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
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
b0005	-18	50	44	50	14.7	RyhB	1	65	1	7	14.12	-11.73	-40.55	-1.23338	UGAUAAAAGGAGUAACCUGUGAAAAAGAUGCAAUCUAUCGUACUCGCACUUUCCCUGGUUCUGGUCGC&GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUA	(((((...(((((((..(((((.......(((((...((((.((..((.(((((..((((((((((((&))))))))))....))....)))))...))..)).)))).)))))))))))))))))...)))))	GAAUAACAACCGCCGUUCUCAUCGAGUAAUCUCCGGAUAUCGACCCAUAACGGGCAAUGAUAAAAGGAGUAACCUGUGAAAAAGAUGCAAUCUAUCGUACUCGCACUUUCCCUGGUUCUGGUCGCUCCCAUGGCAGCACAGGCUGCGGAA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0190705	0.9496255	yaaX	944747	DUF2502 family putative periplasmic protein
b0156	-11	13	3	9	5.27	RyhB	37	59	41	47	3.29	-11.5	-20.06	-1.2092	UGGAGCAAAAUAUGAGUGAUGACG&CGACAUUGCUCACAUUGCUUCCA	((((((((....(((((((((.((&)).)))))))))..)))).))))	UACCAGGGUAUUAGAUAAUGGCGAUUAUUAUUGGGUUAGAAUUUGCCCAAUUGCCGAUGUCGUUUGGAGCAAAAUAUGAGUGAUGACGUAGCACUGCCGCUGGAGUUUACCGACGCAGCAGCCAACAAAGUUAAAAGCCUGAUCGCUGAC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0215456	0.9496255	erpA	944857	iron-sulfur cluster insertion protein
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
b0313	54	75	56	62	0.92	RyhB	40	61	53	59	3.3	-15.35	-19.57	-1.61401	ACUGGAAGCAAUAAAUGAAGUG&CAUUGCUCACAUUGCUUCCAGU	((((((((((((......((((&))))......))))))))))))	GACACAUUUUAUAUUGAACGUCCAAUCAAUAACCGCUUUAAUAGAUAAACACCGCUGAUGAAUGGAGUGGCGAAAAUGCCCAAAUUGGGGAUGCAGUCGAUCCGGCGCAGACAACUGAUCGACGCCACACUGGAAGCAAUAAAUGAAGUG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0024857	0.8637808	betI	944981	choline-inducible betIBA-betT divergent operon transcriptional repressor
b1013	-75	-34	-47	-41	10.22	RyhB	7	44	14	20	13	-12.26	-35.48	-1.28911	CGAUGAGAGUGCAGAAGGUCGAGGCCGGGCGGGGGUUUUGCU&AGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUG	(((((...((((...((((.....((..(((((((((((.((&)).)))))))))))))...))))....))))..)))))	CGAUGAGAGUGCAGAAGGUCGAGGCCGGGCGGGGGUUUUGCUAUCCUGUUGCCAAUCUACAAGAGGGGAGAGCGCAUGACGCAAGGCGCAGUGAAAACAACGGGUAAACGUUCGCGCGCAGUAAGCGCGAAGAAAAAAGCGAUUCUUAGC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0143473	0.9496255	rutR	945075	rut operon transcriptional repressor for
b0528	57	74	58	64	3.72	RyhB	42	61	54	60	3.3	-13.77	-20.79	-1.44788	ACUGGAAGGCUGGAGCGA&UUGCUCACAUUGCUUCCAGU	((((((((..((((((((&)))))).))...))))))))	CGAUGACGGUUGCCACGCUGAUUGAAAACACGCUACAGGCGUGCGUUGAAUAUCAUGAUCCACAGGAUGAGUAACAUGGCGACAUUUUCUUUAGGUAAACAUCCGCACGUUGAGCUGUGCGACUUGCUGAAACUGGAAGGCUGGAGCGAA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0062158	0.9291058	ybcJ	945158	ribosome-associated protein putative RNA-binding protein
b1588	-19	-1	-10	-4	5.91	RyhB	40	56	43	49	3.21	-11.03	-20.15	-1.15978	AAGCAAUAAGUGAGUAAUG&CAUUGCUCACAUUGCUU	(((((((..((((((((((&)))))))))))))))))	AUCGAAAAAAUAUAACCCACGACAACCAUAAAUUCUGGCAUGACAUUUUGUUUGAAAAGCAAUAAGUGAGUAAUGAUGAAAAUCCAUACCACAGAGGCGCUCAUGAAGGCUGAAAUCAGCCGUAGAAGUCUGAUGAAAACCUCCGCACUU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0275701	0.9496255	ynfF	945268	S- and N-oxide reductase A subunit periplasmic
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
b0968	-11	6	-2	5	3.42	RyhB	37	58	38	44	3.22	-13.79	-20.43	-1.44998	GGAGAGCAGCAAUGUCG&CGACAUUGCUCACAUUGCUUCC	(((.(((((((((((((&)))))))))......)))))))	GCAAAGAAAUGGGCGUCAUUGUCCGGAGUUUUCCAUGGAUUUGCAACGCGUCCAUUAAGGAUAAGGAGAGCAGCAAUGUCGAAAGUCUGCAUAAUUGCCUGGGUUUACGGGCGAGUUCAGGGCGUAGGAUUUCGCUACACCACACAGUAC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0061458	0.9291058	yccX	945304	weak acylphosphatase

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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