; 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/Paracoccidioides_brasiliensis_Pb18_MO/genome/Paracoccidioides_brasiliensis_Pb18_MO_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Paracoccidioides_brasiliensis_Pb18_MO/genome/Paracoccidioides_brasiliensis_Pb18_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/Paracoccidioides_brasiliensis_Pb18_MO/genome/Paracoccidioides_brasiliensis_Pb18_MO_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Paracoccidioides_brasiliensis_Pb18_MO/genome/Paracoccidioides_brasiliensis_Pb18_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      	8733
; 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	0.3408908736975	2977
taa	taa	0.2412687507157	2107
tag	tag	0.2053131798924	1793
ttt	ttt	0.0128249169816	112
att	att	0.0096186877362	84
tat	tat	0.0088171304248	77
aat	aat	0.0069849994275	61
aaa	aaa	0.0069849994275	61
ata	ata	0.0060689339288	53
atg	atg	0.0058399175541	51
ttc	ttc	0.0054963929921	48
tgt	tgt	0.0053818848048	47
ctt	ctt	0.0050383602428	44
tta	tta	0.0048093438681	42
atc	atc	0.0048093438681	42
ttg	ttg	0.0046948356808	41
cat	cat	0.0043513111187	38
tct	tct	0.0043513111187	38
gtt	gtt	0.0043513111187	38
aga	aga	0.0040077865567	35
caa	caa	0.0037787701821	33
cct	cct	0.0036642619947	32
gtg	gtg	0.0036642619947	32
tac	tac	0.0035497538074	31
tgg	tgg	0.0034352456201	30
gat	gat	0.0034352456201	30
ccc	ccc	0.0034352456201	30
aca	aca	0.0033207374327	29
aac	aac	0.0033207374327	29
tcc	tcc	0.0032062292454	28
tca	tca	0.0032062292454	28
gta	gta	0.0029772128707	26
gaa	gaa	0.0028627046834	25
cca	cca	0.0028627046834	25
ctc	ctc	0.0028627046834	25
aag	aag	0.0028627046834	25
tgc	tgc	0.0027481964960	24
gct	gct	0.0026336883087	23
tcg	tcg	0.0026336883087	23
ggg	ggg	0.0025191801214	22
cgt	cgt	0.0024046719340	21
acc	acc	0.0024046719340	21
gac	gac	0.0024046719340	21
gga	gga	0.0024046719340	21
cac	cac	0.0024046719340	21
ggt	ggt	0.0022901637467	20
gag	gag	0.0022901637467	20
agg	agg	0.0021756555594	19
gtc	gtc	0.0021756555594	19
cta	cta	0.0020611473720	18
act	act	0.0020611473720	18
ctg	ctg	0.0019466391847	17
cag	cag	0.0018321309974	16
acg	acg	0.0017176228100	15
cga	cga	0.0017176228100	15
agc	agc	0.0017176228100	15
gcc	gcc	0.0017176228100	15
agt	agt	0.0016031146227	14
gcg	gcg	0.0014886064354	13
gca	gca	0.0014886064354	13
ccg	ccg	0.0013740982480	12
ggc	ggc	0.0012595900607	11
cgg	cgg	0.0011450818734	10
cgc	cgc	0.0010305736860	9
; Host name	nic45
; Job started	2011_11_26.223253
; Job done	2011_11_26.223254
; Seconds	0.18