; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1/genome/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1/genome/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1_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_e1520_ensembl_72_GCA_000190815.1/genome/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1/genome/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4673
; Sum of sequence lengths      	14019
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4673
; total oligo occurrences      	4673
; 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	0.6171624224267	2884
tga	tga	0.2991654183608	1398
tag	tag	0.0744703616520	348
ggc	ggc	0.0010699764605	5
gca	gca	0.0008559811684	4
tat	tat	0.0006419858763	3
ctg	ctg	0.0004279905842	2
caa	caa	0.0004279905842	2
tgc	tgc	0.0004279905842	2
gtg	gtg	0.0004279905842	2
ttc	ttc	0.0002139952921	1
tgt	tgt	0.0002139952921	1
cca	cca	0.0002139952921	1
att	att	0.0002139952921	1
ttt	ttt	0.0002139952921	1
gat	gat	0.0002139952921	1
atg	atg	0.0002139952921	1
gcg	gcg	0.0002139952921	1
aac	aac	0.0002139952921	1
tta	tta	0.0002139952921	1
gct	gct	0.0002139952921	1
aat	aat	0.0002139952921	1
acg	acg	0.0002139952921	1
cgt	cgt	0.0002139952921	1
tac	tac	0.0002139952921	1
gac	gac	0.0002139952921	1
ccc	ccc	0.0002139952921	1
tgg	tgg	0.0002139952921	1
gtc	gtc	0.0002139952921	1
aag	aag	0.0002139952921	1
tca	tca	0.0002139952921	1
agc	agc	0.0002139952921	1
cac	cac	0.0002139952921	1
; Host name	jolitorax
; Job started	2013-09-30.210616
; Job done	2013-09-30.210616
; Seconds	1.72
;	user	1.72
;	system	0.09
;	cuser	0
;	csystem	0