; 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/Coccidioides_posadasii_RMSCC_3488_MO/genome/Coccidioides_posadasii_RMSCC_3488_MO_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Coccidioides_posadasii_RMSCC_3488_MO/genome/Coccidioides_posadasii_RMSCC_3488_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/Coccidioides_posadasii_RMSCC_3488_MO/genome/Coccidioides_posadasii_RMSCC_3488_MO_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Coccidioides_posadasii_RMSCC_3488_MO/genome/Coccidioides_posadasii_RMSCC_3488_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      	9938
; 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	0.5335077480378	5302
ctc	ctc	0.0233447373717	232
ctt	ctt	0.0193197826524	192
atc	atc	0.0177098007647	176
cga	cga	0.0176091768968	175
caa	caa	0.0169048098209	168
cgc	cgc	0.0152948279332	152
cag	cag	0.0128798551016	128
ctg	ctg	0.0122761118937	122
gga	gga	0.0120748641578	120
aaa	aaa	0.0116723686859	116
att	att	0.0112698732139	112
ccc	ccc	0.0110686254780	110
cac	cac	0.0108673777420	108
ttt	ttt	0.0106661300060	106
gtt	gtt	0.0104648822701	104
cct	cct	0.0095592674582	95
cgg	cgg	0.0090561481183	90
ggc	ggc	0.0089555242504	89
gtc	gtc	0.0087542765144	87
cca	cca	0.0087542765144	87
ttc	ttc	0.0077480378346	77
gaa	gaa	0.0077480378346	77
tga	tga	0.0077480378346	77
gac	gac	0.0076474139666	76
ccg	ccg	0.0072449184947	72
gat	gat	0.0072449184947	72
agc	agc	0.0071442946267	71
cat	cat	0.0070436707587	70
ggg	ggg	0.0070436707587	70
cta	cta	0.0065405514188	65
tct	tct	0.0062386798149	62
aac	aac	0.0060374320789	60
gcc	gcc	0.0060374320789	60
cgt	cgt	0.0059368082109	59
aga	aga	0.0058361843429	58
gca	gca	0.0056349366070	56
tgc	tgc	0.0056349366070	56
ata	ata	0.0056349366070	56
gag	gag	0.0055343127390	55
gct	gct	0.0054336888710	54
tca	tca	0.0051318172671	51
tcg	tcg	0.0048299456631	48
aat	aat	0.0047293217951	47
gtg	gtg	0.0047293217951	47
tcc	tcc	0.0044274501912	44
ttg	ttg	0.0044274501912	44
gta	gta	0.0043268263232	43
ggt	ggt	0.0041255785872	41
tgt	tgt	0.0038237069833	38
acg	acg	0.0037230831153	37
aca	aca	0.0035218353794	35
acc	acc	0.0032199637754	32
tgg	tgg	0.0030187160394	30
tat	tat	0.0029180921715	29
gcg	gcg	0.0027168444355	27
aag	aag	0.0027168444355	27
act	act	0.0025155966995	25
taa	taa	0.0025155966995	25
tac	tac	0.0021131012276	21
agg	agg	0.0020124773596	20
tta	tta	0.0019118534916	19
agt	agt	0.0019118534916	19
tag	tag	0.0015093580197	15
; Host name	nic47
; Job started	2011_11_26.223249
; Job done	2011_11_26.223249
; Seconds	0.17