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
111 0.005938 0.1855 b0962 helD -11.18 0.082726 7 -- 19 71 -- 82 DNA helicase IV  
112 0.005982 0.1855 b1820 yobD -7.30 0.411799 229 -- 243 1 -- 14 UPF0266 family inner membrane protein  
113 0.005997 0.1855 b1765 ydjA -10.36 0.119141 118 -- 144 49 -- 76 putative oxidoreductase  
114 0.006011 0.1855 b0422 xseB -10.73 0.101337 104 -- 119 73 -- 87 exonuclease VII small subunit  
115 0.006085 0.1855 b3030 parE -11.34 0.077071 10 -- 31 65 -- 86 DNA topoisomerase IV subunit B  
116 0.006112 0.1855 b1260 trpA -12.39 0.048115 172 -- 199 63 -- 89 tryptophan synthase alpha subunit  
117 0.006292 0.1893 b1769 ydjE -12.05 0.056060 116 -- 139 36 -- 59 putative MFS sugar transporter membrane protein b1775
118 0.006444 0.1913 b0189 rof -9.63 0.163299 226 -- 241 29 -- 45 modulator of Rho-dependent transcription termination  
119 0.006508 0.1913 b3834 ubiJ -9.73 0.156135 145 -- 181 28 -- 78 aerobic ubiquinone synthesis protein SCP2 family protein  
120 0.006631 0.1913 b0825 fsaA -14.24 0.020734 15 -- 76 31 -- 86 fructose-6-phosphate aldolase 1 b3946

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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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2