; 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/Cryptococcus_neoformans_var._neoformans_JEC21_MO/genome/Cryptococcus_neoformans_var._neoformans_JEC21_MO_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Cryptococcus_neoformans_var._neoformans_JEC21_MO/genome/Cryptococcus_neoformans_var._neoformans_JEC21_MO_start_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/Cryptococcus_neoformans_var._neoformans_JEC21_MO/genome/Cryptococcus_neoformans_var._neoformans_JEC21_MO_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Cryptococcus_neoformans_var._neoformans_JEC21_MO/genome/Cryptococcus_neoformans_var._neoformans_JEC21_MO_start_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      	6272
; 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
atg	atg	0.3839285714286	2408
ctt	ctt	0.0347576530612	218
ctc	ctc	0.0334821428571	210
caa	caa	0.0279017857143	175
cac	cac	0.0220025510204	138
cat	cat	0.0218431122449	137
atc	atc	0.0176977040816	111
cca	cca	0.0170599489796	107
ccc	ccc	0.0161033163265	101
cag	cag	0.0161033163265	101
cct	cct	0.0157844387755	99
att	att	0.0156250000000	98
cga	cga	0.0156250000000	98
aaa	aaa	0.0151466836735	95
gtc	gtc	0.0145089285714	91
gca	gca	0.0130739795918	82
cgc	cgc	0.0129145408163	81
gaa	gaa	0.0121173469388	76
cgt	cgt	0.0110012755102	69
gtt	gtt	0.0110012755102	69
gcc	gcc	0.0106823979592	67
ccg	ccg	0.0105229591837	66
aac	aac	0.0103635204082	65
agc	agc	0.0102040816327	64
ttc	ttc	0.0097257653061	61
ata	ata	0.0097257653061	61
gct	gct	0.0094068877551	59
cta	cta	0.0094068877551	59
gta	gta	0.0089285714286	56
tcc	tcc	0.0087691326531	55
aat	aat	0.0084502551020	53
ctg	ctg	0.0084502551020	53
ttt	ttt	0.0082908163265	52
tct	tct	0.0082908163265	52
tgc	tgc	0.0078125000000	49
gac	gac	0.0076530612245	48
aga	aga	0.0076530612245	48
acc	acc	0.0074936224490	47
gat	gat	0.0071747448980	45
act	act	0.0070153061224	44
gtg	gtg	0.0070153061224	44
gga	gga	0.0066964285714	42
cgg	cgg	0.0062181122449	39
tat	tat	0.0062181122449	39
tca	tca	0.0057397959184	36
aca	aca	0.0055803571429	35
ggc	ggc	0.0055803571429	35
aag	aag	0.0054209183673	34
ggt	ggt	0.0051020408163	32
tac	tac	0.0046237244898	29
gcg	gcg	0.0041454081633	26
tcg	tcg	0.0039859693878	25
gag	gag	0.0036670918367	23
agt	agt	0.0036670918367	23
acg	acg	0.0033482142857	21
tga	tga	0.0031887755102	20
tgt	tgt	0.0028698979592	18
taa	taa	0.0028698979592	18
ggg	ggg	0.0028698979592	18
tta	tta	0.0020727040816	13
ttg	ttg	0.0015943877551	10
tag	tag	0.0014349489796	9
tgg	tgg	0.0012755102041	8
agg	agg	0.0011160714286	7
; Host name	nic48
; Job started	2011_11_26.230540
; Job done	2011_11_26.230542
; Seconds	0.16