Input and runtime details for job 4596356 (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 4596356 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:10:48 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:13:48 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:14:50 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:16:49 CET 2020
	Job Completed		@ Mon Jan 27 14:17:02 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4596356&toolName=IntaRNA ( 30 days expiry )

Description of the job

FnrS - 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
b3770	-75	-56	-62	-56	3.72	FnrS	1	24	1	7	9.45	-10.78	-23.95	-1.09836	UCGCACACGUUGCCAUCUGC&GCAGGUGAAUGCAACGUCAAGCGA	((((..((((((((((((((&)))))))...)))))))...))))	UCGCACACGUUGCCAUCUGCCAGAGCACAACCACAUCACAACAAAUCCGCGCCUGAGCGCAAAAGGAAUAUAAAAAUGACCACGAAGAAAGCUGAUUACAUUUGGUUCAAUGGGGAGAUGGUUCGCUGGGAAGACGCGAAGGUGCAUGUG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0154393	0.9422174	ilvE	948278	branched-chain amino acid aminotransferase
b1817	-75	-47	-70	-64	4.53	FnrS	57	88	77	83	4.63	-10.21	-19.37	-1.04028	CGAUUCGAUUGUGGACGACGAUUCAAAAA&UUUUUGAAUUACUGCAUAGCACAAUUGAUUCG	(((.(((((((((.......(((((((((&)))))))))..........))))))))).)))	CGAUUCGAUUGUGGACGACGAUUCAAAAAUACAUCUGGCACGUUGAGGUGUUAACGAUAAUAAAGGAGGUAGCAAGUGACCAUUGCUAUUGUUAUAGGCACACAUGGUUGGGCUGCAGAGCAGUUGCUUAAAACGGCAGAAAUGCUGUUA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0225023	0.9422174	manX	946334	fused mannose-specific PTS enzymes: IIA component/IIB component
b2676	-72	-66	-72	-66	0.35	FnrS	1	7	1	7	2.34	-10.89	-13.58	-1.10957	CGCCUGC&GCAGGUG	(((((((&)))))))	AUCCGCCUGCGUCAGAUGGCGCUGGAAGGCACUGAAAUUGAAGGCUGCGUCUCCUGUGCACUUUAAGGAAUAUCUAUGAAACUCUCACGUAUCAGCGCCAUCAACUGGAACAAGAUAUCUGACGAUAAAGAUCUGGAGGUGUGGAAUCGC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0143339	0.9422174	nrdF	947149	ribonucleoside-diphosphate reductase 2 beta subunit ferritin-like protein
b0642	-72	-63	-71	-65	2.78	FnrS	68	77	70	76	1.76	-10.63	-15.17	-1.08307	UGCUAUGCGG&CUGCAUAGCA	((((((((((&))))))))))	CUAUGCUAUGCGGAUCUGAAAAACCACCUCAACGCUACAUUUGUAGCCGUAUUGAAAACAGGACCACUGGCUGCCAUGCAAGAGCAAUACCGCCCGGAAGAGAUAGAAUCCAAAGUACAGCUUCAUUGGGAUGAGAAGCGCACAUUUGAA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.017071	0.9422174	leuS	947497	leucyl-tRNA synthetase
b2799	-72	-54	-62	-56	2.19	FnrS	58	78	60	66	3.57	-10.07	-15.83	-1.02602	GUGCUGGAGAAAUUCAAAA&UUUUGAAUUACUGCAUAGCAC	((((((.((.(((((((((&))))))))).)).))..))))	GUAGUGCUGGAGAAAUUCAAAACCUAUGGGUUACGAAUUGAAGAGUAAUUUCGUAAAGCAACAAGGAGAAGGAUGAUGGCUAACAGAAUGAUUCUGAACGAAACGGCAUGGUUUGGUCGGGGUGCUGUUGGGGCUUUAACCGAUGAGGUG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0246323	0.9422174	fucO	947273	L-12-propanediol oxidoreductase
b1305	-72	-60	-66	-60	0.76	FnrS	42	54	42	48	1.64	-9.99	-12.39	-1.01787	GAAGCAAGACAAU&AUUGUCUUACUUC	((((.((((((((&)))))))).))))	AAUGAAGCAAGACAAUCAAUAAUAACAUCCAGGCGGCGUCCGAACGCGCCGCCGCUCAUCGUCUAAGGAGUACUUAUGAGCGCGCUAUUUCUGGCUAUUCCGUUAACCAUUUUUGUGCUGUUUGUUUUACCGAUCUGGUUAUGGCUGCAU	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0259293	0.9422174	pspB	945893	psp operon transcription co-activator
b4141	-71	-55	-61	-55	6.59	FnrS	73	88	73	79	2.24	-10.44	-19.27	-1.06372	CGAAUCUGAUUGUGCUA&UAGCACAAUUGAUUCG	((((((..(((((((((&))))))))).))))))	UAAGCGAAUCUGAUUGUGCUACCAUCGAAAAUCUACGCAGUUGCCCAAAAUUUGGGCGCAAUCGGACAUCAACCCAUGAGUGGACUCAAACAAGAACUGGGGCUGGCCCAGGGCAUUGGCCUGCUAUCGACGUCAUUAUUAGGCACUGGC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0193611	0.9422174	yjeH	948656	putative transporter
b0846	-67	-52	-64	-58	0.37	FnrS	43	61	52	58	2.19	-11.38	-13.94	-1.15949	AGAAGAGGGAAGACAA&UUGUCUUACUUCCUUUUUU	((((((((((((((((&))))))...))))))))))	UCAAAAUAAGAAGAGGGAAGACAACAUUAGCAAGGUUGUGUACAUUUGUACACAAUUGCAGAGAGAGGAAAUGACAUGCGUCGCGCUAACGAUCCGCAACGGCGAGAAAAAAUUAUCCAGGCCACGCUGGAGGCGGUGAAACUUUACGGA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0102296	0.9422174	rcdA	945473	transcriptional regulator of csgD and ybiJI autoregulator
b2279	-65	-31	-37	-31	8.9	FnrS	43	92	43	49	5.85	-11.54	-26.29	-1.17579	CGUGCGGGUGAAGUGCUGAGCAAUCGUAAAGACGA&UUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACG	(((((((((.(((((((..(((...((((((((((&)))))))................))))))..)))))..)).)))))))))	UCGUGAAGAGCGUGCGGGUGAAGUGCUGAGCAAUCGUAAAGACGACAGCGCGAAAAGAAAAACGGAGGAGCACGCAUGAUCCCCUUACAACAUGGACUGAUCCUCGCGGCAAUCUUAUUCGUUCUUGGCUUAACCGGUCUGGUUAUCCGU	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0091414	0.9422174	nuoK	947580	NADH:ubiquinone oxidoreductase membrane subunit K
b0753	-64	-55	-61	-55	2.2	FnrS	1	10	1	7	2.78	-11.69	-16.67	-1.19108	AUUCACCUGC&GCAGGUGAAU	((((((((((&))))))))))	CAAUGCCUUAUAUUCACCUGCAAAUGCACUGUUGGAAGAGGUUAUCCGACAUAACGACCAUAACAGGAGCAUCCUAUGAAAAUGACAAAACUGGCCACAUUAUUUCUGACUGCCACUCUAAGCCUUGCCAGCGGUGCCGCACUGGCUGCC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0082179	0.9422174	ybgS	945356	putative periplasmic 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

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching