; 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_albo-atrum_VaMs.102_MO/genome/Verticillium_albo-atrum_VaMs.102_MO_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Verticillium_albo-atrum_VaMs.102_MO/genome/Verticillium_albo-atrum_VaMs.102_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_albo-atrum_VaMs.102_MO/genome/Verticillium_albo-atrum_VaMs.102_MO_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Verticillium_albo-atrum_VaMs.102_MO/genome/Verticillium_albo-atrum_VaMs.102_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      	9924
; 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	0.4469971785570	4436
tag	tag	0.2529222087868	2510
taa	taa	0.1974002418380	1959
ttc	ttc	0.0037283353486	37
caa	caa	0.0031237404272	31
ctc	ctc	0.0030229746070	30
aaa	aaa	0.0029222087868	29
ctg	ctg	0.0028214429665	28
cca	cca	0.0027206771463	27
ccc	ccc	0.0026199113261	26
tca	tca	0.0026199113261	26
ttg	ttg	0.0025191455058	25
agc	agc	0.0024183796856	24
cgc	cgc	0.0024183796856	24
atg	atg	0.0023176138654	23
gtc	gtc	0.0023176138654	23
tcc	tcc	0.0022168480451	22
ttt	ttt	0.0022168480451	22
tcg	tcg	0.0021160822249	21
acc	acc	0.0021160822249	21
cac	cac	0.0021160822249	21
tgc	tgc	0.0020153164047	20
cat	cat	0.0019145505844	19
atc	atc	0.0019145505844	19
cag	cag	0.0019145505844	19
tgt	tgt	0.0018137847642	18
gct	gct	0.0018137847642	18
gca	gca	0.0018137847642	18
gat	gat	0.0018137847642	18
acg	acg	0.0015114873035	15
tac	tac	0.0015114873035	15
ccg	ccg	0.0015114873035	15
cct	cct	0.0015114873035	15
aac	aac	0.0015114873035	15
tct	tct	0.0015114873035	15
agg	agg	0.0014107214833	14
gaa	gaa	0.0014107214833	14
gac	gac	0.0014107214833	14
tat	tat	0.0014107214833	14
att	att	0.0013099556630	13
ctt	ctt	0.0013099556630	13
tta	tta	0.0013099556630	13
gtg	gtg	0.0013099556630	13
aga	aga	0.0013099556630	13
cgg	cgg	0.0013099556630	13
agt	agt	0.0013099556630	13
cta	cta	0.0012091898428	12
cga	cga	0.0012091898428	12
ggc	ggc	0.0012091898428	12
tgg	tgg	0.0012091898428	12
ggg	ggg	0.0012091898428	12
cgt	cgt	0.0011084240226	11
aca	aca	0.0011084240226	11
act	act	0.0011084240226	11
ggt	ggt	0.0010076582023	10
gta	gta	0.0010076582023	10
gcc	gcc	0.0010076582023	10
gag	gag	0.0009068923821	9
aag	aag	0.0009068923821	9
gtt	gtt	0.0009068923821	9
gcg	gcg	0.0007053607416	7
aat	aat	0.0006045949214	6
ata	ata	0.0005038291012	5
gga	gga	0.0005038291012	5
; Host name	nic42
; Job started	2011_11_26.223259
; Job done	2011_11_26.223300
; Seconds	0.17