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
lmo0181 -54 -34 LhrA2 158 179 -15.02 0.0151521 0.9011628 sugar ABC transporter substrate-binding protein
lmo1401 -52 9 LhrA2 155 204 -13.43 0.0344502 0.9493467
lmo2811 -50 -8 LhrA2 160 203 -14.59 0.0190178 0.9128702 trmE tRNA modification GTPase TrmE
lmo0390 -50 -8 LhrA2 167 211 -13.46 0.0339368 0.9493467 uracil-DNA glycosylase
lmo0850 -49 -18 LhrA2 148 170 -14.84 0.0166718 0.9082262
lmo1666 -46 7 LhrA2 157 204 -16.3 0.0075316 0.863511 peptidoglycan-linked protein
lmo2809 -46 -2 LhrA2 161 211 -13.64 0.0310006 0.9493467 hypothetical secreted protein
lmo0184 -42 10 LhrA2 158 203 -14.64 0.0185255 0.9128702 oligo-16-glucosidase
lmo2327 -39 14 LhrA2 155 208 -14.96 0.0156437 0.9011628 lmo2327
lmo2596 -36 -21 LhrA2 171 186 -13.45 0.0341071 0.9493467 rpsI 30S ribosomal protein S9
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