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
b3101	22	45	38	44	9.04	CyaR	19	46	20	26	4.56	-11.01	-24.61	-1.16613	GGUGUACUGGUAGCGCGCAUUUUA&UAAAAUGCUAGCUGUACCAGGAACCACC	((((..((((((..((((((((((&))))))))..))..))))))....))))	GACAGCAACGACGCUAAUACCGCGCCAUUGCACAAAAAAACAAUCAGCAGCCUGAGUGGCGCAGUGGAGAGUAUGAUGAAAAAAUUAGAAGAUGUUGGUGUACUGGUAGCGCGCAUUUUAAUGCCGAUUCUGUUUAUUACCGCUGGCUGG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0279455	0.9277422	yqjF	947608	putative quinol oxidase subunit
b2667	-64	-42	-48	-42	7.3	CyaR	20	48	20	26	4.56	-10.49	-22.35	-1.11106	GAGGCUGGUAUAUGUUGCAUUUU&AAAAUGCUAGCUGUACCAGGAACCACCUC	((((((((((((.((((((((((&))))))).)))))))))))......))))	UUUACGCUGCUGAGGCUGGUAUAUGUUGCAUUUUUAGUUUAGAGUUUACUUAAUUUAGAAAAUACUUAAAUAAAUAUGACUGAACUCGCGCAAUUACAGGCCAGUGCCGAACAGGCAGCGGCCUUAUUGAAAGCAAUGAGCCACCCUAAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0372843	0.9277422	ygaV	947136	tributyltin-inducible repressor of ygaVP
b3456	45	74	68	74	9.45	CyaR	15	42	15	21	4.57	-14.38	-28.4	-1.52307	GUUCUUUGUGCUGGCGGGCGUCUUUAUGGG&CCCAUAAAAUGCUAGCUGUACCAGGAAC	((((((.((((..((..((((.((((((((&))))))))))))..)).)))).))))))	CUCAUUCGCCCUGCUGAUUCUGGUGCUGCUGGUGAUGCCGACCGGUAUUCUGGGUCGCCCGGAGGUAGAGAAAGUAUGAAACCGAUGCAUAUUGCAAUGGCGCUGCUCUCUGCCGCGAUGUUCUUUGUGCUGGCGGGCGUCUUUAUGGGC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0034603	0.779419	livM	947966	branched-chain amino acid ABC transporter permease
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
b4523	-72	-41	-64	-58	7.48	CyaR	15	49	35	41	4.57	-11.84	-23.89	-1.25404	GGCGGUUUUUCUUGGUUCUGCACUUUUCUGGG&CCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCC	((.(((..((((((((...((..((((.((((&)))).)))).....))...))))))))..))).))	GCUGGCGGUUUUUCUUGGUUCUGCACUUUUCUGGGUGGUUGUCGCACUGCUGAUUUGGAAAGUGUGGGGAUAACUAUGGUCGGUCAGGAGCAACUGGAGUCGUCACCAUUAUGCCAGCAUAGUGACAAUGAAACAGAAACGAAACGGGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0173235	0.9277422	yciX	1450257	uncharacterized protein
b1599	-11	21	-11	-5	13.23	CyaR	13	49	43	49	4.57	-11.69	-29.49	-1.23816	GGAGGUGAACCAUGGCGCAGUUUGAAUGGGUU&AACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCC	(((((((..((.(((..(((((...(((((((&)))))))........)))))..)))))...)))))))	CCACCCUGGUCGCCGGGAUUGUGUUGAUAAAAUCAGGUACCCGUAAAGCGCGUAAACCUGAACUGGAGGUGAACCAUGGCGCAGUUUGAAUGGGUUCACGCCGCCUGGCUGGCAUUGGCAAUCGUGCUGGAAAUCGUUGCUAACGUCUUU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0189186	0.9277422	mdtI	947333	multidrug efflux system transporter
b1956	-12	22	1	7	9.49	CyaR	16	49	29	35	4.57	-11.27	-25.33	-1.19367	GGAGUCGUCAGGGUGCAGCACGAGACAAAAAUGG&CCAUAAAAUGCUAGCUGUACCAGGAACCACCUCC	((((...((..((((((((...((.((...((((&))))....)))).))))))))..)).....))))	AAUUAUCGCUGUUUUGCGGUACGCUAUCGCCAGGUUAUGCCAGAAUCAUAAAAAAGCAGGUUGGGAGUCGUCAGGGUGCAGCACGAGACAAAAAUGGAAAACCAGAGCUGGUUGAAAAAACUCGCACGCCGCCUGGGGCCUGGUCAUGUC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0241156	0.9277422	yedQ	946471	putative membrane-anchored diguanylate cyclase
b4470	-58	-29	-42	-36	4.35	CyaR	17	45	23	29	4.57	-10.38	-19.3	-1.09941	GUGUGUUUCUCCGUUCCUGGCAUUUUCUUG&CAUAAAAUGCUAGCUGUACCAGGAACCAC	(((.((((((..((..((((((((((..((&)).))))))))))....)).)))))))))	GUCACUGGUUUGUUGCUGUGUGUUUCUCCGUUCCUGGCAUUUUCUUGAUUUACCUGAAAUUUUAAGGUUUUUAAUAUGUUUGAUUCGACUUUAAAUCCGUUAUGGCAGCGUUACAUCCUCGCCGUUCAGGAGGAAGUAAAACCGGCGCUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0395854	0.9277422	yhaM	2847723	putative L-serine dehydratase alpha chain
b1873	45	70	64	70	9.01	CyaR	11	49	11	17	4.59	-10.94	-24.54	-1.15872	GGUUGUGGUUGGUGGCGGCGGGUUAU&AUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCC	((..((((((..((((((((((((((&)))))))...........))))..)))..))))))..))	UAUGCAAGCGGUUAAUUCGUUGUAUAUUUAAUUAUACAAUGAUUUCGGUGUCCAGUAAUUUAAUUAGAGGAAUCUAUGCGAGGGAAAAAACGCAUUGGGUUAUUGUUUUUGCUGAUAGCGGUUGUGGUUGGUGGCGGCGGGUUAUUGCUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0290661	0.9277422	torY	946490	TMAO reductase III (TorYZ) cytochrome c-type subunit
b2039	31	74	38	44	10.37	CyaR	2	46	32	38	4.6	-16.65	-31.62	-1.7635	GGUGGUUCUGGUACACGUCUUUAUCCUGUGACUAUGGCUGUCAG&CUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACC	(((((((((((((((...((......((((..((((....((((&))))....))))...)))).......)).)))))))).)))))))	ACGACUACAGCAAUUUAAUAGUUUUUGCAUCUUGUUCGUGAUGGUGGAGCAAGAUGAAUUAAAAGGAAUGAUGAAAUGAAAAUGCGUAAAGGUAUUAUUUUAGCGGGUGGUUCUGGUACACGUCUUUAUCCUGUGACUAUGGCUGUCAGU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0006569	0.4585162	rfbA	945154	glucose-1-phosphate thymidylyltransferase

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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