; 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/Trichoderma_atroviride/genome/Trichoderma_atroviride_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Trichoderma_atroviride/genome/Trichoderma_atroviride_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/Trichoderma_atroviride/genome/Trichoderma_atroviride_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Trichoderma_atroviride/genome/Trichoderma_atroviride_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      	12114
; 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
taa	taa	0.3387815750371	4104
tga	tga	0.3024599636784	3664
tag	tag	0.2478124484068	3002
cca	cca	0.0225359088658	273
gag	gag	0.0052005943536	63
gat	gat	0.0037147102526	45
gaa	gaa	0.0034670629024	42
aag	aag	0.0034670629024	42
gac	gac	0.0030543173188	37
gca	gca	0.0024764735017	30
tgg	tgg	0.0023939243850	29
ggc	ggc	0.0023113752683	28
ctg	ctg	0.0023113752683	28
gga	gga	0.0021462770348	26
atc	atc	0.0019811788014	24
gct	gct	0.0018160805679	22
ttg	ttg	0.0018160805679	22
aaa	aaa	0.0018160805679	22
cct	cct	0.0017335314512	21
agg	agg	0.0016509823345	20
att	att	0.0016509823345	20
ctt	ctt	0.0016509823345	20
gcg	gcg	0.0015684332178	19
agc	agc	0.0015684332178	19
cag	cag	0.0015684332178	19
ctc	ctc	0.0015684332178	19
cgg	cgg	0.0015684332178	19
cga	cga	0.0014858841010	18
ttt	ttt	0.0014858841010	18
aga	aga	0.0014858841010	18
atg	atg	0.0014033349843	17
ttc	ttc	0.0013207858676	16
gtg	gtg	0.0013207858676	16
aac	aac	0.0013207858676	16
ggg	ggg	0.0013207858676	16
aat	aat	0.0012382367509	15
ggt	ggt	0.0012382367509	15
tct	tct	0.0012382367509	15
gtt	gtt	0.0012382367509	15
gcc	gcc	0.0012382367509	15
tat	tat	0.0011556876341	14
caa	caa	0.0010731385174	13
tac	tac	0.0010731385174	13
ccc	ccc	0.0010731385174	13
tca	tca	0.0010731385174	13
cgt	cgt	0.0009905894007	12
cta	cta	0.0009080402840	11
ccg	ccg	0.0009080402840	11
tcg	tcg	0.0009080402840	11
gtc	gtc	0.0009080402840	11
gta	gta	0.0009080402840	11
tta	tta	0.0008254911672	10
cat	cat	0.0008254911672	10
ata	ata	0.0008254911672	10
cgc	cgc	0.0007429420505	9
agt	agt	0.0007429420505	9
acg	acg	0.0006603929338	8
aca	aca	0.0005778438171	7
tgt	tgt	0.0004952947003	6
acc	acc	0.0004952947003	6
act	act	0.0004952947003	6
tcc	tcc	0.0004127455836	5
tgc	tgc	0.0002476473502	3
cac	cac	0.0002476473502	3
; Host name	nic43
; Job started	2011_11_26.223341
; Job done	2011_11_26.223347
; Seconds	0.16