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IntaRNA 4596356

Input and runtime details for job 4596356 (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 4596356 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:10:48 CET 2020
?IntaRNA Started@ Mon Jan 27 14:13:48 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:14:50 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:16:49 CET 2020
?Job Completed@ Mon Jan 27 14:17:02 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4596356&toolName=IntaRNA ( 30 days expiry )

Description of the job

FnrS - 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) Start(seed-Q) Energy p-value fdr gene annotation
b0123 -50 -21 FnrS 1 31 -14.36 0.0010196 0.9422174 cueO multicopper oxidase (laccase)
b2936 -58 -49 FnrS 1 10 -13.18 0.0026891 0.9422174 loiP Phe-Phe periplasmic metalloprotease OM lipoprotein low salt-inducible Era-binding heat shock protein
b1112 -36 -15 FnrS 1 22 -12.35 0.0050791 0.9422174 bhsA biofilm cell surface and signaling protein
b2210 -40 -33 FnrS 1 8 -11.75 0.0078728 0.9422174 mqo malate dehydrogenase FAD/NAD(P)-binding domain
b1869 66 73 FnrS 1 8 -11.72 0.0080437 0.9422174 yecN MAPEG family inner membrane protein
b0753 -64 -55 FnrS 1 10 -11.69 0.0082179 0.9422174 ybgS putative periplasmic protein
b1685 66 74 FnrS 1 9 -11.63 0.0085766 0.9422174 ydiH uncharacterized protein
b0404 15 22 FnrS 1 8 -11.4 0.0100874 0.9422174 acpH acyl carrier protein (ACP) phosphodiesterase ACP hydrolyase
b4216 -29 -22 FnrS 1 8 -11.27 0.0110445 0.9422174 ytfJ putative transcriptional regulator
b4656 -62 -55 FnrS 1 8 -11.13 0.0121669 0.9422174 yjhY pseudogene zinc finger protein family
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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