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
lmo0057	-22	7	-2	5	4.24	LhrA2	157	181	159	165	2.24	-16.2	-22.68	-1.52753	ACACAGCGGGAGUGGGACAUGAAUGAAGA&UUUUCAUUCAUCUCAUUGGCCGUGU	((((.((...(((((((..((((((((((&))))))))))))))))).)).))))	GCUUUUUCUAAACAUAGAAAGCUUAUGCCUAAAAAGGUAUUUAUAUAAAAAAGACACAGCGGGAGUGGGACAUGAAUGAAGAAAGUAAAAUGGAGUAUUUUACUCUUUUUAGUCUUGGCGAUUUUUCUUUCGGCAGGAAUUACUUAUUUG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0079642	0.863511		986071
lmo2768	30	51	41	47	4.37	LhrA2	161	179	165	171	2.1	-16.16	-22.63	-1.52376	AUGGCGUAAUAUGAGAUGGAUG&CAUUCAUCUCAUUGGCCGU	(((((.....((((((((((((&))))))))))))..)))))	UUUCACGGUGCAUUUAGCAAAUGAUAAAAUAGAUUAUUACGAGAUUUAAAACAGACGGGAGGGACAAGGCUAAUAAUGUUUAAUCGAGGGUUAUGGUACCGGGAAUGGCGUAAUAUGAGAUGGAUGCUUUUGGGUGUUGUGAUACUAUUU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0081436	0.863511		986273	hypothetical membrane protein
lmo1828	11	21	14	20	0.66	LhrA2	201	211	202	208	2.18	-16.11	-18.95	-1.51905	GCAUGACGGGA&UCCCGUUAUGC	(((((((((((&)))))))))))	UGGUAUAAUAAGAAGUCAGAACAAAUUUCAAGUAAUCUUAGAGGGAACUUUAAGUUAUGAAAGGUGUCUUGCCAAAUGGUGAAAAGCAUGACGGGAUUUGGGCGUGCCACAAAAGAAUUUGAAGCGUUCAAAGUAACCAUUGAAUUAAAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0083732	0.863511		985886
lmo0197	-23	48	42	48	12.01	LhrA2	99	173	99	105	12.2	-16.05	-40.26	-1.51339	AAUGGGAUAAGGAGUGACUAAUAAUGCAAGUAACAGAUGUGAGAUUACGUCGUGUAGAAACUGAUGGAAGA&UCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUU	((((((((...((((((..(((((((.....(((((((((..(((((.(((((.......((..(((((((&)))))))..)).)))))...)))))..))))))))).............))))))).....))))))))))))))	AUAAAUACCUAAGAUUUUAGCUGGGAUAAGCAGAUUCUUUUUGAAAGAGGCAAAUGGGAUAAGGAGUGACUAAUAAUGCAAGUAACAGAUGUGAGAUUACGUCGUGUAGAAACUGAUGGAAGAAUGAGAGCGAUUGCUUCAAUCACUUUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0086566	0.863511		987024	regulatory protein SpoVG
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
lmo0482	44	69	61	67	3.37	LhrA2	172	210	174	180	7.54	-15.99	-26.9	-1.50773	CAGAAUGGCUAGAGGCACACGGUCAA&UUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUG	((.(((((...(((((((((((((((&)))))))))).............)))))...))))).))	AAUAGCAUUGCUUGUGAACCAUAAAACAGCUAUAAUCUUUAUAGACGAAAACAAGACCUGAAAAGAGGCUGAACAAUGGAAAAAAGCUCCAUUUAUGGAUUAACAUGGACAAAUUUAACAGAAUGGCUAGAGGCACACGGUCAAAAGAAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.008949	0.863511		986229	ribosomal RNA large subunit methyltransferase N
lmo1203	-27	-2	-9	-3	5.56	LhrA2	155	181	156	162	2.25	-15.88	-23.69	-1.49736	ACACUGCAAUAGAGAGGGUGAAAACA&UGUUUUCAUUCAUCUCAUUGGCCGUGU	((((.(((((.(((((((((((((((&))))))))))).))))))).)).))))	GUCUAGGCGAAAAUCCACUUAUCCAAUCCCAAUUUAUCGACCAUAUCCACACUGCAAUAGAGAGGGUGAAAACACGUGGCUAAAUUUUACGGCAUUGGUACAGGUCCCGGAGAUAGCAAGUUAGUCACGAUGGAAGCAGCAGAAAGACUC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0095091	0.863511	cbiL	986075	cobalt-precorrin-2 C(20)-methyltransferase
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
lmo1952	-9	31	25	31	10.06	LhrA2	161	204	161	167	7.05	-15.84	-32.95	-1.49359	GGGAUUGGCGUGACGUUUGAACGGCUUGGAACAAUGAAUG&CAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCC	(((((.((((((((((....(((((...((...(((((((&))))))).))....))))).......))))).)))))..)))))	AUUGUCGCUCGGCUUCUUAGUAUGCUACUAUAUAAAAGAACUUUUAAAAAUCUAUAAUGUAAAGGUGGGAUUGGCGUGACGUUUGAACGGCUUGGAACAAUGAAUGUAAAUGCAGAAGGACAUCUCGAAAUUGGAGGGGUGGACACUUUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0097207	0.863511	lysA	987983	diaminopimelate decarboxylase
lmo2486	-27	32	26	32	2.54	LhrA2	159	195	159	165	6.6	-15.82	-24.96	-1.4917	CAUAGAUAUAAGAAAGGAAGAGCUAACAUGGAAAAAAAAUUAAGAAGAUCAAGAGUGGA&UUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUG	(((((((((..........((((((.(((((..........((..((((...(((((((&)))))))))))..))..))))))))))))))))))))	UAAAAUAAUUAAACGAAAUCUAGCGCCGUGCAAGCGCGCUAGAUUUUACAUAGAUAUAAGAAAGGAAGAGCUAACAUGGAAAAAAAAUUAAGAAGAUCAAGAGUGGACCGGAAAGUCGGCGGUGUGUUUGGUGGACUAGCUGAGUUUCUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0098281	0.863511		987324	lmo2486

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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