; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_88_0221_ensembl_72_GCA_000305455.1/genome/Escherichia_coli_88_0221_ensembl_72_GCA_000305455.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_88_0221_ensembl_72_GCA_000305455.1/genome/Escherichia_coli_88_0221_ensembl_72_GCA_000305455.1_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_88_0221_ensembl_72_GCA_000305455.1/genome/Escherichia_coli_88_0221_ensembl_72_GCA_000305455.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_88_0221_ensembl_72_GCA_000305455.1/genome/Escherichia_coli_88_0221_ensembl_72_GCA_000305455.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	2103
; Sum of sequence lengths      	6309
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	2103
; total oligo occurrences      	2103
; 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	0.5164051355207	1086
tga	tga	0.3176414645744	668
tag	tag	0.0656205420827	138
cgg	cgg	0.0061816452687	13
tgc	tgc	0.0057061340942	12
ggg	ggg	0.0052306229196	11
aaa	aaa	0.0042796005706	9
gaa	gaa	0.0033285782216	7
gct	gct	0.0033285782216	7
ggc	ggc	0.0033285782216	7
gcg	gcg	0.0028530670471	6
ccg	ccg	0.0028530670471	6
ctt	ctt	0.0023775558726	5
acg	acg	0.0023775558726	5
tgg	tgg	0.0023775558726	5
gca	gca	0.0023775558726	5
ggt	ggt	0.0023775558726	5
cag	cag	0.0023775558726	5
aga	aga	0.0023775558726	5
gga	gga	0.0023775558726	5
agg	agg	0.0019020446981	4
cca	cca	0.0019020446981	4
tct	tct	0.0019020446981	4
caa	caa	0.0019020446981	4
ata	ata	0.0019020446981	4
agc	agc	0.0019020446981	4
cac	cac	0.0019020446981	4
ttc	ttc	0.0014265335235	3
att	att	0.0014265335235	3
cga	cga	0.0014265335235	3
tcg	tcg	0.0014265335235	3
cat	cat	0.0014265335235	3
aag	aag	0.0014265335235	3
gtt	gtt	0.0014265335235	3
gcc	gcc	0.0014265335235	3
tgt	tgt	0.0009510223490	2
gat	gat	0.0009510223490	2
ctg	ctg	0.0009510223490	2
atg	atg	0.0009510223490	2
aac	aac	0.0009510223490	2
aat	aat	0.0009510223490	2
cta	cta	0.0009510223490	2
gac	gac	0.0009510223490	2
aca	aca	0.0009510223490	2
acc	acc	0.0009510223490	2
tcc	tcc	0.0009510223490	2
cct	cct	0.0009510223490	2
tca	tca	0.0009510223490	2
ttg	ttg	0.0009510223490	2
atc	atc	0.0009510223490	2
ttt	ttt	0.0004755111745	1
cgc	cgc	0.0004755111745	1
cgt	cgt	0.0004755111745	1
gta	gta	0.0004755111745	1
tac	tac	0.0004755111745	1
gag	gag	0.0004755111745	1
gtc	gtc	0.0004755111745	1
act	act	0.0004755111745	1
gtg	gtg	0.0004755111745	1
tat	tat	0.0004755111745	1
agt	agt	0.0004755111745	1
; Host name	jolitorax
; Job started	2013-09-30.045933
; Job done	2013-09-30.045933
; Seconds	1.31
;	user	1.31
;	system	0.11
;	cuser	0
;	csystem	0