; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2/genome/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2_start_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2/genome/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2_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_dec4d_ensembl_72_GCA_000249435.2/genome/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2/genome/Escherichia_coli_dec4d_ensembl_72_GCA_000249435.2_start_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5539
; Sum of sequence lengths      	16617
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5539
; total oligo occurrences      	5539
; 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	0.8367936450623	4635
gtg	gtg	0.1113919480051	617
ttg	ttg	0.0480231088644	266
ggt	ggt	0.0005416140097	3
cgc	cgc	0.0005416140097	3
gtt	gtt	0.0003610760065	2
gaa	gaa	0.0001805380032	1
ggc	ggc	0.0001805380032	1
ggg	ggg	0.0001805380032	1
ctt	ctt	0.0001805380032	1
att	att	0.0001805380032	1
ttt	ttt	0.0001805380032	1
gct	gct	0.0001805380032	1
aac	aac	0.0001805380032	1
tcc	tcc	0.0001805380032	1
aat	aat	0.0001805380032	1
cga	cga	0.0001805380032	1
gac	gac	0.0001805380032	1
agc	agc	0.0001805380032	1
; Host name	jolitorax
; Job started	2013-09-30.172817
; Job done	2013-09-30.172817
; Seconds	1.87
;	user	1.87
;	system	0.06
;	cuser	0
;	csystem	0.01