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
b3879	-45	-26	-42	-36	4.37	CyaR	13	40	30	36	4.57	-13.58	-22.52	-1.43834	UCCGGUGCAGUUUUUGGGUU&AACCCAUAAAAUGCUAGCUGUACCAGGA	((((((((((((..((((((&)))))).........))))))))).)))	AACCCUCUCCCCAAAGGGGCGAGGGGACCGUCCGGUGCAGUUUUUGGGUUUGACAUCAGCCUCACGGGAGGCUGUAUGUCGUUAAUUAAGGUGCCUUGUAUGCAAAUCACCAAUAUGCAUUGCAGUGGACAGACCGUUUCACUUGCCGCG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0058953	0.8662988	yihR	948375	putative sulphoquinovose mutarotase
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
b1041	54	73	67	73	5.82	CyaR	10	34	10	16	1.48	-11.4	-18.7	-1.20744	UGCAGCCGCAGCAGGUUAUG&CAUAACCCAUAAAAUGCUAGCUGUA	((((((...(((((((((((&))))))).......)))).))))))	AAAUACAGGUUGCGUUAACAACCAAGUUGAAAUGAUUUAAUUUCUUAAAUGUACGACCAGGUCCAGGGUGACAACAUGAAAAACAAAUUGUUAUUUAUGAUGUUAACAAUACUGGGUGCGCCUGGGAUUGCAGCCGCAGCAGGUUAUGAU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.022384	0.9277422	csgB	947391	curlin nucleator protein minor subunit in curli complex
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
b3770	36	54	36	42	5.82	CyaR	35	52	46	52	4.41	-14.65	-24.88	-1.55167	UGGGGAGAUGGUUCGCUGG&CCAGGAACCACCUCCUUA	(((((((.((((((.((((&)))))))))).)))))))	UCGCACACGUUGCCAUCUGCCAGAGCACAACCACAUCACAACAAAUCCGCGCCUGAGCGCAAAAGGAAUAUAAAAAUGACCACGAAGAAAGCUGAUUACAUUUGGUUCAAUGGGGAGAUGGUUCGCUGGGAAGACGCGAAGGUGCAUGUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0028743	0.779419	ilvE	948278	branched-chain amino acid aminotransferase
b1628	65	73	66	72	1.72	CyaR	10	18	11	17	0.17	-11.62	-13.51	-1.23074	UGGGUUAUG&CAUAACCCA	(((((((((&)))))))))	UAAUGCCAUUGCGUUAAUUACCGCAGGUCUUAUGUCUCUGGCCUUUAUGGGCUUUAGUGGUUUGGUGAAGUUGUAAUGAAUGCUAUCUGGAUUGCCGUUGCCGCCGUGAGCCUGCUGGGCCUGGCGUUUGGCGCCAUUCUGGGUUAUGCC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0197074	0.9277422	rsxB	946146	SoxR iron-sulfur cluster reduction factor component putative iron-sulfur protein
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
b1278	-56	-30	-56	-50	7.85	CyaR	10	41	35	41	4.6	-12.73	-25.18	-1.34831	UUCCUGGAACUGGCGUUUUCAGUUAUG&CAUAACCCAUAAAAUGCUAGCUGUACCAGGAA	(((((((..((((((((((..((((((&))))))....)))))))))).....)))))))	GGCACAAAUCUGUCAAUUUUUCCUGGAACUGGCGUUUUCAGUUAUGAUUGUGGGACUUAUCAAAAAGGAGAGGCCAUGCGUUCGAUUGCCAGACGUACCGCAGUGGGAGCUGCACUAUUGCUUGUCAUGCCAGUAGCCGUAUGGAUUUCU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0101143	0.9277422	pgpB	945863	phosphatidylglycerophosphatase B
b2174	60	70	61	67	1.46	CyaR	31	41	34	40	3.25	-10.95	-15.66	-1.15978	UUCCUGGUAUA&UGUACCAGGAA	(((((((((((&)))))))))))	CGCGCUGUUGAAGCUUCGUUUAGCGACUACCGCGUAAGGUUGCCUGCGUUUUUCAGUAAGAUAAUUAGAGAAAAUAUGAUUAAAAAUUUGCCGCAAAUAGUGUUGUUGAAUAUUGUCGGCCUCGCGCUGUUUCUUUCCUGGUAUAUCCCC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0289036	0.9277422	lpxT	946693	lipid A 1-diphosphate synthase undecaprenyl pyrophosphate:lipid A 1-phosphate phosphotransferase
b2636	-57	-40	-55	-49	2.03	CyaR	9	23	15	21	0.17	-11.73	-13.93	-1.24239	UUUUGUGGGAAUUUAUGU&ACAUAACCCAUAAAA	(((((((((...((((((&)))))))))))))))	CGGCGUGCCGGUGGGUAUUUUUGUGGGAAUUUAUGUCUUUGCCAAAGUGGUUCGUCUGAUUUCAGGGAAAAAAUAAUGAAACGUAAAACACUACCUCUGCUGGCGCUGGUUGCCACCUCUCUGUUUCUGAGCGCCUGCGAUGACAGGAGU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0184807	0.9277422	yfjS	945668	CP4-57 prophage uncharacterized protein

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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