; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_3431_ensembl_72_GCA_000184765.2/genome/Escherichia_coli_3431_ensembl_72_GCA_000184765.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_3431_ensembl_72_GCA_000184765.2/genome/Escherichia_coli_3431_ensembl_72_GCA_000184765.2_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_3431_ensembl_72_GCA_000184765.2/genome/Escherichia_coli_3431_ensembl_72_GCA_000184765.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_3431_ensembl_72_GCA_000184765.2/genome/Escherichia_coli_3431_ensembl_72_GCA_000184765.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5210
; Sum of sequence lengths      	15630
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5210
; total oligo occurrences      	5210
; 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	0.5827255278311	3036
tga	tga	0.3320537428023	1730
tag	tag	0.0735124760077	383
atg	atg	0.0007677543186	4
aat	aat	0.0007677543186	4
acc	acc	0.0007677543186	4
gat	gat	0.0005758157390	3
tcg	tcg	0.0005758157390	3
ttg	ttg	0.0005758157390	3
ttc	ttc	0.0003838771593	2
cga	cga	0.0003838771593	2
ggg	ggg	0.0003838771593	2
ccg	ccg	0.0003838771593	2
gca	gca	0.0003838771593	2
aag	aag	0.0003838771593	2
gtg	gtg	0.0003838771593	2
gcc	gcc	0.0003838771593	2
tgt	tgt	0.0001919385797	1
agg	agg	0.0001919385797	1
ttt	ttt	0.0001919385797	1
ctg	ctg	0.0001919385797	1
cgc	cgc	0.0001919385797	1
gcg	gcg	0.0001919385797	1
gct	gct	0.0001919385797	1
tta	tta	0.0001919385797	1
aac	aac	0.0001919385797	1
acg	acg	0.0001919385797	1
cgt	cgt	0.0001919385797	1
tac	tac	0.0001919385797	1
gta	gta	0.0001919385797	1
gac	gac	0.0001919385797	1
ggc	ggc	0.0001919385797	1
cat	cat	0.0001919385797	1
aaa	aaa	0.0001919385797	1
gtc	gtc	0.0001919385797	1
act	act	0.0001919385797	1
ctc	ctc	0.0001919385797	1
tca	tca	0.0001919385797	1
gtt	gtt	0.0001919385797	1
gga	gga	0.0001919385797	1
agt	agt	0.0001919385797	1
; Host name	jolitorax
; Job started	2013-09-30.023046
; Job done	2013-09-30.023047
; Seconds	1.76
;	user	1.76
;	system	0.08
;	cuser	0
;	csystem	0.01