; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec11e_ensembl_72_GCA_000250195.2/genome/Escherichia_coli_dec11e_ensembl_72_GCA_000250195.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec11e_ensembl_72_GCA_000250195.2/genome/Escherichia_coli_dec11e_ensembl_72_GCA_000250195.2_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_dec11e_ensembl_72_GCA_000250195.2/genome/Escherichia_coli_dec11e_ensembl_72_GCA_000250195.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec11e_ensembl_72_GCA_000250195.2/genome/Escherichia_coli_dec11e_ensembl_72_GCA_000250195.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5174
; Sum of sequence lengths      	15522
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5174
; total oligo occurrences      	5174
; 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	0.5852338616158	3028
tga	tga	0.3241206030151	1677
tag	tag	0.0856204097410	443
gaa	gaa	0.0003865481252	2
ggc	ggc	0.0003865481252	2
ggt	ggt	0.0003865481252	2
cgc	cgc	0.0003865481252	2
aac	aac	0.0003865481252	2
cca	cca	0.0001932740626	1
tgg	tgg	0.0001932740626	1
gca	gca	0.0001932740626	1
ctg	ctg	0.0001932740626	1
tcg	tcg	0.0001932740626	1
acc	acc	0.0001932740626	1
gag	gag	0.0001932740626	1
aaa	aaa	0.0001932740626	1
tct	tct	0.0001932740626	1
cct	cct	0.0001932740626	1
gta	gta	0.0001932740626	1
cgg	cgg	0.0001932740626	1
agc	agc	0.0001932740626	1
gcc	gcc	0.0001932740626	1
cac	cac	0.0001932740626	1
aca	aca	0.0001932740626	1
; Host name	jolitorax
; Job started	2013-09-30.124835
; Job done	2013-09-30.124836
; Seconds	0.32
;	user	0.32
;	system	0.03
;	cuser	0
;	csystem	0