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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
PMM0835 -64 -58 Yfr1 21 27 -7.8 0.0664486 0.8607323
PMM0503 -73 -67 Yfr1 21 27 -6.83 0.1199653 0.8751146 precorrin-6x reductase
PMM1613 59 65 Yfr1 21 27 -6.69 0.1298531 0.8751146 zinc metallopeptidase
PMM1604 -72 -66 Yfr1 21 27 -6.15 0.1738046 0.8751146
PMM0702 60 66 Yfr1 21 27 -5.66 0.2221596 0.8751146
PMM0792 57 63 Yfr1 21 27 -4.64 0.3492182 0.8751146
PMM0538 2 9 Yfr1 20 27 -4.7 0.3408079 0.8751146
PMM1689 24 32 Yfr1 20 29 -5.58 0.2308453 0.8751146 pyrG CTP synthetase
PMM1707 36 44 Yfr1 20 29 -5.26 0.2678137 0.8751146 argG argininosuccinate synthase
PMM0224 54 72 Yfr1 12 29 -6.64 0.13353 0.8751146 aroC chorismate synthase
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