; oligo-analysis  -quick -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i /software/CC/bio/opt/rsat/rsa-tools//data/genomes/Saccharomyces_kudriavzevii/genome/Saccharomyces_kudriavzevii_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//data/genomes/Saccharomyces_kudriavzevii/genome/Saccharomyces_kudriavzevii_start_codon_frequencies
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. 
; Program version              	1.163
; Quick counting mode          
; Oligomer length              	3
; Input file                   	$RSAT/data/genomes/Saccharomyces_kudriavzevii/genome/Saccharomyces_kudriavzevii_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/data/genomes/Saccharomyces_kudriavzevii/genome/Saccharomyces_kudriavzevii_start_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	0
; Sum of sequence lengths      	0
; discarded residues           	NA (quick mode)	 (other letters than ACGT)
; discarded occurrences        	NA (quick mode)	 (contain discarded residues)
; nb possible positions        	NA (quick mode)
; total oligo occurrences      	6371
; alphabet size                	4
; nb possible oligomers        	64
; oligomers tested for significance	0
; Threshold values
;	Parameter      	Lower	Upper
;	ms_P           	none	1
;	occ_P          	none	1
; Sequences:
;
; 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	0.9122586721080	5812
att	att	0.0053366818396	34
aat	aat	0.0048657981479	31
aaa	aaa	0.0039240307644	25
aga	aga	0.0031392246115	20
atc	atc	0.0029822633809	19
tgg	tgg	0.0026683409198	17
aag	aag	0.0025113796892	16
aca	aca	0.0023544184586	15
ata	ata	0.0021974572281	14
acg	acg	0.0020404959975	13
gtg	gtg	0.0020404959975	13
tga	tga	0.0020404959975	13
ttc	ttc	0.0018835347669	12
aac	aac	0.0018835347669	12
tca	tca	0.0018835347669	12
agg	agg	0.0017265735363	11
gat	gat	0.0017265735363	11
gct	gct	0.0017265735363	11
gtt	gtt	0.0017265735363	11
tat	tat	0.0017265735363	11
ttt	ttt	0.0015696123058	10
acc	acc	0.0015696123058	10
act	act	0.0015696123058	10
ttg	ttg	0.0015696123058	10
ctg	ctg	0.0014126510752	9
caa	caa	0.0014126510752	9
taa	taa	0.0014126510752	9
gtc	gtc	0.0014126510752	9
agt	agt	0.0014126510752	9
tac	tac	0.0012556898446	8
tcc	tcc	0.0012556898446	8
tgt	tgt	0.0010987286140	7
ctt	ctt	0.0010987286140	7
cta	cta	0.0010987286140	7
tgc	tgc	0.0010987286140	7
ggg	ggg	0.0010987286140	7
gca	gca	0.0010987286140	7
tta	tta	0.0009417673835	6
gta	gta	0.0009417673835	6
ctc	ctc	0.0009417673835	6
gaa	gaa	0.0007848061529	5
cga	cga	0.0007848061529	5
tcg	tcg	0.0007848061529	5
cat	cat	0.0007848061529	5
agc	agc	0.0007848061529	5
cca	cca	0.0006278449223	4
cgc	cgc	0.0006278449223	4
tct	tct	0.0006278449223	4
ccg	ccg	0.0006278449223	4
cag	cag	0.0006278449223	4
gag	gag	0.0006278449223	4
cac	cac	0.0006278449223	4
gcc	gcc	0.0006278449223	4
gcg	gcg	0.0004708836917	3
gac	gac	0.0004708836917	3
ccc	ccc	0.0004708836917	3
ggt	ggt	0.0004708836917	3
cgt	cgt	0.0003139224612	2
ggc	ggc	0.0003139224612	2
cct	cct	0.0003139224612	2
tag	tag	0.0001569612306	1
gga	gga	0.0001569612306	1
; Host name	nic54
; Job started	2011_11_26.225821
; Job done	2011_11_26.225822
; Seconds	0.16