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
51 0.002608 0.1727 b2299 yfcD -9.22 0.194301 162 -- 171 49 -- 58 putative NUDIX hydrolase  
52 0.002619 0.1727 b2720 hycF -12.75 0.040951 8 -- 55 44 -- 94 formate hydrogenlyase complex iron-sulfur protein  
53 0.002649 0.1727 b2289 lrhA -9.83 0.149509 112 -- 119 68 -- 75 transcriptional repressor of flagellar motility and chemotaxis genes  
54 0.002681 0.1727 b3201 lptB -14.37 0.019597 275 -- 293 64 -- 82 lipopolysaccharide export ABC transporter ATPase  
55 0.002731 0.1727 b2480 bcp -8.89 0.222722 156 -- 187 28 -- 56 peroxiredoxin; thiol peroxidase thioredoxin-dependent  
56 0.002848 0.1727 b0797 rhlE -14.47 0.018687 57 -- 89 53 -- 82 ATP-dependent RNA helicase  
57 0.002848 0.1727 b2059 wcaA -10.75 0.100075 282 -- 295 72 -- 85 putative glycosyl transferase  
58 0.002925 0.1727 b0427 yajR -11.14 0.084219 218 -- 238 54 -- 78 putative transporter  
59 0.002989 0.1727 b2713 hydN -12.16 0.053402 276 -- 298 54 -- 76 formate dehydrogenase-H [4Fe-4S] ferredoxin subunit b3573
60 0.003031 0.1727 b3432 glgB -10.57 0.108575 114 -- 123 51 -- 60 1 4-alpha-glucan branching enzyme  

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