Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1786318

Input and runtime details for job 1786318 (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 1786318 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:20:27 CET 2018
?Processing Started@ Fri Feb 16 15:20:56 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:01:46 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:01:53 CET 2018
?Job Completed@ Fri Feb 16 22:02:22 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

The job description you specified

ArcZ


Output download complete results [zip]

Downloadable files

[csv]
[txt]
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[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
198 0.01217 0.2164 b1236 galU -11.62 0.068156 187 -- 208 56 -- 74 glucose-1-phosphate uridylyltransferase  
150 0.008837 0.2059 b0453 ybaY -11.57 0.069675 268 -- 294 71 -- 94 outer membrane lipoprotein  
38 0.002093 0.1727 b1174 minE -11.55 0.070176 37 -- 55 69 -- 87 cell division topological specificity factor  
173 0.01023 0.2071 b3297 rpsK -11.54 0.070538 32 -- 43 48 -- 59 30S ribosomal subunit protein S11  
125 0.006795 0.1914 b3003 yghA -11.52 0.071261 264 -- 274 70 -- 80 putative oxidoreductase b2902
168 0.009959 0.2071 b0727 sucB -11.51 0.071542 30 -- 47 72 -- 88 dihydrolipoyltranssuccinase  
85 0.004761 0.1855 b2077 iceT -11.46 0.073016 53 -- 74 64 -- 86 putative citrate/iron-citrate/zinc-citrate efflux transporter  
29 0.001588 0.1727 b4371 rsmC -11.43 0.073969 145 -- 160 74 -- 89 16S rRNA m(2)G1207 methyltransferase SAM-dependent  
115 0.006085 0.1855 b3030 parE -11.34 0.077071 10 -- 31 65 -- 86 DNA topoisomerase IV subunit B  
181 0.0108 0.2089 b1683 sufB -11.33 0.077347 153 -- 175 52 -- 74 component of SufBCD Fe-S cluster assembly scaffold  

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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Feeds the job parameters to the input page to resubmit the job.

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Results are computed with CopraRNA version 2.1.2