cov    pid   1 [        .         .         .         .         :         .         .         . 80 
1 TRA5_LACLA/2-372    100.0% 100.0%     TQFTTELLNFLAQ-------KQDIDEFFRTSLETAMNDLLQAELSAFLGYEPYDKVGYNSGNSRNGSYSRQFETKYG-TV    
2 TRA3_RHIME/2-379     99.2%  28.9%     AIEKELLDQLLAGRDPS--EVFGKDGLLDDLKKALSERILNAELDDHLDVERLEGGPANR---RNGSSKKTVLTGTS-KM    
3 I6Y941_MYCTU/30-405  97.3%  28.8%     --ERALVGDLVRQARAEGVALTGPDGLLKALTKTVLEAALQEEMTEHLGYDRHAAAGRGSGNSRNGSRNKKVITDACGQV    
4 Q3Y3U6_ENTFC/1-382   99.5%  25.3%     MTQVHFTFESEEIQAII--NESGANDTAKTLMTIMFNQLMEEQRNQYIQANAYERSEERQ-SQRNGYYDRSFTTRIG-TL    
5 Q5HPJ6_STAEQ/1-380   99.2%  26.7%     MTQVHFTLKSEEIQSII--EYSVKDDVSKNILTTVFNQLMENQRTEYIQAKEYERTENRQ-SQRNGYYERSFTTRVG-TL    
6 TRA5_RHIME/1-377     99.2%  29.7%     MTKTEGKTASAAVKD----ILLSNPDGLREVIRTVMQEVLEAEMDEALGAAKGERTPERL-GYRSGHYGRTLITRVG-KL    
7 TRA1_MYCTU/1-380     98.9%  27.1%     MTSSH-LIDTEQLLADQ--LAQASPDLLRGLLSTFIAALMGAEADALCGAGYRERSDERS-NQRNGYRHRDFDTRAA-TI    
8 O06367_MYCTU/1-380   98.9%  26.6%     MALPQ-SALSELLDAFR--TGDGV-DLIRDAVRLVLQELSELEATERIGAARYERSDTRV-TDRNGARSRVLSTQAG-DV    
9 A1T2J4_MYCVP/6-378   97.3%  28.7%     ------SALLEVLDALR--TADAG-ERITQACEIVYQALIDAELTAKIGAALHERTETRS-NQRNGSRPRTLSTVAG-DL    
  consensus/100%                        ......................s..th.pt.hphh.tth.t.phsthhtht.htts..t....RsG...+.h.T.hs.ph    
  consensus/90%                         ......................s..th.pt.hphh.tth.t.phsthhtht.htts..t....RsG...+.h.T.hs.ph    
  consensus/80%                         ....t..h......t.....h.s..thhcthhphhhptlhptphsthltht.h-ts.tp..s.RNG.ht+ph.Tthu.pl    
  consensus/70%                         h...p.hht..thts.....hpu.s-hh+shhphhhptlhptEhsthlssthhE+stppp.spRNG.hpRsh.Tpsu.pl    

                         cov    pid  81          .         1         .         .         .         .         :         . 160
1 TRA5_LACLA/2-372    100.0% 100.0%     QLSIPRDRNGNFSP-ALLPAYGRRDDHLEEMVIKLYQTGVTTREISDIIERMYG-HHYSPATISNISKATQENVATFHER    
2 TRA3_RHIME/2-379     99.2%  28.9%     TLTIPRDRAGTFDP-KLIARYQRRFPDFDDKIISMYARGMTVREIQGHLEELYG-IDVSPDLISAVTDTVLEAVGEWQNR    
3 I6Y941_MYCTU/30-405  97.3%  28.8%     EIAVPRDRNGTFEP-VIVGKRKRRVTDVDRVVLSLYAKGLTTGEIAAHFADVYG-VSVSKDTISRITDRVIEEMQAWWSR    
4 Q3Y3U6_ENTFC/1-382   99.5%  25.3%     ELHVPRTRDGKFSP-TIFERYQRSEKALIAAMIEMVISGVSTRKVTKTVELLTDGATVSKSFVSNLMKQLDPFVFEWRNR    
5 Q5HPJ6_STAEQ/1-380   99.2%  26.7%     ELKVPRTRDGHFSP-TVFERYQRNEKALMASMLEMYVSGVSTRKVSKIVEELCG-KSVSKSFVSSLTEQLEPMVNEWQNR    
6 TRA5_RHIME/1-377     99.2%  29.7%     ELRVPQDRSGHFST-ELFERYQRSERALVATLAEMYVQGVSTRKVKAITEELCGHA-FSASSISAINKRLDESLKAFAER    
7 TRA1_MYCTU/1-380     98.9%  27.1%     DVAIPKLRQGSYFPDWLLQRRKRAERALTSVVATCYLLGVSTRRMERLVETLGVTK-LSKSQVSIMAKELDEAVEAFRTR    
8 O06367_MYCTU/1-380   98.9%  26.6%     ELRIPKLRKGSFFP-AILEPRRRIDQALYAVVMEAYVHGISTRAVDDLVEAMGVETGISKSEVSRICAGLDEIVGAFRTR    
9 A1T2J4_MYCVP/6-378   97.3%  28.7%     ELRIPKLRSGSFFP-ALLERRRRVDQCLFAVVMEAYLHGTSTRKVDDLVKALGADSGISKSEVSRICKDLDTEVGAFRDR    
  consensus/100%                        pltlPp.RtGpa.s..lh..htR...th.t.hhphh..Ghostthtthht.hhs...hS.s.lS.h.tth...h.ta.pR    
  consensus/90%                         pltlPp.RtGpa.s..lh..htR...th.t.hhphh..Ghostthtthht.hhs...hS.s.lS.h.tth...h.ta.pR    
  consensus/80%                         pltlP+.RpGpF.P.hlhtthpR..psl.thhhphYhpGhoTRclpthhcthhs.h.hS.s.lStlsctl...lttatpR    
  consensus/70%                         -LplP+.RsGpF.P.tlht+hpRt-psL.sslhphYhpGloTRclpthlEtlhs.ttlStu.lStlscplpp.VttapsR    

                         cov    pid 161          .         .         .         2         .         .         .         . 240
1 TRA5_LACLA/2-372    100.0% 100.0%     SLEAN-YSVLFLDGTYLPLR-RGTVSK-ECIHIALGITPEGQKAVLGYEIA--PNENNASWSTLLDKLQNQGIQQVSLVV    
2 TRA3_RHIME/2-379     99.2%  28.9%     PLELC-YPLVFFDAIRVKIR-DEGFVRNKAVYVALAVLADGSKEILGLWIE--QTEGAKFWLRVMNELKNRGCQDILIAV    
3 I6Y941_MYCTU/30-405  97.3%  28.8%     PLEKV-YAAVFIDAIMVKIR--DGQVRNRPVYAAIGVDLDGHKDILGMWAGEGDGESAKFWLAVLTDLRNRGVKDIFFLV    
4 Q3Y3U6_ENTFC/1-382   99.5%  25.3%     SLEGSEYPFFMCDALYMKVR-ENHRIVSKGVYIGIGIDSDGRRTILGFDVQ--DGESEDNWDTVFQSFVQRGLFGVKLVI    
5 Q5HPJ6_STAEQ/1-380   99.2%  26.7%     LLSEKNYPYLMTDVLYIKVR-EENRVLSKSCHIAIGITKDGDREIIGFMIQ--SGESEETWTTFFEYLKERGLQGTELVI    
6 TRA5_RHIME/1-377     99.2%  29.7%     SLEEP-FAYLILDARYEKVR-EAGVVMSQAVLIAVGIDWDGRRQILSVEMA--GRESRSAWKDFLVRLKGRGLKGVELVV    
7 TRA1_MYCTU/1-380     98.9%  27.1%     PLDAGPYTFLAADALVLKVR-EAGRVVGVHTLIATGVNAEGYREILGIQVT--SAEDGAGWLAFFRDLVARGLSGVALVT    
8 O06367_MYCTU/1-380   98.9%  26.6%     TLGHIEFPYVYLDATYLNVRNGTGQVVSMAVIVASGIAADGSREILGLDVG--DSEDETFWRGFLTSLKGRGLGGVRLVI    
9 A1T2J4_MYCVP/6-378   97.3%  28.7%     PLGEQRFPYVFLDATYCKAR-VNHRVVSQAVVIATGVAADGRREVLGFEVG--DSEDGAFWTAFLRSLKSRGLAGVQLVI    
  consensus/100%                        .Lt...ashhhhDshh..hR..tt..h...hhhu.ul..-G.+tlluh.ht...tEstt.W.thh..h.tpGh.th.hhh    
  consensus/90%                         .Lt...ashhhhDshh..hR..tt..h...hhhu.ul..-G.+tlluh.ht...tEstt.W.thh..h.tpGh.th.hhh    
  consensus/80%                         sLtt..ashlhhDuhhhplR..tt.lhs.sshlAhGls.-Gp+plLGh.ht..ssEstt.W.shhppLhtRGltsl.lll    
  consensus/70%                         sLpt..ashlhhDAhhhKlR.tsshVhspslhlAhGlshDGp+pILGh.lt..ssEstthWhshhppLpsRGltsltLVl    

                         cov    pid 241          :         .         .         .         .         3         .         . 320
1 TRA5_LACLA/2-372    100.0% 100.0%     TDGFKGLEQIISQAYPLAKQQRCLIHISRNLASKVKRADRAVILEQFKTIYRAENLEMAVQALENFIA-EWK-PKYRKVM    
2 TRA3_RHIME/2-379     99.2%  28.9%     VDGLKGFPEAITAVFPQTIVQTCIVHLIRHSLEFVSYKDRRTVVPALRAIYRARDAEAGLKALEAFEEGYWG-QKYPAIA    
3 I6Y941_MYCTU/30-405  97.3%  28.8%     CDGLKGLPDSVSAAFPLATVQTCIIHLIRNTFRYASRKYWDKISVDLKPIYTAASAAEARLRYEEFAEKWGK--PYPAIT    
4 Q3Y3U6_ENTFC/1-382   99.5%  25.3%     SDAHKGLVKAVRKNFLGASWQRCQAHFLRNIFDKLPKKVSSDVKDELKSIFKASELELTRERKEHFLEKYGCDSKLSAAC    
5 Q5HPJ6_STAEQ/1-380   99.2%  26.7%     SDAHKGLVSAIRKSFTNVSWQRCQVHFLRNIFTTIPKKNSKSFREAVKGIFKFTDINLAREAKNRLIHDYIDQPKYSKAC    
6 TRA5_RHIME/1-377     99.2%  29.7%     SDDHAGLVAAIGEVIPEAAWQRCYVHFLRNALDHLPRKHGDDCLQELRWLYDRRDLDEAKADLAAWLGKWSV--RYPRLT    
7 TRA1_MYCTU/1-380     98.9%  27.1%     SDAHAGLVAAIGATLPAAAWQRCRTHYAANLMAATPKPSWPWVRTLLHSIYDQPDAESVVAQYDRVLDALTD--KLPAVA    
8 O06367_MYCTU/1-380   98.9%  26.6%     SDQHAGLVKALKRCFQGAGHQRCRVHFARNLLAHVPKDKADMVASMFRMIFSAPDAEAVHATWEGVRDRLAA--SFPKIG    
9 A1T2J4_MYCVP/6-378   97.3%  28.7%     SDAHAGLRAAIDAVLIGSAWQRCRVHFLRNVLAQVPKGSAEMVAAAIRTIFAQPDAEHVREQLDTIAGMLGR--QFPKVE    
  consensus/100%                        sDthtGh.t.lttsh..s..QpC.hHh.tp.ht.h.h.....h...h+.lat..pht.sh.thtth.t.......h.th.    
  consensus/90%                         sDthtGh.t.lttsh..s..QpC.hHh.tp.ht.h.h.....h...h+.lat..pht.sh.thtth.t.......h.th.    
  consensus/80%                         sDshtGL.tulttsh..sthQpC.hHhhRNhhthhs+t..t.hh..h+.Iapt.shp.shtthpthht.hht..phstht    
  consensus/70%                         oDuatGLstAlptsh.tushQRChlHhhRNhhstls+tptp.lhttl+sIapt.-h-.shtth-thhtthht..pastls    

                         cov    pid 321          .         .         :         .         .         .         . ] 392
1 TRA5_LACLA/2-372    100.0% 100.0%     ESLENTD-NLLTFYQFPYQIWHSIYSTNLIESLNKEIKRQTKKKVLFPNEEALERYLVTLFED---YNFKQS    
2 TRA3_RHIME/2-379     99.2%  28.9%     QSWRRNWEHVVPFFAFPEGVRRIIYTTNAIEALNSKLRRAVRSRGHFPGDEAAMKLLYLVLNN-AAEQWKRA    
3 I6Y941_MYCTU/30-405  97.3%  28.8%     RLWDSAWEEFIPFLDYDVEIRRVPCSTNAIESLNARYRRAVRARGHFPNEQSALKTLYLVTRSL-D------    
4 Q3Y3U6_ENTFC/1-382   99.5%  25.3%     DILENGFEDAIQILSFPENIRRRIRTTNVLERLNEEIRRRERVIRIFPNINSITRIIGTLLMEK-DTEWLA-    
5 Q5HPJ6_STAEQ/1-380   99.2%  26.7%     ASLDDGFEDAFQYT-VQGNSHNRLKSTNLIERLNQEVRRREKIIRIFPNQTSANRLIGAVLMDL-HDEWIY-    
6 TRA5_RHIME/1-377     99.2%  29.7%     SWVEETIEQTLTFFRLPRQHHKHLKSTNMLERLNEEIRRRTYVVRIFPNTESCLRLVRALAVET-HENWMEA    
7 TRA1_MYCTU/1-380     98.9%  27.1%     EHLDTARTDLLAFTAFPKQIWRQIWSNNPQERLNREVRRRTDVVGIFPDRASIIRLVGAVLAEQ-HDEWIEG    
8 O06367_MYCTU/1-380   98.9%  26.6%     PLMDDARAEVLAFTAFPKAHWQKIWSTNPLERINKEIKRRSRVVGIFPNPAAVIRLVGAVLADM-HDEWQAS    
9 A1T2J4_MYCVP/6-378   97.3%  28.7%     TMLREAAEDITAFADFPAAHWKKIWSTNPLERLNKEIKRRTDVVGVFPNPAALLRLAGSVLVEA-HDEWQV-    
  consensus/100%                        ..hcps..phh.hh.h..t.hp..hosN..EtlNtch+Rt...hhhFPs.tuh.+hhh.lh.p.........    
  consensus/90%                         ..hcps..phh.hh.h..t.hp..hosN..EtlNtch+Rt...hhhFPs.tuh.+hhh.lh.p.........    
  consensus/80%                         t.hcpshtphh.ahths.thhp.lhoTN.lEpLNpcl+Rt.chhthFPs.tuh.+hlhhlh.p..t.pa...    
  consensus/70%                         p.h-pshpchlsFhtaPtthh+plhSTN.lEpLNpEl+RpscshtlFPN.tuhhRllhslhh-..cppW...