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
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
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
b1152	63	72	66	72	3.03	CyaR	30	39	30	36	4.27	-11.44	-18.74	-1.21168	CCUGGUGCAG&CUGUACCAGG	((((((((((&))))))))))	UUUACGCCUACAAAGUGAAAGCAUUUGGCGAAGUGGCUGAACUGCUGCCCGUCGAUCCCGGCUGUGUGGUAUAUGCGCUGGGAAGGUGUCAGCGAUGGCCUGAAGGUGACCGCCGGGAGUGUUAUUCAGCGCGAUGACCUGGUGCAGUAC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0218742	0.9277422	jayE	945703	pseudogene e14 prophagePhage or Prophage Related
b3139	33	73	67	73	11.91	CyaR	1	39	1	7	4.6	-11.9	-28.41	-1.2604	CCUGGCGGCGUUAGUUUUUGUUCUGGGGAUUGAUUUUUGGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGG	(((((((((..(((..(((....((((...((.((((((((&)))))))).))...))))..)))..)))))))..)))))	CGUCCCUGGCGAUCAAAAAGAACAAAUCCCUGACUAAAUCUAAAAUCGCCUUAAUAUUGGUUUGAGGUAAUAAAAAUGCAUGAAAUAACCCUACUUCAGGGAUUAUCCCUGGCGGCGUUAGUUUUUGUUCUGGGGAUUGAUUUUUGGCUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0167203	0.9277422	agaC	947652	N-acetylgalactosamine-specific enzyme IIC component of PTS
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
b3215	60	73	67	73	5.91	CyaR	36	51	36	42	3.22	-10.88	-20.01	-1.15237	AGGGAUGGUUCCUG&CAGGAACCACCUCCUU	((((((((((((((&)))))))))..)))))	UCGCAAACAGUGCAUAACAUAUAUUAACAAUAUGUUUCUGCGUUAUUUAUCAUUAUUACAGGAGUUUUAAUUUAAAUGCUCAGACACAUUACAUUCACUGUAUUUAUAACAACAUCAAUGAAUACCUUAGCCACAGGGAUGGUUCCUGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0300585	0.9277422	yhcA	947741	putative periplasmic chaperone protein
b0107	67	75	67	73	1.61	CyaR	40	48	42	48	2.76	-10.82	-15.19	-1.14601	GAGGUGGUU&AACCACCUC	(((((((((&)))))))))	AUUCAAAGUGACAGCGCAUUGCAGCAAGCCUGCGAAGAUGUCUUCCGCUUUGAUGACGCCAACUAAGGAGCGGCAAUGAAUAUUCCACAGCUCACUGCCCUGUGUCUGCGUUAUCAUGGAGUCUUGCUGGAUGCCAGCGAAGAGGUGGUU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0310812	0.9277422	hofB	947481	T2SE secretion family protein P-loop ATPase superfamily protein
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
b0675	61	74	68	74	4.01	CyaR	29	42	29	35	4.29	-10.45	-18.75	-1.10682	GUACCGGGUGCAGC&GCUGUACCAGGAAC	((.((.((((((((&)))))))).)).))	UUUGCUCCAGCAUUUGCUGGAAAAUUAAUGUGCUUUUAUAGUGGCGCUUAUUGUUGUCAAUAUUCUGGGUAGUCCAUGACCAUUAAAAAUGUAAUUUGCGAUAUCGACGGCGUGCUGAUGCACGAUAACGUCGCCGUACCGGGUGCAGCG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0381068	0.9277422	umpH	945283	UMP phosphatase
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

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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