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
b3365	-9	12	2	8	4.28	RyhB	38	57	42	48	3.21	-10.98	-18.47	-1.15452	GAGGCAAAAAUGAGCAAAGUC&GACAUUGCUCACAUUGCUUC	(((((((...(((((((..((&))..)))))))..)))))))	AAUUUGAUUUACAUCAAUAAGCGGGGUUGCUGAAUCGUUAAGGUAGGCGGUAAUAGAAAAGAAAUCGAGGCAAAAAUGAGCAAAGUCAGACUCGCAAUUAUCGGUAACGGUAUGGUCGGCCAUCGCUUUAUCGAAGAUCUUCUUGAUAAA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0282964	0.9496255	nirB	947868	nitrite reductase large subunit NAD(P)H-binding
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
b3492	-66	-42	-64	-58	5.23	RyhB	42	65	57	63	3.3	-10.96	-19.49	-1.15242	UGAUGCUGGUGCGACCACUGAGGAA&UUGCUCACAUUGCUUCCAGUAUUA	(((((((((.((((....((((.((&)).))))..))))..)))))))))	UAGUAAUAUUGAUGCUGGUGCGACCACUGAGGAAUCUUUACAAUUCACGCCCGUUUUUUCUAAGAGGAGCGCAACGUGGAAAGGUUUGAUGCCAUUAUUAUAGGCGCUGGUGCGGCGGGUAUGUUCUGUUCUGCGCUGGCAGGUCAGGCA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.028592	0.9496255	yhiN	947996	putative oxidoreductase
b0681	57	71	58	64	3.86	RyhB	32	46	39	45	5.54	-10.92	-20.32	-1.14821	AGCAAUGUCGGGCUU&AAGCACGACAUUGCU	((((((((((.((((&)))).))))))))))	CGCUACUUUUUUAAUUUUUAUUUUUUCGCUGUUCACCUUUGGUGCAGCAAUUUAUACGUCAAAGAGGAUUAACCCAUGCGUACGUUUAGUGGCAAACGUAGUACGCUGGCGCUGGCUAUCGCCGGUGUUACAGCAAUGUCGGGCUUUAUG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0291917	0.9496255	chiP	945296	chitoporin uptake of chitosugars
b2714	60	72	66	72	7.05	RyhB	26	38	26	32	5.77	-10.91	-23.73	-1.14716	CGUGCUUUCAGGU&ACCUGAAAGCACG	(((((((((((((&)))))))))))))	UCCCGCCGAUUGUGCAAGGACAAUCGGCAAACGGUGCAGUACACUGCGUUGAUUGCGUGUAAAGGGAUGAAAAUGAUGACGACGAUGCUGGAAGUGGCGAAGCGCGCCGGGGUUUCAAAAGCGACCGUUUCCCGCGUGCUUUCAGGUAAU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0293435	0.9496255	ascG	947305	asc operon transcriptional repressor prpBC operon repressor
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
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
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
b4281	-9	2	-7	-1	2.98	RyhB	36	46	38	44	2	-10.82	-15.8	-1.1377	AGCAAUGUCGU&ACGACAUUGCU	(((((((((((&)))))))))))	CCCACAUACUUCGGCGUAAUAUCCAUCGGGACAGCCCGGAUAGGCCCAAUGGUCAGCUCAUCGGCCAGCAAUGUCGUGAACUGUGAGACGAAACAGCGUACACAGUUUGAAUGUAUCUACUUUUCCCAAUACUGGGCGAAGGGAGAUUUU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0307429	0.9496255	yjhD	948809	pseudogene KpLE2 phage-like element
b1279	-12	4	-9	-3	7.4	RyhB	46	61	52	58	3.24	-10.81	-21.45	-1.13665	ACGGGAAGUAAUGUGA&UCACAUUGCUUCCAGU	((.(((((((((((((&))))))))))))).))	AAAAUGGUACUUUAAAGGGCUAUUGCGGUAAGUUGACCAUAAUUUAUUCGCUCUAACCACAUAACGGGAAGUAAUGUGAAAUAUUUACUCAUUUUCUUACUGGUGUUAGCGAUCUUCGUGAUUUCGGUCACGUUGGGUGCGCAGAACGAU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0309022	0.9496255	yciS	944936	DUF1049 family inner membrane protein function unknown

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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