Freiburg RNA Tools
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IFF
IntaRNA 4627738

Input and runtime details for job 4627738 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_003210
? 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 4627738 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:20:43 CET 2020
?Processing Started@ Mon Jan 27 14:22:37 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:24:00 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:24:55 CET 2020
?Job Completed@ Mon Jan 27 14:25:04 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=4627738&toolName=IntaRNA ( 30 days expiry )

The job description you specified

LhrA2 - Listeria monocytogenes


? Output download complete results [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_003210 Listeria monocytogenes EGD-e

Sort by selecting a column name
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
lmo1229 -3 28 LhrA2 147 182 -17.22 0.0044601 0.863511
lmo1575 -14 28 LhrA2 150 181 -13.9 0.02717 0.9474659
lmo0137 -20 28 LhrA2 154 207 -13.49 0.0334303 0.9493467 peptide ABC transporter permease
lmo0835 -20 29 LhrA2 146 186 -18.17 0.0025454 0.863511 peptidoglycan binding protein
lmo1984 -14 29 LhrA2 157 201 -15.62 0.0109651 0.863511 ilvB acetolactate synthase
lmo2146 -8 30 LhrA2 172 211 -13.99 0.0259491 0.9474659 LysR family transcriptional regulator
lmo1952 -9 31 LhrA2 161 204 -15.84 0.0097207 0.863511 lysA diaminopimelate decarboxylase
lmo0131 -8 31 LhrA2 165 204 -15.78 0.0100463 0.863511
lmo2486 -27 32 LhrA2 159 195 -15.82 0.0098281 0.863511 lmo2486
lmo2282 -21 35 LhrA2 157 205 -15.26 0.0133252 0.8878302 protein gp21
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