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IntaRNA 6571257

Input and runtime details for job 6571257 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? 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 6571257 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:18:03 CET 2020
?Processing Started@ Mon Jan 27 14:20:22 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:21:19 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:22:25 CET 2020
?Job Completed@ Mon Jan 27 14:22:35 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

The job description you specified

Spot42 - E. coli


? Output download complete results [zip]

Downloadable files

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


heatmap

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

Sort by selecting a column name
Target Start(T) End(T) Query Start(Q) End(Q) Energy Seq(Q) p-value fdr gene annotation
b3224 -61 -50 Spot42 1 12 -16.33 0.0003958 0.8439588 nanT sialic acid transporter
b2797 -68 -54 Spot42 55 69 -15.99 0.0004824 0.8439588 sdaB L-serine dehydratase 2
b0757 -17 39 Spot42 1 59 -14.73 0.001003 0.9238006 galK galactokinase
b0885 -27 -10 Spot42 42 58 -13.52 0.0020193 0.9238006 aat leucyl/phenylalanyl-tRNA-protein transferase
b1398 -10 -2 Spot42 1 9 -13.17 0.0024709 0.9238006 paaK phenylacetyl-CoA ligase
b1927 -50 -39 Spot42 48 59 -13.13 0.0025285 0.9238006 amyA cytoplasmic alpha-amylase
b1212 15 28 Spot42 43 56 -13.07 0.0026174 0.9238006 prmC RF-1 and RF-2 N5-glutamine methyltransferase
b2801 -39 -29 Spot42 46 56 -12.84 0.002988 0.9238006 fucP L-fucose transporter
b2935 63 75 Spot42 52 64 -12.34 0.003983 0.9238006 tktA transketolase 1 thiamine triphosphate-binding
b1302 -35 6 Spot42 21 57 -11.97 0.004925 0.9238006 puuE 4-aminobutyrate aminotransferase PLP-dependent
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