; 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/Verticillium_albo-atrum_VaMs.102_MO/genome/Verticillium_albo-atrum_VaMs.102_MO_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Verticillium_albo-atrum_VaMs.102_MO/genome/Verticillium_albo-atrum_VaMs.102_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/Verticillium_albo-atrum_VaMs.102_MO/genome/Verticillium_albo-atrum_VaMs.102_MO_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Verticillium_albo-atrum_VaMs.102_MO/genome/Verticillium_albo-atrum_VaMs.102_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      	9927
; 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	0.9003727208623	8938
atc	atc	0.0057419159867	57
acc	acc	0.0049360330412	49
aca	aca	0.0045330915684	45
aac	aac	0.0037272086229	37
gac	gac	0.0035257378866	35
gcc	gcc	0.0031227964138	31
acg	acg	0.0030220610456	30
gca	gca	0.0028205903093	28
gtc	gtc	0.0025183842047	25
gaa	gaa	0.0025183842047	25
gcg	gcg	0.0023169134683	23
gag	gag	0.0022161781001	22
aat	aat	0.0019139719956	19
cga	cga	0.0019139719956	19
ggc	ggc	0.0019139719956	19
agg	agg	0.0018132366274	18
gct	gct	0.0018132366274	18
agc	agc	0.0018132366274	18
aaa	aaa	0.0018132366274	18
ctc	ctc	0.0018132366274	18
cac	cac	0.0018132366274	18
gat	gat	0.0017125012592	17
agt	agt	0.0017125012592	17
tct	tct	0.0016117658910	16
ggg	ggg	0.0016117658910	16
act	act	0.0015110305228	15
aga	aga	0.0015110305228	15
tca	tca	0.0015110305228	15
cat	cat	0.0014102951546	14
gtg	gtg	0.0014102951546	14
cca	cca	0.0014102951546	14
caa	caa	0.0013095597864	13
ccg	ccg	0.0013095597864	13
ggt	ggt	0.0013095597864	13
tcc	tcc	0.0013095597864	13
ccc	ccc	0.0013095597864	13
gga	gga	0.0013095597864	13
ctt	ctt	0.0012088244183	12
cct	cct	0.0012088244183	12
ctg	ctg	0.0012088244183	12
cag	cag	0.0012088244183	12
aag	aag	0.0011080890501	11
ata	ata	0.0011080890501	11
gtt	gtt	0.0011080890501	11
tgc	tgc	0.0009066183137	9
tga	tga	0.0009066183137	9
tac	tac	0.0008058829455	8
tcg	tcg	0.0008058829455	8
ttg	ttg	0.0008058829455	8
cgg	cgg	0.0008058829455	8
att	att	0.0007051475773	7
cgt	cgt	0.0007051475773	7
cta	cta	0.0007051475773	7
gta	gta	0.0007051475773	7
ttc	ttc	0.0006044122091	6
ttt	ttt	0.0005036768409	5
tgt	tgt	0.0003022061046	3
cgc	cgc	0.0003022061046	3
tat	tat	0.0003022061046	3
tta	tta	0.0002014707364	2
tgg	tgg	0.0002014707364	2
taa	taa	0.0002014707364	2
tag	tag	0.0001007353682	1
; Host name	nic42
; Job started	2011_11_26.223249
; Job done	2011_11_26.223249
; Seconds	0.18