; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_bl21_de3_asm956v1_ensembl_72_GCA_000009565.2/genome/Escherichia_coli_bl21_de3_asm956v1_ensembl_72_GCA_000009565.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_bl21_de3_asm956v1_ensembl_72_GCA_000009565.2/genome/Escherichia_coli_bl21_de3_asm956v1_ensembl_72_GCA_000009565.2_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/Escherichia_coli_bl21_de3_asm956v1_ensembl_72_GCA_000009565.2/genome/Escherichia_coli_bl21_de3_asm956v1_ensembl_72_GCA_000009565.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_bl21_de3_asm956v1_ensembl_72_GCA_000009565.2/genome/Escherichia_coli_bl21_de3_asm956v1_ensembl_72_GCA_000009565.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4208
; Sum of sequence lengths      	12624
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4208
; total oligo occurrences      	4208
; 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	0.6409220532319	2697
tga	tga	0.2825570342205	1189
tag	tag	0.0660646387833	278
cgc	cgc	0.0066539923954	28
ggc	ggc	0.0009505703422	4
cct	cct	0.0009505703422	4
gag	gag	0.0009505703422	4
tca	tca	0.0004752851711	2
ggg	ggg	0.0002376425856	1
aga	aga	0.0002376425856	1
; Host name	jolitorax
; Job started	2013-09-30.104209
; Job done	2013-09-30.104209
; Seconds	1.67
;	user	1.67
;	system	0.07
;	cuser	0
;	csystem	0