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	geneID	annotation
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
lmo1709	21	41	34	40	4.42	LhrA2	163	181	164	170	2.15	-14.62	-21.19	-1.37855	ACGCGAAAUCGAUGAGAUGAA&UUCAUCUCAUUGGCCGUGU	(((((....((((((((((((&))))))))))))..)))))	UUCCAGAUUACUUUAUUUCUAAGGGGUUUCGAGCUAUAAUAGUAAAUAGUGGAAAUUUUAGGAGGGAAUGAAAAGAUGAUCACACUCAAAUCAAGACGCGAAAUCGAUGAGAUGAAAGCAGCAGGAAAAAUCCUUGCCGAUACGCAUAAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0187209	0.9128702	985602	methionine aminopeptidase
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
lmo0139	52	72	60	66	1.88	LhrA2	166	186	174	180	2.73	-16.03	-20.64	-1.5115	GAACAAUCCGCGGCCAAAGAU&AUCUCAUUGGCCGUGUAGUUC	((((....(((((((((((((&))))..)))))))))..))))	UUGAAAGAAUUAGGCGCAUCAUUUACUCGCAAAGACCAAGAGCUUGAACGGAGCAUGGGAUUGGGGGGUAAAUAAAUGGAUGCAAAGAGCCAGCAAGCGGAGGCGCAAUUGCAACUGCUGAAAAAAGAACAAUCCGCGGCCAAAGAUUUU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0087531	0.863511	986775	lmo0139
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
lmo2797	-16	53	47	53	11.21	LhrA2	153	209	153	159	8.55	-13.46	-33.22	-1.26917	AUAAGGGGGUACGGGCAUGUUAUUGGACCGAGUAACUUUAGAGGAUAUUGAGGUAAAUUUAAAAGCAGA&UUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAU	((((.(((((...((((......(((((.....((((.....((....((((((.(((...((((((((&)))))))).))).))))))....))....))))...)))))))))..))))).))))	UUGGAGCGAGAGUCGCUGGCGGAGGUAGAUUUAACAGAAAUAAUGGCUGAAUAUAAUAAAUAAGGGGGUACGGGCAUGUUAUUGGACCGAGUAACUUUAGAGGAUAUUGAGGUAAAUUUAAAAGCAGAAGACUGGCGGGAAGCUAUCCAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0339368	0.9493467	986733	PTS mannitol transporter subunit IIA
lmo0302	-15	26	14	20	4.67	LhrA2	167	204	176	182	6.87	-14.58	-26.12	-1.37478	GGAGAUGAAUAGAUGAUGAAAAAAACAGUACACGGAUGGGA&UCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCC	((.((((((((((..(((((........(((((((((((((&))))))...))))))).))))).)))))...)))))))	UUGGUUUGGAAUUUAAAGGUUACUAGGAUAUGAUGAUAGUUAGAGAGAAAAUAUUACAUAGGAGAUGAAUAGAUGAUGAAAAAAACAGUACACGGAUGGGAAAUAAUAUCUAGUUUAGACGUACGAGUAUACCAAGAUGAAGCUGGCGGG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0191177	0.9128702	987513	lmo0302
lmo0835	-20	29	-7	-1	6.44	LhrA2	146	186	173	179	7.37	-18.17	-31.98	-1.71329	GAACUUUGGAGGAAUGGUCAGUGAGUAAAAAUGUAAAAAAAAUAGUGAU&AUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUC	(((((........((((((((((((....((((.((((.((((((((((&)))))))))).))))))))...))))))))))))..)))))	UUGUAUCGCAUGUGCUUUUACCAGAUGAAUUAAAUGUACGUUGCAAAAUGUAUGAGAACUUUGGAGGAAUGGUCAGUGAGUAAAAAUGUAAAAAAAAUAGUGAUAACUCUCUUUGCAUUAAUAAUGACAGUAGGAUUAGCAAGUGGGUUC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0025454	0.863511	985352	peptidoglycan binding protein
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
lmo2793	-2	47	-2	5	12.63	LhrA2	115	174	168	174	7.79	-13.69	-34.11	-1.29086	CAGUGAGGUUUUUGAAGAUAAUUGGACAUGCAGUUGGUGUCAUUAGUUG&CAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUG	(((((((((...(((((((((......(((...((((((((((((((((&))))))))..............))))))))...)))...)))))))))...)))))))))	UUUCACCGAAGAAGAGACAGAUGAUUUUUAUCAAAUUACCAUUCAAAUUCCUAAAAAGAAAUAAGAGGUGUAGCAGUGAGGUUUUUGAAGAUAAUUGGACAUGCAGUUGGUGUCAUUAGUUGUUUGAUGGUACUUCCAUCUUUCGUAAUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0302275	0.9493467	985066	lmo2793

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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