Input and runtime details for job 1972078 (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 1972078 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:13:56 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:16:07 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:17:05 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:18:21 CET 2020
	Job Completed		@ Mon Jan 27 14:18:31 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1972078&toolName=IntaRNA ( 30 days expiry )

Description of the job

MicC - 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
b1771	-14	4	-9	-3	4.42	MicC	2	19	8	14	3.65	-11	-19.07	-1.13379	GAUAAUGAAGGCAAAUGA&UUAUAUGCCUUUAUUGUC	(((((((((((((.((((&)))).)))))))))))))	GGUGCCACCACCGGCGUAAAAAACAGAAAGCUGGUCGAACAAUUGCUGGAAGAAUACGAAGGAUAAUGAAGGCAAAUGAAAAAGAUACCUUUAGGCACAACGGAUAUUACGCUUUCGCGAAUGGGGUUGGGGACAUGGGCCAUUGGCGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0138425	0.9679271	ydjG	946283	methylglyoxal reductase NADH-dependent
b4297	57	71	65	71	4.42	MicC	39	53	39	45	4.75	-10.98	-20.15	-1.13173	GCACGCCGAUGGCCC&GGGCCAUUGCAUUGC	(((...(((((((((&)))))))))...)))	CAUCUGAAGAAGCAAAAGAUAAAGUCCACGUGCUGCUUACCGCGCAGGGCAUUUUACCAGUCUGAGGAGAAACUCAUGUCUGUUCGCAAUAUUUUUGCUGACGAGAGCCACGAUAUUUACACCGUCAGAACGCACGCCGAUGGCCCGGAC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0140126	0.9679271	yjhG	946829	putative dehydratase
b4478	-9	3	-9	-3	4.56	MicC	43	54	48	54	3.22	-12.96	-20.74	-1.33581	GGCAGUGCAAUG&CAUUGCAUUGCC	((((((((((((&))))))))))))	UCGCGCCGGGCAAUCCGUAGAGCGCACCGCGCAGCAGGCAGCAGCAUUUGUUAAGGCGUAUCGAGAGGCAGUGCAAUGAAAAUCACCAAAAUUACCACGUAUCGUUUACCUCCCCGCUGGAUGUUCCUGAAAAUUGAAACCGAUGAAGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0040051	0.8150379	dgoD	2847765	D-galactonate dehydratase
b1535	-13	20	-7	-1	4.73	MicC	33	63	51	57	10.92	-11.71	-27.36	-1.20697	AAAAGGAGUGGCAAUGAUCAAGAAGACAACGGA&UCUGUUGGGCCAUUGCAUUGCCACUGAUUUU	((((..((((((((((..(((.....(((((((&))))))).....)))))))))))))..))))	AUGAAAAUAUUGACGUAAUUUUGCUUUUCUCUCGUUAGAAUAGCGCGCACAAGGAACUGUGAAAAAGGAGUGGCAAUGAUCAAGAAGACAACGGAAAUUGAUGCCAUCUUGUUAAAUCUCAAUAAGGCUAUCGAUGCCCACUACCAGUGG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0089209	0.9679271	dgcZ	946075	diguanylate cyclase zinc-sensing
b4230	-10	7	1	7	4.75	MicC	47	65	47	53	4.06	-11.03	-19.84	-1.13688	GGAGAACAGUGUGAUGC&GCAUUGCCACUGAUUUUCC	(((((((((((((((((&))))))).)))).))))))	AGGUGGCGGAGAUCCCGCUGGCAGAGCUUUCCGUUCCGGCGAUCAUGAACGCCAUUGCGGCGUAAGGAGAACAGUGUGAUGCCUCAAUCUCUUCCGGACACCACUACGCCAAAAAGGCGCUUUCGCUGGCCGACGGGGAUGCCGCAGCUG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0135909	0.9679271	ytfT	948743	putative sugar ABC transporter permease
b1406	58	71	58	64	4.77	MicC	41	53	47	53	3.87	-10.5	-19.14	-1.08225	GCGAUGCAACUGGC&GCCAUUGCAUUGC	(((((((((.((((&)))))))))))))	CACCUUCGCAUUAUUUAUCUCUUUUCGUUUCUAUACUGAUUUUUCUUAAUCCGUUUUAUUACAGGGCAGGGUGCGAUGAGCAGCAAUACAUUUACUCUCGGUACAAAAUCCGUUAACCGUCUUGGUUAUGGCGCGAUGCAACUGGCAGGU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0187361	0.9679271	ydbC	945980	putative NAD(P)-binding oxidoreductase
b2501	-15	7	-7	-1	4.87	MicC	40	65	51	57	6.2	-10.33	-21.4	-1.06473	GGAGUAAAAGUGGUAAUGGGUC&GGCCAUUGCAUUGCCACUGAUUUUCC	(((.....((((((((((((((&))))....)))))))))).....)))	AGUUGGACAUCUGCCAAUAUUGCUCGCCAUAAUAUCCAGGCAGUGUCCCGUGAAUAAAACGGAGUAAAAGUGGUAAUGGGUCAGGAAAAGCUAUACAUCGAAAAAGAGCUCAGUUGGUUAUCGUUCAAUGAACGCGUGCUUCAGGAAGCG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0207409	0.9679271	ppk	946971	polyphosphate kinase component of RNA degradosome
b4393	-12	11	1	7	4.89	MicC	35	55	39	45	8.89	-13.36	-27.14	-1.37704	UGGCGACAUAUUAUGGCCCAACA&UGUUGGGCCAUUGCAUUGCCA	((((((......(((((((((((&)))))))))))....))))))	AUAUGCUAUCGUACUCUUUAGCGAGUACAACCGGGGGAGGCAUUUUGCUUCCCCCGCUAACAAUGGCGACAUAUUAUGGCCCAACAAUCACCCUAUUCAGCAGCGAUGGCAGAACAGCGUCACCAGGAGUGGUUACGUUUUGUCGACCUG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0030764	0.7974595	trpR	948917	transcriptional repressor tryptophan-binding
b2986	36	51	41	47	5.28	MicC	38	55	42	48	4.76	-10.36	-20.4	-1.06782	UGGUAGCGAUGGUUCA&UGGGCCAUUGCAUUGCCA	((((((((((((((((&)))))))))))..)))))	CUGAAUUACGCUUUCAUAAAAACAUAUUAACCAAAUAAAUAUUUUUAAUGGAUAUUUAAAUUAAAGGAUAUAUUCAUGCAGUCAAUAACACCUCCAUUAAUUGCCGUUAUUGGUAGCGAUGGUUCAGGCAAGUCAACGGUGUGUGAACAU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0203731	0.9679271	yghT	947477	putative ATP-binding protein
b1218	-28	-2	-18	-12	5.36	MicC	45	65	52	58	4.26	-13.27	-22.89	-1.36776	GGGAAGUAUGCAGUGGCGGAAGUGUAA&UUGCAUUGCCACUGAUUUUCC	(((((((...(((((((...(((((((&)))))))))))))))))))))	CAAAAUGAGCAGUAAAAAUGUCCGGAAGACACCAAAAAGUUGUCGCAGGGAAGUAUGCAGUGGCGGAAGUGUAAGGUGAUAACGCGUGAUUUCUUGAUGAAUGCCGAUUGUAAAACGGCAUUUGGUGCCAUUGAAGAAUCACUCUUAUGG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0032656	0.7974595	chaC	945793	cation transport regulator

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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