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
b2150	-48	-22	-28	-22	7.03	Spot42	1	24	1	7	7.99	-9.49	-24.51	-0.978151	GAGCAUUUAUCUCAAGCACUACCCUGC&GUAGGGUACAGAGGUAAGAUGUUC	(((((((((((((......((((((((&))))))))..))))).))))))))	ACACUUCAUUAACUCUACUGCCCCGCCGAGCAUUUAUCUCAAGCACUACCCUGCAUAAGAAAAACCGGAGAUACCAUGAAUAAGAAGGUGUUAACCCUGUCUGCUGUGAUGGCCAGCAUGUUAUUCGGUGCCGCUGCACACGCUGCUGAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0202101	0.9238006	mglB	949041	methyl-galactoside transporter subunit
b2506	-51	-37	-49	-43	1.09	Spot42	55	68	60	66	6.05	-11.81	-18.95	-1.21728	AUUCAGCCAAAUACC&GGAUUUGGCUGAAU	((((((((((((.((&))))))))))))))	ACCACGACGUAUAACGAAACGCGUAUUCAGCCAAAUACCAAAUGUCCUGAAAAGAGCUAAUAAUCAGGAGGAGUCAUGAAGAAAGUUUUUCUUUGCGCCAUCUUAGCCUCCUUAAGCUAUCCGGCUAUCGCCUCAUCAUUGCAGGAUCAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0053979	0.9238006	yfgI	945168	nalidixic acid resistance protein putative periplasmic protein
b1487	61	69	62	68	2.83	Spot42	48	56	49	55	1.57	-9.48	-13.88	-0.97712	CCGGUUGCG&CGUAAUCGG	(((((((((&)))))))))	ACCCUCUGCUCGCUGAUCAAUUCUCUUGUUUUAUAUCCCCUGGCACACAGCACGUCAGUUAAUCAGGAAACUGUCAUGAAGAGAUCGAUAUCGUUUCGUCCCACAUUGCUCGCGCUCGUCCUUGCCACAAAUUUCCCGGUUGCGCACGCC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0203245	0.9238006	ddpA	946052	DD-dipeptide ABC transporter periplasmic binding protein
b3503	-75	-69	-75	-69	0.06	Spot42	1	7	1	7	2.01	-9.14	-11.21	-0.942075	ACCCUGC&GUAGGGU	(((((((&)))))))	ACCCUGCCUGUGCUGUUUGUGACGCUGGCUGCGCUGGCGCUACGUCUCUCUUUCACUUUGUAAUGAGAUACUGAUAUGAGCAACAUUACCAUUUAUCACAACCCGGCCUGCGGCACGUCGCGUAAUACGCUGGAGAUGAUCCGCAACAGC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0246155	0.9238006	arsC	948018	arsenate reductase
b2622	62	69	62	68	1.3	Spot42	49	56	50	56	0.3	-9.01	-10.61	-0.928676	CCGAUUAC&GUAAUCGG	((((((((&))))))))	ACCUUUUAGGCCCAUUGAUAGGCCCAACGAAAAGCUCUAUUGUUUACGUUGGGCCUAAACGCAGGGAGACUCCCCAUGGCAAGAAAAACCAAGCCGUUAACUGAUACGGAAAUCAAAGCCGCCAAACCUAAAGAUGCCGAUUACCAGCUU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0264814	0.9238006	intA	946160	CP4-57 prophage integrase
b1792	-68	-32	-53	-47	5.05	Spot42	40	73	52	58	9.22	-9.23	-23.5	-0.951352	AAGAAAUUCGCUAAUAUCCGGUGCUAUAGUGACGUAA&UUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUU	((((.(((((((((.(((((((......((((.((((&)))).))))...)))))))))))).)))).))))	AGAGACAAAGAAAUUCGCUAAUAUCCGGUGCUAUAGUGACGUAACAAAUCAUGCGUGAAAGGGAGAACAAACACGAUGAAUAUUCAGUGCAAACGCGUUUAUGAUCCGGCUGAACAGAGCGAUGGUUAUCGCAUACUGGUCGACCGCCUC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0234	0.9238006	yeaO	945675	DUF488 family 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
b0882	-74	-44	-66	-60	5.82	Spot42	3	32	18	24	8.8	-9.02	-23.64	-0.929707	GGGAGAAUGAGCAUCCAUUGCUGUGUACGCU&AGGGUACAGAGGUAAGAUGUUCUAUCUUUC	((((((..(((((((.....((..((((.((&)).))))..))....)))))))..))))))	AGGGAGAAUGAGCAUCCAUUGCUGUGUACGCUAGAAAAAGCCUGAAUGCAGGCAUAAAAAUUGGGGGAGGUGCCUAUGCUCAAUCAAGAACUGGAACUCAGUUUAAAUAUGGCUUUCGCCAGAGCGCGCGAGCACCGUCAUGAGUUUAUG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0263331	0.9238006	clpA	945764	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity
b0333	-32	-26	-32	-26	0.27	Spot42	1	7	1	7	2.01	-10	-12.28	-1.03072	ACCCUAC&GUAGGGU	(((((((&)))))))	AGGUCGGAUAAGACGCAUAGCGUCGCAUCCGACAACAAUCUCGACCCUACAAAUGAUAACAAUGACGAGGACAACAUGAGCGACACAACGAUCCUGCAAAACAGUACCCAUGUCAUUAAACCGAAAAAAUCUGUGGCACUUUCUGGCGUU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0151462	0.9238006	prpC	947528	2-methylcitrate synthase
b3664	17	32	17	23	7.49	Spot42	40	56	50	56	3.32	-10.58	-21.39	-1.0905	CCGAUUACGUGAGUAA&UUACUUCACGUAAUCGG	((((((((((((((((&)))).))))))))))))	AUAAUUAUCACUGAACCGUUGUUGUCAUUUGUUUUACAAAAGCAAGGGAUUAAAUCUCCUCCAAUGGACAAAAAAAUGAAUAAUGACAAUACCGAUUACGUGAGUAAUGAAUCAGGGACGCUUUCGCGAUUAUUUAAACUACCUCAGCAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0108957	0.9238006	adeQ	948174	adenine permease high affinity adenine:H+ symporter

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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