Input and runtime details for job 6571257 (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 6571257 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:18:03 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:20:22 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:21:19 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:22:25 CET 2020
	Job Completed		@ Mon Jan 27 14:22:35 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

Description of the job

Spot42 - 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
b2357	-27	-17	-23	-17	3.22	Spot42	55	65	55	61	6.03	-10.32	-19.57	-1.0637	CAGCCAGAUCC&GGAUUUGGCUG	(((((((((((&)))))))))))	AAAACGCGAAGACCCGUACUUCAAAGCCAGUUACGACAAUGUGGACUACAGCCAGAUCCCGGCAGGAUUCAGGGGGUGAGCAUGAGUCUUUUGAAUGACGUUCAGAAAUUCAUUGAAGCCCAUCCGGGCUGUACUUCCGGAGACAUUGCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0126314	0.9238006	yfdN	946419	CPS-53 (KpLE1) prophage uncharacterized protein
b1927	-50	-39	-49	-43	2.49	Spot42	48	59	52	58	1.57	-13.13	-17.19	-1.35333	AAUCCGAUUACG&CGUAAUCGGAUU	((((((((((((&))))))))))))	CUGAAUGAGUCGAUGGCUCGCGAAUAAUCCGAUUACGGCUACGCUUCUAAUGUUCCCCUUGAAUGGAGUCGAAGAAUGCGUAAUCCCACGCUGUUACAAUGUUUUCACUGGUAUUACCCGGAAGGCGGUAAGCUCUGGCCUGAACUGGCC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0025285	0.9238006	amyA	946434	cytoplasmic alpha-amylase
b0718	20	33	25	31	3.34	Spot42	1	14	3	9	5.33	-10.35	-19.02	-1.06679	CUUUUGUAUCCUGC&GUAGGGUACAGAGG	((((((((((((((&))))))))))))))	GCUGGAUUAUAAAUAAGUAUUAUUUUGGCGGCAUCAUCGCCGCCUUUCAUAAAAUAUUUAUCAGGUAUGGACACCGUGAAUAUUUAUCGACUCUCUUUUGUAUCCUGCCUGGUCAUGGCGAUGCCUUGCGCAAUGGCGGUCGAAUUCAAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0124179	0.9238006	ybgQ	946537	putative outer membrane protein
b2216	-57	-49	-55	-49	1.3	Spot42	3	11	3	9	3.43	-10.78	-15.51	-1.11111	CUGUACCCU&AGGGUACAG	(((((((((&)))))))))	AGAGUCUGGAAUUUCACACUGUACCCUUUAUACUGCCCUAUCACUUCGCGAAGUUUUAACAGGUCAUAAACACGAAUGCGUCAGAAAGAGACAACGGCCACGACCCGCUUUUCACUCCUACCGGGGAGCAUUACCCGCUUCUUUUUACUG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.009723	0.9238006	rcsD	946717	phosphotransfer intermediate protein in two-component regulatory system with RcsBC
b2294	-75	-67	-73	-67	1.57	Spot42	48	56	48	54	1.57	-8.74	-11.88	-0.900847	CUGAUUACG&CGUAAUCGG	(((((((((&)))))))))	CUGAUUACGCAUAUAAAAGAAGGCAUACUCAGCCUUCUUUUUUUUCACCGUAGUAGAGUGAUACAGGAGUCAACAAUGGAAAUGACCAACGCGCAACGUCUUAUUUUGUCUAAUCAGUACAAGAUGAUGACUAUGCUCGAUCCGGCAAAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0308106	0.9238006	yfbU	946767	UPF0304 family protein
b2319	3	19	13	19	6.68	Spot42	20	36	20	26	4.78	-9.12	-20.58	-0.940014	GUCUGAAGGCUGGAACA&UGUUCUAUCUUUCAGAC	(((((((((.(((((((&))))))).)))))))))	GGCACGUUAAUCUCUUCUUCAUGCUCUCUGCUGUAACAUUGGCAGGGAGCUUUGCUAUUUCUGGAGUAAACCACCAUGUCUGAAGGCUGGAACAUUGCCGUCCUGGGCGCAACUGGCGCUGUGGGCGAAGCCCUGCUUGAAACGCUGGCU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0248939	0.9238006	usg	946797	putative semialdehyde dehydrogenase
b1921	60	75	61	67	0.19	Spot42	49	65	58	64	6.17	-9.65	-16.01	-0.994642	CAGCCAGACCCAUUGC&GUAAUCGGAUUUGGCUG	((((((((((..((((&))))..)).))))))))	CGGUUACGCACUAAACUGGGUAAGUUAUAACGUCAGUAAAUGCCGCACUUUAACUUUGACUACCAGGAGUUCUUAAUGAUGGUGCAGCACCUGAAAAGACGGCCAUUAAGCCGCUAUCUUAAAGACUUUAAACACAGCCAGACCCAUUGC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0184641	0.9238006	fliZ	946833	RpoS antagonist putative regulator of FliA activity
b4311	-27	-16	-22	-16	3.92	Spot42	1	12	1	7	3.46	-11.59	-18.97	-1.1946	UCUGUAUCCUAC&GUAGGGUACAGA	((((((((((((&))))))))))))	UAUUACACAACAUAAAUGCUAAUUGUUUAUGCGGGCUUUGUAUUGCUUUCUGUAUCCUACAAAUGAGUGAAAUUUAUGAAAAAGGCUAAAAUACUUUCUGGCGUAUUAUUACUGUGCUUUUCGUCCCCAUUAAUUUCUCAGGCUGCGACA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0061225	0.9238006	nanC	946843	N-acetylnuraminic acid outer membrane channel protein
b2407	-22	-16	-22	-16	0.8	Spot42	1	7	1	7	2.01	-8.77	-11.58	-0.903939	ACCCUAC&GUAGGGU	(((((((&)))))))	AAGUGUAUUGGUAAGAGCCGGGACAACCUCGCUAUAAAAAGGCGUUAGAUUCCACCCUACAGAAAAAGGAUAUGUAUGUCUCAGGUUCAAUUUUCUCAUAACCCGCUGUUUUGCAUAGAUAUUAUCAAGACUUAUAAACCUGAUUUCACG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0302973	0.9238006	xapA	946878	purine nucleoside phosphorylase 2 nicotinamide 1-beta-D-riboside synthase
b1300	-28	-13	-28	-22	3.43	Spot42	44	58	52	58	2.61	-9.81	-15.85	-1.01113	AUCUGAUAGACGUGAA&UUCACGUAAUCGGAU	(((((((..(((((((&))))))).)))))))	CAUACGGCCCGGGGAUCUCUGCGCCCUGACGUUCACAAACUGCAUAUAUCUGAUAGACGUGAAACAGGAGUCAUAAUGAAUUUUCAUCAUCUGGCUUACUGGCAGGAUAAAGCGUUAAGUCUCGCCAUUGAAAACCGCUUAUUUAUUAAC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0168668	0.9238006	puuC	947003	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase succinate semialdehyde dehydrogenase

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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