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
b4463	-61	-51	-61	-55	5.72	CyaR	36	46	40	46	3.13	-10.37	-19.22	-1.09835	GGUGGUUUCUG&CAGGAACCACC	(((((((((((&)))))))))))	CGCUAACCCAUAACGGUGGUUUCUGUUUUCUCUUAUUAAUGAUUAUUCCAUUUUUAUUAUCAGGAAGGAAUUACUAUGUCUUUAUCUCGCGCAGCGAUUGUCGACCAGCUAAAGGAAAUUGUUGGUGCAGAUCGCGUAAUUACCGAUGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0398007	0.9277422	ygcU	2847709	putative FAD-linked oxidoreductase
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
b4144	-25	-8	-14	-8	4.43	CyaR	15	32	15	21	1.44	-10.34	-16.21	-1.09517	CAGCUCAUUGAUUAUGGG&CCCAUAAAAUGCUAGCUG	(((((((((..(((((((&)))))))))))..)))))	UGGUCAUCUUUCUAGUAUAAGAUUCAGACACGGACGACGCGAGUGGCGUCCAGCUCAUUGAUUAUGGGGAAUAACAUGCACGUAAAAUACUUAGCAGGGAUUGUCGGUGCCGCGCUACUGAUGGCGGGUUGUAGCUCCAGCAACGAAUUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.040453	0.9277422	yjeI	948664	DUF4156 family lipoprotein
b1220	58	71	59	65	5.88	CyaR	25	36	29	35	1.42	-10.33	-17.63	-1.09411	GGUACAGCUAACGC&GCUAGCUGUACC	((((((((((..((&))))))))))))	AUACGACAAAAGUUGCCAGUAAUCGUUAUUCUUUAAGGCUAUGGUUUUUCAUUAUUACCGGAAGUUACCGACGUUUUGAGCCGUUUCGUUCCUCGCAUUAUCCCGUUUUAUUUACUCUUGCUUGUAGCAGGCGGUACAGCUAACGCACAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0406726	0.9277422	ychO	945801	putative invasin
b4040	30	39	31	37	2.12	CyaR	21	30	23	29	1.38	-10.32	-13.82	-1.09305	GCUGGCGUUU&AAAUGCUAGC	((((((((((&))))))))))	CGAUUAAGCGGUAAACCGCUGUUGCUAACAGAACUGUUUUUACCGGCGUCACCGUUGUACUAAGAGGAAAAAAAUAUGGAGUGGAGUCUGACGCAGAAUAAGCUGCUGGCGUUUCAUCGCUUAAUGCGUACGGAUAAGCCAAUUGGCGCG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0408932	0.9277422	ubiA	948540	p-hydroxybenzoate octaprenyltransferase
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
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
b3535	-30	-21	-30	-24	1.64	CyaR	27	36	30	36	1.17	-10.28	-13.09	-1.08882	GGUACGGUUA&UAGCUGUACC	((((((((((&))))))))))	ACAAUAAACCGGCGAAAUGCUCACGGUUAGAAUUGUCUCAUGAACGGUACGGUUAUUUCAUAGGGAUCAAGCAAAAUGAAUAACAAUGAACCAGAUACUCUGCCUGAUCCCGCGAUAGGCUAUAUCUUCCAGAAUGAUAUUGUGGCGUUA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0417863	0.9277422	yhjR	948051	DUF2629 family protein
b0989	-32	-16	-32	-26	5.97	CyaR	20	35	29	35	1.43	-10.27	-17.67	-1.08776	GUGCAGCGCAGUAUUUU&AAAAUGCUAGCUGUAC	(((((((..((((((((&)))))))).)))))))	GCGGUCUUAAAUAUCGCUGGCUUUAUUUUAUUAACCCCGUAUAGUGCAGCGCAGUAUUUUCAGUAAGGAAUUUGUUUGUCCCGUAAAAUGACAGGAAUUGUCAAAACCUUUGAUCGCAAAAGCGGCAAAGGAUUCAUUAUCCCCUCCGAC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0420123	0.9277422	cspH	945590	stress protein member of the CspA-family
b2131	33	47	33	39	5.71	CyaR	1	16	10	16	0.91	-10.25	-16.87	-1.08564	GGUUAUGUUGGCAGC&GCUGAAAAACAUAACC	(((((((((..((((&))))...)))))))))	GCUAACCCCGCCAUUAUCAACUAUGCUUUUCUCUUAAUUCGCUGAAAACAACAGUAAAAGAAUGAGGAAAGCAUCAUGCCACUCUUAAAGCUCUGGGCAGGUUCACUGGUUAUGUUGGCAGCCGUGAGCCUGCCGCUACAGGCGGCUUCC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0424675	0.9277422	osmF	946681	putative ABC transporter periplasmic binding 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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