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
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
PA4017	36	45	36	42	1.57	PrrF1	37	46	40	46	3.67	-12.67	-17.91	-1.26347	CGCGACCGGU&ACUGGUCGCG	((((((((((&))))))))))	AAACCGGCGAGGGCGCGGCGGGCAAAUAGAUACGCCGCGCACUACGCUCAUUGGUGUGGAAGGGGAGAAACACACAUGCACUCGACGCCCAAGCGCGUUCUGCUCGCCGGCGCGACCGGUCUUACCGGCGAGCACCUGUUGGAUCGGAUA	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0104813	0.9556607		878987	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA0119	53	73	67	73	8.72	PrrF1	101	121	101	107	2.24	-19.45	-30.41	-1.93959	AAGUCGUGAUUGGCCUGGUGA&UCAUCAGGCUAAUCACGGUUU	(((((((((((((((((((((&)))))))))))))))))))))	AACUGGUCAGACCGGUAAUACCACAAUAAAAAUGCGUUCAUCGCCCGCCUCCGCGAGGCCCGAUGGAAGCGCCGAAUGGAGACUCCUGCGAUGUUCAUCAAGCGCUGUUCCCGCUCGAUAUUCCUGCAAGUCGUGAUUGGCCUGGUGAUA	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	6.97e-05	0.1650844		877578	C4-dicarboxylate transporter DctA
PA1329	-8	7	-1	6	3.11	PrrF1	98	110	99	105	2.16	-11.84	-17.11	-1.1807	AGCACUCGAUGAGGA&UCCUCAUCAGGCU	(((.((.((((((((&)))))))))))))	AACUUGAAAGUCUACGUAGGAGAAGGCCGGUUCUGUUAAAGCUUCGACCUUUCUAGACUGGCCCGCAAGCACUCGAUGAGGACGCCGGCCAUGUCUACCCACCUGUCUCUGCAACAUGCCCAACGCUGCAUCGCGGCGGCCAUUGCCGAA	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0171905	0.9556607		880896	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4236	-22	-7	-13	-7	5.8	PrrF1	96	112	96	102	4.92	-11.12	-21.84	-1.1089	UUAGCCGUUGAGGAGA&UCUCCUCAUCAGGCUAA	((((((..((((((((&))))))))...))))))	AAUCCCUGGUCCACGCUGAUGAUUUCCGUGUAGCCGCUUCGCUUCAUAGCACGUUAGCCGUUGAGGAGAGAGUAAAUGGAAGAGAAGACCCGCCUGACCACUGCCGCUGGCGCACCGGUGGUCGAUAACCAGAACGUGCAGACCGCCGGU	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0259669	0.9556607	katA	881831	catalase
PA3974	-13	33	27	33	13.63	PrrF1	43	79	43	49	17.62	-11.84	-43.09	-1.1807	ACUGCGGGGCAUCAUGCGGCACUGGCUGAUUCUCUUUCUUCUUGCG&CGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGU	(((((((((..((...(((((((((((((..........(((((((&))))))))))))))))..)))).))..))).))))))	ACAACGCUCGCCAAGGGCGGACCAUGACAAGGGAGGUGGGGCUCCCGGUCCGUUCGAGGAGCACUGCGGGGCAUCAUGCGGCACUGGCUGAUUCUCUUUCUUCUUGCGUUGCCGUGCCUGGCGGGUGCGGUGAGCUUCAACGAGCAGGUC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0171905	0.9556607	ladS	878890	lost adherence sensor LadS
PA2715	44	55	46	52	5.75	PrrF1	71	82	74	80	4.1	-16.49	-26.34	-1.64441	CCGACUGCGUGG&CCACGCAGUCGG	((((((((((((&))))))))))))	ACAAGUACGUGCCGGCGCGCCUGGAACGGCUGGCGACGCCCGCCGCUACGAACGCCUGAGCCAGGGAGGACGAUCAUGACCUUCGUCGUGCUGGAAGAAUGCAUCCGCUGCAAACACACCGACUGCGUGGAAGUCUGUCCCGUGGACUGC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.000796	0.5386646		882611	ferredoxin
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)'
PA2509	8	29	9	15	4.78	PrrF1	104	121	114	120	2.23	-11.21	-18.22	-1.11788	AAGCCGUGAUCCAAAGCCUCGA&UCAGGCUAAUCACGGUUU	((((((((((.....((((.((&))))))..))))))))))	ACCCGCUCGGUAUCGAGCGAGCCUUGAGCAGCGAACCGUCGAAAACCCGACCGCAACCCUGGUGGACCCCCGAGAAUGAGCCAAGCCGUGAUCCAAAGCCUCGAGUCGAUCAUCGUCGACCUGCCGACCAUCCGCCCGCACAAGCUGGCC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0246826	0.9556607	catB	882968	muconate cycloisomerase I
PA1283	25	36	28	34	5.71	PrrF1	35	46	37	43	3.67	-12.06	-21.44	-1.20264	CGUGACCAGUUG&CAACUGGUCGCG	((((((((((((&))))))))))))	ACGGGAAUUGCGCGCCACGGGCGGGCGCGUGAAAAUAUAAAUACAUACGUAUGGAUUUAAACUCAAGAGGUAGCCAUGGGACGCCGACGAACGAUCGACCGUGACCAGUUGCUCGAUGCCGCCGAGGCGGUGAUCGCCCGCGAGGGCGCG	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0151084	0.9556607		881458	transcriptional regulator

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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