; 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/Arthroderma_otae_CBS_113480_MO/genome/Arthroderma_otae_CBS_113480_MO_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Arthroderma_otae_CBS_113480_MO/genome/Arthroderma_otae_CBS_113480_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/Arthroderma_otae_CBS_113480_MO/genome/Arthroderma_otae_CBS_113480_MO_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Arthroderma_otae_CBS_113480_MO/genome/Arthroderma_otae_CBS_113480_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      	8762
; 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	0.3593928326866	3149
taa	taa	0.3291485962109	2884
tag	tag	0.2934261584113	2571
ttt	ttt	0.0013695503310	12
aaa	aaa	0.0013695503310	12
aat	aat	0.0007989043597	7
tca	tca	0.0007989043597	7
gat	gat	0.0006847751655	6
aca	aca	0.0006847751655	6
acc	acc	0.0006847751655	6
tta	tta	0.0005706459712	5
tct	tct	0.0005706459712	5
cta	cta	0.0005706459712	5
ggg	ggg	0.0005706459712	5
att	att	0.0004565167770	4
ctt	ctt	0.0004565167770	4
gct	gct	0.0004565167770	4
cat	cat	0.0004565167770	4
tcc	tcc	0.0004565167770	4
tgg	tgg	0.0003423875827	3
gtc	gtc	0.0003423875827	3
act	act	0.0003423875827	3
cct	cct	0.0003423875827	3
cac	cac	0.0003423875827	3
ttc	ttc	0.0002282583885	2
tgt	tgt	0.0002282583885	2
cca	cca	0.0002282583885	2
atg	atg	0.0002282583885	2
aac	aac	0.0002282583885	2
gta	gta	0.0002282583885	2
tac	tac	0.0002282583885	2
cga	cga	0.0002282583885	2
ccc	ccc	0.0002282583885	2
ggt	ggt	0.0002282583885	2
tcg	tcg	0.0002282583885	2
ctc	ctc	0.0002282583885	2
ata	ata	0.0002282583885	2
gtt	gtt	0.0002282583885	2
tat	tat	0.0002282583885	2
gaa	gaa	0.0001141291942	1
ctg	ctg	0.0001141291942	1
gcg	gcg	0.0001141291942	1
caa	caa	0.0001141291942	1
acg	acg	0.0001141291942	1
cgt	cgt	0.0001141291942	1
tgc	tgc	0.0001141291942	1
ggc	ggc	0.0001141291942	1
gca	gca	0.0001141291942	1
ccg	ccg	0.0001141291942	1
gag	gag	0.0001141291942	1
aag	aag	0.0001141291942	1
aga	aga	0.0001141291942	1
gtg	gtg	0.0001141291942	1
ttg	ttg	0.0001141291942	1
gcc	gcc	0.0001141291942	1
agc	agc	0.0001141291942	1
; Host name	nic47
; Job started	2011_11_26.223250
; Job done	2011_11_26.223251
; Seconds	0.16