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
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
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
lmo0181	-54	-34	-50	-44	5.65	LhrA2	158	179	168	174	2.11	-15.02	-22.78	-1.41627	AUGGCAAUGAGCGGAAUGAAA&UUUCAUUCAUCUCAUUGGCCGU	(((((((((((..((((((((&))))))))..))))))).))))	CAAAAAUAUUUCAUCCAAGGAAUGGCAAUGAGCGGAAUGAAAGAAUAAAAAACCAACAAAAAAGGAGUGUUACAAAUGAAAAAAGGUUUAUUAUUGUUAAUGGUAGUUGUACUGUCUGUAUUUGGUCUUUCGGCUUGCGGCGGUGGCAGU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0151521	0.9011628		986977	sugar ABC transporter substrate-binding protein
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
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
lmo1481	1	24	10	16	4.01	LhrA2	151	181	159	165	3.36	-15.05	-22.42	-1.4191	AUGCUGCCAGAAUGGAAACAGAUA&UAUUUGUUUUCAUUCAUCUCAUUGGCCGUGU	((((.(((((((((((((((((((&))))))))))))))).......)))).))))	UGAAAUAAAACUUGCUAUCUCUUAUUUCAUGUUUUACCAUAGAAAGAGAAAUAAGAGUGAAGCGAGGCGAAAUGAAUGCUGCCAGAAUGGAAACAGAUACGCUCCAAAAAAAUAACGCCGGUGUAUUUAAUCAUCGGUACAGAAGAUUAU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0149116	0.9011628	holA	986943	DNA polymerase III subunit delta
lmo0649	-9	5	-9	-3	2.94	LhrA2	190	204	198	204	4.18	-14.7	-21.82	-1.38609	GGGAUGAGCAUGGA&UCUAUGCCUCAUCCC	((((((((((((((&)))))).))))))))	AUUAAUUACAACGGGAGUAACCGUGAUUUUUUGGCGUAGAAAAUACUUUUAAUAUAUAGAAAACGAGGGAUGAGCAUGGAAAAACAAACAUACGAAAAAUUAGCAUAUUAUACAAUCAAAGAAAAAAUUCUCAGUGGAAAGCUUCAUGUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0179502	0.9128702		986557	transcriptional regulator
lmo2074	-69	-43	-58	-52	1.85	LhrA2	147	173	155	161	1.7	-18.23	-21.78	-1.71894	AAUGGAAGAAUGGGAACAAAUAAGCGA&UCAUUAUUUGUUUUCAUUCAUCUCAUU	((((((.((((((((((((((((..((&)).)))))))))))))))).)).))))	GAAAUUAAUGGAAGAAUGGGAACAAAUAAGCGAAGAACUGGAAUCCAUAUAAUCUACAUAAAAAAGGAGCAAACAAUGAAAAAGAUUUUAAUUAUUUCUAGUUCGAUUAUCGUUGGUUUACUUGUUAUUAUUACCAUUUGUGCUAGUUUU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0024551	0.863511		987923
lmo0444	5	27	7	13	5.55	LhrA2	157	181	173	179	2.24	-13.98	-21.77	-1.3182	AUAUGGUCAAAAAUGAGUGGAAA&UUUUCAUUCAUCUCAUUGGCCGUGU	((((((((((..(((((((((((&)))))))))))....))))))))))	UCUGGAAUCUAUAUACUUGAAUUUGUAAGUAAGAGAUAAAGUAUAGCUCAAGAAACUGAAGGAGGAAAUAUGAGUAUGAAUAUGGUCAAAAAUGAGUGGAAAAAACUAUUUCAUAAUAAGGUACUAUUAAUAUCUUUUAUCGCAAUUCUU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0260822	0.9474659		985173

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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