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
b0646	-74	-67	-73	-67	0.06	Spot42	1	8	1	7	2.09	-10.27	-12.42	-1.05855	UACCCUAC&GUAGGGUA	((((((((&))))))))	UUACCCUACCUUGUCCUGGCAACCAUUGGCUUACUAUUCUGCAUGCCCGGAAACGCUUAAGGAUAUGAGCGACCUAUGAAAAAUUGCUGGAAGAUCCUCGAUAUAGAGGAAACGACUGACGUCGAUAUUAUCCGCCGCGCUUAUCUGGCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0129952	0.9238006	djlB	945245	putative HscC co-chaperone uncharacterized J domain-containing protein
b0705	41	48	41	47	1.46	Spot42	49	56	50	56	0.3	-9.4	-11.16	-0.968874	CCGAUUAC&GUAAUCGG	((((((((&))))))))	UAUUCCUUAUUACCUAAAGCUGUUUUUCAUAGCUUAUACAUGAUCAAAUACUCCUUACAUAAAUAAGGUGAACAAAUGGAACUUAAAAAAUUGAUGGAACAUAUUUCUAUUAUUCCCGAUUACAGAUAAGCCUGGAAAGUAGAGCAUAAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0212627	0.9238006	ybfL	947075	pseudogene DDE domain transposase familyputative factor Not classified putative receptor protein
b0718	20	33	25	31	3.34	Spot42	1	14	3	9	5.33	-10.35	-19.02	-1.06679	CUUUUGUAUCCUGC&GUAGGGUACAGAGG	((((((((((((((&))))))))))))))	GCUGGAUUAUAAAUAAGUAUUAUUUUGGCGGCAUCAUCGCCGCCUUUCAUAAAAUAUUUAUCAGGUAUGGACACCGUGAAUAUUUAUCGACUCUCUUUUGUAUCCUGCCUGGUCAUGGCGAUGCCUUGCGCAAUGGCGGUCGAAUUCAAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0124179	0.9238006	ybgQ	946537	putative outer membrane protein
b0721	-55	-44	-50	-44	6.86	Spot42	4	15	4	10	5.8	-10.51	-23.17	-1.08328	ACCUCUGUGCCC&GGGUACAGAGGU	((((((((((((&))))))))))))	CUCCAGGUAACAGAAAGUUAACCUCUGUGCCCGUAGUCCCCAGGGAAUAAUAAGAACAGCAUGUGGGCGUUAUUCAUGAUAAGAAAUGUGAAAAAACAAAGACCUGUUAAUCUGGACCUACAGACCAUCCGGUUCCCCAUCACGGCGAUA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0113383	0.9238006	sdhC	945316	succinate dehydrogenase membrane subunit binds cytochrome b556
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
b0757	-17	39	7	13	11.38	Spot42	1	59	28	34	12.67	-14.73	-38.78	-1.51825	AAUCCGGAGUGUAAGAAAUGAGUCUGAAAGAAAAAACACAAUCUCUGUUUGCCAAC&GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUU	((((((..(((.(((.((...((((((((((...((((..((((((((...((.((&)).))..))))))))....))))...))))))))))...)).)))))).....))))))	CUGACCGCAGAACAGGCAGCAGAGCGUUUGCGCGCAGUCAGCGAUAUCCAUUUUCGCGAAUCCGGAGUGUAAGAAAUGAGUCUGAAAGAAAAAACACAAUCUCUGUUUGCCAACGCAUUUGGCUACCCUGCCACUCACACCAUUCAGGCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.001003	0.9238006	galK	945358	galactokinase
b0774	9	28	16	22	4.03	Spot42	4	24	12	18	7.99	-9.09	-21.11	-0.936922	GGACGAUCUUGCCUUUGACC&GGGUACAGAGGUAAGAUGUUC	((((.((((((((((((.((&))...))))))))))))))))	AAAACGUGUUUUUUGUUGUUAAUUCGGUGUAGACUUGUAAACCUAAAUCUUUUCAAUUUGGUUUACAAGUCGAUUAUGACAACGGACGAUCUUGCCUUUGACCAACGCCAUAUCUGGCACCCAUACACAUCCAUGACCUCCCCUCUGCCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0253174	0.9238006	bioA	945376	78-diaminopelargonic acid synthase PLP-dependent
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
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
b0882	-74	-44	-66	-60	5.82	Spot42	3	32	18	24	8.8	-9.02	-23.64	-0.929707	GGGAGAAUGAGCAUCCAUUGCUGUGUACGCU&AGGGUACAGAGGUAAGAUGUUCUAUCUUUC	((((((..(((((((.....((..((((.((&)).))))..))....)))))))..))))))	AGGGAGAAUGAGCAUCCAUUGCUGUGUACGCUAGAAAAAGCCUGAAUGCAGGCAUAAAAAUUGGGGGAGGUGCCUAUGCUCAAUCAAGAACUGGAACUCAGUUUAAAUAUGGCUUUCGCCAGAGCGCGCGAGCACCGUCAUGAGUUUAUG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0263331	0.9238006	clpA	945764	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity

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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