# cmscan :: search sequence(s) against a CM database # INFERNAL 1.1.4 (Dec 2020) # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: virus.fasta # target CM database: Rfam.cm # output directed to file: data/output.txt # tabular output of hits: data/table.txt # tabular output format: 2 # model-specific thresholding: GA cutoffs # Rfam pipeline mode: on [strict filtering] # clan information read from file: Rfam.clanin # skipping overlaps in tbl output: yes # HMM-only mode for 0 basepair models: no # number of worker threads: 2 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: NC_045512.2 [L=29903] Description: Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome Hit scores: rank E-value score bias modelname start end mdl trunc gc description ---- --------- ------ ----- ----------------- ------ ------ --- ----- ---- ----------- (1) ! 2.1e-124 415.9 0.0 Sarbecovirus-3UTR 29536 29870 + cm no 0.40 Sarbecovirus 3'UTR (2) ! 6.2e-103 342.8 0.0 Sarbecovirus-5UTR 1 299 + cm no 0.45 Sarbecovirus 5'UTR (3) ! 1.7e-48 189.4 0.0 bCoV-3UTR 29518 29870 + cm no 0.41 Betacoronavirus 3'UTR (4) ! 6.1e-40 158.8 0.0 bCoV-5UTR 1 299 + cm no 0.45 Betacoronavirus 5'UTR (5) ! 1.6e-16 80.9 0.0 Corona_FSE 13469 13550 + cm no 0.54 Coronavirus frameshifting stimulation element (6) ! 9.1e-11 55.7 0.0 s2m 29727 29769 + cm no 0.56 Coronavirus 3' stem-loop II-like motif (s2m) (7) ! 4e-08 55.1 0.0 Corona_pk3 29603 29662 + cm no 0.35 Coronavirus 3' UTR pseudoknot Hit alignments: >> Sarbecovirus-3UTR Sarbecovirus 3'UTR rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc ---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ---- (1) ! 2.1e-124 415.9 0.0 cm 1 335 [] 29536 29870 + .. 1.00 no 0.40 NC ::::::::::::<<<<<<--<<-<<<<<<<<<<<--<<<---<<______>>--->>>->>>>>>>>>>>>>>>>>>>--------[[ CS Sarbecovirus-3UTR 1 UcAUGauGACCACaCaaGGCaGAugGgCuauguaAACGuUUUCGCaaUUCCGUUUaCGAuacauaGcCcaCuCuuGuGcAGAAUGAau 88 UCAUG +GACCACACAAGGCAGAU:G:CUAU:UAAACGUUUUCGC++UUCCGUUUACGAUA:AUAG:C:ACUCUUGUGCAGAAUGAAU NC_045512.2 29536 UCAUGCAGACCACACAAGGCAGAUGGGCUAUAUAAACGUUUUCGCUUUUCCGUUUACGAUAUAUAGUCUACUCUUGUGCAGAAUGAAU 29623 **************************************************************************************** PP NC [[[[,<<<<<<<<<-<<____>>-->>>>>>>>>,((((((--((((((((((--((--(((-(((-----((((((((<-<<-<<<_ CS Sarbecovirus-3UTR 89 uCuCGuaaCuacacAgCACAAGcAGguguaGuuaACuuuaaUcuCaCauaGCaAUCuUUaaucaauGUGUAacauuaGGGAGGACucG 176 UCUCGUAACUACA:A:CACAAG:AG:UGUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCA:UGUGUAACAUUAGGGAGGACU:G NC_045512.2 29624 UCUCGUAACUACAUAGCACAAGUAGAUGUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAGUGUGUAACAUUAGGGAGGACUUG 29711 **************************************************************************************** PP v v NC ___>>>>>->,,<<<<<<<<<----<<<-<<<<_____>>-->>-->>>--->>>>>->>>>,<<<<________>>>>,,,,,,,,, CS Sarbecovirus-3UTR 177 AAAgaGCCACCACauuuuCacCGAGgccAcGcGGAGUACgAUCgAGggcACAguGaauaauGCuaGGGAGAGCUGCCuaUAUGGAAGA 264 AAA:AGCCACCACAUUUUCACCGAG:C ACGCGGAGUACGAUCGAG G:ACAGUGAA AAUGCUAGGGAGAGCUGCCUAUAUGGAAGA NC_045512.2 29712 AAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGUGUACAGUGAACAAUGCUAGGGAGAGCUGCCUAUAUGGAAGA 29799 **************************************************************************************** PP NC ,,))))))))-----)))-)))--))---)))))------)))))--))))-))<<____>>]]]]]]::: CS Sarbecovirus-3UTR 265 GCCCuaauguGUAAAauuAauuUUaGUAGuGCuaUCCCCAuGuGaUUuuaaUaGCuUCUUaGGaGaauGAC 335 GCCCUAAUGUGUAAAA:UAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC NC_045512.2 29800 GCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC 29870 *********************************************************************** PP >> Sarbecovirus-5UTR Sarbecovirus 5'UTR rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc ---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ---- (2) ! 6.2e-103 342.8 0.0 cm 1 298 [] 1 299 + [. 0.99 no 0.45 vv vv NC ::::::<<<<<<<-<<<____>>>>>..>>>>>,,,,,,.,,,,<<<<<_____>>>>>,<<<<_______>>>>,,,,,,,,<<<<<<<<- CS Sarbecovirus-5UTR 1 AuauuAgGcuuuuACCuaccCaGGaa..aagCcAAccAA.uuUcGauCuCUUGUaGauCUGuuCUcUAAAcGaaCUUUAAAAUCuGcGuggC 89 AU+ AGG:UU ACCU+CCCAGG AA:CCAACCAA UUUCGAUCUCUUGUAGAUCUGUUCUCUAAACGAACUUUAAAAUCUG:GUG:C NC_045512.2 1 AUUAAAGGUUUAUACCUUCCCAGGUAacAAACCAACCAAcUUUCGAUCUCUUGUAGAUCUGUUCUCUAAACGAACUUUAAAAUCUGUGUGGC 92 ************************6666***********999************************************************** PP v NC <<-<<<<-<<<_____>>>->>>>>>->>>>>>>>------------------------((((((((((((-(((((---(((-(((-(((( CS Sarbecovirus-5UTR 90 uGUCgCucgGCUGcAUGCcuaGcGCacccaCgCaGUAUAAauAaUAAuaAAuUUUAcUGuCGuuGaCagGgaaCgaGUAACuCGuCcauCuu 181 UGUC:CUC:GCUGCAUGC:UAG:GCAC:CAC:CAGUAUAA+UAAUAA +AA UUACUGUCGUUGACAGG AC:AGUAACUCGUC:AUCUU NC_045512.2 93 UGUCACUCGGCUGCAUGCUUAGUGCACUCACGCAGUAUAAUUAAUAACUAA--UUACUGUCGUUGACAGGACACGAGUAACUCGUCUAUCUU 182 ***************************************************..9************************************** PP NC <<<--<<<<<<-<<<<<______>>>>>-->>>>>>------>>><<<<<<<-<<______>>>>>>>>><<<____>>>))))-))))))- CS Sarbecovirus-5UTR 182 CuGCAGgCuGCUcaCGGUUUCGUCCGugUUGCaGcCGAUCAUCaGCacacCcAGGUUUcGUCCgGguguGaCCGAAAGGuaaGaUgGaGaGC 273 CUGCAGGCUGCU:ACGGUUUCGUCCGU:UUGCAGCCGAUCAUCAGCACA:C:AGGUUUCGUCC:G:UGUGACCGAAAGGUAAGAU:GAGAGC NC_045512.2 183 CUGCAGGCUGCUUACGGUUUCGUCCGUGUUGCAGCCGAUCAUCAGCACAUCUAGGUUUCGUCCGGGUGUGACCGAAAGGUAAGAUGGAGAGC 274 ******************************************************************************************** PP v NC ))))))))))---)))))))::::: CS Sarbecovirus-5UTR 274 CucGucCcuGGuuuCaaCGaGAAAA 298 CU:GU CCUGGUUUCAACGAGAAAA NC_045512.2 275 CUUGUCCCUGGUUUCAACGAGAAAA 299 ************************* PP >> bCoV-3UTR Betacoronavirus 3'UTR rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc ---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ---- (3) ! 1.7e-48 189.4 0.0 cm 1 327 [] 29518 29870 + .. 0.93 no 0.41 v vvvv v v vvvv NC :::::::::::::.:...::::::::::::::<<<<<.-<<--<<<<<<-<<<<--<<<<--<<______>>-->>>>---->>>>->>>>>>> CS bCoV-3UTR 1 auauuauuAugcU.a...AcUuuuaAaugUAacgAGa.augaagccuAuugcGacAcugggugGUAACCCCccgccagaaAguCgcgaUaggcc 89 U+++ U+A+GC A C U+ A A AC:AG A :+ G:CUAU ++ A C:: +U:G CC:++ ::GA+A AUAG:C: NC_045512.2 29518 CUCAACUCAGGCCuAaacUCAUGCAGACCACACAAGGcAGAUGGGCUAUAUAAA--CGUUUUCGCUUUUCCGUUUACGAUAU-----AUAGUCU 29604 *********55553356644445556666669999985677889******9977..********999999********9955.....******* PP v v v v v NC >->>>>>---------[[[[[[[,<<<<<<<<<<___________>>>>>>>>>>,,,,,(((((((((((((((((.---(((---------- CS bCoV-3UTR 90 aCuCUcguaCAGAAUGgAuUCuuGcugccacaAcAGuacAAGAAGgUuguggcagaCCUuuauuAucucauuGcuau.guUauuuuaaAgUgUg 182 C CU:GU CAGAAUG AUUCU: U::C:::A:AG ACAAG+AG:U:::G::A CUUUA:::UC:CAU:GC: U +UUA:: AGUGUG NC_045512.2 29605 ACUCUUGUGCAGAAUGAAUUCUC-GUAACUACAUAGCACAAGUAGAUGUAGUUAA--CUUUAAUCUCACAUAGCAAUcUUUAAUC---AGUGUG 29692 ***********************.9*****************************9..8889****************99999999...****** PP v v NC ---((((((((,,,,,,,,,,,,,,.......<<<<<<<<______............___.......______>>>->>>>>,.......... CS bCoV-3UTR 183 UAacugguggGAGaAauUgaaAAAG.......aCuuuCgcCuAuGC............aUA.......ugaacagcGAaaaGuG.......... 240 UAAC::::GGGAG A UUGAAA+AG A:U UC:CC+A+GC UG+ACAG:GAA A:UG NC_045512.2 29693 UAACAUUAGGGAGGACUUGAAAGAGccaccacAUUUUCACCGAGGCcacgcggaguac---gaucgagUGUACAGUGAACAAUGcuagggagag 29783 ********************99999**********************99999885555...5555666************************** PP v v NC ...<<<___>>>,,,,,))))))))---------------)))---)))))))------)))))))))),,,,<<____>>]]]]]]]:: CS bCoV-3UTR 241 ...CCcauagGGAAGAGCccaccagUGUaAAaUuUUcAaaaauauaauagCaauuccauugagaUaauaaUGGCUUuUUAGaaGAaUcgC 327 CC:AUA:GGAAGAGCCC::::GUGUAAAAUU AA+::UA +A :GC:AU+CC +UG:GA:::UAAU+GCUU UUAG:AGAAU +C NC_045512.2 29784 cugCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUU---AAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC 29870 **********************************...9999************************************************* PP >> bCoV-5UTR Betacoronavirus 5'UTR rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc ---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ---- (4) ! 6.1e-40 158.8 0.0 cm 1 310 [] 1 299 + [. 0.97 no 0.45 v v v NC ::::::<<<<<-<<<<<______>>>>>-->>>>>,,,,...,,,<<<<<_____>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<---<<<- CS bCoV-5UTR 1 GAaUaagaGuGAaUaGCuUcCGuGCuAuCcCaCucaCCU...CuCGauCUCUUGUAGauCUuuUcUUUaAACGAACUUuAAAAAaAagcguuCcugcg 95 +UAA::GU: UA:CUUCC +G:UA C :AC::ACC UCGAUCUCUUGUAGAUCU UUCU+UAAACGAACUUUAAAA +::G: UG NC_045512.2 1 A-UUAAAGGUUUAUACCUUCCCAGGUAACAAACCAACCAacuUUCGAUCUCUUGUAGAUCUGUUCUCUAAACGAACUUUAAAA---UCUGU--GUGGC 92 *.************************************7***99***************************************...*****..***** PP v v v v v v NC --<<<<<<<<<_____>>>>>>>>>-->>>-->>>>>,,,,,......,..,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<_____ CS bCoV-5UTR 96 UugccgucggcUGCaUgccgacggcuugcaaUacgcuuaAcA......A..UUuuaauUUcaUUcaaaUaAuAUuUUUCAgUcAGaGaGUgGugUaUc 185 U C::U :GCUGCAUGC: A::G ++ CA :C:: UA++A A UUA+U UC UU+A A +A A+ U A U +GU+UAUC NC_045512.2 93 UGUCACUCGGCUGCAUGCUUAGUGCACUCAC-GCAG-UAUAAuuaauaAcuAAUUACUGUCGUUGACAGGACACGAGUAACU--------CGUCUAUC 180 *******************************.****.777778****9555578899999**********************........******** PP v v v NC ____>>>,,,,,,,,,,,<<---<<<______>>>>>,,,,,,,,,,,,,,,,,<<<<<<<-<<<______>>>>>>>>>>::::::::::::::::: CS bCoV-5UTR 186 uugugCcUCugGguCaCAacaaucgGUUuCGUCcgguucGuggcgAAUuaugAGcacggccUcggUUUCGuccgggccgugGaauuucgaUGggugug 283 UU UGC GG +C :: CGGUUUCGUCCG::U+G +GC+ AU AU AGCAC::C: +GGUUUCGUCC :G::GUG++ + + G+U G + G NC_045512.2 181 UUCUGC----AGGCUGCUUA---CGGUUUCGUCCGUGUUGCAGCCGAUCAUCAGCACAUCU-AGGUUUCGUCC-GGGUGUGACCGAAAGGUAAGAUGG 269 ******....**********...**************************************.***********.***************999999998 PP NC :::::::::::::::::::::.....:::::: CS bCoV-5UTR 284 uccGaacucAGcugAGAagUU.....aGagAA 310 + GA C ++G + UU AGA AA NC_045512.2 270 A--GAGCCUUGUCCCUGGUUUcaacgAGAAAA 299 8..999999999999988888*********** PP >> Corona_FSE Coronavirus frameshifting stimulation element rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc ---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ---- (5) ! 1.6e-16 80.9 0.0 cm 1 82 [] 13469 13550 + .. 1.00 no 0.54 v v NC :::::::<<<<<<<<--<<_____>>->>>>>>>>--<<-<<<<-<<<____>>>>>->>->>::::::::::::::::::: CS Corona_FSE 1 GAGUacGGGGuuCuAGUccuGCcCggCUaGaaCCCUGcgccacuGGuccugagaCagAugucgUuuuaAGgGCuUUUGAuaU 82 G+GU+ G:GGU:::AGU:C+GCCCG:CU:::ACC:UGCG CAC:GG :CU+ : C:GAUGUCGU+U+ AGGGCUUUUGA+AU NC_045512.2 13469 GGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCACUAGUACUGAUGUCGUAUACAGGGCUUUUGACAU 13550 ********************************************************************************** PP >> s2m Coronavirus 3' stem-loop II-like motif (s2m) rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc ---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ---- (6) ! 9.1e-11 55.7 0.0 cm 1 43 [] 29727 29769 + .. 1.00 no 0.56 v v NC :<<<<<----<<<-<<<<_____>>-->>-->>>--->>>>>: CS s2m 1 ggguGCCGaGGCCACGCgGAGUAcGAUCGAGGGUACAGCaccu 43 ::::CCGAGGC ACGCGGAGUACGAUCGAG GUACAG::::+ NC_045512.2 29727 UUUCACCGAGGCCACGCGGAGUACGAUCGAGUGUACAGUGAAC 29769 ******************************************* PP >> Corona_pk3 Coronavirus 3' UTR pseudoknot rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc ---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ---- (7) ! 4e-08 55.1 0.0 cm 1 61 [] 29603 29662 + .. 0.96 no 0.35 NC :::::::::::::::::::::::::::<<<<<<<<<___________>>>>>>>>>::::: CS Corona_pk3 1 CUACUCUUGuACAGAAUGGuAauCcaGUauaaUAacAGUaCAAGaAGguUAuuauAUAuuA 61 CUACUCUUGU CAGAAUG++ UC++GUA:::: A:AG ACAAG+AG:U ::::UA UU NC_045512.2 29603 CUACUCUUGUGCAGAAUGAA-UUCUCGUAACUACAUAGCACAAGUAGAUGUAGUUAACUUU 29662 ******************66.********88888***************88888******* PP Internal CM pipeline statistics summary: ---------------------------------------- Query sequence(s): 1 (59806 residues searched) Query sequences re-searched for truncated hits: 1 (667.9 residues re-searched, avg per model) Target model(s): 3934 (464097 consensus positions) Windows passing local HMM SSV filter: 155505 (0.103); expected (0.06) Windows passing local HMM Viterbi filter: 34995 (0.02176); expected (0.02) Windows passing local HMM Viterbi bias filter: 25051 (0.01437); expected (0.02) Windows passing local HMM Forward filter: 1640 (0.00121); expected (0.0002) Windows passing local HMM Forward bias filter: 1047 (0.0007709); expected (0.0002) Windows passing glocal HMM Forward filter: 757 (0.0005877); expected (0.0002) Windows passing glocal HMM Forward bias filter: 699 (0.0005285); expected (0.0002) Envelopes passing glocal HMM envelope defn filter: 691 (0.0003461); expected (0.0002) Envelopes passing local CM CYK filter: 182 (7.975e-05); expected (0.0001) Total CM hits reported: 7 (6.183e-06); includes 0 truncated hit(s) # CPU time: 43.26u 1.50s 00:00:44.76 Elapsed: 00:00:27.06 // [ok]