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IntaRNA 8164948

Input and runtime details for job 8164948 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_003210
? 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 8164948 (server version trunk)

?Job Submitted & Queued@ Sat Feb 17 12:29:40 CET 2018
?Processing Started@ Sat Feb 17 12:29:57 CET 2018
?IntaRNA Finished & Post-Processing@ Sat Feb 17 13:50:24 CET 2018
?Post-Processing Finished@ Sat Feb 17 13:50:24 CET 2018
?Job Completed@ Sat Feb 17 13:50:28 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=8164948&toolName=IntaRNA ( 30 days expiry )

The job description you specified

LhrA2 - example

? Output download complete results [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_003210 Listeria monocytogenes EGD-e

Sort by selecting a column name:
p-value fdr value Target Position Query Position Energy Gene Annotation
2e-07 0.00055 lmo1883 72 -- 103 LhrA2 139 -- 170 -26.67430   chitinase
0.0004807 0.68888 lmo1187 14 -- 47 LhrA2 153 -- 183 -19.53020   ethanolamine utilization protein EutQ
0.001088 0.88402 lmo2074 6 -- 33 LhrA2 147 -- 174 -18.48090    
0.0024256 0.88402 lmo1611 5 -- 29 LhrA2 149 -- 173 -17.37880   aminopeptidase
0.0029225 0.88402 lmo1507 50 -- 79 LhrA2 147 -- 174 -17.11180   response regulator
0.0030852 0.88402 lmo0057 53 -- 82 LhrA2 157 -- 185 -17.03340    
0.0033078 0.88402 lmo1875 49 -- 79 LhrA2 150 -- 181 -16.93200   ABC transporter ATP-binding protein
0.0034082 0.88402 lmo1229 73 -- 103 LhrA2 147 -- 182 -16.88830    
0.0040804 0.88402 lmo2308 62 -- 82 LhrA2 147 -- 170 -16.62290   single-stranded DNA-binding protein
0.0044658 0.88402 lmo2446 53 -- 80 LhrA2 163 -- 188 -16.48830   glycosidase

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