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: https://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
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
lmo0143	-75	-5	-71	-65	11.9	LhrA2	92	157	147	153	12.35	-13.99	-38.24	-1.31915	AUGAAUGAUGAUUAUGGUAUUGAAAAAUGUUUGAGUAAAAUGACAGCACUUUUGUCUAGGGAUGAGGAUAC&GUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGU	(((((((((((((.((((..((((..((((((((.((........((..((((((...((((.((((((((&)))))).)))))).))))))..))...)).))))))))...))))...)))).)))))))))))))	AUGAAUGAUGAUUAUGGUAUUGAAAAAUGUUUGAGUAAAAUGACAGCACUUUUGUCUAGGGAUGAGGAUACCACAAUGAAAUAUUUAGAAAAUUGCGAUGCGGAUAAUUUAUAUUGGAUAAGUGAAAUCUUUGAAGAUAUUUCUGCCAAU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0259491	0.9474659		986794	lmo0143
lmo2251	-12	5	-8	-2	4.27	LhrA2	149	165	155	161	1.57	-13.92	-19.76	-1.31255	GAAUGAGAACAAGUGAU&AUUAUUUGUUUUCAUUC	(((((((((((((((((&)))))))))))))))))	CAUCGUUAAUUUACUUUGUACUAACAUUUAGCCUGUCGAGACUACUAGGUGUUGCUGAAAGGAGAAUGAGAACAAGUGAUUAAUAUUAAAAAUUUACACAAACAUUUUGGCAAAUUAGAAGUCUUAAAAGGUAUUGACCUUGAAAUCGCA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0268942	0.9474659		984693	amino acid ABC transporter ATP-binding protein
lmo1798	21	65	21	27	3.39	LhrA2	129	169	163	169	6.56	-13.42	-23.37	-1.2654	AGAUGAACUUGAAAAUAAAAUUAUUGAUCAAUUGACAGAAGCAGA&UCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCU	(((((((..((((((((((..((.((((..........(((((((&)))))))..........)))).)))))))))))))))))))	AUAGAGCCACAAUACAACGAUUCCCUGUCGCUAAGAAAAUUUAGCGGCAGGGAAAUUAUAAAAGGAGUGGUACAUAUGCCUUGGAGAGGUAUAUUAGAUGAACUUGAAAAUAAAAUUAUUGAUCAAUUGACAGAAGCAGAAGAGCACGCC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.034623	0.9493467		985932
lmo2308	-14	7	1	7	2.95	LhrA2	147	170	147	153	1.67	-16.63	-21.25	-1.56808	GAGAGGGAAGACGAAUGAUGA&UCAUUAUUUGUUUUCAUUCAUCUC	((((..(((((((((((((((&))))))))))))))).....))))	ACCAGAUGCACAUAUAAAAUUAAUUGAAGAUGAAAAUUUGCUUGAUUGCGAAUUGAUGAAAGAGAGGGAAGACGAAUGAUGAAUCGUGUAGUACUUGUAGGACGAUUAACAAAAGAUCCGGAUUUACGUUACACUCCAGCAGGCGUAGCA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0062544	0.863511		984487	single-stranded DNA-binding protein
lmo1717	-6	17	11	17	3.74	LhrA2	147	170	147	153	1.67	-15.35	-20.76	-1.44738	GAGACGAUGAAAAUGGAUAGUGA&UCAUUAUUUGUUUUCAUUCAUCUC	((((.((((((((((((((((((&)))))))))))))))).)).))))	AUAUUACACUUAGCUAAAUGGAAUGUUCUUCCAUUUAAAAAUAAAUGUGAAUAAUAAUACAUAAAGUAGGAGACGAUGAAAAUGGAUAGUGAAACACUAUUAUUAGAUGUAAAGAAAUUAGGAGAAAGAGUAUCUACGCUUAAGGAUUCG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0126946	0.8870739		985593
lmo0850	-49	-18	-35	-29	3.09	LhrA2	148	170	159	165	1.67	-14.84	-19.6	-1.39929	GAGAAAAAUAAAAAGAAUGAAAACAAAUUUUG&CAUUAUUUGUUUUCAUUCAUCUC	((((..........((((((((((((((..((&))..)))))))))))))).))))	AGAGAAUAUGUUAAAGUAAGGAAAGAGAGAAAAAUAAAAAGAAUGAAAACAAAUUUUGAAGAUGGAGUGAUGAGAUUGGAUAAUAAUCAAAAAGACUUAAAUCAAGUAAUCCGUCAGCUCAAAGAAAAAGGAAUUGUCGUUGAAAAAACA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0166718	0.9082262		985319
lmo1631	-59	-38	-51	-45	4.57	LhrA2	148	170	155	161	1.67	-13.79	-20.03	-1.30029	GAAUGACGGAAAACAAAUGAUG&CAUUAUUUGUUUUCAUUCAUCUC	((((((..((((((((((((((&))))))))))))))..)))).))	CUGAAUCAAUUGGUACGAAUGACGGAAAACAAAUGAUGGAAAACUUUAUUCAUAUAGUGGAAGGGGCGCGAGAAAAUGGAAAUCUUACUACAAAAAGUAUAUGACCAAGAAAAUUUAUCCAAAGAAGAAAUGAAUAUUAUCGCAACAGAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0287341	0.9493467	trpD	985706	anthranilate phosphoribosyltransferase
lmo1109	-23	11	5	11	4.04	LhrA2	141	172	141	147	2.36	-13.88	-20.28	-1.30877	AUGAGUGAAAGGAGAAACAACACAUGAAUUUUGG&CCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAU	(((((((((..(((((.(((...(((.(((((((&))))))))))...)))))))).)))).)))))	CUCUCAACUGAUAGAACGUGUUGAGAGGUAUUUUAUUAACCGCAAGAAAUACAUGAGUGAAAGGAGAAACAACACAUGAAUUUUGGACAAAACUUAUACAACUGGUUUUUGAGUAACGCACAAUCCCUUGUCUUACUGGCAAUCGUAGUC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0274484	0.9474659		986220
lmo1883	-5	28	1	7	4.58	LhrA2	139	173	161	167	3.22	-25.95	-33.75	-2.44688	AGUAGAUGAAUGGAAAACAAGUAAUGGUUGGUG&CACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUU	((((((((((((.((((((((((((((((((((&))))..))))))))))))))))))))))))).)))	UUUCACUAUGUUGGGUAUUUUCUAGUAGCUCCAAAAAAGUAAGUUUGGGGUAGAUAAAGUAAGGGGGAAAAGUAGAUGAAUGGAAAACAAGUAAUGGUUGGUGGUUUGUCUUUACUUUUAGUUGGUGCGGGACUGGGGGCAUUUGGCAGU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	9.7e-06	0.0277905		986008	chitinase

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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