Input and runtime details for job 6571257 (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 6571257 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:18:03 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:20:22 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:21:19 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:22:25 CET 2020
	Job Completed		@ Mon Jan 27 14:22:35 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

Description of the job

Spot42 - 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
b2150	-48	-22	-28	-22	7.03	Spot42	1	24	1	7	7.99	-9.49	-24.51	-0.978151	GAGCAUUUAUCUCAAGCACUACCCUGC&GUAGGGUACAGAGGUAAGAUGUUC	(((((((((((((......((((((((&))))))))..))))).))))))))	ACACUUCAUUAACUCUACUGCCCCGCCGAGCAUUUAUCUCAAGCACUACCCUGCAUAAGAAAAACCGGAGAUACCAUGAAUAAGAAGGUGUUAACCCUGUCUGCUGUGAUGGCCAGCAUGUUAUUCGGUGCCGCUGCACACGCUGCUGAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0202101	0.9238006	mglB	949041	methyl-galactoside transporter subunit
b2506	-51	-37	-49	-43	1.09	Spot42	55	68	60	66	6.05	-11.81	-18.95	-1.21728	AUUCAGCCAAAUACC&GGAUUUGGCUGAAU	((((((((((((.((&))))))))))))))	ACCACGACGUAUAACGAAACGCGUAUUCAGCCAAAUACCAAAUGUCCUGAAAAGAGCUAAUAAUCAGGAGGAGUCAUGAAGAAAGUUUUUCUUUGCGCCAUCUUAGCCUCCUUAAGCUAUCCGGCUAUCGCCUCAUCAUUGCAGGAUCAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0053979	0.9238006	yfgI	945168	nalidixic acid resistance protein putative periplasmic protein
b1921	60	75	61	67	0.19	Spot42	49	65	58	64	6.17	-9.65	-16.01	-0.994642	CAGCCAGACCCAUUGC&GUAAUCGGAUUUGGCUG	((((((((((..((((&))))..)).))))))))	CGGUUACGCACUAAACUGGGUAAGUUAUAACGUCAGUAAAUGCCGCACUUUAACUUUGACUACCAGGAGUUCUUAAUGAUGGUGCAGCACCUGAAAAGACGGCCAUUAAGCCGCUAUCUUAAAGACUUUAAACACAGCCAGACCCAUUGC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0184641	0.9238006	fliZ	946833	RpoS antagonist putative regulator of FliA activity
b3685	-51	-36	-49	-43	4.25	Spot42	54	68	60	66	6.15	-11.08	-21.48	-1.14203	AUUCAGCCAUAAUCCG&CGGAUUUGGCUGAAU	(((((((((.((((((&)))))))))))))))	CUAUAAGGCAAAUCUGCUUCACCGAUUCAGCCAUAAUCCGUAGCAAUUAAAAUGUUAUCUCAAGAGAAAUGGACGAUGAGUGAUAUAGCAUUAACGGUCAGUAUUCUGGCUUUGGUGGCAGUCGUCGGUUUGUUUAUCGGCAACGUCAAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0081942	0.9238006	yidE	948193	putative transporter
b2319	3	19	13	19	6.68	Spot42	20	36	20	26	4.78	-9.12	-20.58	-0.940014	GUCUGAAGGCUGGAACA&UGUUCUAUCUUUCAGAC	(((((((((.(((((((&))))))).)))))))))	GGCACGUUAAUCUCUUCUUCAUGCUCUCUGCUGUAACAUUGGCAGGGAGCUUUGCUAUUUCUGGAGUAAACCACCAUGUCUGAAGGCUGGAACAUUGCCGUCCUGGGCGCAACUGGCGCUGUGGGCGAAGCCCUGCUUGAAACGCUGGCU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0248939	0.9238006	usg	946797	putative semialdehyde dehydrogenase
b1695	43	63	57	63	3.26	Spot42	48	71	48	54	7.47	-8.85	-19.58	-0.912185	AGUAUUCGCGAACUGAUUACG&CGUAAUCGGAUUUGGCUGAAUAUU	(((((((((.(((((((((((&)))))))))..)).)).)))))))	UGGACGAAAGAUUAUUUAUCGAUGCGGCGAUGGGUUUUGUCCUGCCUGAAGCGGCUCAUUAACAGGAGUAUAAUGAUGGAUUUUUCUUUAACUGAAGAACAAGAACUGCUGCUGGCCAGUAUUCGCGAACUGAUUACGACUAACUUUCCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.028969	0.9238006	ydiO	945626	putative acyl-CoA dehydrogenase
b0307	57	71	59	65	1.25	Spot42	48	60	52	58	1.58	-10.37	-13.2	-1.06885	AGAUCCGAUCAUGCG&CGUAAUCGGAUUU	(((((((((..((((&)))))))))))))	GAUUACAACGGGAAGGGCAGAAAGUCAAAGUGAUGCAUAUUGCUGAAGUGUUGAUGAGCCGCUGAGGAUAUAAAGAUGUCGAUCAAAACCAGUAAUACAGAUUUUAAGACACGCAUCCGUCAGCAAAUUGAAGAUCCGAUCAUGCGCAAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0122776	0.9238006	ykgF	944980	ferridoxin-like LutB family protein putative electron transport chain YkgEFG component
b3816	-71	-41	-47	-41	5.45	Spot42	4	37	4	10	11.32	-10.38	-27.15	-1.06988	GGUCUGAAACCCAAUUUGUUUCUGUGUGCCC&GGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACC	(((((((((....((((....((.(((((((&))))))).))...))))........)))))))))	UAAUGGUCUGAAACCCAAUUUGUUUCUGUGUGCCCACCGAACUGUCCGAUAUUUUAAGCAUUGGGAGUCCCGGUCAUGCUGAGCGCAUUUCAACUGGAAAAUAACCGACUGACCCGGCUGGAAGUCGAAGAGUCACAACCCCUUGUAAAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.012208	0.9238006	corA	948351	magnesium/nickel/cobalt transporter
b3238	-21	-5	-21	-15	2.8	Spot42	39	54	48	54	3.87	-9.61	-16.28	-0.990519	GAUUAUGUCGAGGUAAA&UUUACUUCACGUAAUC	((((((((.((((((((&))))))))))))))))	UUAGUGUAUACUUGAUUUUGUGAUAUGGGUCACGAAACAAAGGCCCAGCUAAAAGAUUAUGUCGAGGUAAAAAUCAUGAAAAUCAAAACCACUGUUGCUGCAUUAAGCGUACUUUCUGUUCUCUCUUUCGGUGCAUUCGCUGCCGACUCC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0188861	0.9238006	yhcN	947835	cadmium and peroxide resistance protein stress-induced
b4465	-18	-2	-18	-12	3.4	Spot42	39	56	50	56	3.89	-8.82	-16.11	-0.909092	CUGAUUACAGAGGUAAA&UUUACUUCACGUAAUCGG	((((((((.((((((((&))))))))..))))))))	UAUUGGCGAUCCAAAACUCGACACUUUAUUUAAUCAAUUAACCGCCGAACAUAAACACUGAUUACAGAGGUAAAAAUGAAAACCAAAGUUGCUGCUAUUUAUGGCAAGCGGGAUGUCCGUCUGCGCGUAUUUGAACUGCCAGAAAUUACC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0294603	0.9238006	yggP	2847686	putative Zn-binding dehydrogenase

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

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching