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IntaRNA 4197128

Input and runtime details for job 4197128 (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 4197128 (server version trunk)

?Job Submitted & Queued@ Wed Sep 27 16:47:05 CEST 2017
?Processing Started@ Wed Sep 27 16:47:21 CEST 2017
?IntaRNA Finished & Post-Processing@ Wed Sep 27 17:28:02 CEST 2017
?Post-Processing Finished@ Wed Sep 27 17:28:03 CEST 2017
?Job Completed@ Wed Sep 27 17:28:07 CEST 2017
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=4197128&toolName=IntaRNA ( 30 days expiry )

The job description you specified

RyhB - example

? Output download complete results [zip]

Downloadable files

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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
0.0001433 0.46232 b1683 83 -- 108 RyhB 38 -- 66 -21.43070 sufB component of SufBCD Fe-S cluster assembly scaffold
0.0002853 0.46232 b1181 93 -- 144 RyhB 37 -- 88 -20.31170 ycgN UPF0153 family cysteine cluster protein
0.0003631 0.46232 b0894 38 -- 59 RyhB 42 -- 62 -19.91150 dmsA dimethyl sulfoxide reductase anaerobic subunit A
0.0006013 0.47608 b3743 115 -- 138 RyhB 37 -- 60 -19.05930 asnC transcriptional activator of asnA autorepressor
0.0006231 0.47608 b4255 11 -- 33 RyhB 39 -- 61 -18.99840 rraB protein inhibitor of RNase E
0.0014144 0.70681 b3885 128 -- 150 RyhB 41 -- 66 -17.56810 yihX alpha-D-glucose-1-phosphate phosphatase anomer-specific
0.0017673 0.70681 b2170 43 -- 69 RyhB 2 -- 24 -17.16990 setB lactose/glucose efflux system
0.0019348 0.70681 b0181 2 -- 72 RyhB 5 -- 88 -17.00680 lpxA UDP-N-acetylglucosamine acetyltransferase
0.0021128 0.70681 b2822 109 -- 139 RyhB 37 -- 63 -16.84760 recC exonuclease V (RecBCD complex) gamma chain
0.0021345 0.70681 b4019 66 -- 82 RyhB 43 -- 58 -16.82910 metH homocysteine-N5-methyltetrahydrofolate transmethylase B12-dependent

Details of Selected Interaction Download Interaction Details

Target

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