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 geneID annotation
lmo0551 -68 -3 LhrA2 154 204 -15.63 0.0109054 0.863511 lmo0551
lmo1454 -29 16 LhrA2 154 211 -14.13 0.02415 0.9474659 rpoD RNA polymerase sigma factor RpoD
lmo2327 -39 14 LhrA2 155 208 -14.96 0.0156437 0.9011628 lmo2327
lmo2308 -14 7 LhrA2 147 170 -16.63 0.0062544 0.863511 single-stranded DNA-binding protein
lmo2314 -15 17 LhrA2 171 207 -14.04 0.0252928 0.9474659 lmo2314
lmo0926 56 74 LhrA2 155 175 -15.07 0.0147533 0.9011628 TetR family transcriptional regulator
lmo2765 -13 18 LhrA2 155 199 -15.86 0.0096143 0.863511 PTS cellbiose transporter subunit IIA
lmo2299 37 63 LhrA2 155 181 -15.54 0.0114532 0.863511 portal protein
lmo2282 -21 35 LhrA2 157 205 -15.26 0.0133252 0.8878302 protein gp21
lmo2251 -12 5 LhrA2 149 165 -13.92 0.0268942 0.9474659 amino acid ABC transporter ATP-binding protein
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