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IntaRNA 7119295

Input and runtime details for job 7119295 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_005072
? 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 7119295 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:23:26 CET 2020
?Processing Started@ Mon Jan 27 14:25:03 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:25:25 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:26:09 CET 2020
?Job Completed@ Mon Jan 27 14:26:17 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=7119295&toolName=IntaRNA ( 30 days expiry )

The job description you specified

Yfr1 - Prochlorococcus marinus


? Output download complete results [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_005072 Prochlorococcus marinus subsp. pastoris str. CCMP1986

Sort by selecting a column name
Target Start(T) End(T) Query Start(Q) End(Q) Energy RRI subseqs p-value fdr gene annotation
PMM0951 69 75 Yfr1 31 37 -4.03 0.4402471 0.8909401 carA carbamoyl phosphate synthase small subunit
PMM1518 58 65 Yfr1 30 37 -4.51 0.3678018 0.8751146
PMM0296 -67 -58 Yfr1 27 37 -4.7 0.3408079 0.8751146 similar to Arabidopsis thaliana photosystem II assembly protein
PMM1137 -5 4 Yfr1 29 37 -7.17 0.098354 0.8607323 cytochrome b(C-terminal)/b6/petD
PMM0693 -39 -31 Yfr1 29 37 -6.63 0.1342748 0.8751146
PMM0657 -57 -49 Yfr1 29 37 -5.79 0.2085211 0.8751146 vanadium/alternative nitrogenase delt
PMM1346 18 34 Yfr1 32 51 -5.29 0.2641976 0.8751146
PMM0464 64 70 Yfr1 20 26 -8.22 0.0502434 0.8607323 Tat family protein secretion protein
PMM1312 -61 -55 Yfr1 20 26 -6.14 0.1747091 0.8751146 PIN domain superfamily protein
PMM0648 50 56 Yfr1 20 26 -6.12 0.1765282 0.8751146 glucose-methanol-choline (GMC) oxidoreductase:NAD binding site
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