Freiburg RNA Tools
IntaRNA - Results
BIF
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IntaRNA 4144073

Input and runtime details for job 4144073 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? All repliconsyes
? Extract sequences aroundstart codon
? nt up (1-300)75
? nt down (1-300)75

Output Parameters

? Number of (sub)optimal interactions1
? Suboptimal interaction overlap can overlap in query
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (each)0
? Seed position (query)not provided
? Seed position (target)not provided

Folding Parameters

? Temperature for energy computation37.0
? Access. query: folding window size150
? Access. query: max. basepair distance100
? Access. target: folding window size150
? Access. target: max. basepair distance100
? Energy parameter set (Vienna package) Turner model, 2004

Job ID 4144073 (server version 4.4.2)

?Job Submitted & Queued@ Mon Mar 06 14:22:09 CET 2017
?Processing Started@ Mon Mar 06 14:22:22 CET 2017
?IntaRNA Finished & Post-Processing@ Mon Mar 06 15:30:06 CET 2017
?Post-Processing Finished@ Mon Mar 06 15:30:06 CET 2017
?Job Completed@ Mon Mar 06 15:30:08 CET 2017
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=4144073&toolName=IntaRNA ( 30 days expiry )

The job description you specified

FnrS - example

? Output download complete results [zip]

Downloadable files

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[txt]
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heatmap

? Identified Interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name:
p-value fdr value Target Position Query Position Energy Gene Annotation
7.71e-05 0.32275 b0946 27 -- 74 FnrS 44 -- 89 -18.94720 zapC FtsZ stabilizer
0.0002292 0.35679 b0123 26 -- 55 FnrS 1 -- 31 -17.66950 cueO multicopper oxidase (laccase)
0.0002558 0.35679 b2531 61 -- 139 FnrS 2 -- 58 -17.53530 iscR isc operon transcriptional repressor suf operon transcriptional activator oxidative stress- and iron starvation-inducible autorepressor
0.0004669 0.45892 b1813 66 -- 103 FnrS 15 -- 54 -16.78140 nudL putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase
0.0005483 0.45892 b1841 33 -- 103 FnrS 20 -- 76 -16.57490 yobA CopC family protein
0.0007497 0.47399 b0884 53 -- 139 FnrS 1 -- 71 -16.16600 infA translation initiation factor IF-1
0.0010155 0.47399 b0483 20 -- 60 FnrS 51 -- 91 -15.76090 ybaQ putative DNA-binding transcriptional regulator
0.0010933 0.47399 b1847 51 -- 65 FnrS 72 -- 87 -15.66110 yebF extracellular Colicin M immunity family protein
0.0011177 0.47399 b2513 55 -- 80 FnrS 37 -- 63 -15.63120 yfgM ancillary SecYEG translocon subunit putative anti-RcsB factor
0.0011326 0.47399 b3136 19 -- 58 FnrS 4 -- 49 -15.61320 agaS tagatose-6-phosphate ketose/aldose isomerase

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

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Results are computed with IntaRNA version 2.0.1 (wrapper 1.1.2) linking Vienna RNA package 2.3.1