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
b4153	-59	-48	-59	-53	3.06	MicC	47	58	52	58	3.37	-9.99	-16.42	-1.02969	CGGUGGCGAAGC&GCAUUGCCACUG	(((((((((.((&)).)))))))))	CAGCUAAACGCGUUUACGGUGGCGAAGCGGAUGCAGCCGAUAAGGCGGAAGCAGCCAAUAAGAAGGAGAAGGCGAAUGGCUGAGAUGAAAAACCUGAAAAUUGAGGUGGUGCGCUAUAACCCGGAAGUCGAUACCGCACCGCAUAGCGCA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0253678	0.9679271	frdB	948666	fumarate reductase (anaerobic) Fe-S subunit
b2920	2	18	9	15	3.47	MicC	51	66	53	59	2.9	-13.62	-19.99	-1.40384	UGGAAACUCAGUGGACA&UGCCACUGAUUUUCCA	((((((.(((((((.((&))))))))).))))))	AGGGAUGAACGCUUUCCUCGAAAAACGUAAACCUAAUUUCGUUGGUCAUUAAUCCCUGCGAACGAAGGAGUAAAAAUGGAAACUCAGUGGACAAGGAUGACCGCCAAUGAAGCGGCAGAAAUUAUCCAGCAUAACGACAUGGUGGCAUUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0025864	0.7974595	scpC	947402	propionyl-CoA:succinate CoA transferase
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
b0034	61	72	66	72	3.52	MicC	53	64	53	59	2.77	-10.82	-17.11	-1.11524	GAAAAUCGGUGG&CCACUGAUUUUC	((((((((((((&))))))))))))	AUUUUAAUAUGGCCUUGUUUAAUUGCUUCAAAACGAGUCAUAGCCAGACUUUUAAUUUGUGAAACUGGAGUUCGUAUGUGUGAAGGAUAUGUUGAAAAACCACUCUACUUGUUAAUCGCCGAAUGGAUGAUGGCUGAAAAUCGGUGGGUG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0154461	0.9679271	caiF	944795	cai operon transcriptional activator
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
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
b3617	-16	4	-10	-4	4.14	MicC	47	69	58	64	4.31	-12.98	-21.43	-1.33787	UGUCUGGAGAAUCGCAAUGC&GCAUUGCCACUGAUUUUCCAACA	(((.((((((((((((((((&)))))))....))))))))))))	GUUAACGCGUUAUCUCGUCGCGACCUAUAAGUUUGGGUAAUAUGUGCUGGAAUUUGCCCUGUCUGGAGAAUCGCAAUGCGUGGAGAAUUUUAUCAGCAGUUAACCAACGAUCUGGAAACCGCACGGGCGGAAGGGUUGUUUAAAGAAGAG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.003953	0.8150379	kbl	948138	glycine C-acetyltransferase
b4328	60	71	61	67	1.26	MicC	53	65	58	64	2.8	-11.97	-16.03	-1.23377	GGAAGAUCGGGG&CCACUGAUUUUCC	((((((((((((&)).))))))))))	AUCAUUACGGUCUGCGUGAUUAACGCAUUGCUGUCGAUCUGGGUUAUGCAGCUUAUUGUUUAACAAGGAGUUACCAUGAUUGAUUAUACCGCAGCCGGUUUUACCCUGCUGCAGGGAGCGCAUUUGUAUGCGCCGGAAGAUCGGGGAAUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.007574	0.9679271	iadA	948853	isoaspartyl dipeptidase
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
b4664	-70	-61	-70	-64	1.66	MicC	56	65	59	65	0.92	-10.92	-13.5	-1.12554	GGGGAGUCAG&CUGAUUUUCC	((((((((((&))))))))))	CAAUCGGGGAGUCAGCAGGGGGCUGAAACGGGAAAGCCCCUCCCGAAGAAGGGGGCCUUACAGAAGGAAAGGGUUAUGAUGAAGCUCGUCAUCAUACUGAUUGUGUUGUUACUCGUAAGUUUCGCAGCUUAUUAACAGCCAAUCAGAGGG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0145348	0.9679271	ibsD	7751628	toxic membrane 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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