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
b1535	-13	20	-7	-1	4.73	MicC	33	63	51	57	10.92	-11.71	-27.36	-1.20697	AAAAGGAGUGGCAAUGAUCAAGAAGACAACGGA&UCUGUUGGGCCAUUGCAUUGCCACUGAUUUU	((((..((((((((((..(((.....(((((((&))))))).....)))))))))))))..))))	AUGAAAAUAUUGACGUAAUUUUGCUUUUCUCUCGUUAGAAUAGCGCGCACAAGGAACUGUGAAAAAGGAGUGGCAAUGAUCAAGAAGACAACGGAAAUUGAUGCCAUCUUGUUAAAUCUCAAUAAGGCUAUCGAUGCCCACUACCAGUGG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0089209	0.9679271	dgcZ	946075	diguanylate cyclase zinc-sensing
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
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
b2091	4	16	7	13	2.38	MicC	50	62	53	59	2.89	-10.87	-16.14	-1.12039	AAAUCAGUGGUGA&UUGCCACUGAUUU	(((((((((((((&)))))))))))))	ACAAGAGAAAGUCGUUCUCGCAGAAUAAUUUUUACCUGAGGGGGAGGUUAUCCCCCUUAACAAUCAGGAGUUUUUAUGAAAUCAGUGGUGAAUGAUACUGAUGGUAUCGUGCGCGUUGCAGAAAGCGUCAUUCCUGAAAUUAAACAUCAG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0149839	0.9679271	gatD	946598	galactitol-1-phosphate dehydrogenase Zn-dependent and NAD(P)-binding
b1833	43	54	47	53	1.99	MicC	7	18	8	14	3.26	-10.92	-16.17	-1.12554	ACAGUGAGGGCA&UGCCUUUAUUGU	((((((((((((&))))))))))))	UAAAUGCGUUAAUGCUCAAGAUCAUUCCCAUCAUGGGUUAAGAUUAAUGUUAAUUCUUAUUACAUUUGGCACGUCAUGGCUCUUAACACACCACAAAUUACGCCGACAAAAAAGAUAACAGUGAGGGCAAUCGGCGAGGAACUGCCGCGU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0145348	0.9679271	yebS	946353	inner membrane PqiA domain protein
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
b2103	43	53	46	52	2.54	MicC	47	57	48	54	3.03	-10.8	-16.37	-1.11317	AGUGGUGGUGC&GCAUUGCCACU	(((((((((((&)))))))))))	CAGAAGCGAGGGGCCAGGCAGUUUUGUUCCACAUUUCCUUGAUGCGCUCUGGCAAUUGACGCAGGAGGUGCAGGCAUGAAACGAAUUAACGCUCUGACGAUUGCCGGUACUGAUCCGAGUGGUGGUGCGGGGAUUCAGGCCGAUCUUAAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0156347	0.9679271	thiD	946459	hydroxy-methylpyrimidine kinase and hydroxy-phosphomethylpyrimidine kinase
b0002	27	37	29	35	1.67	MicC	50	60	52	58	2.87	-12.71	-17.25	-1.31004	AUCAGUGGCAA&UUGCCACUGAU	(((((((((((&)))))))))))	CAGGAAACACAGAAAAAAGCCCGCACCUGACAGUGCGGGCUUUUUUUUUCGACCAAAGGUAACGAGGUAACAACCAUGCGAGUGUUGAAGUUCGGCGGUACAUCAGUGGCAAAUGCAGAACGUUUUCUGCGUGUUGCCGAUAUUCUGGAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0047142	0.8384433	thrA	945803	Bifunctional aspartokinase/homoserine dehydrogenase 1
b3673	-10	11	5	11	4.26	MicC	7	25	7	13	4.73	-9.9	-18.89	-1.02041	AUCCGUGAUAAUGAAAAGGCA&UGCCUUUAUUGUCACAGAU	(((.((((((((..(((((((&))))))))))))))).)))	GAUAGAUUCCUCUCCCGCAUUUAUGGGAAUGCGUAGUGACUUAUUCUAAUUAUUUUUAUAAAAGCAUCCGUGAUAAUGAAAAGGCAAAGAAACGUCAAUUUGUUAUUGAUGUUGGUAUUACUCGUGGCCGUCGGUCAGAUGGCGCAAACC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0267449	0.9679271	emrD	948180	multidrug efflux system protein
b2215	-67	-15	-49	-43	14.91	MicC	1	70	42	48	12.16	-21.53	-48.6	-2.21913	AUGAGGGUUAAUCAGUAUGCAGUGGCAUAAAAAAGCAAAUAAAGGCAUAUAAC&GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAU	(((..((..(((((((((((((((((((((((.....((((((((((((((((&))))))))))))))))........))))))..........))))))))))....)))))))..))..)))	ACUGAUUAAUGAGGGUUAAUCAGUAUGCAGUGGCAUAAAAAAGCAAAUAAAGGCAUAUAACAGAGGGUUAAUAACAUGAAAGUUAAAGUACUGUCCCUCCUGGUCCCAGCUCUGCUGGUAGCAGGCGCAGCAAACGCUGCUGAAGUUUAC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	5.2e-06	0.0190476	ompC	946716	outer membrane porin protein C

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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