; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_3030_1_ensembl_72_GCA_000225085.2/genome/Escherichia_coli_3030_1_ensembl_72_GCA_000225085.2_start_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_3030_1_ensembl_72_GCA_000225085.2/genome/Escherichia_coli_3030_1_ensembl_72_GCA_000225085.2_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_3030_1_ensembl_72_GCA_000225085.2/genome/Escherichia_coli_3030_1_ensembl_72_GCA_000225085.2_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_3030_1_ensembl_72_GCA_000225085.2/genome/Escherichia_coli_3030_1_ensembl_72_GCA_000225085.2_start_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5346
; Sum of sequence lengths      	16038
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5346
; total oligo occurrences      	5346
; 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	0.8357650579873	4468
gtg	gtg	0.1118593340816	598
ttg	ttg	0.0480733258511	257
cag	cag	0.0005611672278	3
ccg	ccg	0.0003741114852	2
ggt	ggt	0.0003741114852	2
gcc	gcc	0.0003741114852	2
ggc	ggc	0.0001870557426	1
ggg	ggg	0.0001870557426	1
gca	gca	0.0001870557426	1
ctg	ctg	0.0001870557426	1
acc	acc	0.0001870557426	1
gag	gag	0.0001870557426	1
aaa	aaa	0.0001870557426	1
aac	aac	0.0001870557426	1
ctc	ctc	0.0001870557426	1
tcc	tcc	0.0001870557426	1
cga	cga	0.0001870557426	1
cac	cac	0.0001870557426	1
atc	atc	0.0001870557426	1
tat	tat	0.0001870557426	1
; Host name	jolitorax
; Job started	2013-09-30.022331
; Job done	2013-09-30.022332
; Seconds	1.8
;	user	1.8
;	system	0.08
;	cuser	0
;	csystem	0