; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Salmonella_enterica_serovar_Typhimurium_ST4_74_uid84393/genome/Salmonella_enterica_serovar_Typhimurium_ST4_74_uid84393_stop_codons.wc -o $RSAT/public_html/data/genomes/Salmonella_enterica_serovar_Typhimurium_ST4_74_uid84393/genome/Salmonella_enterica_serovar_Typhimurium_ST4_74_uid84393_stop_codon_frequencies
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. 
; Program version              	1.169
; Slow counting mode           
; Oligomer length              	3
; Input file                   	$RSAT/public_html/data/genomes/Salmonella_enterica_serovar_Typhimurium_ST4_74_uid84393/genome/Salmonella_enterica_serovar_Typhimurium_ST4_74_uid84393_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Salmonella_enterica_serovar_Typhimurium_ST4_74_uid84393/genome/Salmonella_enterica_serovar_Typhimurium_ST4_74_uid84393_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4842
; Sum of sequence lengths      	14526
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4842
; total oligo occurrences      	4842
; alphabet size                	4
; nb possible oligomers        	64
; oligomers tested for significance	0
;
; 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
taa	taa	0.5863279636514	2839
tga	tga	0.3186699710863	1543
tag	tag	0.0950020652623	460
; Host name	rsat-tagc
; Job started	2014-06-20.055431
; Job done	2014-06-20.055431
; Seconds	0.34
;	user	0.34
;	system	0.02
;	cuser	0
;	csystem	0