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

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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
101 0.005473 0.1855 b1129 phoQ -8.66 0.244665 211 -- 219 79 -- 87 sensory histidine kinase in two-component regulatory system with PhoP  
102 0.005508 0.1855 b0659 ybeY -7.73 0.351978 30 -- 54 64 -- 89 ssRNA-specific endoribonuclease; 16S rRNA 3' end maturation and quality control co-endoribonuclease working with RNase R; rRNA transcription antitermination factor  
103 0.005609 0.1855 b2912 fau -11.92 0.059425 103 -- 124 64 -- 85 5-formyltetrahydrofolate cyclo-ligase family protein  
104 0.005642 0.1855 b1476 fdnI -8.74 0.236866 280 -- 291 51 -- 62 formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible  
105 0.005654 0.1855 b0004 thrC -10.56 0.108775 227 -- 299 1 -- 79 L-threonine synthase  
106 0.005731 0.1855 b0867 amiD -15.82 0.010089 39 -- 60 64 -- 86 1 6-anhydro-N-acetylmuramyl-L-alanine amidase Zn-dependent; OM lipoprotein  
107 0.005754 0.1855 b3447 ggt -8.41 0.270031 252 -- 270 52 -- 70 gamma-glutamyltranspeptidase  
108 0.005783 0.1855 b3951 pflD -15.90 0.009733 233 -- 258 63 -- 86 putative glycine radical domain-containing pyruvate formate-lyase b0823
109 0.005919 0.1855 b3807 cyaY -12.33 0.049473 23 -- 64 29 -- 73 iron-dependent inhibitor of iron-sulfur cluster formation; frataxin; iron-binding and oxidizing protein  
110 0.005921 0.1855 b0156 erpA -16.74 0.006653 106 -- 166 29 -- 94 iron-sulfur cluster insertion protein  

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