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
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
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
b2416	-14	10	-5	2	4.99	CyaR	2	27	11	17	1.47	-12.38	-18.84	-1.31124	AGUAAGGUAGGGUUAUGAUUUCAG&CUGAAAAACAUAACCCAUAAAAUGCU	((((...((((((((((.((((((&))))))..)))))))).))...))))	UCUGGUUAAACUGAUGGCGGAACUCGAGUAAUUUCCCGGGUUCUUUUAAAAAUCAGUCACAAGUAAGGUAGGGUUAUGAUUUCAGGCAUUUUAGCAUCCCCGGGUAUCGCUUUCGGUAAAGCUCUGCUUCUGAAAGAAGACGAAAUUGUC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0125381	0.9277422	ptsI	946879	PEP-protein phosphotransferase of PTS system (enzyme I)
b4513	25	54	48	54	8.09	CyaR	11	35	11	17	1.47	-12.16	-21.72	-1.28794	GUAUUGCUGGUGUUUUUAUUACUGGGUUAU&AUAACCCAUAAAAUGCUAGCUGUAC	(((..(((((((((((......((((((((&)))))))).)))))))))))..)))	CGCAGAUUUUUGCGAAAUCUUUGCAGCCAGAAUUCUACCCUUCCGGUAUCACUUUUAGGCCACUGGAGGUGCACUGUGAGUGCAGGCGUGAUAACCGGCGUAUUGCUGGUGUUUUUAUUACUGGGUUAUCUGGUUUAUGCCCUGAUCAAU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0143201	0.9277422	kdpF	948946	potassium ion accessory transporter subunit
b3423	37	59	51	57	6.83	CyaR	9	38	11	17	4.53	-12.11	-23.47	-1.28264	CUGGUUAAACAGCAGGGUUAUGU&ACAUAACCCAUAAAAUGCUAGCUGUACCAG	(((((...(((((.(((((((((&)))))))))...........))))))))))	UAGCCGUGGGUUUAGCGAUGGCUUUUGUUGAUUCGCUCAAUGCGCGAAAACGAAAAUAAUUCCAGGGAUUUAUAAAUGAAACAAACACAACGUCACAACGGUAUUAUCGAACUGGUUAAACAGCAGGGUUAUGUCAGUACCGAAGAGCUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0147559	0.9277422	glpR	947926	pseudogene DNA-binding transcriptional repressorregulator Energy metabolism carbon: Anaerobic respiration repressor of the glp operon
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
b1701	55	62	55	61	1.51	CyaR	10	17	11	17	0.16	-11.42	-13.09	-1.20956	GGGUUAUG&CAUAACCC	((((((((&))))))))	UGAUUUUCGCUACGGCUAAUCAUGCAUCCCACAGGCCCGCAUCUCGGGCCUGAUGUUCUGUUUCGAGAGUCCAACAUGAAAGUGACAUUAACGUUUAACGAACAACGUCGUGCGGCGUAUCGUCAGCAAGGGUUAUGGGGCGAUGCUUCG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0221278	0.9277422	fadK	946213	short chain acyl-CoA synthetase anaerobic
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
b3105	24	45	38	44	5.02	CyaR	10	30	11	17	1.46	-10.91	-17.39	-1.15554	GCUGGAAGCACUACGGGUUAUG&CAUAACCCAUAAAAUGCUAGC	(((((.........((((((((&))))))))........)))))	UGGUAAGGGGCUGGACGCUACAUUGUUAGCCAGAUAUUCUGCCCGGUAUGUUCAAAUUUCCUGAAUGAGAACGAAAUGGCCAAAGAAAGGGCAUUAACGCUGGAAGCACUACGGGUUAUGGAUGCGAUCGAUCGCCGGGGCAGUUUUGCG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0295585	0.9277422	yhaJ	947621	LysR family putative transcriptional regulator
b0698	-65	-36	-42	-36	9.85	CyaR	11	35	11	17	1.47	-10.39	-21.71	-1.10047	GUAUUGCUGGUGUUUUUAUUACUGGGUUAU&AUAACCCAUAAAAUGCUAGCUGUAC	(((..(((((((((((......((((((((&)))))))).)))))))))))..)))	GAUAACCGGCGUAUUGCUGGUGUUUUUAUUACUGGGUUAUCUGGUUUAUGCCCUGAUCAAUGCGGAGGCGUUCUGAUGGCUGCGCAAGGGUUCUUACUGAUCGCCACGUUUUUACUGGUGUUAAUGGUGCUGGCGCGUCCUUUAGGCAGC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0393711	0.9277422	kdpA	946045	potassium translocating ATPase subunit A

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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