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
lmo0131	-8	31	25	31	8.96	LhrA2	165	204	165	171	6.92	-15.78	-31.66	-1.48793	GGGAUAAGAUGGAUAUCUCGAGCACGGAAAUAUGGGAUG&CAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCC	(((((.((((((((((......(((((....((((((((&))))))))...)))))......))))))))..)).)))))	AAUGUAAUGAUAAAAUUUGGCUAUAUUUUCAUUUCGAUGGAAAAAAGGGUAAACUAGAGAAAAAGGAGGGAUAAGAUGGAUAUCUCGAGCACGGAAAUAUGGGAUGCGAUUAGGAGAAAUAGUUACUUACUUUAUUAUCAACCAAAAGUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0100463	0.863511		986722
lmo1875	-25	4	-14	-8	3.72	LhrA2	150	179	161	167	3.97	-15.67	-23.36	-1.47756	ACGAACAGGAAAUGGAUGGGAAUAAAUGA&UUAUUUGUUUUCAUUCAUCUCAUUGGCCGU	(((..((.((.((((((((((((((((((&)))))))))))))))))).))..))..)))	UAAUCUAAGGUAUUUGAUAUGUUCUAUGUUUUCCGCUAGAAUAGAUAAGGACGAACAGGAAAUGGAUGGGAAUAAAUGAAACAAUUAAAAGUGGAAAAUUUAACAAAAACAUAUGGUGAAAAAAGCCUGUUUGAAAAUAUCUCGCUAACG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0106699	0.863511		985821	ABC transporter ATP-binding protein
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
lmo1984	-14	29	22	28	5.18	LhrA2	157	201	158	164	6.99	-15.62	-27.79	-1.47284	AUGAGGUGAUAAGCGUGAUUGAUACGACGAAGACAAAUGAAAA&UUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAU	((((((..(((..(((((...(((((.((((((..((((((((&))))))))..)))..)))..)))))...)))))..))).))))))	UGUAACUAGCGCCCACACUGGUGGUAUUUUGCAAAUUCCAGAAGAUUUAAUCGACUAAAAAAUGAGGUGAUAAGCGUGAUUGAUACGACGAAGACAAAUGAAAAAGCGACAAAAAAGCAAAAUAAAAGUGGAGCGGAACUUUUAAUUGAC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0109651	0.863511	ilvB	984805	acetolactate synthase
lmo1258	24	74	54	60	7.74	LhrA2	157	207	176	182	7.27	-15.61	-30.62	-1.4719	AGCGACAGAUGGGCUAGAUUUACAUUUACAUAUAUGGGAUGAAGUUGAAAA&UUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUU	((((...(((((((((((....(((..((.(((((((((((((..((((((&)))))))))))).......)))))))))..))))))).))).)))).))))	AAUAAAAGGCAGUGAAAUAGUGAAAAUAACUACCAGAUGUUAUACUAAUAUUAAGAUGAAAUGGGAGGGAGACACAUGUACAAACAAAUGAAAUUAAAAGCGACAGAUGGGCUAGAUUUACAUUUACAUAUAUGGGAUGAAGUUGAAAAU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.011025	0.863511		985992	lmo1258
lmo0191	-75	-47	-58	-52	5.04	LhrA2	154	182	159	165	2.3	-15.56	-22.9	-1.46718	UAUAUGGUUAGACCAUGGAGUGAAGGCGA&UUGUUUUCAUUCAUCUCAUUGGCCGUGUA	((((((((((.......((((((((((((&)))))))))))).......))))))))))	UAUAUGGUUAGACCAUGGAGUGAAGGCGAGAACGAUACAAAUAUAAAUUAUUAAUGAAUGAGAGGGGUCAAAGAAAUGAAAAUUAUUUUUAAUGCAGAUGAUUUUGGGAUUAGCCCGGGAGCAGUUUAUGGUAUUUUAGAGUCGUAUAAG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0113293	0.863511		987017	phospho-beta-glucosidase
lmo1584	-2	11	-2	5	2.47	LhrA2	169	181	175	181	2	-15.55	-20.02	-1.46624	ACAUGGCUAAUGA&UCAUUGGCCGUGU	(((((((((((((&)))))))))))))	UUAAAUUAACUGGUACACUUAAAGCGCCAAGAAUGAUGUAUUUAUAUGGAGAAUAAUGUGAGAGGAGAGGCGCACAUGGCUAAUGAAAAUGUUACUUUUGAAAGUAAACGCCAAGUCUAUCAUUAUGAACCAUCUAUUCCGAAAGAAGAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0113911	0.863511		986942
lmo2299	37	63	56	62	6.01	LhrA2	155	181	156	162	2.25	-15.54	-23.8	-1.4653	AUGCGGAGAAUGGGACUAUUGAAAGCA&UGUUUUCAUUCAUCUCAUUGGCCGUGU	((((((..(((((((....((((((((&))))))))....)))))))..))))))	ACGUGUGAUGCUUUUCAGUACUAUGUAAAAGACAAUCUAAGGAAGUUAGGGCUCAAAUACUAGGGGGGGGAAACCUUGAUUAACCAAAUAAUCGCAAGCGUGAAAGGAGUGAUGCGGAGAAUGGGACUAUUGAAAGCACUGAAAGAUGUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0114532	0.863511		984584	portal protein
lmo0196	-2	56	47	53	14.05	LhrA2	156	208	159	165	7.39	-15.48	-36.92	-1.45964	UAAUGGAGAUUACAGAUGUGAGAUUACGACGUGUUGAGACAGAUGGGAGAAUGAAAGC&GUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUA	((((((.(((...((((((((.(((((.(((.(((((......(((((((((((((((&)))))))))).)))))))))))))))))))))))))).......)))))))))	UUUCUCGAGUGUGUACUUAAGUUGCAUGUGAGCAUUGUUUACUAGCAGCGCAACUAGAUUAAGGUGGUGAAGAUAAUGGAGAUUACAGAUGUGAGAUUACGACGUGUUGAGACAGAUGGGAGAAUGAAAGCUAUUUCUUCAAUAACGAUU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0118324	0.8692263		987023	regulatory protein SpoVG
lmo0205	-28	-2	-12	-6	5.2	LhrA2	160	186	164	170	2.96	-15.42	-23.58	-1.45398	GAACGAAAGAAAAAGUGAGGUGAAUGA&UCAUUCAUCUCAUUGGCCGUGUAGUUC	((((.........((((((((((((((&)))))))))))))).........))))	GGCGUUUAUCAAAAUUAUUCAAUUAAGAAAAAAUAAUUAAAAACACAGAACGAAAGAAAAAGUGAGGUGAAUGAUAUGAAAUUCAAAAAGGUGGUUCUAGGUAUGUGCUUGAUCGCAAGUGUUCUAGUCUUUCCGGUAACGAUAAAAGCA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0122233	0.8754939	plcB	987036	phospholipase C

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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