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
b3106	-28	-17	-24	-18	3.1	FnrS	48	59	49	55	0.77	-10.14	-14.01	-1.03315	AAAAGGAAGUAA&UUACUUCCUUUU	((((((((((((&))))))))))))	CCGGGCAGAAUAUCUGGCUAACAAUGUAGCGUCCAGCCCCUUACCAUAAAAGGAAGUAAAGAGAGGUCAAGAAUUAUGAUUACUACCCGAACUGCCAGGCAGUGUGGACAAGCAGACUACGGAUGGUUGCAGGCCCGGUAUACUUUUUCC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0235457	0.9422174	yhaK	947620	redox-sensitive bicupin
b4236	56	68	62	68	2.71	FnrS	37	49	37	43	3.22	-12.7	-18.63	-1.29398	AAGACAAUAUGGA&UCCAUAUUGUCUU	(((((((((((((&)))))))))))))	GUACGUGACCCGGUCGAAUGAGCGUAGUCGUCGAUGAGGCAGUGUGAAGGAUGAAGUGUAAAUAAAAAAGGAACUAUUCUUGCAGUCUCCUCGUUGGUAUUCAGUUCGGCGUCAUUUGCUGCUGAUCUCGAAGACAAUAUGGAAACCCUC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0039014	0.9422174	cybC	948758	pseudogene truncated cytochrome b562 cytochrome b(562)
b1048	23	35	28	34	1.77	FnrS	64	78	65	71	3.45	-10.89	-16.11	-1.10957	GUGCUGCAGUAAU&AUUACUGCAUAGCAC	(((((((((((((&))))))))..)))))	UCCAUUAAAAUAGAUCGGAUCGAUAUAAGCACACAAAGGGGGAAGUGCUUACUAAUUAUGAAACAUAAACUACAAAUGAUGAAAAUGCGUUGGUUGAGUGCUGCAGUAAUGUUAACCCUGUAUACAUCUUCAAGCUGGGCUUUCAGUAUU	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0143339	0.9422174	opgG	945005	OPG biosynthetic periplasmic beta-16 branching glycosyltransferase
b3282	-40	-26	-32	-26	1.98	FnrS	37	52	37	43	3.41	-11.08	-16.47	-1.12892	AGUAAACAAUGUGGA&UCCAUAUUGUCUUACU	(((((((((((((((&)))))))))).)))))	AGAAAACCGCGCAGGGUGUAAAACACUUUUGUGCCAGUAAACAAUGUGGAAAGCCGGUUUCGGCGGAAUAAUAACGUGAAUAAUAACCUGCAAAGAGACGCUAUCGCAGCUGCGAUAGAUGUUCUCAAUGAAGAACGUGUCAUCGCCUAU	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0125922	0.9422174	tsaC	947783	tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein threonine-dependent ADP-forming ATPase
b1847	-25	-11	-18	-12	0.31	FnrS	72	87	73	79	2.18	-15.67	-18.16	-1.59659	GAAUCAUUGUGCUAU&AUAGCACAAUUGAUUC	(((((((((((((((&))))))))).))))))	GCGGCCUGAAGCAACUUGCGCUCCUGACAAUUUGUACCAUGCUUUCUCCUGAAUCAUUGUGCUAUGGAGAAAAACAUGAAAAAAAGAGGGGCGUUUUUAGGGCUGUUGUUGGUUUCUGCCUGCGCAUCAGUUUUCGCUGCCAAUAAUGAA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0003127	0.5665147	yebF	946363	extracellular Colicin M immunity family protein
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
b0846	-67	-52	-64	-58	0.37	FnrS	43	61	52	58	2.19	-11.38	-13.94	-1.15949	AGAAGAGGGAAGACAA&UUGUCUUACUUCCUUUUUU	((((((((((((((((&))))))...))))))))))	UCAAAAUAAGAAGAGGGAAGACAACAUUAGCAAGGUUGUGUACAUUUGUACACAAUUGCAGAGAGAGGAAAUGACAUGCGUCGCGCUAACGAUCCGCAACGGCGAGAAAAAAUUAUCCAGGCCACGCUGGAGGCGGUGAAACUUUACGGA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0102296	0.9422174	rcdA	945473	transcriptional regulator of csgD and ybiJI autoregulator
b1266	10	29	16	22	5.17	FnrS	61	89	68	74	4.63	-10.53	-20.33	-1.07289	ACGAAUUAUGCAGUGAUUUA&UGAAUUACUGCAUAGCACAAUUGAUUCGU	((((((((((((((((((((&)))))))))))))).........))))))	CAGCUCAUUUCAGAAUAUUUGCCAGAACCGUUAUGAUGUCGGCGCAAAAAACAUUAUCCAGAACGGGAGUGCGCCUUGAGCGACACGAAUUAUGCAGUGAUUUACGACCUGCACAGCCAUACCACAGCUUCCGAUGGCUGCCUGACGCCA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0182438	0.9422174	yciV	945857	PHP domain protein
b2085	51	75	55	61	7.41	FnrS	44	80	70	76	5.62	-10.85	-23.88	-1.10549	UUGUGCUGUGCAUAAUGAUGAGACA&UGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAA	((((((((((((((((..(((((((&))))))).............)))).))))))))))))	UCAAUUAUAAUAAUCAUGCCAUUAUUAUAUUUAAACACUAGAGAGUGUCGUUGGUAUUUAAUGGGGGAAGGUGAGAUGAAAAAGAUAGCUGCUAUAUCAUUAAUUAGUAUUUUUAUUAUGUCUGGUUGUGCUGUGCAUAAUGAUGAGACA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0147273	0.9422174	yegR	946613	uncharacterized protein
b2152	1	42	1	7	18.71	FnrS	4	41	35	41	15.28	-11.51	-45.5	-1.17274	AUGGAGCGCAACGUCACGCUCGAUUUUGUUCGCGGCGUCGCC&GGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAU	(((((((((((((((.((((.((.......((..((((((((&)))).))))..)))).))))...)))))))))))))))	UCAAAUCCAGUCAGAAUACGCGCCACGAGUUUCUGCGCGCUGUGCGUCAUCACAACUGAUUAAAAGGCAGGAACCAUGGAGCGCAACGUCACGCUCGAUUUUGUUCGCGGCGUCGCCAUUCUGGGGAUCCUGCUAUUAAACAUCAGCGCC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.009337	0.9422174	yeiB	949044	DUF418 family putative inner membrane 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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