; oligo-analysis  -quick -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Legionella_pneumophila_ATCC_43290_uid86885/genome/Legionella_pneumophila_ATCC_43290_uid86885_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Legionella_pneumophila_ATCC_43290_uid86885/genome/Legionella_pneumophila_ATCC_43290_uid86885_start_codon_frequencies
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. 
; Program version              	1.165
; Quick counting mode          
; Oligomer length              	3
; Input file                   	$RSAT/public_html/data/genomes/Legionella_pneumophila_ATCC_43290_uid86885/genome/Legionella_pneumophila_ATCC_43290_uid86885_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Legionella_pneumophila_ATCC_43290_uid86885/genome/Legionella_pneumophila_ATCC_43290_uid86885_start_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	0
; Sum of sequence lengths      	0
; discarded residues           	NA (quick mode)	 (other letters than ACGT)
; discarded occurrences        	NA (quick mode)	 (contain discarded residues)
; nb possible positions        	NA (quick mode)
; total oligo occurrences      	2928
; alphabet size                	4
; nb possible oligomers        	64
; oligomers tested for significance	0
; Threshold values
;	Parameter      	Lower	Upper
;	ms_P           	none	1
;	occ_P          	none	1
; Sequences:
;
; column headers
;	1	seq            	oligomer sequence
;	2	id             	oligomer identifier
;	3	obs_freq       	observed relative frequency
;	4	occ            	observed occurrences
#seq	id	obs_freq	occ
atg	atg	0.6936475409836	2031
ttg	ttg	0.1267076502732	371
gtg	gtg	0.0744535519126	218
ctg	ctg	0.0481557377049	141
att	att	0.0269808743169	79
ata	ata	0.0181010928962	53
atc	atc	0.0116120218579	34
tcc	tcc	0.0003415300546	1
; Host name	nic42
; Job started	2012-05-05.025501
; Job done	2012-05-05.025501
; Seconds	0.16
;	user	0.16
;	system	0.05
;	cuser	0.15
;	csystem	0.05