; 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/Verticillium_dahliae_VdLs.17_MO/genome/Verticillium_dahliae_VdLs.17_MO_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Verticillium_dahliae_VdLs.17_MO/genome/Verticillium_dahliae_VdLs.17_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/Verticillium_dahliae_VdLs.17_MO/genome/Verticillium_dahliae_VdLs.17_MO_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Verticillium_dahliae_VdLs.17_MO/genome/Verticillium_dahliae_VdLs.17_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      	10367
; 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	0.3861290633742	4003
tag	tag	0.2665187614546	2763
taa	taa	0.1823092505064	1890
ttc	ttc	0.0080061734349	83
ttg	ttg	0.0054017555706	56
ctc	ctc	0.0048229960451	50
atc	atc	0.0047265361242	49
ccc	ccc	0.0047265361242	49
acc	acc	0.0045336162824	47
tcc	tcc	0.0041477765988	43
ctg	ctg	0.0041477765988	43
tgc	tgc	0.0041477765988	43
cca	cca	0.0039548567570	41
tca	tca	0.0039548567570	41
agc	agc	0.0038583968361	40
atg	atg	0.0037619369152	39
gtc	gtc	0.0037619369152	39
aac	aac	0.0035690170734	37
caa	caa	0.0033760972316	35
tcg	tcg	0.0033760972316	35
ttt	ttt	0.0033760972316	35
cac	cac	0.0033760972316	35
cgc	cgc	0.0030867174689	32
gac	gac	0.0029902575480	31
cct	cct	0.0028937976271	30
tct	tct	0.0028937976271	30
cag	cag	0.0028937976271	30
aaa	aaa	0.0028937976271	30
gcc	gcc	0.0028937976271	30
tgt	tgt	0.0027973377062	29
cat	cat	0.0027973377062	29
gtg	gtg	0.0026044178644	27
gat	gat	0.0026044178644	27
acg	acg	0.0025079579435	26
gct	gct	0.0024114980226	25
ccg	ccg	0.0024114980226	25
cgt	cgt	0.0023150381017	24
ggc	ggc	0.0023150381017	24
ctt	ctt	0.0022185781808	23
tgg	tgg	0.0022185781808	23
gtt	gtt	0.0022185781808	23
aag	aag	0.0021221182599	22
tat	tat	0.0021221182599	22
aca	aca	0.0019291984181	20
ggt	ggt	0.0018327384972	19
act	act	0.0018327384972	19
ggg	ggg	0.0018327384972	19
gcg	gcg	0.0017362785763	18
tac	tac	0.0017362785763	18
cta	cta	0.0017362785763	18
gaa	gaa	0.0016398186553	17
att	att	0.0015433587344	16
gag	gag	0.0015433587344	16
agt	agt	0.0015433587344	16
cga	cga	0.0014468988135	15
tta	tta	0.0013504388926	14
gca	gca	0.0013504388926	14
gta	gta	0.0013504388926	14
aga	aga	0.0012539789717	13
cgg	cgg	0.0012539789717	13
agg	agg	0.0010610591299	11
aat	aat	0.0007716793672	8
gga	gga	0.0007716793672	8
ata	ata	0.0002893797627	3
; Host name	nic41
; Job started	2011_11_26.223256
; Job done	2011_11_26.223256
; Seconds	0.15