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
b1485	-11	12	-10	-4	2.97	CyaR	25	49	42	48	4.55	-16.69	-24.21	-1.76774	GGAGGUGGUGAAUGAUGCUAAGC&GCUAGCUGUACCAGGAACCACCUCC	(((((((((...((..((((.((&)))))).....))...)))))))))	UUAUGUGCUGGUCAACCUGGUGGUGGAUUUGCUCUAUUUGUGGAUUGAUCCGCGUAUCGGACGUGGAGGUGGUGAAUGAUGCUAAGCGAGGAAACGUCCGCCGUACGCCCACAAAAACAAACGCGAUUUAACGGUGCAAAACUGGUAUGG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0006365	0.4585162	ddpC	946028	DD-dipeptide ABC transporter permease
b1498	53	75	62	68	4.83	CyaR	21	44	29	35	4.55	-16.06	-25.44	-1.70101	UGGCAUCUGGUAUGGCUGCAUUU&AAAUGCUAGCUGUACCAGGAACCA	(((...(((((((((((((((((&)))))).)))))))))))...)))	UAACUUCACUUACAUCCACUUAUUUCUCUUCGUAAAAUUACUUUGGAAUUAAGUACAAUAAGAAGAGGAACAUUUAUGAAGUCUGCAUUAAAGAAAAGUGUCGUAAGUACCUCGAUAUCUUUGAUACUGGCAUCUGGUAUGGCUGCAUUU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0010357	0.5783349	ydeN	945957	putative Ser-type periplasmic non-aryl sulfatase
b2742	53	72	66	72	6.49	CyaR	24	44	24	30	4.55	-12.91	-23.95	-1.36737	UGGUUUCGCUAUGGCUGGCA&UGCUAGCUGUACCAGGAACCA	(((((((..(((((((((((&)))))))))))...)))))))	UUUUCCAGUGUUCAGUAGGGUGCCUUGCACGGUAAUUAUGUCACUGGUUAUUAACCAAUUUUUCCUGGGGGAUAAAUGAGCGCGGGAAGCCCAAAAUUCACCGUUCGCCGCAUUGCGGCUUUGUCACUGGUUUCGCUAUGGCUGGCAGGC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0090413	0.9277422	nlpD	947011	activator of AmiC murein hydrolase activity lipoprotein
b2957	43	68	53	59	7.84	CyaR	22	43	29	35	4.55	-12.83	-25.22	-1.3589	GGUUUUAGUGGUGCAGCAUUGGCAUU&AAUGCUAGCUGUACCAGGAACC	((((....(((((((((..(((((((&))))))))))))))))..))))	UAAAUUGUUUAACGUCAAAUUUCCCAUACAGAGCUAAGGGAUAAUGCGUAGCGUUCACGUAACUGGAGGAAUGAAAUGGAGUUUUUCAAAAAGACGGCACUUGCCGCACUGGUUAUGGGUUUUAGUGGUGCAGCAUUGGCAUUACCCAAU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0095047	0.9277422	ansB	947454	periplasmic L-asparaginase 2
b1421	46	71	50	56	6.45	CyaR	23	47	38	44	4.55	-11.58	-22.58	-1.22651	AGGUUGGUUCCGUUAUUUGCCUGCAU&AUGCUAGCUGUACCAGGAACCACCU	(((.(((((((.......((..((((&))))..)).......))))))))))	UUUUGGUCAUAAGUAAUUACCGUCAAGUGCCGAUGACUUUCUAUCAGGAGUAAACCUGGACGAGAGACAACGGUAAUGAAUACAACUCCCUCACAGCGAUUAGGUUUUUUGCAUCACAUCAGGUUGGUUCCGUUAUUUGCCUGCAUUCUA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0201714	0.9277422	trg	945995	methyl-accepting chemotaxis protein III ribose and galactose sensor receptor
b3412	-55	-38	-45	-39	7.86	CyaR	23	40	24	30	4.55	-11.17	-23.58	-1.18308	UCCCGGUACUGUUAGCAU&AUGCUAGCUGUACCAGGA	(((.(((((.((((((((&)))))))).))))).)))	AUUCGGCAUAGCCAGCAUAAUCCCGGUACUGUUAGCAUAUGUUCAUCCUUGUAAGUCAAAAGAGAACAAUAGCGGAUGAAUAACAUCUGGUGGCAGACCAAAGGUCAGGGGAAUGUUCAUCUUGUGCUGCUGCACGGAUGGGGACUGAAU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0255288	0.9277422	bioH	947916	pimeloyl-ACP methyl ester carboxylesterase
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
b2025	47	72	47	53	7.32	CyaR	25	47	41	47	4.55	-10.83	-22.7	-1.14707	AGGUGGUGAAAGGCGUACAGUUUCGC&GCUAGCUGUACCAGGAACCACCU	(((((((.......((((((((..((&)).)))))))).....)))))))	UGGCACUGGUGUGCGCGGCGUAAUAGUUGGUCGGGCAUUACUGGAAGGUAAAUUCACCGUGAAGGAGGCCAUCGCAUGCUGGCAAAACGCAUAAUCCCAUGUCUCGACGUUCGUGAUGGUCAGGUGGUGAAAGGCGUACAGUUUCGCAAC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0309086	0.9277422	hisF	946516	imidazole glycerol phosphate synthase catalytic subunit with HisH
b0886	47	75	69	75	10.01	CyaR	24	49	24	30	4.55	-10.31	-24.87	-1.09199	GGAUGUUAAGUCUUGGUAUUGUGCUGGCA&UGCUAGCUGUACCAGGAACCACCUCC	(((.((....((((((((....(((((((&)))))))..))))))))...)).)))	GGACGUUACGCGGAAUUAAGUGUGGCUGGUGGCCCAUUCGCCACAUUACUGGCCCAUCGUCAGGAGGAGAUUUAAAUGCGCGCUUUGCUACCCUAUCUGGCACUGUAUAAACGUCAUAAAUGGAUGUUAAGUCUUGGUAUUGUGCUGGCA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0411148	0.9277422	cydC	945504	glutathione/cysteine ABC transporter export permease/ATPase
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

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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