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
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
b3541	-74	-53	-74	-68	4.21	CyaR	14	30	24	30	1.4	-14.49	-20.1	-1.53472	GCUGGCAUUUAACCUGAUGGGU&ACCCAUAAAAUGCUAGC	((((((((((......((((((&)))))).))))))))))	UGCUGGCAUUUAACCUGAUGGGUGACGGUCUGCGUGACGCGCUCGAUCCCAAACUGAAGCAGUAAGAGGUUCGAGAUGGCGUUAUUAAAUGUAGAUAAAUUAUCGGUGCAUUUCGGCGACGAAAGCGCGCCGUUCCGCGCCGUAGACCGC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0032095	0.779419	dppD	948065	dipeptide/heme ABC transporter ATPas
b1179	-75	-58	-74	-68	5.23	CyaR	16	32	25	31	1.44	-12.63	-19.3	-1.33772	CAGCUGGCUGGCUUGUGG&CCAUAAAAUGCUAGCUG	((((((((....((((((&))))))...))))))))	CAGCUGGCUGGCUUGUGGCGCGGGUUUCAUUGAUGUUAGCUUAUGCCAAAACCUGGCAUCUUAAAGAGUAAAAGUAUGUUUUGUGUGAUUUAUCGAAGCAGCAAGCGUGACCAGACCUAUUUAUAUGUCGAAAAAAAAGACGAUUUUUCG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0107592	0.9277422	ycgL	946226	UPF0745 family protein
b1615	-74	-64	-74	-68	2.11	CyaR	24	35	29	35	1.42	-12.16	-15.69	-1.28794	GUGCAGCAGCA&UGCUAGCUGUAC	(((((((((((&)))).)))))))	AGUGCAGCAGCAAUUAAUCAGCGAUAUCACUAAUUAAUAUUCAAUAAAAAUAAUCAGAACAUCAAAGGUGCAACUAUGAGAAAAAUAGUGGCCAUGGCCGUUAUUUGCCUGACGGCUGCCUCUGGCCUUACCUCUGCUUAUGCGGCGCAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0143201	0.9277422	uidC	944820	putative outer membrane porin for beta-glucuronides porin protein
b0426	-75	-65	-73	-67	4.35	CyaR	30	40	32	38	4.28	-11.54	-20.17	-1.22227	UCCUGGUGCAG&CUGUACCAGGA	(((((((((((&)))))))))))	UCCUGGUGCAGGACUGUCGGUUAUUUAACUUUGCGGGUAUUAUGCUUCGCAUCAAAAAUGAAGGGAGAGGAAAAGAUGCCAUCUUUCGAUAUUGUCUCUGAAGUUGAUCUUCAGGAAGCACGUAACGCGGUCGAUAACGCGAGCCGCGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0206453	0.9277422	yajQ	945063	phage Phi6 host factor ATP/GTP binding protein
b0764	-72	-62	-72	-66	0.7	CyaR	17	27	21	27	1.13	-11.66	-13.49	-1.23498	AGCAUUUUAUG&CAUAAAAUGCU	(((((((((((&)))))))))))	GAAAGCAUUUUAUGAUUAUCUGAAGGGACCGCAGGCAGCGGAAAUCUUUAAACGUUACGGAUUUACAAUCAAGUAAUGAUACUGACCGAUCCAGAAUGGCAGGCAGUUUUAUUAAGCCUGAAAGUUUCUUCCCUGGCUGUGCUGUUUAGC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0192531	0.9277422	modB	945361	molybdate ABC transporter permease chlorate resistance protein
b0694	-75	-66	-72	-66	0	CyaR	41	49	41	47	2.77	-10.81	-13.58	-1.14495	GGAAGGUGGU&ACCACCUCC	((.(((((((&)))))))))	GGAAGGUGGUGCCUGUUUUCGUGUUACACUUCCCCAGCAAACUGCCCCUGAACUUGAAGAAUUUCAUGAGGAUAUGUGACAAACGUUCUGAUUGUUGAAGAUGAACAGGCUAUUCGUCGCUUUCUGCGCACGGCGCUGGAGGGCGACGGG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0312546	0.9277422	kdpE	945302	response regulator in two-component regulatory system with KdpD
b4074	-70	-57	-70	-64	5.13	CyaR	35	48	42	48	3.13	-18.4	-26.66	-1.94885	GAGGUGGUUUCUGG&CCAGGAACCACCUC	((((((((((((((&))))))))))))))	GAAAAGAGGUGGUUUCUGGACGUAUUCCUUCCUGAAGUCGGUUUUCUGGCGUUGUUGUUAAGUCUCGGGGUCAACGUGUUGACCCCGUUGACGGCCUUCGCGGGAGUGCGGUUGCGCUGGCCUGCCAUGAUGCGACUCACUUGCAUCGGC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0001518	0.2119128	nrfE	948579	heme lyase (NrfEFG) for insertion of heme into c552 subunit NrfE
b4686	-70	-59	-70	-64	1.79	CyaR	19	30	24	30	1.38	-11.09	-14.26	-1.17461	GCUGGUAUUUUA&UAAAAUGCUAGC	((((((((((((&))))))))))))	AAAUUGCUGGUAUUUUACGCUUUACUGUUCCGAUAAGUUCAGUAUGAUCUUGCCCGGAAAACGGGGAGAGUCAUUAUGCUGGAAUCAAUAAUUAAUCUGGUAUCGAGUGGCGCAGUUGACAGCCACACACCGCAAACUGCCGUUGCUGCC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0267126	0.9277422	yshB	7751621	uncharacterized protein
b4523	-72	-41	-64	-58	7.48	CyaR	15	49	35	41	4.57	-11.84	-23.89	-1.25404	GGCGGUUUUUCUUGGUUCUGCACUUUUCUGGG&CCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCC	((.(((..((((((((...((..((((.((((&)))).)))).....))...))))))))..))).))	GCUGGCGGUUUUUCUUGGUUCUGCACUUUUCUGGGUGGUUGUCGCACUGCUGAUUUGGAAAGUGUGGGGAUAACUAUGGUCGGUCAGGAGCAACUGGAGUCGUCACCAUUAUGCCAGCAUAGUGACAAUGAAACAGAAACGAAACGGGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0173235	0.9277422	yciX	1450257	uncharacterized 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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