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
b0333	51	74	56	62	2.7	MicC	6	28	17	23	4.89	-11.71	-19.3	-1.20697	AAAAUCUGUGGCACUUUCUGGCGU&AUGCCUUUAUUGUCACAGAUUUU	(((((((((((((.......((((&))))......)))))))))))))	AGGUCGGAUAAGACGCAUAGCGUCGCAUCCGACAACAAUCUCGACCCUACAAAUGAUAACAAUGACGAGGACAACAUGAGCGACACAACGAUCCUGCAAAACAGUACCCAUGUCAUUAAACCGAAAAAAUCUGUGGCACUUUCUGGCGUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0089209	0.9679271	prpC	947528	2-methylcitrate synthase
b2746	36	51	37	43	6.88	MicC	38	55	48	54	4.76	-11.7	-23.34	-1.20594	UGGCGGUGAAGGCCCA&UGGGCCAUUGCAUUGCCA	((((((((((((((((&)))))).)).))))))))	UAAAGUCACGCGCCCGGAAGAUUUGGCACUGGCCGAGUUUUACCUCACCCGAACCAUCCAUCAGGAGAAUACAUAAUGCGAAUUGGACACGGUUUUGACGUACAUGCCUUUGGCGGUGAAGGCCCAAUUAUCAUUGGUGGCGUACGCAUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.008977	0.9679271	ispF	945057	2C-methyl-D-erythritol 24-cyclodiphosphate synthase
b1065	-67	-40	-47	-41	9.38	MicC	46	69	47	53	4.32	-11.69	-25.39	-1.20491	UGAUGGGAAAAGUCUUAGCGGCAAUGCA&UGCAUUGCCACUGAUUUUCCAACA	((.(((((((....((((.(((((((((&))))))))).))))))))))).))	CCCCGAAGUGAUGGGAAAAGUCUUAGCGGCAAUGCAGAAUAGAAAGUGCUCAUCUUUUAUUUCCCGGGAGGGGAAAUGUCCCGCGUGUCGCAGGCGAGGAACCUGGGUAAAUAUUUCCUGCUCAUCGAUAAUAUGCUGGUCGUGCUGGGG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0090334	0.9679271	mdtH	946920	multidrug resistance efflux transporter conferring overexpression resistance to norfloxacin and enoxacin
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
b2771	-18	-8	-14	-8	0.99	MicC	9	19	9	15	0.94	-11.47	-13.4	-1.18223	GACAAUGAAGG&CCUUUAUUGUC	(((((((((((&)))))))))))	GCGAUGACGGGGCGUUGCCUUUUCGGCUUCUCAGGCGAGAAGCCGUUCUUAUUACCGGACAAUGAAGGGGUAAAGAUGAACACUUCACCGGUGCGAAUGGAUGAUUUACCGCUUAACCGUUUUCACUGCCGCAUUGCUGCGCUCACUUUC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0103621	0.9679271	ygcS	947238	putative MFS sugar transporter membrane protein
b3943	29	43	29	35	8.34	MicC	40	55	49	55	4.59	-11.46	-24.39	-1.1812	UGGCAAUCAGUGGCC&GGCCAUUGCAUUGCCA	(((((((((((((((&)))))))).)))))))	GCUGCUUGCUGGCAGUCGCUGAACGUUCUUUACCAGCGUAUAGUGGGCGAACGAAAACUACACACUGGAUCUCUCAUGUCUGCCGCAGGAAAGAGCAACCCACUGGCAAUCAGUGGCCUGGUUGUGCUCACACUUAUCUGGAGUUAUAGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0104267	0.9679271	yijE	948445	EamA-like transporter family protein
b1891	33	54	45	51	6.3	MicC	45	65	48	54	4.26	-11.45	-22.01	-1.18017	GGAUAUUCAGCUGGCAAUGGAA&UUGCAUUGCCACUGAUUUUCC	(((...((((.((((((((.((&)).))))))))))))...)))	CAUCAUGCUCUCAACACGCUUGCUGAAUGAUGUUAAUCAGCCUGAAGAAGCGCUGCGCAAGAAAAGGGCCUGAUCAUGAGUGAAAAAAGCAUUGUUCAGGAAGCGCGGGAUAUUCAGCUGGCAAUGGAAUUGAUCACCCUGGGCGCUCGU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0104916	0.9679271	flhC	947280	flagellar class II regulon transcriptional activator with FlhD
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)
b0301	-74	-54	-73	-67	5.81	MicC	45	66	59	65	4.27	-11.24	-21.32	-1.15853	UGGAAAGUCACAUCGAUGCGA&UUGCAUUGCCACUGAUUUUCCA	((((((((((...((((((((&))))))))....))))))))))	CUGGAAAGUCACAUCGAUGCGAAUUGAUAAUAAUUCAACCGCAACAGCAGUAUUGUAUAAAUAAGGAUGUUCACAAUGGAAAAAUACCUGCACCUGUUAAGUCGGGGAGAUAAAAUUGGCCUGACAUUGAUUCGUCUGAGUAUUGCAAUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.011947	0.9679271	rclC	944974	reactive chlorine species (RCS) stress resistance inner membrane protein
b1384	14	37	30	36	5.92	MicC	41	66	42	48	5.82	-11.12	-22.86	-1.14616	UGGAUAAUGAGUUUCAGCAAUGGC&GCCAUUGCAUUGCCACUGAUUUUCCA	((((.(((.(((..((((((((((&))))))))..))..))).))).))))	GUCAGGCUCAUUAGCUUCGUUUAUUGCAACACAAAUGCAACAAUAAAAAUACAUUUCACAGAGCGAAAACGUGCCAUGAACCCCGCAGUGGAUAAUGAGUUUCAGCAAUGGCUUUCCCAAAUCAAUCAGGUAUGCGGAAAUUUUACCGGA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0128619	0.9679271	feaR	945941	transcriptional activator for tynA and feaB

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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