Input and runtime details for job 7814698 (precomputed example)

Sequence Parameters

	Query ncRNA (short) in FASTA		[.fa]
	Index first query position		1
	Target RNA (long) in FASTA		[.fa]
	Target NCBI RefSeq ID		NC_002516
	All replicons		yes
	Extract sequences around		start codon
	nt upstream (1-300)		75
	nt downstream (1-300)		75
	Index first target position		-75

Output Parameters

	Number of interactions per RNA pair		1
	Suboptimal interaction overlap		can overlap in query
	Max. interaction length		not provided
	Max. absolute energy of an interaction		0
	Max. delta energy above mfe of an interaction		100
	No lonely base pairs		yes
	No GU at helix ends		yes

Seed Parameters

	Min. number of basepairs in seed		7
	Max. Number of mismatches in seed		0
	Maximal energy		0
	Minimal unpaired probability (per RNA)		0
	Seed position (query)		not provided
	Seed position (target)		not provided
	Ignore seeds with GU base pairs		no
	Ignore seeds with GU ends		yes

Folding Parameters

	Temperature for energy computation		37.0
	Access. query: folding window size		150
	Access. query: max. basepair distance		100
	Access. target: folding window size		150
	Access. target: max. basepair distance		100
	Energy parameter set (Vienna package)		Turner model, 2004

Job ID 7814698 (server version trunk)

	Job Submitted & Queued		@ Fri Jan 07 21:23:03 CET 2022
	Pre-Processing Started		@ Fri Jan 07 21:23:24 CET 2022
	IntaRNA Started		@ Fri Jan 07 21:25:48 CET 2022
	IntaRNA Finished & Post-Processing		@ Fri Jan 07 21:26:49 CET 2022
	Post-Processing Finished		@ Fri Jan 07 21:27:12 CET 2022
	Job Completed		@ Fri Jan 07 21:27:13 CET 2022

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7814698&toolName=IntaRNA ( 30 days expiry )

Description of the job

PrrF1 - Pseudomonas aeruginosa

Output [zip]

Downloadable files

	IntaRNA result table:		[csv]
	Target region plot		[png] [pdf]
	Query region plot		[png] [pdf]
	Functional enrichment file		[txt]
	Functional annotation chart		[html] [pdf] [png]

Target region plot

Query region plot

Function

Identified Interactions for NC_002516 Pseudomonas aeruginosa PAO1

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)	Start(seed-T)	End(seed-T)	ED(T)	Query	Start(Q)	End(Q)	Start(seed-Q)	End(seed-Q)	ED(Q)	Energy	E(hybrid)	E_norm	RRI subseqs	RRI details	Seq(T)	Seq(Q)	p-value	fdr	gene	geneID	annotation
PA2659	-9	17	10	16	3.85	PrrF1	75	99	76	82	6.14	-15.78	-25.77	-1.57361	GAGAUUCCCAUGAAGAAACUGACUGC&GCAGUCGGACUCUUCAGAUUAUCUC	(((((.....((((((..((((((((&))))))))..))))))....)))))	AGCUUCAAUUAAGAGCGCCCGGUUAAUCUGCAAACCGUCGAAAGCAACACGAUUGAUUCCCACGGAGAGAUUCCCAUGAAGAAACUGACUGCCCUGUUCGCCGCCACCGCCAUCGCCCUGACUGCCGGCCUGGCCCAGGCCCGCGACCUC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0013402	0.5771389		882368	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA2264	-30	-9	-28	-22	6.47	PrrF1	99	121	113	119	2.24	-15.57	-24.28	-1.55267	AAACCGUGAUGAUCCAGAGAGG&CCUCAUCAGGCUAAUCACGGUUU	((((((((((...((.((((((&)))).)).))...))))))))))	ACACAUGAACUUAUAAUUAGCCUGCUAAUCAUUAUCAGAAAGACGAAACCGUGAUGAUCCAGAGAGGACCCCACCAUGCCCGAUGACAAGGCCGUCAACGGCCGCCGCGACUUCCUGCGCAAGACCCUGACCGUGAUCCCGGCGGUGACC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0015572	0.5837442		877991	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA0007	-4	13	-3	4	4.07	PrrF1	104	120	113	119	2.23	-15.53	-21.83	-1.54868	AACCGUGAAACGCCUGA&UCAGGCUAAUCACGGUU	((((((((...((((((&))))))...))))))))	UGUUUCCACCACAGGUGGAGCGGGCGUGACGACGGGGAGUUCCGGGGCGUCUGCCCGUUCCCAAGGACGGUAACCGUGAAACGCCUGAAAAAGACACUGCACCUUUCAAGCUUGUCCCUCGCUUCCCUGGCUCUUUCUUCCGCCGCCCUG	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.001602	0.5837442		877575	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA1464	28	51	45	51	8.54	PrrF1	68	89	68	74	8.02	-15.33	-31.89	-1.52873	GAAGAUCCGAUCCUGCAGUGGGUC&GACCCACGCAGUCGGACUCUUC	((((((((((..((((.(((((((&)))))))))))))))).)))))	GCCGUCAAGCGCCUGCACGGCGACCAUUGAUAGACAGCUUCCGCCACUUGCGGCGGUUUUCGAGAGGUUAGGGGAAUGAGCAAAGCCACCGCGCAAAGCGCCGAAGAUCCGAUCCUGCAGUGGGUCACCUUCCGCCUGGACAACGAGAGC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0018445	0.6240997		882080	purine-binding chemotaxis protein
PA3767	-40	-23	-30	-24	8.83	PrrF1	98	121	99	105	2.24	-15.05	-26.12	-1.50081	AGACCGGCCUGAUGGGGA&UCCUCAUCAGGCUAAUCACGGUUU	((((((((((((((((((&))))))))))))......))))))	GUGGAUGUUCCACUGCCACGUCAUCGACCAUAUGGAGACCGGCCUGAUGGGGACCAUCGCGGUCGGCGAGGCCUGGUGCGGGUGACUAAGCUGAUCAGCAACGGCAAGGGCUACCCGACGGUAAAAGGUGUGCGUCCGAUCAUCGAUCGC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0022411	0.6680946		880561	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA3255	-74	-60	-67	-61	2.74	PrrF1	101	115	102	108	2.12	-15.04	-19.9	-1.49981	UGAUGAGCCUGGUGA&UCAUCAGGCUAAUCA	((((.((((((((((&)))))))))).))))	UUGAUGAGCCUGGUGAUCUUCGACCUGGACGAGACCAUGAUCCACGGCGACUGCUCCAGCCUGUGGAGCCAGCGCAUGGCGAGUCUCGGCUGGGUCGACGAAUCCUUCGUCCGCCGCGACGCCGAACUGAUGGAGCAGUACGCCGAAGGC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0022566	0.6680946		882418	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA1432	25	50	25	31	6.46	PrrF1	70	89	83	89	5.86	-14.9	-27.22	-1.48585	GAAGAGUUCGAUAAAAAACUGCUGGG&CCCACGCAGUCGGACUCUUC	(((((((((((.......((((((((&)))).)))))))))))))))	AUCUAUCUCAUUUGCUAGUUAUAAAAUUAUGAAAUUUGCAUAAAUUCUUCAGCUUCCUAUUUGGAGGAAGUGAAGAUGAUCGUACAAAUUGGUCGGCGCGAAGAGUUCGAUAAAAAACUGCUGGGCGAGAUGCACAAGUUGCGUGCUCAA	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0024845	0.6765752	lasI	881777	acyl-homoserine-lactone synthase
PA0365	43	52	43	49	0.65	PrrF1	101	110	104	110	2.11	-14.85	-17.61	-1.48087	AGCCUGAUGA&UCAUCAGGCU	((((((((((&))))))))))	UACAAGCUGUUCGUGCGCUGAACCGGGGCGCGUGCGGCGCCCCCUCAUUCCUACGCUGCAGGUGACAUAACAACAAUGAGCGACACCACCCUUGAAAGCGCCGGCCUGUCCCGACGCAGCCUGAUGAAAGUCGGCCUGAUCGGCGGCGCC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0025709	0.6765752		879873	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4756	52	64	52	58	4.34	PrrF1	107	119	113	119	2.23	-14.73	-21.3	-1.4689	AUCGUGAUUGGCC&GGCUAAUCACGGU	(((((((((((((&)))))))))))))	UCGGCGCCCUGUUCGUCGGCUUUGGUGUGAAGCUGGCCACCGCAACCCUGUCCUGAUUAUUGCAACGAGAGUCCCAUGCCAAAACGUACAGACAUAAAGAGCAUCCUGAUCCUCGGUGCCGGCCCCAUCGUGAUUGGCCAGGCCUGCGAA	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0027896	0.6954913	carB	881743	carbamoyl phosphate synthase large subunit
PA5164	-13	4	-3	4	2.89	PrrF1	101	121	101	107	2.24	-14.59	-19.72	-1.45494	AGACCGUGUACUGAUGA&UCAUCAGGCUAAUCACGGUUU	((((((((..(((((((&)))))))......))))))))	AAAACUCGCCGCGCCGCUGGCCAAGAACGGCUACGGCCAAUACCUCAAGCGCCUGCUGACCGAGACCGUGUACUGAUGAAAGCGACCCGCCUGGCAAUUCCCGACGUCAUCCUCUUCGAACCCCGGGUGUUCGGCGACGAUCGCGGAUUC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0030663	0.7262532	rmlC	879991	dTDP-4-dehydrorhamnose 35-epimerase

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

Energy

Hybridization Energy

Unfolding Energy - Target

Unfolding Energy - Query

Position - Target

Position - Query

Position Seed - Target

Position Seed - Query

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When using IntaRNA please cite :

Martin Mann, Patrick R. Wright, and Rolf Backofen
IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
Nucleic Acids Research, 2017, 45 (W1), W435–W439.
Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Anke Busch, Andreas S. Richter, and Rolf Backofen
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Bioinformatics, 2008, 24 (24), 2849-56.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with IntaRNA version 3.2.0 linking Vienna RNA package 2.4.14

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