; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_ec1849_ensembl_72_GCA_000303495.1/genome/Escherichia_coli_ec1849_ensembl_72_GCA_000303495.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_ec1849_ensembl_72_GCA_000303495.1/genome/Escherichia_coli_ec1849_ensembl_72_GCA_000303495.1_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_ec1849_ensembl_72_GCA_000303495.1/genome/Escherichia_coli_ec1849_ensembl_72_GCA_000303495.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_ec1849_ensembl_72_GCA_000303495.1/genome/Escherichia_coli_ec1849_ensembl_72_GCA_000303495.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	3671
; Sum of sequence lengths      	11013
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	3671
; total oligo occurrences      	3671
; 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	0.5450830836284	2001
tga	tga	0.3067284118769	1126
tag	tag	0.0858076818306	315
gaa	gaa	0.0043584854263	16
cag	cag	0.0029964587306	11
ccg	ccg	0.0027240533914	10
cgt	cgt	0.0024516480523	9
acc	acc	0.0024516480523	9
gcc	gcc	0.0024516480523	9
ctg	ctg	0.0021792427132	8
tgc	tgc	0.0019068373740	7
ggg	ggg	0.0019068373740	7
gca	gca	0.0019068373740	7
aaa	aaa	0.0019068373740	7
act	act	0.0019068373740	7
atg	atg	0.0016344320349	6
ggt	ggt	0.0016344320349	6
cac	cac	0.0016344320349	6
ttc	ttc	0.0013620266957	5
cgg	cgg	0.0013620266957	5
att	att	0.0010896213566	4
gat	gat	0.0010896213566	4
cgc	cgc	0.0010896213566	4
tta	tta	0.0010896213566	4
aat	aat	0.0010896213566	4
tgg	tgg	0.0010896213566	4
tcg	tcg	0.0010896213566	4
cct	cct	0.0010896213566	4
tat	tat	0.0010896213566	4
tgt	tgt	0.0008172160174	3
agg	agg	0.0008172160174	3
cga	cga	0.0008172160174	3
gac	gac	0.0008172160174	3
ggc	ggc	0.0008172160174	3
aga	aga	0.0008172160174	3
ttg	ttg	0.0008172160174	3
ata	ata	0.0008172160174	3
agc	agc	0.0008172160174	3
cca	cca	0.0005448106783	2
gct	gct	0.0005448106783	2
aac	aac	0.0005448106783	2
gta	gta	0.0005448106783	2
aca	aca	0.0005448106783	2
cat	cat	0.0005448106783	2
aag	aag	0.0005448106783	2
gtg	gtg	0.0005448106783	2
tca	tca	0.0005448106783	2
ttt	ttt	0.0002724053391	1
gcg	gcg	0.0002724053391	1
tct	tct	0.0002724053391	1
caa	caa	0.0002724053391	1
acg	acg	0.0002724053391	1
cta	cta	0.0002724053391	1
ccc	ccc	0.0002724053391	1
gag	gag	0.0002724053391	1
gtc	gtc	0.0002724053391	1
tcc	tcc	0.0002724053391	1
gtt	gtt	0.0002724053391	1
atc	atc	0.0002724053391	1
agt	agt	0.0002724053391	1
; Host name	jolitorax
; Job started	2013-09-30.224219
; Job done	2013-09-30.224219
; Seconds	1.58
;	user	1.58
;	system	0.1
;	cuser	0
;	csystem	0