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
b1343	21	34	28	34	1.43	Spot42	11	24	11	17	7	-8.89	-17.32	-0.916308	GAAUGUUUUGCCUC&GAGGUAAGAUGUUC	((((((((((((((&))))))))))))))	AUUGUCGCAUCGUGAGCGUAGAUCUGCGAGGAUACGCGCCUGCUAACUUUGCGUCGAUGACCACGAGAAUAGAUUGUGACCGCUUUUUCUACCCUGAAUGUUUUGCCUCCCGCCCAACUCACGAACCUUAAUGAGUUGGGUUAUUUAACC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0283265	0.9238006	dbpA	947153	ATP-dependent RNA helicase specific for 23S rRNA
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
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
b0728	-20	-9	-20	-14	2.59	Spot42	23	34	28	34	3.29	-9.01	-14.89	-0.928676	CUGAAGGAUGGA&UCUAUCUUUCAG	((((((((((((&))))))))))))	CAAUGCCCGGAAGCGAUACGAAAUAUUCGGUCUACGGUUUAAAAGAUAACGAUUACUGAAGGAUGGACAGAACACAUGAACUUACAUGAAUAUCAGGCAAAACAACUUUUUGCCCGCUAUGGCUUACCAGCACCGGUGGGUUAUGCCUGU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0264814	0.9238006	sucC	945312	succinyl-CoA synthetase beta subunit
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
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
b3908	-12	16	10	16	4.66	Spot42	1	34	1	7	9.12	-9.96	-23.74	-1.02659	CUGGAGAUGAAUAUGAGCUAUACCCUGC&GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAG	((((((((((((((...((.((((((((&)))))))).)).......)))))).))).)))))	CAUUUAAUUAACUAUAAUGAACCAACUGCUUACGCGGCAUUAACAAUCGGCCGCCCGACAAUACUGGAGAUGAAUAUGAGCUAUACCCUGCCAUCCCUGCCGUAUGCUUACGAUGCCCUGGAACCGCACUUCGAUAAGCAGACCAUGGAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0154934	0.9238006	sodA	948403	superoxide dismutase Mn
b3078	-27	-20	-26	-20	0.44	Spot42	1	8	1	7	2.09	-10.33	-12.86	-1.06473	UACCCUAC&GUAGGGUA	((((((((&))))))))	CCAUAACAAAUAACAACUACGGCGGCAAAAGGAGUUUGCCGCCACCGCUACCCUACUCAUUUUCGGAGAUGUGUUAUGUCUGAUACCAAACGUAAUACAAUCGGCAAAUUCGGCUUGCUCUCGCUGACUUUUGCCGCCGUUUACAGCUUU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0125598	0.9238006	ygjI	947579	putative transporter
b2801	-39	-29	-39	-33	2.87	Spot42	46	56	50	56	1.84	-12.84	-17.55	-1.32344	CCGAUUACGUG&CACGUAAUCGG	(((((((((((&)))))))))))	CCCGAACUCGCUGGUUUUGCACUUUUGAAAACAUAACCGAUUACGUGCUUAAGCUUCUGAACCUAAGAGGAUGCUAUGGGAAACACAUCAAUACAAACGCAGAGUUACCGUGCGGUAGAUAAAGAUGCAGGGCAAAGCAGAAGUUACAUU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.002988	0.9238006	fucP	947487	L-fucose transporter
b1751	-14	-2	-13	-7	3.61	Spot42	21	33	26	32	4.03	-9.65	-17.29	-0.994642	UGAAGGAUAGAAC&GUUCUAUCUUUCA	(((((((((((((&)))))))))))))	CCCGACACAAACAUGUGGAUCUGUCUGCUUCGCGCCGCAGCCCACUUACUCACCCAAAAAAUGAAGGAUAGAACGAUGUUGCAACAUUAUUCAGUGUCAUGGAAAAAAGGACUGGCUGCACUCUGUUUACUGGCUGUUGCUGGGCUUAGC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0184641	0.9238006	ydjY	946248	putative ferrodoxin-like lipoprotein

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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