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
PMM1180	3	9	3	9	1.75	Yfr1	32	38	32	38	0.34	-5.59	-7.68	-0.61395	GAUUUGG&CCAAAUC	(((((((&)))))))	ACCAAUUUAGGAUUGAAUUCAUUAGUUCUGCUGAUAGUCUUUUUAAAGUAGAUUUAUGAUUUGUACCUUAAAAGAAUGAUUUGGCCUUUUAGACGUAAGUCAAAAAAAAGAAUGGCUCGUAUAGUAAUUGAUGAGCCAAUAACAAGUUCA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.2297474	0.8751146	sppA	1726722	signal peptide peptidase SppA (protease IV)
PMM1689	24	32	26	32	4.22	Yfr1	20	29	20	26	1.88	-5.58	-11.68	-0.612851	UGGAGGAGU&ACUCCUCACA	(((((((((&))))))).))	AACUAUUUAUGGAUGAUCAAUAAAUUUUUUGUUUAAAUAAAGUAUAAGGAGGUUGUGCUUAAUUAAAAAUAUUGCAUGUCAAAGUUUGUUUUUGUUACUGGAGGAGUCGUUUCUAGCAUAGGUAAAGGUAUUGUUGCCGCAAGCUUAGGA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.2308453	0.8751146	pyrG	1727199	CTP synthetase
PMM0712	-72	-65	-72	-66	1.65	Yfr1	12	19	13	19	5.25	-5.54	-12.44	-0.608458	AUGGGGUU&AACCCCAU	((((((((&))))))))	CGAAUGGGGUUACAGCUGCAGGCUUGCAGAUCUUACUGAAUAUGUAAUCAAAAAAGAGAUUUAAUUUAUGUCUUUAUGAAGUUAUCUAAUAUUCAACAAUAUAGUGUUGUAACAGCAAACUAUUGGGCGUUCACGCUUACUGACGGCGCA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.2352719	0.8751146		1726305	major facilitator superfamily multidrug-efflux transporter
PMM1443	61	75	69	75	1.19	Yfr1	19	31	19	25	3.39	-5.46	-10.04	-0.599672	UGUUGUUCAGGAGUA&UACUCCUCACACA	(((.((..(((((((&))))))).)))))	UAAAAUUUUGGAUUGGCGAAUUUUAUAAAAAAAUGGAAGAAUGAAUUAGAAGAUAUUUAAAAACUAAUCUUUUUAAUGGAACCAAAUGUCUACAUUCUAAUUUUACUUAUAAUUAUAAUUUUAGUAGGUUCAGCAUGUUGUUCAGGAGUA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.2442923	0.8751146		1725821
PMM1166	-58	-52	-58	-52	3.33	Yfr1	23	29	23	29	0.92	-5.42	-9.67	-0.595279	UGUGGGG&CCUCACA	(((((((&)))))))	AGACGUUCCUGCUGAGAUGUGGGGGUGGAAUGGAAGAACCUUUGCUUAAUAAUUAUUAUUUUAGGUAUUAAUUAAAUGGAAAUAAAUAAAUUAGUUGAUUUAAACAGUCUUAGAACUGCUCCGCAAUUAAGCAGCAGUCAAGUAAAAAAA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.248886	0.8751146		1726936
PMM1454	19	25	19	25	2.68	Yfr1	30	36	30	36	0.34	-5.35	-8.37	-0.587591	UUUGGUG&CACCAAA	(((((((&)))))))	UUCCUAAAAGUUAAUGUUGCUUUUAAUUCUUAUUAGCAAUAUUUAAAAAUAAUUUUUUAAUUUCAACUGAAAGAUAUGUUGGCCUUUGAUUUUUUUGGUGCUACUGAAGGUGGUUUAUUUGAUAUAAAUGCCACUUUGCCUCUCAUGGCA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.2570582	0.8751146	atpG	1725865	ATP synthase F0F1 subunit B'
PMM0933	32	38	32	38	2.03	Yfr1	32	38	32	38	0.34	-5.33	-7.7	-0.585394	GAUUUGG&CCAAAUC	(((((((&)))))))	UUUUUUGAUAAGCCCAUACUAUUUAGUAAAGAUAUAAGAUGUACAUUUAAUUUAAACAUAUUAUUUCUAUUUUGGAUGAAUUUUAAGAACCAUCAUCAAAAAAAAAGAUUUGGACAACAUUGGUUGGUUAAUAAUCUGAUAUUAGAGAAA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.2594242	0.8751146	ksgA	1725616	dimethyladenosine transferase
PMM1346	18	34	28	34	5.07	Yfr1	32	51	32	38	11.19	-5.29	-21.55	-0.581001	CGAGCAGGGUGAUUUGG&CCAAAUCGCCCGAUUUAUCG	(((...(((((((((((&)))))))))))......)))	AGUAAGAAAUUGAAAAAAGAUGAUUUCAUAAUAAAAGAAUUUAUAGAUGAUGCUUUUGAUUUGAAAUCACACUUAAUGGAAUUUUUGUCUAUCGAGCAGGGUGAUUUGGAUGGGUUCCUCGAAAACGCAAAGAUGGAUUUAGCCAAUCUU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.2641976	0.8751146		1726816
PMM1707	36	44	38	44	4.52	Yfr1	20	29	20	26	1.88	-5.26	-11.66	-0.577706	UGGAGGAGU&ACUCCUCACA	(((((((((&))))))).))	AUAUUAGUUUUUAAUAAAAUUUAGAAAGCUGAAAGUAAUUAGGAUUUCAGCUUUCUUUACUGGAGGUAAAUUUUAAUGCAGCAGGUAAAAAAAGUUGUUCUUGCAUAUUCUGGAGGAGUUGAUACUAGUGUCUGCAUUCCAUAUUUAAAA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.2678137	0.8751146	argG	1727295	argininosuccinate synthase
PMM0876	-43	-36	-43	-37	3.25	Yfr1	20	27	21	27	1.88	-5.23	-10.36	-0.574411	UGGGGGGU&ACUCCUCA	((((((((&))))))))	UCAUACAUUUCUUAAAAAAGGGUUGACGAAUAUGGGGGGUAAAGAGGUAAUAAUUUUAAUAAGGUUUUUUUCAUUAUGGAUUGGGACUUCACUGAAAACAUAGCAUUUAAAUCCCUAAUUGAAGCUUUUAAAGAAUGUGAUGAAACAUCA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.2714606	0.8751146		1727209

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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