; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_frik920_ensembl_72_GCA_000302715.1/genome/Escherichia_coli_frik920_ensembl_72_GCA_000302715.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_frik920_ensembl_72_GCA_000302715.1/genome/Escherichia_coli_frik920_ensembl_72_GCA_000302715.1_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_frik920_ensembl_72_GCA_000302715.1/genome/Escherichia_coli_frik920_ensembl_72_GCA_000302715.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_frik920_ensembl_72_GCA_000302715.1/genome/Escherichia_coli_frik920_ensembl_72_GCA_000302715.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	6075
; Sum of sequence lengths      	18225
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	6075
; total oligo occurrences      	6075
; 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	0.5693827160494	3459
tga	tga	0.3349794238683	2035
tag	tag	0.0834567901235	507
aat	aat	0.0006584362140	4
gcc	gcc	0.0006584362140	4
cca	cca	0.0004938271605	3
aac	aac	0.0004938271605	3
ggg	ggg	0.0004938271605	3
ggt	ggt	0.0004938271605	3
tcc	tcc	0.0004938271605	3
aga	aga	0.0004938271605	3
gtg	gtg	0.0004938271605	3
agc	agc	0.0004938271605	3
ttc	ttc	0.0003292181070	2
tgt	tgt	0.0003292181070	2
ctt	ctt	0.0003292181070	2
gat	gat	0.0003292181070	2
ctg	ctg	0.0003292181070	2
tta	tta	0.0003292181070	2
ccc	ccc	0.0003292181070	2
ggc	ggc	0.0003292181070	2
ccg	ccg	0.0003292181070	2
cag	cag	0.0003292181070	2
tca	tca	0.0003292181070	2
cgg	cgg	0.0003292181070	2
gaa	gaa	0.0001646090535	1
ttt	ttt	0.0001646090535	1
cgc	cgc	0.0001646090535	1
atg	atg	0.0001646090535	1
gct	gct	0.0001646090535	1
tct	tct	0.0001646090535	1
caa	caa	0.0001646090535	1
tac	tac	0.0001646090535	1
gta	gta	0.0001646090535	1
tgc	tgc	0.0001646090535	1
gac	gac	0.0001646090535	1
aca	aca	0.0001646090535	1
gca	gca	0.0001646090535	1
cat	cat	0.0001646090535	1
gag	gag	0.0001646090535	1
ctc	ctc	0.0001646090535	1
gtt	gtt	0.0001646090535	1
cac	cac	0.0001646090535	1
; Host name	jolitorax
; Job started	2013-10-01.033750
; Job done	2013-10-01.033751
; Seconds	1.93
;	user	1.93
;	system	0.1
;	cuser	0
;	csystem	0.01