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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 Seq(Q) p-value fdr gene annotation
PMM1119 -3 7 Yfr1 22 31 -11.27 0.0038187 0.7904709 som porin
PMM0173 41 68 Yfr1 20 38 -10.31 0.0097181 0.8607323
PMM0417 -71 -63 Yfr1 28 36 -9.92 0.0136924 0.8607323
PMM1634 5 11 Yfr1 22 28 -9.17 0.0251876 0.8607323 gyrB DNA gyrase subunit B
PMM0494 -36 -28 Yfr1 22 30 -9.16 0.0253828 0.8607323 ppa inorganic pyrophosphatase
PMM1193 -63 -43 Yfr1 36 58 -9.03 0.0280368 0.8607323 tetrapyrrole methylase family protein
PMM1121 -3 6 Yfr1 23 31 -8.64 0.0374112 0.8607323 som porin
PMM0384 -48 -42 Yfr1 22 28 -8.55 0.0399051 0.8607323 spnII-interrupted-C
PMM1021 12 18 Yfr1 21 27 -8.47 0.0422349 0.8607323 pili assembly chaperone
PMM1448 62 68 Yfr1 21 27 -8.28 0.0482169 0.8607323
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