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
b3197	10	40	34	40	9.83	CyaR	1	35	1	7	1.49	-13.72	-25.04	-1.45317	GUAGAGUUACAACCGGGUUUUGACUUUCAGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUAC	(((.(((((((...(((((.((..(((((((&)))))))..)).)))))......)).))))).)))	CUGGCGGAUUUAUCGUAUGGCUGGCGAUGUUGUACUGGUUAUCGCCAAUACUCGUUGAAUAACUGGAAACGCAUUAUGUCGCACGUAGAGUUACAACCGGGUUUUGACUUUCAGCAAGCAGGUAAAGAAGUCCUGGCGAUUGAACGUGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0053801	0.8345133	kdsD	947734	D-arabinose 5-phosphate isomerase
b1115	37	45	38	44	0.27	CyaR	9	17	10	16	0.16	-12.46	-12.89	-1.31971	GGGUUAUGU&ACAUAACCC	(((((((((&)))))))))	CAGAUACCCAUUACACCUCGGGUCAUAACCCGCAGGAUCAACCGCAUGUAAAUUAAAAAAGAGCGUGUUGUCCUGAUGAAACAAAAAGAGCUAUGGAUUAACCAGAUCAAAGGGUUAUGUAUUUGUCUGGUGGUGAUUUAUCACUCGGUC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0119418	0.9277422	ycfT	945679	inner membrane protein
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
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
b1445	17	47	36	42	9.96	CyaR	1	33	10	16	1.49	-12.58	-24.03	-1.33242	ACAUGCUUGUUUUUUAUGCGGUUAUGGCAGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGU	(((.(((....(((((((.(((((((.((((&)))).....))))))))))))))....))))))	GUGAAAAAACUUGAUGCACGUCAAAAAAUGACGCAUAUUUGCGCGCGUUUUAUUCAUCUGGCUGGACGCCCGUACAUGUCUCUCUAUCAACACAUGCUUGUUUUUUAUGCGGUUAUGGCAGCAAUCGCAUUUCUUAUCACCUGGUUUCUU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0110954	0.9277422	ydcX	945936	DUF2566 family protein
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
b3492	28	49	35	41	10.02	CyaR	9	43	29	35	4.6	-10.65	-25.27	-1.128	GGCGCUGGUGCGGCGGGUAUGU&ACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACC	((..((((((((((((((((((&)))).))))...........))))))))))...))	UAGUAAUAUUGAUGCUGGUGCGACCACUGAGGAAUCUUUACAAUUCACGCCCGUUUUUUCUAAGAGGAGCGCAACGUGGAAAGGUUUGAUGCCAUUAUUAUAGGCGCUGGUGCGGCGGGUAUGUUCUGUUCUGCGCUGGCAGGUCAGGCA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0341505	0.9277422	yhiN	947996	putative oxidoreductase
b4322	9	50	18	24	10.82	CyaR	1	48	32	38	4.6	-10.65	-26.07	-1.128	GACCUGGCGCUGGUACGGCCCAAACGAUCCGGUUUCUUUAGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUC	((..(((..((((((((((.((........((((..((((((&))))))......)))).......))...))))))))))...)))..))	CAUCCGGAUACCUAAACAACUCCAGGGUUCCGCGUCUCUUUGCUGUGGAACCCACUAUGUGAAAGAGGAAAAAUCAUGGAACAGACCUGGCGCUGGUACGGCCCAAACGAUCCGGUUUCUUUAGCUGAUGUCCGUCAGGCGGGCGCAACU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0341505	0.9277422	uxuA	947082	mannonate hydrolase
b0465	33	50	44	50	5.81	CyaR	1	26	1	7	1.46	-10.58	-17.85	-1.12059	GCAUUUUGUUUUUUCAGC&GCUGAAAAACAUAACCCAUAAAAUGC	((((((((((((((((((&)))))))))........)))))))))	GGUUCACUGCGUCGUGAUAUUCUUGCGGUUUGACUUUUUCAGGUCGUUCUUCAGGUUCAGAAACCUUCAUUCAUCAUGACUAUGUUCCAGUAUUACAAACGAUCACGGCAUUUUGUUUUUUCAGCAUUUAUUGCUUUUGUUUUUGUCUUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0354913	0.9277422	mscK	945132	mechanosensitive channel protein intermediate conductance K+ regulated
b1891	40	52	42	48	5.44	CyaR	16	32	24	30	1.44	-11.35	-18.23	-1.20215	CAGCUGGCAAUGG&CCAUAAAAUGCUAGCUG	(((((((((((((&))))....)))))))))	CAUCAUGCUCUCAACACGCUUGCUGAAUGAUGUUAAUCAGCCUGAAGAAGCGCUGCGCAAGAAAAGGGCCUGAUCAUGAGUGAAAAAAGCAUUGUUCAGGAAGCGCGGGAUAUUCAGCUGGCAAUGGAAUUGAUCACCCUGGGCGCUCGU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0230363	0.9277422	flhC	947280	flagellar class II regulon transcriptional activator with FlhD

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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