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
1 0 0 b3209 elbB -118.30 0.000000 1 -- 83 1 -- 83 isoprenoid biosynthesis protein with amidotransferase-like domain  
18 0.001002 0.1727 b2284 nuoF -9.91 0.144715 4 -- 28 1 -- 36 NADH:ubiquinone oxidoreductase chain F  
40 0.002113 0.1727 b2314 dedD -12.04 0.056230 10 -- 25 1 -- 19 membrane-anchored periplasmic protein involved in septation  
76 0.003978 0.182 b0336 codB -6.71 0.504284 39 -- 48 1 -- 11 cytosine transporter  
82 0.004565 0.1855 b4144 yjeI -10.12 0.132253 163 -- 240 1 -- 93 DUF4156 family lipoprotein  
92 0.004911 0.1855 b3732 atpD -9.01 0.211333 117 -- 128 1 -- 11 F1 sector of membrane-bound ATP synthase beta subunit  
105 0.005654 0.1855 b0004 thrC -10.56 0.108775 227 -- 299 1 -- 79 L-threonine synthase  
112 0.005982 0.1855 b1820 yobD -7.30 0.411799 229 -- 243 1 -- 14 UPF0266 family inner membrane protein  
129 0.007194 0.1964 b3401 hslO -8.25 0.287762 98 -- 107 1 -- 10 heat shock protein Hsp33  
133 0.007533 0.1993 b2194 ccmH -11.64 0.067570 191 -- 199 1 -- 9 heme lyase CcmH subunit  

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