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
b1778	-35	-24	-30	-24	2.52	RyhB	43	54	43	49	3.19	-12.27	-17.98	-1.29016	GUAAUGUGAGCA&UGCUCACAUUGC	((((((((((((&))))))))))))	UUUUGCCAGUUGGUGUUAAUGUUUUGUUAGAAUCAGUCACGUAAUGUGAGCACGAUUAAAGUGAGAUGUGAGCAAAUGGCUAAUAAACCUUCGGCAGAAGAACUGAAAAAAAAUUUGUCCGAGAUGCAGUUUUACGUGACGCAGAAUCAU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0142698	0.9496255	msrB	947188	methionine sulfoxide reductase B
b3543	-67	-48	-57	-51	2.65	RyhB	41	58	44	50	3.21	-12.11	-17.97	-1.27334	GGAAUUGAUUUGUGAGCAAU&AUUGCUCACAUUGCUUCC	((((......((((((((((&))))))))))....))))	UAAGGGCGGGAAUUGAUUUGUGAGCAAUACAGACACGCAGUUCCAGGCUGCGGGUCACUAUAGAGAAUCCGGGUUAUGUUGCAGUUUAUUCUCCGACGUUUGGGACUCGUCAUCCCCACGUUUAUCGGUAUUACCCUUCUCACAUUUGCC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0155581	0.9496255	dppB	948063	dipeptide/heme ABC transporter permease
b2727	-7	4	-6	1	4.77	RyhB	39	49	42	48	1.15	-12.05	-17.97	-1.26703	GUGAGCGAUGU&ACAUUGCUCAC	(((((((((((&)))))))))))	CAUGGUGACAUGCUGCAGAUUGUGGCAGACGACGGUUUACAGAUUCGGCGGAUAGAAAUAGACCAGGAGUGAGCGAUGUGUACAACAUGCGGUUGCGGUGAAGGCAACCUGUAUAUCGAGGGUGAUGAACAUAACCCUCAUUCCGCGUUU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0160688	0.9496255	hypB	947194	GTP hydrolase involved in nickel liganding into hydrogenases
b0624	35	48	35	41	3.25	RyhB	53	66	60	66	2.88	-11.71	-17.84	-1.23128	GUGGUACGGGAAGC&GCUUCCAGUAUUAC	(((((((.((((((&)))))).)))))))	GUCGUAAAAUUCGCCAACGACGAUUAUUCGGCGUUACACUUAUCACUCAUACAAAUCAAAUAGCAGGAUUUUGCAGUGUUACAACUUCUUUUAGCAGUUUUUAUUGGCGGUGGUACGGGAAGCGUGGCGAGAUGGCUGUUAAGUAUGCGA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0192746	0.9496255	flc	945798	fluoride efflux channel dual topology membrane protein
b2830	62	74	68	74	1.12	RyhB	44	56	44	50	3.2	-13.5	-17.82	-1.41949	AGGUAAUGUGGGC&GCUCACAUUGCUU	(((((((((((((&)))))))))))))	GCAGAGAGUGGUUUACCGUCUUCCUGGAGUAUGAAACAAUCAUUCGUAUAUAAAGCUUUAUUUUGAGGUAGUCCGGUGAUUGAUGACGAUGGCUACCGCCCAAACGUAGGUAUCGUGAUUUGUAAUCGCCAGGGGCAGGUAAUGUGGGCC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0072388	0.9291058	rppH	947300	RNA pyrophosphohydrolase
b3084	-35	-25	-32	-26	2.76	RyhB	37	47	38	44	1.15	-13.75	-17.66	-1.44578	GGGCAAUGUCG&CGACAUUGCUC	(((((((((((&)))))))))))	CGAAAAAGAGAAAAAGGGUAUACUCACGCACCCUUUUCAGGGGCAAUGUCGAAAUUUUAUCAUUCAGGAGGGCCGAUGAGCCACUUAGACAACGGUUUCCGUUCACUGACACUACAACGUUUUCCGGCGACGGAUGACGUUAACCCGCUA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0062866	0.9291058	rlmG	947589	23S rRNA m(2)G1835 methyltransferase SAM-dependent
b2155	-55	-41	-50	-44	3.08	RyhB	41	57	44	50	3.2	-11.36	-17.64	-1.19448	GAAGAUGUGAGCGAU&AUUGCUCACAUUGCUUC	(((((((((((((((&)))))))))))..))))	CGUACGCAAGGGGACGUGAAGAAGAUGUGAGCGAUAACCCAUUUUAUUUUCGUAGUUACCUCAUGGAGAUAUGGAAUGUUUAGGUUGAACCCUUUCGUACGGGUCGGGCUGUGUUUGUCCGCUAUUUCUUGUGCAUGGCCUGUGUUAGCG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0231967	0.9496255	cirA	949042	colicin IA outer membrane receptor and translocator ferric iron-catecholate transporter
b3991	-75	-66	-75	-69	2.89	RyhB	40	49	43	49	1.15	-13.4	-17.44	-1.40898	GUGAGCAGUG&CAUUGCUCAC	((((((((((&))))))))))	GUGAGCAGUGGGCGCAACAUAUCGUGCAGGAUGGCGACCAGAUCCUGCUUUUUCAGGUUAUUGCAGGGGGUUGAAAUGUUACGUAUUGCGGACAAAACGUUUGAUUCACAUCUGUUUACCGGCACAGGGAAAUUCGCUUCUUCACAACUG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0076567	0.9291058	thiG	948493	thiamine biosynthesis ThiGH complex subunit
b4551	57	73	67	73	3.25	RyhB	39	58	39	45	3.21	-10.85	-17.31	-1.14085	GGAUUCAAUGGCGAUGU&ACAUUGCUCACAUUGCUUCC	(((..((((((((((((&)))))))...)))))..)))	GAGAUUUUCCAGCGUGAAAUGCAACAAGAACGACGCCAGCUGGACGGCUGGGAUGAAUUUGAGUAGAGGGUAAAGAUGGCAAUCCGAAAACGUUUUAUUGCGGGCGCAAAAUGCCCGGCCUGUCAGGCGCAGGAUUCAAUGGCGAUGUGG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0302697	0.9496255	yheV	1450290	DUF2387 family putative metal-binding protein
b2283	-15	-6	-13	-7	0.75	RyhB	52	61	53	59	2.88	-13.04	-16.67	-1.37112	ACUGGAAGCA&UGCUUCCAGU	((((((((((&))))))))))	ACCUGCUGAAAGAGCGCUGGUAACCGAAUUUCGAUUAACGCUCAGUCUCUGACUGAGAAAACUGGAAGCAUGCUAAUGGCUACAAUUCAUGUAGACGGCAAAGAAUACGAGGUCAACGGAGCGGACAACCUGCUGGAAGCUUGUCUGUCU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0093579	0.9291058	nuoG	946762	NADH:ubiquinone oxidoreductase chain G

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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