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
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
b0814	-9	26	20	26	8.49	CyaR	1	48	1	7	4.6	-14.33	-27.42	-1.51778	GAGGUGGUUAUGAAAAAAAUUGCAUGUCUUUCAGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUC	(((((((((.((.........((((((.(((((((&))))))).)))............))).........))..)))))))))	AAUCGCGAAGAGUUUCCCAUUAAUUUUUGAUAUAUUUAAAACUUAGGACUUAUUUGAAUCACAUUUGAGGUGGUUAUGAAAAAAAUUGCAUGUCUUUCAGCACUGGCCGCAGUUCUGGCUUUCACCGCAGGUACUUCCGUAGCUGCGACU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0035802	0.779419	ompX	944967	outer membrane protein X
b1167	-41	-13	-33	-27	4.55	CyaR	4	33	18	24	1.49	-14.31	-20.35	-1.51566	ACAGCAUAAUUUUAUUGGGUUAAUAUUUC&GAAAAACAUAACCCAUAAAAUGCUAGCUGU	(((((...(((((((.((((((...((((&))))....)))))))))))))....)))))	UCAUCUUAUUUUUGUCUGUCGCUUUAGACUAUACACAGCAUAAUUUUAUUGGGUUAAUAUUUCUACGAGGCUGACAUGAAUAAUUCAAUCCCAGAGAGAUUUAUUUUUCAAUGUGCUUUGUUUAAAAAUCUCGAGAGGGAGGUGUUCAUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0036291	0.779419	ymgC	945090	Blue light low temperature and stress induced protein
b4350	-75	-45	-75	-69	4.79	CyaR	15	36	30	36	1.45	-14.19	-20.43	-1.50295	GGUACAGAAAGCUAAGAUGAGAUGUUAUGGG&CCCAUAAAAUGCUAGCUGUACC	(((((((..(((.........((.(((((((&))))))).)))))..)))))))	GGUACAGAAAGCUAAGAUGAGAUGUUAUGGGCCUUAAAUAUUUGGACAGGCCCGCACAGCAAUGGAUUAAUAACAAUGAUGAAUAAAUCCAAUUUUGAAUUCCUGAAGGGCGUCAACGACUUCACUUAUGCCAUCGCCUGUGCGGCGGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0039361	0.7849708	hsdR	948878	endonuclease R Type I restriction enzyme
b4547	23	35	29	35	2.33	CyaR	34	46	34	40	3.2	-13.97	-19.5	-1.47965	GGUGGAUUCUGGU&ACCAGGAACCACC	(((((.(((((((&))))))).)))))	CUACUUGCCCGUAUGUAUCAACGUAUCAUGGAACAGCUCGUCGCCUGAUGAGUGGUUCUGCAAGAGGAAAUAAGCAUGGACUGGCUGGCUAAAUAUUGGUGGAUUCUGGUGAUUGUCUUUUUGGUAGGCGUCCUGCUGAACGUGAUUAAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.004561	0.8345133	ypfN	1450286	putative membrane protein UPF0370 family
b0435	-63	-44	-55	-49	2.84	CyaR	21	36	26	32	1.43	-13.8	-18.07	-1.46164	GGUAAAAGCGGCUAGUAUUU&AAAUGCUAGCUGUACC	((((....((((((((((((&))))))))))))))))	UGCAAUGGAAACGGUAAAAGCGGCUAGUAUUUAAAGGGAUGGAUGACAUCUCAGCGUUGUCGGAGGAGAUAUUUCAUGAUGAUACGUGAGCGGAUAGAAGAAAAAUUAAGGGCGGCGUUCCAACCCGUAUUCCUCGAAGUAGUGGAUGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0051044	0.8345133	bolA	947043	stationary-phase morphogene transcriptional repressor for mreB also regulator for dacA dacC and ampC
b1250	28	58	41	47	10.19	CyaR	1	33	14	20	1.49	-13.78	-25.46	-1.45952	ACAGCAACAAAUUUAUGGGUGACCCUUCGGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGU	(((((......(((((((((.....((((((&)))))).......)))))))))......)))))	UUCACGCGCUGCAUGUAUGUUCAGAAAAUGUGCACGCUAAGAUAAUUAAACAAAAUUGUGGUUACAGAGGUAUCAGUGAGUCACUGGGCUACAUUCAAACAAACAGCAACAAAUUUAUGGGUGACCCUUCGGCACGACAUUCUCGCGCUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0051721	0.8345133	kch	945841	voltage-gated potassium channel
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
b3879	-45	-26	-42	-36	4.37	CyaR	13	40	30	36	4.57	-13.58	-22.52	-1.43834	UCCGGUGCAGUUUUUGGGUU&AACCCAUAAAAUGCUAGCUGUACCAGGA	((((((((((((..((((((&)))))).........))))))))).)))	AACCCUCUCCCCAAAGGGGCGAGGGGACCGUCCGGUGCAGUUUUUGGGUUUGACAUCAGCCUCACGGGAGGCUGUAUGUCGUUAAUUAAGGUGCCUUGUAUGCAAAUCACCAAUAUGCAUUGCAGUGGACAGACCGUUUCACUUGCCGCG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0058953	0.8662988	yihR	948375	putative sulphoquinovose mutarotase
b3861	52	70	64	70	5.37	CyaR	31	49	31	37	3.25	-13.18	-21.8	-1.39597	GGUGGUGGCACAUGGUACA&UGUACCAGGAACCACCUCC	((.(((((....(((((((&)))))))....))))).))	UGCAUCCUGCCGCUGGACAUUAUUUCAGCAUAAGUGGAUAUUCAAAGUUUUGCUGUUUUAUCAGGGAAUAUUUAUAUGAUACGUAAGUCAGCUACAGGUGUUAUUGUUGCGUUAGCCGUAAUCUGGGGUGGUGGCACAUGGUACACAGGU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.007625	0.9277422	yihF	948352	DUF945 family 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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