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]
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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
102 0.005508 0.1855 b0659 ybeY -7.73 0.351978 30 -- 54 64 -- 89 ssRNA-specific endoribonuclease; 16S rRNA 3' end maturation and quality control co-endoribonuclease working with RNase R; rRNA transcription antitermination factor  
65 0.003263 0.1727 b2584 pka -7.67 0.359085 49 -- 62 69 -- 82 protein lysine acetyltransferase  
44 0.002208 0.1727 b1859 znuB -7.63 0.365449 19 -- 38 72 -- 88 zinc ABC transporter permease  
159 0.009346 0.2062 b3661 nlpA -7.63 0.365650 232 -- 240 1 -- 9 cytoplasmic membrane lipoprotein-28  
145 0.008374 0.2033 b0068 thiB -7.61 0.367750 229 -- 244 73 -- 87 thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein  
197 0.01211 0.2164 b0495 ybbA -7.53 0.379415 88 -- 97 1 -- 10 putative ABC transporter ATPase  
43 0.002187 0.1727 b2222 atoA -7.38 0.400797 260 -- 273 68 -- 82 acetyl-CoA:acetoacetyl-CoA transferase beta subunit  
94 0.005015 0.1855 b2703 srlE -7.35 0.404948 254 -- 271 70 -- 86 glucitol/sorbitol-specific enzyme IIB component of PTS  
90 0.004828 0.1855 b2149 mglA -7.32 0.409352 216 -- 239 61 -- 86 methyl-galactoside ABC transporter ATPase  
112 0.005982 0.1855 b1820 yobD -7.30 0.411799 229 -- 243 1 -- 14 UPF0266 family inner membrane protein  

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)

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Results are computed with CopraRNA version 2.1.2