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IntaRNA 6571257

Input and runtime details for job 6571257 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? 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 6571257 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:18:03 CET 2020
?Processing Started@ Mon Jan 27 14:20:22 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:21:19 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:22:25 CET 2020
?Job Completed@ Mon Jan 27 14:22:35 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

The job description you specified

Spot42 - E. coli


? Output download complete results [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
b0774 9 28 Spot42 4 24 -9.09 0.0253174 0.9238006 bioA 78-diaminopelargonic acid synthase PLP-dependent
b2582 6 19 Spot42 4 16 -9.03 0.0261856 0.9238006 trxC thioredoxin 2
b1867 51 72 Spot42 5 25 -9.93 0.0157589 0.9238006 yecD isochorismatase family protein
b1586 -1 24 Spot42 5 28 -9.23 0.0234 0.9238006 ynfD DUF1161 family periplasmic protein
b2602 -71 -60 Spot42 7 18 -10.62 0.0106505 0.9238006 yfiL lipoprotein
b0954 28 49 Spot42 9 31 -9.87 0.0163036 0.9238006 fabA beta-hydroxydecanoyl thioester dehydrase
b1004 -75 -56 Spot42 10 32 -9.83 0.0166769 0.9238006 wrbA NAD(P)H:quinone oxidoreductase
b2561 -7 16 Spot42 11 32 -10.17 0.0137542 0.9238006 yfhH putative DNA-binding transcriptional regulator
b1343 21 34 Spot42 11 24 -8.89 0.0283265 0.9238006 dbpA ATP-dependent RNA helicase specific for 23S rRNA
b3690 -4 11 Spot42 17 31 -9.42 0.0210242 0.9238006 cbrA colicin M resistance protein FAD-binding protein putative oxidoreductase
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