; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_88_1042_ensembl_72_GCA_000316345.1/genome/Escherichia_coli_88_1042_ensembl_72_GCA_000316345.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_88_1042_ensembl_72_GCA_000316345.1/genome/Escherichia_coli_88_1042_ensembl_72_GCA_000316345.1_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_88_1042_ensembl_72_GCA_000316345.1/genome/Escherichia_coli_88_1042_ensembl_72_GCA_000316345.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_88_1042_ensembl_72_GCA_000316345.1/genome/Escherichia_coli_88_1042_ensembl_72_GCA_000316345.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	3407
; Sum of sequence lengths      	10221
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	3407
; total oligo occurrences      	3407
; 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	0.5406515996478	1842
tga	tga	0.3149398297623	1073
tag	tag	0.0724977986498	247
tgg	tgg	0.0038156736131	13
tca	tca	0.0035221602583	12
ggg	ggg	0.0032286469034	11
ccg	ccg	0.0032286469034	11
aaa	aaa	0.0032286469034	11
agc	agc	0.0032286469034	11
tgc	tgc	0.0029351335486	10
gct	gct	0.0026416201937	9
ggc	ggc	0.0023481068389	8
cgc	cgc	0.0020545934840	7
gcg	gcg	0.0020545934840	7
cgg	cgg	0.0020545934840	7
gcc	gcc	0.0020545934840	7
cca	cca	0.0017610801291	6
atg	atg	0.0017610801291	6
gca	gca	0.0017610801291	6
tgt	tgt	0.0014675667743	5
agg	agg	0.0014675667743	5
tct	tct	0.0014675667743	5
cag	cag	0.0014675667743	5
ctg	ctg	0.0011740534194	4
aac	aac	0.0011740534194	4
ggt	ggt	0.0011740534194	4
aag	aag	0.0011740534194	4
aga	aga	0.0011740534194	4
ttc	ttc	0.0008805400646	3
gaa	gaa	0.0008805400646	3
caa	caa	0.0008805400646	3
acg	acg	0.0008805400646	3
cgt	cgt	0.0008805400646	3
gag	gag	0.0008805400646	3
gtc	gtc	0.0008805400646	3
ctc	ctc	0.0008805400646	3
act	act	0.0008805400646	3
cct	cct	0.0008805400646	3
gtg	gtg	0.0008805400646	3
ttg	ttg	0.0008805400646	3
gga	gga	0.0008805400646	3
tat	tat	0.0008805400646	3
gat	gat	0.0005870267097	2
aat	aat	0.0005870267097	2
gta	gta	0.0005870267097	2
acc	acc	0.0005870267097	2
cac	cac	0.0005870267097	2
atc	atc	0.0005870267097	2
ttt	ttt	0.0002935133549	1
cta	cta	0.0002935133549	1
cga	cga	0.0002935133549	1
gac	gac	0.0002935133549	1
aca	aca	0.0002935133549	1
ccc	ccc	0.0002935133549	1
cat	cat	0.0002935133549	1
ata	ata	0.0002935133549	1
gtt	gtt	0.0002935133549	1
; Host name	jolitorax
; Job started	2013-09-30.050535
; Job done	2013-09-30.050536
; Seconds	1.53
;	user	1.53
;	system	0.08
;	cuser	0
;	csystem	0