Input and runtime details for job 8403881 (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 8403881 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:15:25 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:18:18 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:19:13 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:20:45 CET 2020
	Job Completed		@ Mon Jan 27 14:20:57 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8403881&toolName=IntaRNA ( 30 days expiry )

Description of the job

RyhB - 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
b2170	-33	-7	-33	-27	3.48	RyhB	2	24	18	24	7.69	-17.18	-28.35	-1.80643	CUCCGCGUCUUCCUCUUCCAGUGAUCG&CGAUCAGGAAGACCCUCGCGGAG	(((((((......((((((..((((((&))))))))))))....)))))))	UUUGAUUUCGCUGUCUGUUUAUUUUCUGACAAGCAGCGUAAACUCCGCGUCUUCCUCUUCCAGUGAUCGACCAGCAUGCAUAACUCCCCCGCAGUCUCCAGCGCGAAAUCGUUUGACCUGACCUCGACGGCGUUUUUAAUCGUUGCCUUU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0008131	0.5651045	setB	946673	lactose/glucose efflux system
b1227	47	67	54	60	12.39	RyhB	2	22	9	15	7.55	-13.21	-33.15	-1.389	CCGGGGCGGUCUUCCUGAUUG&CGAUCAGGAAGACCCUCGCGG	((((((.((((((((((((((&))))))))))))))))).)))	CACUGCGCAUCAGCGUCGCUUUGCCGGUGCCGUCGCGCCGCAAUAUCUGAAUAUCACCACCGGAGGACAGCACUAAUGCAAUUCCUGAAUAUGUUCUUCUUUGAUAUCUACCCGUACAUAGCCGGGGCGGUCUUCCUGAUUGGUAGCUGG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0085143	0.9291058	narI	945808	nitrate reductase 1 gamma (cytochrome b(NR)) subunit
b3777	15	47	35	41	9.19	RyhB	51	84	56	62	14.45	-11.41	-35.05	-1.19973	CAGCCCUAAGGUUGGUGAAAUACUGGAAUGCAA&UUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUG	((((((...(((((((((((((((((((.((((&))))))))))))))..))).)))))).)).))))	CAUUAGACUUAGAAAAUAUCGGGUCGUAACGUUGUGUUAUUACUUUUUCAGAGUUUACUAAGGAGAGGUUUACUCGUGGCGAUUAAUUUCAGCCCUAAGGUUGGUGAAAUACUGGAAUGCAACUUUGGUAACUAUCCUGUUAGCCAAAAU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0225939	0.9496255	yifN	2847676	PemK toxin family pseudogene
b3032	-67	-43	-49	-43	8.96	RyhB	40	63	40	46	3.3	-10.86	-23.12	-1.1419	AUACUGUUUAGCACAUGGAGCGAUG&CAUUGCUCACAUUGCUUCCAGUAU	((((((...((((.(((((((((((&)))))))).)))))))..))))))	UGGUUGCGAUACUGUUUAGCACAUGGAGCGAUGGCGAUUCCGGUUUAUUAGCGUCGUGAAACCUAAGGACACCAUUUGGAAAGCCUGUUAACCCUUCCUCUGGCUGGUGAGGCCAGAGUCAGGAUUUUACAAAUUACCGACACUCACCUG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0301134	0.9496255	cpdA	947515	3'5' cAMP phosphodiesterase
b1269	-46	8	2	8	15.9	RyhB	42	90	42	48	14.91	-11.89	-42.7	-1.2502	AAAAGCAUAUCAGACGCCUGGGAAGGCGACACCAAAAGGAAGCUCUAUGAGCGA&UUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	((((((....(((.(((((((...(((..........((((((....(((((((&)))))))....))))))...........)))..))))))))))))))))	CAGAUGUAAGUUCUGACUCACUGUUGCACAAAAGCAUAUCAGACGCCUGGGAAGGCGACACCAAAAGGAAGCUCUAUGAGCGAAAAGCUACAGAAAGUGCUGGCGCGUGCCGGCCACGGUUCUCGCCGUGAAAUCGAAUCUAUUAUUGAA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0175092	0.9496255	rluB	945840	23S rRNA pseudouridine(2605) synthase
b3248	19	35	29	35	5.01	RyhB	18	35	18	24	9.68	-12.53	-27.22	-1.3175	GCUUCCGGUUCUCCGCG&CGCGGAGAACCUGAAAGC	(((((.(((((((((((&))))))))))).)).)))	UGGGGUGCUCUGGCCGUGGAUUUUCUUGCUGAUGCGCAAAGUCCGUCAGCAGUUUGCAGUGCAAUAAAGGUUUCUAUGACUUCUCUGUAUUUAGCUUCCGGUUCUCCGCGUCGUCAGGAGUUACUUGCGCAACUUGGCGUGACCUUUGAA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0123886	0.9496255	yhdE	947753	dTTP/UTP pyrophosphatase m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase
b2253	-13	5	-2	5	4.92	RyhB	38	58	38	44	3.21	-12.03	-20.16	-1.26493	GGAAGGAAAAGCAAUGUC&GACAUUGCUCACAUUGCUUCC	(((((.((.(((((((((&)))))))))....)).)))))	CAAAUGGCAAAAUAUACACAACACUCUUUAUAGCAAAUAUAAGUGGACAGGUAUUCAAUGGCGGAAGGAAAAGCAAUGUCAGAAUUUUUGCCUUUUUCGCGACCAGCAAUGGGCGUGGAGGAACUCGCUGCAGUUAAAGAGGUUCUCGAA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0162426	0.9496255	arnB	947375	uridine 5'-(beta-1-threo-pentapyranosyl-4-ulose diphosphate) aminotransferase PLP-dependent
b0728	-74	-59	-66	-60	1.61	RyhB	50	64	51	57	2.98	-10.97	-15.56	-1.15347	AAUGCCCGGAAGCGAU&AUUGCUUCCAGUAUU	(((((..(((((((((&))))))))).)))))	CAAUGCCCGGAAGCGAUACGAAAUAUUCGGUCUACGGUUUAAAAGAUAACGAUUACUGAAGGAUGGACAGAACACAUGAACUUACAUGAAUAUCAGGCAAAACAACUUUUUGCCCGCUAUGGCUUACCAGCACCGGUGGGUUAUGCCUGU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0284439	0.9496255	sucC	945312	succinyl-CoA synthetase beta subunit
b3867	-13	5	-6	1	8.94	RyhB	38	58	43	49	3.21	-10.87	-23.02	-1.14295	GGAAGGAGUGAGCAUGUC&GACAUUGCUCACAUUGCUUCC	(((((..(((((((((((&)))).)))))))....)))))	CAACCGGCUGAUGACCCGAAACGGGCAUCCGCCGGUACGCCGUAGCCGCCAGAGACGCCAUCGGAAGGAGUGAGCAUGUCUGUACAGCAAAUCGACUGGGAUCUGGCCCUGAUCCAGAAAUAUAACUAUUCCGGGCCACGAUACACCUCG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0299579	0.9496255	hemN	948362	coproporphyrinogen III oxidase SAM and NAD(P)H dependent oxygen-independent
b4308	25	59	46	52	9.14	RyhB	53	90	60	66	14.49	-11.59	-35.22	-1.21866	AAAAGUGCAGCAUCUGGCAGCGUAAUGCAGGUAGC&GCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	(((((..(((((((((((.(((((((((.((..((&))..)).)))))))...))..))))))))))).)))))	GAACUCCCAGCAAGACCCUGUAAAUAAUUCUGUGUAACUGCCCACGAUUAAAGGUGGCCGCUCAGGCGGUCACCGUAUUCGAUAAUAAAUGGGUCUGGAAAAAGUGCAGCAUCUGGCAGCGUAAUGCAGGUAGCCCAGUUCAACUCUCAC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0205432	0.9496255	yjhR	944740	pseudogene helicase family putative frameshift suppressor

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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