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
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
STM3630	-43	-2	-21	-15	6.19	GcvB	51	92	66	72	10.1	-20.93	-37.22	-2.02929	UUGCAAAGGGCAAAACAACAUACAUCACAAUUGGAGCAGAAG&CUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAA	(((((((...((.((((((((((((((((((((.((((((((&)))))).))..))))))))))).))))))))).)))))))))	AAAAAACAAAAAAGGCCGGGCGGUAAAAGCCUUUGCAAAGGGCAAAACAACAUACAUCACAAUUGGAGCAGAAGAAUGAGUAUUUCCUUGAAGAAGUCAGGGAUGCUGAAGCUUGGUUUGAGCCUGGUGGCCAUGACCGUUGCAGCAAGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	9.35e-05	0.2036716	dppA	1255154	ABC transporter substrate-binding protein
STM1107	4	61	6	12	17.59	GcvB	36	82	74	80	10.87	-20.55	-49.01	-1.99245	AGCGACACAUCAUCUGCACUUCCGGAAAGCCCCGAGUCUGUCAGUUCGCACAACGCGC&GCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUU	(((((((((.((((...((..(((..(((((...((((((((((.......(((((((&)))))))))))))))))...))))).)))..)))))).)))))))))	UUAAGCCUGGCCCCGUAAGCGCAGCGCUACCGGGCAACCGUAGUACCCUACAAAAUUCCCAUCAGAGGAAAAAAAAUGAGCGACACAUCAUCUGCACUUCCGGAAAGCCCCGAGUCUGUCAGUUCGCACAACGCGCUCAGCACGGGUCAA	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0001353	0.2036716	hpaX	1252625	4-hydroxyphenylacetate permease
STM3251	-5	39	5	11	7.81	GcvB	45	87	72	78	12.16	-20.16	-40.13	-1.95464	AACGCAUGAACAUAACAAUCGCAACAUUGGGUGAAUUGCUCGUC&GAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUU	((((((..(((((((((.(((((((..((((..((..(((((((&)))))))..))..))))..))))))))))))))))..))))))	CCAACAGCUAUACCAAUAACGAAUGUCUGACCUGGAUAAACCCGACCCUGCAUCAGGCAAGAUGAAGGACAACGCAUGAACAUAACAAUCGCAACAUUGGGUGAAUUGCUCGUCGAGUUUCUGGCAAAAAAAGAGAACCAGGGAUUUUCC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0001949	0.2200421		1254774	sugar kinase
STM4398	-30	6	-22	-16	2.15	GcvB	125	169	153	159	9.4	-19.27	-30.82	-1.86835	CACAACACAGACAGGUACAGGAAGAAAAACAUGGUA&UACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUG	(((...(((((((((((((((((((((((...((((&)))).))))))..)))))))).......))))))))).....)))	UGAUAACAGGAUCGUCGUAUCAUAGACCAAAGGCCGUAGAGCCCGCACAACACAGACAGGUACAGGAAGAAAAACAUGGUAGAUCAGGUAAAAGUCGCAGCCGACGAACAGGCUCCGGCUGAACAGUCGCUACGGCGCAAUCUUACAAAC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.000428	0.3847632	cycA	1255924	D-serine/D-alanine/glycine transporter
STM0369	2	69	8	14	12.59	GcvB	31	91	80	86	17.22	-18.82	-48.63	-1.82471	UGACAGACACGACGAUCCUGCAAAACAACACGCAUGUCAUUAAGCCUAAAAAAUCGGUCGCGCUUUCC&GGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCA	((.((((((((((((.....((..(((((.((...((((..(((((((.....((((.((((..((((&))))..))))..))))))))))).))))...)))))))..)).....))))))))))))))	CACUACGUUUAACCCGCCUACGGUACGGCCUACACGCCUCAAUACCCUACACAUUACAAUAAUGACGAGGACAAUAUGACAGACACGACGAUCCUGCAAAACAACACGCAUGUCAUUAAGCCUAAAAAAUCGGUCGCGCUUUCCGGCGUA	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0006231	0.3847632	prpC	1251888	2-methylcitrate synthase
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
STM0001	-71	-15	-35	-29	4	GcvB	141	186	155	161	8.64	-18.71	-31.35	-1.81405	GGCGGGCAGAUACUUUAACCAAUAUAGGAAUACAAGACAGACAAAUAAAAAUGACAG&CUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCC	(((((((...(((.((((.((.(((.((........(((((((......((((((((&)))).)))).....)))))))))))).)).)))).))))).)))))	CUUAGGCGGGCAGAUACUUUAACCAAUAUAGGAAUACAAGACAGACAAAUAAAAAUGACAGAGUACACAACAUCCAUGAACCGCAUCAGCACCACCACCAUUACCACCAUCACCAUUACCACAGGUAACGGUGCGGGCUGACGCGUACAG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0006816	0.3847632	thrL	1251519	thr operon leader peptide
STM3344	-70	-27	-61	-55	11.46	GcvB	48	102	83	89	15.57	-18.35	-45.38	-1.77915	CGCGGGCAACGAGCACAACCACGCGGCACAGCAACCGCAAGUUC&GGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCG	(((((((..((((((((((.((((((((((.((((((.((((((&))))))........)))))))).)))))))).))))))))))......)))))))	GUUUACGCGGGCAACGAGCACAACCACGCGGCACAGCAACCGCAAGUUCUUGACAUCUAAUCGGGAUUAUAGGCAAUGGCUGAAAAUCAAUACUACGGCACUGGUCGCCGCAAAAGUUCCGCAGCUCGCGUGUUCAUCAAACCGGGCAAC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0009093	0.4343002	rpsI	1254867	30S ribosomal protein S9
STM1098	-69	-36	-51	-45	4.7	GcvB	62	90	69	75	8.25	-18.25	-31.2	-1.76945	GCAUUUGCACAAUAACGACGACAUCAAUCAACUG&CGGUUGUGAUGUUGUGUUGUUGUGUUUGC	(((....(((((((((.(((((((((..((((((&))))))))))))))))))))))))..)))	GGUUUCGCAUUUGCACAAUAACGACGACAUCAAUCAACUGGAUAAGCUGCUGAAAUAACGCGGCAGGAGGUUCUCAUGCAAGUAGAUGAACAACGUCUGCGUUUUCGCGAUGCGAUGGCAAGUCUGGCGGCAGCGGUCAACAUCGUAACC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0009836	0.4343002	hpaC	1252616	4-hydroxyphenylacetate 3-monooxygenase reductase component

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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