; 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/Scheffersomyces_stipitis_CBS_6054_MO/genome/Scheffersomyces_stipitis_CBS_6054_MO_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Scheffersomyces_stipitis_CBS_6054_MO/genome/Scheffersomyces_stipitis_CBS_6054_MO_stop_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/Scheffersomyces_stipitis_CBS_6054_MO/genome/Scheffersomyces_stipitis_CBS_6054_MO_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Scheffersomyces_stipitis_CBS_6054_MO/genome/Scheffersomyces_stipitis_CBS_6054_MO_stop_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      	4540
; 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
tag	tag	0.3660792951542	1662
taa	taa	0.2947136563877	1338
tga	tga	0.1819383259912	826
aag	aag	0.0074889867841	34
gat	gat	0.0063876651982	29
tat	tat	0.0063876651982	29
gaa	gaa	0.0061674008811	28
aaa	aaa	0.0061674008811	28
aat	aat	0.0059471365639	27
ttc	ttc	0.0057268722467	26
ttt	ttt	0.0057268722467	26
ttg	ttg	0.0055066079295	25
tct	tct	0.0052863436123	24
att	att	0.0048458149780	22
gac	gac	0.0046255506608	21
cag	cag	0.0041850220264	19
tgg	tgg	0.0039647577093	18
tac	tac	0.0037444933921	17
gag	gag	0.0035242290749	16
aac	aac	0.0033039647577	15
caa	caa	0.0033039647577	15
atg	atg	0.0030837004405	14
tgt	tgt	0.0028634361233	13
act	act	0.0028634361233	13
cct	cct	0.0026431718062	12
gtt	gtt	0.0026431718062	12
tta	tta	0.0024229074890	11
atc	atc	0.0024229074890	11
gct	gct	0.0022026431718	10
tgc	tgc	0.0022026431718	10
cat	cat	0.0022026431718	10
gtc	gtc	0.0022026431718	10
ata	ata	0.0022026431718	10
agg	agg	0.0019823788546	9
tcg	tcg	0.0019823788546	9
agc	agc	0.0019823788546	9
cca	cca	0.0017621145374	8
ctt	ctt	0.0017621145374	8
cgt	cgt	0.0017621145374	8
gca	gca	0.0017621145374	8
aga	aga	0.0017621145374	8
tcc	tcc	0.0015418502203	7
agt	agt	0.0015418502203	7
ggc	ggc	0.0013215859031	6
acc	acc	0.0013215859031	6
ctc	ctc	0.0013215859031	6
tca	tca	0.0013215859031	6
gcc	gcc	0.0013215859031	6
acg	acg	0.0011013215859	5
aca	aca	0.0011013215859	5
gga	gga	0.0011013215859	5
cac	cac	0.0011013215859	5
ctg	ctg	0.0008810572687	4
ccg	ccg	0.0008810572687	4
gtg	gtg	0.0008810572687	4
cgc	cgc	0.0006607929515	3
ccc	ccc	0.0006607929515	3
ggt	ggt	0.0006607929515	3
cta	cta	0.0004405286344	2
cga	cga	0.0004405286344	2
gcg	gcg	0.0002202643172	1
gta	gta	0.0002202643172	1
ggg	ggg	0.0002202643172	1
; Host name	nic54
; Job started	2011_11_26.225011
; Job done	2011_11_26.225011
; Seconds	0.15