-
Notifications
You must be signed in to change notification settings - Fork 2
/
output.txt
222 lines (190 loc) · 17.6 KB
/
output.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
# 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]