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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
?IntaRNA 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/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

Description of the job

Spot42 - E. coli

? Output [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

Show rows: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 all
Sort by selecting a column name.
Target Start(T) End(T) Query Start(Q) End(Q) Energy RRI subseqs p-value fdr gene annotation
b1343 21 34 Spot42 11 24 -8.89 0.0283265 0.9238006 dbpA ATP-dependent RNA helicase specific for 23S rRNA
b2659 -45 -24 Spot42 1 24 -10.83 0.0094499 0.9238006 csiD carbon starvation protein
b2150 -48 -22 Spot42 1 24 -9.49 0.0202101 0.9238006 mglB methyl-galactoside transporter subunit
b1586 -1 24 Spot42 5 28 -9.23 0.0234 0.9238006 ynfD DUF1161 family periplasmic protein
b3238 -21 -5 Spot42 39 54 -9.61 0.0188861 0.9238006 yhcN cadmium and peroxide resistance protein stress-induced
b0774 9 28 Spot42 4 24 -9.09 0.0253174 0.9238006 bioA 78-diaminopelargonic acid synthase PLP-dependent
b0882 -74 -44 Spot42 3 32 -9.02 0.0263331 0.9238006 clpA ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity
b3816 -71 -41 Spot42 4 37 -10.38 0.012208 0.9238006 corA magnesium/nickel/cobalt transporter
b1398 -10 -2 Spot42 1 9 -13.17 0.0024709 0.9238006 paaK phenylacetyl-CoA ligase
b2619 67 75 Spot42 1 9 -8.94 0.0275429 0.9238006 ratA toxic UPF0083 family protein inhibitor of 70S ribosome formation
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



		 
	

			





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