Freiburg RNA Tools
IntaRNA - Results
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IntaRNA 1683303

Input and runtime details for job 1683303 (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 1683303 (server version trunk)

?Job Submitted & Queued@ Sat Feb 17 12:27:11 CET 2018
?Processing Started@ Sat Feb 17 12:27:27 CET 2018
?IntaRNA Finished & Post-Processing@ Sat Feb 17 13:20:08 CET 2018
?Post-Processing Finished@ Sat Feb 17 13:20:08 CET 2018
?Job Completed@ Sat Feb 17 13:20:13 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=1683303&toolName=IntaRNA ( 30 days expiry )

The job description you specified

FnrS - 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
0.0001208 0.25588 b1847 51 -- 65 FnrS 72 -- 87 -15.66110 yebF extracellular Colicin M immunity family protein
0.0001252 0.25588 b2513 55 -- 80 FnrS 37 -- 63 -15.63120 yfgM ancillary SecYEG translocon subunit putative anti-RcsB factor
0.0002087 0.28429 b2501 70 -- 106 FnrS 55 -- 94 -15.19720 ppk polyphosphate kinase component of RNA degradosome
0.0003748 0.38289 b1841 59 -- 79 FnrS 38 -- 60 -14.67150 yobA CopC family protein
0.0005601 0.45767 b1476 45 -- 60 FnrS 41 -- 57 -14.29260 fdnI formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible
0.0008323 0.56677 b4002 47 -- 67 FnrS 36 -- 54 -13.90350 zraP Zn-dependent periplasmic chaperone
0.0010631 0.60637 b0585 85 -- 103 FnrS 46 -- 63 -13.65510 fes enterobactin/ferrienterobactin esterase
0.0012178 0.60637 b0723 47 -- 70 FnrS 67 -- 90 -13.51460 sdhA succinate dehydrogenase flavoprotein subunit
0.0013356 0.60637 b1557 13 -- 36 FnrS 69 -- 91 -13.41800 cspB Qin prophage cold shock protein
0.0016809 0.63401 b2936 18 -- 27 FnrS 1 -- 10 -13.17350 loiP Phe-Phe periplasmic metalloprotease OM lipoprotein low salt-inducible Era-binding heat shock protein

Details of Selected Interaction Download Interaction Details

Target

Query

		

		

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Results are computed with IntaRNA version 2.1.0 (wrapper 1.1.3) linking Vienna RNA package 2.4.3