; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2/genome/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2/genome/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2_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_dec13e_ensembl_72_GCA_000250395.2/genome/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2/genome/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4927
; Sum of sequence lengths      	14781
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4927
; total oligo occurrences      	4927
; 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	0.6068601583113	2990
tga	tga	0.3072863811650	1514
tag	tag	0.0791556728232	390
aaa	aaa	0.0008118530546	4
agg	agg	0.0006088897909	3
atc	atc	0.0006088897909	3
gaa	gaa	0.0004059265273	2
ctg	ctg	0.0004059265273	2
gcg	gcg	0.0004059265273	2
aac	aac	0.0004059265273	2
ata	ata	0.0004059265273	2
tgt	tgt	0.0002029632636	1
gat	gat	0.0002029632636	1
gca	gca	0.0002029632636	1
ggt	ggt	0.0002029632636	1
cgc	cgc	0.0002029632636	1
tcg	tcg	0.0002029632636	1
cag	cag	0.0002029632636	1
gag	gag	0.0002029632636	1
ctc	ctc	0.0002029632636	1
gta	gta	0.0002029632636	1
tac	tac	0.0002029632636	1
agc	agc	0.0002029632636	1
ccc	ccc	0.0002029632636	1
; Host name	jolitorax
; Job started	2013-09-30.135824
; Job done	2013-09-30.135825
; Seconds	1
;	user	1
;	system	0.01
;	cuser	0
;	csystem	0