; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec11b_ensembl_72_GCA_000250135.2/genome/Escherichia_coli_dec11b_ensembl_72_GCA_000250135.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec11b_ensembl_72_GCA_000250135.2/genome/Escherichia_coli_dec11b_ensembl_72_GCA_000250135.2_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_dec11b_ensembl_72_GCA_000250135.2/genome/Escherichia_coli_dec11b_ensembl_72_GCA_000250135.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec11b_ensembl_72_GCA_000250135.2/genome/Escherichia_coli_dec11b_ensembl_72_GCA_000250135.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5269
; Sum of sequence lengths      	15807
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5269
; total oligo occurrences      	5269
; 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	0.5896754602391	3107
tga	tga	0.3289049155437	1733
tag	tag	0.0753463655343	397
gag	gag	0.0005693680015	3
cct	cct	0.0005693680015	3
tgg	tgg	0.0003795786677	2
cgc	cgc	0.0003795786677	2
aag	aag	0.0003795786677	2
atc	atc	0.0003795786677	2
ttc	ttc	0.0001897893338	1
ggc	ggc	0.0001897893338	1
gaa	gaa	0.0001897893338	1
tgt	tgt	0.0001897893338	1
ggg	ggg	0.0001897893338	1
ctt	ctt	0.0001897893338	1
att	att	0.0001897893338	1
gca	gca	0.0001897893338	1
ctg	ctg	0.0001897893338	1
cat	cat	0.0001897893338	1
aaa	aaa	0.0001897893338	1
gct	gct	0.0001897893338	1
act	act	0.0001897893338	1
gtg	gtg	0.0001897893338	1
cgg	cgg	0.0001897893338	1
tgc	tgc	0.0001897893338	1
gac	gac	0.0001897893338	1
agc	agc	0.0001897893338	1
; Host name	jolitorax
; Job started	2013-09-30.122816
; Job done	2013-09-30.122816
; Seconds	1.53
;	user	1.53
;	system	0.07
;	cuser	0
;	csystem	0