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
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
b0698	-65	-36	-42	-36	9.85	CyaR	11	35	11	17	1.47	-10.39	-21.71	-1.10047	GUAUUGCUGGUGUUUUUAUUACUGGGUUAU&AUAACCCAUAAAAUGCUAGCUGUAC	(((..(((((((((((......((((((((&)))))))).)))))))))))..)))	GAUAACCGGCGUAUUGCUGGUGUUUUUAUUACUGGGUUAUCUGGUUUAUGCCCUGAUCAAUGCGGAGGCGUUCUGAUGGCUGCGCAAGGGUUCUUACUGAUCGCCACGUUUUUACUGGUGUUAAUGGUGCUGGCGCGUCCUUUAGGCAGC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0393711	0.9277422	kdpA	946045	potassium translocating ATPase subunit A
b2667	-64	-42	-48	-42	7.3	CyaR	20	48	20	26	4.56	-10.49	-22.35	-1.11106	GAGGCUGGUAUAUGUUGCAUUUU&AAAAUGCUAGCUGUACCAGGAACCACCUC	((((((((((((.((((((((((&))))))).)))))))))))......))))	UUUACGCUGCUGAGGCUGGUAUAUGUUGCAUUUUUAGUUUAGAGUUUACUUAAUUUAGAAAAUACUUAAAUAAAUAUGACUGAACUCGCGCAAUUACAGGCCAGUGCCGAACAGGCAGCGGCCUUAUUGAAAGCAAUGAGCCACCCUAAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0372843	0.9277422	ygaV	947136	tributyltin-inducible repressor of ygaVP
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
b1579	-61	-38	-48	-42	6.33	CyaR	9	32	13	19	1.48	-13.17	-20.98	-1.39491	CAGCGGGCUUGUAAUGGGUUAAGU&ACAUAACCCAUAAAAUGCUAGCUG	((((..((.....((((((((.((&)).)))))))).....))..))))	GGGAAUAUCUGCGGCAGCGGGCUUGUAAUGGGUUAAGUGAUAACAGAUGUCUGGAAAUAUAGGGGCAAAUCCACAGGUGAACUACGCUCCUCUGUUUGUUACGCAAUAAAAACUGGUGUUUUCGACUAUGCAAAACAGUUUCCCUCCUCA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0076736	0.9277422	intQ	946130	pseudogene Qin prophage phage integrase familyPhage or Prophage Related
b4463	-61	-51	-61	-55	5.72	CyaR	36	46	40	46	3.13	-10.37	-19.22	-1.09835	GGUGGUUUCUG&CAGGAACCACC	(((((((((((&)))))))))))	CGCUAACCCAUAACGGUGGUUUCUGUUUUCUCUUAUUAAUGAUUAUUCCAUUUUUAUUAUCAGGAAGGAAUUACUAUGUCUUUAUCUCGCGCAGCGAUUGUCGACCAGCUAAAGGAAAUUGUUGGUGCAGAUCGCGUAAUUACCGAUGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0398007	0.9277422	ygcU	2847709	putative FAD-linked oxidoreductase
b3284	-60	-47	-59	-53	2.73	CyaR	16	31	24	30	1.42	-10.6	-14.75	-1.12271	AGUUAGCAGGAUGG&CCAUAAAAUGCUAGCU	((((((((..((((&))))....))))))))	AACUACUCGAACUGGAGUUAGCAGGAUGGAUCGCAGCUGUACCCGGCGGCUAUGUCCGAUUGAGGAGGGCAUGCCAUGUUCGACGUACUAAUGUAUUUGUUUGAAACCUAUAUUCACACAGAAGCUGAGUUGCGUGUGGAUCAAGACAAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0351035	0.9277422	smg	947781	DUF494 family putative periplasmic protein
b2859	-59	-36	-46	-40	6.61	CyaR	9	32	13	19	1.48	-12.89	-20.98	-1.36526	CAGCGGGCUUGUAAUGGGUUAAGU&ACAUAACCCAUAAAAUGCUAGCUG	((((..((.....((((((((.((&)).)))))))).....))..))))	ACGGGAAUAUCUGCGGCAGCGGGCUUGUAAUGGGUUAAGUGAUAACAGAUGUCUGGAAAUAUAGGGGCAAAUCCAAUAAACAAUUGGAAUUUACUUCCAUUGAUCUGUUUACUCAGUGGUUGUCACUUUUAUCGAGAAAGGUUUGCAGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0091552	0.9277422	ygeO	947325	pseudogene orgA family part of T3SS PAI ETT2 remnant
b4470	-58	-29	-42	-36	4.35	CyaR	17	45	23	29	4.57	-10.38	-19.3	-1.09941	GUGUGUUUCUCCGUUCCUGGCAUUUUCUUG&CAUAAAAUGCUAGCUGUACCAGGAACCAC	(((.((((((..((..((((((((((..((&)).))))))))))....)).)))))))))	GUCACUGGUUUGUUGCUGUGUGUUUCUCCGUUCCUGGCAUUUUCUUGAUUUACCUGAAAUUUUAAGGUUUUUAAUAUGUUUGAUUCGACUUUAAAUCCGUUAUGGCAGCGUUACAUCCUCGCCGUUCAGGAGGAAGUAAAACCGGCGCUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0395854	0.9277422	yhaM	2847723	putative L-serine dehydratase alpha chain

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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