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
lmo1229	-3	28	7	13	3.75	LhrA2	147	182	167	173	5.55	-17.22	-26.52	-1.62371	UACGUGGCAAAUGAGAGAAAUAAAGUAGUGA&UCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUA	((((((((.(((((((((((..(((((((((&)))))))))..)))).....))))))).))))))))	UUUUCUUUCCUGCUUUUUCGUGAUAAGAUUAUGACAAGUAGCGGCCUAAACGAAUUUGGGCGAGGAGGAAUUUACGUGGCAAAUGAGAGAAAUAAAGUAGUGACAACAAUUUACGGUAGAGAAUAUACGAUUGUUGGCGUAGAAACAACA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0044601	0.863511		985608
lmo1572	1	26	9	15	8.3	LhrA2	157	179	165	171	2.12	-17.19	-27.61	-1.62088	AUGGCGAAUGAGAUGGAAUUUGAGAA&UUUUCAUUCAUCUCAUUGGCCGU	(((((.(((((((((((...((((((&))))))))))))))))).)))))	GUCUUGAUUUGCAAAAUAAGUUAAGUUUUAUUUUAAGCAUUCAUGUGAAAGCACCUGGAGUAGGGGGUGAAGUUGAUGGCGAAUGAGAUGGAAUUUGAGAAACCGAUUUUAGAAUUAAAAAGUAAGAUCGCUGACUUAAAAGAGUACAAU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0045383	0.863511	accA	986992	acetyl-CoA carboxylase carboxyltransferase subunit alpha
lmo2615	-18	25	19	25	6.27	LhrA2	155	202	155	161	7.03	-17.05	-30.35	-1.60768	GAAGGAGGGACAUAUUACAUGCCUGAGCAAAUUGAUGGAAACA&UGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUC	((..(((((((((((((((((((((((.....(((((((((((&)))))))).))).))))..)).))))))))..)))))....)))).))	GGCCGCGUGAAAGCUCUUGCUGAAGCAGCUCGCGAAAAUGGACUAGAAUUUUAAUAAGAAGGAGGGACAUAUUACAUGCCUGAGCAAAUUGAUGGAAACAAAUUAGAUUUAGAAGAACGCGUUGUUACAAUCAACCGUGUUGCUAAAGUA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0049203	0.863511	rpsE	987198	30S ribosomal protein S5
lmo1161	-12	36	19	25	8.89	LhrA2	158	204	170	176	7.06	-16.94	-32.89	-1.59731	GGAGGUGGAAAAAUGGAUAUUUUACAAACAGCCAAUGAACGAAUGGAA&UUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCC	((.((((.....((((((((.......((.((((((((..((((((((&))))))))...)))))))).)).......))))))))....))))))	AGCGAACGCGGCAGAUAUUGCUGGCACGAAUUUUGCAAAAAUAAUCAAGUCGUGAUCUGGUAAGGAGGUGGAAAAAUGGAUAUUUUACAAACAGCCAAUGAACGAAUGGAACAGCUUGCAGCGCUAAUGAAUAAAGAUAUCGAACAAAAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0052414	0.863511		986144	ethanolamine utilization protein EutJ
lmo1507	-25	4	-11	-5	2.75	LhrA2	147	173	155	161	1.7	-16.85	-21.3	-1.58882	AAUGUAAGAGGAGUGAGAACAGAAUAUGA&UCAUUAUUUGUUUUCAUUCAUCUCAUU	((((..(((.(((((((((((((..((((&))))..))))))))))))).)))))))	CGCGAAAAAAAUAAUUUGGCUUGAUUAUUAGGUCUAAUUAGGCUAGUUUUAAUGUAAGAGGAGUGAGAACAGAAUAUGAAAUUACUUAUGAUAGAAGAUAAUGUAAGUGUCUGUGAAAUGAUAGAAAUGUUCUUUAUGAAAGAAGAAAUU	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0055185	0.863511		987756	response regulator
lmo1403	-17	22	16	22	6.24	LhrA2	169	208	169	175	7.22	-16.71	-30.17	-1.57562	UAAGGGAUGAUGAGAUAAUGACAGAAUAUACACCAAUGA&UCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUA	(((.((..((((((.....((((((((((((.(((((((&)))))))..))))).))).)))).....)))))))).)))	UCUUUUGCGGUCGCGGGAAAAUGAAACUUUAUGCUAUAAUGAGAGGAUGAAAAAGAAGUAAGGGAUGAUGAGAUAAUGACAGAAUAUACACCAAUGAUUAAGCAGUACUUGGAAAUCAAAGACAAAUAUCAAGAUGCUUUCUUAUUUUUC	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0059768	0.863511	mutS	985419	DNA mismatch repair protein MutS
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
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
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
lmo1666	-46	7	-7	-1	7.72	LhrA2	157	204	164	170	7.08	-16.3	-31.1	-1.53696	GGGAUAAAAUAAUUGGGGGACUUUUAAAAAAGGGAGAUGGGGAUGAAUGAAAA&UUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCC	((((.........((((((((..........((......((((((((((((((&)))))))))))))).....))...........)))....)))))))))	GGAAUAACAUGACAAUAGCUUUAGGAAUGGGGAUAAAAUAAUUGGGGGACUUUUAAAAAAGGGAGAUGGGGAUGAAUGAAAAGUAAAUUUUUUAUAGGCAUGAUGACUUUUUUGCUAUCAUUAAUUUGUCUUACUGGAAUGAAAGCAGAA	AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG	0.0075316	0.863511		985661	peptidoglycan-linked protein

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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