Freiburg RNA Tools
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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 RRI subseqs p-value fdr gene annotation
lmo1941 23 69 LhrA2 156 207 -15.29 0.0131118 0.8878302
lmo2074 -69 -43 LhrA2 147 173 -18.23 0.0024551 0.863511
lmo1835 -25 28 LhrA2 154 207 -18.61 0.0019491 0.863511 carB carbamoyl-phosphate synthetase
lmo2106 -29 22 LhrA2 159 207 -14.28 0.0223506 0.9474659
lmo0197 -23 48 LhrA2 99 173 -16.05 0.0086566 0.863511 regulatory protein SpoVG
lmo0137 -20 28 LhrA2 154 207 -13.49 0.0334303 0.9493467 peptide ABC transporter permease
lmo1507 -25 4 LhrA2 147 173 -16.85 0.0055185 0.863511 response regulator
lmo2759 -28 4 LhrA2 141 173 -14.73 0.0176689 0.9128702
lmo2654 -5 11 LhrA2 167 184 -14.34 0.0216662 0.9474659 fus elongation factor G
lmo1659 23 35 LhrA2 169 181 -13.48 0.0335984 0.9493467 lmo1659
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