; 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/Cryptococcus_neoformans_var._neoformans_JEC21_MO/genome/Cryptococcus_neoformans_var._neoformans_JEC21_MO_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Cryptococcus_neoformans_var._neoformans_JEC21_MO/genome/Cryptococcus_neoformans_var._neoformans_JEC21_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/Cryptococcus_neoformans_var._neoformans_JEC21_MO/genome/Cryptococcus_neoformans_var._neoformans_JEC21_MO_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Cryptococcus_neoformans_var._neoformans_JEC21_MO/genome/Cryptococcus_neoformans_var._neoformans_JEC21_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      	6273
; 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	0.1128646580583	708
tag	tag	0.1050534034752	659
tga	tga	0.1001115893512	628
ttt	ttt	0.0253467240555	159
tat	tat	0.0218396301610	137
atg	atg	0.0212019767256	133
ata	ata	0.0207237366491	130
cat	cat	0.0196078431373	123
att	att	0.0192890164196	121
ttg	ttg	0.0188107763431	118
tta	tta	0.0180137095489	113
tca	tca	0.0180137095489	113
tgt	tgt	0.0178542961900	112
gta	gta	0.0164195759605	103
tct	tct	0.0159413358839	100
aga	aga	0.0151442690897	95
aat	aat	0.0146660290132	92
atc	atc	0.0145066156544	91
aaa	aaa	0.0143472022956	90
ctt	ctt	0.0141877889367	89
gca	gca	0.0141877889367	89
gat	gat	0.0141877889367	89
tgc	tgc	0.0137095488602	86
aca	aca	0.0133907221425	84
gtt	gtt	0.0132313087837	83
caa	caa	0.0122748286306	77
tcg	tcg	0.0121154152718	76
tac	tac	0.0119560019130	75
gaa	gaa	0.0119560019130	75
cag	cag	0.0111589351188	70
aag	aag	0.0108401084011	68
agt	agt	0.0103618683246	65
ctg	ctg	0.0102024549657	64
ttc	ttc	0.0098836282480	62
cta	cta	0.0097242148892	61
cga	cga	0.0097242148892	61
gct	gct	0.0086083213773	54
tgg	tgg	0.0086083213773	54
gtg	gtg	0.0086083213773	54
cac	cac	0.0086083213773	54
cca	cca	0.0084489080185	53
agc	agc	0.0079706679420	50
aac	aac	0.0079706679420	50
agg	agg	0.0078112545831	49
gag	gag	0.0078112545831	49
act	act	0.0076518412243	48
ctc	ctc	0.0076518412243	48
gac	gac	0.0074924278655	47
gtc	gtc	0.0071736011478	45
ggt	ggt	0.0070141877889	44
tcc	tcc	0.0066953610713	42
acg	acg	0.0065359477124	41
acc	acc	0.0065359477124	41
cgt	cgt	0.0062171209947	39
gcc	gcc	0.0062171209947	39
gga	gga	0.0057388809182	36
gcg	gcg	0.0054200542005	34
ggc	ggc	0.0052606408417	33
cct	cct	0.0052606408417	33
cgg	cgg	0.0049418141240	31
ccc	ccc	0.0047824007652	30
ggg	ggg	0.0047824007652	30
cgc	cgc	0.0038259206121	24
ccg	ccg	0.0035070938945	22
; Host name	nic48
; Job started	2011_11_26.230547
; Job done	2011_11_26.230547
; Seconds	0.15