; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec1c_ensembl_72_GCA_000249095.2/genome/Escherichia_coli_dec1c_ensembl_72_GCA_000249095.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec1c_ensembl_72_GCA_000249095.2/genome/Escherichia_coli_dec1c_ensembl_72_GCA_000249095.2_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_dec1c_ensembl_72_GCA_000249095.2/genome/Escherichia_coli_dec1c_ensembl_72_GCA_000249095.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec1c_ensembl_72_GCA_000249095.2/genome/Escherichia_coli_dec1c_ensembl_72_GCA_000249095.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5357
; Sum of sequence lengths      	16071
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5357
; total oligo occurrences      	5357
; 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	0.5811088295688	3113
tga	tga	0.3298487959679	1767
tag	tag	0.0798954638790	428
cgt	cgt	0.0007466865783	4
att	att	0.0005600149337	3
atg	atg	0.0005600149337	3
gtt	gtt	0.0005600149337	3
agg	agg	0.0003733432892	2
ttt	ttt	0.0003733432892	2
tac	tac	0.0003733432892	2
ggc	ggc	0.0003733432892	2
ccg	ccg	0.0003733432892	2
tcg	tcg	0.0003733432892	2
aaa	aaa	0.0003733432892	2
ttg	ttg	0.0003733432892	2
cgg	cgg	0.0003733432892	2
cca	cca	0.0001866716446	1
gct	gct	0.0001866716446	1
aat	aat	0.0001866716446	1
acg	acg	0.0001866716446	1
cga	cga	0.0001866716446	1
gac	gac	0.0001866716446	1
ggg	ggg	0.0001866716446	1
tgg	tgg	0.0001866716446	1
gca	gca	0.0001866716446	1
ggt	ggt	0.0001866716446	1
ctc	ctc	0.0001866716446	1
tcc	tcc	0.0001866716446	1
aag	aag	0.0001866716446	1
tca	tca	0.0001866716446	1
gga	gga	0.0001866716446	1
cac	cac	0.0001866716446	1
gcc	gcc	0.0001866716446	1
agc	agc	0.0001866716446	1
; Host name	jolitorax
; Job started	2013-09-30.152326
; Job done	2013-09-30.152327
; Seconds	1.83
;	user	1.83
;	system	0.08
;	cuser	0
;	csystem	0