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
b4361	-33	-23	-33	-27	0.83	Spot42	55	65	59	65	6.03	-9.75	-16.61	-1.00495	CAGCCAAAUUC&GGAUUUGGCUG	(((((((((((&)))))))))))	CGGACUGCCGAAACGAGAUGUGAAUACGGUCAGCGAACCUGACAGCCAAAUUCCACCAGGAUUCAGAGGGUAACGAUGAAAAACGUUGGCGACCUGAUGCAACGCCUGCAAAAAAUGAUGCCUGCCCAUAUCAAACCCGCAUUCAAAACG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0174491	0.9238006	dnaC	948864	DNA biosynthesis protein
b3051	19	28	22	28	2.51	Spot42	3	12	3	9	3.46	-10.36	-16.33	-1.06782	UCUGUGCCCU&AGGGUACAGA	((((((((((&))))))))))	UGCAACGCGAUAUUUGGCGGAAAAUAAUCCCUGGCCCCAAAUAUUGUAAUUUAUUAAUCAAAAGGAAAUUUAAUAAUGGAUGAUAUUGUUAAUUCUGUGCCCUCCUGGAUGUUUACCGCAAUUAUUGCCGUAUGCAUUCUGUUUAUUAUU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0123476	0.9238006	yqiK	947537	PHB family membrane protein function unknown
b3238	-21	-5	-21	-15	2.8	Spot42	39	54	48	54	3.87	-9.61	-16.28	-0.990519	GAUUAUGUCGAGGUAAA&UUUACUUCACGUAAUC	((((((((.((((((((&))))))))))))))))	UUAGUGUAUACUUGAUUUUGUGAUAUGGGUCACGAAACAAAGGCCCAGCUAAAAGAUUAUGUCGAGGUAAAAAUCAUGAAAAUCAAAACCACUGUUGCUGCAUUAAGCGUACUUUCUGUUCUCUCUUUCGGUGCAUUCGCUGCCGACUCC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0188861	0.9238006	yhcN	947835	cadmium and peroxide resistance protein stress-induced
b4465	-18	-2	-18	-12	3.4	Spot42	39	56	50	56	3.89	-8.82	-16.11	-0.909092	CUGAUUACAGAGGUAAA&UUUACUUCACGUAAUCGG	((((((((.((((((((&))))))))..))))))))	UAUUGGCGAUCCAAAACUCGACACUUUAUUUAAUCAAUUAACCGCCGAACAUAAACACUGAUUACAGAGGUAAAAAUGAAAACCAAAGUUGCUGCUAUUUAUGGCAAGCGGGAUGUCCGUCUGCGCGUAUUUGAACUGCCAGAAAUUACC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0294603	0.9238006	yggP	2847686	putative Zn-binding 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
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
b3683	5	16	5	11	0.51	Spot42	55	66	60	66	6.04	-9.25	-15.8	-0.953413	UCAGUCAAAUUC&GGAUUUGGCUGA	((((((((((((&))))))))))))	CCUAUCCUCGCUCCAGGCCUGCCGCAUAACCAAUCAGGCUUCCUACUUACAGAAUUGAGAAAAGAGGAUGUGGAAAUGCUCAGUCAAAUUCAACGCUUUGGCGGCGCGAUGUUCACGCCAGUGCUGCUGUUUCCCUUCGCCGGGAUUGUG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.023138	0.9238006	glvC	2847721	pseudogene arbutin specific enzyme IIC component of PTSenzyme Transport of small molecules: Carbohydrates organic acids alcohols PTS system arbutin-like IIB component PTS system arbutin-like IIC component
b1347	-46	-34	-43	-37	1.2	Spot42	20	32	23	29	4.03	-10.44	-15.67	-1.07607	GAAAGAUGGAAUA&UGUUCUAUCUUUC	(((((((((((((&)))))))))))))	GUUAUGGUGGAAGUGAAAAAGAAGCACUCGAAAGAUGGAAUAAACGAACCACUGGAAAUAAUAAUGGAGGUGUUCAUGUAUAAAAUUACCGCCACUAUUGAAAAGGAAGGUGGCACUCCUACUAACUGGACAAGAUAUUCAAAAUCUAAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0117987	0.9238006	ydaC	947504	DUF1187 family protein Rac prophage putative double-strand break reduction protein
b2221	-36	-27	-35	-29	1.58	Spot42	1	11	4	10	3.43	-10.63	-15.64	-1.09565	CUGUACCCAC&GUAGGGUACAG	((((((((((&)).))))))))	CAAUAAUCUCAUUCUGGCACUCCCCUUGCUAUUGCCUGACUGUACCCACAACGGUGUAUGCAAGAGGGAUAAAAAAUGAAAACAAAAUUGAUGACAUUACAAGACGCCACCGGCUUCUUUCGUGACGGCAUGACCAUCAUGGUGGGCGGA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.01059	0.9238006	atoD	947525	acetyl-CoA:acetoacetyl-CoA transferase alpha subunit
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

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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