Input and runtime details for job 6571257 (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 6571257 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:18:03 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:20:22 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:21:19 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:22:25 CET 2020
	Job Completed		@ Mon Jan 27 14:22:35 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

Description of the job

Spot42 - 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
b1623	-58	-51	-57	-51	1.86	Spot42	1	8	1	7	2.09	-9.03	-12.98	-0.930738	UACCCUGC&GUAGGGUA	((((((((&))))))))	GCGCAAUCGUGGAUUUUUACCCUGCUUUGUUUUUAUAAUGGUGCGCACUUUUAUAUCCAGAAAAAGAGUGCGACCAUGAUUGAUACCACCCUGCCAUUAACUGAUAUCCAUCGCCACCUUGAUGGCAACAUUCGUCCCCAGACCAUUCUU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0261856	0.9238006	add	945851	adenosine deaminase
b0369	-53	-46	-52	-46	2.08	Spot42	1	8	1	7	2.09	-8.81	-12.98	-0.908062	UACCCUGC&GUAGGGUA	((((((((&))))))))	GACAACUUUCGUAAAACAUCCCUACCCUGCUUCAGGUAUACUAUGCCCCUCGAUUCCACAAACAUCAGGCAGACCAUGACAGACUUAAUCCAACGCCCUCGUCGCCUGCGCAAAUCUCCUGCGCUGCGCGCUAUGUUUGAAGAGACAACA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0296259	0.9238006	hemB	945017	5-aminolevulinate dehydratase (porphobilinogen synthase)
b2582	6	19	13	19	2.49	Spot42	4	16	4	10	6.57	-9.03	-18.09	-0.930738	UACCGUUUGUACCC&GGGUACAGAGGUA	((((.(((((((((&)))))))))))))	CCGAUAAUAUGUAACAUAUUAGAAACAUACCGGCGUCGUUGCCGAUAAGUCUCCUUACUCAUCCCGAGGUUAGUUAUGAAUACCGUUUGUACCCAUUGUCAGGCCAUCAAUCGCAUUCCCGACGAUCGGAUCGAAGAUGCGGCAAAAUGC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0261856	0.9238006	trxC	947062	thioredoxin 2
b1596	63	73	63	69	1.46	Spot42	56	66	60	66	5.97	-10.86	-18.29	-1.11936	UCAGCCAAAUC&GAUUUGGCUGA	(((((((((((&)))))))))))	UAUUAGACAGAACAAUUCGAUUUUCCUACCCUAUGUAUAAGCCUGAUCUACAGGCAUAUUUAGCAAGGAUUUCAAGUGAGCCGUACUACAACUGUUGAUGGCGCUCCGGCAAGCGACACUGACAAGCAAAGCAUUUCUCAGCCAAAUCAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0092897	0.9238006	ynfM	946138	putative arabinose efflux transporter
b1391	56	67	61	67	4.67	Spot42	55	66	55	61	6.04	-10.65	-21.36	-1.09771	UCAGCCAGAUCC&GGAUUUGGCUGA	((((((((((((&))))))))))))	UGGACCCAUGCUGGCAGAAAUGCAGUAUCUCCAGCGUGUCUUGCCCGGUCAGCAAUGGUAACAGAGGAGAUGGGUAUGCAACGUCUGGCCACCAUUGCACCGCCACAGGUUCAUGAGAUAUGGGCGCUACUCAGCCAGAUCCCGGACCCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0104701	0.9238006	paaD	945959	ring 12-phenylacetyl-CoA epoxidase subunit
b3683	5	16	5	11	0.51	Spot42	55	66	60	66	6.04	-9.25	-15.8	-0.953413	UCAGUCAAAUUC&GGAUUUGGCUGA	((((((((((((&))))))))))))	CCUAUCCUCGCUCCAGGCCUGCCGCAUAACCAAUCAGGCUUCCUACUUACAGAAUUGAGAAAAGAGGAUGUGGAAAUGCUCAGUCAAAUUCAACGCUUUGGCGGCGCGAUGUUCACGCCAGUGCUGCUGUUUCCCUUCGCCGGGAUUGUG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.023138	0.9238006	glvC	2847721	pseudogene arbutin specific enzyme IIC component of PTSenzyme Transport of small molecules: Carbohydrates organic acids alcohols PTS system arbutin-like IIB component PTS system arbutin-like IIC component
b0347	-21	-6	-14	-8	7.38	Spot42	41	57	43	49	3.3	-8.74	-19.42	-0.900847	UCCGAGUCGUGAGGUA&UACUUCACGUAAUCGGA	(((((..(((((((((&)))))))))...)))))	UACAUGUUUUUAACAAAAUAAGUUGCGCUGUACUGUGCGCGCAACGACAUUUUGUCCGAGUCGUGAGGUACUGAAAUGGCAAUACAACACCCUGACAUCCAGCCUGCUGUUAACCAUAGCGUUCAGGUGGCGAUCGCUGGUGCCGGCCCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0308106	0.9238006	mhpA	945197	3-(3-hydroxyphenyl)propionate hydroxylase
b3921	-74	-67	-73	-67	0.43	Spot42	50	57	50	56	0.29	-9.55	-10.27	-0.984335	UCCGAUUA&UAAUCGGA	((((((((&))))))))	CUCCGAUUAAAACGAUAUCUGUCGCCCUUGUCAAAAGGGUAGAAUCCUGGAAAAGACAACCAUCAAGGAACUUACAUGACCAUACAGCAAUGGUUAUUCUCAUUUAAAGGGCGUAUUGGACGCCGUGAUUUCUGGAUUUGGAUAGGCCUG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0195371	0.9238006	yiiR	948417	DUF805 family putative inner membrane protein
b1302	-35	6	-34	-28	9.35	Spot42	21	57	50	56	12.11	-11.97	-33.43	-1.23377	UCCGAUUAACCGUGAAGAGUCAAAAGGUGUGAAACAUGAGC&GUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGA	((((((((..(((((((.....((((((.((((....((((&)))).....)))).))))))..)))))))))))))))	CGGCGUAUUACAGCCUGCGCGAUCGUCUGGGCGUUUAAUUUCCGAUUAACCGUGAAGAGUCAAAAGGUGUGAAACAUGAGCAACAAUGAAUUCCAUCAGCGUCGUCUUUCUGCCACUCCGCGCGGGGUUGGCGUGAUGUGUAACUUCUUC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.004925	0.9238006	puuE	945446	4-aminobutyrate aminotransferase PLP-dependent
b3092	6	69	55	61	11.46	Spot42	1	57	5	11	12.67	-10.14	-34.27	-1.04515	UCCGUUUAUGACUGAAGAUUUCCUGUUAGAUACCGAAUUUGCCCGCCGUCUGUAUCACGACUAC&GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGA	((((.(((((..(((((.....(((..(((((....(((((((.....((((((((....((((&))))))))))))))))).))....)))))..)))........)))))))))).))))	CUGGAAAUUGGUGUGAUAACUUUGUCAGCAUCGCACCAUAAGCAAGCUAGCUCACUCGUUGAGAGGAAGACGAAAAUGACUCCGUUUAUGACUGAAGAUUUCCUGUUAGAUACCGAAUUUGCCCGCCGUCUGUAUCACGACUACGCAAAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0139903	0.9238006	uxaC	947599	uronate isomerase

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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