Input and runtime details for job 7119295 (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_005072
	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 7119295 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:23:26 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:25:03 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:25:25 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:26:09 CET 2020
	Job Completed		@ Mon Jan 27 14:26:17 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7119295&toolName=IntaRNA ( 30 days expiry )

Description of the job

Yfr1 - Prochlorococcus marinus

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_005072 Prochlorococcus marinus subsp. pastoris str. CCMP1986

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
PMM0792	57	63	57	63	4.68	Yfr1	21	27	21	27	1.88	-4.64	-11.2	-0.509611	UGAGGAG&CUCCUCA	(((((((&)))))))	GAAAUCUUAAAGGUUAAUCCCGCAGGCAAUUCUGAUGAAAAAACACCUAUAGUAUUAAUAAGGAAUAAUAUAUAAAUGAAACAAGAUUCAAAUCAUAUUUUGAAUUCUAAUAAAGAUAGAAAAGUUACCUUUGAGGAGCUUCAUAUUCGU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.3492182	0.8751146		1726832
PMM1107	2	18	12	18	2.2	Yfr1	19	34	19	25	3.65	-4.63	-10.48	-0.508513	UGGCAAAAUUAGGAGUA&UACUCCUCACACACCA	(((.......(((((((&)))))))......)))	AUUAUAGGAUUGUAAUUUUUUAUUAGCUAGAAUUAGUCGGUUAGUAAAUUGUCUAAAUCAAAGAGUUAUCAAUUUAUGGCAAAAUUAGGAGUAAAUAUAGAUCAUAUUGCAAAUGUCAGGCAGGCUAGGCAGACUGUAGAACCAGAUCCU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.3506303	0.8751146	pdxJ	1727142	pyridoxine 5'-phosphate synthase
PMM1605	-52	-46	-52	-46	2.67	Yfr1	20	26	20	26	1.88	-4.62	-9.17	-0.507415	GGGGAGU&ACUCCUC	(((((((&)))))))	UCUUUAACAACUACUAUAGAACCGGGGAGUAUUGGUUUAUUCGAAAAUUCCAUAGAAAUAAAUUACAUAUAAACUAUGAUAAAUCAUAAUGAGUGGUUAAUUGUUGGCUUAAUAACAUCUCCUCAAGGCAUUAAUGGAAAAAUCAAGAUU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.3520454	0.8751146	rimM	1726286	16S rRNA-processing protein RimM
PMM0843	35	43	37	43	7.01	Yfr1	30	38	30	36	0.34	-4.56	-11.91	-0.500825	GAUUUGGUG&CACCAAAUC	(((((((((&)))))))))	CUCUUGAAAGUGAUGAUUUUCAACCAUCAAUUAGAUAAUCUGAUCUUAACAAAGAGCUAAAGUUAUAAGAUUCAAAUGGUAUCUGCGAGUAUUAAAUCUUCCGAAAUUAGAUUUGGUGAAUGUAAUAAAAAACUUCUUGAAGAAGUCAUU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.3605969	0.8751146	tldD	1727285	modulator of DNA gyrase TldD
PMM0446	45	51	45	51	1.75	Yfr1	31	37	31	37	0.34	-4.54	-6.63	-0.498628	AUUUGGU&ACCAAAU	(((((((&)))))))	AUUUUCCAUUAACAAACAAUGCAAAAUUAAAAAAAUUGAAUAUGUUGAAAAUAUAAAUAAGAUUUAUUUCCUCAAUUGUUAAAUAAAAACUUUUAUUUAAUACUUAUAAUUUCCGUUGUAUUUGGUAUAUCUUUUUGGAUCGGAUUUAAU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.3634704	0.8751146	ctaC	1727092	cytochrome c oxidase subunit 2
PMM1216	37	43	37	43	2.02	Yfr1	32	38	32	38	0.34	-4.53	-6.89	-0.49753	GGUUUGG&CCAAAUC	(((((((&)))))))	UUUCUCCAGCUUUUACAUCAAGUUUCUCACUGGCAGAUUUAAUAAUUAAUUCUUCAAAAUUAAAUAAAGAAUAAUAUGGACAAAAAGUUAAAAGUUUUAUUAUUAGCGGCAGGUUUGGGAACAAGAUUAAAACCAUUAACAAAUAAUGUC	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.3649114	0.8751146		1726669	sugar-phosphate nucleotidyl transferase
PMM1518	58	65	59	65	4.45	Yfr1	30	37	30	36	0.34	-4.51	-9.3	-0.495333	AUUUGGUG&CACCAAAU	((((((((&))))))))	GUUAGAGCAAAUUCCGUCUAAAAUAUCAUUUAAGGCUAAACCCAUUUCUUCUCGUAAAUAAUAAAAAGACAUUUUAUGAAAGAACAUAUAGACCCUACCUCACUAUUUAAGCAAACUAAUUUUUCAAACACUAUUUGGUGGAAAGUAAAA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.3678018	0.8751146		1725898
PMM0017	23	29	23	29	4.39	Yfr1	29	35	29	35	0.32	-4.48	-9.19	-0.492038	UUGGUGU&ACACCAA	(((((((&)))))))	AAGAAGAUAUUGAUUCAGAGAAUCCUAUCUCUGAAGAAAAUUAAAUCCUUUUUAUGAAUAGUUGAGUAUUAUUUAAUGGCCGACUUUUAUCAAAUACUUGGUGUUUCAAGAGAUGCUGAUGCUAAUACUUUAAAGAGUGCUUAUAGAAAG	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.3721584	0.8754181	dnaJ	1726455	molecular chaperone DnaJ
PMM0389	68	74	68	74	4.35	Yfr1	29	35	29	35	0.32	-4.36	-9.03	-0.478859	UUGGUGU&ACACCAA	(((((((&)))))))	UAUUGAAUCGGAGAUCUUAUCCCAAACGUUUGCUUUGCCAAGAAUUCAUAGUUAAUUGAAUUUUGUUAUUAAUUUAUGGGAAUUAGAAAUACUCUAAAAAAUCUGCUUGGUUUUAAAAGUGAUCUUGCAUCAUUAACAGUAGUUGGUGUA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.3898285	0.8909401	cobI/cbiL	1726325	precorrin-2 C20-methyltransferase
PMM0665	-1	6	-1	6	2.04	Yfr1	14	20	14	20	5.25	-4.34	-11.63	-0.476662	UAUGGGG&CCCCAUA	(((((((&)))))))	CAUUAUUCGAGGGGAUACCGUCUAAAAUAUUAGUUCUUGAACAAGGAAAGAUUAAAGAAUUAAUGAAAAAAAAUUAUGGGGGAUAAAAUUGUACGCGCAACUGCGGCUAAUGGUGGAAUAAGGUUAGUUGCGGUAUUAACAACAGAUUCA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.3928103	0.8909401	hslO	1726016	heat shock protein 33

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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