Input and runtime details for job 4935127 (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_003197
	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 4935127 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:12:23 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:14:40 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:16:11 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:17:25 CET 2020
	Job Completed		@ Mon Jan 27 14:17:35 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4935127&toolName=IntaRNA ( 30 days expiry )

Description of the job

GcvB - 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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
STM3261	59	74	68	74	0.94	GcvB	54	69	54	60	6.65	-14.26	-21.85	-1.38259	CACAACUGCAAGCCGA&UUGGCUUACGGUUGUG	((((((((.(((((((&))))))).))))))))	CGGCGCUACAGCAAAGUCAAAUCGCCUCUUAAUUUUAGGGGAGCAAUCGCUCCCCUCACCUUCCUGGAGAAUGUUAUGAAAUCAGUGGUUAUUCACGCUGAGGGAGACGUGCGCGUUGAAGAACGUCCCUUACCACAACUGCAAGCCGAG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0148769	0.7904009		1254784	galactitol-1-phosphate 5-dehydrogenase
STM1571	-69	-46	-53	-47	3	GcvB	65	89	66	72	6.66	-15.24	-24.9	-1.47761	CAGUCACAAAGCAUGACAUCACAA&UUGUGAUGUUGUGUUGUUGUGUUUG	((..((((((((((((((((((((&))))))))))))))).)))))..))	UCAGGACAGUCACAAAGCAUGACAUCACAAAAAGCAACGCUAAUAGGGCUUGUUGCCAUCGUUCUGUGGAGCACGAUGGUUGGGUUAAUUCGCGGCGUCAGCGAAGGUCUCGGACCGGUAGGCGGCGCAGCCAUGAUCUAUUCAUUAAGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0081593	0.7799855	yddG	1253089	putative permease
STM3564	-44	-17	-25	-19	1.58	GcvB	65	90	67	73	6.67	-14.37	-22.62	-1.39326	GCAAAAAACAAAACAUAUAACAUCACGA&UUGUGAUGUUGUGUUGUUGUGUUUGC	((((...(((.(((((((((((((((((&)))))))))))))).))).)))))))	UUUAUAAAAAGUACAGUCUGCUUUUUAACCAGCAAAAAACAAAACAUAUAACAUCACGAAUGGGGAUACAGGCACAUGAAACGGAAAGCGAAAACAAUAAUCGCAGGGAUUGUUGCAUUAGCAGUCUCGCAGGGGGCAAUGGCAGAUGAU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.013933	0.7904009	livK	1255087	leucine ABC transporter subunit substrate-binding protein LivK
STM1351	-23	26	18	24	10.93	GcvB	145	186	147	153	6.71	-15.56	-33.2	-1.50864	GGCAUAAAAGGGGCUACGGCAUUAUGAGUUCGGACAAUAAGGUGAAUGU&ACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCC	(((......((.(((((..(((((((....((((((....(((((((((&))))))))).))))))..)))))))......))))).)))))	AACUAUCCUGUCACAUGCGAAAAAAAUUGGACUGGUGAAUCUAUUAAAAGACGGCAUAAAAGGGGCUACGGCAUUAUGAGUUCGGACAAUAAGGUGAAUGUUGACGUCAAAUUGGGCGUAAAUAAAUUUUACGUAGAUGAAGGACACCCA	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0066498	0.7419678	ydiT	1252869	ferredoxin family protein
STM1871	-72	-28	-46	-40	5.98	GcvB	143	187	154	160	6.86	-14.41	-27.25	-1.39714	UGGCGAUACAGGACAGGAAAUUACAACGGACGGUGGAUCAGGUAC&GUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCA	(((((.......(((...((((((.((((((((.((.....((((&)))).....)))))))))).....))))))..))).....)))))	GGCUGGCGAUACAGGACAGGAAAUUACAACGGACGGUGGAUCAGGUACAACUUCAUAGCGCAAAACCACACGCCAGUGGCGCUUAUUGAAAAACUAAAAGGAACGGACUCAUUCACUGUGUCCGCAUGGAUUGAUCGCUAUGAGGUUUUA	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0136032	0.7904009		1253392	putative phage integrase protein
STM0069	-71	-52	-71	-65	3.48	GcvB	60	81	75	81	6.88	-14.87	-25.23	-1.44174	ACAGCACAUGCGCAACCGUA&UACGGUUGUGAUGUUGUGUUGU	((((((((..((((((((((&))))))))))....))))))))	GCCUACAGCACAUGCGCAACCGUAGACCGGAUAAGGUGUUUACGCCGCCAUCCGGCAAAAAACCGAGGUACAACUAUGAGCUAUUACGCCUUUGAAGGACUGAUCCCGGUGGUGCAUCCGGACGCGUUUGUCCACCCCAGCGCCGUGCUG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0102821	0.7883581	caiE	1251587	phenylacetic acid degradation protein PaaY
STM1856	-40	-18	-39	-33	1.92	GcvB	64	87	80	86	7.14	-17.01	-26.07	-1.64922	AACACAACAUAUAACAUUAUAAC&GUUGUGAUGUUGUGUUGUUGUGUU	(((((((((((((((((((((((&))))))))))))))).))))))))	AUAUCUGUAUGGCUGCUUUUAAGCAACAAUACUCUAACACAACAUAUAACAUUAUAACUUACAAUAGGUUAACAAAUGGAAUUACAGCUUAUGCUUAACCACUUUUUCGAGCGCGUCAGAAAGGAUGCAAAUUUCAACGCAUUUCUAAUC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0024848	0.659913		1253375	similar to E. coli orf hypothetical protein (AAC74245.1) Blastp hit to AAC74245.1 (134 aa) 40% identity in aa 1 - 127
STM4007	-39	-20	-26	-20	2.82	GcvB	63	85	63	69	7.27	-13.85	-23.94	-1.34284	CACGACGACCGACCAUGACC&GGUUGUGAUGUUGUGUUGUUGUG	((((((((((((((((((((&)))))))..)))).)))))))))	CGGCGACACGGCCAGCAGAAUUGAAGAUCUCGUUACCACGACGACCGACCAUGACCAAUCCGGGAGAGUACAAGUAUGUCCGCUGAACACGUUUUGACGAUGCUGAACGAGCACGAAGUGAAGUUUGUCGAUCUGCGCUUCACCGAUACC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0189185	0.8629894	glnA	1255533	type I glutamate--ammonia ligase
STM1033	42	70	60	66	5.67	GcvB	132	162	137	143	7.38	-15.02	-28.07	-1.45628	GACAGCAGGGAACGGACGCGGGGAGGGAA&UUUCACUUCCUGUACAUUUACCCUGUCUGUC	((((((((((........(((((((((((&)))).)))))))........))))).)))))	ACGAAAACCGUAAGCUGGGACUGGUAUUUGAUACUGAUCCGGCACAUGACCCGGGGGAACAGGAUAAUGCCGGAAGUGAAGACAACAGUGGCGGCGAUAAAAAUGCCGCCGGUGAUGACAGCAGGGAACGGACGCGGGGAGGGAAGCAGU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0093682	0.7883581		1252551	Gifsy-2 prophage Clp protease-like protein
STM0532	-28	7	-7	-1	2.42	GcvB	131	164	138	144	7.56	-14.18	-24.16	-1.37484	UGGACAACAAAUAGUAAAAGGAUAGGGAAUGAAAA&UUUUCACUUCCUGUACAUUUACCCUGUCUGUCCA	(((((((((....(((((...(((((((.((((((&)))))).)))))))...)))))..))).))))))	GCGCUGGGGCACACCUCUGGUGCGGAUACGCUGCUGGGGUUCUGGCUUGGACAACAAAUAGUAAAAGGAUAGGGAAUGAAAACGUUGGUAGUUGCUCUUGGCGGCAACGCAUUAUUGCAGCGCGGAGAAGCGCUAACGGCAGAGAAUCAA	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0155989	0.7979576	arcC	1252052	putative carbamate kinase

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