; 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/Chlamydophila_pneumoniae_AR39_uid57809/genome/Chlamydophila_pneumoniae_AR39_uid57809_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Chlamydophila_pneumoniae_AR39_uid57809/genome/Chlamydophila_pneumoniae_AR39_uid57809_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/Chlamydophila_pneumoniae_AR39_uid57809/genome/Chlamydophila_pneumoniae_AR39_uid57809_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Chlamydophila_pneumoniae_AR39_uid57809/genome/Chlamydophila_pneumoniae_AR39_uid57809_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      	1112
; 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	0.7850719424460	873
gtg	gtg	0.1178057553957	131
ttg	ttg	0.0971223021583	108
; Host name	nic42
; Job started	2012-05-05.012855
; Job done	2012-05-05.012855
; Seconds	0.17
;	user	0.17
;	system	0.02
;	cuser	0.14
;	csystem	0.03