; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2/genome/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2/genome/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2_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_epeca14_ensembl_72_GCA_000188755.2/genome/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2/genome/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5876
; Sum of sequence lengths      	17628
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5876
; total oligo occurrences      	5876
; 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	0.5616065350579	3300
tga	tga	0.3384955752212	1989
tag	tag	0.0793056501021	466
gcg	gcg	0.0010211027910	6
gct	gct	0.0008509189925	5
ctg	ctg	0.0006807351940	4
ttt	ttt	0.0006807351940	4
gta	gta	0.0006807351940	4
ccc	ccc	0.0006807351940	4
aca	aca	0.0006807351940	4
tgg	tgg	0.0006807351940	4
ggt	ggt	0.0006807351940	4
cag	cag	0.0006807351940	4
cgg	cgg	0.0006807351940	4
ttc	ttc	0.0005105513955	3
gaa	gaa	0.0005105513955	3
ccg	ccg	0.0005105513955	3
gag	gag	0.0005105513955	3
gtt	gtt	0.0005105513955	3
cac	cac	0.0005105513955	3
atc	atc	0.0005105513955	3
cca	cca	0.0003403675970	2
att	att	0.0003403675970	2
ctt	ctt	0.0003403675970	2
gat	gat	0.0003403675970	2
atg	atg	0.0003403675970	2
tct	tct	0.0003403675970	2
acg	acg	0.0003403675970	2
cgt	cgt	0.0003403675970	2
tac	tac	0.0003403675970	2
tgc	tgc	0.0003403675970	2
cga	cga	0.0003403675970	2
aaa	aaa	0.0003403675970	2
aag	aag	0.0003403675970	2
ttg	ttg	0.0003403675970	2
ata	ata	0.0003403675970	2
gcc	gcc	0.0003403675970	2
tat	tat	0.0003403675970	2
tgt	tgt	0.0001701837985	1
agg	agg	0.0001701837985	1
tta	tta	0.0001701837985	1
gac	gac	0.0001701837985	1
ggc	ggc	0.0001701837985	1
ggg	ggg	0.0001701837985	1
gca	gca	0.0001701837985	1
tcg	tcg	0.0001701837985	1
acc	acc	0.0001701837985	1
cat	cat	0.0001701837985	1
gtc	gtc	0.0001701837985	1
ctc	ctc	0.0001701837985	1
act	act	0.0001701837985	1
tcc	tcc	0.0001701837985	1
cct	cct	0.0001701837985	1
gtg	gtg	0.0001701837985	1
tca	tca	0.0001701837985	1
gga	gga	0.0001701837985	1
agc	agc	0.0001701837985	1
; Host name	jolitorax
; Job started	2013-10-01.015131
; Job done	2013-10-01.015132
; Seconds	2
;	user	2
;	system	0.07
;	cuser	0
;	csystem	0