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
PMM0229	-75	-67	-73	-67	2.33	Yfr1	22	31	22	28	1.55	-7.62	-11.5	-0.836905	UGGUGAGGA&UCCUCACACA	(((((((((&))))))).))	UGGUGAGGACUUUUGAAACUAAAAGGUAUAAAUUAAUAUCCGAUUACAUUCAUCUUAUUGAAGAGGAACAAUUGGAUGAACGUUAAAUCUAAAGAAUUAAAAGUUAAGGUUCUUUUAUUAAUUACUGGAAGUAUUGCUGCAGUAAGGAUC	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0745694	0.8607323	dfp	1727066	p-pantothenate cysteine ligase and p-pantothenenoylcysteine decarboxylase
PMM1335	-75	-69	-75	-69	0.25	Yfr1	32	38	32	38	0.34	-7.58	-8.17	-0.832511	GAUUUGG&CCAAAUC	(((((((&)))))))	GAUUUGGGAAGGUAAAAGGUGAAGCUCAUGUUGAUGGGAAGUUGGUUUGCUCAGGCGAAUUAAUGUUUUCAUUAGUUGAUUAAAAACAUGGAGAUUAAAAAUACUAAUUUUAAAGGUGCAAUAGUUCAUCCAAAUGCAUUGGUUGAUUCA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0764774	0.8607323	lpxA	1726818	UDP-N-acetylglucosamine acyltransferase
PMM1120	-75	-69	-75	-69	3.56	Yfr1	22	28	22	28	1.55	-7.05	-12.16	-0.774302	GUGAGGA&UCCUCAC	(((((((&)))))))	GUGAGGAAAUUCUCAAGUUAGUGAAUUUUAUUUUUCAUAAUUUCAGUUACUAUAAUUAUUAGAAAACAAAAUAUAUUGAAAAAAAUUGACUUAUUAAAAAAAAUUGAAGAAGCAAAAAUAAAACAAAAAGCAGGAAAUUCUUUAGAGGCA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.1056045	0.8607323		1726966	TPR repeat-containing sulfotransferase
PMM1096	-75	-69	-75	-69	2.62	Yfr1	20	26	20	26	1.88	-6.25	-10.75	-0.686438	GGGGAGU&ACUCCUC	(((((((&)))))))	GGGGAGUGAACUUGAAUAUGUAGAUGAAGUUACUUUAGCAAGAGCCUUAGAAGGAAGAACAAAUUUAAUUUAAAAAUGAAAAAUAAAAAUCAGAUGAAAGUAGAAAAAAUUUUAAGGCUUCCUUCUUGGAUAAAGUUUCCUAUUAGCAAA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.1649446	0.8751146	lipA,lip	1727018	lipoyl synthase
PMM0021	-74	-68	-74	-68	0.17	Yfr1	14	20	14	20	5.25	-6.53	-11.95	-0.71719	UAUGGGG&CCCCAUA	(((((((&)))))))	AUAUGGGGGCUGGAGAUUGUCAUAACUUAUGGUCAAUUUUAAAAAAUAAAAAUACUUUAAAUAAUUAAAUAAUUAAUGAAAAAUAUUACUUUUAAAGAGAAAAUAAACCUUUCUAAUUAUACGACUAUAAAAGUUGGUGGAUUUGCGGAA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.141895	0.8751146	murB	1726721	UDP-N-acetylenolpyruvoylglucosamine reductase
PMM0503	-73	-67	-73	-67	2.87	Yfr1	21	27	21	27	1.88	-6.83	-11.58	-0.750139	UGAGGAG&CUCCUCA	(((((((&)))))))	UCUGAGGAGCGCUAUUUAUUACGGCUUGAAUUAAACAAUGAUUCAUUAACUUUCUAUUUAAUUACAAAUAUCUUGAUGCACAAUUCAGAAAAUUGCCACGAAAAUGUUUGGAUCCUUUCAGGAACUUCAGAUGGACCAGUCAUAGUUAAC	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.1199653	0.8751146		1726491	precorrin-6x reductase
PMM1604	-72	-66	-72	-66	3.57	Yfr1	21	27	21	27	1.88	-6.15	-11.6	-0.675455	UGAGGAG&CUCCUCA	(((((((&)))))))	CCUUGAGGAGAUGUUAUUAAGCCAACAAUUAACCACUCAUUAUGAUUUAUCAUAGUUUAUAUGUAAUUUAUUUCUAUGGAAUUUUCGAAUAAACCAAUACUCCCCGGUUCUAUAGUAGUUGUUAAAGAUGUUAAUUCUAUUUAUAGAGGU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.1738046	0.8751146		1725848
PMM1592	-72	-66	-72	-66	2.5	Yfr1	30	36	30	36	0.34	-5.87	-8.71	-0.644702	UUUGGUG&CACCAAA	(((((((&)))))))	UUUUUUGGUGAAACCUGGACUGAAAAUUUUAUUAAUAAUUUUCUUUUUACUUUAAAUCAUAAUCCUCUAAAAUAAAUGUUAAUUCAAAAUACUAUUUUUUAUAGCCAAGAAUGGCGAUGGGCUAAAUUUAUAAAAUUCUUAAUUUCUCAG	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.2004204	0.8751146	pebB	1726486	phycoerythrobilin:ferredoxin oxidoreductase
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
PMM0417	-71	-63	-69	-63	2.71	Yfr1	28	36	28	34	0.34	-9.92	-12.97	-1.08951	UUUGGUGUG&CACACCAAA	(((((((((&)))))))))	AAAUUUUGGUGUGAUUUAUAUCUAAAAGGGAUUAGGUUUAUAUUUAAUUUCCUCUUUACUAAUUAAUUUAAAUUUAUGACAGGGUUUUUAUAUUUUUUGGGAAAUACUUUGAGAUGGCCCGCUUUAAAACCAAAAGAAUUUUUUUCUUUA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0136924	0.8607323		1726396

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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