; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_ec4422_ensembl_72_GCA_000267365.1/genome/Escherichia_coli_ec4422_ensembl_72_GCA_000267365.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_ec4422_ensembl_72_GCA_000267365.1/genome/Escherichia_coli_ec4422_ensembl_72_GCA_000267365.1_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_ec4422_ensembl_72_GCA_000267365.1/genome/Escherichia_coli_ec4422_ensembl_72_GCA_000267365.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_ec4422_ensembl_72_GCA_000267365.1/genome/Escherichia_coli_ec4422_ensembl_72_GCA_000267365.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	3176
; Sum of sequence lengths      	9528
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	3176
; total oligo occurrences      	3176
; 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	0.5588790931990	1775
tga	tga	0.3003778337531	954
tag	tag	0.0768261964736	244
tgc	tgc	0.0034634760705	11
aaa	aaa	0.0028337531486	9
ttc	ttc	0.0025188916877	8
agg	agg	0.0025188916877	8
ctg	ctg	0.0022040302267	7
ttg	ttg	0.0022040302267	7
gca	gca	0.0018891687657	6
acc	acc	0.0018891687657	6
cgg	cgg	0.0018891687657	6
agc	agc	0.0018891687657	6
gaa	gaa	0.0015743073048	5
tgt	tgt	0.0015743073048	5
cga	cga	0.0015743073048	5
aca	aca	0.0015743073048	5
ggc	ggc	0.0015743073048	5
ggg	ggg	0.0015743073048	5
tcc	tcc	0.0015743073048	5
gtg	gtg	0.0015743073048	5
ata	ata	0.0015743073048	5
gcc	gcc	0.0015743073048	5
ttt	ttt	0.0012594458438	4
aac	aac	0.0012594458438	4
tgg	tgg	0.0012594458438	4
act	act	0.0012594458438	4
tca	tca	0.0012594458438	4
atc	atc	0.0012594458438	4
agt	agt	0.0012594458438	4
cca	cca	0.0009445843829	3
acg	acg	0.0009445843829	3
gta	gta	0.0009445843829	3
ccc	ccc	0.0009445843829	3
ccg	ccg	0.0009445843829	3
cat	cat	0.0009445843829	3
aag	aag	0.0009445843829	3
aga	aga	0.0009445843829	3
gat	gat	0.0006297229219	2
caa	caa	0.0006297229219	2
cgt	cgt	0.0006297229219	2
tac	tac	0.0006297229219	2
ggt	ggt	0.0006297229219	2
gag	gag	0.0006297229219	2
cac	cac	0.0006297229219	2
ctt	ctt	0.0003148614610	1
att	att	0.0003148614610	1
cgc	cgc	0.0003148614610	1
atg	atg	0.0003148614610	1
gcg	gcg	0.0003148614610	1
gct	gct	0.0003148614610	1
tct	tct	0.0003148614610	1
aat	aat	0.0003148614610	1
gac	gac	0.0003148614610	1
tcg	tcg	0.0003148614610	1
gtc	gtc	0.0003148614610	1
gga	gga	0.0003148614610	1
tat	tat	0.0003148614610	1
; Host name	jolitorax
; Job started	2013-10-01.004313
; Job done	2013-10-01.004313
; Seconds	1.53
;	user	1.53
;	system	0.12
;	cuser	0
;	csystem	0