; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec10c_ensembl_72_GCA_000250035.2/genome/Escherichia_coli_dec10c_ensembl_72_GCA_000250035.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec10c_ensembl_72_GCA_000250035.2/genome/Escherichia_coli_dec10c_ensembl_72_GCA_000250035.2_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_dec10c_ensembl_72_GCA_000250035.2/genome/Escherichia_coli_dec10c_ensembl_72_GCA_000250035.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec10c_ensembl_72_GCA_000250035.2/genome/Escherichia_coli_dec10c_ensembl_72_GCA_000250035.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5888
; Sum of sequence lengths      	17664
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5888
; total oligo occurrences      	5888
; 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	0.5715013586957	3365
tga	tga	0.3415421195652	2011
tag	tag	0.0813519021739	479
ccg	ccg	0.0005095108696	3
tgt	tgt	0.0003396739130	2
tgg	tgg	0.0003396739130	2
atg	atg	0.0003396739130	2
gag	gag	0.0003396739130	2
aag	aag	0.0003396739130	2
ctc	ctc	0.0003396739130	2
cgt	cgt	0.0003396739130	2
ccc	ccc	0.0003396739130	2
ttt	ttt	0.0001698369565	1
cgc	cgc	0.0001698369565	1
tcg	tcg	0.0001698369565	1
cag	cag	0.0001698369565	1
gcg	gcg	0.0001698369565	1
aaa	aaa	0.0001698369565	1
aac	aac	0.0001698369565	1
tta	tta	0.0001698369565	1
aat	aat	0.0001698369565	1
cct	cct	0.0001698369565	1
ata	ata	0.0001698369565	1
agc	agc	0.0001698369565	1
aca	aca	0.0001698369565	1
agt	agt	0.0001698369565	1
; Host name	jolitorax
; Job started	2013-09-30.115810
; Job done	2013-09-30.115810
; Seconds	0.92
;	user	0.92
;	system	0.06
;	cuser	0
;	csystem	0