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IntaRNA 4596356

Input and runtime details for job 4596356 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? All repliconsyes
? Extract sequences aroundstart codon
? nt upstream (1-300)75
? nt downstream (1-300)75
? Index first target position-75

Output Parameters

? Number of interactions per RNA pair1
? Suboptimal interaction overlap can overlap in query
? Max. interaction lengthnot provided
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100
? No lonely base pairsyes
? No GU at helix endsyes

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (per RNA)0
? Seed position (query)not provided
? Seed position (target)not provided
? Ignore seeds with GU base pairsno
? Ignore seeds with GU endsyes

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 4596356 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:10:48 CET 2020
?Processing Started@ Mon Jan 27 14:13:48 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:14:50 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:16:49 CET 2020
?Job Completed@ Mon Jan 27 14:17:02 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=4596356&toolName=IntaRNA ( 30 days expiry )

The job description you specified

FnrS - E. coli


? Output download complete results [zip]

Downloadable files

[csv]
[png] [pdf]
[png] [pdf]
[txt]
[html] [pdf] [png]


heatmap

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

Sort by selecting a column name
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
b0483 -56 -16 FnrS 51 91 -15.77 0.0002842 0.5665147 ybaQ putative DNA-binding transcriptional regulator
b1847 -25 -11 FnrS 72 87 -15.67 0.0003127 0.5665147 yebF extracellular Colicin M immunity family protein
b1841 -43 4 FnrS 38 76 -15.32 0.000434 0.5665147 yobA CopC family protein
b0123 -50 -21 FnrS 1 31 -14.36 0.0010196 0.9422174 cueO multicopper oxidase (laccase)
b4002 -29 -18 FnrS 43 54 -13.88 0.0015278 0.9422174 zraP Zn-dependent periplasmic chaperone
b2501 -6 31 FnrS 55 94 -13.4 0.0022581 0.9422174 ppk polyphosphate kinase component of RNA degradosome
b2552 -31 24 FnrS 20 85 -13.23 0.0025851 0.9422174 hmp fused nitric oxide dioxygenase/dihydropteridine reductase 2
b0585 18 28 FnrS 46 56 -13.23 0.0025851 0.9422174 fes enterobactin/ferrienterobactin esterase
b2936 -58 -49 FnrS 1 10 -13.18 0.0026891 0.9422174 loiP Phe-Phe periplasmic metalloprotease OM lipoprotein low salt-inducible Era-binding heat shock protein
b2078 -48 -8 FnrS 53 92 -13.16 0.0027318 0.9422174 baeS sensory histidine kinase in two-component regulatory system with BaeR
Rows: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 all

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

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Results are computed with IntaRNA version 3.1.3 linking Vienna RNA package 2.4.14