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
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
PMM1607	-27	-21	-27	-21	4.89	Yfr1	23	29	23	29	0.92	-4.65	-10.46	-0.51071	UGUGAGG&CCUCACA	(((((((&)))))))	AGCAUAUCUUAAUUUUUUUAAUUUCUUUGUAAGACAAUAGUAUUAUAUUGUGAGGUUCUCAAAGACAAUUUUUACAUGUCACACGCAGUUAAGAUUUAUGACACAUGCAUUGGAUGUACCCAAUGUGUAAGGGCAUGCCCACUAGAUGUU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.347809	0.8751146	psaC	1726501	photosystem I subunit VII
PMM1613	59	65	59	65	3.28	Yfr1	21	27	21	27	1.88	-6.69	-11.85	-0.734763	UGAGGAG&CUCCUCA	(((((((&)))))))	UGGUUAAUAAACGUUCGCAGAUGGCCUCAAAAACCAACGAAAGAUUUGAUGAAAUUUAUAGCUCUGAAAUAAUAAAUGGAAAGAGAUAAAUUGUUAAAAAAAAUUGAUUCAAUCAAGGAUGAACUUAUUAAUAUGAGGAGGCACAUUCAU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.1298531	0.8751146		1726505	zinc metallopeptidase
PMM1627	27	33	27	33	2.88	Yfr1	21	27	21	27	1.88	-6.26	-11.02	-0.687536	UGGGGAG&CUCCUCA	(((((((&)))))))	UAAUUAAACUUUAAUUCAAAAAAAAAAAAAUCGUUUUCGAUUAAUUAUUCUUAGUUUAGAAAAAAUUUUUAGUCUAUGAAAAAAACAAAAGUUAUUUGUAUUGGGGAGGCUUUAAUAGAUAGAAUCAAGAAUAAAUCAAAUCAAGAAUUU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.164077	0.8751146		1726533	carbohydrate kinase
PMM1634	5	11	5	11	1.13	Yfr1	22	28	22	28	1.55	-9.17	-11.85	-1.00714	GUGAGGA&UCCUCAC	(((((((&)))))))	UAUCCCGAUGGUAAAUUUAAUGAAACACCUUUUAAAAAUAACAUUUUAAAAGUUUUAUUUUAUUUUUUAUAUUAAAUGAGUGAGGAAAAAAGAUCUAAUAAAAUCUCCAAUGACUAUGGUGCUGAUCAGAUACAGGUUUUAGAGGGAUUA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0251876	0.8607323	gyrB	1725995	DNA gyrase subunit B
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
PMM1678	26	32	26	32	3.02	Yfr1	29	35	29	35	0.32	-5.87	-9.21	-0.644702	UUGGUGU&ACACCAA	(((((((&)))))))	AUUUAGUAUUAUUUUGACAAAAAAAGUCAUCAAAGACGAUUUAUUUUCUUAAAAUUAAAGAAAACUAAUUACAAAAUGGAUGCAUUACUAGUUAAAGAUAUUGGUGUAAAAGCUUUAUUGGUUGGUGGAGCAGUGCUUGUUUCUUUUUGG	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.2004204	0.8751146		1727342
PMM1685	47	53	47	53	1.44	Yfr1	32	38	32	38	0.34	-5.83	-7.61	-0.640309	GAUUUGG&CCAAAUC	(((((((&)))))))	ACAAAACCCAAAAGAUUUUCAGCGGCUUUGGGAAGUUGCUAAAAAAACACUAAUGAGAGAAAAAUUGAAAAAAAAAUGAAAGAUAUGCCAACUUGGAUAGAUGAGUACCACAAAGGCUCAAGAUUUGGACUUAAUGGGAAAGUAUUACUU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.204443	0.8751146	speE	1727184	spermidine synthase
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
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

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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