; 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_kudriavzevii/genome/Saccharomyces_kudriavzevii_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//data/genomes/Saccharomyces_kudriavzevii/genome/Saccharomyces_kudriavzevii_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_kudriavzevii/genome/Saccharomyces_kudriavzevii_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/data/genomes/Saccharomyces_kudriavzevii/genome/Saccharomyces_kudriavzevii_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      	6370
; 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	0.3522762951334	2244
tga	tga	0.3095761381476	1972
tag	tag	0.2117739403454	1349
tcc	tcc	0.0124018838305	79
gcc	gcc	0.0062794348509	40
aag	aag	0.0056514913658	36
aaa	aaa	0.0047095761381	30
tca	tca	0.0047095761381	30
aca	aca	0.0037676609105	24
atg	atg	0.0036106750392	23
caa	caa	0.0034536891680	22
gga	gga	0.0034536891680	22
gaa	gaa	0.0031397174254	20
aac	aac	0.0031397174254	20
att	att	0.0029827315542	19
gat	gat	0.0028257456829	18
aat	aat	0.0028257456829	18
agg	agg	0.0026687598116	17
cag	cag	0.0026687598116	17
aga	aga	0.0025117739403	16
ttg	ttg	0.0025117739403	16
ctg	ctg	0.0023547880691	15
gtg	gtg	0.0023547880691	15
acg	acg	0.0021978021978	14
gtt	gtt	0.0021978021978	14
cga	cga	0.0020408163265	13
tgg	tgg	0.0020408163265	13
gac	gac	0.0018838304553	12
agt	agt	0.0018838304553	12
gag	gag	0.0017268445840	11
gtc	gtc	0.0017268445840	11
act	act	0.0017268445840	11
atc	atc	0.0017268445840	11
ttt	ttt	0.0015698587127	10
ccg	ccg	0.0015698587127	10
tcg	tcg	0.0015698587127	10
cct	cct	0.0015698587127	10
ata	ata	0.0015698587127	10
gca	gca	0.0014128728414	9
acc	acc	0.0014128728414	9
cac	cac	0.0014128728414	9
cca	cca	0.0012558869702	8
ctt	ctt	0.0012558869702	8
tac	tac	0.0012558869702	8
cta	cta	0.0012558869702	8
tct	tct	0.0010989010989	7
ccc	ccc	0.0010989010989	7
agc	agc	0.0010989010989	7
tat	tat	0.0010989010989	7
ggt	ggt	0.0009419152276	6
cgg	cgg	0.0009419152276	6
gct	gct	0.0007849293564	5
cat	cat	0.0007849293564	5
ctc	ctc	0.0007849293564	5
tgt	tgt	0.0006279434851	4
gcg	gcg	0.0006279434851	4
tgc	tgc	0.0006279434851	4
ggg	ggg	0.0006279434851	4
ttc	ttc	0.0003139717425	2
tta	tta	0.0001569858713	1
cgt	cgt	0.0001569858713	1
gta	gta	0.0001569858713	1
ggc	ggc	0.0001569858713	1
; Host name	nic54
; Job started	2011_11_26.225825
; Job done	2011_11_26.225826
; Seconds	0.15