; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2/genome/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2_start_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2/genome/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2_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_dec13e_ensembl_72_GCA_000250395.2/genome/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2/genome/Escherichia_coli_dec13e_ensembl_72_GCA_000250395.2_start_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4927
; Sum of sequence lengths      	14781
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4927
; total oligo occurrences      	4927
; 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	0.8321493809620	4100
gtg	gtg	0.1087883093160	536
ttg	ttg	0.0539882281307	266
cag	cag	0.0008118530546	4
gag	gag	0.0006088897909	3
gaa	gaa	0.0004059265273	2
ggg	ggg	0.0004059265273	2
acg	acg	0.0004059265273	2
tgt	tgt	0.0002029632636	1
gat	gat	0.0002029632636	1
ctg	ctg	0.0002029632636	1
ccg	ccg	0.0002029632636	1
cgc	cgc	0.0002029632636	1
tcg	tcg	0.0002029632636	1
acc	acc	0.0002029632636	1
aaa	aaa	0.0002029632636	1
tct	tct	0.0002029632636	1
aat	aat	0.0002029632636	1
cgg	cgg	0.0002029632636	1
gcc	gcc	0.0002029632636	1
; Host name	jolitorax
; Job started	2013-09-30.135817
; Job done	2013-09-30.135818
; Seconds	0.36
;	user	0.36
;	system	0.02
;	cuser	0
;	csystem	0