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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
b1901 -37 -30 Spot42 1 8 -11.04 0.0083834 0.9238006 araF L-arabinose ABC transporter periplasmic binding protein
b3078 -27 -20 Spot42 1 8 -10.33 0.0125598 0.9238006 ygjI putative transporter
b0646 -74 -67 Spot42 1 8 -10.27 0.0129952 0.9238006 djlB putative HscC co-chaperone uncharacterized J domain-containing protein
b3878 60 67 Spot42 1 8 -10.22 0.0133694 0.9238006 yihQ putative sulpholipid alpha-glucosidase alpha-glucosyl fluoride glucosidase
b2715 -28 -21 Spot42 1 8 -9.51 0.0199833 0.9238006 ascF cellobiose/arbutin/salicin-specific PTS enzymes IIB and IC components
b1862 13 20 Spot42 1 8 -9.04 0.0260389 0.9238006 yebB DUF830 family protein
b1623 -58 -51 Spot42 1 8 -9.03 0.0261856 0.9238006 add adenosine deaminase
b0369 -53 -46 Spot42 1 8 -8.81 0.0296259 0.9238006 hemB 5-aminolevulinate dehydratase (porphobilinogen synthase)
b1398 -10 -2 Spot42 1 9 -13.17 0.0024709 0.9238006 paaK phenylacetyl-CoA ligase
b3311 17 25 Spot42 1 9 -9.59 0.0191007 0.9238006 rpsQ 30S ribosomal subunit protein S17
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