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
b2239	56	74	62	68	6.41	MicC	41	66	47	53	5.82	-14.71	-26.94	-1.51618	UGGGAAGCAGUGCAAUGGC&GCCAUUGCAUUGCCACUGAUUUUCCA	(((((((((((((((((((&))))))))))))).......))))))	UGUUGAUUGUUGUGAUGAUUGGCGAAAAACGUCGCCAUGAACAAUUACUGCAAGAACGCAACGGAGGCUAAUGGCAUGAAAUUGACGCUGAAAAACCUUAGCAUGGCGAUCAUGAUGAGCACUAUAGUCAUGGGAAGCAGUGCAAUGGCG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0012277	0.7974595	glpQ	946725	periplasmic glycerophosphodiester phosphodiesterase
b0553	14	23	14	20	2.38	MicC	49	58	52	58	2.9	-10.68	-15.96	-1.10081	CAGUGGCAAU&AUUGCCACUG	((((((((((&))))))))))	AAUCACAUUGAUUAGAUGAAUAUUUAUCGCGCAGUGACAUCAUUUUUUAAUAAUAGUUCAAAAAAAGGGCUCACGAUGAAAAAAUUAACAGUGGCAAUUUCUGCUGUAGCUGCAUCAGUACUAAUGGCGAUGUCUGCUCAGGCAGCUGAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0168124	0.9679271	nmpC	946786	DLP12 prophage truncated outer membrane porin (pseudogene)IS phage Tn Phage or Prophage Related outer membrane porin protein locus of qsr prophage
b4297	57	71	65	71	4.42	MicC	39	53	39	45	4.75	-10.98	-20.15	-1.13173	GCACGCCGAUGGCCC&GGGCCAUUGCAUUGC	(((...(((((((((&)))))))))...)))	CAUCUGAAGAAGCAAAAGAUAAAGUCCACGUGCUGCUUACCGCGCAGGGCAUUUUACCAGUCUGAGGAGAAACUCAUGUCUGUUCGCAAUAUUUUUGCUGACGAGAGCCACGAUAUUUACACCGUCAGAACGCACGCCGAUGGCCCGGAC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0140126	0.9679271	yjhG	946829	putative dehydratase
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
b2422	-39	-29	-38	-32	5.46	MicC	56	66	59	65	0.93	-9.83	-16.22	-1.01319	UGGAGAAUCAG&CUGAUUUUCCA	(((((((((((&)))))))))))	UCACCCUGUUUUUAAAAAGUAUGUUGCAGUGGCGCCUGGAGAAUCAGGAAAAACGCGCACAGCAGGAGGAACAUCAUGAGCAUUGAGAUUGCCAAUAUUAAGAAGUCGUUUGGUCGCACCCAGGUGCUGAACGAUAUCUCACUGGAUAUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.027864	0.9679271	cysA	946889	sulfate/thiosulfate transporter subunit
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
b2445	51	64	58	64	5.87	MicC	50	63	50	56	2.99	-10.98	-19.84	-1.13173	AGAAUCAGUGGCGA&UUGCCACUGAUUUU	((((((((((((((&))))))))))))))	GAAGUUAAUCAAAGCGGAUAUCCACGCCCAGCUGAAGGCCUGUGAUUGCGAUAUUUCUGAAUGACAGGUGGAAUCAUGAAACACGUUUUUAAAUAUCUUGAUUUUGCAGAAGACCGCGAACACGCAGAAUCAGUGGCGACCAAAGAGUUA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0140126	0.9679271	yffN	946930	CPZ-55 prophage uncharacterized protein
b2501	-15	7	-7	-1	4.87	MicC	40	65	51	57	6.2	-10.33	-21.4	-1.06473	GGAGUAAAAGUGGUAAUGGGUC&GGCCAUUGCAUUGCCACUGAUUUUCC	(((.....((((((((((((((&))))....)))))))))).....)))	AGUUGGACAUCUGCCAAUAUUGCUCGCCAUAAUAUCCAGGCAGUGUCCCGUGAAUAAAACGGAGUAAAAGUGGUAAUGGGUCAGGAAAAGCUAUACAUCGAAAAAGAGCUCAGUUGGUUAUCGUUCAAUGAACGCGUGCUUCAGGAAGCG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0207409	0.9679271	ppk	946971	polyphosphate kinase component of RNA degradosome
b2550	-75	-62	-73	-67	2.48	MicC	43	56	48	54	3.24	-13.61	-19.33	-1.40281	GUGGCAGUGUAUUG&CAUUGCAUUGCCAC	(((((((((((.((&)).)))))))))))	GUGGCAGUGUAUUGAACAAUCUGGCAAUGUUUUCGCGGAAUAAUCACGCAAUUAACUAAACAAGGUUUAGUGAAGAUGAGAGCCUGCAUUAAUAAUCAACAGAUUCGCCACCAUAACAAAUGCGUGAUUCUGGAACUGCUGUACCGGCAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0026038	0.7974595	yphH	947023	putative DNA-binding transcriptional regulator
b2573	48	57	51	57	2.53	MicC	56	65	56	62	0.92	-10.66	-14.11	-1.09874	GGGAGAUCAG&CUGAUUUUCC	((((((((((&))))))))))	CUUGCUCAAAUUGCAGCUAAUGGAGUGGCGUUUCGAUAGCGCGUGGAAAUUUGGUUUGGGGAGACUUUACCUCGGAUGAGCGAGCAGUUAACGGACCAGGUCCUGGUUGAACGGGUCCAGAAGGGAGAUCAGAAAGCCUUUAACUUACUG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0170166	0.9679271	rpoE	947050	RNA polymerase sigma E factor

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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