; 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_capsulatus_H143_MO/genome/Ajellomyces_capsulatus_H143_MO_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Ajellomyces_capsulatus_H143_MO/genome/Ajellomyces_capsulatus_H143_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_capsulatus_H143_MO/genome/Ajellomyces_capsulatus_H143_MO_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Ajellomyces_capsulatus_H143_MO/genome/Ajellomyces_capsulatus_H143_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      	9481
; 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	0.7966459234258	7553
caa	caa	0.0104419365046	99
ctc	ctc	0.0090707731252	86
ctt	ctt	0.0068558168970	65
ctg	ctg	0.0066448686847	63
cga	cga	0.0059065499420	56
cac	cac	0.0054846535176	52
cat	cat	0.0051682311992	49
cgc	cgc	0.0051682311992	49
gac	gac	0.0051682311992	49
atc	atc	0.0048518088809	46
ttt	ttt	0.0048518088809	46
cag	cag	0.0048518088809	46
gga	gga	0.0047463347748	45
att	att	0.0045353865626	43
cca	cca	0.0045353865626	43
gtc	gtc	0.0043244383504	41
cct	cct	0.0042189642443	40
gaa	gaa	0.0041134901382	39
gtt	gtt	0.0041134901382	39
ccg	ccg	0.0040080160321	38
aaa	aaa	0.0040080160321	38
ccc	ccc	0.0037970678199	36
gat	gat	0.0035861196076	34
aac	aac	0.0035861196076	34
ttc	ttc	0.0034806455015	33
ggc	ggc	0.0032696972893	31
cta	cta	0.0028478008649	27
gag	gag	0.0028478008649	27
agc	agc	0.0028478008649	27
cgg	cgg	0.0028478008649	27
tac	tac	0.0027423267588	26
aca	aca	0.0027423267588	26
gct	gct	0.0026368526527	25
aat	aat	0.0026368526527	25
ttg	ttg	0.0026368526527	25
ggg	ggg	0.0026368526527	25
cgt	cgt	0.0025313785466	24
gca	gca	0.0025313785466	24
aga	aga	0.0023204303344	22
gcc	gcc	0.0023204303344	22
tct	tct	0.0022149562282	21
tca	tca	0.0022149562282	21
tgc	tgc	0.0021094821221	20
tat	tat	0.0020040080160	19
agg	agg	0.0018985339099	18
ggt	ggt	0.0017930598038	17
ata	ata	0.0017930598038	17
tcg	tcg	0.0016875856977	16
acc	acc	0.0016875856977	16
tcc	tcc	0.0016875856977	16
gcg	gcg	0.0015821115916	15
tga	tga	0.0015821115916	15
gtg	gtg	0.0014766374855	14
gta	gta	0.0014766374855	14
act	act	0.0013711633794	13
tgg	tgg	0.0012656892733	12
aag	aag	0.0012656892733	12
tta	tta	0.0011602151672	11
agt	agt	0.0011602151672	11
tgt	tgt	0.0010547410611	10
acg	acg	0.0010547410611	10
tag	tag	0.0009492669550	9
taa	taa	0.0009492669550	9
; Host name	nic48
; Job started	2011_11_26.223256
; Job done	2011_11_26.223257
; Seconds	0.15