; 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_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Paracoccidioides_brasiliensis_Pb18_MO/genome/Paracoccidioides_brasiliensis_Pb18_MO_start_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_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Paracoccidioides_brasiliensis_Pb18_MO/genome/Paracoccidioides_brasiliensis_Pb18_MO_start_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
atg	atg	0.7946868201076	6940
caa	caa	0.0095041795488	83
ctt	ctt	0.0092751631742	81
ctc	ctc	0.0080155731135	70
aaa	aaa	0.0077865567388	68
cca	cca	0.0058399175541	51
cga	cga	0.0052673766174	46
cac	cac	0.0052673766174	46
ccc	ccc	0.0051528684301	45
gtt	gtt	0.0051528684301	45
ctg	ctg	0.0050383602428	44
cag	cag	0.0050383602428	44
gga	gga	0.0046948356808	41
ttt	ttt	0.0043513111187	38
cat	cat	0.0042368029314	37
gaa	gaa	0.0042368029314	37
cgc	cgc	0.0040077865567	35
att	att	0.0038932783694	34
tct	tct	0.0038932783694	34
atc	atc	0.0037787701821	33
aac	aac	0.0037787701821	33
gca	gca	0.0036642619947	32
ata	ata	0.0036642619947	32
gac	gac	0.0034352456201	30
cgg	cgg	0.0034352456201	30
aca	aca	0.0033207374327	29
gtc	gtc	0.0033207374327	29
tcc	tcc	0.0033207374327	29
gat	gat	0.0033207374327	29
gct	gct	0.0032062292454	28
aat	aat	0.0030917210581	27
ggg	ggg	0.0030917210581	27
cta	cta	0.0029772128707	26
acc	acc	0.0029772128707	26
gag	gag	0.0028627046834	25
act	act	0.0026336883087	23
tac	tac	0.0025191801214	22
ttg	ttg	0.0025191801214	22
ccg	ccg	0.0024046719340	21
tat	tat	0.0024046719340	21
ttc	ttc	0.0022901637467	20
agc	agc	0.0022901637467	20
tca	tca	0.0022901637467	20
agg	agg	0.0021756555594	19
acg	acg	0.0021756555594	19
cct	cct	0.0021756555594	19
gtg	gtg	0.0021756555594	19
tta	tta	0.0020611473720	18
tgc	tgc	0.0019466391847	17
aga	aga	0.0019466391847	17
gcc	gcc	0.0019466391847	17
tga	tga	0.0018321309974	16
ggt	ggt	0.0016031146227	14
gcg	gcg	0.0014886064354	13
ggc	ggc	0.0014886064354	13
taa	taa	0.0013740982480	12
tgt	tgt	0.0012595900607	11
tcg	tcg	0.0011450818734	10
aag	aag	0.0011450818734	10
cgt	cgt	0.0010305736860	9
tgg	tgg	0.0009160654987	8
gta	gta	0.0009160654987	8
agt	agt	0.0006870491240	6
tag	tag	0.0005725409367	5
; Host name	nic45
; Job started	2011_11_26.223240
; Job done	2011_11_26.223240
; Seconds	0.18