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
PA1196	36	55	47	53	7.22	PrrF1	103	121	105	111	2.23	-11.73	-21.18	-1.16973	AAGCGGUGAACUGGCCUGGU&AUCAGGCUAAUCACGGUUU	((((.((((..(((((((((&))))))))).)))).))))	GGAUGCUCGGUCGCGCUGCGUCGAAGAUGGGACAACUGACGAGAUUUCGACAUCCGGGAAACCGAGGGGGAGAGCAUGGCGCUUGUCGAGGAACCGACGAUUUCCACGCGAAGCGGUGAACUGGCCUGGUUGGUGGACUGCCUGGCGCCG	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0183269	0.9556607		878419	transcriptional regulator
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
PA1216	-28	15	9	15	10	PrrF1	78	119	78	84	12.11	-13.13	-35.24	-1.30934	ACCACGAGAGCCUACUGGAGAUUACCCAAUGAAGCAGUUCGAC&GUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGU	(((..((.(((((...((((((.......(((((.((((((((&)))))))))))))....)))))).....)))))..))..)))	CCUCGGCGGCAGCGGCACCUACAUCAAUUUCGUCCACAAGGGCGAUUACCACGAGAGCCUACUGGAGAUUACCCAAUGAAGCAGUUCGACAAGCACGCAGACGCCUACAACGUGGUCCGCGGCAAGAUCGCCUAUCCGGAUUCGCUCUAC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0078947	0.9556607		878403	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4430	-16	4	-6	1	7.87	PrrF1	101	119	104	110	2.24	-11.46	-21.57	-1.14281	ACCAGGAGAAAGCCUGAUGA&UCAUCAGGCUAAUCACGGU	(((..((...((((((((((&))))))))))..))..)))	GAACCUGCCGAUUCCGCCUUAUACGUUCGAUGCUGACGACGUCAUCACCAUCGGCGUGGACCAGGAGAAAGCCUGAUGAACAAGUUCAUGGCUUGGGUCGAUGCGCGUUUUCCCGCGACCAAGAUGUGGGAAGACCAUCUGAGCAAGUAC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0214121	0.9556607		880944	cytochrome b
PA1248	4	22	15	21	5.15	PrrF1	101	119	102	108	2.24	-11.83	-19.22	-1.17971	ACCAUGCGCCGCCUGAUGA&UCAUCAGGCUAAUCACGGU	(((.((....(((((((((&)))))))))....)).)))	GAGCGCUCGCUGCUCAAUUACCUGUUCAAGCCCCUGUUCGACCGCGCCCACGUGGCGCUGGCGGAGAACUGACCGAUGACCAUGCGCCGCCUGAUGACCUGGCUGUUCGGCGCCUUCCUGUUGCUGCUGCGCGAGGACGCCUUCGCCCUC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0172911	0.9556607	aprF	881227	alkaline protease secretion protein AprF
PA0916	-13	-1	-8	-2	2.41	PrrF1	107	119	108	114	2.23	-13.58	-18.22	-1.35422	ACCGAGGUUAGCC&GGCUAAUCACGGU	((((.((((((((&)))))))).))))	CGCGGCGCUGCCGCUAGAAUUGCGCACUUUUUGAUCAGAGGCGCCAGCAAGCGCGCCCGCCUACCGAGGUUAGCCAUGUCCACCCCCACUCCCAAAGUCGGCUUCGUCAGUCUUGGAUGCCCCAAGGCGCUGGUCGACUCCGAGCGCAUC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.005944	0.9377188		880629	ribosomal protein S12 methylthiotransferase RimO
PA1205	-16	-3	-9	-3	5	PrrF1	104	119	104	110	2.23	-11.66	-18.89	-1.16275	ACCGGAGAGCCUGA&UCAGGCUAAUCACGGU	((((((.(((((((&)))))))..)).))))	GCAGCAGUUGCAGGCCCUGCAGCUAUGGGUGCGCCGCCUGCGCGGUUGAAUGCCUCGUCACCGGAGAGCCUGAACAUGAGCAAUACCGAAGAGCGUUGCGACCUGUCCUCCUCGCGGGACUGUCCGGAACGCCACGAACACCUGCUGCAA	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0190852	0.9556607		882088	quercetin 23-dioxygenase
PA4656	25	38	29	35	5.43	PrrF1	100	119	103	109	2.24	-12.22	-19.89	-1.2186	ACCGGCCUGAUGGG&CUCAUCAGGCUAAUCACGGU	((((((((((((((&))))))))))......))))	GAUGCACGGUCAUCGGGCAGAUCGAUGUCCAGGGUCCAGACUGAAAGGGCACGCAGGCAAAACGAGGAGACAGCCAUGCACAUUCUCUUGACCGGCGGUACCGGCCUGAUGGGUCGCCGCCUGUGCGCCCGCUGGCGACAGGCCGGACAC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0137418	0.9556607		881319	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA3263	-66	-51	-58	-52	9.16	PrrF1	104	119	105	111	2.23	-11.58	-22.97	-1.15478	ACCGGGGUUGGCCUGA&UCAGGCUAAUCACGGU	((((.(((((((((((&))))))))))).))))	UAGCGACGGACCGGGGUUGGCCUGAGCCGCCAGCGGCGGAAUAAUGGGUCCUUUGUGCCCGGAGAGAACGACCCCAUGUGGUUCCGCAAUCUGCUCGUCUACCGCCUCACCCAGGAUCUGCAACUGGAUGCCGAUUCCCUCGAGAAAGCC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0199868	0.9556607		882426	recombination associated protein RdgC
PA1336	43	53	43	49	2.27	PrrF1	107	119	113	119	2.23	-11.82	-16.32	-1.17871	ACCGUGAAGCC&GGCUAAUCACGGU	(((((((((((&))))..)))))))	CUGCCGGCCGUGCCGGAAAACCGCCCGCUCCGCCGCCCAUCGUGGCGGCGGGCUGGCCUAGCCGCGACGACUGUGAUGGAAUCCCCCGACCCGCCCUGCAGCGUACCUCCGUCACUGACCGUGAAGCCCCGCCUCGUCCGCCAGUUGCUG	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0173922	0.9556607		879303	two-component sensor

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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