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
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
b3139	13	19	13	19	0.4	Spot42	1	7	1	7	2.01	-9.42	-11.83	-0.970936	ACCCUAC&GUAGGGU	(((((((&)))))))	CGUCCCUGGCGAUCAAAAAGAACAAAUCCCUGACUAAAUCUAAAAUCGCCUUAAUAUUGGUUUGAGGUAAUAAAAAUGCAUGAAAUAACCCUACUUCAGGGAUUAUCCCUGGCGGCGUUAGUUUUUGUUCUGGGGAUUGAUUUUUGGCUG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0210242	0.9238006	agaC	947652	N-acetylgalactosamine-specific enzyme IIC component of PTS
b3690	-4	11	-2	5	3.57	Spot42	17	31	23	29	4.24	-9.42	-17.23	-0.970936	AAAGAUGGAACAUUU&AGAUGUUCUAUCUUU	(((((((((((((((&)))))))))))))))	CCCGCCAUCAUACUUCACAAGGACUUCACUUUCAGACAAUAGUCUUUUGCCAUCGUGAUGAAUGUGAGUGAAAAGAUGGAACAUUUCGACGUGGCGAUUAUUGGCCUCGGCCCGGCAGGAUCGGCGUUGGCACGAAAGUUAGCAGGCAAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0210242	0.9238006	cbrA	948197	colicin M resistance protein FAD-binding protein putative oxidoreductase
b0705	41	48	41	47	1.46	Spot42	49	56	50	56	0.3	-9.4	-11.16	-0.968874	CCGAUUAC&GUAAUCGG	((((((((&))))))))	UAUUCCUUAUUACCUAAAGCUGUUUUUCAUAGCUUAUACAUGAUCAAAUACUCCUUACAUAAAUAAGGUGAACAAAUGGAACUUAAAAAAUUGAUGGAACAUAUUUCUAUUAUUCCCGAUUACAGAUAAGCCUGGAAAGUAGAGCAUAAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0212627	0.9238006	ybfL	947075	pseudogene DDE domain transposase familyputative factor Not classified putative receptor protein
b4174	-75	-61	-68	-62	2.14	Spot42	42	57	43	49	3.26	-9.36	-14.76	-0.964751	UCUGAAGCGUGGAGU&ACUUCACGUAAUCGGA	(((((..((((((((&))))))))...)))))	UCUGAAGCGUGGAGUCAUAUCCUCUGGCGUCGAAAGACAACAGGGAUCACCGCAUAACAAAUAUGGAGCACAAACAUGGCGUGGAAUCAGCCCGGUAAUAACGGACAAGACCGCGACCCGUGGGGAAGCAGCAAACCUGGCGGCAACUCU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0217476	0.9238006	hflK	948698	modulator for HflB protease specific for phage lambda cII repressor
b0969	-24	-15	-21	-15	0.31	Spot42	50	59	50	56	0.3	-9.29	-9.9	-0.957536	AGUCUGAUUA&UAAUCGGAUU	((((((((((&))))))))))	CUUUCAUAGCCUCGCUUUAUGCGGGGCUUUGUUUUUUGUUACACUGCCGCCAGUCUGAUUAAGGUAGUAAUAAUUAUGCUGAUCUUCGAAGGUAAAGAGAUAGAAACGGAUACCGAAGGCUAUCUCAAAGAAAGCAGCCAGUGGAGUGAG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0226226	0.9238006	tusE	945023	mnm(5)-s(2)U34-tRNA 2-thiolation sulfurtransferase
b1056	68	75	68	74	1.16	Spot42	49	56	50	56	0.3	-9.26	-10.72	-0.954444	CCGAUUAC&GUAAUCGG	((((((((&))))))))	CAUCAUUUCAUCGAUAAAGACGACACUCUGAAGCGCAUGCUGGGAAAGUCGUCAUCUGACUAUGGAGUAUAAAAAAUGAAAAAAAGCCUGCUUGGUUUAACCUUCGCGUCCCUGAUGUUCUCUGCCGGUUCAGCGGUUGCCGCCGAUUAC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.023008	0.9238006	yceI	946145	periplasmic high pH-inducible lipid-binding protein
b2548	-17	-11	-17	-11	1.11	Spot42	1	7	1	7	2.01	-9.25	-12.37	-0.953413	ACCCUAC&GUAGGGU	(((((((&)))))))	GAGCGGCACGCGCUGCCGCUCAUCACAAAAUAAUUAGAAUAAGCCGUUGUUAAUAAAAACCCUACAGGAGGCUCUAUGCCUACAAAAAUGAGAACAACCCGUAAUCUAUUAUUAAUGGCUACGCUAUUAGGUAGCGCACUAUUUGCCAGG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.023138	0.9238006	yphF	947020	putative sugar ABC transporter periplasmic binding protein
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
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

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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