Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 3429477

Input and runtime details for job 3429477 (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 3429477 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:26:36 CET 2018
?Processing Started@ Fri Feb 16 15:27:01 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 20:15:20 CET 2018
?Post-Processing Finished@ Fri Feb 16 20:15:27 CET 2018
?Job Completed@ Fri Feb 16 20:15:52 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

The job description you specified

OxyS

Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
[png] [pdf] [ps]
[png] [pdf] [ps]
[html] [pdf]
[png] [pdf]
[txt] [svg]


heatmap

? Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

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 0 0 b3961 oxyR -149.65 0.000000 1 -- 105 1 -- 105 oxidative and nitrosative stress transcriptional regulator  
2 0.0001834 0.3 b2729 hypD -13.53 0.025234 75 -- 91 71 -- 87 hydrogenase maturation protein  
3 0.0006202 0.5173 b3310 rplN -11.54 0.056896 6 -- 16 77 -- 87 50S ribosomal subunit protein L14  
4 0.0006326 0.5173 b3230 rpsI -11.95 0.048152 221 -- 251 74 -- 108 30S ribosomal subunit protein S9  
5 0.0009313 0.5385 b3829 metE -12.51 0.038445 233 -- 242 75 -- 84 5-methyltetrahydropteroyltriglutamate- homocysteine S-methyltransferase  
6 0.001078 0.5385 b0849 grxA -11.19 0.065759 209 -- 232 58 -- 81 glutaredoxin 1 redox coenzyme for ribonucleotide reductase (RNR1a)  
7 0.001275 0.5385 b2175 mepS -13.85 0.022182 178 -- 188 25 -- 35 murein DD-endopeptidase space-maker hydrolase mutational suppressor of prc thermosensitivity outer membrane lipoprotein weak murein LD-carboxypeptidase  
8 0.001355 0.5385 b3915 fieF -13.87 0.021962 2 -- 39 50 -- 90 ferrous iron and zinc transporter  
9 0.0016 0.5385 b1709 btuD -9.25 0.141890 185 -- 194 75 -- 84 vitamin B12 ABC transporter ATPase  
10 0.001846 0.5385 b2099 yegU -13.29 0.027829 185 -- 270 5 -- 83 ADP-ribosylglycohydrolase family protein  

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

		

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:
Feeds the job parameters to the input page to resubmit the job.

de.NBI usability assessment

Please support us by filling this short quality survey for evaluating this de.NBI service.

When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2