Input and runtime details for job 1972078 (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 1972078 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:13:56 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:16:07 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:17:05 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:18:21 CET 2020
	Job Completed		@ Mon Jan 27 14:18:31 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1972078&toolName=IntaRNA ( 30 days expiry )

Description of the job

MicC - 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
b0170	-75	-65	-71	-65	0.66	MicC	39	48	39	45	4.7	-11.94	-17.3	-1.23068	GCAUAUGGCCC&GGGCCAUUGC	(((.(((((((&))))))))))	GCAUAUGGCCCCCUUUUUCACUUUUAUAUCUGUGCGGUUUAAUGCCGGGCAGAUCACAUCUCCGAGGAUUUUAGAAUGGCUGAAAUUACCGCAUCCCUGGUAAAAGAGCUGCGUGAGCGUACUGGCGCAGGCAUGAUGGAUUGCAAAAAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.007719	0.9679271	tsf	944866	translation elongation factor EF-Ts
b2118	34	64	58	64	5.65	MicC	7	42	7	13	11.66	-10.57	-27.88	-1.08947	GCCCAACUGGAACUGAAAUAUAAAAAAGGCA&UGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGC	(((((((.((((.((((((((((.(((((((&))))))).)))).....)))))).)))).)))))))	UUCUCCGUAAUCGAUGCCAUCACCGCCAGCGAGCUAAUUAACGAUAUUGAAGCCCUGUUUGAAUAAGGAAAGAGCAUGGACAAGGAAUUACCGUGGCUGGCGGAUAACGCCCAACUGGAACUGAAAUAUAAAAAAGGCAAAACGCCGCUC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0179646	0.9679271	yehI	946649	DUF4132 domain-containing protein
b1406	58	71	58	64	4.77	MicC	41	53	47	53	3.87	-10.5	-19.14	-1.08225	GCGAUGCAACUGGC&GCCAUUGCAUUGC	(((((((((.((((&)))))))))))))	CACCUUCGCAUUAUUUAUCUCUUUUCGUUUCUAUACUGAUUUUUCUUAAUCCGUUUUAUUACAGGGCAGGGUGCGAUGAGCAGCAAUACAUUUACUCUCGGUACAAAAUCCGUUAACCGUCUUGGUUAUGGCGCGAUGCAACUGGCAGGU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0187361	0.9679271	ydbC	945980	putative NAD(P)-binding oxidoreductase
b1152	17	28	17	23	3.49	MicC	37	48	42	48	5.33	-10.21	-19.03	-1.05236	GCGAUGGCCUGA&UUGGGCCAUUGC	((((((((((((&))))))))))))	UUUACGCCUACAAAGUGAAAGCAUUUGGCGAAGUGGCUGAACUGCUGCCCGUCGAUCCCGGCUGUGUGGUAUAUGCGCUGGGAAGGUGUCAGCGAUGGCCUGAAGGUGACCGCCGGGAGUGUUAUUCAGCGCGAUGACCUGGUGCAGUAC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0222753	0.9679271	jayE	945703	pseudogene e14 prophagePhage or Prophage Related
b1093	-8	1	-8	-2	0.86	MicC	57	65	59	65	0.83	-9.81	-11.5	-1.01113	GGAAAAUCA&UGAUUUUCC	(((((((((&)))))))))	GACACCCUGACCGCCUCGGCGCUGAACGAACCUUCAGCGAUGGCAGCGGCGCUCGAGCUUUAAAAGAGGAAAAUCAUGAAUUUUGAAGGAAAAAUCGCACUGGUAACCGGUGCAAGCCGCGGAAUUGGCCGCGCAAUUGCUGAAACGCUC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0281917	0.9679271	fabG	945645	3-oxoacyl-[acyl-carrier-protein] reductase
b0572	-60	-37	-60	-54	9.67	MicC	45	65	59	65	4.26	-9.78	-23.71	-1.00804	GGAAAAUCAGAGCCUGGCGAGUAA&UUGCAUUGCCACUGAUUUUCC	((((((((((....((((((((((&)))).))))))))))))))))	CAUUUUUCUGUCACCGGAAAAUCAGAGCCUGGCGAGUAAAGUUGGCGGCAUAAAAUCACCAGAAAUUAUGAGCCUAUGUCUCCUUGUAAACUUCUGCCAUUUUGUGUGGCCCUUGCGCUAACCGGUUGUUCACUGGCACCGGAUUAUCAG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.02869	0.9679271	cusC	946288	copper/silver efflux system outer membrane component
b2331	-26	-17	-26	-20	0.32	MicC	56	65	59	65	0.92	-10.33	-11.57	-1.06473	GGAAAAUUAG&CUGAUUUUCC	((((((((((&))))))))))	AAAAAUACGUUUAAAACGAUCGAUUGCGCUACGAGUCGGGUAAACUGUAGGAAAAUUAGAAAUAGAGACAGAUAAAUGAAAAAGAAAACAACACUUAGCGAGGAGGACCAGGCUCUGUUUCGCCAGUUGAUGGCGGGGACUCGCAAGAUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0207409	0.9679271	smrB	944847	putative DNA endonuclease
b4328	60	71	61	67	1.26	MicC	53	65	58	64	2.8	-11.97	-16.03	-1.23377	GGAAGAUCGGGG&CCACUGAUUUUCC	((((((((((((&)).))))))))))	AUCAUUACGGUCUGCGUGAUUAACGCAUUGCUGUCGAUCUGGGUUAUGCAGCUUAUUGUUUAACAAGGAGUUACCAUGAUUGAUUAUACCGCAGCCGGUUUUACCCUGCUGCAGGGAGCGCAUUUGUAUGCGCCGGAAGAUCGGGGAAUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.007574	0.9679271	iadA	948853	isoaspartyl dipeptidase
b0688	-10	5	-3	4	3.94	MicC	41	54	42	48	3.89	-10.86	-18.69	-1.11936	GGACAAAGCAAUGGC&GCCAUUGCAUUGCC	((.(((.((((((((&)))))))).)))))	CGAUGCAAUUCCCGGCGGAAUUGAUUGAGAAGGUUUGCGGAACUAUCUAAAACGUUGCAGACAAAGGACAAAGCAAUGGCAAUCCACAAUCGUGCAGGCCAACCUGCACAACAGAGUGAUUUGAUUAACGUCGCCCAACUGACGGCGCAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0150753	0.9679271	pgm	945271	phosphoglucomutase
b4230	-10	7	1	7	4.75	MicC	47	65	47	53	4.06	-11.03	-19.84	-1.13688	GGAGAACAGUGUGAUGC&GCAUUGCCACUGAUUUUCC	(((((((((((((((((&))))))).)))).))))))	AGGUGGCGGAGAUCCCGCUGGCAGAGCUUUCCGUUCCGGCGAUCAUGAACGCCAUUGCGGCGUAAGGAGAACAGUGUGAUGCCUCAAUCUCUUCCGGACACCACUACGCCAAAAAGGCGCUUUCGCUGGCCGACGGGGAUGCCGCAGCUG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0135909	0.9679271	ytfT	948743	putative sugar ABC transporter permease

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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