; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_ec1856_ensembl_72_GCA_000303455.1/genome/Escherichia_coli_ec1856_ensembl_72_GCA_000303455.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_ec1856_ensembl_72_GCA_000303455.1/genome/Escherichia_coli_ec1856_ensembl_72_GCA_000303455.1_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_ec1856_ensembl_72_GCA_000303455.1/genome/Escherichia_coli_ec1856_ensembl_72_GCA_000303455.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_ec1856_ensembl_72_GCA_000303455.1/genome/Escherichia_coli_ec1856_ensembl_72_GCA_000303455.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	2810
; Sum of sequence lengths      	8430
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	2810
; total oligo occurrences      	2810
; 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	0.5466192170819	1536
tga	tga	0.2967971530249	834
tag	tag	0.0758007117438	213
ggg	ggg	0.0042704626335	12
cag	cag	0.0039145907473	11
gca	gca	0.0032028469751	9
ggt	ggt	0.0032028469751	9
gtg	gtg	0.0032028469751	9
cgc	cgc	0.0028469750890	8
gac	gac	0.0024911032028	7
atc	atc	0.0024911032028	7
ctg	ctg	0.0021352313167	6
aac	aac	0.0021352313167	6
aat	aat	0.0021352313167	6
aga	aga	0.0021352313167	6
cgg	cgg	0.0021352313167	6
tct	tct	0.0017793594306	5
tgc	tgc	0.0017793594306	5
ccg	ccg	0.0017793594306	5
aag	aag	0.0017793594306	5
tcc	tcc	0.0017793594306	5
cac	cac	0.0017793594306	5
gcc	gcc	0.0017793594306	5
agc	agc	0.0017793594306	5
ttc	ttc	0.0014234875445	4
gat	gat	0.0014234875445	4
cat	cat	0.0014234875445	4
ctc	ctc	0.0014234875445	4
tca	tca	0.0014234875445	4
gaa	gaa	0.0010676156584	3
att	att	0.0010676156584	3
gcg	gcg	0.0010676156584	3
acg	acg	0.0010676156584	3
ggc	ggc	0.0010676156584	3
tgg	tgg	0.0010676156584	3
acc	acc	0.0010676156584	3
gtc	gtc	0.0010676156584	3
act	act	0.0010676156584	3
cct	cct	0.0010676156584	3
ttg	ttg	0.0010676156584	3
tgt	tgt	0.0007117437722	2
ctt	ctt	0.0007117437722	2
cca	cca	0.0007117437722	2
agg	agg	0.0007117437722	2
atg	atg	0.0007117437722	2
gct	gct	0.0007117437722	2
caa	caa	0.0007117437722	2
cgt	cgt	0.0007117437722	2
gta	gta	0.0007117437722	2
aca	aca	0.0007117437722	2
gga	gga	0.0007117437722	2
gtt	gtt	0.0007117437722	2
tat	tat	0.0007117437722	2
ttt	ttt	0.0003558718861	1
tac	tac	0.0003558718861	1
cga	cga	0.0003558718861	1
ccc	ccc	0.0003558718861	1
ata	ata	0.0003558718861	1
agt	agt	0.0003558718861	1
; Host name	jolitorax
; Job started	2013-09-30.225453
; Job done	2013-09-30.225453
; Seconds	1.48
;	user	1.48
;	system	0.08
;	cuser	0
;	csystem	0