; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec9d_ensembl_72_GCA_000249955.2/genome/Escherichia_coli_dec9d_ensembl_72_GCA_000249955.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec9d_ensembl_72_GCA_000249955.2/genome/Escherichia_coli_dec9d_ensembl_72_GCA_000249955.2_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_dec9d_ensembl_72_GCA_000249955.2/genome/Escherichia_coli_dec9d_ensembl_72_GCA_000249955.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec9d_ensembl_72_GCA_000249955.2/genome/Escherichia_coli_dec9d_ensembl_72_GCA_000249955.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5611
; Sum of sequence lengths      	16833
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5611
; total oligo occurrences      	5611
; 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	0.5815362680449	3263
tga	tga	0.3286401710925	1844
tag	tag	0.0825164854750	463
atg	atg	0.0007128854037	4
ccg	ccg	0.0005346640528	3
gga	gga	0.0005346640528	3
ttc	ttc	0.0003564427018	2
att	att	0.0003564427018	2
tgc	tgc	0.0003564427018	2
gac	gac	0.0003564427018	2
gtg	gtg	0.0003564427018	2
tgt	tgt	0.0001782213509	1
ctt	ctt	0.0001782213509	1
ctg	ctg	0.0001782213509	1
cgc	cgc	0.0001782213509	1
tct	tct	0.0001782213509	1
aat	aat	0.0001782213509	1
cgt	cgt	0.0001782213509	1
tac	tac	0.0001782213509	1
ggg	ggg	0.0001782213509	1
gca	gca	0.0001782213509	1
cag	cag	0.0001782213509	1
acc	acc	0.0001782213509	1
cat	cat	0.0001782213509	1
aaa	aaa	0.0001782213509	1
gtc	gtc	0.0001782213509	1
act	act	0.0001782213509	1
cct	cct	0.0001782213509	1
aga	aga	0.0001782213509	1
gtt	gtt	0.0001782213509	1
agc	agc	0.0001782213509	1
atc	atc	0.0001782213509	1
; Host name	jolitorax
; Job started	2013-09-30.201610
; Job done	2013-09-30.201611
; Seconds	2.09
;	user	2.1
;	system	0.07
;	cuser	0
;	csystem	0