; 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/Puccinia_graminis_f._sp._tritici_MO/genome/Puccinia_graminis_f._sp._tritici_MO_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Puccinia_graminis_f._sp._tritici_MO/genome/Puccinia_graminis_f._sp._tritici_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/Puccinia_graminis_f._sp._tritici_MO/genome/Puccinia_graminis_f._sp._tritici_MO_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Puccinia_graminis_f._sp._tritici_MO/genome/Puccinia_graminis_f._sp._tritici_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      	18358
; 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	0.8916548643643	16369
gac	gac	0.0109489051095	201
aac	aac	0.0063187711080	116
ggg	ggg	0.0059919381196	110
gag	gag	0.0058285216254	107
acc	acc	0.0054472164724	100
atc	atc	0.0050659113193	93
gaa	gaa	0.0050114391546	92
gcc	gcc	0.0046301340015	85
aag	aag	0.0040854123543	75
ggc	ggc	0.0036496350365	67
gga	gga	0.0032683298834	60
agc	agc	0.0032683298834	60
gat	gat	0.0031593855540	58
aca	aca	0.0031049133893	57
act	act	0.0028325525656	52
aaa	aaa	0.0026691360715	49
agg	agg	0.0023423030831	43
gct	gct	0.0022333587537	41
gcg	gcg	0.0020699422595	38
aga	aga	0.0019609979301	36
aat	aat	0.0019065257653	35
gca	gca	0.0017975814359	33
gtg	gtg	0.0017431092712	32
gtc	gtc	0.0015796927770	29
att	att	0.0015252206123	28
ata	ata	0.0014162762828	26
gtt	gtt	0.0013073319534	24
caa	caa	0.0010894432945	20
ggt	ggt	0.0010894432945	20
cac	cac	0.0008715546356	16
agt	agt	0.0008170824709	15
acg	acg	0.0007626103061	14
gta	gta	0.0007081381414	13
ctt	ctt	0.0006536659767	12
ttt	ttt	0.0006536659767	12
cat	cat	0.0005991938120	11
cca	cca	0.0005447216472	10
ctc	ctc	0.0004902494825	9
ccc	ccc	0.0004357773178	8
cga	cga	0.0003813051531	7
ccg	ccg	0.0003813051531	7
tgt	tgt	0.0003268329883	6
tcc	tcc	0.0003268329883	6
tac	tac	0.0002723608236	5
tcg	tcg	0.0002723608236	5
ttg	ttg	0.0002723608236	5
ttc	ttc	0.0002178886589	4
cgt	cgt	0.0002178886589	4
cag	cag	0.0002178886589	4
cct	cct	0.0002178886589	4
tca	tca	0.0002178886589	4
tat	tat	0.0002178886589	4
cta	cta	0.0001634164942	3
tgc	tgc	0.0001634164942	3
tgg	tgg	0.0001634164942	3
cgg	cgg	0.0001634164942	3
ctg	ctg	0.0000544721647	1
cgc	cgc	0.0000544721647	1
tag	tag	0.0000544721647	1
taa	taa	0.0000544721647	1
tga	tga	0.0000544721647	1
; Host name	nic42
; Job started	2011_11_26.230549
; Job done	2011_11_26.230549
; Seconds	0.16