Input and runtime details for job 4627738 (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_003210
	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 4627738 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:20:43 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:22:37 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:24:00 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:24:55 CET 2020
	Job Completed		@ Mon Jan 27 14:25:04 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4627738&toolName=IntaRNA ( 30 days expiry )

Description of the job

LhrA2 - Listeria monocytogenes

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_003210 Listeria monocytogenes EGD-e

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
lmo0390	-50	-8	-26	-20	7.87	LhrA2	167	211	180	186	7.74	-13.46	-29.07	-1.26917	GUAUAAUGGAAGGACAAAAUCAUGGAACUACUGAGACGGGAGA&UCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGC	(((((((((.(((.((....(((.(((((((....((((((((&)))).....))))))))))))))....)))))....)))))))))	UUUUGACAGUUGCUUGAGGUGAAAAGUAUAAUGGAAGGACAAAAUCAUGGAACUACUGAGACGGGAGAAUUAAAAAUGGUAAAAACAUGGGAAGAAUUUUUAAAACAAGAAGCAAAACAGCCUUAUUUUAUAGAAUUAAUGGAAGCAGUC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0339368	0.9493467		987648	uracil-DNA glycosylase
lmo2282	-21	35	-1	6	10.94	LhrA2	157	205	183	189	7.12	-15.26	-33.32	-1.4389	CGGGAACUAGGAGGAGUAAACAUGAACUAUAAACAGUUUUACACAUAUGAUGAAAA&UUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCG	(((((.....((((..((.((((((((((((..((((.........((((((((((&)))))).))))...))))....)))))))))))).))..)))).)))))	AACGGAUAAUGCUAAUCCUAGCUAUAUAAGUCUUUCUGGUAUUAGCUAUGAAGUCGGGAACUAGGAGGAGUAAACAUGAACUAUAAACAGUUUUACACAUAUGAUGAAAAUGGCGAUUAUCUCGAAACAAUACUUGUGUUUGAAGAUGAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0133252	0.8878302		984600	protein gp21
lmo1246	-20	5	-3	4	2.75	LhrA2	184	206	185	191	5.47	-13.51	-21.73	-1.27389	AUGAGGAAAUGAGGACUGACAUGAA&UUCAUGUCUAUGCCUCAUCCCGU	(((.(((..(((((...((((((((&))))))))....)))))))))))	GGAUAAAGUACAAACAAUUCGUUCCAUCAUUUGUGAAAAAAUAUGGUAUGAUGAUAUGAGGAAAUGAGGACUGACAUGAAUAAUUUAAAAUUAAGUGAAGAAAUUAAAAGAGCGAUUAAUGAACUAGGAUAUACAGAAGCAACACCUGUU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0330966	0.9493467		986011	ATP-dependent RNA helicase
lmo2765	-13	18	-4	3	4.17	LhrA2	155	199	186	192	6.93	-15.86	-26.96	-1.49547	GAGGAAAAUAGACAUGAAUGAAAUGGAAACA&UGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUC	((((...((((((((((((((((((((((((&))))))))))....))))............)))))))))).))))	UUGAAACAGCAACACAUAAAAACCAAGCUGGCCUACUCGGCGCAGUGUAUCACUUUUUACAGGAGGAAAAUAGACAUGAAUGAAAUGGAAACAGUUAUUUUUGGCAUGAUUAGCCAAGUUGGUUCUGCGAGAAGCAGUUACUUAGAAGGA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0096143	0.863511		984518	PTS cellbiose transporter subunit IIA
lmo0184	-42	10	-33	-27	5	LhrA2	158	203	188	194	7.03	-14.64	-26.67	-1.38044	GGAGAAAAAAUAGACAAAAUUACAAGGGCGGGAAUUUAAUCGAUGAAAGAAA&UUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCC	(((......(((((((.(((((((.((....((........((((((.((((&)))).)))))))).....)).)))))))..)))))))......)))	UUGCAGCAAAAAGUAACUACUAUACAAGUGUUUGGAGAAAAAAUAGACAAAAUUACAAGGGCGGGAAUUUAAUCGAUGAAAGAAAAAGAUUGGUGGAAAAAAAGCGUAGUGUACCAAAUCUAUCCAAAGAGUUUUAAUGAUUCGAAUGGU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0185255	0.9128702		987008	oligo-16-glucosidase
lmo1767	11	63	28	34	14.05	LhrA2	158	213	191	197	8.5	-13.96	-36.51	-1.31632	AUGCAUAUAGUAAAGCAGGCGUGGACGUAGAAGCUGGCUAUCAAGUAGUGGAA&UUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAU	(((((((.........((((((((((((.(((.(((((((...((.(((((((&)))))))...))...)))))....)))))))))))))))))........)))))))	ACCCCUUUAUACGAUUAUGAAGCGGAAUAUUUAGCGAGCUUAGAAGCAGAAAAAUAAUGAGGAGUGACAAAUCGAAUGGCAGAAAAUGCAUAUAGUAAAGCAGGCGUGGACGUAGAAGCUGGCUAUCAAGUAGUGGAACGCAUCAAAAAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0263503	0.9474659	purM	985975	phosphoribosylaminoimidazole synthetase
lmo2314	-15	17	-10	-4	5.96	LhrA2	171	207	192	198	7.1	-14.04	-27.1	-1.32386	AGCGGAGGCGUAAAUAUGGAAUUAUAUGCAAU&AUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUU	((((((((((((.((((.((((((((((((((&))))..)))))))))))))).)))))))....)))))	GGAAAUUAAAGGCAUACCUGGAGGCGAAAUAUAUUGGCAGUUUGCUGUUCUUGUUGAGGAAGCGGAGGCGUAAAUAUGGAAUUAUAUGCAAUAGUUGACGAGGAUUUACAGGUUGCUAAACAUCGUAGUAAAGGAACUCUAGCAGUGUUU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0252928	0.9474659		984495	lmo2314
lmo2146	-8	30	7	13	8.39	LhrA2	172	211	193	199	7.72	-13.99	-30.1	-1.31915	GUGUUACGAUGGAUGAGGCAUUAAGAACAUAUAUCCGA&UUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGC	((((.(((..(((((((((((...((((.((((.((((&))))...))))))))......)))))))))))))).))))	UUACCAUUCCUGAUUUUAUUAGUAAAAUUUAUAUUAAUUAUAUUAUUGAUAAGUUAUUUUUAUGGAGGUGUUACGAUGGAUGAGGCAUUAAGAACAUAUAUCCGAGUAGUAGAAUUGCAAAGUUUUACAAAAGCAGCUGAAGAAUUACAC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0259491	0.9474659		984701	LysR family transcriptional regulator
lmo0851	-12	20	-12	-6	4.34	LhrA2	172	200	194	200	6.62	-17.88	-28.84	-1.68594	UGAGGCAUAUACAUGAAAAAAGAAGCGGUUAA&UUGGCCGUGUAGUUCAUGUCUAUGCCUCA	(((((((((.(((((((........(((((((&))))))).....))))))).)))))))))	UUACGCAAAAAUGUUGUAUGAUGGAGUGGAAGGCUUUUGUCAUAGAAGAAAAUAGAAAUAGAGUGAGGCAUAUACAUGAAAAAAGAAGCGGUUAACCAACAAUCUAUUUAUGUGCAUAUUGAUCAUGUUAUUAAUAAUGUGGCGACAAGC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0030274	0.863511		985315	lmo0851
lmo0551	-68	-3	-65	-59	5.24	LhrA2	154	204	196	202	7.09	-15.63	-27.96	-1.47378	GGAGGUGAGGGAAGAAAUUCGGUGAAACUGCACGAUAAAAAAAGGAUAUCAGAAAGAGGAGAAUAA&UUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCC	((.(((((((..(((.......((((.((((((..........((.....(((.....((((((((&)))))))).....)))......))))))))))))..)))...)))))))))	AUUUUAAGGAGGUGAGGGAAGAAAUUCGGUGAAACUGCACGAUAAAAAAAGGAUAUCAGAAAGAGGAGAAUAAUAAUGACAAGUAGAACAGUAAAGGUAACAACAGCGAGUUUAUUAGCAUUAGGAUUGAUUGUGGCACCAGUACUUUCU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0109054	0.863511		984417	lmo0551

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