; oligo-analysis  -quick -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i /software/CC/bio/opt/rsat/rsa-tools//data/genomes/Pichia_stipitis_CBS_6054/genome/Pichia_stipitis_CBS_6054_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//data/genomes/Pichia_stipitis_CBS_6054/genome/Pichia_stipitis_CBS_6054_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/data/genomes/Pichia_stipitis_CBS_6054/genome/Pichia_stipitis_CBS_6054_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/data/genomes/Pichia_stipitis_CBS_6054/genome/Pichia_stipitis_CBS_6054_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      	5104
; 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	0.9874608150470	5040
aga	aga	0.0009796238245	5
agg	agg	0.0005877742947	3
caa	caa	0.0005877742947	3
taa	taa	0.0005877742947	3
aaa	aaa	0.0005877742947	3
ttg	ttg	0.0005877742947	3
ata	ata	0.0005877742947	3
agt	agt	0.0005877742947	3
ttc	ttc	0.0003918495298	2
cca	cca	0.0003918495298	2
tta	tta	0.0003918495298	2
acg	acg	0.0003918495298	2
cta	cta	0.0003918495298	2
ccc	ccc	0.0003918495298	2
ggc	ggc	0.0003918495298	2
acc	acc	0.0003918495298	2
cat	cat	0.0003918495298	2
act	act	0.0003918495298	2
cct	cct	0.0003918495298	2
gaa	gaa	0.0001959247649	1
gat	gat	0.0001959247649	1
tct	tct	0.0001959247649	1
tgc	tgc	0.0001959247649	1
aca	aca	0.0001959247649	1
ccg	ccg	0.0001959247649	1
cag	cag	0.0001959247649	1
tcg	tcg	0.0001959247649	1
aag	aag	0.0001959247649	1
tcc	tcc	0.0001959247649	1
gtg	gtg	0.0001959247649	1
tga	tga	0.0001959247649	1
cgg	cgg	0.0001959247649	1
gtt	gtt	0.0001959247649	1
agc	agc	0.0001959247649	1
atc	atc	0.0001959247649	1
; Host name	nic47
; Job started	2011_11_26.224931
; Job done	2011_11_26.224931
; Seconds	0.15