; 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_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Ajellomyces_capsulatus_H143_MO/genome/Ajellomyces_capsulatus_H143_MO_stop_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_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Ajellomyces_capsulatus_H143_MO/genome/Ajellomyces_capsulatus_H143_MO_stop_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
tga	tga	0.3259149878705	3090
taa	taa	0.2043033435292	1937
tag	tag	0.1878493829765	1781
ttc	ttc	0.0168758569771	160
ttt	ttt	0.0162430123405	154
ttg	ttg	0.0117076257779	111
tcc	tcc	0.0091762472313	87
atc	atc	0.0082269802763	78
tat	tat	0.0081215061702	77
ctc	ctc	0.0080160320641	76
att	att	0.0073831874275	70
tct	tct	0.0071722392153	68
aaa	aaa	0.0063284463664	60
tac	tac	0.0061174981542	58
ctg	ctg	0.0061174981542	58
aat	aat	0.0060120240481	57
tgg	tgg	0.0059065499420	56
gtc	gtc	0.0059065499420	56
aac	aac	0.0059065499420	56
atg	atg	0.0058010758359	55
tgc	tgc	0.0058010758359	55
gtt	gtt	0.0058010758359	55
cat	cat	0.0056956017298	54
ctt	ctt	0.0053791794115	51
aag	aag	0.0052737053053	50
gtg	gtg	0.0051682311992	49
cag	cag	0.0051682311992	49
tgt	tgt	0.0050627570931	48
gag	gag	0.0048518088809	46
gat	gat	0.0048518088809	46
ccc	ccc	0.0044299124565	42
cac	cac	0.0043244383504	41
tcg	tcg	0.0040080160321	38
acc	acc	0.0037970678199	36
agg	agg	0.0035861196076	34
gcg	gcg	0.0035861196076	34
cct	cct	0.0031642231832	30
cgt	cgt	0.0030587490771	29
ccg	ccg	0.0030587490771	29
act	act	0.0030587490771	29
gac	gac	0.0030587490771	29
tta	tta	0.0029532749710	28
acg	acg	0.0027423267588	26
agc	agc	0.0027423267588	26
cgc	cgc	0.0027423267588	26
tca	tca	0.0027423267588	26
gct	gct	0.0026368526527	25
ata	ata	0.0026368526527	25
agt	agt	0.0026368526527	25
gcc	gcc	0.0025313785466	24
ggc	ggc	0.0024259044405	23
cca	cca	0.0023204303344	22
ggg	ggg	0.0023204303344	22
caa	caa	0.0022149562282	21
gaa	gaa	0.0021094821221	20
gga	gga	0.0020040080160	19
ggt	ggt	0.0017930598038	17
cgg	cgg	0.0017930598038	17
aca	aca	0.0016875856977	16
aga	aga	0.0014766374855	14
gca	gca	0.0012656892733	12
cta	cta	0.0011602151672	11
gta	gta	0.0011602151672	11
cga	cga	0.0006328446366	6
; Host name	nic48
; Job started	2011_11_26.223356
; Job done	2011_11_26.223357
; Seconds	0.15