; 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_posadasii_RMSCC_3488_MO/genome/Coccidioides_posadasii_RMSCC_3488_MO_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Coccidioides_posadasii_RMSCC_3488_MO/genome/Coccidioides_posadasii_RMSCC_3488_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_posadasii_RMSCC_3488_MO/genome/Coccidioides_posadasii_RMSCC_3488_MO_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Coccidioides_posadasii_RMSCC_3488_MO/genome/Coccidioides_posadasii_RMSCC_3488_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      	9930
; 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	0.2528700906344	2511
taa	taa	0.1644511581067	1633
tag	tag	0.1259818731118	1251
aaa	aaa	0.0425981873112	423
caa	caa	0.0246727089627	245
gaa	gaa	0.0221550855992	220
tca	tca	0.0162134944612	161
ata	ata	0.0146022155086	145
gca	gca	0.0135951661631	135
tta	tta	0.0131923464250	131
aga	aga	0.0124874118832	124
ttt	ttt	0.0115810674723	115
aca	aca	0.0113796576032	113
gga	gga	0.0108761329305	108
gta	gta	0.0106747230614	106
cca	cca	0.0101711983887	101
ttg	ttg	0.0094662638469	94
cta	cta	0.0093655589124	93
ttc	ttc	0.0085599194361	85
aag	aag	0.0083585095670	83
cga	cga	0.0080563947633	80
gag	gag	0.0080563947633	80
atg	atg	0.0072507552870	72
gtg	gtg	0.0070493454179	70
tcc	tcc	0.0065458207452	65
tgg	tgg	0.0062437059416	62
atc	atc	0.0062437059416	62
tgc	tgc	0.0062437059416	62
ctg	ctg	0.0061430010070	61
tat	tat	0.0060422960725	60
tct	tct	0.0058408862034	58
ctt	ctt	0.0055387713998	55
gat	gat	0.0055387713998	55
gcg	gcg	0.0054380664653	54
gtt	gtt	0.0052366565962	52
agc	agc	0.0051359516616	51
ggg	ggg	0.0051359516616	51
ggc	ggc	0.0050352467271	50
gtc	gtc	0.0050352467271	50
cag	cag	0.0050352467271	50
ccc	ccc	0.0049345417925	49
att	att	0.0048338368580	48
ctc	ctc	0.0048338368580	48
cac	cac	0.0048338368580	48
tac	tac	0.0045317220544	45
gac	gac	0.0042296072508	42
tcg	tcg	0.0041289023162	41
aac	aac	0.0041289023162	41
gcc	gcc	0.0041289023162	41
agg	agg	0.0039274924471	39
aat	aat	0.0039274924471	39
cat	cat	0.0039274924471	39
cct	cct	0.0037260825780	37
acc	acc	0.0035246727090	35
cgg	cgg	0.0035246727090	35
tgt	tgt	0.0030211480363	30
ccg	ccg	0.0030211480363	30
cgc	cgc	0.0028197381672	28
act	act	0.0027190332326	27
acg	acg	0.0026183282981	26
agt	agt	0.0024169184290	24
gct	gct	0.0023162134945	23
cgt	cgt	0.0019133937563	19
ggt	ggt	0.0019133937563	19
; Host name	nic47
; Job started	2011_11_26.223303
; Job done	2011_11_26.223304
; Seconds	0.18