSQGTSESDFLNFQ--FVLTLK 2 7300689/20-252 99.6% 54.5% FENTTITK-VSGFDEN-PTSSLIEIHGRIPSLIHK-GDYFSMGR--------VWIVQMNSTGESLSDFQNFR--FVLKLK 3 7301542/40-274 97.8% 23.6% FANTKVKE-SRVSKKD----FSWQTKIYLPKMRLD-GRYEMAGR--------ILLIPLSGSGKIFIEIDDLD--ILLLTK 4 7301544/17-251 97.8% 19.8% FGKMLIKE-SKVSKKD----FSWLTKIYLPQMRID-GHYKMVGR--------ILLVPLQGNGKIVMEIDDLD--ILMTTK 5 7301541/26-258 97.8% 20.8% AGQALVLE-SSWDPNH----YVARTLISVPKLRFN-FDYKVKGH--------VSALNLNGHGKGYFEAENAL--LLLELA 6 7300097/32-259 97.4% 23.9% ISKHTVNE-LRLEPSK----LKFILSLTFPKLHME-SDYSIKGK--------IMMMPLLGDGHCKVDLVNIT--MRTELI 7 7300096/42-270 97.0% 20.4% PSNATVRR-ASLDLER----RLLNFELELPRLRIR-AKYNLKGN--------ILLLPLVGSGDVAMALKNVHTTVYTRIS 8 7296800/20-249 97.0% 22.5% VSNITVTN-IRSDLDS----LQFQLTCEIPRIRVK-AQYRSTGV--------LILVKASGAGDYWGEYEGVKAKIYFKAV 9 7296799/19-246 96.5% 17.8% ASNFKVTS-LKLSEGS----EPFKAKIVMPKLKIE-AKYTSSGV--------LLILPASGGGDFHANFEGVSADLTGKTS 10 7301295/18-249 98.7% 21.5% IKDQRIVK-VKGFGRDLT--AKHEVKIVTKTFSLV-GPYNIQGK--------VLILPISGTGQSNMTMVNVR--AIVSFS 11 3261846/27-260 99.1% 20.0% LANSMMVKSLKGFTKDLTRPLKLTLLLDNPELEVR-AKYDVDGK--------LLILPIVSKGDLTIRLNDVHTKVWITAE 12 7301297/21-250 98.3% 22.2% LHQGVAKR-VSGFTRDLS--RSIELVMEVPEIGVR-GPYSVDGR--------ILILPITGNGIADIRLTRTK--VRAQIK 13 7301176/12-238 97.0% 23.1% MISTSKIQRYRTDLDK----HLIICDSRTDRIEMI-GDYEMSGR--------ILLLPITGHGKANVTLINTK--IEHRLI 14 6560645/18-239 94.8% 20.1% LKSSIIDD-VKWDLKS----KKFEIHYHAD-CTVK-GHYTAAGR--------ILVLPITGDGDMKLKLKNLNIKLYISYE 15 5052546/33-262 97.4% 17.0% LSEGIVDK-VNFRLKDG--RVRMEILSHVPQMFVE-GLYKADIK--------LNDLKLNPKGAFNITMTDVA--MRARPI 16 7298030/22-250 97.4% 18.3% FSSNRAKE-VSVKLNGD--KVKLRLVTQMPKLNIV-GSYKADMQ--------VNQLQLKPKGEFNVTLLDVE--AITVTD 17 7298031/93-323 97.0% 14.3% ISQLQVNS-VAANFTDN--GFIIKLGVELPQLKAG-GHFKADVK--------FGGLRLVPKGPFNITIDNIKATILTDGH 18 7300762/37-260 95.2% 17.0% WARSEVTK-FHADPED----QRIVYTQYFPDKSLE-GEYEFAAK--------MLGTEMNRKGHWNLTLYDY---SQTTSV 19 505621 95.7% 14.1% MKSCFLNK-FWMNFEK----RYASMEMICD-LQMK-GHYKLFSN-SSLIRNLLDGDTLHGDGNGGLKFEKMK--MSFDFR 20 7287790 96.5% 12.3% LNDFDIDE-MKVNAIT----SKVTYKFTFRDVNVD-TQYDLSVL----LKKYGFTINLIGAGHAKFAIKDMV--IWGTMK 21 7287791 97.0% 15.5% LEGMEIKK-MKVSYTF---SKKVKFHFNFPELKAS-AHYLDTNTFVNLLKELGLSVRYESSGPLSFSLQNLS--IQGEFK 22 7287789 96.1% 10.3% LDQYEIIT-MNMDVIR----SRLTFNINFASLNFT-TDYEMDM---------GSGYRIKRNGGAFFALEDLN--IQGRIS 23 7287793 97.4% 11.0% LDGYEFSK-LEWNNIL----HTIKFDMNFPKISLKSTNYKLNLL------ARLFGADFSLWGDGALSLELIN--FRAYGS 24 7295803 92.6% 11.1% LSKFRIDK-MNLDLKE----MRFNGGLQLDQMLVK-GQYTLSS------------FFSKANGPFTVVLKNVY--AEATAF 25 6625564 95.7% 15.0% LKNQQISD-FQMDTKA----KTVLLKTKAD-LHIV-GDIVIELT--------EQSKSFTGLYTADTNVIGA---VRYGYN 26 726332 95.2% 11.9% LKNQQISD-FKMDTDK----KSVVLKTKAI-LNIV-ADLKIEFT--------KQNKVFNGPYIAKATALGS---SQYGYS 27 Q26300 95.7% 11.9% LKNQKISD-FRMDTTR----KSVLLKTQAD-LNVV-ADVVIELS--------KQSKSFAGVMNIQASIIGG---AKYSYD 28 Q9V3P4 94.8% 13.1% LNDFNIQK-FKLNVIT----SKITFDFLFKNIDTTAQKYDTDTL---IDALRQLGLSVEYEGSGELLFDLVNLRIAGTLK consensus/100% ..t..h.p..............h.h......h.h....h......................h.....h........h... consensus/90% htp..h.p..ph...t......h.h...h..h.h..s.h................h.h...h...hth.th...h.h.h. consensus/80% htp..lpc.hphp.pp......h.hth.hsphph..upYphth.........h..h.htstGth.hph.sh...h.hph. consensus/70% hpphplpc.hphshpp....hphphphphsplphp.ucYphpsp........h.hh.hpupGphthph.shp..hhhphp cov pid 161 . . . 2 . . . . 240 1 7300690/20-253 100.0% 100.0% VRVEYR-NNKRYLKIYELVPNIRLDR---WIMWLDNFFPD-------NEDLTIAVNNLFNRNWVEFW-NELEPGILRLFE 2 7300689/20-252 99.6% 54.5% VIMEYR-NNKRYLKIYELTPFVTMDR---WVFWLDNFFES-------NTDMTIAINQVFNLHWVEFW-NELEPTNLKIFA 3 7301542/40-274 97.8% 23.6% IRLYEK-GGFTFDNVTAVQVQLNLSK---VRTYLDNLFNG------RSKEVERSTNEFFNENWRDFY-EALKPLIVETVE 4 7301544/17-251 97.8% 19.8% TRLYEK-GGYTFYNVTSVKVKVDVGK---VRTRLDNLFNG------HSKEVEDSTNQFFNDNWKDVF-EALRPLVVETVE 5 7301541/26-258 97.8% 20.8% VKPLAT-SDGYFADVQSVKVNFREIK--QFRIKLENLFGG-------NKDLEDTAHILFNENWRDFF-EVLRPAVEQTVG 6 7300097/32-259 97.4% 23.9% GQEYKK-NGANFLKINTVKVKYELSD---VHIHLDNLFNG-------DKALGDRMNEFLNENWKALA-EEVRPLMTKALV 7 7300096/42-270 97.0% 20.4% LRNETR-TGDEIIHIDEMKVGFDVGA---MRIHLKNLFNG-------NEILAASINSFLNQNGKEVI-AELRPDLELGLA 8 7296800/20-249 97.0% 22.5% ANEGP--DGRTYLTTDSVKMDFNVKE---IQMGVDNIANG-------NTVIQAALNLFINSNSQELL-KEMKPALRTKLT 9 7296799/19-246 96.5% 17.8% IHAF---KGANYLHIDALSLVLDVKD---VKMSISGAFNN-------NRILLEATNLFLRENSQVVL-EAMQAQLQKKLA 10 7301295/18-249 98.7% 21.5% GKPLVK-NGETYLDVTDLKITMKPES---SHYHFSNLFNG-------DKALGDNMNVFLNENSEAIY-KETAKAIDRSFG 11 3261846/27-260 99.1% 20.0% PVKRS--DGHTYLNITDYKTATKIKG---GHFDLSNLFND-------NKELRDSTLKVLNLEWSTLA-LDVQPKINEACA 12 7301297/21-250 98.3% 22.2% LKRVSKGDHQTYAEVMNIKVELDPSH---VTYQLENLFNG-------QKDLSENMHALINENWKDIF-NELKPGIGEAFG 13 7301176/12-238 97.0% 23.1% GEPFEK-DGVKYMRLKDYRVSFDPKR---VYMNFENLFND--------KTLSDGMNRFLNENWETVF-NELKVGYAKSFG 14 6560645/18-239 94.8% 20.1% VEKGA--DGKDHIAPKKLDYDFEVVD--NAQFSLTNLFNG-------NKELSDTMLKFLNENWKQIS-LEFGKPLMDVAA 15 5052546/33-262 97.4% 17.0% GELYER-DGHTYLRLTKLETEPKVGD---LKFYANGLVPD--------PVLNDVILDFINQYWRQLY-QAMLPETLDTWQ 16 7298030/22-250 97.4% 18.3% GEVYEK-DGHRFFRLKNIDSKPKIKD---LVIKANGIFAD--------PELDKIALNVANQYWRDIY-GIMLPETRQFWQ 17 7298031/93-323 97.0% 14.3% IEQLP--SGQQRLSLHRLNANVNIGD---AKVVANGIFSD--------RNLNAMILNLVNENLPEIT-RVGIPATREQWA 18 7300762/37-260 95.2% 17.0% RRIGG------PGSLIKVHVEVDRIG--GMELHIENLLQG--------QPLNQLADGVINSMWQLGL-PFIKPMINELVS 19 505621 95.7% 14.1% FKVEQR-GGDNFLNIDSESSKFNVDILRGASFAADNLYLG-------DVEASATIMKVMNQHWKLVM-DGTALPFMYKIK 20 7287790 96.5% 12.3% YSLG---VISGNLKLKSLEVRTHLGE---VDSEIEGILGD--------GSINEKMNEYLAEAVELAI-NENEDLIADTIE 21 7287791 97.0% 15.5% YKMPF---IFGSIKIYKFSCAVGLGG---VSSNIGGVMGN--------GRINEFINDMLDKEIPAFI-NGNQEQISAKIE 22 7287789 96.1% 10.3% YSLG---VFTSQLRVKDVLIYPSVGN---VNSQIENLSKYRIFNRKLNEIIEEFVTLTINENTDFVA-AWLLIVAAKPTN 23 7287793 97.4% 11.0% FVIRPK-SATSGVYAKSWKVNWELEE---AKSQTTGFMNS--------RLYTKFINDLIVEYLDIMI-NDNPTEVSQFME 24 7295803 92.6% 11.1% LAVER----DGQLATDRIKIDITFSD---MTMDFQNLGLV-------GSVFQSVVNGAPNLVFDAMK-PFMLQEADKKLR 25 6625564 95.7% 15.0% LKNDD--NGVQHFEVQPETFTCESIG--EPKITLSSDLSSAL-----EKDSGNNSLEPDMEPLKTLR-QAAICKIAEACY 26 726332 95.2% 11.9% FTKK---DDKEYFVVGSEENACEIIG--EPDVEIGEELQKAL-----LNDADAKAMKPDYEANKVALRKKTLCHIVEAAY 27 Q26300 95.7% 11.9% LQDDS--KGVKHFEVGQETISCESIG--EPAVNLNPELADAL-----LKDPDTTHYRKDYEAHAVGIRQRSLCKIVELCY 28 Q9V3P4 94.8% 13.1% YKLP---MLWGSAKITSLKTTISLES---VTSDITGFMGN--------GKINRAINSQLENIVVKGI-NGNQDAISETIE consensus/100% ......................t..........ht..............................h............h. consensus/90% h.........t.hth.t.p...p..t.......hps.h.s..........htt.h..........hh.......h.t.h. consensus/80% hp........t.hpltphphthp..t...hphthpshhts........t.hpt.h.thhsp.ht.hh.t.h...h.phht consensus/70% hp.....sstphhplpphpsphphtp...hphplsslhss........ptlspth.phhNpthpthh.pthhsth.ctht cov pid 241 : . ] 265 1 7300690/20-253 100.0% 100.0% TVFLS---LFEDLFEKVPYDDLFLA 2 7300689/20-252 99.6% 54.5% AEDVE-KCHFGDSTCLVRSINALIK 3 7301542/40-274 97.8% 23.6% NILYD---VMSTVFHLIPANFFVED 4 7301544/17-251 97.8% 19.8% RTLLD---LLHKTFALFPASFFVED 5 7301541/26-258 97.8% 20.8% GVLLD---RFKKTFVYVPATYLIKD 6 7300097/32-259 97.4% 23.9% DILRA---SVDKLFASFSYDDLLPM 7 7300096/42-270 97.0% 20.4% DIFHG---LWNNVFSKMPTKLWLV- 8 7296800/20-249 97.0% 22.5% LVIRN---FMDRIFAKIPLDEWINL 9 7296799/19-246 96.5% 17.8% SEFGK---LANQLLKNVPVEQFYVD 10 7301295/18-249 98.7% 21.5% KLYLG---VVKGVFSKLPYAKFFAD 11 3261846/27-260 99.1% 20.0% KAFSA---IVQSLWANIPYDEFFEK 12 7301297/21-250 98.3% 22.2% LIAKS---VVDRIFGKLPLEQLFVV 13 7301176/12-238 97.0% 23.1% IIFRE---LSNKLFEKVPFDNIFLS 14 6560645/18-239 94.8% 20.1% KSIFK---NVITFFAKEAIEDIAEV 15 5052546/33-262 97.4% 17.0% PLILK---STNDFFAALPFDMLVTK 16 7298030/22-250 97.4% 18.3% PLMLR---MFNEAFELVPIDQFLKE 17 7298031/93-323 97.0% 14.3% PILIA---HINEFFAKVPIEKFLVQ 18 7300762/37-260 95.2% 17.0% TAFTD---IFNESFRHFPLEKFLAT 19 505621 95.7% 14.1% GLFYD---LTQKYFNNVPVKIISMM 20 7287790 96.5% 12.3% SIALP---AVNSVLDDISIAEIISG 21 7287791 97.0% 15.5% EIFVP---LANAHLTGHKIWYLFSL 22 7287789 96.1% 10.3% PQLLNSDDPVQRELERQAKEETVHL 23 7287793 97.4% 11.0% ELIVP---PMNLVLDNLAWYEITAI 24 7295803 92.6% 11.1% SEINV---MIQKTLGERRLPNSITP 25 6625564 95.7% 15.0% ISVVH---NIRASAKILPASSFFEN 26 726332 95.2% 11.9% VTVIH---NIRAVAKLFPKEAFFLD 27 Q26300 95.7% 11.9% VDVVH---NIRAVAKILPSTAFFTD 28 Q9V3P4 94.8% 13.1% NAIVP---RVNKMLKG--KDFWTVV consensus/100% .............h........... consensus/90% ..hh.....hpt.ht...h..hh.. consensus/80% ..hht....hpthht.hsht.hh.. consensus/70% .hhht...hhpphhtthshpthh..