; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_ec1846_ensembl_72_GCA_000303555.1/genome/Escherichia_coli_ec1846_ensembl_72_GCA_000303555.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_ec1846_ensembl_72_GCA_000303555.1/genome/Escherichia_coli_ec1846_ensembl_72_GCA_000303555.1_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_ec1846_ensembl_72_GCA_000303555.1/genome/Escherichia_coli_ec1846_ensembl_72_GCA_000303555.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_ec1846_ensembl_72_GCA_000303555.1/genome/Escherichia_coli_ec1846_ensembl_72_GCA_000303555.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4310
; Sum of sequence lengths      	12930
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4310
; total oligo occurrences      	4310
; 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	0.5645011600928	2433
tga	tga	0.3011600928074	1298
tag	tag	0.0737819025522	318
tgc	tgc	0.0025522041763	11
ggg	ggg	0.0025522041763	11
gaa	gaa	0.0020881670534	9
cat	cat	0.0020881670534	9
cgg	cgg	0.0020881670534	9
agc	agc	0.0020881670534	9
tat	tat	0.0020881670534	9
gcg	gcg	0.0018561484919	8
ggc	ggc	0.0018561484919	8
tgg	tgg	0.0018561484919	8
ggt	ggt	0.0016241299304	7
cag	cag	0.0016241299304	7
tca	tca	0.0016241299304	7
tta	tta	0.0013921113689	6
aat	aat	0.0013921113689	6
cgt	cgt	0.0013921113689	6
gtc	gtc	0.0013921113689	6
aga	aga	0.0013921113689	6
ata	ata	0.0013921113689	6
atc	atc	0.0013921113689	6
gct	gct	0.0011600928074	5
acc	acc	0.0011600928074	5
act	act	0.0011600928074	5
cac	cac	0.0011600928074	5
tgt	tgt	0.0009280742459	4
gat	gat	0.0009280742459	4
tct	tct	0.0009280742459	4
ccg	ccg	0.0009280742459	4
ttg	ttg	0.0009280742459	4
ttc	ttc	0.0006960556845	3
att	att	0.0006960556845	3
cca	cca	0.0006960556845	3
ctg	ctg	0.0006960556845	3
cgc	cgc	0.0006960556845	3
aac	aac	0.0006960556845	3
caa	caa	0.0006960556845	3
gta	gta	0.0006960556845	3
ccc	ccc	0.0006960556845	3
aaa	aaa	0.0006960556845	3
aag	aag	0.0006960556845	3
gga	gga	0.0006960556845	3
gtt	gtt	0.0006960556845	3
gcc	gcc	0.0006960556845	3
agt	agt	0.0006960556845	3
agg	agg	0.0004640371230	2
ttt	ttt	0.0004640371230	2
atg	atg	0.0004640371230	2
cta	cta	0.0004640371230	2
cga	cga	0.0004640371230	2
gca	gca	0.0004640371230	2
tcg	tcg	0.0004640371230	2
ctc	ctc	0.0004640371230	2
cct	cct	0.0004640371230	2
acg	acg	0.0002320185615	1
gac	gac	0.0002320185615	1
aca	aca	0.0002320185615	1
gag	gag	0.0002320185615	1
; Host name	jolitorax
; Job started	2013-09-30.222118
; Job done	2013-09-30.222119
; Seconds	1.72
;	user	1.72
;	system	0.06
;	cuser	0
;	csystem	0.01