; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_frik523_ensembl_72_GCA_000303275.1/genome/Escherichia_coli_frik523_ensembl_72_GCA_000303275.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_frik523_ensembl_72_GCA_000303275.1/genome/Escherichia_coli_frik523_ensembl_72_GCA_000303275.1_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_frik523_ensembl_72_GCA_000303275.1/genome/Escherichia_coli_frik523_ensembl_72_GCA_000303275.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_frik523_ensembl_72_GCA_000303275.1/genome/Escherichia_coli_frik523_ensembl_72_GCA_000303275.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	3432
; Sum of sequence lengths      	10296
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	3432
; total oligo occurrences      	3432
; 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	0.5300116550117	1819
tga	tga	0.3015734265734	1035
tag	tag	0.0777972027972	267
gtg	gtg	0.0040792540793	14
cgg	cgg	0.0037878787879	13
ggg	ggg	0.0034965034965	12
cag	cag	0.0034965034965	12
gcc	gcc	0.0034965034965	12
gat	gat	0.0032051282051	11
ggc	ggc	0.0032051282051	11
ctg	ctg	0.0026223776224	9
cgt	cgt	0.0026223776224	9
ttg	ttg	0.0026223776224	9
aat	aat	0.0023310023310	8
gca	gca	0.0023310023310	8
aaa	aaa	0.0023310023310	8
gaa	gaa	0.0020396270396	7
cgc	cgc	0.0020396270396	7
gcg	gcg	0.0020396270396	7
gct	gct	0.0020396270396	7
aac	aac	0.0020396270396	7
gac	gac	0.0020396270396	7
ttc	ttc	0.0017482517483	6
acc	acc	0.0017482517483	6
aga	aga	0.0017482517483	6
agc	agc	0.0017482517483	6
atc	atc	0.0017482517483	6
tgt	tgt	0.0014568764569	5
tgg	tgg	0.0014568764569	5
ggt	ggt	0.0014568764569	5
cat	cat	0.0014568764569	5
gtc	gtc	0.0014568764569	5
cac	cac	0.0014568764569	5
att	att	0.0011655011655	4
agg	agg	0.0011655011655	4
ttt	ttt	0.0011655011655	4
tgc	tgc	0.0011655011655	4
aca	aca	0.0011655011655	4
act	act	0.0011655011655	4
ctc	ctc	0.0011655011655	4
aag	aag	0.0011655011655	4
gga	gga	0.0011655011655	4
tct	tct	0.0008741258741	3
caa	caa	0.0008741258741	3
acg	acg	0.0008741258741	3
tcc	tcc	0.0008741258741	3
tat	tat	0.0008741258741	3
cca	cca	0.0005827505828	2
ctt	ctt	0.0005827505828	2
atg	atg	0.0005827505828	2
tac	tac	0.0005827505828	2
cga	cga	0.0005827505828	2
ccc	ccc	0.0005827505828	2
ccg	ccg	0.0005827505828	2
gag	gag	0.0005827505828	2
cct	cct	0.0005827505828	2
agt	agt	0.0005827505828	2
tcg	tcg	0.0002913752914	1
tca	tca	0.0002913752914	1
; Host name	jolitorax
; Job started	2013-10-01.033041
; Job done	2013-10-01.033042
; Seconds	1.57
;	user	1.57
;	system	0.08
;	cuser	0
;	csystem	0