; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2/genome/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2_start_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2/genome/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2_start_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_epeca14_ensembl_72_GCA_000188755.2/genome/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2/genome/Escherichia_coli_epeca14_ensembl_72_GCA_000188755.2_start_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5876
; Sum of sequence lengths      	17628
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5876
; total oligo occurrences      	5876
; 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
atg	atg	0.8116065350579	4769
gtg	gtg	0.1218515997277	716
ttg	ttg	0.0490129339687	288
aaa	aaa	0.0010211027910	6
atc	atc	0.0010211027910	6
ctg	ctg	0.0008509189925	5
aac	aac	0.0008509189925	5
gac	gac	0.0008509189925	5
cca	cca	0.0006807351940	4
att	att	0.0006807351940	4
gat	gat	0.0006807351940	4
gct	gct	0.0006807351940	4
ggc	ggc	0.0006807351940	4
cag	cag	0.0006807351940	4
ttt	ttt	0.0005105513955	3
cgc	cgc	0.0005105513955	3
gcg	gcg	0.0005105513955	3
cga	cga	0.0005105513955	3
gag	gag	0.0005105513955	3
gaa	gaa	0.0003403675970	2
aat	aat	0.0003403675970	2
acg	acg	0.0003403675970	2
cgt	cgt	0.0003403675970	2
tgg	tgg	0.0003403675970	2
ccg	ccg	0.0003403675970	2
ggt	ggt	0.0003403675970	2
cat	cat	0.0003403675970	2
ctc	ctc	0.0003403675970	2
tcc	tcc	0.0003403675970	2
cct	cct	0.0003403675970	2
cgg	cgg	0.0003403675970	2
cac	cac	0.0003403675970	2
ttc	ttc	0.0001701837985	1
tgt	tgt	0.0001701837985	1
ctt	ctt	0.0001701837985	1
tta	tta	0.0001701837985	1
tct	tct	0.0001701837985	1
caa	caa	0.0001701837985	1
tac	tac	0.0001701837985	1
gga	gga	0.0001701837985	1
agc	agc	0.0001701837985	1
gcc	gcc	0.0001701837985	1
agt	agt	0.0001701837985	1
; Host name	jolitorax
; Job started	2013-10-01.015129
; Job done	2013-10-01.015130
; Seconds	1.93
;	user	1.93
;	system	0.08
;	cuser	0
;	csystem	0