Freiburg RNA Tools
IntaRNA - Results
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IntaRNA 8753634

Input and runtime details for job 8753634 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_002516
? 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 8753634 (server version 4.4.2)

?Job Submitted & Queued@ Mon Mar 06 14:24:54 CET 2017
?Processing Started@ Mon Mar 06 14:25:07 CET 2017
?IntaRNA Finished & Post-Processing@ Mon Mar 06 15:53:52 CET 2017
?Post-Processing Finished@ Mon Mar 06 15:53:52 CET 2017
?Job Completed@ Mon Mar 06 15:53:54 CET 2017
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=8753634&toolName=IntaRNA ( 30 days expiry )

The job description you specified

PrrF1 - example

? Output download complete results [zip]

Downloadable files

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[txt]
[png] [pdf] [ps]
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heatmap

? Identified Interactions for NC_002516 Pseudomonas aeruginosa PAO1

Sort by selecting a column name:
p-value fdr value Target Position Query Position Energy Gene Annotation
5.35e-05 0.19891 PA5206 32 -- 137 PrrF1 35 -- 119 -20.30400 argE acetylornithine deacetylase
8.85e-05 0.19891 PA3621 119 -- 130 PrrF1 71 -- 82 -19.76620 fdxA ferredoxin I
0.000115 0.19891 PA0119 131 -- 148 PrrF1 101 -- 118 -19.47710   C4-dicarboxylate transporter DctA
0.0001546 0.20054 PA1103 60 -- 82 PrrF1 81 -- 102 -19.14320   flagellar assembly protein FliH
0.000242 0.23305 PA0151 113 -- 148 PrrF1 39 -- 82 -18.62140   TonB-dependent receptor
0.0002696 0.23305 PA2831 50 -- 70 PrrF1 99 -- 118 -18.49260   'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
0.0003201 0.23721 PA5490 56 -- 116 PrrF1 67 -- 120 -18.28510 cc4 cytochrome C4
0.0004338 0.28125 PA1571 43 -- 69 PrrF1 96 -- 121 -17.91060   'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
0.0006044 0.34831 PA5491 60 -- 91 PrrF1 75 -- 108 -17.49060   cytochrome
0.0007685 0.39863 PA2264 45 -- 68 PrrF1 98 -- 122 -17.17870   'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'

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