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
PMM1405	68	75	68	74	2.69	Yfr1	12	19	13	19	5.25	-4.34	-12.28	-0.476662	AUGGGGUU&AACCCCAU	((((((((&))))))))	AAUGUGACUAGCUGACAAAUUAAUAUUUUCGACCUAUUGUUAACAAUUAGUUAAGUAAAAGUAAAGAUUAAGAUUAUGGCAAAAUCAAAAGUGAAGGGGGGAAAAGCUAUUUUAUCUCCAAAAACUCCAACUAUUUUGGCAGAUGGGGUU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.3928103	0.8909401		1725967
PMM0135	52	58	52	58	1.81	Yfr1	31	37	31	37	0.34	-4.27	-6.42	-0.468974	AUUUGGU&ACCAAAU	(((((((&)))))))	UUAAUUCUUACAGCAAGAGGUACAGGAUAUCUGUUUCAAAGGAUAGUUGAUAUAUCUCCAUUUGACGGUAAAUAGAUGGAAAAAGAUUCUUCUAUUAAAAAGUCUAGAGCUAUAAGAAGAUUAGUUAUUUGGUAUAAAAGAAAUUCUGCU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.403326	0.8909401	plsX	1726261	glycerol-3-phosphate acyltransferase PlsX
PMM1647	17	23	17	23	1.9	Yfr1	14	20	14	20	5.25	-4.25	-11.4	-0.466778	UAUGGGG&CCCCAUA	(((((((&)))))))	GAUCUUUUAUCAUUAAAAUUUAAUUUACUUUAUCUUAAAGAAAGCAUAAUUAUAAUAAGAUUCUUUUUUGCAGAUAUGCCAAUACAAAUAAUAUGGGGAAAUGAUUUAAAUGCAAGUAAUAAGUUUAUAAAACAAAUAAUUGAUGAAAAA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.4063526	0.8909401		1726055	DNA polymerase III subunit delta
PMM0484	-13	-7	-13	-7	2.32	Yfr1	31	37	31	37	0.34	-4.22	-6.88	-0.463483	AUUUGGU&ACCAAAU	(((((((&)))))))	CAUUUUGUUUAAUUUCAAAAUAAUUUAAGAUUUAAAAUUAUUUGCUAUCUUAAUUUUACAUAAUUUGGUAAAAAAUUGUUAAUAGCAACUUGGAAUGUAAACUCUGUAAGAACAAGGCUUUCUCAAAUUAUUAAUUGGAUUAAAGAGGUA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.4109104	0.8909401	xthA	1726771	exodeoxyribonuclease III
PMM0913	-47	-41	-47	-41	1.97	Yfr1	14	20	14	20	5.25	-4.18	-11.4	-0.459089	UAUGGGG&CCCCAUA	(((((((&)))))))	CGUUACAACUCAAUGAAGGGGUUGUUUAUAUGGGGCAGAUAGAAGACGAUGAGGAUGCACUAGAUAAAUAUAAGUAUGUCUAGGAAUAUAUCUCUUAAAGAAGCCUUUAAUAUGGCUGGUAAAACUUUAGUUUCAAACAAAUUAAGAAGU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.4170203	0.8909401		1726817	ABC transporter
PMM1264	38	44	38	44	3.16	Yfr1	32	38	32	38	0.34	-4.16	-7.66	-0.456893	GAUUUGG&CCAAAUC	(((((((&)))))))	UCUUACCCAAAAAAAAUCAUACAGGUACGGAACUCGUUCUUUUAGUUUAUAAUAAACCCACAAUUGAUAUUAAUCAUGCCAAUAAGACAAGACGAUAAUCAGCCUAAUAGAAGAUUUGGAAUAGUAAAUAUCAUUUUAAUUGGACUCGGA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.420089	0.8909401	ftsH3	1726562	cell division protein FtsH3
PMM1030	10	17	11	17	0.3	Yfr1	49	56	49	55	9.5	-4.09	-13.89	-0.449205	AAGCCCGA&UCGGGCUU	((((((((&))))))))	AGUUGUUUAAAAAAGACAUUAAUCGUAUGAUUCGUUAUGAUCAAAAAAGCAGGACAUUAAAAGAUCUUGAAAAUAAUGGUAACCAAGCCCGACAUUACCAAAAGACAAGAGCAACUUCUUGAAGAACUUAAAAAAUGUGAUGAUGAAUUG	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.4308989	0.8909401		1726150	ferric uptake regulator family protein
PMM1423	36	42	36	42	1.62	Yfr1	31	37	31	37	0.34	-4.08	-6.04	-0.448106	AUUUGGU&ACCAAAU	(((((((&)))))))	UUAUCAAAAAGCUAAGAAUAGUUAAGCAGGCAAAUCCAUCUAGUAUUUGUGACUCUGUUCUUAAAAGUUAAAAAAAUGCAAUUAAAGUCUUUUACACCAUUGGUUGCAGUAUUUGGUACUUCAUUUCUUAUAACUAUUACUUUGAUUAAA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.4324518	0.8909401		1726752
PMM0951	69	75	69	75	1.53	Yfr1	31	37	31	37	0.34	-4.03	-5.9	-0.442615	AUUUGGU&ACCAAAU	(((((((&)))))))	UCUAUGAGUAAAGCAGAGCCUUGGAAUAAAUUUUUACUUUUGAAAAACUACCUUGAAUCAUAAUAAAUUUAAUUAAUGAAUCAUCUUUUUAAGAAAAAUGCAAAACUUGUUUUGAGUAAUGGGAUUACUUUUACUGGUUAUUCAUUUGGU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.4402471	0.8909401	carA	1726175	carbamoyl phosphate synthase small subunit
PMM1144	-58	-52	-58	-52	4.42	Yfr1	30	36	30	36	0.34	-4	-8.76	-0.43932	UUUGGUG&CACCAAA	(((((((&)))))))	CAAAUACCUCAAUGGUUUUUGGUGAUGCCAAGAAAGUUUUAAGUGAGUUAAUUGGAGAAUUAAAGGAUCUAGGAGUUGGCGAUAAAUAGUAAUCUCUCAUUUAAGUUUUCAGAUUAUAUAAACAAAAGACCUUUUAGACAGGCUUUCCCU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.4449483	0.8909401		1726314	hydrolase of the alpha/beta-hydrolase fold

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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