; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec5a_ensembl_72_GCA_000249495.2/genome/Escherichia_coli_dec5a_ensembl_72_GCA_000249495.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec5a_ensembl_72_GCA_000249495.2/genome/Escherichia_coli_dec5a_ensembl_72_GCA_000249495.2_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_dec5a_ensembl_72_GCA_000249495.2/genome/Escherichia_coli_dec5a_ensembl_72_GCA_000249495.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec5a_ensembl_72_GCA_000249495.2/genome/Escherichia_coli_dec5a_ensembl_72_GCA_000249495.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5311
; Sum of sequence lengths      	15933
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5311
; total oligo occurrences      	5311
; 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	0.5963095462248	3167
tga	tga	0.3168894746752	1683
tag	tag	0.0815289022783	433
tgg	tgg	0.0003765769158	2
ccg	ccg	0.0003765769158	2
ctg	ctg	0.0003765769158	2
cct	cct	0.0003765769158	2
gac	gac	0.0003765769158	2
ttc	ttc	0.0001882884579	1
gaa	gaa	0.0001882884579	1
cgc	cgc	0.0001882884579	1
cag	cag	0.0001882884579	1
acc	acc	0.0001882884579	1
atg	atg	0.0001882884579	1
gag	gag	0.0001882884579	1
gtc	gtc	0.0001882884579	1
aac	aac	0.0001882884579	1
gct	gct	0.0001882884579	1
aag	aag	0.0001882884579	1
ctc	ctc	0.0001882884579	1
tcc	tcc	0.0001882884579	1
aat	aat	0.0001882884579	1
caa	caa	0.0001882884579	1
gta	gta	0.0001882884579	1
gcc	gcc	0.0001882884579	1
atc	atc	0.0001882884579	1
; Host name	jolitorax
; Job started	2013-09-30.174804
; Job done	2013-09-30.174805
; Seconds	1.93
;	user	1.93
;	system	0.08
;	cuser	0
;	csystem	0