; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2/genome/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2/genome/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2_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_dec4d_ensembl_72_GCA_000249435.2/genome/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2/genome/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5539
; Sum of sequence lengths      	16617
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5539
; total oligo occurrences      	5539
; 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	0.5831377504965	3230
tga	tga	0.3273153998917	1813
tag	tag	0.0819642534754	454
acg	acg	0.0005416140097	3
ggc	ggc	0.0005416140097	3
ata	ata	0.0005416140097	3
gaa	gaa	0.0003610760065	2
gat	gat	0.0003610760065	2
cgc	cgc	0.0003610760065	2
tgg	tgg	0.0003610760065	2
ccg	ccg	0.0003610760065	2
ttg	ttg	0.0003610760065	2
agg	agg	0.0001805380032	1
ctg	ctg	0.0001805380032	1
gcg	gcg	0.0001805380032	1
aac	aac	0.0001805380032	1
tct	tct	0.0001805380032	1
cgt	cgt	0.0001805380032	1
tgc	tgc	0.0001805380032	1
gca	gca	0.0001805380032	1
ggt	ggt	0.0001805380032	1
tcg	tcg	0.0001805380032	1
cag	cag	0.0001805380032	1
aaa	aaa	0.0001805380032	1
gtc	gtc	0.0001805380032	1
act	act	0.0001805380032	1
cct	cct	0.0001805380032	1
tca	tca	0.0001805380032	1
cgg	cgg	0.0001805380032	1
gtt	gtt	0.0001805380032	1
gcc	gcc	0.0001805380032	1
agc	agc	0.0001805380032	1
atc	atc	0.0001805380032	1
; Host name	jolitorax
; Job started	2013-09-30.172817
; Job done	2013-09-30.172818
; Seconds	1.84
;	user	1.84
;	system	0.09
;	cuser	0
;	csystem	0