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
60 0.003031 0.1727 b3432 glgB -10.57 0.108575 114 -- 123 51 -- 60 1 4-alpha-glucan branching enzyme  
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  
29 0.001588 0.1727 b4371 rsmC -11.43 0.073969 145 -- 160 74 -- 89 16S rRNA m(2)G1207 methyltransferase SAM-dependent  
42 0.002147 0.1727 b0082 rsmH -13.18 0.033634 23 -- 49 70 -- 94 16S rRNA m(4)C1402 methyltransferase SAM-dependent  
80 0.004451 0.1855 b3578 yiaN -12.19 0.052777 198 -- 212 52 -- 66 2 3-diketo-L-gulonate TRAP transporter large permease protein  
200 0.01246 0.2193 b0425 panE -12.07 0.055655 285 -- 293 54 -- 62 2-dehydropantoate reductase NADPH-specific  
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  
147 0.008705 0.2059 b0071 leuD -8.42 0.269085 76 -- 114 1 -- 54 3-isopropylmalate dehydratase small subunit  
173 0.01023 0.2071 b3297 rpsK -11.54 0.070538 32 -- 43 48 -- 59 30S ribosomal subunit protein S11  
33 0.001709 0.1727 b0023 rpsT -12.95 0.037339 65 -- 78 72 -- 85 30S ribosomal subunit protein S20  

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