; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Drosophila_melanogaster/genome/Drosophila_melanogaster_start_codons.wc -o $RSAT/public_html/data/genomes/Drosophila_melanogaster/genome/Drosophila_melanogaster_start_codon_frequencies.tab
; 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/Drosophila_melanogaster/genome/Drosophila_melanogaster_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Drosophila_melanogaster/genome/Drosophila_melanogaster_start_codon_frequencies.tab
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	21313
; Sum of sequence lengths      	63939
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	21313
; total oligo occurrences      	21313
; 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	0.9929151222259	21162
agt	agt	0.0011260732886	24
ctg	ctg	0.0007507155257	16
ttc	ttc	0.0003753577629	8
aat	aat	0.0003753577629	8
act	act	0.0002815183222	6
ctc	ctc	0.0002815183222	6
gtt	gtt	0.0002815183222	6
gat	gat	0.0002345986018	5
ctt	ctt	0.0001876788814	4
gtg	gtg	0.0001876788814	4
ata	ata	0.0001876788814	4
gaa	gaa	0.0001407591611	3
gct	gct	0.0001407591611	3
tct	tct	0.0001407591611	3
aca	aca	0.0001407591611	3
gca	gca	0.0001407591611	3
cat	cat	0.0001407591611	3
cct	cct	0.0001407591611	3
agc	agc	0.0001407591611	3
aac	aac	0.0000938394407	2
gac	gac	0.0000938394407	2
ggc	ggc	0.0000938394407	2
ggt	ggt	0.0000938394407	2
gcc	gcc	0.0000938394407	2
cac	cac	0.0000938394407	2
atc	atc	0.0000938394407	2
tat	tat	0.0000938394407	2
tgt	tgt	0.0000469197204	1
agg	agg	0.0000469197204	1
att	att	0.0000469197204	1
ttt	ttt	0.0000469197204	1
tta	tta	0.0000469197204	1
caa	caa	0.0000469197204	1
acg	acg	0.0000469197204	1
cgt	cgt	0.0000469197204	1
tac	tac	0.0000469197204	1
gta	gta	0.0000469197204	1
tgc	tgc	0.0000469197204	1
ccc	ccc	0.0000469197204	1
ggg	ggg	0.0000469197204	1
tcg	tcg	0.0000469197204	1
acc	acc	0.0000469197204	1
aaa	aaa	0.0000469197204	1
aag	aag	0.0000469197204	1
aga	aga	0.0000469197204	1
ttg	ttg	0.0000469197204	1
gga	gga	0.0000469197204	1
; Host name	n52
; Job started	2017-04-15.082913
; Job done	2017-04-15.082914
; Seconds	0.31
;	user	0.31
;	system	0.03
;	cuser	0
;	csystem	0