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
b1140	-67	-42	-66	-60	5.94	MicC	44	68	61	67	4.39	-9.8	-20.13	-1.0101	GUUGGGGAGUUGGUAACACCUGUAAU&AUUGCAUUGCCACUGAUUUUCCAAC	((((((((((((((..((..((((((&)))))).))..))))))))))))))	CCGAGUUAGUUGGGGAGUUGGUAACACCUGUAAUCAAGAAAAAUGACUCAUUACUUUUGCAACGGAUUUUGAGUAAUGGCAGCCAGACCGCGUAAGAAUAAUGUUUCAGUCCCUAACUUAUAUCCGCUUUAUAGUAGGAAGGUAAAUAAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0283569	0.9679271	intE	948034	e14 prophage putative integrase
b2314	-9	11	1	7	5.95	MicC	45	65	50	56	4.26	-13.85	-24.06	-1.42754	GGAGAAGCGGUGGCAAGUAA&UUGCAUUGCCACUGAUUUUCC	((((((.(((((((((((((&)))).))))))))).))))))	AAGACACCGUGCUGGUGUGUGGUUCUUUCCACACGGUCGCACAUGUCAUGGAAGUGAUUGACGCGAGGAGAAGCGGUGGCAAGUAAGUUUCAGAAUCGGUUAGUGGGCACGAUCGUGCUGGUGGCGCUGGGGGUGAUUGUACUUCCAGGG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0022155	0.7974595	dedD	944971	membrane-anchored periplasmic protein involved in septation
b1507	-16	4	-7	-1	6.02	MicC	47	63	51	57	3.74	-9.86	-19.62	-1.01629	AAAAUCUGGAGUGGUAAUGC&GCAUUGCCACUGAUUUU	((((((...(((((((((((&)))))))))))))))))	UGAACUCUCAAUGACGCUAUGCGACGCGAAAAAUGCCUCGCCAGAAUCAACAGAACAGCAAAAUCUGGAGUGGUAAUGCCUAAACUUGUCACUUGGAUGAACAACCAGCGGGUAGGCGAGUUAACGAAGUUAGCCAACGGCGCGCACACC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0273792	0.9679271	hipA	946064	inactivating GltX kinase facilitating persister formation toxin of HipAB TA pair autokinase
b0393	-71	-57	-67	-61	6.05	MicC	40	55	45	51	4.59	-16.11	-26.75	-1.66049	UGGCAAUGCAAGGCC&GGCCAUUGCAUUGCCA	(((((((((((((((&)))).)))))))))))	GGAUUGGCAAUGCAAGGCCGCCGACAAUUCGUUAUCAUGCCCGCUAAAUUUAACGACAAGGCCGUGGAAAUUAUCAUGCUGUGGUUCAAAAAUUUAAUGGUUUACCGUCUUAGCCGCGAGAUUUCGCUGCGUGCAGAAGAGAUGGAAAAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0004508	0.7974595	rdgC	948585	nucleoid-associated ssDNA and dsDNA binding protein competitive inhibitor of RecA function
b1676	-60	-49	-60	-54	6.14	MicC	39	54	48	54	4.76	-10.62	-21.52	-1.09462	GGCAGUGCGCCC&GGGCCAUUGCAUUGCC	((((((((((((&))))....))))))))	CCGGAUUCGCUUUCCGGCAGUGCGCCCAGAAAGCAAGUUUCUCCCAUCCUUCUCAACUUAAAGACUAAGACUGUCAUGAAAAAGACCAAAAUUGUUUGCACCAUCGGACCGAAAACCGAAUCUGAAGAGAUGUUAGCUAAAAUGCUGGAC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.017432	0.9679271	pykF	946179	pyruvate kinase I
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
b1891	33	54	45	51	6.3	MicC	45	65	48	54	4.26	-11.45	-22.01	-1.18017	GGAUAUUCAGCUGGCAAUGGAA&UUGCAUUGCCACUGAUUUUCC	(((...((((.((((((((.((&)).))))))))))))...)))	CAUCAUGCUCUCAACACGCUUGCUGAAUGAUGUUAAUCAGCCUGAAGAAGCGCUGCGCAAGAAAAGGGCCUGAUCAUGAGUGAAAAAAGCAUUGUUCAGGAAGCGCGGGAUAUUCAGCUGGCAAUGGAAUUGAUCACCCUGGGCGCUCGU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0104916	0.9679271	flhC	947280	flagellar class II regulon transcriptional activator with FlhD
b2239	56	74	62	68	6.41	MicC	41	66	47	53	5.82	-14.71	-26.94	-1.51618	UGGGAAGCAGUGCAAUGGC&GCCAUUGCAUUGCCACUGAUUUUCCA	(((((((((((((((((((&))))))))))))).......))))))	UGUUGAUUGUUGUGAUGAUUGGCGAAAAACGUCGCCAUGAACAAUUACUGCAAGAACGCAACGGAGGCUAAUGGCAUGAAAUUGACGCUGAAAAACCUUAGCAUGGCGAUCAUGAUGAGCACUAUAGUCAUGGGAAGCAGUGCAAUGGCG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0012277	0.7974595	glpQ	946725	periplasmic glycerophosphodiester phosphodiesterase
b3005	-12	11	3	9	6.42	MicC	46	65	48	54	4.07	-9.93	-20.42	-1.0235	GGAUAAUAUCCGAUGGCAAUGCA&UGCAUUGCCACUGAUUUUCC	(((....(((...((((((((((&))))))))))..)))..)))	GACCUGGAUCUGGAAGCCAGCGCCGCUGCGCAUCCGGUUCGUGUCGCACAAAAAUUACGCGCAGGAUAAUAUCCGAUGGCAAUGCAUCUUAACGAAAACCUCGACGAUAACGGCGAAAUGCAUGAUAUCAACGUGACGCCGUUUAUCGAC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0262783	0.9679271	exbD	946345	membrane spanning protein in TonB-ExbB-ExbD complex
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

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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