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IntaRNA 6571257

Input and runtime details for job 6571257 (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 6571257 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:18:03 CET 2020
?Processing Started@ Mon Jan 27 14:20:22 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:21:19 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:22:25 CET 2020
?Job Completed@ Mon Jan 27 14:22:35 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

The job description you specified

Spot42 - 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
b4361 -33 -23 Spot42 55 65 -9.75 0.0174491 0.9238006 dnaC DNA biosynthesis protein
b1751 -14 -2 Spot42 21 33 -9.65 0.0184641 0.9238006 ydjY putative ferrodoxin-like lipoprotein
b1921 60 75 Spot42 49 65 -9.65 0.0184641 0.9238006 fliZ RpoS antagonist putative regulator of FliA activity
b3709 -53 -42 Spot42 1 13 -9.62 0.0187797 0.9238006 tnaB tryptophan transporter of low affinity
b3238 -21 -5 Spot42 39 54 -9.61 0.0188861 0.9238006 yhcN cadmium and peroxide resistance protein stress-induced
b0511 -28 10 Spot42 18 58 -9.6 0.0189931 0.9238006 ybbW putative allantoin transporter
b3311 17 25 Spot42 1 9 -9.59 0.0191007 0.9238006 rpsQ 30S ribosomal subunit protein S17
b3921 -74 -67 Spot42 50 57 -9.55 0.0195371 0.9238006 yiiR DUF805 family putative inner membrane protein
b2715 -28 -21 Spot42 1 8 -9.51 0.0199833 0.9238006 ascF cellobiose/arbutin/salicin-specific PTS enzymes IIB and IC components
b2150 -48 -22 Spot42 1 24 -9.49 0.0202101 0.9238006 mglB methyl-galactoside transporter subunit
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