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
lmo0788	-23	-4	-11	-5	4.93	LhrA2	197	212	198	204	3.03	-14.54	-22.5	-1.37101	UGCGUAACGAAAGGGAUGAG&CUCAUCCCGUUAUGCA	((((((((....((((((((&))))))))))))))))	AAGCGAAGUACAAUUAACGGAUGAUAUGUGAAAUCAUAUACAUAUUAAGUAGUGCGUAACGAAAGGGAUGAGAAAAUGAUUCAUGCAGGAUUAGAUGUAGGAUCAACAACAGCAAAGGCCGUAGCACUUAAUGACCAGGGGGAUAUUUUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0195222	0.9163749		985448	lmo0788
lmo0661	46	71	65	71	6.26	LhrA2	156	186	156	162	3.01	-14.51	-23.78	-1.36818	GAAGUACACUCUGCCUGGAUGGAAAC&GUUUUCAUUCAUCUCAUUGGCCGUGUAGUUC	(((.(((((...((((((((((((((&))))))))))).......))).))))).)))	AGAAAAUAGAUAAUACGAAAACCGCCCAGUGUUUGGGCGGUUUUUUAUUAUAAUAAAAGUUAGGAGAUGAGUUCAAUGAAAGUAAGCAAAUCAUUUGAAGUAUUCGCGAAAGAAGCUCCCGAAGUACACUCUGCCUGGAUGGAAACCGUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0198308	0.9163749		984999
lmo2654	-5	11	-2	5	0.62	LhrA2	167	184	175	181	2.5	-14.34	-17.46	-1.35215	ACAACAUGGCUAGAGA&UCUCAUUGGCCGUGUAGU	((.(((((((((((((&))))..))))))))).))	UCGUUGGUAAAAAAAUCACUGACAAAUUCCAGGCGUAUUGCCUGAAAAAUUGUUUUAUGGAAGGAGAAAUACAACAUGGCUAGAGAGUUCUCCUUAGAAAAGACUCGUAAUAUUGGUAUCAUGGCCCACAUUGAUGCGGGUAAAACUACC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0216662	0.9474659	fus	986619	elongation factor G
lmo0292	3	49	39	45	1.83	LhrA2	155	203	159	165	7.05	-14.32	-23.2	-1.35026	GGACGAGAAAGAAAAGAAUUUAAAUGAAAACAGCGAGAAUGAAAGCA&UGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCC	(((.(((..(((...(((((...(((........(((((((((((((&))))))))))).))........)))..)))))...)))....))).)))	UUUUCAUCGUUUUUUCAUAUUUGGGGUUUAUUAUGGAAGUAUAUAAAUGCGAAAUUUGCAGAGAGGAAGGAAGACAUGGACGAGAAAGAAAAGAAUUUAAAUGAAAACAGCGAGAAUGAAAGCACGCCGAAAAGAGAGGUCGAGGAUACU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0218921	0.9474659		987455	heat-shock protein htrA serine protease
lmo0066	-22	6	-3	4	8.22	LhrA2	158	199	160	166	6.89	-14.3	-29.41	-1.34838	GAGGUAUAAGGAGGCCAGAUGAAUGAAA&UUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUC	((((((((....((((((((((((((((&)))))))))))....)))))..............))))))))	AAACCAUGGUUGAUGCAGACAGAGAUAUUGCUGAAAAAAUUAUCGCAGCUUUAGAGGUAUAAGGAGGCCAGAUGAAUGAAAGAAGUCAACUACCGAGAAGACGACUGGCGUGAAGCCAAAAGUGCCCUCGCUCCAUUUGCCGCAGCGAAU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0221203	0.9474659		986392	toxin
lmo2106	-29	22	-29	-23	8.45	LhrA2	159	207	201	207	7.26	-14.28	-29.99	-1.34649	AAUGGGAACAGCAACAUAGAGGUGAAAAAAUGUCUUUAAAGAUGAAGUGGA&UUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUU	(((((((..((...((((((..((((.....(((.....(((((((.((((&)))))))))))....))).......))))..)))))).))..)))))))	AUAAUGAUAGGGAUAACGUUUAAAGGAUGACAAAAUAUUGAUAAUAAAUGGGAACAGCAACAUAGAGGUGAAAAAAUGUCUUUAAAGAUGAAGUGGAUUAUAGCGAUCAGUAUUAUCAUUGUACUUUUAGUCGUGGGGUGGUUUCUUGGG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0223506	0.9474659		984749
lmo2445	-67	-36	-44	-38	1.3	LhrA2	157	177	159	165	1.89	-14.24	-17.43	-1.34272	GGCUAUAUUGAAAGGAGUGGAAUGAAUGAAAA&UUUUCAUUCAUCUCAUUGGCC	(((((.........(((....(((((((((((&))))))))))))))..)))))	GAAAGGGUGGCUAUAUUGAAAGGAGUGGAAUGAAUGAAAAAAAUAAUUGGACUGACGUUUGUUGCUAUUUGUUGAAUUUUAUUUGCACCAACAAUCAAAGCACAAGCAGAUACAGUUCCGUUACCAGCGCCUAUUAUAGAGGCUUUCCCG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0228179	0.9474659		987394	internalin
lmo0200	-10	14	-10	-4	4.26	LhrA2	175	204	198	204	6.62	-14.21	-25.09	-1.33989	GGGAUGAGACAUGAACGCUCAAGC&GCCGUGUAGUUCAUGUCUAUGCCUCAUCCC	((((((((((((((((......((&))......)))))))))......)))))))	AACAAUUGUUGUUACUGCCUAAUGUUUUUAGGGUAUUUUAAAAAAGGGCGAUAAAAAACGAUUGGGGGAUGAGACAUGAACGCUCAAGCAGAAGAAUUCAAAAAAUAUUUAGAAACUAACGGGAUAAAACCAAAACAAUUUCAUAAAAAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0231743	0.9474659	prfA	987031	listeriolysin positive regulatory protein
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

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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