cov    pid   1 [        .         .         .         .         :         .         .         . 80 
 1 TRF1_SALSA     100.0% 100.0%     VKWCVKSEQELRKCHDLAAKVA--------EFSCVRKDGSFECIQAIKGGEADAITLDGGDIYTAGLTNYGLQPIIAEDY    
 2 TRF2_SALSA     100.0% 100.0%     VKWCVKSEQELRKCHDLAAKVA--------EFSCVRKDGSFECIQAIKGGEADAITLDGGDIYTAGLTNYGLQPIIAEDY    
 3 TRF_BLADI       96.2%  22.1%     YKVCVPEGALES-CHRMSQE-------SDLHMTCVAARDRIECLDKIKHREADFAPVDPEDMYVAAKIPQQDFIIFKEIR    
 4 TRF_MANSE       96.8%  20.4%     YKLCVPAAYMKD-CEQMLEVPTK----SKVALECVPARDRVECLSFVQQRQADFVPVDPEDMYVASKIPNQDFVVFQEYR    
 5 TRFE_ANAPL      98.4%  47.8%     VRWCTISSAEEKKCNSLKDHMQQERVT----LSCVQKATYLDCIKAISNNEADAISLDGGQVFEAGLAPYKLKPIAAEVY    
 6 TRFE_BOVIN      96.8%  41.0%     VRWCTISTHEANKCASFRENVLRILES-GPFVSCVKKTSHMDCIKAISNNEADAVTLDGGLVYEAGLKPNNLKPVVAEFH    
 7 TRFE_CHICK      98.4%  46.4%     IRWCTISSPEEKKCNNLRDLTQQERIS----LTCVQKATYLDCIKAIANNEADAISLDGGQAFEAGLAPYKLKPIAAEVY    
 8 TRFE_HORSE      97.1%  42.1%     VRWCTVSNHEVSKCASFRDSMKSIVPA-PPLVACVKRTSYLECIKAIADNEADAVTLDAGLVFEAGLSPYNLKPVVAEFY    
 9 TRFE_HUMAN      96.8%  42.8%     VRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFY    
10 TRFE_PIG        97.1%  41.3%     VRWCTISNQEANKCSSFRENMSKAVKN-GPLVSCVKKSSYLDCIKAIRDKEADAVTLDAGLVFEAGLAPYNLKPVVAEFY    
11 TRFE_RABIT      96.8%  42.5%     VRWCAVNDHEASKCANFRDSMKKVLPEDGPRIICVKKASYLDCIKAIAAHEADAVTLDAGLVHEAGLTPNNLKPVVAEFY    
12 TRFE_XENLA      99.4%  48.8%     VRWCVKSNSELKKCKDLVDTCKNKEI----KLSCVEKSNTDECSTAIQEDHADAICVDGGDVYKGSLQPYNLKPIMAENY    
13 TRFL_BOVIN      97.8%  41.0%     VRWCTISQPEWFKCRRWQWRMKKLGAP---SITCVRRAFALECIRAIAEKKADAVTLDGGMVFEAGRDPYKLRPVAAEIY    
14 TRFL_HUMAN      97.8%  41.9%     VQWCAVSQPEATKCFQWQRNMRKVRGP---PVSCIKRDSPIQCIQAIAENRADAVTLDGGFIYEAGLAPYKLRPVAAEVY    
15 TRFL_MOUSE      97.8%  39.6%     VQWCAVSNSEEEKCLRWQNEMRKVGGP---PLSCVKKSSTRQCIQAIVTNRADAMTLDGGTLFDAGKPPYKLRPVAAEVY    
16 TRFL_PIG        96.8%  39.4%     VRWCVISTAEYSKCRQWQSKIRRTNP-----IFCIRRASPTDCIRAIAAKRADAVTLDGGLVFEAG--QYKLRPVAAEIY    
17 TRFM_HUMAN      96.2%  38.6%     VRWCATSDPEQHKCGNMSEAFREAGIQP--SLLCVRGTSADHCVQLIAAQEADAITLDGGAIYEAG-KEHGLKPVVGEVY    
18 TRF1_SAL_2      90.5%  33.2%     IKWCAVGHAEKGKCDTWTINSFADGE---SKISCQDAPTVEECIKKIMRKEADAIAVDGGEVYTAG-KCG-LVPVMVEQY    
19 TRF2_SAL_2      90.5%  33.1%     IKWCAVGHAEKGKCDTWTINSFADGE---SKISCQDAPTVEECIKKIMRKEADAIAVDGGEVYTAG-KCG-LVPVMVEQY    
20 TRF_BLA_2       91.1%  32.0%     VRFCVTSDAELEKCRVLKRAAYSRDIR--PAFDCVREAGLHECLRTVRDDGADVITLDGGEVFVAQ-RQYNLKPIVAEQY    
21 TRF_MAN_2       81.0%  19.9%     VRLCVTSNVALSKCRAMSVFAFSRDIR--PILDCVQENSEDACLKSVQDNGSDLASVDDMRVAAAA-KKYNLHPVFHEVY    
22 TRFE_ANA_2      89.8%  31.6%     IQWCAVGKDEKSKCDRWSVVSNG-------EVECTILDDNKDCIVKITKGEADAISLDGGFVYTAG-VCG-LVPVVGESY    
23 TRFE_BOV_2      89.5%  29.9%     VKWCAIGHQERTKCDRWSGFSGG-------AIECETAENTEECIAKIMKGEADAMSLDGGYLYIAG-KCG-LVPVLAENY    
24 TRFE_CHI_2      89.8%  30.0%     IQWCAVGKDEKSKCDRWSVVSNG-------DVECTVVDETKDCIIKIMKGEADAVALDGGLVYTAG-VCG-LVPVMAERY    
25 TRFE_HOR_2      90.2%  31.5%     VKWCAIGHHEKVKCDEWSVNSGG-------NIECESAQSTEDCIAKIVKGEADAMSLDGGFIYIAG-KCG-LVPVLAENY    
26 TRFE_HUM_2      89.8%  32.7%     VKWCALSHHERLKCDEWSVNSVG-------KIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAG-KCG-LVPVLAENY    
27 TRFE_PIG_2      89.8%  30.5%     VRWCAIGHEETQKCDAWSINSGG-------KIECVSAENTEDCIAKIVKGEADAMSLDGGYIYIAG-KCG-LVPVLAENY    
28 TRFE_RAB_2      89.8%  31.3%     VKWCALSHHERLKCDEWSVTSGG-------LIECESAETPEDCIAKIMNGEADAMSLDGGYVYIAG-QCG-LVPVLAENY    
29 TRFE_XEN_2      89.8%  32.6%     VRWCTQSKAEKTKCDDWTTISGG-------AIECTEASTAEECIVQILKGDADAVTLDGGYMYTAG-LCG-LVPVMGEYY    
30 TRFL_BOV_2      90.2%  30.9%     VVWCAVGPEEQKKCQQWSQQSGQ-------NVTCATASTTDDCIVLVLKGEADALNLDGGYIYTAG-KCG-LVPVLAENR    
31 TRFL_HUM_2      90.2%  30.7%     VVWCAVGEQELRKCNQWSGLSEG-------SVTCSSASTTEDCIALVLKGEADAMSLDGGYVYTAC-KCG-LVPVLAENY    
32 TRFL_MOU_2      90.2%  31.9%     VTWCAVGSEEKRKCDQWNRASRG-------RVTCISFPTTEDCIVAIMKGDADAMSLDGGYIYTAG-KCG-LVPVLAENQ    
33 TRFL_PIG_2      88.6%  33.1%     VVWCAVGPEELRKCRQWSSQSSQ-------NLNCSLASTTEDCIVQVLKGEADAMSLDGGFIYTAG-KCG-LVPVLAENQ    
34 TRFM_HUM_2      95.9%  30.2%     LRWCVLSTPEIQKCGDMAVAFRRQRLK--PEIQCVSAKSPQHCMERIQAEQVDAVTLSGEDIYTAG-KKYGLVPAAGEHY    
   consensus/100%                   h.hCs.t......C..h..............h.C.......tC...l.tttsDhhslss..hh.u.........hh.E..    
   consensus/90%                    lpaCshut.E..KCtpht....t........htC..tts..cCl.hl.ttpADshslDut.ha.Au.....LhPlhsE.h    
   consensus/80%                    lpWCshup.EhpKCtphp....t........lpC.ptts..-ClttIhttcADAhsLDuG.la.Au.hsh.LhPlhuE.Y    
   consensus/70%                    V+WCsluptEhpKCpphp.t.tt.......tlpCsptssh.-CIttIhps-ADAhoLDGG.lYpAG.tsh.LhPVhAE.Y    

                     cov    pid  81          .         1         .         .         .         .         :         . 160
 1 TRF1_SALSA     100.0% 100.0%     G------------EDSDTCYYAVAVAKKGT--AFGFKTLRGKKSCHTGLGKSAGWNIPIGTLVTESQIRWAGIEDRP---    
 2 TRF2_SALSA     100.0% 100.0%     G------------EDSDTCYYAVAVAKKGT--AFGFKTLRGKKSCHTGLGKSAGWNIPIGTLVTESQIRWAGIEDRP---    
 3 TRF_BLADI       96.2%  22.1%     TKEE---------PDEEFRYEAVCVIHKDLD-ITSIHGLQGLKSCHTGVGRNVGYKIPITKLRHMGVLGPLNNSDLTPRE    
 4 TRF_MANSE       96.8%  20.4%     TDEE---------PDAPFRYEAVIVVHKDLP-INNLDQLKGLRSCHTGVNRNVGYKIPLTMLMKRAVFPKMNDHSISPKE    
 5 TRFE_ANAPL      98.4%  47.8%     ERS----------GGSTTSYYAVAVVKKGT--DFMIKDLRGKTSCHTGLGRSAGWNIPIGTLIHREDIEWEGIESGI---    
 6 TRFE_BOVIN      96.8%  41.0%     GTK----------DNPQTHYYAVAVVKKDT--DFKLNELRGKKSCHTGLGRSAGWNIPMAKLYKELPD--PQES------    
 7 TRFE_CHICK      98.4%  46.4%     EHT----------EGSTTSYYAVAVVKKGT--EFTVNDLQGKTSCHTGLGRSAGWNIPIGTLLHRGAIEWEGIESGS---    
 8 TRFE_HORSE      97.1%  42.1%     GSK----------TEPQTHYYAVAVVKKNS--NFQLNQLQGKKSCHTGLGRSAGWNIPIGLLYWQLPE--PRES------    
 9 TRFE_HUMAN      96.8%  42.8%     GSK----------EDPQTFYYAVAVVKKDS--GFQMNQLRGKKSCHTGLGRSAGWNIPIGLLYCDLPE--PRKP------    
10 TRFE_PIG        97.1%  41.3%     GQK----------DNPQTHYYAVAVVKKGS--NFQWNQLQGKRSCHTGLGRSAGWIIPMGLLYDQLPE--PRKP------    
11 TRFE_RABIT      96.8%  42.5%     GSK----------ENPKTFYYAVALVKKGS--NFQLNELQGKKSCHTGLGRSAGWNIPIGLLYCDLPE--PRKP------    
12 TRFE_XENLA      99.4%  48.8%     GSH----------TETDTCYYAVAVVKKSS--KFTFDELKDKKSCHTGIGKTAGWNIIIGLLLERKLLKWAGPDSET---    
13 TRFL_BOVIN      97.8%  41.0%     GTK----------ESPQTHYYAVAVVKKGS--NFQLDQLQGRKSCHTGLGRSAGWIIPMGILRPYLSWTESLEP------    
14 TRFL_HUMAN      97.8%  41.9%     GTE----------RQPRTHYYAVAVVKKGG--SFQLNELQGLKSCHTGLRRTAGWNVPTGTLRPFLNWTGPPEP------    
15 TRFL_MOUSE      97.8%  39.6%     GTK----------EQPRTHYYAVAVVKNSS--NFHLNQLQGLRSCHTGIGRSAGWKIPIGTLRPYLNWNGPPAS------    
16 TRFL_PIG        96.8%  39.4%     GTE----------ENPQTYYYAVAVVKKGF--NFQLNQLQGRKSCHIGLGRSAGWNIPIGLLRRFLDWAGPPEP------    
17 TRFM_HUMAN      96.2%  38.6%     D------------QEVGTSYYAVAVVRRSS--HVTIDTLKGVKSCHTGINRTVGWNVPVGYLVESGRLSVMGCD------    
18 TRF1_SAL_2      90.5%  33.2%     DAD------LCSAPGEASSYYAVAVAKKGSG--LTWKTLKGKRSCHTGLGRTAGWNIPMGLIHQ----ETNDCDFT----    
19 TRF2_SAL_2      90.5%  33.1%     DAD------LCSAPGEASSYYAVAVAKKGSG--LTWKTLKGKRSCHTGLGRTAGWNIPMGLIHQ----ETNDCDFT----    
20 TRF_BLA_2       91.1%  32.0%     GEH-----------GSL--YYAVAVVRKDSTY-QSIEDLRGAKSCHTGYGRNAGWNVPLYTLLSKELISKNSCPYSSA--    
21 TRF_MAN_2       81.0%  19.9%     GEL-----------KTP--NYAVAVVKKGTAY-NKIDDLRGKKSCHSSYSTFSGLHAPLFYLINKRAIQSDHCVKN----    
22 TRFE_ANA_2      89.8%  31.6%     EDETQCS----KDEEQPAYYFAVAVVKKSSA--ITWNNLQGKKSCHTAVGRTAGWNIPMGLIHN----KTGSCDFD----    
23 TRFE_BOV_2      89.5%  29.9%     KTE-GES----CKNTPEKGYLAVAVVKTSDAN-INWNNLKDKKSCHTAVDRTAGWNIPMGLLYS----KINNCKFD----    
24 TRFE_CHI_2      89.8%  30.0%     DDESQCS----KTDERPASYFAVAVARKDSN--VNWNNLKGKKSCHTAVGRTAGWVIPMGLIHN----RTGTCNFD----    
25 TRFE_HOR_2      90.2%  31.5%     ETRSGSA----CVDTPEEGYHAVAVVKSSSDPDLTWNSLKGKKSCHTGVDRTAGWNIPMGLLYS----EIKHCEFD----    
26 TRFE_HUM_2      89.8%  32.7%     NKS--DN----CEDTPEAGYFAVAVVKKSASD-LTWDNLKGKKSCHTAVGRTAGWNIPMGLLYN----KINHCRFD----    
27 TRFE_PIG_2      89.8%  30.5%     KTE-GEN----CVNTPEKGYLAVAVVKKSSGPDLNWNNLKGKKSCHTAVDRTAGWNIPMGLLYN----KINSCKFD----    
28 TRFE_RAB_2      89.8%  31.3%     EST--D-----CKKAPEEGYLSVAVVKKSNPD-INWNNLEGKKSCHTAVDRTAGWNIPMGLLYN----RINHCRFD----    
29 TRFE_XEN_2      89.8%  32.6%     DQDDLTPC-QRSCSQAKGVYYAVAIVKKGTQ--VSWSNLRGVKTCHTAVGRTAGWNIPVGLITS----ETANCDFA----    
30 TRFL_BOV_2      90.2%  30.9%     KSSKHSS--LDCVLRPTEGYLAVAVVKKANEG-LTWNSLKDKKSCHTAVDRTAGWNIPMGLIVN----QTGSCAFD----    
31 TRFL_HUM_2      90.2%  30.7%     KSQQSSDPDPNCVDRPVEGYLAVAVVRRSDTS-LTWNSVKGKKSCHTAVDRTAGWNIPMGLLFN----QTGSCKFD----    
32 TRFL_MOU_2      90.2%  31.9%     KSSKSNG--LDCVNRPVGGYLAVAAVRREDAG-FTWSSLRGKKSCHTAVDRTAGWNIPMGLLAN----QTRSCKFN----    
33 TRFL_PIG_2      88.6%  33.1%     KSRQSSS--SDCVHRPTQGYFAVAVVRKANGG-ITWNSVRGTKSCHTAVDRTAGWNIPMGLLVN----QTGSCKFD----    
34 TRFM_HUM_2      95.9%  30.2%     APE-----------DSSNSYYVVAVVRRDSSHAFTLDELRGKRSCHAGFGSPAGWDVPVGALIQRGFIRPKDCDVLTA--    
   consensus/100%                   t.............t......sVhhh+pt......hptlpshpoCH.uhtp.sGh.h.hhhlh.................    
   consensus/90%                    t.............t....YhAVAVs++ss...hphppLpGh+SCHTuls+suGWplPhshlh.................    
   consensus/80%                    tpp...........ps.t.YhAVAVV++ss...hphppLpGt+SCHTulsRoAGWsIPhGhLhp....t..tp.......    
   consensus/70%                    tpp..........ppspptYaAVAVVKKus...hphspLcGKKSCHTulsRoAGWNIPhGhLhp....phsspp......    

                     cov    pid 161          .         .         .         2         .         .         .         . 240
 1 TRF1_SALSA     100.0% 100.0%     -VESAVSDFFNASCAPGATMG------------SKLCQLCKG-----------DCSRSHKEPYYDYAGAFQCLKDGAGDV    
 2 TRF2_SALSA     100.0% 100.0%     -VESAVSDFFNASCAPGATMG------------SKLCQLCKG-----------DCSRSHKEPYYDYAGAFQCLKDGAGDV    
 3 TRF_BLADI       96.2%  22.1%     NELHALSHLFSEACLVGKWAPDPAQNQALKAKYPNLCALCEHP-----------EICDYPDKYSGYDGALRCLAEHGGQV    
 4 TRF_MANSE       96.8%  20.4%     NELKALSTFFAKSCIVGKWSPDPKTNSAWKSQYSHLCSMCEHP-----------ERCDYPDNYSGYEGALRCLAHNNGEV    
 5 TRFE_ANAPL      98.4%  47.8%     -SEQAVAKFFSASCVPGAT------------IEQKLCRQCKGD-------A--KTKCLRNGPYSGYSGAFQCLKDGKGDV    
 6 TRFE_BOVIN      96.8%  41.0%     -IQRAAANFFSASCVPCADQ----------SSFPKLCQLCAGK-------GTDKCACSNHEPYFGYSGAFKCLMEGAGDV    
 7 TRFE_CHICK      98.4%  46.4%     -VEQAVAKFFSASCVPGAT------------IEQKLCRQCKGD-------P--KTKCARNAPYSGYSGAFHCLKDGKGDV    
 8 TRFE_HORSE      97.1%  42.1%     -LQKAVSNFFAGSCVPCADR----------TAVPNLCQLCVGK-------GTDKCACSNHEPYFGYSGAFKCLADGAGDV    
 9 TRFE_HUMAN      96.8%  42.8%     -LEKAVANFFSGSCAPCADG----------TDFPQLCQLCPG------------CGCSTLNQYFGYSGAFKCLKDGAGDV    
10 TRFE_PIG        97.1%  41.3%     -IEKAVASFFSSSCVPCADP----------VNFPKLCQQCAGK-------GAEKCACSNHEPYFGYAGAFNCLKEDAGDV    
11 TRFE_RABIT      96.8%  42.5%     -LEKAVASFFSGSCVPCADG----------ADFPQLCQLCPG------------CGCSSVQPYFGYSGAFKCLKDGLGDV    
12 TRFE_XENLA      99.4%  48.8%     -WRNAVSKFFKASCVPGAKE-------------PKLSQLCAGI-------KEHKCSRSNNEPYYNYAGAFKCLQDDQGDV    
13 TRFL_BOVIN      97.8%  41.0%     -LQGAVAKFFSASCVPCIDR----------QAYPNLCQLCKGE-------GENQCACSSREPYFGYSGAFKCLQDGAGDV    
14 TRFL_HUMAN      97.8%  41.9%     -IEAAVARFFSASCVPGADK----------GQFPNLCRLCAGT-------GENKCAFSSQEPYFSYSGAFKCLRDGAGDV    
15 TRFL_MOUSE      97.8%  39.6%     -LEEAVSKFFSKSCVPGAQK----------DRFPNLCSSCAGT-------GANKCASSPEEPYSGYAGALRCLRDNAGDV    
16 TRFL_PIG        96.8%  39.4%     -LQKAVAKFFSQSCVPCADG----------NAYPNLCQLCIGK-------GKDKCACSSQEPYFGYSGAFNCLHKGIGDV    
17 TRFM_HUMAN      96.2%  38.6%     -VLKAVSDYFGGSCVPGAGET---------SYSESLCRLCRGDSS-----GEGVCDKSPLERYYDYSGAFRCLAEGAGDV    
18 TRF1_SAL_2      90.5%  33.2%     ------KYFS-KGCAPGSE-VGSP-----------FCAQCKGSGKA-VG-DEYRCKARSEEQYYGYTGAFRCLVEDAGDV    
19 TRF2_SAL_2      90.5%  33.1%     ------KYFS-KGCAPGSE-VGSP-----------FCAQCKGSGKA-RGGDEDRCKARSEEQYYGYTGAFRCLVEDAGDV    
20 TRF_BLA_2       91.1%  32.0%     ----LSSYFSGGSCVPGAQLPENNPANQNPDS---LCSICAGNLDAPNNDPAWKCSASNDESFFGYSGAFRCLASGEGQV    
21 TRF_MAN_2       81.0%  19.9%     ----LGEFFSGGSCLPGVDKPENNPSGDDVSK---LKKQCG------SDSSAWKCLEED-----------------RGDV    
22 TRFE_ANA_2      89.8%  31.6%     ------DYFS-EGCAPGSP-PNSR-----------LCKLCQGSGEN-LL---EKCVASSHEKYYGYTGALRCLVE-QGDV    
23 TRFE_BOV_2      89.5%  29.9%     ------EFFS-AGCAPGSP-RNSS-----------LCALCIGSEKG-TG---KECVPNSNERYYGYTGAFRCLVE-KGDV    
24 TRFE_CHI_2      89.8%  30.0%     ------EYFS-EGCAPGSP-PNSR-----------LCQLCQGSGGI-PP---EKCVASSHEKYFGYTGALRCLVE-KGDV    
25 TRFE_HOR_2      90.2%  31.5%     ------KFFR-EGCAPGYR-RNST-----------LCNLCIGSASG-PG---RECEPNNHERYYGYTGAFRCLVE-KGDV    
26 TRFE_HUM_2      89.8%  32.7%     ------EFFS-EGCAPGSK-KDSS-----------LCKLCMGSGL-------NLCEPNNKEGYYGYTGAFRCLVE-KGDV    
27 TRFE_PIG_2      89.8%  30.5%     ------QFFG-EGCAPGSQ-RNSS-----------LCALCIGSERA-PG---RECLANNHERYYGYTGAFRCLVE-KGDV    
28 TRFE_RAB_2      89.8%  31.3%     ------EFFR-QGCAPGSQ-KNSS-----------LCELCIGP---------SVCAPNNREGYYGYTGAFRCLVE-KGDV    
29 TRFE_XEN_2      89.8%  32.6%     ------SYVG-ESCAPGSD-VKSN-----------LCALCIGDPEK-LSEREKKCSPSASEAYYGYSGAFRCLVE-KGQV    
30 TRFL_BOV_2      90.2%  30.9%     ------EFFS-QSCAPGAD-PKSR-----------LCALCAGDDQG-L----DKCVPNSKEKYYGYTGAFRCLAEDVGDV    
31 TRFL_HUM_2      90.2%  30.7%     ------EYFS-QSCAPGSD-PRSN-----------LCALCIGDEQG-E----NKCVPNSNERYYGYTGAFRCLAENAGDV    
32 TRFL_MOU_2      90.2%  31.9%     ------EFFS-QSCAPGAD-PKSN-----------LCALCIGDEKG-E----NKCAPNSKERYQGYTGALRCLAEKAGNV    
33 TRFL_PIG_2      88.6%  33.1%     ------EFFS-QSCAPGSQ-PGSN-----------LCALCVGNDQG-V----DKCVPNSNERYYGYTGAFRCLAENAGDV    
34 TRFM_HUM_2      95.9%  30.2%     ----VSEFFN-ASCVPVNN-PKNYP-----SS---LCALCVGDEQG-----RNKCVGNSQERYYGYRGAFRCLVENAGDV    
   consensus/100%                   ......t.h..tuChss..................hpt.C..............p......................GpV    
   consensus/90%                    ......t.F..tuCsPst.................LCt.C.G............s..p..p.Y.sYsGAhpCLhc.tGpV    
   consensus/80%                    ......t.F..tuCsPsup................LCt.ChG............C.sssp-.Y.GYsGAh+CLh-.tGDV    
   consensus/70%                    ......phF..tSCsPGup................LCtLChGp..........cCsssspE.YaGYoGAF+CLh-ttGDV    

                     cov    pid 241          :         .         .         .         .         3         .         . 320
 1 TRF1_SALSA     100.0% 100.0%     AFIKPLAVPAAEKAS---------------YELLCKDG---TRASIDSYKTCHLARVPAHAVVSR-KDPE--LANRIYNK    
 2 TRF2_SALSA     100.0% 100.0%     AFIKPLAVPAAEKAS---------------YELLCKDG---TRASIDSYKTCHLARVPAHAVVSR-KDPE--LANRIYNK    
 3 TRF_BLADI       96.2%  22.1%     AWTKVYYVKKHFGMAIGAGEAVPTGQNPDDYAYLCPDA---TKKPITG-KPCIWAARPWQGYMAN------HDLDNDIAD    
 4 TRF_MANSE       96.8%  20.4%     AFTKVIFTRKFFGLPVGTTPASPSNENPEEFRYLCVDG---SKAPITG-KACSWAARPWQGLIGH------NDVLAKLAP    
 5 TRFE_ANAPL      98.4%  47.8%     AFVKHTTVQENAPE------------EKDEYELLCLDG---SRQPVDSYKTCNWARVAAHAVVARDDS-KIDDIWSFLGM    
 6 TRFE_BOVIN      96.8%  41.0%     AFVKHSTVFDNLPNPE----------DRKNYELLCGDN---TRKSVDDYQECYLAMVPSHAVVARTVGGKEDVIWELLNH    
 7 TRFE_CHICK      98.4%  46.4%     AFVKHTTVNENAPD------------QKDEYELLCLDG---SRQPVDNYKTCNWARVAAHAVVARDDN-KVEDIWSFLSK    
 8 TRFE_HORSE      97.1%  42.1%     AFVKHSTVLENLPQEA----------DRDEYQLLCRDN---TRKSVDEYKDCYLASIPSHAVVARSVDGKEDLIWGLLNQ    
 9 TRFE_HUMAN      96.8%  42.8%     AFVKHSTIFENLANKA----------DRDQYELLCLDN---TRKPVDEYKDCHLAQVPSHTVVARSMGGKEDLIWELLNQ    
10 TRFE_PIG        97.1%  41.3%     AFVKHSTVLENLPDKA----------DRDQYELLCRDN---TRRPVDDYENCYLAQVPSHAVVARSVDGQEDSIWELLNQ    
11 TRFE_RABIT      96.8%  42.5%     AFVKQETIFENLPSKD----------ERDQYELLCLDN---TRKPVDEYEQCHLARVPSHAVVARSVDGKEDLIWELLNQ    
12 TRFE_XENLA      99.4%  48.8%     AFVKQSTVPEEFHKD---------------YELLCPDN---TRKSIKEYKNCNLAKVPAHAVLTRGRDDKSKDIIEFLQE    
13 TRFL_BOVIN      97.8%  41.0%     AFVKETTVFENLPEKA----------DRDQYELLCLNN---SRAPVDAFKECHLAQVPSHAVVARSVDGKEDLIWKLLSK    
14 TRFL_HUMAN      97.8%  41.9%     AFIRESTVFEDLSDEA----------ERDEYELLCPDN---TRKPVDKFKDCHLARVPSHAVVARSVNGKEDAIWNLLRQ    
15 TRFL_MOUSE      97.8%  39.6%     AFTRGSTVFEELPNKA----------ERDQYKLLCPDN---TWKPVTEYKECHLAQVPSHAVVSRSTNDKEEAIWELLRQ    
16 TRFL_PIG        96.8%  39.4%     AFVKESTVFENLPQKA----------DRDKYELLCPDN---TRKPVEAFRECHLARVPSHAVVARSVNGKENSIWSLLYQ    
17 TRFM_HUMAN      96.2%  38.6%     AFVKHSTVLENTDGKTLPSWG--QALLSQDFELLCRDG---SRADVTEWRQCHLARVPAHAVVVR-ADTDGGLIFRLLNE    
18 TRF1_SAL_2      90.5%  33.2%     AFIKHTIVPESTDGNGPD-WAKDL--KSSDFELLCQD---GTTQPVTKFSECHLAKVPAHAVITRPET-RGDVVSILLEL    
19 TRF2_SAL_2      90.5%  33.1%     AFIKHTIVPESTDGNGPD-WAKDL--KSSDFELLCQD---GTTQPVTKFSECHLAKVPAHAVITRPET-RGDVVSILLEL    
20 TRF_BLA_2       91.1%  32.0%     AFVKHTTVPENTDGHNQAAWTAGL--RSEDFELLCAD---GGRASINEYSRCHLAEVPPHMVVTSNDK-TDIQLNEIRHA    
21 TRF_MAN_2       81.0%  19.9%     AFVS----------S---ADLSHF--DANQYELLCLNRDAGGRDVLSSFATCNVAMAPSRTWVAAKD---FLSDVSIAHT    
22 TRFE_ANA_2      89.8%  31.6%     AFIKHSTVGENVSGSNKDDWAKGL--TRDDFELLCTN---GKRAKTMDYKTCHLAKVPTHAVVARPEK-ANKIRELLEGQ    
23 TRFE_BOV_2      89.5%  29.9%     AFVKDQTVIQNTDGNNNEAWAKNL--KKENFEVLCKD---GTRKPVTDAENCHLARGPNHAVVSRKDK-ATCVEKILNKQ    
24 TRFE_CHI_2      89.8%  30.0%     AFIQHSTVEENTGGKNKADWAKNL--QMDDFELLCTD---GRRANVMDYRECNLAEVPTHAVVVRPEK-ANKIRDLLERQ    
25 TRFE_HOR_2      90.2%  31.5%     AFVKHQTVEQNTDGRNPDDWAKDL--KSENFKLLCPD---GTRKSVTEFKSCYLARAPNHAVVSRKEK-AACVCQELHNQ    
26 TRFE_HUM_2      89.8%  32.7%     AFVKHQTVPQNTGGKNPDPWAKNL--NEKDYELLCLD---GTRKPVEEYANCHLARAPNHAVVTRKDK-EACVHKILRQQ    
27 TRFE_PIG_2      89.8%  30.5%     AFVKDQVVQQNTDGKNKDDWAKDL--KQMDFELLCQN---GAREPVDNAENCHLARAPNHAVVARDDK-VTCVAEELLKQ    
28 TRFE_RAB_2      89.8%  31.3%     AFVKSQTVLQNTGGRNSEPWAKDL--KEEDFELLCLD---GTRKPVSEAHNCHLAKAPNHAVVSRKDK-AACVKQKLLDL    
29 TRFE_XEN_2      89.8%  32.6%     GFAKHTTVFENTDGKNPAGWAKDL--KSEDFELLCPD---GSRAPVTDYKRCNLAEVPAHAVVTLPDK-REQVAKIVVNQ    
30 TRFL_BOV_2      90.2%  30.9%     AFVKNDTVWENTNGESTADWAKNL--NREDFRLLCLD---GTRKPVTEAQSCHLAVAPNHAVVSRSDR-AAHVKQVLLHQ    
31 TRFL_HUM_2      90.2%  30.7%     AFVKDVTVLQNTDGNNNEAWAKDL--KLADFALLCLD---GKRKPVTEARSCHLAMAPNHAVVSRMDK-VERLKQVLLHQ    
32 TRFL_MOU_2      90.2%  31.9%     AFLKDSTVLQNTDGKNTEEWARNL--KLKDFELLCLD---DTRKPVTEAKNCHLAIAPNHAVVSRTDK-VEVLQQVLLDQ    
33 TRFL_PIG_2      88.6%  33.1%     AFVKDVTVLDNTNGQNTQEWAREL--RSDDFELLCLN---GTRKPVTEAQNCHLAVAPSHAVVSRKEK-AAQVEQMLLTE    
34 TRFM_HUM_2      95.9%  30.2%     AFVRHTTVFDNTNGHNSEPWAAEL--RSEDYELLCPN---GARAEVSQFAACNLAQIPPHAVMVRPDTNIFTVYGLLDKA    
   consensus/100%                   uahp..........................athLC.s....tht.h.t.t.C.hA.hs.phhhs................    
   consensus/90%                    AFh+..hl.pth.t...............pacLLC.s....s+tslpthppC.hA.hPsHuVlsp..t........h.t.    
   consensus/80%                    AFlKp.sV.pshstp...........p.ppacLLC.D....sRtslsphppCpLAtsPsHAVVsR..p...p.h..lhpt    
   consensus/70%                    AFlKcpTV.cNhssps..........ppcpaELLC.D....oRpsVspacpCaLApsPsHAVVuR.tp.ttphh..Llpp    

                     cov    pid 321          .         .         :         .         .         .         .         4 400
 1 TRF1_SALSA     100.0% 100.0%     LVA---------VKDFNLFSSDG---YAAKNLMFKDSAQKLVQLPTTTDSFLYLGAEYMSTIRSLKK---SQATGASSRA    
 2 TRF2_SALSA     100.0% 100.0%     LVA---------VKDFNLFSSDG---YAAKNLMFKDSAQKLVQLPTTTDSFLYLGAEYMSTIRSLKK---SQATGASSRA    
 3 TRF_BLADI       96.2%  22.1%     LRAK--------ISLADTIGETE------NADWLSKVLDLNNKTIPIDNQGPYSPENYLNKANYTDVI--ERDTGAPHRP    
 4 TRF_MANSE       96.8%  20.4%     LREK--------VKQLADSGAAD------KPEWFTKVLGLSEKIHHVADNIPIKPIDYLNKANYTEVI--ERGHGAPELV    
 5 TRFE_ANAPL      98.4%  47.8%     QAYSLGVDT---TSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPELMDSQLYLGFEYYSAIQSLRKD--QLTVGPRENK    
 6 TRFE_BOVIN      96.8%  41.0%     AQEHFGKDK---PDNFQLFQSPHG-----KDLLFKDSADGFLKIPSKMDFELYLGYEYVTALQNLRESKPPDSSKDEC-M    
 7 TRFE_CHICK      98.4%  46.4%     AQSDFGVDT---KSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMRKD--QLTPSPRENR    
 8 TRFE_HORSE      97.1%  42.1%     AQEHFGTEK---SKDFHLFSSPHG-----KDLLFKDSALGFLRIPPAMDTWLYLGYEYVTAIRNLREDIRPEVPKDECKK    
 9 TRFE_HUMAN      96.8%  42.8%     AQEHFGKDK---SKEFQLFSSPHG-----KDLLFKDSAHGFLKVPPRMDAKMYLGYEYVTAIRNLREGTCPEAPTDECKP    
10 TRFE_PIG        97.1%  41.3%     AQEHFGRDK---SPDFQLFSSSHG-----KDLLFKDSANGFLKIPSKMDSSLYLGYQYVTALRNLREEISPDSSKNECKK    
11 TRFE_RABIT      96.8%  42.5%     AQEHFGKDK---SGDFQLFSSPHG-----KNLLFKDSAYGFFKVPPRMDANLYLGYEYVTAVRNLREGICPDPLQDECKA    
12 TRFE_XENLA      99.4%  48.8%     AQK---------TQECKLFSSP----VWGRDLIFKDSAVSLIPLPSSMDSFLFLGADYFQCIQALKEGV-KEDDSAAQVK    
13 TRFL_BOVIN      97.8%  41.0%     AQEKFGKNK---SRSFQLFGSPPGQ----RDLLFKDSALGFLRIPSKVDSALYLGSRYLTTLKNLRET--AEEVKARYTR    
14 TRFL_HUMAN      97.8%  41.9%     AQEKFGKDK---SPKFQLFGSPSGQ----KDLLFKDSAIGFSRVPPRIDSGLYLGSGYFTAIQNLRKS--EEEVAARRAR    
15 TRFL_MOUSE      97.8%  39.6%     SQEKFGKKQ---ASGFQLFASPSGQ----KDLLFKESAIGFVRVPQKVDVGLYLTFSYTTSIQNLNKK--QQDVIATKAR    
16 TRFL_PIG        96.8%  39.4%     SQKKFGKSN---PQEFQLFGSPGQQ----KDLLFRDATIGFLKIPSKIDSKLYLGLPYLTAIQGLRET--AAEVEARQAK    
17 TRFM_HUMAN      96.2%  38.6%     GQRLFSHE----GSSFQMFSSEAYG---QKDLLFKDSTSELVPIATQT-YEAWLGHEYLHAMKGLL-CD-----PNRLPP    
18 TRF1_SAL_2      90.5%  33.2%     QA-KFGS-SG-SDSSFRMFQSSVE-----KNLLFKDSTKCLQEIPKGTKYQDFLGKEYMIAMQSLRKCSDS-------TS    
19 TRF2_SAL_2      90.5%  33.1%     QA-KFGS-SG-SDSSFRMFQSSVE-----KNLLFKDSTKCLQEIPKGTKYQDFLGKEYMIAMQSLRKCSDS-------TS    
20 TRF_BLA_2       91.1%  32.0%     IL-AAGDLYSRRPDLFKLFGDFGGT----KDLLFKNSATGLLSVE----NGSPLMQRYSEILEVIRACE---------NQ    
21 TRF_MAN_2       81.0%  19.9%     PL-SLAQMLATRPDLFNIYGEFLKN----NNVIFNNAAKGLATTE----KLD--FEKFKTIHDVISSCG---------LA    
22 TRFE_ANA_2      89.8%  31.6%     EK-LFGLHGT-EKERFMMFQSQT------KDLLFKALTKCLVKLRQGITYKEFLGDEYYASVASLNTCN---------PS    
23 TRFE_BOV_2      89.5%  29.9%     QD-DFGKSVTDCTSNFCLFQSNS------KDLLFRDDTKCLASIA-KKTYDSYLGDDYVRAMTNLRQCS---------TS    
24 TRFE_CHI_2      89.8%  30.0%     EK-RFGVNGS-EKSKFMMFESQN------KDLLFKDLTKCLFKVREGTTYKEFLGDKFYTVISSLKTCN---------PS    
25 TRFE_HOR_2      90.2%  31.5%     QA-SYGKNGSHCPDKFCLFQSAT------KDLLFRDDTQCLANLQPTTTYKTYLGEKYLTAVANLRQCS---------TS    
26 TRFE_HUM_2      89.8%  32.7%     QH-LFGSNVTDCSGNFCLFRSET------KDLLFRDDTVCLAKLHDRNTYEKYLGEEYVKAVGNLRKCS---------TS    
27 TRFE_PIG_2      89.8%  30.5%     QA-QFGRHVTDCSSSFCMFKSNT------KDLLFRDDTQCLARVG-KTTYESYLGADYITAVANLRKCS---------TS    
28 TRFE_RAB_2      89.8%  31.3%     QV-EYGNTVADCSSKFCMFHSKT------KDLLFRDDTKCLVDLRGKNTYEKYLGADYIKAVSNLRKCS---------TS    
29 TRFE_XEN_2      89.8%  32.6%     QS-LYGRKGF-QKDIFQMFQSTGG-----KDLLFKDSTQCLLEIPSKTTMQEFLGDKYHTAVTSLNKCS---------TS    
30 TRFL_BOV_2      90.2%  30.9%     QA-LFGKNGKNCPDKFCLFKSET------KNLLFNDNTECLAKLGGRPTYEEYLGTEYVTAIANLKKCS---------TS    
31 TRFL_HUM_2      90.2%  30.7%     QA-KFGRNGSDCPDKFCLFQSET------KNLLFNDNTECLARLHGKTTYEKYLGPQYVAGITNLKKCS---------TS    
32 TRFL_MOU_2      90.2%  31.9%     QV-QFGRNGQRCPGEFCLFQSKT------KNLLFNDNTECLAKIPGKTTSEKYLGKEYVIATERLKQCS---------SS    
33 TRFL_PIG_2      88.6%  33.1%     QA-QFGRYGKDCPDKFCLFRSET------KNLLFNDNTECLAQLQGKTTYEKYLGSEYVTAIAT----------------    
34 TRFM_HUM_2      95.9%  30.2%     QD-LFGDDHN--KNGFKMFDSSNYH---GQDLLFKDATVRAVPVGEKTTYRGWLGLDYVAALEGMSSQQCSGAAAPAPGA    
   consensus/100%                   ...............h...t.........ps.hhpt.h.....h.............a...ht.................    
   consensus/90%                    .............t.FphFts........+sLhFpcss.hh.pl....p...aLs.pYhtthtshp..............    
   consensus/80%                    tt..hu......sppFphFtS.t......KsLLFpDss.thhpl..ths.t.aLG.cYhpshpslppt...........t    
   consensus/70%                    tt.paGpph...sspFphFpS.s......KsLLF+Dss.shhcl.tths.t.aLG.cYhsulpsL+ps..........tt    

                     cov    pid 401          .] 411
 1 TRF1_SALSA     100.0% 100.0%     -----------    
 2 TRF2_SALSA     100.0% 100.0%     -----------    
 3 TRF_BLADI       96.2%  22.1%     -----------    
 4 TRF_MANSE       96.8%  20.4%     -----------    
 5 TRFE_ANAPL      98.4%  47.8%     -----------    
 6 TRFE_BOVIN      96.8%  41.0%     -----------    
 7 TRFE_CHICK      98.4%  46.4%     -----------    
 8 TRFE_HORSE      97.1%  42.1%     -----------    
 9 TRFE_HUMAN      96.8%  42.8%     -----------    
10 TRFE_PIG        97.1%  41.3%     -----------    
11 TRFE_RABIT      96.8%  42.5%     -----------    
12 TRFE_XENLA      99.4%  48.8%     -----------    
13 TRFL_BOVIN      97.8%  41.0%     -----------    
14 TRFL_HUMAN      97.8%  41.9%     -----------    
15 TRFL_MOUSE      97.8%  39.6%     -----------    
16 TRFL_PIG        96.8%  39.4%     -----------    
17 TRFM_HUMAN      96.2%  38.6%     Y----------    
18 TRF1_SAL_2      90.5%  33.2%     DLEKACTFHSC    
19 TRF2_SAL_2      90.5%  33.1%     DLEKACTFHSC    
20 TRF_BLA_2       91.1%  32.0%     PTP--------    
21 TRF_MAN_2       81.0%  19.9%     -----------    
22 TRFE_ANA_2      89.8%  31.6%     DLLQVCTFLED    
23 TRFE_BOV_2      89.5%  29.9%     KLLEACTFHKP    
24 TRFE_CHI_2      89.8%  30.0%     DILQMCSFLEG    
25 TRFE_HOR_2      90.2%  31.5%     RLLEACTFHRV    
26 TRFE_HUM_2      89.8%  32.7%     SLLEACTFRRP    
27 TRFE_PIG_2      89.8%  30.5%     KLLEACTFHSA    
28 TRFE_RAB_2      89.8%  31.3%     RLLEACTFHKH    
29 TRFE_XEN_2      89.8%  32.6%     RLLAACTFHAA    
30 TRFL_BOV_2      90.2%  30.9%     PLLEACAFLTR    
31 TRFL_HUM_2      90.2%  30.7%     PLLEACEFLRK    
32 TRFL_MOU_2      90.2%  31.9%     PLLEACAFLTQ    
33 TRFL_PIG_2      88.6%  33.1%     -----------    
34 TRFM_HUM_2      95.9%  30.2%     PLLPLLLPALA    
   consensus/100%                   ...........    
   consensus/90%                    ...........    
   consensus/80%                    ...........    
   consensus/70%                    ...........