; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_93_0055_ensembl_72_GCA_000316445.1/genome/Escherichia_coli_93_0055_ensembl_72_GCA_000316445.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_93_0055_ensembl_72_GCA_000316445.1/genome/Escherichia_coli_93_0055_ensembl_72_GCA_000316445.1_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_93_0055_ensembl_72_GCA_000316445.1/genome/Escherichia_coli_93_0055_ensembl_72_GCA_000316445.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_93_0055_ensembl_72_GCA_000316445.1/genome/Escherichia_coli_93_0055_ensembl_72_GCA_000316445.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	2878
; Sum of sequence lengths      	8634
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	2878
; total oligo occurrences      	2878
; 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	0.5503822098680	1584
tga	tga	0.2953439888812	850
tag	tag	0.0747046560111	215
ggg	ggg	0.0034746351633	10
ctg	ctg	0.0031271716470	9
aac	aac	0.0031271716470	9
gtg	gtg	0.0031271716470	9
tgt	tgt	0.0027797081306	8
cgc	cgc	0.0027797081306	8
ggc	ggc	0.0027797081306	8
tgg	tgg	0.0027797081306	8
ccg	ccg	0.0027797081306	8
aaa	aaa	0.0027797081306	8
atg	atg	0.0024322446143	7
tgc	tgc	0.0024322446143	7
cga	cga	0.0024322446143	7
gac	gac	0.0024322446143	7
gcc	gcc	0.0024322446143	7
gct	gct	0.0020847810980	6
cgg	cgg	0.0020847810980	6
gga	gga	0.0020847810980	6
acc	acc	0.0017373175817	5
ttc	ttc	0.0013898540653	4
ttt	ttt	0.0013898540653	4
gat	gat	0.0013898540653	4
cag	cag	0.0013898540653	4
gtc	gtc	0.0013898540653	4
ctc	ctc	0.0013898540653	4
agt	agt	0.0013898540653	4
aat	aat	0.0010423905490	3
acg	acg	0.0010423905490	3
gca	gca	0.0010423905490	3
tcg	tcg	0.0010423905490	3
aag	aag	0.0010423905490	3
ata	ata	0.0010423905490	3
atc	atc	0.0010423905490	3
tat	tat	0.0010423905490	3
gaa	gaa	0.0006949270327	2
att	att	0.0006949270327	2
gcg	gcg	0.0006949270327	2
cgt	cgt	0.0006949270327	2
tac	tac	0.0006949270327	2
gta	gta	0.0006949270327	2
ggt	ggt	0.0006949270327	2
cat	cat	0.0006949270327	2
gag	gag	0.0006949270327	2
cct	cct	0.0006949270327	2
aga	aga	0.0006949270327	2
tca	tca	0.0006949270327	2
gtt	gtt	0.0006949270327	2
agc	agc	0.0006949270327	2
agg	agg	0.0003474635163	1
ctt	ctt	0.0003474635163	1
cca	cca	0.0003474635163	1
aca	aca	0.0003474635163	1
ccc	ccc	0.0003474635163	1
ttg	ttg	0.0003474635163	1
; Host name	jolitorax
; Job started	2013-09-30.062640
; Job done	2013-09-30.062640
; Seconds	1.47
;	user	1.47
;	system	0.1
;	cuser	0
;	csystem	0