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
185 0.01108 0.2089 b0662 ubiF -8.33 0.279302 272 -- 292 6 -- 27 2-octaprenyl-3-methyl-6-methoxy-1 4-benzoquinol oxygenase  
129 0.007194 0.1964 b3401 hslO -8.25 0.287762 98 -- 107 1 -- 10 heat shock protein Hsp33  
142 0.00825 0.2033 b3457 livH -8.25 0.287512 56 -- 64 3 -- 11 branched-chain amino acid ABC transporter permease  
75 0.003854 0.1809 b0606 ahpF -8.17 0.297536 59 -- 82 64 -- 85 alkyl hydroperoxide reductase F52a subunit FAD/NAD(P)-binding  
153 0.009069 0.2059 b3529 yhjK -8.15 0.299018 186 -- 212 47 -- 74 cyclic-di-GMP phosphodiesterase  
66 0.003275 0.1727 b0394 mak -8.12 0.303293 18 -- 92 5 -- 77 manno(fructo)kinase  
160 0.009416 0.2062 b2095 gatZ -8.10 0.305092 155 -- 170 18 -- 33 D-tagatose 1 6-bisphosphate aldolase 2 subunit b3132
20 0.001165 0.1727 b1763 topB -8.06 0.310309 3 -- 10 34 -- 41 DNA topoisomerase III  
134 0.007678 0.1993 b3139 agaC -7.83 0.338422 255 -- 275 57 -- 74 N-acetylgalactosamine-specific enzyme IIC component of PTS  
195 0.01197 0.2159 b0738 tolR -7.83 0.338188 180 -- 193 26 -- 40 membrane spanning protein in TolA-TolQ-TolR complex  

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