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
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
b3943	29	43	29	35	8.34	MicC	40	55	49	55	4.59	-11.46	-24.39	-1.1812	UGGCAAUCAGUGGCC&GGCCAUUGCAUUGCCA	(((((((((((((((&)))))))).)))))))	GCUGCUUGCUGGCAGUCGCUGAACGUUCUUUACCAGCGUAUAGUGGGCGAACGAAAACUACACACUGGAUCUCUCAUGUCUGCCGCAGGAAAGAGCAACCCACUGGCAAUCAGUGGCCUGGUUGUGCUCACACUUAUCUGGAGUUAUAGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0104267	0.9679271	yijE	948445	EamA-like transporter family protein
b3996	-15	-6	-15	-9	1.93	MicC	45	54	48	54	3.15	-9.78	-14.86	-1.00804	GGUAGUGCAA&UUGCAUUGCC	((((((((((&))))))))))	UAUUCAAAAACUGCUCAGUGAGAAAUGUAAAAACCAUGUUAAACAUGCCAGUGAUGCAAAGGUAGUGCAAGAGCUAUGGAUCGUAUAAUUGAAAAAUUAGAUCACGGCUGGUGGGUCGUCAGCCAUGAACAAAAAUUAUGGUUGCCGAAG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.02869	0.9679271	nudC	948498	NADH pyrophosphatase
b4032	-14	21	7	13	8.43	MicC	31	65	39	45	10.96	-14.02	-33.41	-1.44507	GGGAGAUAACAAAAAUGGCAAUGGUCCAACCGAAA&UUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCC	(((((((..........(((((((((((((.((((&)))).)))))))))))))..........)))))))	CCUGCUGGUGGGUGCGCUGGCGAUAGUGAACCUGAAAGCCACGCGAAUGAAGUUUGAUUAAGGGAGAUAACAAAAAUGGCAAUGGUCCAACCGAAAUCGCAAAAAGCUCGUUUAUUUAUUACUCACCUGCUACUGCUACUUUUUAUCGCA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0019743	0.7974595	malG	948530	maltose transporter subunit
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
b4153	-59	-48	-59	-53	3.06	MicC	47	58	52	58	3.37	-9.99	-16.42	-1.02969	CGGUGGCGAAGC&GCAUUGCCACUG	(((((((((.((&)).)))))))))	CAGCUAAACGCGUUUACGGUGGCGAAGCGGAUGCAGCCGAUAAGGCGGAAGCAGCCAAUAAGAAGGAGAAGGCGAAUGGCUGAGAUGAAAAACCUGAAAAUUGAGGUGGUGCGCUAUAACCCGGAAGUCGAUACCGCACCGCAUAGCGCA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0253678	0.9679271	frdB	948666	fumarate reductase (anaerobic) Fe-S subunit
b4187	-2	10	-2	5	2.55	MicC	41	52	46	52	2.27	-9.78	-14.6	-1.00804	CAGUGCACUGGC&GCCAUUGCAUUG	(((((((.((((&)))).)))))))	UAGCAAUCUCUUUCUGUCAUGAAUCCAUGGCAGUGACCAUACUAAUGGUGACUGCCAUUGAUGGAGGGAGACACAGUGCACUGGCAAACUCACACCGUUUUUAAUCAACCUAUACCAUUAAAUAACAGCAACUUAUACCUGUCUGAUGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.02869	0.9679271	aidB	948710	DNA alkylation damage repair protein flavin-containing DNA binding protein weak isovaleryl CoA dehydrogenase
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
b4255	-59	-46	-59	-53	3.93	MicC	42	54	48	54	3.49	-12.39	-19.81	-1.27706	GGCAAUGUCAGUGG&CCAUUGCAUUGCC	(((((((.((((((&)))))))))))))	UUGUCACAAAGGUGGAGGCAAUGUCAGUGGUGUGUGACAAUAAGAGUAUCGGCAGGACAUUAAGAGGAAUGAGCCAUGGCAAACCCGGAACAACUGGAAGAACAGCGUGAAGAAACACGUUUGAUUAUUGAAGAAUUACUGGAAGAUGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0057958	0.9230441	rraB	948773	protein inhibitor of RNase E
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

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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