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
25 0.001541 0.1727 b1948 fliP -12.25 0.051366 190 -- 216 44 -- 71 flagellar biosynthesis protein  
80 0.004451 0.1855 b3578 yiaN -12.19 0.052777 198 -- 212 52 -- 66 2 3-diketo-L-gulonate TRAP transporter large permease protein  
95 0.005084 0.1855 b3182 dacB -12.18 0.052827 253 -- 263 2 -- 12 D-alanyl-D-alanine carboxypeptidase  
59 0.002989 0.1727 b2713 hydN -12.16 0.053402 276 -- 298 54 -- 76 formate dehydrogenase-H [4Fe-4S] ferredoxin subunit b3573
50 0.002535 0.1727 b1879 flhA -12.13 0.054078 218 -- 247 64 -- 89 putative flagellar export pore protein  
200 0.01246 0.2193 b0425 panE -12.07 0.055655 285 -- 293 54 -- 62 2-dehydropantoate reductase NADPH-specific  
117 0.006292 0.1893 b1769 ydjE -12.05 0.056060 116 -- 139 36 -- 59 putative MFS sugar transporter membrane protein b1775
40 0.002113 0.1727 b2314 dedD -12.04 0.056230 10 -- 25 1 -- 19 membrane-anchored periplasmic protein involved in septation  
186 0.01109 0.2089 b3234 degQ -11.96 0.058310 267 -- 277 3 -- 13 serine endoprotease periplasmic  
103 0.005609 0.1855 b2912 fau -11.92 0.059425 103 -- 124 64 -- 85 5-formyltetrahydrofolate cyclo-ligase family 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