Input and runtime details for job 3751556 (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 3751556 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:09:18 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:12:06 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:12:59 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:14:52 CET 2020
	Job Completed		@ Mon Jan 27 14:15:02 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3751556&toolName=IntaRNA ( 30 days expiry )

Description of the job

CyaR - 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
b0814	-9	26	20	26	8.49	CyaR	1	48	1	7	4.6	-14.33	-27.42	-1.51778	GAGGUGGUUAUGAAAAAAAUUGCAUGUCUUUCAGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUC	(((((((((.((.........((((((.(((((((&))))))).)))............))).........))..)))))))))	AAUCGCGAAGAGUUUCCCAUUAAUUUUUGAUAUAUUUAAAACUUAGGACUUAUUUGAAUCACAUUUGAGGUGGUUAUGAAAAAAAUUGCAUGUCUUUCAGCACUGGCCGCAGUUCUGGCUUUCACCGCAGGUACUUCCGUAGCUGCGACU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0035802	0.779419	ompX	944967	outer membrane protein X
b3197	10	40	34	40	9.83	CyaR	1	35	1	7	1.49	-13.72	-25.04	-1.45317	GUAGAGUUACAACCGGGUUUUGACUUUCAGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUAC	(((.(((((((...(((((.((..(((((((&)))))))..)).)))))......)).))))).)))	CUGGCGGAUUUAUCGUAUGGCUGGCGAUGUUGUACUGGUUAUCGCCAAUACUCGUUGAAUAACUGGAAACGCAUUAUGUCGCACGUAGAGUUACAACCGGGUUUUGACUUUCAGCAAGCAGGUAAAGAAGUCCUGGCGAUUGAACGUGAA	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0053801	0.8345133	kdsD	947734	D-arabinose 5-phosphate isomerase
b0704	-71	-37	-43	-37	4.79	CyaR	1	33	1	7	1.49	-13.16	-19.44	-1.39385	ACAGCAGGGAUAGAUGAUUUGGGUGAAAUUUUAGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGU	(((((.....(((((....(((((....(((((((&)))))))......)))))....)).))))))))	AGCAACAGCAGGGAUAGAUGAUUUGGGUGAAAUUUUAGCUAAGAUGAAACAGAGAACAUCGAGAGGAAUAAGAAAAUGAAAAGAGUUUUGUUCUUUUUGCUGAUGAUAUUUGUUAGUUUUGGUGUUAUAGCUGAUUGCGAAAUACAAGCU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0077225	0.9277422	ybfC	947288	putative secreted protein
b3139	33	73	67	73	11.91	CyaR	1	39	1	7	4.6	-11.9	-28.41	-1.2604	CCUGGCGGCGUUAGUUUUUGUUCUGGGGAUUGAUUUUUGGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGG	(((((((((..(((..(((....((((...((.((((((((&)))))))).))...))))..)))..)))))))..)))))	CGUCCCUGGCGAUCAAAAAGAACAAAUCCCUGACUAAAUCUAAAAUCGCCUUAAUAUUGGUUUGAGGUAAUAAAAAUGCAUGAAAUAACCCUACUUCAGGGAUUAUCCCUGGCGGCGUUAGUUUUUGUUCUGGGGAUUGAUUUUUGGCUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0167203	0.9277422	agaC	947652	N-acetylgalactosamine-specific enzyme IIC component of PTS
b2721	-73	-43	-49	-43	7.31	CyaR	1	39	1	7	4.6	-11.06	-22.97	-1.17143	CCUGGGCUGGGUUUGGCUUUGCAUUUUUAGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGG	((((((((((...(((.((....((((((((&))))))))....)).))).......)))))....)))))	UACCUGGGCUGGGUUUGGCUUUGCAUUUUUAGCGUUCGUCUCCUUGCUGGCGGCGUGAUUAAAGAGAGUUUGAGCAUGUCUGAAGAAAAAUUAGGUCAACAUUAUCUCGCCGCGCUGAAUGAGGCAUUUCCGGGCGUCGUGCUGGACCAC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0271691	0.9277422	hycE	947396	hydrogenase 3 large subunit
b0465	33	50	44	50	5.81	CyaR	1	26	1	7	1.46	-10.58	-17.85	-1.12059	GCAUUUUGUUUUUUCAGC&GCUGAAAAACAUAACCCAUAAAAUGC	((((((((((((((((((&)))))))))........)))))))))	GGUUCACUGCGUCGUGAUAUUCUUGCGGUUUGACUUUUUCAGGUCGUUCUUCAGGUUCAGAAACCUUCAUUCAUCAUGACUAUGUUCCAGUAUUACAAACGAUCACGGCAUUUUGUUUUUUCAGCAUUUAUUGCUUUUGUUUUUGUCUUG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0354913	0.9277422	mscK	945132	mechanosensitive channel protein intermediate conductance K+ regulated
b0684	-15	27	21	27	11.55	CyaR	1	48	1	7	4.6	-10.55	-26.7	-1.11741	GAGGUUAUUUCACUCAUGGCUAUCACUGGCAUCUUUUUCGGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUC	(((((..((((.....(((.((.(((((((((.(((((((((&))))))))).............))))))).)))))))))))..)))))	UUCUGCUAUGAUUGCCUUUAUCCGUGGGCAAUUUUCCACCCCCAUUUCAAUAAGUUUCAAGAGGUUAUUUCACUCAUGGCUAUCACUGGCAUCUUUUUCGGCAGCGACACCGGUAAUACCGAAAAUAUCGCAAAAAUGAUUCAAAAACAG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0360802	0.9277422	fldA	945293	flavodoxin 1
b0140	-19	10	-1	6	6.42	CyaR	3	33	7	13	1.49	-10.36	-18.27	-1.09729	ACUCUAUCAGGGAUGGUUUAUGUUUUUUA&UGAAAAACAUAACCCAUAAAAUGCUAGCUGU	((.(((.((...((((.((((((((((((&)))))))))))).))))....)).)))..))	GAAUGAAUAUACAGGGAAUAAUAAUUUCUAUUUUAUAUUAUUCCCUGUUUUAAUUAACUCUAUCAGGGAUGGUUUAUGUUUUUUAACACCAAACAUACAACAGCUUUAUGCUUCGUAACCUGUAUGGCUUUUAGUUCAUCGUCUAUUGCG	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0400171	0.9277422	yadV	944859	putative periplasmic pilin chaperone
b1445	17	47	36	42	9.96	CyaR	1	33	10	16	1.49	-12.58	-24.03	-1.33242	ACAUGCUUGUUUUUUAUGCGGUUAUGGCAGC&GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGU	(((.(((....(((((((.(((((((.((((&)))).....))))))))))))))....))))))	GUGAAAAAACUUGAUGCACGUCAAAAAAUGACGCAUAUUUGCGCGCGUUUUAUUCAUCUGGCUGGACGCCCGUACAUGUCUCUCUAUCAACACAUGCUUGUUUUUUAUGCGGUUAUGGCAGCAAUCGCAUUUCUUAUCACCUGGUUUCUU	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0110954	0.9277422	ydcX	945936	DUF2566 family protein
b1115	37	45	38	44	0.27	CyaR	9	17	10	16	0.16	-12.46	-12.89	-1.31971	GGGUUAUGU&ACAUAACCC	(((((((((&)))))))))	CAGAUACCCAUUACACCUCGGGUCAUAACCCGCAGGAUCAACCGCAUGUAAAUUAAAAAAGAGCGUGUUGUCCUGAUGAAACAAAAAGAGCUAUGGAUUAACCAGAUCAAAGGGUUAUGUAUUUGUCUGGUGGUGAUUUAUCACUCGGUC	GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU	0.0119418	0.9277422	ycfT	945679	inner membrane protein

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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