; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1/genome/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1_start_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1/genome/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1_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_e1520_ensembl_72_GCA_000190815.1/genome/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1/genome/Escherichia_coli_e1520_ensembl_72_GCA_000190815.1_start_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4673
; Sum of sequence lengths      	14019
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4673
; total oligo occurrences      	4673
; 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	0.8574791354590	4007
gtg	gtg	0.1052856837150	492
ttg	ttg	0.0299593408945	140
gta	gta	0.0010699764605	5
cag	cag	0.0006419858763	3
ctg	ctg	0.0004279905842	2
cgc	cgc	0.0004279905842	2
tac	tac	0.0004279905842	2
cgg	cgg	0.0004279905842	2
ttc	ttc	0.0002139952921	1
gaa	gaa	0.0002139952921	1
ggg	ggg	0.0002139952921	1
ctt	ctt	0.0002139952921	1
ttt	ttt	0.0002139952921	1
tcg	tcg	0.0002139952921	1
acc	acc	0.0002139952921	1
gag	gag	0.0002139952921	1
cat	cat	0.0002139952921	1
aaa	aaa	0.0002139952921	1
aac	aac	0.0002139952921	1
gct	gct	0.0002139952921	1
tcc	tcc	0.0002139952921	1
tct	tct	0.0002139952921	1
cgt	cgt	0.0002139952921	1
cta	cta	0.0002139952921	1
cac	cac	0.0002139952921	1
tat	tat	0.0002139952921	1
; Host name	jolitorax
; Job started	2013-09-30.210609
; Job done	2013-09-30.210610
; Seconds	1.95
;	user	1.95
;	system	0.06
;	cuser	0
;	csystem	0.01