; 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_kluyveri/genome/Saccharomyces_kluyveri_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//data/genomes/Saccharomyces_kluyveri/genome/Saccharomyces_kluyveri_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/data/genomes/Saccharomyces_kluyveri/genome/Saccharomyces_kluyveri_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/data/genomes/Saccharomyces_kluyveri/genome/Saccharomyces_kluyveri_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      	6083
; 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
taa	taa	0.3305934571757	2011
tga	tga	0.3059345717574	1861
tag	tag	0.2538221272398	1544
tcc	tcc	0.0069044879171	42
gcc	gcc	0.0065757027782	40
aaa	aaa	0.0052605622226	32
aag	aag	0.0044385993753	27
gga	gga	0.0037810290975	23
tca	tca	0.0036166365280	22
aca	aca	0.0031234588197	19
cag	cag	0.0031234588197	19
atg	atg	0.0029590662502	18
caa	caa	0.0029590662502	18
aac	aac	0.0029590662502	18
cca	cca	0.0027946736807	17
ctg	ctg	0.0027946736807	17
agg	agg	0.0024658885418	15
aat	aat	0.0024658885418	15
gat	gat	0.0024658885418	15
gtg	gtg	0.0023014959724	14
aga	aga	0.0023014959724	14
att	att	0.0021371034029	13
tgg	tgg	0.0021371034029	13
agc	agc	0.0021371034029	13
ttg	ttg	0.0019727108335	12
gaa	gaa	0.0019727108335	12
ccg	ccg	0.0018083182640	11
ttc	ttc	0.0016439256946	10
cat	cat	0.0016439256946	10
atc	atc	0.0016439256946	10
cac	cac	0.0016439256946	10
cct	cct	0.0014795331251	9
cgc	cgc	0.0014795331251	9
tat	tat	0.0014795331251	9
gct	gct	0.0013151405556	8
ttt	ttt	0.0013151405556	8
gag	gag	0.0011507479862	7
gac	gac	0.0011507479862	7
cgg	cgg	0.0011507479862	7
gtt	gtt	0.0011507479862	7
gca	gca	0.0009863554167	6
ggg	ggg	0.0009863554167	6
ata	ata	0.0009863554167	6
ctt	ctt	0.0008219628473	5
gcg	gcg	0.0008219628473	5
acg	acg	0.0008219628473	5
tcg	tcg	0.0008219628473	5
acc	acc	0.0008219628473	5
gtc	gtc	0.0008219628473	5
act	act	0.0008219628473	5
tct	tct	0.0008219628473	5
gta	gta	0.0008219628473	5
ctc	ctc	0.0008219628473	5
tac	tac	0.0006575702778	4
ggt	ggt	0.0006575702778	4
agt	agt	0.0006575702778	4
cgt	cgt	0.0004931777084	3
cga	cga	0.0004931777084	3
ccc	ccc	0.0004931777084	3
tgt	tgt	0.0003287851389	2
ggc	ggc	0.0003287851389	2
tgc	tgc	0.0003287851389	2
tta	tta	0.0001643925695	1
cta	cta	0.0001643925695	1
; Host name	nic49
; Job started	2011_11_26.225358
; Job done	2011_11_26.225358
; Seconds	0.17