; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Shigella_flexneri_2a_301_uid62907/genome/Shigella_flexneri_2a_301_uid62907_stop_codons.wc -o $RSAT/public_html/data/genomes/Shigella_flexneri_2a_301_uid62907/genome/Shigella_flexneri_2a_301_uid62907_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/Shigella_flexneri_2a_301_uid62907/genome/Shigella_flexneri_2a_301_uid62907_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Shigella_flexneri_2a_301_uid62907/genome/Shigella_flexneri_2a_301_uid62907_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4314
; Sum of sequence lengths      	12942
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4314
; total oligo occurrences      	4314
; 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	0.6423273064441	2771
tga	tga	0.2832637923041	1222
tag	tag	0.0744089012517	321
; Host name	rsat-tagc
; Job started	2014-06-20.065331
; Job done	2014-06-20.065331
; Seconds	0.32
;	user	0.32
;	system	0.02
;	cuser	0
;	csystem	0