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
lmo0129	-14	15	-14	-8	2.87	LhrA2	176	203	197	203	6.34	-16.42	-25.63	-1.54828	GGAUGAGGAAAAACAUGACAAAGAUAUGG&CCGUGUAGUUCAUGUCUAUGCCUCAUCC	((((((((....((((((.....((((((&))))))...)))))).....))))))))	GAAUGAAGGUCCCGGAAGUAUUGAAAAAUUUAAUUUUGAUUUUCGAUGCAAAGUCAGGAGAGGAUGAGGAAAAACAUGACAAAGAUAUGGAUUGACGCUGGACACGGUGGUAAGGAUUCAGGUGCGAGUGGUAAUGGACUUGUUGAAAAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0070414	0.863511		986713	N-acetylmuramoyl-L-alanine amidase
lmo2446	-22	16	-3	4	6.66	LhrA2	154	187	164	170	3.16	-17.3	-27.12	-1.63125	UGAAUUAAGGGAGGAAAGUGAGAUGAAGCGAAGAACGA&UUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCA	(((((((.....((..(((((((((((....(((((((&)))))))..)))))))))))..))...)))))))	UAAUAAUUUUGCAAAAUAACACAUCGAAAGUAGUAUAUUUUUAGUAAAAAAGGUGAAUUAAGGGAGGAAAGUGAGAUGAAGCGAAGAACGAGAAAAUGCAGUUUGGUUUUUAUUCUGGGGAUAUUAAUUUUUAGUUGUUUAAGUGGAUUU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0042577	0.863511		987393	glycosidase
lmo1689	-16	16	-1	6	7.38	LhrA2	157	186	167	173	3	-15.11	-25.49	-1.42475	GAAUUACGAGGGGAAAAUGAGAAAAAUGAAGA&UUUUCAUUCAUCUCAUUGGCCGUGUAGUUC	(((((((....((..(((((((..((((((((&))))))))..)))))))..))..)))))))	UUUAUUCCCUGUCUACAUUAUACUACACAUCCGGAGCAACACACAUUAGAAAUCUAUUAGAAUUACGAGGGGAAAAUGAGAAAAAUGAAGAGACUAACUUGGGAUGAAACAAAGAUAACUGCUUUUCAAGAAGCACUCGUUUCCUGGUAU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0144414	0.9011628		985627	A/G-specific adenine glycosylase
lmo2566	-22	16	-3	4	7.18	LhrA2	155	186	164	170	3.01	-14.16	-24.35	-1.33518	GAAAAUCAUGGAGGACAUAGAGAUGAAUAUAGAAAACA&UGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUC	(((...(((((....((..(((((((((...(((((((&))))))))))))))))..)).)))))...)))	AUUUUAAGCCAUUUGUAUCUAAUUUUGCUGUCGGUAUGCUAUAAUAACAAAAAGAAAAUCAUGGAGGACAUAGAGAUGAAUAUAGAAAACACCUUACUAAAACAAGAUGUGUGGCGUUUUAUUGAUAAUACAACGAUUAAUCCAGCUUUC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0237797	0.9474659		984810	lmo2566
lmo1454	-29	16	10	16	7.93	LhrA2	154	211	154	160	7.93	-14.13	-29.99	-1.33235	GCAUUUUGGAAGGAGGAAUACAGGCAGUUAUGAGUGAUAAAACAA&UUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGC	((((...(((..((((..(((((((....((((((((.(((((((&)))))))...))).)))))..))).)))).............)))).)))....))))	AAUGAUGGUAUUAUUACCUAAGAGAAGCCUUUUAAUAAGGUUAGCGGCAUUUUGGAAGGAGGAAUACAGGCAGUUAUGAGUGAUAAAACAAAAAACACAAAACCAGUUGCUGAACUAAGUGUUGAGCAAGUAAAAGAAGCCCUGAUAGAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.02415	0.9474659	rpoD	984456	RNA polymerase sigma factor RpoD
lmo1278	-16	16	4	10	5.6	LhrA2	173	203	180	186	6.78	-13.95	-26.33	-1.31537	GGAGGAGGUUAAAGAAAUGGAAUUACACGCUA&UGGCCGUGUAGUUCAUGUCUAUGCCUCAUCC	(((.((((....(((....(((((((((((((&)))).)))))))))...)))...)))).)))	UGUAACAAAAGAGCAUUUAAAGUCUACUUAUAUGAAACAUCAUCCGAGGGCUUAAAUUUGGAGGAGGUUAAAGAAAUGGAAUUACACGCUACAACGAUAUUUGCUGUUCAACAUGACGGAAAAGCGGCGAUGGCUGGUGACGGUCAAGUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0264853	0.9474659	clpQ	985099	ATP-dependent protease peptidase subunit
lmo1717	-6	17	11	17	3.74	LhrA2	147	170	147	153	1.67	-15.35	-20.76	-1.44738	GAGACGAUGAAAAUGGAUAGUGA&UCAUUAUUUGUUUUCAUUCAUCUC	((((.((((((((((((((((((&)))))))))))))))).)).))))	AUAUUACACUUAGCUAAAUGGAAUGUUCUUCCAUUUAAAAAUAAAUGUGAAUAAUAAUACAUAAAGUAGGAGACGAUGAAAAUGGAUAGUGAAACACUAUUAUUAGAUGUAAAGAAAUUAGGAGAAAGAGUAUCUACGCUUAAGGAUUCG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0126946	0.8870739		985593
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
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
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

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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