; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec9a_ensembl_72_GCA_000249895.2/genome/Escherichia_coli_dec9a_ensembl_72_GCA_000249895.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec9a_ensembl_72_GCA_000249895.2/genome/Escherichia_coli_dec9a_ensembl_72_GCA_000249895.2_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_dec9a_ensembl_72_GCA_000249895.2/genome/Escherichia_coli_dec9a_ensembl_72_GCA_000249895.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec9a_ensembl_72_GCA_000249895.2/genome/Escherichia_coli_dec9a_ensembl_72_GCA_000249895.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5583
; Sum of sequence lengths      	16749
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5583
; total oligo occurrences      	5583
; 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	0.5751388142576	3211
tga	tga	0.3311839512807	1849
tag	tag	0.0838259000537	468
ccg	ccg	0.0008955758553	5
aat	aat	0.0005373455132	3
gcg	gcg	0.0003582303421	2
gct	gct	0.0003582303421	2
tct	tct	0.0003582303421	2
acg	acg	0.0003582303421	2
tgc	tgc	0.0003582303421	2
gac	gac	0.0003582303421	2
ccc	ccc	0.0003582303421	2
tcg	tcg	0.0003582303421	2
cat	cat	0.0003582303421	2
gag	gag	0.0003582303421	2
aaa	aaa	0.0003582303421	2
gtc	gtc	0.0003582303421	2
aag	aag	0.0003582303421	2
cct	cct	0.0003582303421	2
cac	cac	0.0003582303421	2
agt	agt	0.0003582303421	2
gaa	gaa	0.0001791151711	1
ctt	ctt	0.0001791151711	1
gat	gat	0.0001791151711	1
ctg	ctg	0.0001791151711	1
cgt	cgt	0.0001791151711	1
cga	cga	0.0001791151711	1
aca	aca	0.0001791151711	1
ggc	ggc	0.0001791151711	1
tgg	tgg	0.0001791151711	1
act	act	0.0001791151711	1
tcc	tcc	0.0001791151711	1
gtg	gtg	0.0001791151711	1
ttg	ttg	0.0001791151711	1
tca	tca	0.0001791151711	1
gcc	gcc	0.0001791151711	1
; Host name	jolitorax
; Job started	2013-09-30.195759
; Job done	2013-09-30.195800
; Seconds	1.95
;	user	1.95
;	system	0.07
;	cuser	0
;	csystem	0