; 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/Coccidioides_immitis_RMSCC_2394_MO/genome/Coccidioides_immitis_RMSCC_2394_MO_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Coccidioides_immitis_RMSCC_2394_MO/genome/Coccidioides_immitis_RMSCC_2394_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/Coccidioides_immitis_RMSCC_2394_MO/genome/Coccidioides_immitis_RMSCC_2394_MO_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Coccidioides_immitis_RMSCC_2394_MO/genome/Coccidioides_immitis_RMSCC_2394_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      	10406
; 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
tga	tga	0.2457236209879	2557
taa	taa	0.1638477801268	1705
tag	tag	0.1232942533154	1283
aaa	aaa	0.0456467422641	475
caa	caa	0.0240246011916	250
gaa	gaa	0.0226792235249	236
tca	tca	0.0159523351912	166
ata	ata	0.0137420718816	143
aca	aca	0.0130693830482	136
tta	tta	0.0124927926196	130
ttt	ttt	0.0118201037863	123
gga	gga	0.0117240053815	122
aga	aga	0.0115318085720	120
cca	cca	0.0114357101672	119
gca	gca	0.0113396117624	118
gta	gta	0.0113396117624	118
cta	cta	0.0098020372862	102
atg	atg	0.0094176436671	98
ttc	ttc	0.0091293484528	95
aag	aag	0.0091293484528	95
cga	cga	0.0087449548337	91
ttg	ttg	0.0087449548337	91
gag	gag	0.0082644628099	86
gtg	gtg	0.0070151835480	73
ctg	ctg	0.0069190851432	72
tcc	tcc	0.0063424947146	66
tgc	tgc	0.0061502979051	64
tat	tat	0.0061502979051	64
gtc	gtc	0.0060541995003	63
tgg	tgg	0.0059581010955	62
gat	gat	0.0058620026908	61
cag	cag	0.0058620026908	61
atc	atc	0.0057659042860	60
ctt	ctt	0.0055737074765	58
gtt	gtt	0.0053815106669	56
gcg	gcg	0.0052854122622	55
tac	tac	0.0052854122622	55
ctc	ctc	0.0052854122622	55
tcg	tcg	0.0049971170479	52
agc	agc	0.0049971170479	52
ggc	ggc	0.0049010186431	51
ggg	ggg	0.0049010186431	51
aac	aac	0.0048049202383	50
tct	tct	0.0048049202383	50
ccc	ccc	0.0048049202383	50
agg	agg	0.0046127234288	48
att	att	0.0046127234288	48
cac	cac	0.0046127234288	48
gac	gac	0.0042283298097	44
acc	acc	0.0039400345954	41
cct	cct	0.0039400345954	41
cgg	cgg	0.0038439361907	40
cat	cat	0.0037478377859	39
aat	aat	0.0036517393811	38
ccg	ccg	0.0032673457621	34
gcc	gcc	0.0032673457621	34
cgc	cgc	0.0031712473573	33
tgt	tgt	0.0029790505478	31
acg	acg	0.0029790505478	31
gct	gct	0.0026907553335	28
agt	agt	0.0023063617144	24
ggt	ggt	0.0022102633096	23
act	act	0.0022102633096	23
cgt	cgt	0.0017297712858	18
; Host name	nic47
; Job started	2011_11_26.223303
; Job done	2011_11_26.223303
; Seconds	0.17