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
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
b4187	-2	10	-2	5	2.55	MicC	41	52	46	52	2.27	-9.78	-14.6	-1.00804	CAGUGCACUGGC&GCCAUUGCAUUG	(((((((.((((&)))).)))))))	UAGCAAUCUCUUUCUGUCAUGAAUCCAUGGCAGUGACCAUACUAAUGGUGACUGCCAUUGAUGGAGGGAGACACAGUGCACUGGCAAACUCACACCGUUUUUAAUCAACCUAUACCAUUAAAUAACAGCAACUUAUACCUGUCUGAUGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.02869	0.9679271	aidB	948710	DNA alkylation damage repair protein flavin-containing DNA binding protein weak isovaleryl CoA dehydrogenase
b4255	-59	-46	-59	-53	3.93	MicC	42	54	48	54	3.49	-12.39	-19.81	-1.27706	GGCAAUGUCAGUGG&CCAUUGCAUUGCC	(((((((.((((((&)))))))))))))	UUGUCACAAAGGUGGAGGCAAUGUCAGUGGUGUGUGACAAUAAGAGUAUCGGCAGGACAUUAAGAGGAAUGAGCCAUGGCAAACCCGGAACAACUGGAAGAACAGCGUGAAGAAACACGUUUGAUUAUUGAAGAAUUACUGGAAGAUGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0057958	0.9230441	rraB	948773	protein inhibitor of RNase E
b2118	34	64	58	64	5.65	MicC	7	42	7	13	11.66	-10.57	-27.88	-1.08947	GCCCAACUGGAACUGAAAUAUAAAAAAGGCA&UGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGC	(((((((.((((.((((((((((.(((((((&))))))).)))).....)))))).)))).)))))))	UUCUCCGUAAUCGAUGCCAUCACCGCCAGCGAGCUAAUUAACGAUAUUGAAGCCCUGUUUGAAUAAGGAAAGAGCAUGGACAAGGAAUUACCGUGGCUGGCGGAUAACGCCCAACUGGAACUGAAAUAUAAAAAAGGCAAAACGCCGCUC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0179646	0.9679271	yehI	946649	DUF4132 domain-containing protein
b1385	-3	20	12	18	5.43	MicC	1	21	3	9	4.41	-10.7	-20.54	-1.10287	GUGAUGACAGAGCCGCAUGUAGC&GUUAUAUGCCUUUAUUGUCAC	(((((((.((((..(((((((((&))))))))))))).)))))))	GUCACAGCGAAAAAAGUGACUUUUCUUGUCGCUGCGUACACUGAAAUCACACUGGGUAAAUAAUAAGGAAAAGUGAUGACAGAGCCGCAUGUAGCAGUAUUAAGCCAGGUCCAACAGUUUCUCGAUCGUCAACACGGUCUUUAUAUUGAU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0166105	0.9679271	feaB	945933	phenylacetaldehyde dehydrogenase
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
b2830	63	75	63	69	1.12	MicC	40	54	48	54	4.58	-10.17	-15.87	-1.04824	GGUAAUGUGGGCC&GGCCAUUGCAUUGCC	(((((((..((((&))))....)))))))	GCAGAGAGUGGUUUACCGUCUUCCUGGAGUAUGAAACAAUCAUUCGUAUAUAAAGCUUUAUUUUGAGGUAGUCCGGUGAUUGAUGACGAUGGCUACCGCCCAAACGUAGGUAUCGUGAUUUGUAAUCGCCAGGGGCAGGUAAUGUGGGCC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0228099	0.9679271	rppH	947300	RNA pyrophosphohydrolase
b0126	30	44	30	36	2.04	MicC	40	52	46	52	4.54	-9.79	-16.37	-1.00907	CAAUGCACUAUGGUC&GGCCAUUGCAUUG	(((((((..((((((&)))))))))))))	UCUGUGGUUUAAAUCGUCCCGGAGUUGCCCUAUAUUAGCCAAACGUAAUUAUUUGGUUACAGGUCGUUAACCUCCAUGAAAGACAUAGAUACACUCAUCAGCAACAAUGCACUAUGGUCAAAAAUGCUGGUGGAAGAGGAUCCCGGGUUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.028523	0.9679271	can	944832	carbonic anhydrase
b0556	-72	-57	-63	-57	3.89	MicC	42	55	42	48	3.5	-11.05	-18.44	-1.13894	UGGCGGUAAGCAAUGG&CCAUUGCAUUGCCA	(((((((..(((((((&))))))))))))))	CGCUGGCGGUAAGCAAUGGAAAGGCCUGAUGACUCGUCGUGAGAUUGAGCGUGAAGUCUGUUUGUGGGGGCAACAGUGAGCAGAGUAACCGCGAUUAUAUCCGCUCUGAUUAUCUGCAUCAUCGUCAGCCUGUCAUGGGCGGUCAAUCAU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0134256	0.9679271	rzpD	945929	DLP12 prophage putative murein endopeptidase
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

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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