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
STM0283	41	60	54	60	3.62	GcvB	152	169	152	158	2.38	-16.47	-22.47	-1.59687	CAGUAUGUGGCGUGACGGGG&CCCUGUCUGUCCAUAGUG	((.((((.(((..(((((((&))))))).))))))).))	CGGUGGCGGAUAACGGCAGUAAAGCCGGGCGGGCGAAAAACCGUCGGGUGGAAAUUCUGGUAGUGGAGUGAAUGAAUGAUGAAAAAAUCAACCUAUGAUGUGUCUCAUCAUUCGGCAGUAUGUGGCGUGACGGGGGAUUAUUAUCGGAUC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0036267	0.6975035		1251802
STM4083	-40	-22	-40	-34	2.95	GcvB	138	155	149	155	2.38	-13.8	-19.13	-1.33799	AGGGUAAACUGUAGCGGAA&UUCCUGUACAUUUACCCU	((((((((.((((..((((&))))..))))))))))))	UCACGAUUAAAACGAUAACUGUCGGGCUUGUCAAAAGGGUAAACUGUAGCGGAAGGCAAAAUAUAAGGAACUUACAUGACCAUACAGCAAUGGUUAUUCUCAUUUAAAGGGCGUAUCGGACGCCGUGAUUUCUGGAUUUGGAUCGGCCUC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0194729	0.8669559	yiiR	1255610	similar to E. coli orf hypothetical protein (AAC76903.1) Blastp hit to AAC76903.1 (146 aa) 90% identity in aa 1 - 141
STM3574	-53	-35	-43	-37	7.7	GcvB	150	169	152	158	2.39	-15.48	-25.57	-1.50088	CACUAUAACGGGCAGGGUA&UACCCUGUCUGUCCAUAGUG	((((((.((((((((((((&))))))))))))..))))))	GGCCGUGACGGUCAGAUGACAACACUAUAACGGGCAGGGUAUGCUUAUUUCCGCAUUUUCUGACAGGUUAACAGUAUGAGUAAGCCACCGCUUUUCUUCAUUAUAAUCAUUGCAUUAAUCGUAGUUGCCGCGUCGUUCCGCUUCGUUCAG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0070016	0.7528387	yhhM	1255097	similar to E. coli putative receptor (AAC76492.1) Blastp hit to AAC76492.1 (119 aa) 84% identity in aa 1 - 116
STM2925	58	74	59	65	5.88	GcvB	153	170	163	169	2.49	-14.45	-22.82	-1.40102	UCACUAUGGCUGGCAGG&CCUGUCUGUCCAUAGUGA	(((((((((..((((((&))))))...)))))))))	UUUCCCGUGUUCACUUAAUGCGUUGCACGGUUCUUACGUCACUGGUUGUUAACCAAAUUUUUUCCUGGGGGAUAAAUGAGCGCGGGAAGCCCAAAAUUCACCGUUAGUCGCAUUGCGGCACUAUCACUGGUUUCACUAUGGCUGGCAGGU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0132805	0.7904009	nlpD	1254448	lipoprotein NlpD
STM0330	-25	-8	-14	-8	4.13	GcvB	152	170	152	158	2.51	-14.16	-20.8	-1.3729	UCAUUACUUCAGGCAGGG&CCCUGUCUGUCCAUAGUGA	((((((...(((((((((&)))))))))....))))))	CGGCGAUGGUUGCGGCGGCGGCGGUAGCGGGGCAUCUGGUCGAUGUUCGGUCAUUACUUCAGGCAGGGGAAUAAGAUGGAUACGUUUAAGCAAAUCAGCGGGCGAAUUGCGCCGAUGCUGGAACCGAAUAUCGACACUGAUGUGAUUAUG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0157842	0.7979576		1251849	3-isopropylmalate dehydratase small subunit
STM2189	-6	10	2	8	3.03	GcvB	155	171	158	164	2.56	-15.31	-20.9	-1.4844	AUCAUUAUGGGCAGCA&UGUCUGUCCAUAGUGAU	((((((((((((((((&)).))))))))))))))	CGCAGACCGGAUAACGUAUUUCUUUUGCCAUCCGGCGCGGAUAGUCAUAAUUAAAAAGGCCGACAGGGUAUCAUUAUGGGCAGCACGAUUUCUCCGCCGUCGGGUGAAUAUUUGUUGGAAAUGCGUGGCAUUAACAAAUCAUUUCCCGGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0078051	0.7711365	mglA	1253711	galactose/methyl galactoside ABC transporter ATP-binding protein MglA
STM3495	52	64	57	63	3.25	GcvB	181	193	182	188	2.72	-16.35	-22.32	-1.58523	GCAAUAUGGCGGU&ACCGCCAUAUUGC	(((((((((((((&)))))))))))))	GCCAACCACAGAAAAAUGUUUAUUGGACAGGGUGCGACUGACCACGCCUGACAGACUUAGUAAGAUGGGGAAAGCAUGAGCACCAUUCUGAUUUUUAUAGCUGCUUUGCUGGCCUGCUCUCUACUGGCAAUAUGGCGGUUCCGGGUAAAG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0039371	0.6975035	yrfF	1255018	Intracellular growth attenuator protein igaA
STM3786	27	38	30	36	0.47	GcvB	178	189	180	186	2.94	-14.4	-17.81	-1.39617	UGUGGUGGUGUU&AGCACCGCCAUA	((((((((((((&))))))))))))	UCCUGACAGGCCAGAACGUCGACAGUUAUAAAUUUACCGUUAUGAUGGGCAUCCUGUUUGGUGACGGAUGUGCGCAUGAUUUGGUUGAUUCUGGCCACGUUUGUGGUGGUGUUUAUUGUGGGGUUUCGGGUGCUGACAUCGGAUACCCGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.013685	0.7904009	yicN	1255310	similar to E. coli orf hypothetical protein (AAC76686.1) Blastp hit to AAC76686.1 (159 aa) 82% identity in aa 10 - 159
STM2526	-32	-17	-31	-25	0.58	GcvB	71	86	79	85	3.06	-14.36	-18	-1.39229	ACAUAACAACAGAACA&UGUUGUGUUGUUGUGU	(((((((((((.((((&)))).)))))))))))	AUCCAUAGGCAAUUGAUGGGAUGCUCUUUAUAAUCCGCGCCUGACAUAACAACAGAACAUAUUUCAGAGGUAAACAUGGCUAUUGAACGGACUUUUUCCAUCAUUAAACCCAACGCGGUGGCAAAAAACGUUAUUGGCAGCAUCUUUGCG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0140165	0.7904009	ndk	1254048	nucleoside-diphosphate kinase
STM3089	56	73	67	73	1.87	GcvB	157	174	157	163	3.11	-16.07	-21.05	-1.55809	UUAAUCAGUAUGGAUGGA&UCUGUCCAUAGUGAUUAA	(((((((.((((((((((&)))))))))).)))))))	GUAAAAAGGUGUUUUGCCAUAUUUAAUUUCACCUAAGGAGAAUUUAGUUAGCUCAAACUGUUGUGCGGAAUAGUCAUGACAGAAGAUUCUACCAUGAGUCUGAAGGUUGCUGACACUGGCAGUCUGAGUGUUAAUCAGUAUGGAUGGAUU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0047561	0.6975035	yqgD	1254612	similar to E. coli orf hypothetical protein (AAC75978.1) Blastp hit to AAC75978.1 (83 aa) 52% identity in aa 1 - 78

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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