Input and runtime details for job 8403881 (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 8403881 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:15:25 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:18:18 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:19:13 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:20:45 CET 2020
	Job Completed		@ Mon Jan 27 14:20:57 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8403881&toolName=IntaRNA ( 30 days expiry )

Description of the job

RyhB - 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
b3080	-59	-34	-44	-38	3.58	RyhB	1	25	6	12	7.71	-14.07	-25.36	-1.47943	UCCCAGCGACCAAAUCUUCCUGAUGC&GCGAUCAGGAAGACCCUCGCGGAGA	((((.((((.....((((((((((((&)).))))))))))...)))))).))	AAAAUGCCUCUCACGAUCCCAGCGACCAAAUCUUCCUGAUGCAAUAUUUCUACUGGUAAUAAGGACUGUAAUUUCAUGAAAAUAAAAACUAUUUUAACGCCAGUAACCUGCGCUCUGCUGAUAAGUUUUUCCGCCCAUGCCGCUAACGCC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0052402	0.9291058	ygjK	947596	alpha-glucosidase
b4633	-42	-17	-32	-26	9.35	RyhB	37	66	49	55	3.3	-12.21	-24.86	-1.28385	GUAUUUGGGGAGCAAUGGCGAUGACG&CGACAUUGCUCACAUUGCUUCCAGUAUUAC	(((....((((((((((((((((.((&)).))))))...)))))))))).....)))	AAAAUGGACGAGGCACUGGCUGAAAUUGGUUUUGUAUUUGGGGAGCAAUGGCGAUGACGCAUCCUCACGAUAAUAUCCGGGUACCUCACAACACGGCAAGCCUGCAUUGCGGCGCUUCAGUCUCCGCUGCAUACUGUCCAGGUGAGCGCG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0147406	0.9496255	xisD	5625559	pseudogene exisionase in defective prophage DLP12Phage or Prophage Related
b1279	-12	4	-9	-3	7.4	RyhB	46	61	52	58	3.24	-10.81	-21.45	-1.13665	ACGGGAAGUAAUGUGA&UCACAUUGCUUCCAGU	((.(((((((((((((&))))))))))))).))	AAAAUGGUACUUUAAAGGGCUAUUGCGGUAAGUUGACCAUAAUUUAUUCGCUCUAACCACAUAACGGGAAGUAAUGUGAAAUAUUUACUCAUUUUCUUACUGGUGUUAGCGAUCUUCGUGAUUUCGGUCACGUUGGGUGCGCAGAACGAU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0309022	0.9496255	yciS	944936	DUF1049 family inner membrane protein function unknown
b3110	57	75	57	63	2.99	RyhB	44	62	56	62	3.3	-13.55	-19.84	-1.42475	UGCUGGAAUGAGUGAGAGC&GCUCACAUUGCUUCCAGUA	((((((((..((((.((((&)))).))))..))))))))	AAACGUAGACCGCAUAUCGCCUUGAUGCGGCUCGGAAAAAAAUAAUAAGCCCUACAAAAUAUUGAGCGAGAAAUUAUGGAAAUUGCAUCGAAUAAAGGCGUCAUUGCAGACGCUUCGACCCCGGCGGGUCGUGCUGGAAUGAGUGAGAGC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0070381	0.9291058	yhaO	947628	putative transporter
b2211	-12	13	7	13	8.49	RyhB	6	30	6	12	10.22	-11.41	-30.12	-1.19973	CGGGUUUUCUGCAUGGAACUUCUUG&CAGGAAGACCCUCGCGGAGAACCUG	((((((((((((..((..(((((((&)))))))..))..))))))))))))	AAAUAAGAAUUAUUAUUGCUGUGCGCGCGAAGAUGUUUAAACUGCGGGCUGUAAUUCAUUGUCCGGGUUUUCUGCAUGGAACUUCUUGUACUUGUCUGGCGGCAGUAUCGCUGGCCAUUUAUCAGUGUGAUGGCGCUAAGCCUCGCCAGU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0225939	0.9496255	yojI	946705	microcin J25 efflux ABC transporter permease/ATPase
b1189	10	30	13	19	8.06	RyhB	47	66	57	63	3.09	-11.54	-22.69	-1.2134	GUCAUACUGGGAAGUGGUGUG&CACAUUGCUUCCAGUAUUAC	((.(((((((.((((((((((&))))))))))))))))).))	AAUAUUUUCAACUGAGUUAUCAAGAUGUGAUUAGAUUAUUAUUCUUUUACUGUAUCUACCGUUAUCGGAGUGGCUAUGCGAGUUGUCAUACUGGGAAGUGGUGUGGUAGGCGUUGCCAGCGCCUGGUACUUAAAUCAGGCAGGACAUGAG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0210945	0.9496255	dadA	945752	D-amino acid dehydrogenase
b1342	-10	11	-10	-4	7.12	RyhB	41	59	53	59	3.27	-12.25	-22.64	-1.28806	UGGAGGCACUGUGGAAGCGAU&AUUGCUCACAUUGCUUCCA	((((((((.((((..((((((&)))))))))).))))))))	AAUGGGGUGAUGAGAUGUUGCGUAACAGGGCCAGAAGGCUAGACUACAAAAUAAUGCGUUGAUGAUGGAGGCACUGUGGAAGCGAUUAAGGGAUCGGACGUUAAUGUCCCGGAUGCAGUAUUUGCCUGGAUGCUGGAUGGUAGAGGCGGC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0144251	0.9496255	ydaN	945910	putative Zn(II) transporter
b3365	-9	12	2	8	4.28	RyhB	38	57	42	48	3.21	-10.98	-18.47	-1.15452	GAGGCAAAAAUGAGCAAAGUC&GACAUUGCUCACAUUGCUUC	(((((((...(((((((..((&))..)))))))..)))))))	AAUUUGAUUUACAUCAAUAAGCGGGGUUGCUGAAUCGUUAAGGUAGGCGGUAAUAGAAAAGAAAUCGAGGCAAAAAUGAGCAAAGUCAGACUCGCAAUUAUCGGUAACGGUAUGGUCGGCCAUCGCUUUAUCGAAGAUCUUCUUGAUAAA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0282964	0.9496255	nirB	947868	nitrite reductase large subunit NAD(P)H-binding
b3573	47	75	68	74	7.83	RyhB	37	66	38	44	3.3	-11.77	-22.9	-1.23759	GUACCUGUGAAGUGGCUUGCGCAGUGUCG&CGACAUUGCUCACAUUGCUUCCAGUAUUAC	(((.(((.((((.....((.(((((((((&))))))))).)).....)))))))...)))	ACAUUUCCUUCGUUGGAUCAAAGCAGUAGGGACGCGCUCUCUGGCACUCUGCUGUUUUAGUGCAAAGGAGUGAUCAUGAACCGGUUUAUUAUUGCGGAUGCGACGAAAUGUAUCGGUUGCCGUACCUGUGAAGUGGCUUGCGCAGUGUCG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0186683	0.9496255	ysaA	948085	putative hydrogenase 4Fe-4S ferredoxin-type component
b2283	-15	-6	-13	-7	0.75	RyhB	52	61	53	59	2.88	-13.04	-16.67	-1.37112	ACUGGAAGCA&UGCUUCCAGU	((((((((((&))))))))))	ACCUGCUGAAAGAGCGCUGGUAACCGAAUUUCGAUUAACGCUCAGUCUCUGACUGAGAAAACUGGAAGCAUGCUAAUGGCUACAAUUCAUGUAGACGGCAAAGAAUACGAGGUCAACGGAGCGGACAACCUGCUGGAAGCUUGUCUGUCU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0093579	0.9291058	nuoG	946762	NADH:ubiquinone oxidoreductase chain G

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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