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
PA0443	-44	4	-44	-38	10.78	PrrF1	75	113	107	113	11.59	-12.67	-35.04	-1.26347	AUUAGCCCGAUGAGCGAAUAACUAAAAGAAUUCUGGAGAGGCCCAUGC&GCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAU	(((((((.((((((.((((((..........(((((((((.((...((&))....)).))))))))))))).)))))))).)))))))	AGUACUGGUGGUGCGGUACUCCGGCCAUCGCAUUAGCCCGAUGAGCGAAUAACUAAAAGAAUUCUGGAGAGGCCCAUGCAACAGAGCAGAUCGGAAGUGACCGAGCGCGACGGCUUGGUCGAGCUGUCCGCCGGCAGCGACGUACUCGAC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0104813	0.9556607		880435	transporter
PA0796	-5	10	-5	2	4.52	PrrF1	104	118	112	118	2.23	-11.73	-18.48	-1.16973	CCGUGAUGAGCCAGA&UCAGGCUAAUCACGG	(((((((.((((.((&)).)))).)))))))	GCAAUAUCGAGCGCCAGCUGGAACCCCAGCCGGCGAAGCUCGCCUCCGCUUCCUCCACCGUCUAAGAGGUCCGUGAUGAGCCAGACGUCCCUUACCCCCGGCCAGCGCUUCCGCGAAGCCGUGGCCACCGAACACCCGCUGCAGGUGGUC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0183269	0.9556607	prpB	882026	2-methylisocitrate lyase
PA1477	-23	7	-5	2	8.62	PrrF1	98	123	103	109	2.24	-12.15	-23.01	-1.21162	AAGAGCCCUGUAAACAGAGCCUGAUGAUGA&UCCUCAUCAGGCUAAUCACGGUUUUU	(((((((.((.......((((((((((.((&)).))))))))))...)).)))))))	GCCGCCCACGCUUGACCCGGGCUGGCAGCGGAAGGUCUGCCCGGUAUUUCCAAAGAGCCCUGUAAACAGAGCCUGAUGAUGAAUUGGACAUGGUUUCACAAGCUUGGGUCGCCCAAGUGGUUCUACGAGAUCAGCGGCCGCUGGCUGCCC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0143251	0.9556607	ccmC	881087	heme exporter protein CcmC
PA4155	-10	5	-10	-4	3.31	PrrF1	100	114	108	114	2.17	-13.27	-18.75	-1.32331	GAUUGGCACGAUGAG&CUCAUCAGGCUAAUC	(((((((..((((((&))))))..)))))))	CCUUCUAGGCGCCCCGAGAAGCCGGCCCCGCGCAGGGCUGGCCCAGCCCCAGAGCCCAUACAGGAGAUUGGCACGAUGAGUACCCCGAAACGCCUGCACAUCGGCAUGUCGCUGGCCCCCACCUGGCUCAGCGGCGAUGCCUGGCGGCGC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0072326	0.9556607		880176	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA1551	-15	5	-3	4	9.13	PrrF1	100	118	101	107	2.24	-14.25	-25.62	-1.42103	CCGUGGUACGCACUGAUGAG&CUCAUCAGGCUAAUCACGG	(((((((..((.((((((((&))))))))))..)))))))	AGUAGGCGUGCAACUAUUUUCUGACCCUGUCGGCAUGUACCGGCCGGGCGCCCCCCACUGCCGUGGUACGCACUGAUGAGCAAACAGAUUCCCGUUCAAGACGUCACCCCGCCUGCCAAGGGCGACACCAAUAACAACGAUCUCUACGCC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0038469	0.8677507		883008	ferredoxin
PA5351	-10	22	16	22	4.66	PrrF1	71	99	71	77	6.14	-15.79	-26.59	-1.5746	GAGGUAAACAAUGAAGAAGUGGCAAUGCGUGG&CCACGCAGUCGGACUCUUCAGAUUAUCUC	(((((((....((((((.((.....(((((((&))))))).....))))))))..)))))))	GGGCAGGUUGGCGGACAGGGUGGAUUUGUUAUAGGUUGCCGGCGCUGAACCGUGGUAACCCGCCCGAGGUAAACAAUGAAGAAGUGGCAAUGCGUGGUGUGUGGACUGAUCUAUGACGAGGCCAAAGGCUGGCCGGAAGAAGGCAUCGAG	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0013306	0.5771389	rubA1	879562	rubredoxin
PA3745	58	73	58	64	1.83	PrrF1	107	119	113	119	2.23	-11.31	-15.37	-1.12785	ACCGUGACCAACAGCC&GGCUAAUCACGGU	(((((((.....((((&))))..)))))))	GAAUAUGCGGCCUUUCGGGCCGUGGGCCCAGCGUGCAUUCAUUUUGCAAGCACCGACUACAGGAACGAAGUUCACAUGGUAACCAUCCGUCUUGCUCGUGGCGGCUCCAAAAAGCGCCCCUUCUACCACCUGACCGUGACCAACAGCCGC	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0233235	0.9556607	rpsP	880510	30S ribosomal protein S16
PA1389	-4	10	4	10	3.77	PrrF1	104	118	104	110	2.23	-11.6	-17.6	-1.15677	CCUGAUGAGCCUGA&UCAGGCUAAUCACGG	((((((.(((((((&))))))).)))).))	AGGCACAUGCCUGCCGCGGCAGCCCCGCAUCGAUGAGCCGAGCAUCCAGCACUUCUACCAAGUGGAACUUUCCUGAUGAGCCUGAACGGCAGACUGAAAGCUCGUGCGGCCAGCUUCGCUCGCACAGCCUAUCCACCUAUUCUUGGAUCG	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0197578	0.9556607		879276	glycosyl transferase family protein
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
PA2967	-13	21	3	9	6.98	PrrF1	68	101	80	86	9.23	-11.7	-27.91	-1.16674	AGGAGAGAAUCCCAUGAGUCUGCAAGGUAAGGUC&GACCCACGCAGUCGGACUCUUCAGAUUAUCUCCU	((((((.((((....(((((((....((..((((&)))).)).....)))))))....)))).))))))	AUGGCCUGGAUGGCGUCGAGGCGUUCGCCGCCACGCGCGCCGCCCUGGCCUGAGAGAGAGAAAGGAGAGAAUCCCAUGAGUCUGCAAGGUAAGGUCGCAUUGGUAACCGGCGCCAGCCGUGGCAUCGGCCAGGCGAUUGCGCUGGAACUG	UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGGUAAGCUGAGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUUUUGACCCGGCACUUUGCCGGGUCUUUUUUU	0.0186484	0.9556607	fabG	880433	3-oxoacyl-[acyl-carrier-protein] reductase FabG

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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