Freiburg RNA Tools
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IntaRNA 3645355

Input and runtime details for job 3645355 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? All repliconsyes
? Extract sequences aroundstart codon
? nt up (1-300)75
? nt down (1-300)75

Output Parameters

? Number of (sub)optimal interactions1
? Suboptimal interaction overlap can overlap in query
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (each)0
? Seed position (query)not provided
? Seed position (target)not provided

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 3645355 (server version 4.4.2)

?Job Submitted & Queued@ Mon Mar 06 14:24:03 CET 2017
?Processing Started@ Mon Mar 06 14:24:07 CET 2017
?IntaRNA Finished & Post-Processing@ Mon Mar 06 15:21:36 CET 2017
?Post-Processing Finished@ Mon Mar 06 15:21:36 CET 2017
?Job Completed@ Mon Mar 06 15:21:37 CET 2017
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=3645355&toolName=IntaRNA ( 30 days expiry )

The job description you specified

MicC - example

? Output download complete results [zip]

Downloadable files

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[txt]
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heatmap

? Identified Interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name:
p-value fdr value Target Position Query Position Energy Gene Annotation
4.07e-05 0.16251 b2215 9 -- 61 MicC 1 -- 70 -21.51350 ompC outer membrane porin protein C
0.000622 0.74535 b1835 61 -- 86 MicC 35 -- 58 -17.38350 rsmF 16S rRNA m(5)C1407 methyltransferase SAM-dependent
0.0006728 0.74535 b1667 120 -- 141 MicC 34 -- 55 -17.25750 ydhR putative monooxygenase
0.0007467 0.74535 b2859 4 -- 69 MicC 7 -- 65 -17.08980 ygeO pseudogene orgA family part of T3SS PAI ETT2 remnant
0.0011558 0.83046 b4590 93 -- 150 MicC 7 -- 61 -16.37850 ybfK uncharacterized protein
0.001368 0.83046 b0393 5 -- 19 MicC 40 -- 55 -16.10070 rdgC nucleoid-associated ssDNA and dsDNA binding protein competitive inhibitor of RecA function
0.001641 0.83046 b0333 126 -- 149 MicC 6 -- 28 -15.79850 prpC 2-methylcitrate synthase
0.0016638 0.83046 b1579 2 -- 67 MicC 7 -- 65 -15.77550 intQ pseudogene Qin prophage phage integrase familyPhage or Prophage Related
0.0024498 0.87628 b3751 130 -- 149 MicC 41 -- 60 -15.12500 rbsB D-ribose ABC transporter periplasmic binding protein ribose chemotaxis receptor
0.0027954 0.87628 b3354 76 -- 150 MicC 8 -- 70 -14.90070 yheU UPF0270 family protein

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

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Results are computed with IntaRNA version 2.0.1 (wrapper 1.1.2) linking Vienna RNA package 2.3.1