Input and runtime details for job 6571257 (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_000913
	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 6571257 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:18:03 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:20:22 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:21:19 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:22:25 CET 2020
	Job Completed		@ Mon Jan 27 14:22:35 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

Description of the job

Spot42 - E. coli

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_000913 Escherichia coli str. K-12 substr. MG1655

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
b1487	61	69	62	68	2.83	Spot42	48	56	49	55	1.57	-9.48	-13.88	-0.97712	CCGGUUGCG&CGUAAUCGG	(((((((((&)))))))))	ACCCUCUGCUCGCUGAUCAAUUCUCUUGUUUUAUAUCCCCUGGCACACAGCACGUCAGUUAAUCAGGAAACUGUCAUGAAGAGAUCGAUAUCGUUUCGUCCCACAUUGCUCGCGCUCGUCCUUGCCACAAAUUUCCCGGUUGCGCACGCC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0203245	0.9238006	ddpA	946052	DD-dipeptide ABC transporter periplasmic binding protein
b3465	27	38	31	37	4.39	Spot42	54	65	55	61	6.13	-8.75	-19.27	-0.901877	CGGCCAAAUCCG&CGGAUUUGGCUG	((((((((((((&))))))))))))	AAAUAGUCUAUCACUUAACUUAAUUCACAUCACCGCCUGCAAGUAUGUGUUAUCUGGCGGAUUGAGCAAUUUAUCAUGAAAAAACCGAAUCAUUCCGGCAGCGGCCAAAUCCGCAUUAUUGGCGGGCAGUGGCGAGGCCGUAAACUCCCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0306386	0.9238006	rsmD	947977	16S rRNA m(2)G966 methyltransferase SAM-dependent
b1563	62	72	66	72	0.54	Spot42	44	55	44	50	2.6	-9.07	-12.21	-0.93486	CGGUACGUGAA&UUCACGUAAUCG	(((((((((((&))))))).))))	UGCUGAACUUGUGGAGAUAGUGAAAGAACGGCUUCGUAAUCCUAAGCCAGUACGUGUGACGCUGGAUGAACUCUGAUGGCGUAUUUUCUGGAUUUUGACGAGCGGGCACUAAAGGAAUGGCGAAAGCUGGGCUCGACGGUACGUGAACAG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0256036	0.9238006	relE	947549	Qin prophage toxin of the RelE-RelB toxin-antitoxin system
b0835	-52	-36	-52	-46	3	Spot42	1	13	7	13	5.11	-10	-18.11	-1.03072	CUCUGUAGAAUCCCUGC&GUAGGGUACAGAG	(((((((....((((((&)))))))))))))	UGCGAUACAAAUUUUAUCCAGAACUCUGUAGAAUCCCUGCCCUGACCUUUCCUGUAACUGAAUAUUUUUUAAGCUAUGAGCAAAGUAACUCCCCAGCCGAAAAUCGGCUUUGUUUCCCUUGGCUGUCCGAAAAACCUUGUUGAUUCAGAG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0151462	0.9238006	rimO	945465	ribosomal protein S12 methylthiotransferase
b0523	-51	-41	-47	-41	5.97	Spot42	3	13	3	9	5.1	-8.91	-19.98	-0.918369	CUCUGUGCCCU&AGGGUACAGAG	(((((((((((&)))))))))))	UCCUUGCUCUCUUUCCGUGCUAUUCUCUGUGCCCUCUAAAGCCGAGAGUUGUGCACCACAGGAGUUUUAAGACGCAUGUCUUCCCGCAAUAAUCCGGCGCGUGUCGCCAUCGUGAUGGGGUCCAAAAGCGACUGGGCUACCAUGCAGUUC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0280104	0.9238006	purE	949031	N5-carboxyaminoimidazole ribonucleotide mutase
b3709	-53	-42	-48	-42	3.28	Spot42	1	13	1	7	5.11	-9.62	-18.01	-0.99155	CUCUUACCCUAC&GUAGGGUACAGAG	((((((((((((&)))))))).))))	GGCUAUAAGGAUGUUAGCCACUCUCUUACCCUACAUCCUCAAUAACAAAAAUAGCCUUCCUCUAAAGGUGGCAUCAUGACUGAUCAAGCUGAAAAAAAGCACUCUGCAUUUUGGGGUGUUAUGGUUAUAGCAGGUACAGUAAUUGGUGGA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0187797	0.9238006	tnaB	948220	tryptophan transporter of low affinity
b0728	-20	-9	-20	-14	2.59	Spot42	23	34	28	34	3.29	-9.01	-14.89	-0.928676	CUGAAGGAUGGA&UCUAUCUUUCAG	((((((((((((&))))))))))))	CAAUGCCCGGAAGCGAUACGAAAUAUUCGGUCUACGGUUUAAAAGAUAACGAUUACUGAAGGAUGGACAGAACACAUGAACUUACAUGAAUAUCAGGCAAAACAACUUUUUGCCCGCUAUGGCUUACCAGCACCGGUGGGUUAUGCCUGU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0264814	0.9238006	sucC	945312	succinyl-CoA synthetase beta subunit
b4465	-18	-2	-18	-12	3.4	Spot42	39	56	50	56	3.89	-8.82	-16.11	-0.909092	CUGAUUACAGAGGUAAA&UUUACUUCACGUAAUCGG	((((((((.((((((((&))))))))..))))))))	UAUUGGCGAUCCAAAACUCGACACUUUAUUUAAUCAAUUAACCGCCGAACAUAAACACUGAUUACAGAGGUAAAAAUGAAAACCAAAGUUGCUGCUAUUUAUGGCAAGCGGGAUGUCCGUCUGCGCGUAUUUGAACUGCCAGAAAUUACC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0294603	0.9238006	yggP	2847686	putative Zn-binding dehydrogenase
b2294	-75	-67	-73	-67	1.57	Spot42	48	56	48	54	1.57	-8.74	-11.88	-0.900847	CUGAUUACG&CGUAAUCGG	(((((((((&)))))))))	CUGAUUACGCAUAUAAAAGAAGGCAUACUCAGCCUUCUUUUUUUUCACCGUAGUAGAGUGAUACAGGAGUCAACAAUGGAAAUGACCAACGCGCAACGUCUUAUUUUGUCUAAUCAGUACAAGAUGAUGACUAUGCUCGAUCCGGCAAAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0308106	0.9238006	yfbU	946767	UPF0304 family protein
b0878	64	73	66	72	2.3	Spot42	47	56	48	54	1.58	-9.01	-12.89	-0.928676	CUGAUUACGU&ACGUAAUCGG	((((((((((&))))))))))	GUAAAUUUUAGGGUUUUGUUGAUAUUUCGUUGAAGUUAAUGACCCGGAUUGGCAUAUGGAGUAUUCAGAAAAUUUAUGAAAAAGCGGAAAACCGUGAAGAAGCGUUACGUUAUUGCGCUGGUGAUAGUCAUCGCCGGACUGAUUACGUUA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0264814	0.9238006	macA	947322	macrolide transporter membrane fusion protein (MFP) component

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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