; oligo-analysis  -quick -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Ajellomyces_dermatitidis_SLH14081_MO/genome/Ajellomyces_dermatitidis_SLH14081_MO_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Ajellomyces_dermatitidis_SLH14081_MO/genome/Ajellomyces_dermatitidis_SLH14081_MO_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/public_html/data/genomes/Ajellomyces_dermatitidis_SLH14081_MO/genome/Ajellomyces_dermatitidis_SLH14081_MO_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Ajellomyces_dermatitidis_SLH14081_MO/genome/Ajellomyces_dermatitidis_SLH14081_MO_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      	9552
; 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	0.8142797319933	7778
ctc	ctc	0.0106783919598	102
caa	caa	0.0092127303183	88
ctt	ctt	0.0082705192630	79
cga	cga	0.0068048576214	65
atc	atc	0.0062814070352	60
cgc	cgc	0.0058626465662	56
cac	cac	0.0058626465662	56
gtc	gtc	0.0057579564489	55
gaa	gaa	0.0055485762144	53
att	att	0.0054438860972	52
aac	aac	0.0052345058626	50
ctg	ctg	0.0043969849246	42
cca	cca	0.0040829145729	39
cat	cat	0.0040829145729	39
aaa	aaa	0.0040829145729	39
ttt	ttt	0.0038735343384	37
gca	gca	0.0035594639866	34
gac	gac	0.0034547738693	33
cag	cag	0.0034547738693	33
cct	cct	0.0034547738693	33
gga	gga	0.0033500837521	32
gtt	gtt	0.0033500837521	32
ttc	ttc	0.0032453936348	31
ccc	ccc	0.0031407035176	30
gcc	gcc	0.0031407035176	30
ccg	ccg	0.0030360134003	29
cta	cta	0.0029313232831	28
agc	agc	0.0028266331658	27
ata	ata	0.0027219430486	26
aat	aat	0.0025125628141	24
aga	aga	0.0024078726968	23
cgt	cgt	0.0023031825796	22
tgc	tgc	0.0021984924623	21
ggc	ggc	0.0021984924623	21
gag	gag	0.0021984924623	21
cgg	cgg	0.0021984924623	21
aca	aca	0.0020938023451	20
ggg	ggg	0.0020938023451	20
aag	aag	0.0019891122278	19
gat	gat	0.0017797319933	17
gct	gct	0.0017797319933	17
gta	gta	0.0017797319933	17
tcc	tcc	0.0016750418760	16
gtg	gtg	0.0015703517588	15
ggt	ggt	0.0013609715243	13
agg	agg	0.0011515912898	11
gcg	gcg	0.0011515912898	11
taa	taa	0.0011515912898	11
tga	tga	0.0011515912898	11
tgt	tgt	0.0010469011725	10
tta	tta	0.0010469011725	10
tct	tct	0.0010469011725	10
acc	acc	0.0010469011725	10
ttg	ttg	0.0010469011725	10
agt	agt	0.0010469011725	10
tgg	tgg	0.0008375209380	8
tcg	tcg	0.0008375209380	8
act	act	0.0008375209380	8
tca	tca	0.0008375209380	8
acg	acg	0.0007328308208	7
tac	tac	0.0007328308208	7
tat	tat	0.0007328308208	7
; Host name	nic48
; Job started	2011_11_26.223302
; Job done	2011_11_26.223303
; Seconds	0.17