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
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
b0444	28	64	54	60	13.08	CyaR	23	49	30	36	4.55	-11.11	-28.74	-1.17673	GGAGGUCAGGAUUCCACCACCUGUCUGGUGCAGGCAU&AUGCUAGCUGUACCAGGAACCACCUCC	((((((..((.((((..........((((((((((((&))))...))))))))))))))))))))	CAUCGCAAUGAAUAGCUGGUCCGGGUUAAUCGCAGGCGUUACCAUAACGCUUUUAUUGUUCAAGCAGGAUUAUCUAUGAAACGUGCUGUCGUUGUGUUCAGUGGAGGUCAGGAUUCCACCACCUGUCUGGUGCAGGCAUUACAACAAUAU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0264121	0.9277422	queC	947034	7-cyano-7-deazaguanine (preQ0) synthase queuosine biosynthesis
b1825	54	66	57	63	4.28	CyaR	37	49	40	46	3.13	-12.12	-19.53	-1.2837	GGUGGUGGUUCUU&AGGAACCACCUCC	((.((((((((((&)))))))))).))	AUAUCAUUUUUUCAGCACUAGAUUUUCUUCCUCUCCAGCAGUGGUAGAAUAGCGCCUCUACUCAGAGGUGGUGAAAUGAACGAAGUUGUAAAUUCAGGCGUGAUGAACAUUGCGUCUUUGGUUGUAUCGGUGGUGGUUCUUCUUAUCGGG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0146678	0.9277422	yebO	946350	putative inner membrane protein
b3168	49	67	61	67	11.55	CyaR	29	45	29	35	4.3	-11.86	-27.71	-1.25616	GUGGAACGCCUGGUACAGC&GCUGUACCAGGAACCAC	((((....(((((((((((&)))))))))))..))))	GCACUGAUUAUGGCUGCCCGUAAUAUUUGCUGGUUCGGUGACGAAGCGUAAUAAACUGUAGCAGGAAGGAACAGCAUGACAGAUGUAACGAUUAAAACGCUGGCCGCAGAGCGACAGACCUCCGUGGAACGCCUGGUACAGCAAUUUGCU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0171203	0.9277422	infB	947684	translation initiation factor IF-2
b3890	60	67	61	67	2.18	CyaR	29	36	29	35	1.16	-10.64	-13.98	-1.12695	GGUGCAGC&GCUGUACC	((((((((&))))))))	CAAGGGUACUUUUCUCUCCAUAGAUUCAAAAAUGAUAUUGGCGAGAUAUUUAUGAACUCUCUGGCAGGUAUAGAUAUGGGCAGAAUUUUACUCGAUUUAUCGAAUGAGGUGAUUAAGCAACUUGAUGAUCUCGAGGUGCAGCGUAAUCUU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0343392	0.9277422	yiiF	948385	putative thymol sensitivity protein CopG family putative transcriptional regulator
b0412	56	67	61	67	3.66	CyaR	29	39	29	35	4.29	-10.47	-18.42	-1.10894	CCUGUGUGCAGC&GCUGUACCAGG	((((.(((((((&)))))))))))	UGAGAUAAAGGAUCGAUGCUUUCGCUGCUUUUACCCUCUACCAUUAGGCUAAUUGCGACGAGAAAGGGACGACCUAUGAAUACUAACGUUUUUCGACUGCUCCUGCUGGGAAGCCUGUUCAGCCUUAGCGCCUGUGUGCAGCAAAGUGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0376936	0.9277422	yajI	947233	putative lipoprotein
b2957	43	68	53	59	7.84	CyaR	22	43	29	35	4.55	-12.83	-25.22	-1.3589	GGUUUUAGUGGUGCAGCAUUGGCAUU&AAUGCUAGCUGUACCAGGAACC	((((....(((((((((..(((((((&))))))))))))))))..))))	UAAAUUGUUUAACGUCAAAUUUCCCAUACAGAGCUAAGGGAUAAUGCGUAGCGUUCACGUAACUGGAGGAAUGAAAUGGAGUUUUUCAAAAAGACGGCACUUGCCGCACUGGUUAUGGGUUUUAGUGGUGCAGCAUUGGCAUUACCCAAU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0095047	0.9277422	ansB	947454	periplasmic L-asparaginase 2
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
b2174	60	70	61	67	1.46	CyaR	31	41	34	40	3.25	-10.95	-15.66	-1.15978	UUCCUGGUAUA&UGUACCAGGAA	(((((((((((&)))))))))))	CGCGCUGUUGAAGCUUCGUUUAGCGACUACCGCGUAAGGUUGCCUGCGUUUUUCAGUAAGAUAAUUAGAGAAAAUAUGAUUAAAAAUUUGCCGCAAAUAGUGUUGUUGAAUAUUGUCGGCCUCGCGCUGUUUCUUUCCUGGUAUAUCCCC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0289036	0.9277422	lpxT	946693	lipid A 1-diphosphate synthase undecaprenyl pyrophosphate:lipid A 1-phosphate phosphotransferase
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

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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