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
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
b2918	-71	-56	-63	-57	4.03	MicC	38	54	39	45	4.76	-10.85	-19.64	-1.11833	GGCGAUUUAUGGUCCA&UGGGCCAUUGCAUUGCC	((((((..((((((((&))))))))...))))))	UGGCGGCGAUUUAUGGUCCAGGUACACCUAUGCUCGACAGUGUGCGCGACGUACUGAAUCUGAUAAGCCAGCAUCAUGAUUAAUGAAGCCACGCUGGCAGAAAGUAUUCGCCGCUUACGUCAGGGUGAGCGUGCCACACUCGCCCAGGCC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0151672	0.9679271	argK	947412	membrane ATPase/protein kinase
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
b1200	-75	-53	-59	-53	5.77	MicC	40	65	40	46	6.2	-13.35	-25.32	-1.37601	GGAUUCAUCGGCAGUCAGUGGUC&GGCCAUUGCAUUGCCACUGAUUUUCC	(((.(((..((((((((((((((&)))))))).))))))..)))...)))	GGAUUCAUCGGCAGUCAGUGGUCGCCGUGUCGUUGAACAUCAUCCAUGCCCUACCGUAAUUGCUGGAGCAAAAUAAUGAAAAAAUUGAUCAAUGAUGUGCAAGACGUACUGGACGAACAACUGGCAGGACUGGCGAAAGCGCAUCCAUCG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0030969	0.7974595	dhaK	945747	dihydroxyacetone kinase PTS-dependent dihydroxyacetone-binding subunit
b0686	-75	-45	-51	-45	7.31	MicC	40	74	40	46	6.93	-11.49	-25.73	-1.18429	UUAUUUGUUGCAGCCCUGUGGCACAAUGGUC&GGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAA	((((.(((((.......((((((((((((((&))))))))...))))))........))))).))))	UUAUUUGUUGCAGCCCUGUGGCACAAUGGUCAACAUAAUACCCUAACCCGACAACGCGAAAAAAAGAACUUUGCCAUGAAAUUGAAUAUCCGCGCGCAAACUGCACAAAACCAGCACAAUAAUUCUCCCAUCGUUCUUGUCCACGGUCUG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0102341	0.9679271	ybfF	945288	acyl-CoA esterase
b3128	-16	6	-2	5	4.19	MicC	40	66	41	47	6.2	-12.58	-22.97	-1.29664	UGGAGAAUAUUGCACAAUGGCC&GGCCAUUGCAUUGCCACUGAUUUUCCA	((((((((...(((((((((((&))))))))...))).....))))))))	ACCCAAUGAAGUCAUUUAUUUUUAAAUGAGACCAGGUCCUCAUUUUAAUAACCCCUGGCUGGAGAAUAUUGCACAAUGGCCAACAUCGAAAUCAGACAAGAAACGCCAACUGCGUUUUAUAUAAAAGUUCACGACACAGAUAAUGUGGCA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0051283	0.853862	garD	947641	D-galactarate dehydrogenase
b4271	-9	24	-2	5	7.14	MicC	23	54	41	47	9.06	-10.7	-26.9	-1.10287	GGGAAUACGAUGGCAUUAACAGAUAUCAAAGUC&GAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCC	((.(((.(((((((...((((((....((((((&))))))....))))))..))))))).))).))	AUCUACCAACAUAUGUUGGUACAGAUGAUGGUAUUUCCGGUUCGAUAAUGCUUGUACCAACAGGGAGGGAAUACGAUGGCAUUAACAGAUAUCAAAGUCAGAGCAGCCAAGCCAACGGAUAAGCAAUAUUAGCUGACUGAUGGUGGCGGU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0166105	0.9679271	intB	948782	pseudogene integrase homologyIS phage Tn Phage-related functions and prophages KpLE2 phage-like element P4-like integrase
b2215	-67	-15	-49	-43	14.91	MicC	1	70	42	48	12.16	-21.53	-48.6	-2.21913	AUGAGGGUUAAUCAGUAUGCAGUGGCAUAAAAAAGCAAAUAAAGGCAUAUAAC&GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAU	(((..((..(((((((((((((((((((((((.....((((((((((((((((&))))))))))))))))........))))))..........))))))))))....)))))))..))..)))	ACUGAUUAAUGAGGGUUAAUCAGUAUGCAGUGGCAUAAAAAAGCAAAUAAAGGCAUAUAACAGAGGGUUAAUAACAUGAAAGUUAAAGUACUGUCCCUCCUGGUCCCAGCUCUGCUGGUAGCAGGCGCAGCAAACGCUGCUGAAGUUUAC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	5.2e-06	0.0190476	ompC	946716	outer membrane porin protein C
b1346	-13	5	-3	4	7.92	MicC	41	58	42	48	4.26	-14.56	-26.74	-1.50072	CAGAGGUGAUGCGAUGGC&GCCAUUGCAUUGCCACUG	(((.((((((((((((((&)))))))))))))).)))	UUCAUAGCUGAUUAUUAAUAAUCAACAUCGGGCGUCAAUUUCAGUCUAACAUUGGCGCCUGCCAGAGGUGAUGCGAUGGCACAAGUAAUCUUUAAUGAAGAGUGGAUGGUUGAAUACGGCCUGAUGCUUCGCACUGGUCUGGGGGCCAGA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0013626	0.7974595	ydaQ	947399	Rac prophage conserved protein
b3751	56	74	67	73	8.66	MicC	41	59	42	48	4.26	-13.8	-26.72	-1.42239	UCAGUGCGAAUGCGAUGGC&GCCAUUGCAUUGCCACUGA	((((((..(((((((((((&)))))))))))..))))))	AAAGCGGUGGUGAUUUUGCUGGCGGUGCUGGUAGACAACAAAAAGCAGUAAUAACGACUACAGGACAUCUUGAAUAUGAACAUGAAAAAACUGGCUACCCUGGUUUCCGCUGUUGCGCUAAGCGCCACCGUCAGUGCGAAUGCGAUGGCA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0022915	0.7974595	rbsB	948261	D-ribose ABC transporter periplasmic binding protein ribose chemotaxis receptor

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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