Input and runtime details for job 4596356 (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_000913
	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 4596356 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:10:48 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:13:48 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:14:50 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:16:49 CET 2020
	Job Completed		@ Mon Jan 27 14:17:02 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4596356&toolName=IntaRNA ( 30 days expiry )

Description of the job

FnrS - E. coli

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_000913 Escherichia coli str. K-12 substr. MG1655

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
b0657	32	43	37	43	4.44	FnrS	1	12	1	7	6.44	-10.92	-21.8	-1.11262	GCAUUCGCCUGC&GCAGGUGAAUGC	((((((((((((&))))))))))))	GUUCAUGUCAAAAUCCCGGAUGACUCACCCCAGCCGAAGCUGGAUGAAUAAAACCGAAACUGGAUAGAUAACUACAUGGCUUUUGCCUCAUUAAUUGAACGCCAGCGCAUUCGCCUGCUGCUGGCGUUAUUAUUCGGUGCCUGCGGAACG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0140451	0.9422174	lnt	946201	apolipoprotein N-acyltransferase
b1841	-43	4	-16	-10	7.88	FnrS	38	76	53	59	7.45	-15.32	-30.65	-1.56093	GUUAUGCUCUGUAAAAAAGUUAUUACAAAAAGGAAUAGAUAAUAUGG&CCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGC	(((((((..........(((.(((..(((((((((.(((((((((((&)))))))))))...)))))))))..))).))))))))))	AUUGAUGAUCCUCGACUCAGACAUUAGACAAGGUUAUGCUCUGUAAAAAAGUUAUUACAAAAAGGAAUAGAUAAUAUGGCUUCAACUGCACGCUCCCUUCGCUACGCGCUGGCAAUCCUGACCACUUCGUUGGUGACACCUUCCGUCUGG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.000434	0.5665147	yobA	948315	CopC family protein
b4040	-14	8	-14	-8	0.97	FnrS	34	59	53	59	7.46	-12.6	-21.03	-1.28379	AAGAGGAAAAAAAUAUGGAGUG&CGCUCCAUAUUGUCUUACUUCCUUUU	((((((((...(((((((((((&))))))))))).......))))))))	CGAUUAAGCGGUAAACCGCUGUUGCUAACAGAACUGUUUUUACCGGCGUCACCGUUGUACUAAGAGGAAAAAAAUAUGGAGUGGAGUCUGACGCAGAAUAAGCUGCUGGCGUUUCAUCGCUUAAUGCGUACGGAUAAGCCAAUUGGCGCG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0042095	0.9422174	ubiA	948540	p-hydroxybenzoate octaprenyltransferase
b3847	-56	4	-22	-16	10.89	FnrS	38	89	56	62	7.59	-11.7	-30.18	-1.19209	AUGAACGAUGUGCUAAGAUGCGGAGACUUAAGGUCAAAAAAACAGAAGGGUAAAAAAUGG&CCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGU	(((((((((((((((...(((((.....(((..((((((((...((((.....((.((((&)))).))......)))).)))))))).)))))))))))))).)))).)))))	GGCAGAAAUCACGCUCUGGAUGAACGAUGUGCUAAGAUGCGGAGACUUAAGGUCAAAAAAACAGAAGGGUAAAAAAUGGAAUCACUGGCCUCGCUCUAUAAAAAUCAUAUAGCUACCUUACAAGAACGGACUCGCGAUGCGCUGGCGCGC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0081594	0.9422174	pepQ	948335	proline dipeptidase
b0356	59	74	62	68	2.9	FnrS	4	20	11	17	7.73	-11.93	-22.56	-1.21553	UUGACGUUGCACCACC&GGUGAAUGCAACGUCAA	(((((((((((.((((&))))..)))))))))))	UUGACGACACUAUUGAACUGGUUCGUGCCUAUCUUAAAUAGCUGAAUCUAUUACCAUAUUGAGGAAGAGCGAGAGAUGAAAUCACGUGCUGCCGUUGCAUUUGCUCCCGGUAAACCGCUGGAAAUCGUUGAAAUUGACGUUGCACCACCG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0069153	0.9422174	frmA	944988	alcohol dehydrogenase class III glutathione-dependent formaldehyde dehydrogenase
b1112	-36	-15	-21	-15	6.62	FnrS	1	22	1	7	8.09	-12.35	-27.06	-1.25832	GCUUGCGACGUCAUUCAUCUGC&GCAGGUGAAUGCAACGUCAAGC	((((..((((((((((((((((&)))))))))))..)))))))))	GAUCACAUCUAUCAUUUAGUUAUCGAUCGUUAAGUAAUUGCUUGCGACGUCAUUCAUCUGCAUAAGGCCACUAUUAUGAAAAACGUAAAAACCCUCAUCGCUGCGGCGAUUUUAAGCUCCAUGUCAUUUGCCAGCUUUGCGGCUGUCGAA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0050791	0.9422174	bhsA	945492	biofilm cell surface and signaling protein
b0227	53	74	68	74	1.04	FnrS	1	22	1	7	8.09	-10.14	-19.27	-1.03315	GUUUGCCGUUUUCUUCAUUUGC&GCAGGUGAAUGCAACGUCAAGC	(((((.((((...(((((((((&)))))))))...)))).)))))	AAUGGUUUAUUAAGUUUGUUCAGAAACGAUCCGGGAUACACUGCAACAUUAAAGCAUGACCAGCCAUUAUUGAGUAUGUCCUUGCCGUCGAUUCCAUCCUUUGUAUUGUCGGGAUUACUGUUGAUUUGUUUGCCGUUUUCUUCAUUUGCC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0235457	0.9422174	yafL	944899	putative lipoprotein and C40 family peptidase
b3770	-75	-56	-62	-56	3.72	FnrS	1	24	1	7	9.45	-10.78	-23.95	-1.09836	UCGCACACGUUGCCAUCUGC&GCAGGUGAAUGCAACGUCAAGCGA	((((..((((((((((((((&)))))))...)))))))...))))	UCGCACACGUUGCCAUCUGCCAGAGCACAACCACAUCACAACAAAUCCGCGCCUGAGCGCAAAAGGAAUAUAAAAAUGACCACGAAGAAAGCUGAUUACAUUUGGUUCAAUGGGGAGAUGGUUCGCUGGGAAGACGCGAAGGUGCAUGUG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0154393	0.9422174	ilvE	948278	branched-chain amino acid aminotransferase
b3892	-16	-1	-9	-3	3.18	FnrS	31	49	33	39	9.51	-10.14	-22.83	-1.03315	AAGACGAGGAGCGCAA&UUGCGCUCCAUAUUGUCUU	((((((((((((((((&)))))))))...)))))))	CUACGUGGGUGUCGGUCCGAACCGUGCGGAUGAGGAAGAGAAUAAUCUGCACGAAGAGAAAGACGAGGAGCGCAAAUGAAACGACGUGACACCAUCGUGCGCUACACCGCGCCGGAACGUAUCAACCACUGGAUCACCGCCUUCUGCUUC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0235457	0.9422174	fdoI	948383	formate dehydrogenase-O cytochrome b556 subunit
b1759	58	71	62	68	2.71	FnrS	21	36	26	32	12.14	-10.11	-24.96	-1.03009	GCGCAACGCCCCGC&GCGAUGGGCGUUGCGC	(((((((((((.((&))...)))))))))))	AAAUAUAAAGCCUUUCUGAUUGAGCAACAGUGCGGAUAUUAUGGCAUUUUUCGCUUAUCUGCCCGUGUGUAAUUUAUGAAAAUGAUUGAAGUUGUUGCCGCCAUCAUUGAACGUGAUGGCAAAAUUUUACUCGCGCAACGCCCCGCCCAG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.024006	0.9422174	nudG	946277	CTP pyrophosphohydrolase also hydrolyzes 2-hydroxy-dATP 8-hydroxy-dGTP 5-hydroxy-CTP dCTP and 5-methyl-dCTP

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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