; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_e101_ensembl_72_GCA_000241995.1/genome/Escherichia_coli_e101_ensembl_72_GCA_000241995.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_e101_ensembl_72_GCA_000241995.1/genome/Escherichia_coli_e101_ensembl_72_GCA_000241995.1_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_e101_ensembl_72_GCA_000241995.1/genome/Escherichia_coli_e101_ensembl_72_GCA_000241995.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_e101_ensembl_72_GCA_000241995.1/genome/Escherichia_coli_e101_ensembl_72_GCA_000241995.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4915
; Sum of sequence lengths      	14745
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4915
; total oligo occurrences      	4915
; 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	0.6061037639878	2979
tga	tga	0.3062054933876	1505
tag	tag	0.0773143438454	380
gtt	gtt	0.0014242115972	7
atg	atg	0.0010172939980	5
ggt	ggt	0.0008138351984	4
ata	ata	0.0008138351984	4
gat	gat	0.0006103763988	3
aaa	aaa	0.0006103763988	3
acc	acc	0.0004069175992	2
acg	acg	0.0004069175992	2
ttg	ttg	0.0004069175992	2
ttc	ttc	0.0002034587996	1
ggc	ggc	0.0002034587996	1
gaa	gaa	0.0002034587996	1
agg	agg	0.0002034587996	1
att	att	0.0002034587996	1
ctg	ctg	0.0002034587996	1
gag	gag	0.0002034587996	1
gct	gct	0.0002034587996	1
tta	tta	0.0002034587996	1
aac	aac	0.0002034587996	1
tct	tct	0.0002034587996	1
aga	aga	0.0002034587996	1
cgt	cgt	0.0002034587996	1
gta	gta	0.0002034587996	1
cgg	cgg	0.0002034587996	1
gcc	gcc	0.0002034587996	1
cac	cac	0.0002034587996	1
ccc	ccc	0.0002034587996	1
aca	aca	0.0002034587996	1
; Host name	jolitorax
; Job started	2013-09-30.204057
; Job done	2013-09-30.204057
; Seconds	1.72
;	user	1.72
;	system	0.12
;	cuser	0
;	csystem	0.01