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
b1667	45	59	52	58	6.65	MicC	41	55	42	48	3.89	-12.31	-22.85	-1.26881	UGGCGACGCAAUGGC&GCCAUUGCAUUGCCA	((((((.((((((((&)))))))).))))))	UCUGUUUCUUCUCUGUAUCCAAUACGUUAAAAGAUUUACACUGUCUUCGUAUGCGUUAUCAGAAGGAGAAUCGCUAUGGCAACUUUGUUACAACUUCAUUUUGCUUUUAAUGGCCCAUUUGGCGACGCAAUGGCUGAGCAGCUUAAACCA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0061007	0.9311193	ydhR	946177	putative monooxygenase
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
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
b0633	2	18	9	15	6.88	MicC	39	55	42	48	4.76	-9.83	-21.47	-1.01319	UGCGUAAGCAGUGGCUC&GGGCCAUUGCAUUGCCA	((.((((((((((((((&)))))))))).))))))	UGGCUGGGUUCGGGAUUGUAAUGUCAAUCCACACCCACAGGAAAAUGUUGUCGAAAAGCGUGUAAGAGGUGCGCAAUGCGUAAGCAGUGGCUCGGGAUCUGCAUCGCGGCAGGAAUGCUCGCGGCAUGUACAAGCGAUGAUGGUCAGCAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.027864	0.9679271	rlpA	945241	septal ring protein suppressor of prc minor lipoprotein
b1551	-38	-27	-37	-31	7	MicC	47	58	51	57	3.37	-10.03	-20.4	-1.03381	CAGUGGUAGUGC&GCAUUGCCACUG	((((((((((((&))))))))))))	CAUGAAAAAAAUCAUAGUUUUUUUAACUCUGAACCAGCAGUGGUAGUGCCAGCGAUGACUGGAGUUAACACCAUCAUGCGUGAAUAUCCAAAUGGCGAAAAAACACACCUUACUGUAAUGGCCGCAGGGUUUCCAUCUCUGACCGGAGAU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0247772	0.9679271	ynfN	946097	Qin prophage cold shock-induced protein
b4271	-9	24	-2	5	7.14	MicC	23	54	41	47	9.06	-10.7	-26.9	-1.10287	GGGAAUACGAUGGCAUUAACAGAUAUCAAAGUC&GAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCC	((.(((.(((((((...((((((....((((((&))))))....))))))..))))))).))).))	AUCUACCAACAUAUGUUGGUACAGAUGAUGGUAUUUCCGGUUCGAUAAUGCUUGUACCAACAGGGAGGGAAUACGAUGGCAUUAACAGAUAUCAAAGUCAGAGCAGCCAAGCCAACGGAUAAGCAAUAUUAGCUGACUGAUGGUGGCGGU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0166105	0.9679271	intB	948782	pseudogene integrase homologyIS phage Tn Phage-related functions and prophages KpLE2 phage-like element P4-like integrase
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
b4473	52	67	61	67	7.34	MicC	39	54	39	45	4.76	-11.89	-23.99	-1.22552	GGCGAUGAUAUGGUCC&GGGCCAUUGCAUUGCC	(((((((..(((((((&)))))))..)))))))	AAAUCCCCCUCUGAUUGACAGCAUCACUGACCAAUCGCAAAGAUUGCUAAGGCUGCUUAUGGCAGGGAGAUAAGGAUGGUCGAUACAGAAAUUUGGCUGCGUUUAAUGAGUAUCAGCAGCUUGUACGGCGAUGAUAUGGUCCGUAUCGCU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0079665	0.9679271	smf	2847708	DNA recombination-mediator A family protein
b1256	14	29	14	20	7.4	MicC	41	58	52	58	4.26	-10.38	-22.04	-1.06988	CAGUGGCGGCUUUGGC&GCCAUUGCAUUGCCACUG	(((((((.((..((((&))))..))...)))))))	AUCUAUGUAGGAUCAUUUGUUACUCCAAUGUAGGUAUAUUCGUCACGUUUUUAUAACCAUAACGACGGAGCGGAUAUGAAAAAGUUAACAGUGGCGGCUUUGGCAGUAACAACUCUUCUCUCUGGCAGUGCCUUUGCGCAUGAAGCAGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0201313	0.9679271	ompW	945128	outer membrane protein W
b0763	57	71	59	65	7.52	MicC	41	55	47	53	3.89	-11.91	-23.32	-1.22758	UGGCAAUGCACUGGC&GCCAUUGCAUUGCCA	((((((((((.((((&)))).))))))))))	AGCAAUAACUGCUGGGAAAAUUCCGAGUUAGUCGUUAUAUUGUCGCCUACAUAACGUUACAUUAAGGGGUUACCAAUGGCUCGUAAAUGGUUGAACUUGUUUGCCGGGGCGGCACUCUCUUUCGCUGUUGCUGGCAAUGCACUGGCAGAU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0078666	0.9679271	modA	945364	molybdate ABC transporter periplasmic binding protein chlorate resistance 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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