; 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/Verticillium_dahliae_VdLs.17_MO/genome/Verticillium_dahliae_VdLs.17_MO_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Verticillium_dahliae_VdLs.17_MO/genome/Verticillium_dahliae_VdLs.17_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/Verticillium_dahliae_VdLs.17_MO/genome/Verticillium_dahliae_VdLs.17_MO_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Verticillium_dahliae_VdLs.17_MO/genome/Verticillium_dahliae_VdLs.17_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      	10367
; 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	0.8454712067136	8765
atc	atc	0.0096459920903	100
acc	acc	0.0088743127231	92
gac	gac	0.0076203337513	79
aca	aca	0.0069451143050	72
gcg	gcg	0.0062698948587	65
gcc	gcc	0.0055946754124	58
aac	aac	0.0054982154915	57
acg	acg	0.0047265361242	49
ggg	ggg	0.0044371563615	46
gca	gca	0.0041477765988	43
gag	gag	0.0039548567570	41
act	act	0.0036654769943	38
gtc	gtc	0.0034725571525	36
gat	gat	0.0034725571525	36
gaa	gaa	0.0032796373107	34
agg	agg	0.0030867174689	32
gga	gga	0.0029902575480	31
agt	agt	0.0027973377062	29
aga	aga	0.0027008777853	28
ggc	ggc	0.0025079579435	26
aaa	aaa	0.0024114980226	25
gct	gct	0.0023150381017	24
aag	aag	0.0023150381017	24
aat	aat	0.0022185781808	23
cga	cga	0.0022185781808	23
agc	agc	0.0022185781808	23
cca	cca	0.0021221182599	22
ctc	ctc	0.0021221182599	22
gtg	gtg	0.0020256583390	21
ccc	ccc	0.0020256583390	21
gtt	gtt	0.0020256583390	21
cac	cac	0.0020256583390	21
ctt	ctt	0.0019291984181	20
att	att	0.0018327384972	19
tct	tct	0.0017362785763	18
ata	ata	0.0017362785763	18
cat	cat	0.0016398186553	17
ttg	ttg	0.0016398186553	17
tcg	tcg	0.0015433587344	16
cct	cct	0.0015433587344	16
ttc	ttc	0.0014468988135	15
cag	cag	0.0014468988135	15
caa	caa	0.0013504388926	14
cgc	cgc	0.0013504388926	14
tca	tca	0.0013504388926	14
ggt	ggt	0.0011575190508	12
tcc	tcc	0.0011575190508	12
ttt	ttt	0.0011575190508	12
tga	tga	0.0011575190508	12
ccg	ccg	0.0008681392881	9
tgc	tgc	0.0008681392881	9
cgg	cgg	0.0008681392881	9
gta	gta	0.0007716793672	8
cta	cta	0.0006752194463	7
ctg	ctg	0.0005787595254	6
tgt	tgt	0.0004822996045	5
tta	tta	0.0004822996045	5
cgt	cgt	0.0004822996045	5
tac	tac	0.0004822996045	5
tag	tag	0.0003858396836	4
tat	tat	0.0002893797627	3
tgg	tgg	0.0001929198418	2
taa	taa	0.0001929198418	2
; Host name	nic41
; Job started	2011_11_26.223246
; Job done	2011_11_26.223246
; Seconds	0.15