; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_5_0588_ensembl_72_GCA_000215145.2/genome/Escherichia_coli_5_0588_ensembl_72_GCA_000215145.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_5_0588_ensembl_72_GCA_000215145.2/genome/Escherichia_coli_5_0588_ensembl_72_GCA_000215145.2_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_5_0588_ensembl_72_GCA_000215145.2/genome/Escherichia_coli_5_0588_ensembl_72_GCA_000215145.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_5_0588_ensembl_72_GCA_000215145.2/genome/Escherichia_coli_5_0588_ensembl_72_GCA_000215145.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4973
; Sum of sequence lengths      	14919
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4973
; total oligo occurrences      	4973
; 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	0.5942087271265	2955
tga	tga	0.3213352101347	1598
tag	tag	0.0808365171928	402
aaa	aaa	0.0004021717273	2
gtg	gtg	0.0004021717273	2
ttg	ttg	0.0004021717273	2
cac	cac	0.0004021717273	2
att	att	0.0002010858637	1
gca	gca	0.0002010858637	1
ccg	ccg	0.0002010858637	1
gat	gat	0.0002010858637	1
cat	cat	0.0002010858637	1
tta	tta	0.0002010858637	1
aag	aag	0.0002010858637	1
cgt	cgt	0.0002010858637	1
atc	atc	0.0002010858637	1
agt	agt	0.0002010858637	1
; Host name	jolitorax
; Job started	2013-09-30.041937
; Job done	2013-09-30.041938
; Seconds	1.74
;	user	1.74
;	system	0.08
;	cuser	0
;	csystem	0