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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) End(seed-Q) Energy p-value fdr gene annotation
PMM0224 54 72 Yfr1 12 29 -6.64 0.13353 0.8751146 aroC chorismate synthase
PMM0712 -72 -65 Yfr1 12 19 -5.54 0.2352719 0.8751146 major facilitator superfamily multidrug-efflux transporter
PMM1561 35 42 Yfr1 12 19 -4.72 0.3380285 0.8751146
PMM1405 68 75 Yfr1 12 19 -4.34 0.3928103 0.8909401
PMM0021 -74 -68 Yfr1 14 20 -6.53 0.141895 0.8751146 murB UDP-N-acetylenolpyruvoylglucosamine reductase
PMM0665 -1 6 Yfr1 14 20 -4.34 0.3928103 0.8909401 hslO heat shock protein 33
PMM1647 17 23 Yfr1 14 20 -4.25 0.4063526 0.8909401 DNA polymerase III subunit delta
PMM0913 -47 -41 Yfr1 14 20 -4.18 0.4170203 0.8909401 ABC transporter
PMM1443 61 75 Yfr1 19 31 -5.46 0.2442923 0.8751146
PMM1069 -35 -21 Yfr1 19 33 -4.67 0.3449996 0.8751146 folD bifunctional 510-methylene-tetrahydrofolate dehydrogenase/ 510-methylene-tetrahydrofolate cyclohydrolase
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