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
b2077	26	54	26	32	10.15	CyaR	1	30	24	30	1.48	-18.84	-30.47	-1.99546	GUUGGCAAUUGUGGAUUGUGGCUUUCGGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGC	(((((((.((((((.(((((..(((((((&)))))))..))))).))))))..)))))))	CCGGUGGUGUAUCUCUUUUUCGACCGUCUGCGGCUGCGUUUUUCGCGUAAACCUAAACAAACGGUAACCGAGUAAAUGACAGAUCUUCCCGACAGCACCCGUUGGCAAUUGUGGAUUGUGGCUUUCGGCUUCUUUAUGCAGUCGCUGGAC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0001018	0.2119128	iceT	946601	putative citrate/iron-citrate/zinc-citrate efflux transporter
b4074	-70	-57	-70	-64	5.13	CyaR	35	48	42	48	3.13	-18.4	-26.66	-1.94885	GAGGUGGUUUCUGG&CCAGGAACCACCUC	((((((((((((((&))))))))))))))	GAAAAGAGGUGGUUUCUGGACGUAUUCCUUCCUGAAGUCGGUUUUCUGGCGUUGUUGUUAAGUCUCGGGGUCAACGUGUUGACCCCGUUGACGGCCUUCGCGGGAGUGCGGUUGCGCUGGCCUGCCAUGAUGCGACUCACUUGCAUCGGC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0001518	0.2119128	nrfE	948579	heme lyase (NrfEFG) for insertion of heme into c552 subunit NrfE
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
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
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
b1686	60	73	65	71	4.86	CyaR	35	49	37	43	3.13	-15.77	-23.76	-1.67029	GGUGGGGUUCCUGG&CCAGGAACCACCUCC	((.(((((((((((&))))))))).)).))	CUGCCGUAGCCAGGUAAAACGGGUUGAAGGCACGGGGGUACGCCAUCCUGUGCAGGCUUUACUGGAGAUUAUUAAAUGAUAUGGAAACGGAAAAUCACCCUGGAAGCACUGAAUGCUAUGGGUGAAGGAAACAUGGUGGGGUUCCUGGAU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0012872	0.5989771	menI	946190	14-dihydroxy-2-naphthoyl-CoA hydrolase
b1209	-57	-34	-51	-45	9.06	CyaR	11	36	24	30	1.47	-15.14	-25.67	-1.60357	GGUAACGCUAGCAUUAAGGGUUAU&AUAACCCAUAAAAUGCUAGCUGUACC	((((..(((((((((..(((((((&)))))))....)))))))))..))))	ACAUAGACGAUAGCGGACGGUAACGCUAGCAUUAAGGGUUAUAACUGCAACGUAUCUCAAGGACUUGUCAUCACUAUGCCCCUGCCCGAUUUUCGUCUUAUCCGCCUGCUACCGCUGGCUGCUCUUGUGCUCACUGCCUGUUCCGUUACC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0020364	0.7364947	lolB	945775	lipoprotein localization factor
b2556	40	58	48	54	6.05	CyaR	20	38	24	30	4.48	-15.09	-25.62	-1.59827	CUGGUAAUGCUGGCAUUUU&AAAAUGCUAGCUGUACCAG	((((((..(((((((((((&)))))))))))..))))))	UAAUUCCCGGCUUUGUUGUAUCUGAACUUCCCCUCGGUUAGCAUCAGGCUAUUCGCGUCUGACGAGAGUAACACCUUGAAACGCUGGCCCGUUUUUCCCCGCUCAUUACGACAACUGGUAAUGCUGGCAUUUUUGCUGAUUCUGCUGCCC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0021103	0.7364947	glrK	947013	sensor protein kinase regulating glmY sRNA in two-component system with response regulator GlrR
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
b3541	-74	-53	-74	-68	4.21	CyaR	14	30	24	30	1.4	-14.49	-20.1	-1.53472	GCUGGCAUUUAACCUGAUGGGU&ACCCAUAAAAUGCUAGC	((((((((((......((((((&)))))).))))))))))	UGCUGGCAUUUAACCUGAUGGGUGACGGUCUGCGUGACGCGCUCGAUCCCAAACUGAAGCAGUAAGAGGUUCGAGAUGGCGUUAUUAAAUGUAGAUAAAUUAUCGGUGCAUUUCGGCGACGAAAGCGCGCCGUUCCGCGCCGUAGACCGC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0032095	0.779419	dppD	948065	dipeptide/heme ABC transporter ATPas

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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