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
b4595	-48	-34	-48	-42	3.82	CyaR	31	49	43	49	3.25	-12.33	-19.4	-1.30594	GGGGGUGGGGGUAUA&UGUACCAGGAACCACCUCC	((((((((.((((((&)))))).....))))))))	AACGCGGGAAAAGCACUGGUCAGCGUCGGGGGUGGGGGUAUAAUGACCAUUCUGUUAUUGCAUAGAGUAGUUAACAUGAAGCGGAGUAGAACGGAAGUGGGGCGCUGGCGCAUGCAGCGUCAGGCUAGCCGACGUAAAUCGCGUUGGCUU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0129245	0.9277422	yciY	5061502	uncharacterized protein
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
b2036	-19	3	-4	3	4.4	CyaR	17	38	17	23	4.49	-10.41	-19.3	-1.10258	CUGGUUUGCUGAGGAUUUUAUG&CAUAAAAUGCUAGCUGUACCAG	(((((..(((.((.((((((((&)))))))).)))))...)))))	CAACAGAGUGCUUAGUUACGUCACUCAUGCUGAUGUUCGUAAGAAAUAAUAAAUUACUGGUUUGCUGAGGAUUUUAUGUACGAUUAUAUCAUUGUUGGUUCUGGUUUGUUUGGUGCCGUUUGUGCGAAUGAGUUAAAAAAGCUAAACAAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0389456	0.9277422	glf	945235	UDP-galactopyranose mutase FAD/NAD(P)-binding
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
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
b2416	-14	10	-5	2	4.99	CyaR	2	27	11	17	1.47	-12.38	-18.84	-1.31124	AGUAAGGUAGGGUUAUGAUUUCAG&CUGAAAAACAUAACCCAUAAAAUGCU	((((...((((((((((.((((((&))))))..)))))))).))...))))	UCUGGUUAAACUGAUGGCGGAACUCGAGUAAUUUCCCGGGUUCUUUUAAAAAUCAGUCACAAGUAAGGUAGGGUUAUGAUUUCAGGCAUUUUAGCAUCCCCGGGUAUCGCUUUCGGUAAAGCUCUGCUUCUGAAAGAAGACGAAAUUGUC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0125381	0.9277422	ptsI	946879	PEP-protein phosphotransferase of PTS system (enzyme I)
b0675	61	74	68	74	4.01	CyaR	29	42	29	35	4.29	-10.45	-18.75	-1.10682	GUACCGGGUGCAGC&GCUGUACCAGGAAC	((.((.((((((((&)))))))).)).))	UUUGCUCCAGCAUUUGCUGGAAAAUUAAUGUGCUUUUAUAGUGGCGCUUAUUGUUGUCAAUAUUCUGGGUAGUCCAUGACCAUUAAAAAUGUAAUUUGCGAUAUCGACGGCGUGCUGAUGCACGAUAACGUCGCCGUACCGGGUGCAGCG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0381068	0.9277422	umpH	945283	UMP phosphatase
b1152	63	72	66	72	3.03	CyaR	30	39	30	36	4.27	-11.44	-18.74	-1.21168	CCUGGUGCAG&CUGUACCAGG	((((((((((&))))))))))	UUUACGCCUACAAAGUGAAAGCAUUUGGCGAAGUGGCUGAACUGCUGCCCGUCGAUCCCGGCUGUGUGGUAUAUGCGCUGGGAAGGUGUCAGCGAUGGCCUGAAGGUGACCGCCGGGAGUGUUAUUCAGCGCGAUGACCUGGUGCAGUAC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0218742	0.9277422	jayE	945703	pseudogene e14 prophagePhage or Prophage Related
b1041	54	73	67	73	5.82	CyaR	10	34	10	16	1.48	-11.4	-18.7	-1.20744	UGCAGCCGCAGCAGGUUAUG&CAUAACCCAUAAAAUGCUAGCUGUA	((((((...(((((((((((&))))))).......)))).))))))	AAAUACAGGUUGCGUUAACAACCAAGUUGAAAUGAUUUAAUUUCUUAAAUGUACGACCAGGUCCAGGGUGACAACAUGAAAAACAAAUUGUUAUUUAUGAUGUUAACAAUACUGGGUGCGCCUGGGAUUGCAGCCGCAGCAGGUUAUGAU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.022384	0.9277422	csgB	947391	curlin nucleator protein minor subunit in curli complex
b3600	54	72	57	63	6.76	CyaR	14	33	24	30	1.44	-10.46	-18.66	-1.10788	ACUGCUGGCAGACGCGGGU&ACCCAUAAAAUGCUAGCUGU	((.(((((((.....((((&))))......))))))).))	CACGGAGAGGGUUUGGGUGAGGGAAAAGCCUCACCCCAGCCCUCUCGGGUAAAAACAUUGAUGAAGGUUAAUACUAUGAAAGCAUUACAUUUUGGCGCAGGUAAUAUCGGUCGUGGCUUUAUCGGUAAACUGCUGGCAGACGCGGGUAUC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0378997	0.9277422	mtlD	948117	mannitol-1-phosphate dehydrogenase NAD-dependent

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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