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
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
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
lmo0888	-1	37	28	34	15.9	LhrA2	174	211	176	182	7.72	-13.9	-37.52	-1.31066	GCUGAUGGUGAAGCGUGGUGACGUAUACUACGCGGACC&GGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGC	(((((((((((.((((((..((((..(((((((((.((&)))))))))))..)))))))))).)))..)))))).))	GCUAUCGCAUGCGAGUGUACCCAUGUCGAAGCAGAAGCAGAAGACAGGAAUAUUAGUAUUUUAGGAGGUUAAUGGCUGAUGGUGAAGCGUGGUGACGUAUACUACGCGGACCUUUCCCCCGUGGUCGGAAGCGAGCAAGGGGGAAUACGG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.02717	0.9474659		986538
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
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
lmo1724	-57	12	3	9	11.46	LhrA2	156	211	159	165	7.92	-13.58	-32.96	-1.28049	GCAUCGGUUUAGAUGACCAAGCAGCAAUAGAAUUACUAAUAAAAAGGAGCCGCAACCAUGAAUGAAAAC&GUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGC	(((((((....(((((....(((...((((((((((..........(((........((((((((((((&))))))))))))))).........))))))).)))...))).))))))))..))))	UUUUAGAAGAAGCGAAGAGCAUCGGUUUAGAUGACCAAGCAGCAAUAGAAUUACUAAUAAAAAGGAGCCGCAACCAUGAAUGAAAACCUGAUUACAAUUACGGGAUUAACGAAAAAAUAUCGAAAAAGAAAACCAUUAAAUGACAUUAAC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0319523	0.9493467		986662	ABC transporter ATP-binding protein
lmo2759	-28	4	-7	-1	2.74	LhrA2	141	173	146	152	2.37	-14.73	-19.84	-1.38892	AAUUAGAAUGAAGAAAAGAGGUGAUGGUAUGG&CCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUU	(((.(((.(((((((((.((((((((((..((&))...)))))))))).))))).))))))).)))	ACCAGCAAACGAAGAUAAUCGCCUUGCUGGAAAUCGCCUUCAAAAUAAAUUAGAAUGAAGAAAAGAGGUGAUGGUAUGGAAAUAACAAUUGUAAAAGGUGAUAUUACGGAACAAGAAGUGGACGUCAUUGUAAAUGCUGCUAACUCCGGG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0176689	0.9128702		986677
lmo2811	-50	-8	-22	-16	10.77	LhrA2	160	203	167	173	7.01	-14.59	-32.37	-1.37572	GGAUAAGGCUUAUUUGGGCUGAAAUUCUAAUGAGAAAGGAUGA&UCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCC	((((.((((.....((((((......(((((((((..((((((&)))))).)))))))))......)))))).......)))).))))	CAUGUGCCAAAAUUUAUUCAAAAUAGGAUAAGGCUUAUUUGGGCUGAAAUUCUAAUGAGAAAGGAUGAGUAAAGAAUGGAAUUUGAUACUAUUGCUGCAAUCUCAACACCGCCGGGAGAAGGGGCCAUUGCUAUUAUUAGAUUAAGCGGU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0190178	0.9128702	trmE	986680	tRNA modification GTPase TrmE
lmo2809	-46	-2	-11	-5	12.36	LhrA2	161	211	164	170	7.9	-13.64	-33.9	-1.28614	GUAGAAUGGGAUUACAUAGAAGAAGACAGACUGCAGAGGUGAAUG&CAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGC	(((.((((((((..((((((....((...((((((((((((((((&))))))))))........))))))))...))))))....)))))))).)))	AAUGUGGUUUUUUCUUGUUUUUAAUUAAGGUAGAAUGGGAUUACAUAGAAGAAGACAGACUGCAGAGGUGAAUGUGUGAAAAAGAGAUGGAUAAUAGCAACGGUAGUUCUAGUAAUGAUUGUUGCGGGAUUAGGCGUGAAAUUUUAUAUG	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0310006	0.9493467		986696	hypothetical secreted protein
lmo0129	-14	15	-14	-8	2.87	LhrA2	176	203	197	203	6.34	-16.42	-25.63	-1.54828	GGAUGAGGAAAAACAUGACAAAGAUAUGG&CCGUGUAGUUCAUGUCUAUGCCUCAUCC	((((((((....((((((.....((((((&))))))...)))))).....))))))))	GAAUGAAGGUCCCGGAAGUAUUGAAAAAUUUAAUUUUGAUUUUCGAUGCAAAGUCAGGAGAGGAUGAGGAAAAACAUGACAAAGAUAUGGAUUGACGCUGGACACGGUGGUAAGGAUUCAGGUGCGAGUGGUAAUGGACUUGUUGAAAAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0070414	0.863511		986713	N-acetylmuramoyl-L-alanine amidase

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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