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
b2619	67	75	69	75	3.62	Spot42	1	9	1	7	2.1	-8.94	-14.66	-0.921461	GUACCCUAC&GUAGGGUAC	(((((((((&)))))))))	GGGGACAAGGCUCUAUCUUAGCAUGAACCCGAUGUUACCCAGCGCCGGGAUAGCGUUUUUUUUACAGCAGGAUAAAUGAUAUUAUUUGUUGGAUUUUUGUUGAUGGAAAUUGUUAUGCCUCAGAUUAGCCGGACCGCACUGGUACCCUAC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0275429	0.9238006	ratA	945614	toxic UPF0083 family protein inhibitor of 70S ribosome formation
b1695	43	63	57	63	3.26	Spot42	48	71	48	54	7.47	-8.85	-19.58	-0.912185	AGUAUUCGCGAACUGAUUACG&CGUAAUCGGAUUUGGCUGAAUAUU	(((((((((.(((((((((((&)))))))))..)).)).)))))))	UGGACGAAAGAUUAUUUAUCGAUGCGGCGAUGGGUUUUGUCCUGCCUGAAGCGGCUCAUUAACAGGAGUAUAAUGAUGGAUUUUUCUUUAACUGAAGAACAAGAACUGCUGCUGGCCAGUAUUCGCGAACUGAUUACGACUAACUUUCCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.028969	0.9238006	ydiO	945626	putative acyl-CoA dehydrogenase
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
b1182	60	69	62	68	1.35	Spot42	20	29	21	27	1.55	-8.85	-11.75	-0.912185	AGAUGGAGCA&UGUUCUAUCU	((((((((((&))))))))))	GAUGAAGUAAAAUUUAUUAAUAGUUGUAAAACAGGAGUUUCAUUACAAUUUAUAUAUUUAAAGAGGCGAAUGAUUAUGACUGAAAUCGUUGCAGAUAAAACGGUAGAAGUAGUUAAAAACGCAAUCGAAACCGCAGAUGGAGCAUUAGAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.028969	0.9238006	hlyE	945745	hemolysin E
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
b1212	15	28	20	26	4.52	Spot42	43	56	45	51	3.25	-13.07	-20.84	-1.34715	CUGGUUACGUGAAG&CUUCACGUAAUCGG	((((((((((((((&))))))))))))))	GCUGGAUAUGCUGAUUGAACCGAUUAUCCAGGAACAUCAGGCCGACCAACUGGCGGCGUUGUCCGAGCAGGAAUAAUGGAAUAUCAACACUGGUUACGUGAAGCAAUAAGCCAACUUCAGGCGAGCGAAAGCCCGCGGCGUGAUGCUGAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0026174	0.9238006	prmC	945779	RF-1 and RF-2 N5-glutamine methyltransferase
b1623	-58	-51	-57	-51	1.86	Spot42	1	8	1	7	2.09	-9.03	-12.98	-0.930738	UACCCUGC&GUAGGGUA	((((((((&))))))))	GCGCAAUCGUGGAUUUUUACCCUGCUUUGUUUUUAUAAUGGUGCGCACUUUUAUAUCCAGAAAAAGAGUGCGACCAUGAUUGAUACCACCCUGCCAUUAACUGAUAUCCAUCGCCACCUUGAUGGCAACAUUCGUCCCCAGACCAUUCUU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0261856	0.9238006	add	945851	adenosine deaminase
b1385	21	37	31	37	2.01	Spot42	55	71	55	61	6.06	-11.57	-19.64	-1.19254	AGUAUUAAGCCAGGUCC&GGAUUUGGCUGAAUAUU	((((((.((((((((((&)))))))))).))))))	GUCACAGCGAAAAAAGUGACUUUUCUUGUCGCUGCGUACACUGAAAUCACACUGGGUAAAUAAUAAGGAAAAGUGAUGACAGAGCCGCAUGUAGCAGUAUUAAGCCAGGUCCAACAGUUUCUCGAUCGUCAACACGGUCUUUAUAUUGAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.006193	0.9238006	feaB	945933	phenylacetaldehyde dehydrogenase
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
b1398	-10	-2	-8	-2	1.61	Spot42	1	9	1	7	2.1	-13.17	-16.88	-1.35745	GUACCCUAC&GUAGGGUAC	(((((((((&)))))))))	GUGCAUCGGUGUCGGUCAGGGCAUCGCCAUGAUUCUGGAGCGUGUUUGAGCAUAUCAACCUGCGAGUACCCUACAAUGAUAACCAAUACAAAGCUUGACCCGAUUGAAACCGCGUCUGUUGAUGAGUUACAGGCGUUGCAAACACAGCGU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0024709	0.9238006	paaK	945963	phenylacetyl-CoA ligase

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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