; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_8_0566_ensembl_72_GCA_000305175.1/genome/Escherichia_coli_8_0566_ensembl_72_GCA_000305175.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_8_0566_ensembl_72_GCA_000305175.1/genome/Escherichia_coli_8_0566_ensembl_72_GCA_000305175.1_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_8_0566_ensembl_72_GCA_000305175.1/genome/Escherichia_coli_8_0566_ensembl_72_GCA_000305175.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_8_0566_ensembl_72_GCA_000305175.1/genome/Escherichia_coli_8_0566_ensembl_72_GCA_000305175.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	2108
; Sum of sequence lengths      	6324
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	2108
; total oligo occurrences      	2108
; 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	0.6176470588235	1302
tga	tga	0.2836812144213	598
tag	tag	0.0754269449715	159
cgg	cgg	0.0018975332068	4
gac	gac	0.0018975332068	4
ctg	ctg	0.0014231499051	3
gcg	gcg	0.0014231499051	3
cgt	cgt	0.0014231499051	3
atc	atc	0.0014231499051	3
ttc	ttc	0.0009487666034	2
tgt	tgt	0.0009487666034	2
aaa	aaa	0.0009487666034	2
gct	gct	0.0009487666034	2
gtg	gtg	0.0009487666034	2
ttg	ttg	0.0009487666034	2
agt	agt	0.0009487666034	2
gaa	gaa	0.0004743833017	1
tgg	tgg	0.0004743833017	1
cca	cca	0.0004743833017	1
gca	gca	0.0004743833017	1
cag	cag	0.0004743833017	1
acc	acc	0.0004743833017	1
aac	aac	0.0004743833017	1
aag	aag	0.0004743833017	1
cct	cct	0.0004743833017	1
aga	aga	0.0004743833017	1
tca	tca	0.0004743833017	1
gcc	gcc	0.0004743833017	1
cac	cac	0.0004743833017	1
aca	aca	0.0004743833017	1
tat	tat	0.0004743833017	1
; Host name	jolitorax
; Job started	2013-09-30.053137
; Job done	2013-09-30.053137
; Seconds	1.5
;	user	1.51
;	system	0.08
;	cuser	0
;	csystem	0