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
b3743	40	66	42	48	7.94	RyhB	34	60	52	58	6.76	-19.68	-34.38	-2.0693	CUGGAAGCAUUAAUGGGCAAUGCGCGC&GCACGACAUUGCUCACAUUGCUUCCAG	(((((((((....(((((((((((.((&)).)).)))))))))...)))))))))	AGCCUAACUCACUUUUGAUUCAUUAAAAAAGAAGGCUAAAAUAGAAUGAAUCAUCAAUCCGCAUAAGAAAAUCCUAUGGAAAAUUAUCUGAUCGACAAUCUGGACCGUGGCAUCCUGGAAGCAUUAAUGGGCAAUGCGCGCACCGCUUAC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0001586	0.1837117	asnC	948259	transcriptional activator of asnA autorepressor
b3902	43	75	61	67	8.05	RyhB	57	89	67	73	13.55	-11.97	-33.57	-1.25862	AAAGCCACCACCGACGCCUGGCUGAAAGGCUGG&CCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUU	(((((((.((((..((.((((((((((..((((&))))..))..)))))))).)))))).)))))))	CGGAUGCGGCGCGAGCGCCUUAUCCGGCCUACGGGUCGUGCAUCCGACAACACCGAAUUUACAGGAACACAGAACAUGCAAAACAUUACUCAGUCCUGGUUUGUCCAGGGAAUGAUCAAAGCCACCACCGACGCCUGGCUGAAAGGCUGG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0167745	0.9496255	rhaD	948401	rhamnulose-1-phosphate aldolase
b1189	10	30	13	19	8.06	RyhB	47	66	57	63	3.09	-11.54	-22.69	-1.2134	GUCAUACUGGGAAGUGGUGUG&CACAUUGCUUCCAGUAUUAC	((.(((((((.((((((((((&))))))))))))))))).))	AAUAUUUUCAACUGAGUUAUCAAGAUGUGAUUAGAUUAUUAUUCUUUUACUGUAUCUACCGUUAUCGGAGUGGCUAUGCGAGUUGUCAUACUGGGAAGUGGUGUGGUAGGCGUUGCCAGCGCCUGGUACUUAAAUCAGGCAGGACAUGAG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0210945	0.9496255	dadA	945752	D-amino acid dehydrogenase
b4516	-39	-2	-9	-3	8.43	RyhB	21	62	22	28	7.99	-11.31	-27.73	-1.18922	UACUGAUUUAGUGUAUGAUGGUGUUUUUGAGGUUCUCC&GGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUA	(((((....((((((((...(((((((..(((((((((&))))))))).)))))))..))).....))))).....)))))	UUCAUCGCAUGGACAAUACGGGUGAUGCUGCCAACUUACUGAUUUAGUGUAUGAUGGUGUUUUUGAGGUUCUCCAGUGGCUUCUGUUUCUAUCAGCUGUCCCUCCUGUUCAGCUACUGACGGGGUGGUGCGUAACGGCAAAAGCACUGCC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0238147	0.9496255	insA	1450250	IS1 repressor TnpA
b2211	-12	13	7	13	8.49	RyhB	6	30	6	12	10.22	-11.41	-30.12	-1.19973	CGGGUUUUCUGCAUGGAACUUCUUG&CAGGAAGACCCUCGCGGAGAACCUG	((((((((((((..((..(((((((&)))))))..))..))))))))))))	AAAUAAGAAUUAUUAUUGCUGUGCGCGCGAAGAUGUUUAAACUGCGGGCUGUAAUUCAUUGUCCGGGUUUUCUGCAUGGAACUUCUUGUACUUGUCUGGCGGCAGUAUCGCUGGCCAUUUAUCAGUGUGAUGGCGCUAAGCCUCGCCAGU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0225939	0.9496255	yojI	946705	microcin J25 efflux ABC transporter permease/ATPase
b2230	-27	3	-27	-21	8.92	RyhB	40	76	70	76	12.64	-12.71	-34.27	-1.33643	GGCUGGCUAUACACAAGGAAUGUGGCAAUG&CAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCC	((((((((((((...((.((((((((((((&)))))).)))))).))....)))).....))))))))	UUUUGUCGUAUUAGGGCACGGUAAAGUUUGGCUGUGCCCGUAAAAAAUGGCUGGCUAUACACAAGGAAUGUGGCAAUGAGUGGUGAAAAAAAGGCGAAAGGCUGGCGGUUCUAUGGUCUUGUAGGUUUUGGCGCAAUAGCACUGCUUUCC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0112262	0.9496255	yfaA	946618	DUF2138 family protein putative host defense protein
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
b1120	-17	5	-7	-1	9.07	RyhB	46	68	52	58	3.24	-14.88	-27.19	-1.5646	AAGUGGUGCCGGAAGCAAUGGA&UCACAUUGCUUCCAGUAUUACUU	(((((((((.((((((((((((&)).)))))))))).)))))))))	CGUAAAAAUAAACGCCGCCUGCGCGAGCGUUUGCGUCAGCGUAUUUUUUUCAGAGAUAAAGUGGUGCCGGAAGCAAUGGAAAAACCAAGAGUACUCGUACUGACAGGGGCAGGAAUUUCUGCGGAAUCAGGUAUUCGUACCUUUCGCGCC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0032796	0.9291058	cobB	945687	deacetylase of acs and cheY chemotaxis regulator
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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