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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 p-value fdr gene annotation
b1623 -58 -51 Spot42 1 8 -9.03 0.0261856 0.9238006 add adenosine deaminase
b3224 -61 -50 Spot42 1 12 -16.33 0.0003958 0.8439588 nanT sialic acid transporter
b2216 -57 -49 Spot42 3 11 -10.78 0.009723 0.9238006 rcsD phosphotransfer intermediate protein in two-component regulatory system with RcsBC
b0369 -53 -46 Spot42 1 8 -8.81 0.0296259 0.9238006 hemB 5-aminolevulinate dehydratase (porphobilinogen synthase)
b0721 -55 -44 Spot42 4 15 -10.51 0.0113383 0.9238006 sdhC succinate dehydrogenase membrane subunit binds cytochrome b556
b3934 -56 -44 Spot42 41 56 -10.45 0.0117318 0.9238006 cytR Anti-activator for CytR-CRP nucleoside utilization regulon
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
b4553 -64 -42 Spot42 53 74 -11.45 0.006633 0.9238006 ysaB uncharacterized protein
b3709 -53 -42 Spot42 1 13 -9.62 0.0187797 0.9238006 tnaB tryptophan transporter of low affinity
b4621 -48 -41 Spot42 1 8 -11.15 0.0078733 0.9238006 yjbS uncharacterized protein
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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