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IntaRNA 7657267

Input and runtime details for job 7657267 (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 7657267 (server version 4.4.2)

?Job Submitted & Queued@ Mon Mar 06 14:26:24 CET 2017
?Processing Started@ Mon Mar 06 14:26:37 CET 2017
?IntaRNA Finished & Post-Processing@ Mon Mar 06 15:23:39 CET 2017
?Post-Processing Finished@ Mon Mar 06 15:23:39 CET 2017
?Job Completed@ Mon Mar 06 15:23:40 CET 2017
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=7657267&toolName=IntaRNA ( 30 days expiry )

The job description you specified

Spot42 - example

? Output download complete results [zip]

Downloadable files

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


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
0.000332 0.61568 b3224 15 -- 26 Spot42 1 -- 12 -16.32220 nanT sialic acid transporter
0.0004194 0.61568 b2797 8 -- 22 Spot42 55 -- 69 -15.98320 sdaB L-serine dehydratase 2
0.0005403 0.61568 b0757 58 -- 106 Spot42 8 -- 60 -15.61240 galK galactokinase
0.0006216 0.61568 b1302 41 -- 82 Spot42 20 -- 57 -15.40590 puuE 4-aminobutyrate aminotransferase PLP-dependent
0.0013242 0.92325 b2962 101 -- 147 Spot42 1 -- 57 -14.27370 yggX oxidative damage protective factor for iron-sulfur proteins
0.0014089 0.92325 b0885 48 -- 66 Spot42 42 -- 59 -14.17960 aat leucyl/phenylalanyl-tRNA-protein transferase
0.0016663 0.92325 b0882 2 -- 33 Spot42 2 -- 32 -13.92370 clpA ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity
0.0018642 0.92325 b4642 10 -- 38 Spot42 1 -- 28 -13.75170 yoeD pseudogene CP4-44 putative prophage remnantPhage or Prophage Related
0.0027407 0.93293 b1398 66 -- 74 Spot42 1 -- 9 -13.15580 paaK phenylacetyl-CoA ligase
0.0027932 0.93293 b1927 26 -- 37 Spot42 48 -- 59 -13.12620 amyA cytoplasmic alpha-amylase

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