; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_99_0678_ensembl_72_GCA_000316545.1/genome/Escherichia_coli_99_0678_ensembl_72_GCA_000316545.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_99_0678_ensembl_72_GCA_000316545.1/genome/Escherichia_coli_99_0678_ensembl_72_GCA_000316545.1_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_99_0678_ensembl_72_GCA_000316545.1/genome/Escherichia_coli_99_0678_ensembl_72_GCA_000316545.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_99_0678_ensembl_72_GCA_000316545.1/genome/Escherichia_coli_99_0678_ensembl_72_GCA_000316545.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5289
; Sum of sequence lengths      	15867
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5289
; total oligo occurrences      	5289
; 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	0.5933068633012	3138
tga	tga	0.3083758744564	1631
tag	tag	0.0831915295897	440
aaa	aaa	0.0009453582908	5
gat	gat	0.0007562866326	4
ggc	ggc	0.0007562866326	4
ggg	ggg	0.0007562866326	4
ttc	ttc	0.0005672149745	3
aac	aac	0.0005672149745	3
tgg	tgg	0.0005672149745	3
gag	gag	0.0005672149745	3
gtc	gtc	0.0005672149745	3
aga	aga	0.0005672149745	3
gcc	gcc	0.0005672149745	3
cac	cac	0.0005672149745	3
atc	atc	0.0005672149745	3
gcg	gcg	0.0003781433163	2
gct	gct	0.0003781433163	2
tta	tta	0.0003781433163	2
caa	caa	0.0003781433163	2
cgt	cgt	0.0003781433163	2
acc	acc	0.0003781433163	2
cat	cat	0.0003781433163	2
gtg	gtg	0.0003781433163	2
cgg	cgg	0.0003781433163	2
tat	tat	0.0003781433163	2
gaa	gaa	0.0001890716582	1
cca	cca	0.0001890716582	1
ctg	ctg	0.0001890716582	1
cgc	cgc	0.0001890716582	1
tgc	tgc	0.0001890716582	1
cga	cga	0.0001890716582	1
gac	gac	0.0001890716582	1
ccc	ccc	0.0001890716582	1
ccg	ccg	0.0001890716582	1
ggt	ggt	0.0001890716582	1
tcg	tcg	0.0001890716582	1
aag	aag	0.0001890716582	1
tcc	tcc	0.0001890716582	1
tca	tca	0.0001890716582	1
ttg	ttg	0.0001890716582	1
gga	gga	0.0001890716582	1
; Host name	jolitorax
; Job started	2013-09-30.083614
; Job done	2013-09-30.083614
; Seconds	1.8
;	user	1.8
;	system	0.08
;	cuser	0
;	csystem	0.01