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
39 0.002105 0.1727 b3249 mreD -13.67 0.026871 102 -- 115 74 -- 87 cell wall structural complex MreBCD transmembrane component MreD  
14 0.0004762 0.1198 b2286 nuoC -13.55 0.028468 156 -- 179 68 -- 87 NADH:ubiquinone oxidoreductase fused CD subunit  
148 0.008708 0.2059 b1754 ynjB -13.35 0.031185 160 -- 171 50 -- 61 putative ABC transporter periplasmic binding protein  
30 0.001614 0.1727 b3607 cysE -13.31 0.031682 13 -- 32 63 -- 81 serine acetyltransferase  
126 0.006849 0.1914 b2930 yggF -13.28 0.032133 176 -- 191 68 -- 83 fructose 1 6 bisphosphatase isozyme  
45 0.002234 0.1727 b0055 djlA -13.22 0.033048 207 -- 250 35 -- 76 membrane-anchored DnaK co-chaperone DNA-binding protein  
138 0.007886 0.2012 b3991 thiG -13.21 0.033127 237 -- 259 64 -- 85 thiamine biosynthesis ThiGH complex subunit  
140 0.008117 0.2031 b3221 yhcH -13.19 0.033484 158 -- 212 34 -- 73 DUF386 family protein cupin superfamily  
42 0.002147 0.1727 b0082 rsmH -13.18 0.033634 23 -- 49 70 -- 94 16S rRNA m(4)C1402 methyltransferase SAM-dependent  
83 0.004611 0.1855 b1593 ynfK -13.15 0.034145 276 -- 295 66 -- 83 putative dethiobiotin synthetase  

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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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