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
b2069	37	49	38	44	3.81	MicC	46	59	52	58	3.42	-10.11	-17.34	-1.04205	UCAGUGGCGGUCA&UGCAUUGCCACUGA	(((((((((((((&)).)))))))))))	UUCAUAUUCCGGUUGUCGCGACGGCAACAUUUCGCUAAAGUCACGCCCCUUCUUCACCGGCAUGGGGAUUAUUUCGUGUUUAUUGGUUUUGAUUACGGUACAGCAAACUGUUCAGUGGCGGUCAUGCGUGACGGUAAACCGCAUUUGCUA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0236344	0.9679271	yegD	947234	Hsp70 chaperone family protein
b3690	16	45	16	22	13.63	MicC	32	56	50	56	9.02	-10.08	-32.73	-1.03896	GUGGCGAUUAUUGGCCUCGGCCCGGCAGGA&UUCUGUUGGGCCAUUGCAUUGCCAC	((((((((.....((...((((((((((((&))))))))))))...))))))))))	CCCGCCAUCAUACUUCACAAGGACUUCACUUUCAGACAAUAGUCUUUUGCCAUCGUGAUGAAUGUGAGUGAAAAGAUGGAACAUUUCGACGUGGCGAUUAUUGGCCUCGGCCCGGCAGGAUCGGCGUUGGCACGAAAGUUAGCAGGCAAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0240571	0.9679271	cbrA	948197	colicin M resistance protein FAD-binding protein putative oxidoreductase
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
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
b0294	-9	12	-8	-2	5.56	MicC	45	66	59	65	4.27	-9.97	-19.8	-1.02762	UGGAAAGUAGUGACAUGGCAA&UUGCAUUGCCACUGAUUUUCCA	((((((((((((.((..((((&))))..)).)))).))))))))	UACUACGUAUCUUAUUUACUUCCGGUUUACUAAGGAAACUGAAUGCACCUGUAAAAAUUACAGGUUUGGAAAGUAGUGACAUGGCAAAGUGAUUACAGUAGGGACUAUGAGGUUAAAAACCAUAUGGAAUGUCAAAACCGUUCUGAUAAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0256679	0.9679271	ecpR	944966	putative transcriptional regulator for the ecp operon
b3005	-12	11	3	9	6.42	MicC	46	65	48	54	4.07	-9.93	-20.42	-1.0235	GGAUAAUAUCCGAUGGCAAUGCA&UGCAUUGCCACUGAUUUUCC	(((....(((...((((((((((&))))))))))..)))..)))	GACCUGGAUCUGGAAGCCAGCGCCGCUGCGCAUCCGGUUCGUGUCGCACAAAAAUUACGCGCAGGAUAAUAUCCGAUGGCAAUGCAUCUUAACGAAAACCUCGACGAUAACGGCGAAAUGCAUGAUAUCAACGUGACGCCGUUUAUCGAC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0262783	0.9679271	exbD	946345	membrane spanning protein in TonB-ExbB-ExbD complex
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
b1817	-20	-10	-16	-10	0.62	MicC	9	19	9	15	0.94	-9.88	-11.44	-1.01835	GAUAAUAAAGG&CCUUUAUUGUC	(((((((((((&)))))))))))	CGAUUCGAUUGUGGACGACGAUUCAAAAAUACAUCUGGCACGUUGAGGUGUUAACGAUAAUAAAGGAGGUAGCAAGUGACCAUUGCUAUUGUUAUAGGCACACAUGGUUGGGCUGCAGAGCAGUUGCUUAAAACGGCAGAAAUGCUGUUA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0270603	0.9679271	manX	946334	fused mannose-specific PTS enzymes: IIA component/IIB component
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
b4327	3	12	5	11	1.53	MicC	89	98	90	96	4.56	-9.85	-15.94	-1.01526	GGAUGACUGU&ACAGUCGUCC	((((((((((&))))))))))	AAACGGCUUAAACGGUUGUCAGCCGCCCGAAUGGACGUAGAAUGCCCGCAAGGGCGGCUGACAGAGUAAAACGUAAUGGAUGACUGUGGUGCGAUUUUGCAUAAUAUUGAAACCAAAUGGCUUUAUGAUUUUCUGACCCUGGAAAAAUGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0275399	0.9679271	hypT	948852	hypochlorite-responsive transcription 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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