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
b1507	-16	4	-7	-1	6.02	MicC	47	63	51	57	3.74	-9.86	-19.62	-1.01629	AAAAUCUGGAGUGGUAAUGC&GCAUUGCCACUGAUUUU	((((((...(((((((((((&)))))))))))))))))	UGAACUCUCAAUGACGCUAUGCGACGCGAAAAAUGCCUCGCCAGAAUCAACAGAACAGCAAAAUCUGGAGUGGUAAUGCCUAAACUUGUCACUUGGAUGAACAACCAGCGGGUAGGCGAGUUAACGAAGUUAGCCAACGGCGCGCACACC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0273792	0.9679271	hipA	946064	inactivating GltX kinase facilitating persister formation toxin of HipAB TA pair autokinase
b1068	-66	-50	-56	-50	5.69	MicC	51	66	51	57	2.9	-10.2	-18.79	-1.05133	UGGAAAUCGAAGUGGCA&UGCCACUGAUUUUCCA	((((((....(((((((&)))))))...))))))	UCGAAGCCCUGGAAAUCGAAGUGGCAGAACUGAAACAGCGUCUUGAUUCGUUGCUGGCCCAUCUGGGAGAUUAAAGUGAAAAAAUUACGUAUCGGCGUAGUGGGAUUAGGUGGCAUUGCGCAAAAAGCGUGGUUACCGGUGCUGGCGGCA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0224078	0.9679271	yceM	945204	putative oxidoreductase
b4393	-12	11	1	7	4.89	MicC	35	55	39	45	8.89	-13.36	-27.14	-1.37704	UGGCGACAUAUUAUGGCCCAACA&UGUUGGGCCAUUGCAUUGCCA	((((((......(((((((((((&)))))))))))....))))))	AUAUGCUAUCGUACUCUUUAGCGAGUACAACCGGGGGAGGCAUUUUGCUUCCCCCGCUAACAAUGGCGACAUAUUAUGGCCCAACAAUCACCCUAUUCAGCAGCGAUGGCAGAACAGCGUCACCAGGAGUGGUUACGUUUUGUCGACCUG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0030764	0.7974595	trpR	948917	transcriptional repressor tryptophan-binding
b1776	-72	8	-60	-54	13.29	MicC	8	70	57	63	12.15	-10.51	-35.95	-1.08328	AUGUUGACCUCAAAAAUCAUGUGGGUAAGUAUGAUGGCCAUCUAAGCAAAACUAAACACAGAGGAUGACGCAAUGAAAGC&GCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAU	((((((......(((((((.(((.(((((((..((((((.......((.........(((((((((((..(((((((.((&)).))))))).........)))))))))))))))))))))).)))))))))))))).))))))	UUAAUGUUGACCUCAAAAAUCAUGUGGGUAAGUAUGAUGGCCAUCUAAGCAAAACUAAACACAGAGGAUGACGCAAUGAAAGCACUGGCUCGGUUUGGCAAGGCCUUUGGCGGCUACAAGAUGAUUGAUGUCCCACAACCCAUGUGUGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.018624	0.9679271	ydjL	946299	putative Zn-dependent NAD(P)-binding oxidoreductase
b1383	33	62	55	61	9.64	MicC	41	69	42	48	6.46	-12.7	-28.8	-1.30901	UGUUGGGCUGGUAAGCAGCAAUGUAAUGGC&GCCAUUGCAUUGCCACUGAUUUUCCAACA	((((((.......((..(((((((((((((&)))))))))))))..))......))))))	AUGAGAUCAUCAUCAAGGCAGACAAAGAUGUCGAAGAGCUGCUUGAAACUCGUAGCGAUCUUUUCUGAGGUGAUGAUGAAGAAAACAUUACUUCUUUGUGCGUUUCUUGUUGGGCUGGUAAGCAGCAAUGUAAUGGCAUUGACUCUGGAU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0047449	0.8384433	ydbL	945943	DUF1318 family protein
b2374	42	60	54	60	6.8	MicC	38	58	38	44	6.57	-10.67	-24.04	-1.09978	CGGUGUGCAAUCUGGCCCA&UGGGCCAUUGCAUUGCCACUG	(((((.(((((.(((((((&)))))))....))))))))))	GGUUAUUUAUAGAAGAUAUUACGCCUUAAAUAAACGCUAAAUUAACACAUAUUUAAUUAACUAAUAGGUAUUGCUAUGUCAACUCCACUUCAAGGAAUUAAAGUUCUCGAUUUCACCGGUGUGCAAUCUGGCCCAUCUUGUACUCAAAUG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0169142	0.9679271	frc	946842	formyl-CoA transferase NAD(P)-binding
b4496	8	31	19	25	7.77	MicC	39	64	47	53	6.64	-12.68	-27.09	-1.30695	GAAAAGUUCUGGCAAUGCUGGUCC&GGGCCAUUGCAUUGCCACUGAUUUUC	(((((....(((((((((((((((&))))))..)))))))))....)))))	UCCAAAUGUGCUUUUUUUUGGAUAACGGCACUUAUUGAUAUAUUCAUGAAGAUUAUAAUCACAAGGGAAUACAUAAUGAAAAGAAAAGUUCUGGCAAUGCUGGUCCCGGCGUUAUUAGUUGCUGGCGCAGCAAAUGCGGCUGAAGUCUAU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0048068	0.8384433	yedS	2847763	pseudogene outer membrane protein homology putative outer membrane protein
b1466	54	67	59	65	3.06	MicC	42	56	45	51	3.53	-11.27	-17.86	-1.16162	GUGGGAAUGCAAGG&CCAUUGCAUUGCCAC	((((.(((((((((&)).))))))).))))	AUUCAACCUGUUCAACAGUAGCCGUAUCGAUGCCAUCAACAUCACCGAAGUGCGCGACAAAGCGGAGGGCGAAUAAUGCAGAUCCUCAAAGUGAUCGGCCUGUUGAUGGAGUAUCCGGACGAGCUGUUGUGGGAAUGCAAGGAGGACGCG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.011728	0.9679271	narW	946032	nitrate reductase 2 (NRZ) delta subunit (assembly subunit)
b1119	57	75	69	75	7.68	MicC	42	58	42	48	3.69	-11.87	-23.24	-1.22346	CGGUCGGCAGUUGCAGUGG&CCAUUGCAUUGCCACUG	((((.((((((.(((((((&)))))))))))))))))	GGCGCGCCAGUAAUAUUGACCCUGCGCGAGUCCUUAGCGGCCAGUAAAGGCAGUACAUUAAAACAAGGAGCGGCAAUGUAUUACGGGUUUGAUAUUGGUGGAACAAAAAUUGCGCUUGGCGUGUUUGAUAGCGGUCGGCAGUUGCAGUGG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0080676	0.9679271	nagK	945664	N-acetyl-D-glucosamine kinase
b0686	-75	-45	-51	-45	7.31	MicC	40	74	40	46	6.93	-11.49	-25.73	-1.18429	UUAUUUGUUGCAGCCCUGUGGCACAAUGGUC&GGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAA	((((.(((((.......((((((((((((((&))))))))...))))))........))))).))))	UUAUUUGUUGCAGCCCUGUGGCACAAUGGUCAACAUAAUACCCUAACCCGACAACGCGAAAAAAAGAACUUUGCCAUGAAAUUGAAUAUCCGCGCGCAAACUGCACAAAACCAGCACAAUAAUUCUCCCAUCGUUCUUGUCCACGGUCUG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0102341	0.9679271	ybfF	945288	acyl-CoA esterase

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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