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
84 0.004676 0.1855 b0526 cysS -14.43 0.019007 256 -- 269 64 -- 77 cysteinyl-tRNA synthetase  
49 0.00252 0.1727 b3452 ugpA -14.40 0.019328 59 -- 78 52 -- 70 sn-glycerol-3-phosphate ABC transporter permease  
54 0.002681 0.1727 b3201 lptB -14.37 0.019597 275 -- 293 64 -- 82 lipopolysaccharide export ABC transporter ATPase  
77 0.00398 0.182 b2411 ligA -14.36 0.019662 79 -- 95 70 -- 86 DNA ligase NAD(+)-dependent  
120 0.006631 0.1913 b0825 fsaA -14.24 0.020734 15 -- 76 31 -- 86 fructose-6-phosphate aldolase 1 b3946
22 0.001393 0.1727 b0794 ybhF -14.07 0.022426 148 -- 164 67 -- 84 putative ABC transporter ATPase  
154 0.009082 0.2059 b2676 nrdF -13.94 0.023769 159 -- 176 53 -- 69 ribonucleoside-diphosphate reductase 2 beta subunit ferritin-like protein  
196 0.01202 0.2159 b1729 ydjN -13.87 0.024594 143 -- 155 72 -- 84 putative transporter  
156 0.009123 0.2059 b2683 ygaH -13.79 0.025463 164 -- 213 27 -- 86 putative L-valine exporter norvaline resistance 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  

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