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
b2962	26	68	33	39	15.68	Spot42	4	57	44	50	12.67	-10.78	-39.13	-1.11111	UCCUGCAACGUGAAGCAGAAGGUCAGGAUUUUCAGCUGUACCC&GGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGA	(((....((((((((.(((((((((((((......((((((((&))))))))..............)))))...)))))))).))))))))....)))	CCCGUGGAGCGUUUGUUACAGCAGUUACGCACUGGCGCGCCGGUUUAGCGCGUGAGUCGAUAAAGAGGAUGAUUUAUGAGCAGAACGAUUUUUUGUACUUUCCUGCAACGUGAAGCAGAAGGUCAGGAUUUUCAGCUGUACCCCGGCGAG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.009723	0.9238006	yggX	947461	oxidative damage protective factor for iron-sulfur proteins
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
b1391	56	67	61	67	4.67	Spot42	55	66	55	61	6.04	-10.65	-21.36	-1.09771	UCAGCCAGAUCC&GGAUUUGGCUGA	((((((((((((&))))))))))))	UGGACCCAUGCUGGCAGAAAUGCAGUAUCUCCAGCGUGUCUUGCCCGGUCAGCAAUGGUAACAGAGGAGAUGGGUAUGCAACGUCUGGCCACCAUUGCACCGCCACAGGUUCAUGAGAUAUGGGCGCUACUCAGCCAGAUCCCGGACCCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0104701	0.9238006	paaD	945959	ring 12-phenylacetyl-CoA epoxidase subunit
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
b2602	-71	-60	-67	-61	1.23	Spot42	7	18	8	14	7.38	-10.62	-19.23	-1.09462	CUUACCUCUGUA&UACAGAGGUAAG	((((((((((((&))))))))))))	AACCCUUACCUCUGUAUAGAUAAAUUUACACUCCCUUUGAAAACAAUCCGCUAUGCUUUGAAAAAGGAGAAAGAAAUGAUGAAAAAGUUUAUCGCCCCCUUGUUGGCUUUACUGGUUAGCGGAUGUCAGAUUGAUCCUUAUACUCACGCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0106505	0.9238006	yfiL	947106	lipoprotein
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
b0721	-55	-44	-50	-44	6.86	Spot42	4	15	4	10	5.8	-10.51	-23.17	-1.08328	ACCUCUGUGCCC&GGGUACAGAGGU	((((((((((((&))))))))))))	CUCCAGGUAACAGAAAGUUAACCUCUGUGCCCGUAGUCCCCAGGGAAUAAUAAGAACAGCAUGUGGGCGUUAUUCAUGAUAAGAAAUGUGAAAAAACAAAGACCUGUUAAUCUGGACCUACAGACCAUCCGGUUCCCCAUCACGGCGAUA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0113383	0.9238006	sdhC	945316	succinate dehydrogenase membrane subunit binds cytochrome b556
b3934	-56	-44	-51	-45	1.68	Spot42	41	56	42	48	3.3	-10.45	-15.43	-1.0771	CCGAUGUGAAGUA&UACUUCACGUAAUCGG	(((((((((((((&))))))))...)))))	CUAUCUGCUAAAAAUGUUGCCGAUGUGAAGUAAACAUGGAUGUAGUACGCCUGACGUGCCAGGCGAGGAGUGAGUGUGAAAGCGAAGAAGCAGGAAACUGCCGCGACCAUGAAAGACGUUGCCCUCAAGGCAAAAGUCUCUACAGCGACC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0117318	0.9238006	cytR	948427	Anti-activator for CytR-CRP nucleoside utilization regulon
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
b2980	2	16	3	9	3.62	Spot42	18	33	26	32	4.24	-10.39	-18.25	-1.07092	UGAAAGAUGAACGUC&GAUGUUCUAUCUUUCA	(((((((((((((((&))))))).))))))))	AAUCACUUACGUGAUGUGCGUGUUUUGCGAGUUAAGAACAGAAAAAUUGGUCCUACCUGUGCACGAGGUCCGGGAAUGAAAGAUGAACGUCGCCCUAUUUGCGAAGUGGUUGCAGAGAGUAUCGAACGGUUAAUUAUCGACGGCGUACUG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0121389	0.9238006	glcC	947466	glycolate-inducible glc operon transcriptional repressor autorepressor

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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