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
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
STM1498	-54	-38	-48	-42	4.66	GcvB	76	92	80	86	3.94	-16.29	-24.89	-1.57942	UUGCGAACACAACGACA&UGUUGUUGUGUUUGCAA	(((((((((((((((((&)))))))))))))))))	ACGCGCCCGGAGCUCCCCGUUUUGCGAACACAACGACAUUUAAAACUCUUUUUUGGAUGAGCAUAGUGAGCUGUUAUGAAAAUCACCAACCCUGAGGCAUUAAUGGCGGCCAGUCUCAGCCGACGAAGCCUGGUGAAAACCUCCGCUAUC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0041011	0.6975035		1253016	dimethyl sulfoxide reductase subunit A
STM3523	7	24	10	16	5.8	GcvB	72	89	80	86	4.11	-15.15	-25.06	-1.46889	CAAACACAACGGCAUGAC&GUUGUGUUGUUGUGUUUG	((((((((((((((((((&))))))))))))))))))	UCGAGAUAUUUUUCCAGGCCGGGUAGGGCGAAUGCCGCUAUCCGGCGCAAGGUUGGUUACUUUCAGAGAUUAUUCAUGAAACAAACACAACGGCAUGACGCGAUCAUUGAACUGGUAAAAAAACAGGGGUACGUCAGUACGGAAGAGCUG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0086358	0.7799855	glpR	1255046	DeoR/GlpR family transcriptional regulator
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
STM3909	-34	-14	-24	-18	1.56	GcvB	67	88	71	77	6.32	-21.24	-29.12	-2.05935	AAGCGCGACACACAACAUCAC&GUGAUGUUGUGUUGUUGUGUUU	(((((((((((((((((((((&))))))))))).))))))))))	UGGGUUCAUUCGCACAGAUAGCAAUCUGUAAACCGAACAAUAAGCGCGACACACAACAUCACGGAGUACACCAUCAUGGCUAACUACUUUAAUACACUGAAUCUGCGCCAGCAGCUGGCGCAGUUGGGUAAAUGCCGCUUUAUGGGCCGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	6.85e-05	0.2036716	ilvC	1255435	ketol-acid reductoisomerase
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
STM1953	-28	28	18	24	12.25	GcvB	31	87	36	42	16.22	-18.8	-47.27	-1.82278	AACACACCACAACGUUACCGGAGGCUCAAUGCCACUACAUCACUUAACGCGCUUCC&GGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUU	((((((((((((((((((((.((((.(((.(((....(((((...(((((((((((&)))).))))))).))))))))..))))))).)))...))))))))))..)).)))))	AUCGGCGCCUUUUUUAUUUCCGUUAGAUCAACGUGCAUAAUAAAAAGAACACACCACAACGUUACCGGAGGCUCAAUGCCACUACAUCACUUAACGCGCUUCCCUCGCCUGGAGUUUAUCGGCGCGCCGACCCCGCUCGAAUACCUGCCG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0006334	0.3847632	yedO	1253474	D-cysteine desulfhydrase
STM3093	-66	-41	-47	-41	4.25	GcvB	72	101	72	78	11.77	-15.59	-31.61	-1.51155	GCGGACUGAUUGCAUACAGACACAAC&GUUGUGUUGUUGUGUUUGCAAUUGGUCUGC	((((((((((((((((((.(((((((&)))))))...)))))..)))))))))))))	CUUUCCUGAGCGGACUGAUUGCAUACAGACACAACUUUCGUUACGUUGCGGGCUCGUUUUGCUAUGGAGUGUGCAAUGUACCGUAAUUUUUCUUUUGCCGCUGCGUUGCUGGCCGCAGCGUUUUCAGGCCAGGCCCUGGCCGAUGGCAUU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.006522	0.7419678	endA	1254616	deoxyribonuclease I
STM2328	11	48	11	17	9.42	GcvB	32	75	69	75	13.51	-14.14	-37.07	-1.37096	CAACAUCCACUGAAGUCAUCGCUCAUCACUGGGCAUUC&GAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUG	((((((((((((((((((..((((((((....((((((&))))))......))))))))...)))))).))).)).)))))))	CCUCCCCAUGAAUCGAUGUGGCGCCCAUCUGCCGUAAAGAGCAGAGAAACUGGCGCUACUUUUGAUGAGUAAGCAAUGAGUAUGUCAACAUCCACUGAAGUCAUCGCUCAUCACUGGGCAUUCGCUAUCUUUCUUAUCGUUGCCAUUGGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0159714	0.7979576	nuoA	1253850	NADH-quinone oxidoreductase subunit A
STM4558	-7	58	24	30	12.74	GcvB	36	91	63	69	14.51	-14.84	-42.09	-1.43883	UGCGAACAUGAACACGAUUUCUAUCCUCAGCACGACCGAUCUCCCCGCAGCCUGGCAGAUUGAGC&GCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCA	(((((((((((((((((..........((.((((((((.....((...((((...((((....((&))....))))...))))...))....)))))))).))))))))..)))))))))))	UCACGACGCCGGCGUUUAAUGAACUCCGGGCAAACCCGGCGGCACGCGCCGCACUAUGGCAACAAAUCUGCGAACAUGAACACGAUUUCUAUCCUCAGCACGACCGAUCUCCCCGCAGCCUGGCAGAUUGAGCAACGCGCUCAUGCGUUU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0104742	0.7883581	rimI	1256084	ribosomal-protein-alanine N-acetyltransferase

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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