Input and runtime details for job 3751556 (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_000913
	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 3751556 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:09:18 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:12:06 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:12:59 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:14:52 CET 2020
	Job Completed		@ Mon Jan 27 14:15:02 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3751556&toolName=IntaRNA ( 30 days expiry )

Description of the job

CyaR - E. coli

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_000913 Escherichia coli str. K-12 substr. MG1655

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
b0107	67	75	67	73	1.61	CyaR	40	48	42	48	2.76	-10.82	-15.19	-1.14601	GAGGUGGUU&AACCACCUC	(((((((((&)))))))))	AUUCAAAGUGACAGCGCAUUGCAGCAAGCCUGCGAAGAUGUCUUCCGCUUUGAUGACGCCAACUAAGGAGCGGCAAUGAAUAUUCCACAGCUCACUGCCCUGUGUCUGCGUUAUCAUGGAGUCUUGCUGGAUGCCAGCGAAGAGGUGGUU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0310812	0.9277422	hofB	947481	T2SE secretion family protein P-loop ATPase superfamily protein
b0140	-19	10	-1	6	6.42	CyaR	3	33	7	13	1.49	-10.36	-18.27	-1.09729	ACUCUAUCAGGGAUGGUUUAUGUUUUUUA&UGAAAAACAUAACCCAUAAAAUGCUAGCUGU	((.(((.((...((((.((((((((((((&)))))))))))).))))....)).)))..))	GAAUGAAUAUACAGGGAAUAAUAAUUUCUAUUUUAUAUUAUUCCCUGUUUUAAUUAACUCUAUCAGGGAUGGUUUAUGUUUUUUAACACCAAACAUACAACAGCUUUAUGCUUCGUAACCUGUAUGGCUUUUAGUUCAUCGUCUAUUGCG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0400171	0.9277422	yadV	944859	putative periplasmic pilin chaperone
b0222	-56	-30	-38	-32	13.51	CyaR	18	46	20	26	4.56	-11.31	-29.38	-1.19791	GGCGGUAUCCGGUACACUGCAUUUUGU&AUAAAAUGCUAGCUGUACCAGGAACCACC	((.(((.((((((((((((((((((((&))))))))).)).)))))).)))))).))	GCCCGUACUUCUCGCUUUUGGCGGUAUCCGGUACACUGCAUUUUGUCUAUUACAUUUAUGCUGAAGGAUAUCCUCAUGUACCAGGAUCUUAUUCGUAACGAACUGAACGAAGCGGCGGAAACGCUGGCUAACUUUUUAAAAGAUGACGCC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0235704	0.9277422	gmhA	949134	D-sedoheptulose 7-phosphate isomerase
b0412	56	67	61	67	3.66	CyaR	29	39	29	35	4.29	-10.47	-18.42	-1.10894	CCUGUGUGCAGC&GCUGUACCAGG	((((.(((((((&)))))))))))	UGAGAUAAAGGAUCGAUGCUUUCGCUGCUUUUACCCUCUACCAUUAGGCUAAUUGCGACGAGAAAGGGACGACCUAUGAAUACUAACGUUUUUCGACUGCUCCUGCUGGGAAGCCUGUUCAGCCUUAGCGCCUGUGUGCAGCAAAGUGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0376936	0.9277422	yajI	947233	putative lipoprotein
b0426	-75	-65	-73	-67	4.35	CyaR	30	40	32	38	4.28	-11.54	-20.17	-1.22227	UCCUGGUGCAG&CUGUACCAGGA	(((((((((((&)))))))))))	UCCUGGUGCAGGACUGUCGGUUAUUUAACUUUGCGGGUAUUAUGCUUCGCAUCAAAAAUGAAGGGAGAGGAAAAGAUGCCAUCUUUCGAUAUUGUCUCUGAAGUUGAUCUUCAGGAAGCACGUAACGCGGUCGAUAACGCGAGCCGCGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0206453	0.9277422	yajQ	945063	phage Phi6 host factor ATP/GTP binding protein
b0435	-63	-44	-55	-49	2.84	CyaR	21	36	26	32	1.43	-13.8	-18.07	-1.46164	GGUAAAAGCGGCUAGUAUUU&AAAUGCUAGCUGUACC	((((....((((((((((((&))))))))))))))))	UGCAAUGGAAACGGUAAAAGCGGCUAGUAUUUAAAGGGAUGGAUGACAUCUCAGCGUUGUCGGAGGAGAUAUUUCAUGAUGAUACGUGAGCGGAUAGAAGAAAAAUUAAGGGCGGCGUUCCAACCCGUAUUCCUCGAAGUAGUGGAUGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0051044	0.8345133	bolA	947043	stationary-phase morphogene transcriptional repressor for mreB also regulator for dacA dacC and ampC
b0444	28	64	54	60	13.08	CyaR	23	49	30	36	4.55	-11.11	-28.74	-1.17673	GGAGGUCAGGAUUCCACCACCUGUCUGGUGCAGGCAU&AUGCUAGCUGUACCAGGAACCACCUCC	((((((..((.((((..........((((((((((((&))))...))))))))))))))))))))	CAUCGCAAUGAAUAGCUGGUCCGGGUUAAUCGCAGGCGUUACCAUAACGCUUUUAUUGUUCAAGCAGGAUUAUCUAUGAAACGUGCUGUCGUUGUGUUCAGUGGAGGUCAGGAUUCCACCACCUGUCUGGUGCAGGCAUUACAACAAUAU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0264121	0.9277422	queC	947034	7-cyano-7-deazaguanine (preQ0) synthase queuosine biosynthesis
b0465	33	50	44	50	5.81	CyaR	1	26	1	7	1.46	-10.58	-17.85	-1.12059	GCAUUUUGUUUUUUCAGC&GCUGAAAAACAUAACCCAUAAAAUGC	((((((((((((((((((&)))))))))........)))))))))	GGUUCACUGCGUCGUGAUAUUCUUGCGGUUUGACUUUUUCAGGUCGUUCUUCAGGUUCAGAAACCUUCAUUCAUCAUGACUAUGUUCCAGUAUUACAAACGAUCACGGCAUUUUGUUUUUUCAGCAUUUAUUGCUUUUGUUUUUGUCUUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0354913	0.9277422	mscK	945132	mechanosensitive channel protein intermediate conductance K+ regulated
b0607	-14	-8	-14	-8	0.07	CyaR	63	69	63	69	0.93	-10.28	-11.28	-1.08882	AGGGAGA&UCUCCCU	(((((((&)))))))	AACCAGACAAAUAUCAGGGAUAAAUAUUAUAAUCAUGGCGAAUGAUUUGUUCAUGAUUAACAGGGAGAAAGGGUUAUGUAUAAGACAAUCAUUAUGCCAGUUGAUGUAUUUGAAAUGGAAUUGAGCGACAAAGCUGUUCGCCACGCUGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0417863	0.9277422	uspG	945229	universal stress protein UP12
b0675	61	74	68	74	4.01	CyaR	29	42	29	35	4.29	-10.45	-18.75	-1.10682	GUACCGGGUGCAGC&GCUGUACCAGGAAC	((.((.((((((((&)))))))).)).))	UUUGCUCCAGCAUUUGCUGGAAAAUUAAUGUGCUUUUAUAGUGGCGCUUAUUGUUGUCAAUAUUCUGGGUAGUCCAUGACCAUUAAAAAUGUAAUUUGCGAUAUCGACGGCGUGCUGAUGCACGAUAACGUCGCCGUACCGGGUGCAGCG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0381068	0.9277422	umpH	945283	UMP phosphatase

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 3.1.3 linking Vienna RNA package 2.4.14

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