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
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
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
b0885	-27	-10	-17	-11	6.33	Spot42	42	58	43	49	3.26	-13.52	-23.11	-1.39353	AUCCGACUUGCGUGGAGU&ACUUCACGUAAUCGGAU	((((((.(((((((((((&)))))))))))))))))	GGGGCGUUAUUACCAGUUCAAGCAGGGUUUGUAAGCUAUUAUUGAACGAUCCGACUUGCGUGGAGUUUUGCGGUCAUGCGCCUGGUUCAGCUUUCUCGCCAUUCAAUAGCCUUCCCUUCCCCGGAAGGCGCAUUACGUGAGCCUAACGGC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0020193	0.9238006	aat	945490	leucyl/phenylalanyl-tRNA-protein transferase
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
b0559	38	49	38	44	2.17	Spot42	46	58	52	58	1.84	-9.04	-13.05	-0.931768	AUCUGAUUCGUG&CACGUAAUCGGAU	((((((((((((&)))).))))))))	CUCAAACCUUCAUACAGAAAGAUUUGAAGUAAUAUUUUAACCGCUAGAUGAAGAGCAAGCGCAUGGAGCGACAAAAUGAAUAAAGAACAAUCUGCUGAUGAUCCCUCCGUGGAUCUGAUUCGUGUAAAAAAUAUGCUUAAUAGCACCAUU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0260389	0.9238006	ybcW	945175	DLP12 prophage uncharacterized protein
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
b3685	-51	-36	-49	-43	4.25	Spot42	54	68	60	66	6.15	-11.08	-21.48	-1.14203	AUUCAGCCAUAAUCCG&CGGAUUUGGCUGAAU	(((((((((.((((((&)))))))))))))))	CUAUAAGGCAAAUCUGCUUCACCGAUUCAGCCAUAAUCCGUAGCAAUUAAAAUGUUAUCUCAAGAGAAAUGGACGAUGAGUGAUAUAGCAUUAACGGUCAGUAUUCUGGCUUUGGUGGCAGUCGUCGGUUUGUUUAUCGGCAACGUCAAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0081942	0.9238006	yidE	948193	putative transporter
b0511	-28	10	-28	-22	12.54	Spot42	18	58	52	58	12.19	-9.6	-34.33	-0.989488	AUUCGAUACGUGAAAUUAAGAGGGAUUUAUGGAACAUC&GAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAU	((((((((((((((..(((((((((...((((((((((&))))))))))...))...))))))).))))))).)))))))	AAUAUUUUUAUUUUAUUUGUUCCUCAUAGCUAGAUUAAAACAACGUUAUUCGAUACGUGAAAUUAAGAGGGAUUUAUGGAACAUCAGAGAAAACUAUUCCAGCAACGCGGCUAUAGCGAAGAUCUAUUGCCGAAAACGCAAAGCCAGCGG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0189931	0.9238006	ybbW	945138	putative allantoin transporter
b0367	-75	-66	-73	-67	0.27	Spot42	52	61	53	59	2.18	-10.23	-12.68	-1.05442	CAAGUCCGAU&AUCGGAUUUG	((((((((((&))))))))))	CAAGUCCGAUCCACAAUUCAUCGCCAUGCGCGAAUAUGUUUUAAGCCGCGUAUUUGAGCAACGGGAGGCGUUCUCAUGAGUGUGCUCAUUAAUGAAAAACUGCAUUCGCGGCGGCUGAAAUGGCGCUGGCCGCUCUCGCGUCAGGUGACC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0132937	0.9238006	tauC	945026	taurine ABC transporter permease
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

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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