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
b4176	18	67	41	47	18.12	RyhB	31	86	56	62	18.89	-13.5	-50.51	-1.41949	GCUGGCGCUUGCCCUGGUUUUGGUACUGGAAGGUUUAGGGCCGAUGCUUU&AAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGC	(((((((((((..((((((.((((((((((((.....((((((.((((((&)))))))).....))))......))))))))))))...)))))).)))))))))))	GACUGCGGUACAGGUCAAUAAAGCCACCGCAUCCUCAGGGAUGUCGGUGGUUUUCUUUUUCUAUAAGGAUAAUGAAUGAAUUCGACAAUCUGGCUGGCGCUUGCCCUGGUUUUGGUACUGGAAGGUUUAGGGCCGAUGCUUUACCCGAAG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0072388	0.9291058	yjeT	948696	DUF2065 family protein
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
b2819	20	33	23	29	4.07	RyhB	47	62	53	59	3.09	-12.43	-19.59	-1.30698	UACUGGAAGCUGUG&CACAUUGCUUCCAGUA	((((((((((((((&))))..))))))))))	CACAACCCGACCCAACGCCGGGUUGAUUGCCCUGAUGGAUGAGAUGUUUGCCGGUAUGACCCUGGAGGAGGCGUAAUGAAAUUGCAAAAGCAAUUACUGGAAGCUGUGGAGCACAAACAGCUACGCCCGCUGGAUGUGCAAUUUGCCCUG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0130826	0.9496255	recD	947287	exonuclease V (RecBCD complex) alpha chain
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
b3928	30	40	33	39	2.04	RyhB	51	61	52	58	2.88	-13.08	-18	-1.37533	ACUGGAAGCAA&UUGCUUCCAGU	(((((((((((&)))))))))))	UCGUAUUUAUUAAGGCGUCACCGGUAAUCGGGACGAGGAUUUUUAUCCAUCAACGCCUUGCAAUUCAGGAGAGGUAUGACAAUGUCAUUAGAAGUGUUUGAGAAACUGGAAGCAAAAGUACAGCAGGCGAUUGAUACCAUCACUCUGUUG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0091526	0.9291058	zapB	948420	FtsZ stabilizer septal ring assembly factor cell division stimulator
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
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
b2823	42	60	42	48	6.85	RyhB	40	58	52	58	3.21	-14.06	-24.12	-1.47837	GGAGGUAAUGUUGGCGAUG&CAUUGCUCACAUUGCUUCC	(((((((((((..((((((&))))))..)))))))))))	CGAAGUCAUUGAUGGAAACAUUGUUUUUUCGCCACGCGGCUGGAGCGAUUUUUGUCCGCUGAAAGAGAGGGCGUUAUGUCAGCUUCCCUGAAGAAUCAACAAGGCUUUAGCCUGCCGGAGGUAAUGUUGGCGAUGGUGUUGAUGGUGAUG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0052703	0.9291058	ppdC	945797	putative prepilin peptidase-dependent protein
b2120	43	58	48	54	10.52	RyhB	71	86	75	81	11.6	-12.11	-34.23	-1.27334	GCCUGCGCCCGGCUGG&CCAGCCGGGUGCUGGC	(((.((((((((((((&)))))))))))).)))	GUGUCGCCACACAUAAAGAAGCUCACUGGCAGGCUUAUUAUCAAGCCCGCCACCGCCUGCCGUGAGGAAAGAUGCAUGAGCGAGCCGUUAAUUGUCGGCAUCCGGCAUCAUAGUCCGGCCUGCGCCCGGCUGGUGAAAUCGUUAAUCGAA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0155581	0.9496255	yehM	946651	uncharacterized protein
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

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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