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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 p-value fdr gene annotation
PMM0792 57 63 Yfr1 21 27 -4.64 0.3492182 0.8751146
PMM1107 2 18 Yfr1 19 34 -4.63 0.3506303 0.8751146 pdxJ pyridoxine 5'-phosphate synthase
PMM1605 -52 -46 Yfr1 20 26 -4.62 0.3520454 0.8751146 rimM 16S rRNA-processing protein RimM
PMM0843 35 43 Yfr1 30 38 -4.56 0.3605969 0.8751146 tldD modulator of DNA gyrase TldD
PMM0446 45 51 Yfr1 31 37 -4.54 0.3634704 0.8751146 ctaC cytochrome c oxidase subunit 2
PMM1216 37 43 Yfr1 32 38 -4.53 0.3649114 0.8751146 sugar-phosphate nucleotidyl transferase
PMM1518 58 65 Yfr1 30 37 -4.51 0.3678018 0.8751146
PMM0017 23 29 Yfr1 29 35 -4.48 0.3721584 0.8754181 dnaJ molecular chaperone DnaJ
PMM0389 68 74 Yfr1 29 35 -4.36 0.3898285 0.8909401 cobI/cbiL precorrin-2 C20-methyltransferase
PMM0665 -1 6 Yfr1 14 20 -4.34 0.3928103 0.8909401 hslO heat shock protein 33
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