; 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/Aspergillus_flavus_MO/genome/Aspergillus_flavus_MO_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Aspergillus_flavus_MO/genome/Aspergillus_flavus_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/Aspergillus_flavus_MO/genome/Aspergillus_flavus_MO_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Aspergillus_flavus_MO/genome/Aspergillus_flavus_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      	12470
; 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	0.3277465918204	4087
taa	taa	0.2411387329591	3007
tag	tag	0.2397754611067	2990
ttc	ttc	0.0094627105052	118
ttg	ttg	0.0075380914194	94
atg	atg	0.0066559743384	83
tgg	tgg	0.0054530874098	68
tct	tct	0.0051323175621	64
gtg	gtg	0.0050521251002	63
atc	atc	0.0049719326383	62
ttt	ttt	0.0048917401764	61
ctc	ctc	0.0048917401764	61
tgc	tgc	0.0048115477145	60
ctt	ctt	0.0043303929431	54
tcc	tcc	0.0043303929431	54
att	att	0.0042502004812	53
gtc	gtc	0.0040898155573	51
tat	tat	0.0040898155573	51
acc	acc	0.0040096230954	50
gac	gac	0.0040096230954	50
tac	tac	0.0039294306335	49
agc	agc	0.0036888532478	46
ctg	ctg	0.0036888532478	46
ccc	ccc	0.0036888532478	46
gtt	gtt	0.0033680834002	42
tgt	tgt	0.0032878909383	41
gcc	gcc	0.0032878909383	41
tta	tta	0.0032076984763	40
cgc	cgc	0.0031275060144	39
tcg	tcg	0.0030473135525	38
agt	agt	0.0030473135525	38
ggc	ggc	0.0028869286287	36
cat	cat	0.0028869286287	36
cct	cct	0.0028869286287	36
agg	agg	0.0028067361668	35
gag	gag	0.0027265437049	34
ggg	ggg	0.0026463512430	33
aga	aga	0.0025661587811	32
act	act	0.0024057738573	30
gcg	gcg	0.0023255813953	29
gct	gct	0.0023255813953	29
acg	acg	0.0023255813953	29
aaa	aaa	0.0023255813953	29
ccg	ccg	0.0022453889334	28
ggt	ggt	0.0022453889334	28
ata	ata	0.0022453889334	28
cag	cag	0.0021651964715	27
aat	aat	0.0020850040096	26
gat	gat	0.0020850040096	26
aag	aag	0.0020850040096	26
aca	aca	0.0018444266239	23
gaa	gaa	0.0018444266239	23
aac	aac	0.0018444266239	23
tca	tca	0.0018444266239	23
cac	cac	0.0017642341620	22
caa	caa	0.0013632718524	17
gta	gta	0.0013632718524	17
cgg	cgg	0.0013632718524	17
gga	gga	0.0012830793905	16
cta	cta	0.0012028869286	15
cgt	cgt	0.0010425020048	13
gca	gca	0.0010425020048	13
cga	cga	0.0009623095429	12
cca	cca	0.0009623095429	12
; Host name	nic54
; Job started	2011_11_26.223308
; Job done	2011_11_26.223309
; Seconds	0.17