Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 5774122

Input and runtime details for job 5774122 (precomputed example)

Sequence input

? sRNA sequences[.fa]
? Putative target sequences (organism of interest)[.fa]
? Extract sequences aroundstart codon
? nt up (1-300)200
? nt down (1-300)100

CopraRNA parameters

? Consensus prediction off
? p-value combinationno
? p-value filtering (0=off)0

IntaRNA parameters

? Target folding window size150
? Target max. basepair distance100

Job ID 5774122 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:30:38 CET 2018
?Processing Started@ Fri Feb 16 20:16:08 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 23:32:42 CET 2018
?Post-Processing Finished@ Fri Feb 16 23:32:50 CET 2018
?Job Completed@ Fri Feb 16 23:33:10 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

The job description you specified

FsrA


Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
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[png] [pdf]
[txt] [svg]


heatmap

? Conserved, identified interactions for NC_000964 Bacillus subtilis subsp. subtilis str. 168

Sort by selecting a column name:
Rank CopraRNA p-value CopraRNA fdr value Locus Tag Gene Name Energy [kcal/mol] IntaRNA p-value Position mRNA Position sRNA Annotation Additional homologs
1 3.729e-08 0.0001244 bsu14890 ctaC -17.27 0.009980 187 -- 199 23 -- 34 cytochrome c oxidase subunit 2  
2 2.736e-07 0.0004564 bsu10760 yisL -18.52 0.005045 172 -- 193 31 -- 51 'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 15849754 16850406; Product type pm: membrane component'  
3 5.299e-07 0.0005893 bsu18000 citB -22.45 0.000394 173 -- 202 21 -- 50 aconitate hydratase  
4 1.471e-05 0.01227 bsu32200 yutJ -17.92 0.007061 210 -- 239 21 -- 53 NADH dehydrogenase-like protein YutJ  
5 2.545e-05 0.01698 bsu22540 qcrC -19.98 0.002129 169 -- 196 23 -- 48 menaquinol-cytochrome c reductase cytochrome b/c subunit  
6 3.166e-05 0.01761 bsu12160 yjgC -18.77 0.004394 190 -- 206 10 -- 27 oxidoreductase bsu27220 bsu03310
7 4.152e-05 0.01979 bsu05670 ydgJ -17.13 0.010734 234 -- 258 25 -- 49 MarR family transcriptional regulator  
8 5.206e-05 0.02171 bsu37180 fadF -12.43 0.089383 154 -- 199 26 -- 74 'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 17189250; Product type pe : enzyme'  
9 8.212e-05 0.03044 bsu07800 treP -22.21 0.000470 182 -- 210 21 -- 52 PTS system-trehalose-specific transporter subunit EIIBC  
10 0.0001049 0.035 bsu34190 yvfH -16.62 0.013859 188 -- 201 23 -- 36 L-lactate permease  

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

		

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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Results are computed with CopraRNA version 2.1.2