; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_83972_ensembl_72_GCA_000159295.1/genome/Escherichia_coli_83972_ensembl_72_GCA_000159295.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_83972_ensembl_72_GCA_000159295.1/genome/Escherichia_coli_83972_ensembl_72_GCA_000159295.1_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_83972_ensembl_72_GCA_000159295.1/genome/Escherichia_coli_83972_ensembl_72_GCA_000159295.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_83972_ensembl_72_GCA_000159295.1/genome/Escherichia_coli_83972_ensembl_72_GCA_000159295.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5255
; Sum of sequence lengths      	15765
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5255
; total oligo occurrences      	5255
; 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	0.5935299714558	3119
tga	tga	0.3156993339676	1659
tag	tag	0.0757373929591	398
gag	gag	0.0009514747859	5
gcg	gcg	0.0007611798287	4
gga	gga	0.0007611798287	4
gaa	gaa	0.0005708848716	3
aac	aac	0.0005708848716	3
cgt	cgt	0.0005708848716	3
ccc	ccc	0.0005708848716	3
ggg	ggg	0.0005708848716	3
ggt	ggt	0.0005708848716	3
tcg	tcg	0.0005708848716	3
aaa	aaa	0.0005708848716	3
tca	tca	0.0005708848716	3
cgg	cgg	0.0005708848716	3
agg	agg	0.0003805899144	2
atg	atg	0.0003805899144	2
aat	aat	0.0003805899144	2
tgc	tgc	0.0003805899144	2
gac	gac	0.0003805899144	2
tgg	tgg	0.0003805899144	2
acc	acc	0.0003805899144	2
aag	aag	0.0003805899144	2
agc	agc	0.0003805899144	2
atc	atc	0.0003805899144	2
att	att	0.0001902949572	1
cca	cca	0.0001902949572	1
gat	gat	0.0001902949572	1
tta	tta	0.0001902949572	1
caa	caa	0.0001902949572	1
gta	gta	0.0001902949572	1
cta	cta	0.0001902949572	1
aca	aca	0.0001902949572	1
ggc	ggc	0.0001902949572	1
gca	gca	0.0001902949572	1
cat	cat	0.0001902949572	1
gtg	gtg	0.0001902949572	1
ata	ata	0.0001902949572	1
gcc	gcc	0.0001902949572	1
cac	cac	0.0001902949572	1
tat	tat	0.0001902949572	1
; Host name	jolitorax
; Job started	2013-09-30.045252
; Job done	2013-09-30.045252
; Seconds	1.76
;	user	1.76
;	system	0.12
;	cuser	0
;	csystem	0