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
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
b4551	57	72	66	72	3.24	MicC	48	65	48	54	4	-10.34	-17.58	-1.06576	GGAUUCAAUGGCGAUG&CAUUGCCACUGAUUUUCC	(((.(((.((((((((&)))))))).)))...)))	GAGAUUUUCCAGCGUGAAAUGCAACAAGAACGACGCCAGCUGGACGGCUGGGAUGAAUUUGAGUAGAGGGUAAAGAUGGCAAUCCGAAAACGUUUUAUUGCGGGCGCAAAAUGCCCGGCCUGUCAGGCGCAGGAUUCAAUGGCGAUGUGG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0206176	0.9679271	yheV	1450290	DUF2387 family putative metal-binding protein
b2331	-26	-17	-26	-20	0.32	MicC	56	65	59	65	0.92	-10.33	-11.57	-1.06473	GGAAAAUUAG&CUGAUUUUCC	((((((((((&))))))))))	AAAAAUACGUUUAAAACGAUCGAUUGCGCUACGAGUCGGGUAAACUGUAGGAAAAUUAGAAAUAGAGACAGAUAAAUGAAAAAGAAAACAACACUUAGCGAGGAGGACCAGGCUCUGUUUCGCCAGUUGAUGGCGGGGACUCGCAAGAUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0207409	0.9679271	smrB	944847	putative DNA endonuclease
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
b2247	42	62	44	50	6.63	MicC	30	55	47	53	8.97	-10.24	-25.84	-1.05545	UGGCGGUGCGACAGCAGAAAA&UUUUCUGUUGGGCCAUUGCAUUGCCA	(((((((((((((((((((((&)))))))))).....)))))))))))	CGCCAGGGAUAUUUCACGUCUGUUGGGAUGGAAAAGUCCCUUUGACUUACAAGCCUCAUAACAAUGGAGAACAUCAUGACCCUACCAAAAAUUAAACAGGUUCGCGCCUGGUUUACUGGCGGUGCGACAGCAGAAAAAGGCGCUGGCGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.021882	0.9679271	rhmD	945881	L-rhamnonate dehydratase
b1152	17	28	17	23	3.49	MicC	37	48	42	48	5.33	-10.21	-19.03	-1.05236	GCGAUGGCCUGA&UUGGGCCAUUGC	((((((((((((&))))))))))))	UUUACGCCUACAAAGUGAAAGCAUUUGGCGAAGUGGCUGAACUGCUGCCCGUCGAUCCCGGCUGUGUGGUAUAUGCGCUGGGAAGGUGUCAGCGAUGGCCUGAAGGUGACCGCCGGGAGUGUUAUUCAGCGCGAUGACCUGGUGCAGUAC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0222753	0.9679271	jayE	945703	pseudogene e14 prophagePhage or Prophage Related
b1068	-66	-50	-56	-50	5.69	MicC	51	66	51	57	2.9	-10.2	-18.79	-1.05133	UGGAAAUCGAAGUGGCA&UGCCACUGAUUUUCCA	((((((....(((((((&)))))))...))))))	UCGAAGCCCUGGAAAUCGAAGUGGCAGAACUGAAACAGCGUCUUGAUUCGUUGCUGGCCCAUCUGGGAGAUUAAAGUGAAAAAAUUACGUAUCGGCGUAGUGGGAUUAGGUGGCAUUGCGCAAAAAGCGUGGUUACCGGUGCUGGCGGCA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0224078	0.9679271	yceM	945204	putative oxidoreductase
b2830	63	75	63	69	1.12	MicC	40	54	48	54	4.58	-10.17	-15.87	-1.04824	GGUAAUGUGGGCC&GGCCAUUGCAUUGCC	(((((((..((((&))))....)))))))	GCAGAGAGUGGUUUACCGUCUUCCUGGAGUAUGAAACAAUCAUUCGUAUAUAAAGCUUUAUUUUGAGGUAGUCCGGUGAUUGAUGACGAUGGCUACCGCCCAAACGUAGGUAUCGUGAUUUGUAAUCGCCAGGGGCAGGUAAUGUGGGCC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0228099	0.9679271	rppH	947300	RNA pyrophosphohydrolase
b2848	-72	-62	-68	-62	0.69	MicC	44	55	44	50	3.21	-10.16	-14.06	-1.04721	UGGCAUGCAAU&AUUGCAUUGCCA	(((((((((((&))))))).))))	UUAUGGCAUGCAAUAAAAACUAUAACCAACAUGAAGUGGCAAACUGUUUAACCCUGUCUUACCGUGAGGUUAAUCGUGAUUGAUUAUAAAAAAAACUUAUUAUUUAUUUUAGUUUUUAUCAGUGGGUUUAUUCUCUUCACUGUCUAUUCU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0229454	0.9679271	yqeJ	947328	uncharacterized protein
b0907	-13	8	1	7	6.19	MicC	38	56	39	45	4.76	-10.15	-21.1	-1.04618	GUGGUGAGGGGAAAUGGCUCA&UGGGCCAUUGCAUUGCCAC	(((((((.....(((((((((&)))))))))...)))))))	CACAGGAAUAAUGUAUUACCUGUGGUCGCAAUCGAUUGACCGCGGGUUAAUAGCAACGCAACGUGGUGAGGGGAAAUGGCUCAAAUCUUCAAUUUUAGUUCUGGUCCGGCAAUGCUACCGGCAGAGGUGCUUAAACAGGCUCAACAGGAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0230817	0.9679271	serC	945527	3-phosphoserine/phosphohydroxythreonine aminotransferase

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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