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
b3224	-61	-50	-56	-50	1.86	Spot42	1	12	1	7	3.46	-16.33	-21.65	-1.68316	UCUGUACCCUAC&GUAGGGUACAGA	((((((((((((&))))))))))))	GGGAAAUAAACGCAUCUGUACCCUACAAUUUUCAUACCAAAGCGUGUGGGCAUCGCCCACCGCGGGAGACUCACAAUGAGUACUACAACCCAGAAUAUCCCGUGGUAUCGCCAUCUCAACCGUGCACAAUGGCGCGCAUUUUCCGCUGCC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0003958	0.8439588	nanT	947740	sialic acid transporter
b2797	-68	-54	-65	-59	0.35	Spot42	55	69	60	66	6.05	-15.99	-22.39	-1.64812	UGUUCAGCUAAGUCC&GGAUUUGGCUGAAUA	(((((((((((((((&)))))))))))))))	UACUCUCUGUUCAGCUAAGUCCUUUCGCGCCGCUUUCGGGCGGCGCUUCCUCCGUUUUAACGCGAUGUAUUUCCUAUGAUUAGCGUAUUCGAUAUUUUCAAAAUCGGCAUUGGCCCUUCCAGUUCUCAUACCGUUGGACCAAUGAAAGCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0004824	0.8439588	sdaB	947262	L-serine dehydratase 2
b0757	-17	39	7	13	11.38	Spot42	1	59	28	34	12.67	-14.73	-38.78	-1.51825	AAUCCGGAGUGUAAGAAAUGAGUCUGAAAGAAAAAACACAAUCUCUGUUUGCCAAC&GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUU	((((((..(((.(((.((...((((((((((...((((..((((((((...((.((&)).))..))))))))....))))...))))))))))...)).)))))).....))))))	CUGACCGCAGAACAGGCAGCAGAGCGUUUGCGCGCAGUCAGCGAUAUCCAUUUUCGCGAAUCCGGAGUGUAAGAAAUGAGUCUGAAAGAAAAAACACAAUCUCUGUUUGCCAACGCAUUUGGCUACCCUGCCACUCACACCAUUCAGGCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.001003	0.9238006	galK	945358	galactokinase
b0885	-27	-10	-17	-11	6.33	Spot42	42	58	43	49	3.26	-13.52	-23.11	-1.39353	AUCCGACUUGCGUGGAGU&ACUUCACGUAAUCGGAU	((((((.(((((((((((&)))))))))))))))))	GGGGCGUUAUUACCAGUUCAAGCAGGGUUUGUAAGCUAUUAUUGAACGAUCCGACUUGCGUGGAGUUUUGCGGUCAUGCGCCUGGUUCAGCUUUCUCGCCAUUCAAUAGCCUUCCCUUCCCCGGAAGGCGCAUUACGUGAGCCUAACGGC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0020193	0.9238006	aat	945490	leucyl/phenylalanyl-tRNA-protein transferase
b1398	-10	-2	-8	-2	1.61	Spot42	1	9	1	7	2.1	-13.17	-16.88	-1.35745	GUACCCUAC&GUAGGGUAC	(((((((((&)))))))))	GUGCAUCGGUGUCGGUCAGGGCAUCGCCAUGAUUCUGGAGCGUGUUUGAGCAUAUCAACCUGCGAGUACCCUACAAUGAUAACCAAUACAAAGCUUGACCCGAUUGAAACCGCGUCUGUUGAUGAGUUACAGGCGUUGCAAACACAGCGU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0024709	0.9238006	paaK	945963	phenylacetyl-CoA ligase
b1927	-50	-39	-49	-43	2.49	Spot42	48	59	52	58	1.57	-13.13	-17.19	-1.35333	AAUCCGAUUACG&CGUAAUCGGAUU	((((((((((((&))))))))))))	CUGAAUGAGUCGAUGGCUCGCGAAUAAUCCGAUUACGGCUACGCUUCUAAUGUUCCCCUUGAAUGGAGUCGAAGAAUGCGUAAUCCCACGCUGUUACAAUGUUUUCACUGGUAUUACCCGGAAGGCGGUAAGCUCUGGCCUGAACUGGCC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0025285	0.9238006	amyA	946434	cytoplasmic alpha-amylase
b1212	15	28	20	26	4.52	Spot42	43	56	45	51	3.25	-13.07	-20.84	-1.34715	CUGGUUACGUGAAG&CUUCACGUAAUCGG	((((((((((((((&))))))))))))))	GCUGGAUAUGCUGAUUGAACCGAUUAUCCAGGAACAUCAGGCCGACCAACUGGCGGCGUUGUCCGAGCAGGAAUAAUGGAAUAUCAACACUGGUUACGUGAAGCAAUAAGCCAACUUCAGGCGAGCGAAAGCCCGCGGCGUGAUGCUGAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0026174	0.9238006	prmC	945779	RF-1 and RF-2 N5-glutamine methyltransferase
b2801	-39	-29	-39	-33	2.87	Spot42	46	56	50	56	1.84	-12.84	-17.55	-1.32344	CCGAUUACGUG&CACGUAAUCGG	(((((((((((&)))))))))))	CCCGAACUCGCUGGUUUUGCACUUUUGAAAACAUAACCGAUUACGUGCUUAAGCUUCUGAACCUAAGAGGAUGCUAUGGGAAACACAUCAAUACAAACGCAGAGUUACCGUGCGGUAGAUAAAGAUGCAGGGCAAAGCAGAAGUUACAUU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.002988	0.9238006	fucP	947487	L-fucose transporter
b2935	63	75	69	75	2.55	Spot42	52	64	52	58	6.13	-12.34	-21.02	-1.2719	AGCCAAAUCCGGU&AUCGGAUUUGGCU	(((((((((((((&)))))))))))))	UUUCCGGCGUAGCCCAAAACGCGCUGUCGUCAAGUCGUUAAGGGCGUGCCCUUCAUCAUCCGAUCUGGAGUCAAAAUGUCCUCACGUAAAGAGCUUGCCAAUGCUAUUCGUGCGCUGAGCAUGGACGCAGUACAGAAAGCCAAAUCCGGU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.003983	0.9238006	tktA	947420	transketolase 1 thiamine triphosphate-binding
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

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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