Freiburg RNA Tools
IntaRNA - Results
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IFF
IntaRNA 4341560

Input and runtime details for job 4341560 (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 4341560 (server version trunk)

?Job Submitted & Queued@ Wed Sep 27 16:45:23 CEST 2017
?Processing Started@ Wed Sep 27 16:45:36 CEST 2017
?IntaRNA Finished & Post-Processing@ Wed Sep 27 17:17:36 CEST 2017
?Post-Processing Finished@ Wed Sep 27 17:17:37 CEST 2017
?Job Completed@ Wed Sep 27 17:17:41 CEST 2017
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=4341560&toolName=IntaRNA ( 30 days expiry )

The job description you specified

CyaR - 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
4.14e-05 0.1325 b2039 105 -- 150 CyaR 1 -- 47 -20.88970 rfbA glucose-1-phosphate thymidylyltransferase
0.0002547 0.40734 b2077 101 -- 129 CyaR 1 -- 30 -18.83730 iceT putative citrate/iron-citrate/zinc-citrate efflux transporter
0.0005556 0.5924 b4074 6 -- 21 CyaR 32 -- 48 -17.85020 nrfE heme lyase (NrfEFG) for insertion of heme into c552 subunit NrfE
0.0009877 0.63968 b1485 65 -- 92 CyaR 24 -- 49 -17.07730 ddpC DD-dipeptide ABC transporter permease
0.0009998 0.63968 b1498 128 -- 150 CyaR 21 -- 44 -17.06050 ydeN putative Ser-type periplasmic non-aryl sulfatase
0.0013246 0.70624 b3456 120 -- 149 CyaR 15 -- 42 -16.66770 livM branched-chain amino acid ABC transporter permease
0.0022294 0.76799 b4350 1 -- 29 CyaR 10 -- 36 -15.91440 hsdR endonuclease R Type I restriction enzyme
0.0024455 0.76799 b1686 135 -- 148 CyaR 35 -- 49 -15.77690 menI 14-dihydroxy-2-naphthoyl-CoA hydrolase
0.0024673 0.76799 b2859 3 -- 48 CyaR 2 -- 46 -15.76360 ygeO pseudogene orgA family part of T3SS PAI ETT2 remnant
0.0025146 0.76799 b3482 117 -- 146 CyaR 1 -- 35 -15.73520 rhsB Rhs protein with DUF4329 family putative toxin domain putative neighboring cell growth inhibitor

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

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Results are computed with IntaRNA version 2.0.5 (wrapper 1.1.2) linking Vienna RNA package 2.3.1