; 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/Kluyveromyces_waltii/genome/Kluyveromyces_waltii_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//data/genomes/Kluyveromyces_waltii/genome/Kluyveromyces_waltii_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/Kluyveromyces_waltii/genome/Kluyveromyces_waltii_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/data/genomes/Kluyveromyces_waltii/genome/Kluyveromyces_waltii_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      	5349
; 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	0.3834361562909	2051
tga	tga	0.3312768741821	1772
tag	tag	0.2467750981492	1320
aaa	aaa	0.0024303608151	13
atg	atg	0.0022434099832	12
ctg	ctg	0.0020564591512	11
aag	aag	0.0020564591512	11
agg	agg	0.0018695083193	10
aac	aac	0.0016825574874	9
aat	aat	0.0016825574874	9
cag	cag	0.0014956066554	8
atc	atc	0.0013086558235	7
ggc	ggc	0.0009347541597	5
tgg	tgg	0.0009347541597	5
ccg	ccg	0.0009347541597	5
att	att	0.0007478033277	4
ctt	ctt	0.0007478033277	4
caa	caa	0.0007478033277	4
ggt	ggt	0.0007478033277	4
acc	acc	0.0007478033277	4
act	act	0.0007478033277	4
aga	aga	0.0007478033277	4
gtg	gtg	0.0007478033277	4
cgg	cgg	0.0007478033277	4
gaa	gaa	0.0005608524958	3
acg	acg	0.0005608524958	3
cgt	cgt	0.0005608524958	3
cta	cta	0.0005608524958	3
gca	gca	0.0005608524958	3
tcg	tcg	0.0005608524958	3
gtc	gtc	0.0005608524958	3
tcc	tcc	0.0005608524958	3
ata	ata	0.0005608524958	3
agt	agt	0.0005608524958	3
cca	cca	0.0003739016639	2
gat	gat	0.0003739016639	2
tta	tta	0.0003739016639	2
tct	tct	0.0003739016639	2
gac	gac	0.0003739016639	2
ccc	ccc	0.0003739016639	2
ggg	ggg	0.0003739016639	2
gag	gag	0.0003739016639	2
ctc	ctc	0.0003739016639	2
cac	cac	0.0003739016639	2
agc	agc	0.0003739016639	2
tgt	tgt	0.0001869508319	1
cgc	cgc	0.0001869508319	1
gta	gta	0.0001869508319	1
tac	tac	0.0001869508319	1
tgc	tgc	0.0001869508319	1
cat	cat	0.0001869508319	1
cct	cct	0.0001869508319	1
tca	tca	0.0001869508319	1
ttg	ttg	0.0001869508319	1
gga	gga	0.0001869508319	1
gtt	gtt	0.0001869508319	1
gcc	gcc	0.0001869508319	1
tat	tat	0.0001869508319	1
; Host name	nic48
; Job started	2011_11_26.225227
; Job done	2011_11_26.225228
; Seconds	0.16