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
PA5489	-23	26	12	18	9.41	PrrF1	6	53	14	20	18.7	-11.08	-39.19	-1.10492	CUGACCUCGCCUAGGAGUGAACGAUGCGUAACCUGAUUCUCACCGCCAU&AUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAG	((((.(((((((((((((((......(((((..(((((((((...((((&))))...)))))))))...)))))))))))..))))..))))).))))	GACCGCUCCCCCCGGUCGAACUGACCGGGCCGAACCCGGCCGGAGAGCGGCACUGACCUCGCCUAGGAGUGAACGAUGCGUAACCUGAUUCUCACCGCCAUGCUGGCCAUGGCCAGCCUGUUCGGCAUGGCCGCCCAGGCCGACGACUAU	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0265569	0.9556607	dsbA	877731	thiol:disulfide interchange protein DsbA
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
PA3402	25	45	39	45	2.87	PrrF1	40	57	40	46	10.91	-13.64	-27.42	-1.3602	CCGCUGCUGAUCCUCGCGAUC&GGUCGCGAGAUCAGCCGG	(((..(((((((.((((((((&))))))))))))))))))	CCGGCGCGCUUCCGGCCAGCGCAACGGCCUGGCAAUGUACUACCAUCGCCCGGUCGUGUUCAGGAAGCCUGCCCCAUGAAGGGAUGGAAACUCUUUACCCCGCUGCUGAUCCUCGCGAUCGUCGCCAUCACCCUCUACCUGCGCCUGCAC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0057204	0.9377188		879960	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
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)'
PA4235	64	73	64	70	4.22	PrrF1	37	46	40	46	3.67	-11.73	-19.62	-1.16973	CGCGACCAGU&ACUGGUCGCG	((((((((((&))))))))))	UGGCUUGACCCGGAUCAGGCGGAGCCGGGAGCAUAUGCGGCUAGAUUCCUAGUUUUCUCCAGGGAGAGCCCCCCGAUGCAAGGCCAUCCGGAAGUCAUCGAUUACCUCAAUACGCUGUUGACCGGCGAGCUGGCCGCGCGCGACCAGUAC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0183269	0.9556607	bfrA	881830	bacterioferritin
PA4968	6	14	6	12	3.61	PrrF1	38	46	40	46	3.67	-11.52	-18.8	-1.14879	CGCGACCAG&CUGGUCGCG	(((((((((&)))))))))	GGCUGGAAGAUGAAGCCUGGAAGCUGUUACCGUUCGGCUUUCCCUACCGAGUUGAAGCCCAUUAGCCCGUUCCCGAUGACCGCGACCAGCCCAUCCCUGCUGUAUAUCCACGGCUUCAACAGUUCGCCCGAAUCGCACAAGGCGCGUCAG	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0206883	0.9556607		879898	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4420	-36	-14	-20	-14	5.57	PrrF1	40	62	40	46	11.83	-11.37	-28.77	-1.13383	GCUGCCGGACGAACUACGCGACC&GGUCGCGAGAUCAGCCGGUAAGC	((((((((..((.((.(((((((&))))))))).))..)))))).))	GGCUGAAGCCGACCUGGCGGCAAUCAAACAACCCGGUGGGCUGCCGGACGAACUACGCGACCUGAUCCUUUGACUAUGAAUGCCACCUACCGCCAUAUCACCGUUCUGCUCGAGGAGGCCGUUUCCGCACUGGCCCCGCGGGAGGACGGC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0225411	0.9556607		881254	S-adenosyl-methyltransferase MraW
PA0502	4	16	4	10	1.93	PrrF1	34	46	40	46	3.67	-11.3	-16.9	-1.12685	CGUGACCACUUGA&UCAACUGGUCGCG	((((((((.((((&)))).))))))))	UCGAAGCCCUCGGCGAAAGCUGGCGACAGCUGUCGUCUAGCCUUCUGGCAGAGAUCGAAGCCGAGGAGGGAGACGAUGCGUGACCACUUGAUCCUGUUGCCGGGCUGGGGCCUGGGUAGCGCACCGCUGGAACCGCUGCGCGACGCGCUG	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0234563	0.9556607		878654	biotin biosynthesis protein BioH
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
PA0483	25	40	28	34	3.91	PrrF1	40	54	45	51	8.07	-11.7	-23.68	-1.16674	GCCGAUCUCGCCGACC&GGUCGCGAGAUCAGC	((.((((((((.((((&)))))))))))).))	CGCGGCGUCGCAGGAUGUUUCACUGCGCUGCGAGCGCCUUGCCUAUACUCCCGGAAUCGCCCCAGGAGCCUCGCCAUGCCCGUCCAUGCCGCAUCCCUCGCCGAUCUCGCCGACCUGGUUCCGCUGUUUUCCGCCUACCUCGACUUCUAC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0186484	0.9556607		879556	acetyltransferase

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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