; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_fda507_ensembl_72_GCA_000303735.1/genome/Escherichia_coli_fda507_ensembl_72_GCA_000303735.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_fda507_ensembl_72_GCA_000303735.1/genome/Escherichia_coli_fda507_ensembl_72_GCA_000303735.1_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_fda507_ensembl_72_GCA_000303735.1/genome/Escherichia_coli_fda507_ensembl_72_GCA_000303735.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_fda507_ensembl_72_GCA_000303735.1/genome/Escherichia_coli_fda507_ensembl_72_GCA_000303735.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	2548
; Sum of sequence lengths      	7644
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	2548
; total oligo occurrences      	2548
; 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	0.5317896389325	1355
tga	tga	0.2978806907378	759
tag	tag	0.0753532182104	192
cgg	cgg	0.0054945054945	14
ggg	ggg	0.0043171114600	11
ttc	ttc	0.0039246467818	10
gcg	gcg	0.0039246467818	10
tgc	tgc	0.0039246467818	10
atg	atg	0.0035321821036	9
tgg	tgg	0.0035321821036	9
gaa	gaa	0.0027472527473	7
gct	gct	0.0027472527473	7
gcc	gcc	0.0027472527473	7
cgc	cgc	0.0023547880691	6
ccg	ccg	0.0023547880691	6
acc	acc	0.0023547880691	6
gtc	gtc	0.0023547880691	6
ata	ata	0.0023547880691	6
gga	gga	0.0023547880691	6
agc	agc	0.0023547880691	6
tgt	tgt	0.0019623233909	5
agg	agg	0.0019623233909	5
acg	acg	0.0019623233909	5
ggc	ggc	0.0019623233909	5
aaa	aaa	0.0019623233909	5
ctc	ctc	0.0019623233909	5
gtg	gtg	0.0019623233909	5
agt	agt	0.0019623233909	5
cca	cca	0.0015698587127	4
aac	aac	0.0015698587127	4
aca	aca	0.0015698587127	4
gca	gca	0.0015698587127	4
aag	aag	0.0015698587127	4
tcc	tcc	0.0015698587127	4
att	att	0.0011773940345	3
ccc	ccc	0.0011773940345	3
gtt	gtt	0.0011773940345	3
ctg	ctg	0.0007849293564	2
gat	gat	0.0007849293564	2
tct	tct	0.0007849293564	2
caa	caa	0.0007849293564	2
cgt	cgt	0.0007849293564	2
gta	gta	0.0007849293564	2
cta	cta	0.0007849293564	2
ggt	ggt	0.0007849293564	2
cat	cat	0.0007849293564	2
aga	aga	0.0007849293564	2
ttg	ttg	0.0007849293564	2
tca	tca	0.0007849293564	2
tat	tat	0.0007849293564	2
ctt	ctt	0.0003924646782	1
ttt	ttt	0.0003924646782	1
cga	cga	0.0003924646782	1
gac	gac	0.0003924646782	1
cag	cag	0.0003924646782	1
gag	gag	0.0003924646782	1
atc	atc	0.0003924646782	1
; Host name	jolitorax
; Job started	2013-10-01.023535
; Job done	2013-10-01.023535
; Seconds	1.48
;	user	1.48
;	system	0.08
;	cuser	0
;	csystem	0