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
PMM1119	-3	7	1	7	4.08	Yfr1	22	31	22	28	1.55	-11.27	-16.9	-1.23778	UGUGUGAGGA&UCCUCACACA	((((((((((&))))))))))	UGGCCAGCUCGUUUUUUGUCUACUGGUGGUUGUUAAUUCUAGGCAAAUAGAUUAUUUUUAAAUUACUCAAAUUGUGUGAGGAUUUUUAUGAAGCUUUUUAAAAGCUUGUUGGUAGCUCCAGCAACGAUUGGGCUACUAGCUCCAUUUUCA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0038187	0.7904709	som	1726740	porin
PMM0173	41	68	43	49	7.38	Yfr1	20	38	30	36	2.28	-10.31	-19.97	-1.13235	GGUUUGGUGAUUGUGACUCUGCAGGAGU&ACUCCUCACACACCAAAUC	(((((((((..((((.......((((((&)))))))))))))))))))	AAAAAUAGCUGAUAUUAUGGCAAUCCUUGGCUCAAUAGACGUCAUUAUGGGUUCUGUAGACAGGUAAACCUUUUAAUGAAACCUAAAAAUUGGUUGAUUUUAAAAAGGAAAGUAAGGUUUGGUGAUUGUGACUCUGCAGGAGUGAUACAU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0097181	0.8607323		1726254
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
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
PMM0494	-36	-28	-34	-28	4.84	Yfr1	22	30	22	28	1.55	-9.16	-15.55	-1.00604	GUGUGAGGA&UCCUCACAC	(((((((((&)))))))))	AGAUUUCUGCUAAAAAUUUACGUUUUAGAAUUUGAUUGAGUGUGAGGAUGUAGGAUAAAUAAAAAUAAUUUUUUGAUGGCAAACCUUAAUCAACCCCCAAGUAGAGUUACCCCAAAUUUAUUGCAUAUUUUAGAUGCUUUUACAGACAAU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0253828	0.8607323	ppa	1726044	inorganic pyrophosphatase
PMM1193	-63	-43	-61	-55	1.24	Yfr1	36	58	50	56	11.19	-9.03	-21.46	-0.991765	AAAAGCCCGUAAAUCAUCGAU&AUCGCCCGAUUUAUCGGGCUUUU	(((((((((((((((..((((&))))...)))))).)))))))))	AGCUUCCCAGCUAAAAGCCCGUAAAUCAUCGAUAAGAUUUUCAAGAUAAACACCAGAGGGUAAUUUAAUCACUAAAUGAAUAUUAAACAACCAUCUUCUCAUAAAAAUCCAGAACCUGAAAGUAGCGUUUUAUAUAUUGUUGGUACGCCC	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0280368	0.8607323		1726173	tetrapyrrole methylase family protein
PMM1121	-3	6	-2	5	5.15	Yfr1	23	31	24	30	0.92	-8.64	-14.71	-0.948931	UGUGUGAGG&CCUCACACA	(((((((((&)))))))))	AUCAUAGAAAAAGUAUCGUUUGAUACUUGUGAUUAUACUCAGUUAUACAGUAUCUUAAGGUGUCCCUAAUAUUGUGUGAGGCAAUUUAUGAAGCUUUUCAAAAGCUUGCUUGUGGCACCUGCAACUCUUGGUCUUUUAGCACCAAUGACC	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0374112	0.8607323	som	1727082	porin
PMM0384	-48	-42	-48	-42	1.7	Yfr1	22	28	22	28	1.55	-8.55	-11.8	-0.939047	GUGAGGA&UCCUCAC	(((((((&)))))))	AGCUUUAUUCAAAGUAUGAACUAGAUAGUGAGGAAAUAAAUUUUAUUGAAAAGACCAUUAUGAAAAUGGAAUAAUAUGGCUAAAGACUUUUUCUAUAAAAGGUAUGAAGGGAAUCCCAAGAUAUAUGCUUAUUCUGAUUCACAUCCGCAA	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0399051	0.8607323	spnII-interrupted-C	1726323
PMM1021	12	18	12	18	0.63	Yfr1	21	27	21	27	1.88	-8.47	-10.98	-0.93026	UGAGGAG&CUCCUCA	(((((((&)))))))	CAACCAAAAAAAAAUCAUUUAAGUAGUACCAAUACUCAUAAAAUAAAUUAAUAUAGAGUUUGUGAAAAUUUAAUUAUGACUGAUAUUGAGGAGAUAAAAAAGAAGAUAUAUCAAAUUGCAGCUAUUACUGACAGGGGGCAAAGACUGAAC	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0422349	0.8607323		1725891	pili assembly chaperone
PMM1448	62	68	62	68	1.4	Yfr1	21	27	21	27	1.88	-8.28	-11.56	-0.909392	UGAGGAG&CUCCUCA	(((((((&)))))))	AUCUGAUCUACAUAUUAUUAUCGGCGAUGAAGUUGAAGAUAAUCUAUAUAAUAAUCAAUUUGGUAAAUAUCAAAUAUGAACUUAAAAAAGGUUGAUUUUUAUUUAGAUUGGCCAGGAUCAAAAAACAUUAUUCAUUUGAGGAGAUUUAUU	AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU	0.0482169	0.8607323		1726048

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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