; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec7c_ensembl_72_GCA_000249735.2/genome/Escherichia_coli_dec7c_ensembl_72_GCA_000249735.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec7c_ensembl_72_GCA_000249735.2/genome/Escherichia_coli_dec7c_ensembl_72_GCA_000249735.2_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_dec7c_ensembl_72_GCA_000249735.2/genome/Escherichia_coli_dec7c_ensembl_72_GCA_000249735.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec7c_ensembl_72_GCA_000249735.2/genome/Escherichia_coli_dec7c_ensembl_72_GCA_000249735.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5296
; Sum of sequence lengths      	15888
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5296
; total oligo occurrences      	5296
; 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	0.5912009063444	3131
tga	tga	0.3223187311178	1707
tag	tag	0.0804380664653	426
tgt	tgt	0.0003776435045	2
ttt	ttt	0.0003776435045	2
cag	cag	0.0003776435045	2
tcg	tcg	0.0003776435045	2
cgg	cgg	0.0003776435045	2
gac	gac	0.0003776435045	2
ggg	ggg	0.0001888217523	1
agg	agg	0.0001888217523	1
tgg	tgg	0.0001888217523	1
gat	gat	0.0001888217523	1
ctg	ctg	0.0001888217523	1
ccg	ccg	0.0001888217523	1
acc	acc	0.0001888217523	1
atg	atg	0.0001888217523	1
gcg	gcg	0.0001888217523	1
aac	aac	0.0001888217523	1
tta	tta	0.0001888217523	1
tct	tct	0.0001888217523	1
cct	cct	0.0001888217523	1
acg	acg	0.0001888217523	1
tca	tca	0.0001888217523	1
cta	cta	0.0001888217523	1
gga	gga	0.0001888217523	1
agc	agc	0.0001888217523	1
gcc	gcc	0.0001888217523	1
tat	tat	0.0001888217523	1
; Host name	jolitorax
; Job started	2013-09-30.190555
; Job done	2013-09-30.190556
; Seconds	1.82
;	user	1.82
;	system	0.09
;	cuser	0
;	csystem	0