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# cmscan :: search sequence(s) against a CM database
# INFERNAL 1.1.5 (Sep 2023)
# Copyright (C) 2023 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file: BK006935_6_7.fasta
# target CM database: IRES_5S_U2.cm
# tabular output of hits: IRES_5S_U2_Yeast-cmscan.tbl
# number of worker threads: 4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: ENA|BK006935|BK006935.2 [L=230218]
Hit scores:
rank E-value score bias modelname start end mdl trunc gc description
---- --------- ------ ----- --------- ------ ------ --- ----- ---- -----------
------ inclusion threshold ------
(1) ? 0.91 13.5 0.0 U2 52929 53083 + cm no 0.44 U2 spliceosomal RNA
(2) ? 1.3 12.8 5.3 U2 196571 196389 - cm no 0.33 U2 spliceosomal RNA
Hit alignments:
>> U2 U2 spliceosomal RNA
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ? 0.91 13.5 0.0 cm 1 193 [] 52929 53083 + .. 0.80 no 0.44
v v NC
::::::.<<<-<<<<..____>>>>->>>,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,,, CS
U2 1 AUacCU.UCucgGCc..UUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCU*[20]**[18]*aauuauaUUAaauuaAUUUUU 105
U +C UC:C:G UUUU C:A:GAUCAAG G AG UCUGU ++U+AUA AAUU AUU
ENA|BK006935|BK006935.2 52929 CUGGCAaUCCCGGAGugUUUUUGCCAGGAUCAAGAGCAGCUUCUGU---*[ 2]**[ 1]*UUUAAUAAACAAUUCAUUAAG 52998
**********8875544888999*************9999999987......7.....4..333555555566788888888 PP
vv v v vv v v v v NC
,,,,,,,<<<<<<<<----<<<<<__>>>>>-->>>>>>>>,,<<<<<<-<<<<<<___________>>>>>>-->>>>>>: CS
U2 106 ggaacuaGugggggcauuuuggGCUUGCccauugcccccaCacggguugaccuggcaUUGCAcUaccgccagguucagcccA 187
GGAACU+: ::: : U++: U : U : ::: : ::::U C G: U CA U+C :C G U A::::A
ENA|BK006935|BK006935.2 52999 GGAACUUAGCCAUCUGGAUGAUAUGUGCA--GUGGGUGGUUCACAAAUA-GCUCGUCUGCCAGUUCAUCUGGUUGGAUUUGA 53077
88888888888888877664333333322..358999999999999999.8888999*********99999999******** PP
NC
:::::: CS
U2 188 cccuuu 193
C C+UU
ENA|BK006935|BK006935.2 53078 CACCUU 53083
****** PP
>> U2 U2 spliceosomal RNA
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(2) ? 1.3 12.8 5.3 cm 1 193 [] 196571 196389 - .. 0.77 no 0.33
vvvv vvvv v v v NC
::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<~~~~~~>> CS
U2 1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggccc*[ 7]*gg 81
AU C UUC:C U UU+++ +:GAU A U U G A UUCU: CAG +UAAUAUCUG : GG :: ::
ENA|BK006935|BK006935.2 196571 AUUCUUUCCCA---UCUUUAUAUGGAUAAUAUUUUGAA----UUCUAUGCAGAGUAAUAUCUGUUU-GGUAU*[19]*AU 196487
**********5...44444555*******999999999....6********************999.65444...7..33 PP
v vvvv vvvv v v NC
>>>,,,.,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<----<<<<<_~~~~~~>>>>>-->>>>>>>>,,<<<<<<- CS
U2 82 gccaau.uauaUUAaauuaAUUUUUggaacuaGugggggcauuuuggGCU*[ 1]*GCccauugcccccaCacggguuga 155
CC++ UA A UA +UU+ UUUUU G +++ :: ++ +::A+G:: : A
ENA|BK006935|BK006935.2 196486 CCCUUGuUAGAGUAGUUUUUUUUUUUGGUUAGUG---------------G*[10]*---------AAGUCAAUGAAAGCA 196427
3444445666666666666666666666665544...............2...3...........34467899******* PP
v v v v NC
<<<<<<___________>>>>>>-->>>>>>::::::: CS
U2 156 ccuggcaUUGCAcUaccgccagguucagcccAcccuuu 193
:: :: U GCA +++:: ::UU : ::CA CC+
ENA|BK006935|BK006935.2 196426 UAAGUUUUAGCAUCUUUAAUAUAUUUCGUUCAGCCCGG 196389
************************************** PP
Internal CM pipeline statistics summary:
----------------------------------------
Query sequence(s): 1 (460436 residues searched)
Query sequences re-searched for truncated hits: 1 (1166.7 residues re-searched, avg per model)
Target model(s): 3 (664 consensus positions)
Windows passing local HMM SSV filter: 1951 (0.3874); expected (0.35)
Windows passing local HMM Viterbi filter: (off)
Windows passing local HMM Viterbi bias filter: (off)
Windows passing local HMM Forward filter: 932 (0.1928); expected (0.02)
Windows passing local HMM Forward bias filter: 386 (0.09111); expected (0.02)
Windows passing glocal HMM Forward filter: 129 (0.06346); expected (0.02)
Windows passing glocal HMM Forward bias filter: 75 (0.03339); expected (0.02)
Envelopes passing glocal HMM envelope defn filter: 84 (0.01354); expected (0.02)
Envelopes passing local CM CYK filter: 3 (0.0002665); expected (0.0001)
Total CM hits reported: 2 (0.0002441); includes 0 truncated hit(s)
# CPU time: 8.73u 0.20s 00:00:08.93 Elapsed: 00:00:08.28
//
Query: ENA|BK006936|BK006936.2 [L=813184]
Hit scores:
rank E-value score bias modelname start end mdl trunc gc description
---- --------- ------ ----- --------- ------ ------ --- ----- ---- -----------
(1) ! 1.2e-20 98.7 0.1 U2 681858 681747 - cm no 0.33 U2 spliceosomal RNA
Hit alignments:
>> U2 U2 spliceosomal RNA
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ! 1.2e-20 98.7 0.1 cm 1 193 [] 681858 681747 - .. 0.91 no 0.33
v NC
::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>> CS
U2 1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggcccccAuuggg 80
AU+ UCU+:GCCUUUUGGC:+AGAUCAAGUGUAGUAUCUGUUCUU:UCAGU+UAA+A+CUGA:AUG: CC:CA+UG:G
ENA|BK006936|BK006936.2 681858 AUC---UCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAAUGA-CCUCAAUGAG 681783
***...************************************************************999.********** PP
v NC
>>>>,,,.,,,,,,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~::::::: CS
U2 81 ggccaau.uauaUUAaauuaAUUUUUggaacua*[34]**[40]*Acccuuu 193
G+:CA+U U+UUAA+UU AC +UUU
ENA|BK006936|BK006936.2 681782 GCUCAUUaCCUUUUAAUUUG-------------*[ 6]**[ 3]*ACAUUUU 681747
******86555555555443................7.....9..******* PP
Internal CM pipeline statistics summary:
----------------------------------------
Query sequence(s): 1 (1626368 residues searched)
Query sequences re-searched for truncated hits: 1 (1166.7 residues re-searched, avg per model)
Target model(s): 3 (664 consensus positions)
Windows passing local HMM SSV filter: 6996 (0.3917); expected (0.35)
Windows passing local HMM Viterbi filter: (off)
Windows passing local HMM Viterbi bias filter: (off)
Windows passing local HMM Forward filter: 1952 (0.1271); expected (0.005)
Windows passing local HMM Forward bias filter: 311 (0.02308); expected (0.005)
Windows passing glocal HMM Forward filter: 162 (0.01766); expected (0.005)
Windows passing glocal HMM Forward bias filter: 104 (0.01062); expected (0.005)
Envelopes passing glocal HMM envelope defn filter: 109 (0.004945); expected (0.005)
Envelopes passing local CM CYK filter: 7 (0.0001391); expected (0.0001)
Total CM hits reported: 1 (2.294e-05); includes 0 truncated hit(s)
# CPU time: 10.01u 0.30s 00:00:10.31 Elapsed: 00:00:09.27
//
Query: ENA|BK006937|BK006937.2 [L=316620]
Hit scores:
rank E-value score bias modelname start end mdl trunc gc description
---- --------- ------ ----- --------- ------ ------ --- ----- ---- -----------
------ inclusion threshold ------
(1) ? 2.4 14.1 0.3 5S_rRNA 761 644 - cm no 0.41 5S ribosomal RNA
(2) ? 4.7 11.1 0.1 U2 229986 229885 - cm no 0.32 U2 spliceosomal RNA
Hit alignments:
>> 5S_rRNA 5S ribosomal RNA
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ? 2.4 14.1 0.3 cm 1 119 [] 761 644 - .. 0.90 no 0.41
v v v v v v v NC
(((((((((,,,,<<-<<.<<<.---<<--<<<<.<<______>>-->>>>-->>---->>>>>-->><<<-<<----<-<<---- CS
5S_rRNA 1 gccuGcggcCAUAccagc.gcg.aAagcACcgGa.uCCCAUCcGaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcuagGa 83
: :: ::: AUAC + :: G: C:::: CC AUC+G ::::AA:U AAG :: U+ GGC: :G GUA :+GGA
ENA|BK006937|BK006937.2 761 GAGAUGGUAUAUACUGUAgCAUcCGUGUGCGUAUgACCGAUCAGA--AUACAAGUGAAGGUGAGUAUGGCAUGUG--GUAGUGGGA 680
**************9753244314478889999889999999999..89**********9999999*********..********* PP
v NC
-<<____>>----->>->-->>->>>.))))))))): CS
5S_rRNA 84 UGgGuGAcCuCcUGggAAgaccagGu.gccgCaggcc 119
U :G G : G: AAG+: A:GU ::: :: : C
ENA|BK006937|BK006937.2 679 UUAGAG-UGGUAGGAUAAGUAUAUGUgUAUUAUUUAC 644
*99988.689999************************ PP
>> U2 U2 spliceosomal RNA
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(2) ? 4.7 11.1 0.1 cm 1 193 [] 229986 229885 - .. 0.83 no 0.32
v v v v v v NC
::::::<<<-~~~~~~->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>>>>>>,, CS
U2 1 AUacCUUCuc*[12]*aaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggcccccAuugggggccaa 86
A CUU + + AUCAAGUGUAG AUCU UU :A : : UU +A+: : U: G: ::::A U::::+:CAA
ENA|BK006937|BK006937.2 229986 UCAACUUGUU*[ 4]*UUCAUCAAGUGUAGAAUCUAUUUCAAAAUACUUCCCAAUGUCUU-GU-AAGGAGUCCUUUACAA 229911
*******876...4..589****************9999888888888888888888888.88.5566666888888899 PP
NC
,,,,,,,,,,,,,,,,,,~~~~~~::::::: CS
U2 87 uuauaUUAaauuaAUUUU*[82]*Acccuuu 193
+U+ AU A AUUUU ACC+UU
ENA|BK006937|BK006937.2 229910 AUUCAUAACCACGAUUUU*[ 1]*ACCUUUG 229885
888888888888888876...8..******* PP
Internal CM pipeline statistics summary:
----------------------------------------
Query sequence(s): 1 (633240 residues searched)
Query sequences re-searched for truncated hits: 1 (1166.7 residues re-searched, avg per model)
Target model(s): 3 (664 consensus positions)
Windows passing local HMM SSV filter: 2708 (0.3858); expected (0.35)
Windows passing local HMM Viterbi filter: (off)
Windows passing local HMM Viterbi bias filter: (off)
Windows passing local HMM Forward filter: 1345 (0.2002); expected (0.02)
Windows passing local HMM Forward bias filter: 470 (0.08163); expected (0.02)
Windows passing glocal HMM Forward filter: 181 (0.05878); expected (0.02)
Windows passing glocal HMM Forward bias filter: 99 (0.03068); expected (0.02)
Envelopes passing glocal HMM envelope defn filter: 111 (0.01272); expected (0.02)
Envelopes passing local CM CYK filter: 6 (0.0003184); expected (0.0001)
Total CM hits reported: 2 (0.0001156); includes 0 truncated hit(s)
# CPU time: 10.51u 0.39s 00:00:10.90 Elapsed: 00:00:09.15
//
[ok]
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