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
b0031	-30	-8	-28	-22	3.19	FnrS	55	78	69	75	3.63	-10.05	-16.87	-1.02398	GUCUAUGCAAAUUAACAAAAGAG&CUUUUUUGAAUUACUGCAUAGCAC	(((((((((......((((((((&))))))))......))))))).))	GUUUUUGGCUGGCGGCGUAGCGAUGCGCUGGUUACUCUGAAAACGGUCUAUGCAAAUUAACAAAAGAGAAUAGCUAUGCAUGAUGCAAACAUCCGCGUUGCCAUCGCGGGAGCCGGGGGGCGUAUGGGCCGCCAGUUGAUUCAGGCGGCG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.024951	0.9422174	dapB	944762	dihydrodipicolinate reductase
b1656	13	20	13	19	0.9	FnrS	1	8	2	8	2.36	-10.04	-13.3	-1.02296	UUACCUGC&GCAGGUGA	((((((((&))))))))	UUUAAUUUGCUACCCUAUCCAUACGCACAAUAAGGCUAUUGUACGUAUGCAAAUUAAUAAUAAAGGAGAGUAGCAAUGUCAUUCGAAUUACCUGCACUACCAUAUGCUAAAGAUGCUCUGGCACCGCACAUUUCUGCGGAAACCAUCGAG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0251117	0.9422174	sodB	944953	superoxide dismutase Fe
b4650	-27	-10	-25	-19	0.82	FnrS	36	59	51	57	3.82	-10.03	-14.67	-1.02194	AGAAGGAAGAAUAAGGAG&CUCCAUAUUGUCUUACUUCCUUUU	(((((((((((((.((((&)))).))))......)))))))))	GAUGCAAAGAGCAAACUUCAAGAGCUCAAAAAGCUAAAGCGAAUGGAUAGAAGGAAGAAUAAGGAGAAUCCGUAAAAGCAAUAGUUCAUCAGACUGCCGCAGCAGUAGUAUGAUGAUGAAUCAGGGCUGUACUAUAACUAUUAUCGGUAA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0252733	0.9422174	yibS	5625576	pseudogene Rhs family protein
b3755	-17	-3	-14	-8	2.17	FnrS	47	60	51	57	0.87	-10.02	-13.06	-1.02092	AAAAAGGAAGAUAAG&CUUACUUCCUUUUU	((((((((((.((((&))))))))))))))	UGCCGUUUUUGCAACCGUAAUCACACUUCCUGGUGGCAUACUAAGGAGGAAUAAAAAGAAAAAGGAAGAUAAGUAAUGCCUUUAAGCGCACAACAGUUAGCUGCACAGAAAAACCUUUCGUAUGUUCUGGCUGAGAAGCUGGCGCAACGG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0254359	0.9422174	yieP	948263	putative transcriptional regulator
b2562	24	42	31	37	2.74	FnrS	71	89	76	82	4.45	-10.02	-17.21	-1.02092	AUGCAUCAAUUGUGAUAUG&CAUAGCACAAUUGAUUCGU	(((.((((((((((.((((&)))).)))))))))).)))	UGGUGAAAAAACUGGUCUGAGUAAAGAAUGCGCGUAUAAUGCCCGCCCGGUUUGUGUUGUUUUGAGAGUUUCCUUAUGGCGUUGUUAAUCACUAAAAAAUGCAUCAAUUGUGAUAUGUGUGAACCCGAAUGCCCGAAUGAGGCGAUUUCA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0254359	0.9422174	yfhL	947031	putative 4Fe-4S cluster-containing protein
b1305	-72	-60	-66	-60	0.76	FnrS	42	54	42	48	1.64	-9.99	-12.39	-1.01787	GAAGCAAGACAAU&AUUGUCUUACUUC	((((.((((((((&)))))))).))))	AAUGAAGCAAGACAAUCAAUAAUAACAUCCAGGCGGCGUCCGAACGCGCCGCCGCUCAUCGUCUAAGGAGUACUUAUGAGCGCGCUAUUUCUGGCUAUUCCGUUAACCAUUUUUGUGCUGUUUGUUUUACCGAUCUGGUUAUGGCUGCAU	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0259293	0.9422174	pspB	945893	psp operon transcription co-activator
b0147	-41	-17	-27	-21	6.7	FnrS	61	83	65	71	3.74	-9.99	-20.43	-1.01787	CACAUUGUAGCAUCGCGGUAAUUCA&UGAAUUACUGCAUAGCACAAUUG	((.(((((.((...(((((((((((&)))))))))))...)))))))))	ACAAAACGCUCCAGAGGGUUAACAUUCUUCGCGCCACAUUGUAGCAUCGCGGUAAUUCAUAACCGAGUGCCUCACAUGUCUGAACCGCAACGUCUGUUCUUUGCUAUCGACUUACCUGCAGAAAUCCGCGAACAGAUUAUCCAUUGGCGC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0259293	0.9422174	ligT	944848	2'-5' RNA ligase
b0566	-7	20	14	20	9.72	FnrS	65	91	65	71	4.53	-9.97	-24.22	-1.01583	GUGCGAAAUGCAAUUGAGCAGCAGUGA&UUACUGCAUAGCACAAUUGAUUCGUAC	(((((((...((((((.((.(((((((&)))))))...)).)))))).)))))))	CGGCGAACGGGCCGAUCACUCAUGCAGGAAGCAUAGAUCCUUUGAGCGGAGUUUCUGAUAUCUGAGGAGUGCGAAAUGCAAUUGAGCAGCAGUGAACCUUGCGUGGUGAUCCUGACCGAAAAAGAGGUAGAGGUAAGCGUCAAUAACCAU	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.026263	0.9422174	envY	949114	porin thermoregulatory transcriptional activator
b1444	-4	5	-3	4	2.31	FnrS	69	77	70	76	1.75	-9.96	-14.02	-1.01481	UGCUAUGCA&UGCAUAGCA	(((((((((&)))))))))	UUGCCGAUCCUGGGGGCCUGGUGGCUAACCCGCGAAGGCGACAAUGGUCAAUAACCACUGAUACAGGAAUAUGCUAUGCAACAUAAGUUACUGAUUAACGGAGAACUGGUUAGCGGCGAAGGGGAAAAACAGCCUGUCUAUAAUCCGGCA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0264313	0.9422174	patD	945876	gamma-aminobutyraldehyde dehydrogenase
b4551	56	75	68	74	3.27	FnrS	38	56	39	45	3.52	-9.88	-16.67	-1.00666	AGGAUUCAAUGGCGAUGUGG&CCAUAUUGUCUUACUUCCU	((((......((((((((((&)))))))))).....))))	GAGAUUUUCCAGCGUGAAAUGCAACAAGAACGACGCCAGCUGGACGGCUGGGAUGAAUUUGAGUAGAGGGUAAAGAUGGCAAUCCGAAAACGUUUUAUUGCGGGCGCAAAAUGCCCGGCCUGUCAGGCGCAGGAUUCAAUGGCGAUGUGG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.027813	0.9422174	yheV	1450290	DUF2387 family putative metal-binding 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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