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IntaRNA 3751556

Input and runtime details for job 3751556 (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 3751556 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:09:18 CET 2020
?Processing Started@ Mon Jan 27 14:12:06 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:12:59 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:14:52 CET 2020
?Job Completed@ Mon Jan 27 14:15:02 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=3751556&toolName=IntaRNA ( 30 days expiry )

The job description you specified

CyaR - 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 p-value fdr gene annotation
b2077 26 54 CyaR 1 30 -18.84 0.0001018 0.2119128 iceT putative citrate/iron-citrate/zinc-citrate efflux transporter
b4074 -70 -57 CyaR 35 48 -18.4 0.0001518 0.2119128 nrfE heme lyase (NrfEFG) for insertion of heme into c552 subunit NrfE
b1485 -11 12 CyaR 25 49 -16.69 0.0006365 0.4585162 ddpC DD-dipeptide ABC transporter permease
b2039 31 74 CyaR 2 46 -16.65 0.0006569 0.4585162 rfbA glucose-1-phosphate thymidylyltransferase
b1498 53 75 CyaR 21 44 -16.06 0.0010357 0.5783349 ydeN putative Ser-type periplasmic non-aryl sulfatase
b1686 60 73 CyaR 35 49 -15.77 0.0012872 0.5989771 menI 14-dihydroxy-2-naphthoyl-CoA hydrolase
b1209 -57 -34 CyaR 11 36 -15.14 0.0020364 0.7364947 lolB lipoprotein localization factor
b2556 40 58 CyaR 20 38 -15.09 0.0021103 0.7364947 glrK sensor protein kinase regulating glmY sRNA in two-component system with response regulator GlrR
b3770 36 54 CyaR 35 52 -14.65 0.0028743 0.779419 ilvE branched-chain amino acid aminotransferase
b3541 -74 -53 CyaR 14 30 -14.49 0.0032095 0.779419 dppD dipeptide/heme ABC transporter ATPas
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