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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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
31 0.001682 0.1727 b1887 cheW -12.93 0.037697 13 -- 28 70 -- 86 purine-binding chemotaxis protein  
32 0.001707 0.1727 b3606 trmL -13.76 0.025837 263 -- 277 71 -- 85 tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent  
33 0.001709 0.1727 b0023 rpsT -12.95 0.037339 65 -- 78 72 -- 85 30S ribosomal subunit protein S20  
34 0.001871 0.1727 b4485 ytfR -15.36 0.012458 204 -- 227 64 -- 86 putative sugar ABC transporter ATPase  
35 0.001921 0.1727 b1849 purT -12.35 0.048961 166 -- 192 67 -- 88 phosphoribosylglycinamide formyltransferase 2  
36 0.001988 0.1727 b2573 rpoE -9.66 0.161217 247 -- 255 64 -- 72 RNA polymerase sigma E factor  
37 0.002023 0.1727 b2197 ccmE -14.61 0.017549 166 -- 218 48 -- 94 periplasmic heme chaperone  
38 0.002093 0.1727 b1174 minE -11.55 0.070176 37 -- 55 69 -- 87 cell division topological specificity factor  
39 0.002105 0.1727 b3249 mreD -13.67 0.026871 102 -- 115 74 -- 87 cell wall structural complex MreBCD transmembrane component MreD  
40 0.002113 0.1727 b2314 dedD -12.04 0.056230 10 -- 25 1 -- 19 membrane-anchored periplasmic protein involved in septation  

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