; 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/Ajellomyces_capsulatus_NAm1_MO/genome/Ajellomyces_capsulatus_NAm1_MO_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Ajellomyces_capsulatus_NAm1_MO/genome/Ajellomyces_capsulatus_NAm1_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/Ajellomyces_capsulatus_NAm1_MO/genome/Ajellomyces_capsulatus_NAm1_MO_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Ajellomyces_capsulatus_NAm1_MO/genome/Ajellomyces_capsulatus_NAm1_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      	9231
; 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	0.3515328783447	3245
taa	taa	0.2282526270177	2107
tag	tag	0.2013866320009	1859
ttt	ttt	0.0150579568844	139
ttc	ttc	0.0123496912577	114
aaa	aaa	0.0090997725057	84
tat	tat	0.0076914743798	71
ttg	ttg	0.0072581518795	67
tcc	tcc	0.0067164987542	62
ctc	ctc	0.0064998375041	60
att	att	0.0058498537537	54
tct	tct	0.0056331925035	52
aat	aat	0.0047665475030	44
tgg	tgg	0.0046582168779	43
ctt	ctt	0.0044415556278	41
cat	cat	0.0044415556278	41
gtt	gtt	0.0043332250027	40
atg	atg	0.0042248943776	39
tgt	tgt	0.0040082331275	37
ctg	ctg	0.0040082331275	37
ata	ata	0.0038999025024	36
aag	aag	0.0037915718774	35
acc	acc	0.0035749106272	33
atc	atc	0.0034665800022	32
gat	gat	0.0034665800022	32
gag	gag	0.0033582493771	31
aac	aac	0.0033582493771	31
tgc	tgc	0.0033582493771	31
gtc	gtc	0.0032499187520	30
tac	tac	0.0031415881270	29
gtg	gtg	0.0031415881270	29
ccc	ccc	0.0031415881270	29
cac	cac	0.0031415881270	29
act	act	0.0030332575019	28
gaa	gaa	0.0029249268768	27
cag	cag	0.0028165962518	26
tca	tca	0.0028165962518	26
agg	agg	0.0027082656267	25
cct	cct	0.0027082656267	25
gcg	gcg	0.0025999350016	24
tta	tta	0.0024916043766	23
caa	caa	0.0023832737515	22
gac	gac	0.0023832737515	22
ggg	ggg	0.0023832737515	22
cgg	cgg	0.0022749431264	21
gcc	gcc	0.0022749431264	21
gta	gta	0.0021666125014	20
gct	gct	0.0020582818763	19
cgt	cgt	0.0020582818763	19
cca	cca	0.0020582818763	19
aca	aca	0.0019499512512	18
ggt	ggt	0.0019499512512	18
tcg	tcg	0.0019499512512	18
agc	agc	0.0019499512512	18
agt	agt	0.0017332900011	16
ccg	ccg	0.0016249593760	15
cta	cta	0.0015166287509	14
gga	gga	0.0015166287509	14
ggc	ggc	0.0014082981259	13
aga	aga	0.0014082981259	13
acg	acg	0.0012999675008	12
cgc	cgc	0.0012999675008	12
gca	gca	0.0011916368757	11
cga	cga	0.0007583143755	7
; Host name	nic48
; Job started	2011_11_26.223411
; Job done	2011_11_26.223412
; Seconds	0.16