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
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
STM3843	7	49	43	49	16.07	GcvB	37	85	37	43	13.09	-14.9	-44.06	-1.44465	CAUAACGACACUAUCGUCGCCCAGGCAACCCCACCGGGACGCG&CGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUG	(((((((((((...((((((((((.(((.((((.(((((((((&))))))))).))))...))).))...))..))))))..)))))))))))	AACGCUUAUCAGGCCUACAAUCAAAAGGCGGUCAUAUGACCGCCUUUUUUUAUUGCAACAAAGUUGAGACUAACCAUGAGCCAUAACGACACUAUCGUCGCCCAGGCAACCCCACCGGGACGCGGUGGCGUGGGUAUCCUGCGUAUUUCC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0100932	0.7883581	trmE	1255370	tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE
STM4250	10	38	18	24	10.09	GcvB	49	80	66	72	9.49	-14.64	-34.22	-1.41944	CAGCGCACCAUUACACUGAGCGAGAAGCC&GGCUUUUGGCUUACGGUUGUGAUGUUGUGUUG	(((((((.(((((((((((((.(((((((&))))))).)))..))).))))))).)))))))	CCCCGCUGGCUUUUACCUUUUCCAGACUUGCUGCACACUAUUCAGGAGACGUUUGUUUUUAGGAAGGAGCAGCCUAUGUGGUAUCAGCGCACCAUUACACUGAGCGAGAAGCCGCGCGGGUUUCAUCUGAUAACAGAUGAAAUUACCGAU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0118389	0.7904009	yjbQ	1255776	similar to E. coli orf hypothetical protein (AAC77026.1) Blastp hit to AAC77026.1 (138 aa) 78% identity in aa 1 - 138
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
STM3720	14	23	14	20	2.2	GcvB	154	163	157	163	1.28	-14.11	-17.59	-1.36805	GGAUAGACAG&CUGUCUGUCC	((((((((((&))))))))))	AAGCCGCUCGAAUUAAAGAAAGGACAAUAAGAAAAAAUCUGUAAUUAUAAUAAUUAUGCACUCAGUGAGUAAUUUAUGAGUGAGACAAGGAUAGACAGAAUGUCUAACAUUAAAAGUUAUAUUUCAAACCAAAAAAACAUAAUUCAACAU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.016256	0.7979576	yibR	1255244	putative inner membrane protein
STM2096	18	30	24	30	4.12	GcvB	152	164	152	158	1.44	-14.39	-19.95	-1.3952	UGGUAAGACAGGG&CCCUGUCUGUCCA	(((..((((((((&))))))))..)))	UACUCAAUGGGUAAACAAUGUUAAAAGUGGGGCGUAUCAGAGUUGGAUAGAACAGAACUAUGAAGGACGCCAGUAAUGAAUAUCUUACUUUUUGGUAAGACAGGGCAAGUAGGCUGGGAGUUGCAACGUUCUCUGGCACCGGUAGGGAAU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0137672	0.7904009	rfbD	1253617	dTDP-4-dehydrorhamnose reductase
STM1564	19	40	32	38	3.82	GcvB	72	90	74	80	4.11	-16.06	-23.99	-1.55712	GCAAAUACCUCAGCAGCACAAC&GUUGUGUUGUUGUGUUUGC	((((((((...(((((((((((&)))))))))))))))))))	AAUAUUUGCCAUGCUGAAUACGAAUUAAUUUUCUGCGAGCCGUACUAAAUAAAUACAUGUUCACGGAGGCAUUAUAUGUUUACUUAUCACUCAGCAAAUACCUCAGCAGCACAACCGGCCCUGGUCAACGCGAUUGAACAAGGAUUACGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.004788	0.6975035	yddX	1253082	biofilm-dependent modulation protein
STM0634	20	62	49	55	5.65	GcvB	35	77	39	45	11	-16.39	-33.04	-1.58911	CAGAAAGACAACCGGCCGAUCAACACCUACAGGACAAACCGCA&UGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUG	((.((..((((((((((((......(((((((((((...((((&))))))))))).))))...)))))...)))))))....)).))	UUAAAACCAACCCAUAAAUGCAAAAUAUACUAUUUCAUCUAUUAUUCAUAAUACGAAUGAAUUCGGAGCCAGAGCGUGAGUGAUAAUAAUCAGGCAGAAAGACAACCGGCCGAUCAACACCUACAGGACAAACCGCAAAUUUUCAGAACA	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0038311	0.6975035	ybeF	1252154	putative LysR family transcriptional regulator
STM1179	22	44	38	44	7.1	GcvB	35	58	35	41	5.79	-16.06	-28.95	-1.55712	GCCAAAACCGGUCUGGACGCGCA&UGCGUGUUCUGAUGGGCUUUUGGC	(((((((((..((.(((((((((&))))))))).))..)).)))))))	AGGUUAUCACCAGCGUAGAUGAGAACGAAGGGCGAGCUAACCAACUGCUGUCGAUGAGUUAAUACAGGACAUUUUAUGAUCAGUUCAUUAUGGAUCGCCAAAACCGGUCUGGACGCGCAGCAAACCAAUAUGGAUGUGAUUGCCAAUAAC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.004788	0.6975035	flgG	1252697	flagellar basal-body rod protein FlgG
STM3236	25	40	34	40	5.36	GcvB	154	169	154	160	2.34	-15.54	-23.24	-1.5067	CAAUGUGGACAGGCAG&CUGUCUGUCCAUAGUG	((.(((((((((((((&))))))))))))).))	CCGGGCAGAAUAUCUGGCUAACAAUGCAGCGUCCAGCCCCUUAACAUAAAAGGAAGUAAAGAGAGGUUAAUAACGAUGAUUACGACCCGAACCGCCAAACAAUGUGGACAGGCAGACUACGGAUGGCUACAGGCCCGCUAUACCUUCUCC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0067362	0.7419678	yhaK	1254759	similar to E. coli orf hypothetical protein (AAC76141.1) Blastp hit to AAC76141.1 (233 aa) 84% identity in aa 1 - 233

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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