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
lmo1941	23	69	23	29	9.14	LhrA2	156	207	201	207	7.27	-15.29	-31.7	-1.44173	AACGGGAAUACGAAGAACCGGCUGAUUAUGACAUGAGUUCUGAAGGC&GUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUU	((((((((((.(((..((((((((((...((.((((((...((((((&)))))))))))).)))))))))).))..))).)))..........)))))))	AUCAUAUGUAACACUUCUCUGUGCCAAUAAUAGUGCAUAGGAUAAGUUUAGAAAGCACUAAAGGAGGAACUUUGAGUGGUAAAAACAAGAAAAGAAAAACGGGAAUACGAAGAACCGGCUGAUUAUGACAUGAGUUCUGAAGGCCAAGAU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0131118	0.8878302	987990
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
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
lmo2121	32	72	64	70	3.08	LhrA2	153	189	155	161	4.89	-14.83	-22.8	-1.39835	CAUGGACAUUACGGACAACCAAACUAGAUAAAGAAAAUAAA&UUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUG	(((((((...((((....((((...((((.(((((((((((&))))))))).)).))))..))))))))...)))))))	ACAUUUUUGAAAACAAGAUUUUAUAAGACUAGUGAAAAAAGUAUGGCUGCUAGUCGCUAAUUAGGAGGUUUUAGUAUGGCACAGAAGCAAUUAUUUGAAAUCGAACCAUGGACAUUACGGACAACCAAACUAGAUAAAGAAAAUAAACGU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0167603	0.9082262	987891	maltose phosphorylase
lmo1018	51	72	51	57	0.58	LhrA2	158	181	175	181	2.23	-13.69	-16.5	-1.29086	AUAUGGCGCAAAUAGAAUGGAA&UUUCAUUCAUCUCAUUGGCCGUGU	(((((((.(((...((((((((&))))))))......))))))))))	UGGAUUUUUUUGUAUUCAAGCACGCCUUAAAAGGGUAAAAUGAAGGUAAUUAGUUAUUAAAAGGAGCGGAAUAAUAUGUUAGAAGUGAUAGUUCAAAAUCCAAGAGACGCUUACUUAGCGGAAAAAUAUGGCGCAAAUAGAAUGGAAGUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0302275	0.9493467	986357	copper homeostasis protein CutC
lmo0233	38	73	63	69	6.72	LhrA2	157	198	161	167	6.87	-16.51	-30.1	-1.55676	AGGCAUGUGGAUAUGAAUCGGCAAAAUGGAUGGGAA&UUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCU	(((((..((((((((((.((((...(((((((((((&))))))))))).......)))).....)))))))))))))))	CGAAUUUGAUGAAAAGGGUUAACGCGAACAGAUGAUCUGUGGUAAAAUGGAGCAUAUGUAUGGAGGGAUGUAUAAAUGGCUAAAGCAAAAAGGACAACCAAAUUUGUGUGUCAGGCAUGUGGAUAUGAAUCGGCAAAAUGGAUGGGAAAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0066934	0.863511	987204	DNA repair protein RadA
lmo0142a	37	73	41	47	3.57	LhrA2	119	157	147	153	6.71	-14.8	-25.08	-1.39552	AUGAAUGAUGAUUAUGGUAUUGAAAAAUGUUUGAGUA&UAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGU	(((((((((((((.((((..((((..((((((((.((&)).))))))))...))))...)))).)))))))))))))	UGAUUCUUAUACUUACAUAGGUGAUAAAAAAUAGGUAUAUAAAGGCGGGAAAAUACAAUAGACUUAAAAGAAAACAUGAAUAUUGUGCUGUCUGAAAGAAAAAAAUUACAUAUGAAUGAUGAUUAUGGUAUUGAAAAAUGUUUGAGUAAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0170282	0.9082262	16695797
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
lmo0926	56	74	63	69	1.72	LhrA2	155	175	159	165	1.62	-15.07	-18.41	-1.42098	CCAAGAUGAGUGAAAAGCA&UGUUUUCAUUCAUCUCAUUGG	((((((((((((((((.((&)))))))))))))))...)))	UCGUAUUUGUUAUAUUAAAUAUUUUUGCUUUGAAAAAAUACCGCAAAGUUUAAAUGAAACAGGAGGAGAUAAGACGUGGAUGCAGAAGGAGAUAUUAUCCGUCAAAUGCUUGAUUUAACGGAAAAAGAAACCAAGAUGAGUGAAAAGCAG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0147533	0.9011628	984510	TetR family transcriptional regulator
lmo1217	28	75	68	74	7.89	LhrA2	167	211	168	174	7.74	-13.51	-29.14	-1.27389	GCAUUAACAGAUGCAAAAGGUAUUCCCGGUAACGAACGUGCAGUGAGA&UCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGC	((((.(((.((((....((((((.......(((..(((..((((((((&))))))))..)))...))).......))))))))))..)))))))	UUUUUUGCGUUUUCAAAGGAUUUUUAUAAAGAAACUGUUAUAAUGAAAAAGGAGUUUAUAAGGAGGGUUAUUAAUAUGGAUGAACAAUUAAAGAUGUUAAAAGCAUUAACAGAUGCAAAAGGUAUUCCCGGUAACGAACGUGCAGUGAGA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0330966	0.9493467	986057	endo-14-beta-glucanase and to aminopeptidase

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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