; 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/Coprinopsis_cinerea_okayama7#130_MO/genome/Coprinopsis_cinerea_okayama7#130_MO_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Coprinopsis_cinerea_okayama7#130_MO/genome/Coprinopsis_cinerea_okayama7#130_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/Coprinopsis_cinerea_okayama7#130_MO/genome/Coprinopsis_cinerea_okayama7#130_MO_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Coprinopsis_cinerea_okayama7#130_MO/genome/Coprinopsis_cinerea_okayama7#130_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      	10968
; 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	0.8340627279358	9148
ctt	ctt	0.0150437636761	165
ctc	ctc	0.0140408460977	154
cac	cac	0.0086615609044	95
cca	cca	0.0085703865791	94
gtc	gtc	0.0071115973742	78
ccc	ccc	0.0059263311451	65
cga	cga	0.0054704595186	60
gtt	gtt	0.0054704595186	60
caa	caa	0.0052881108680	58
cct	cct	0.0047410649161	52
atc	atc	0.0044675419402	49
cat	cat	0.0037381473377	41
ctg	ctg	0.0037381473377	41
cgc	cgc	0.0036469730124	40
gcc	gcc	0.0036469730124	40
gct	gct	0.0032822757112	36
cag	cag	0.0032822757112	36
ccg	ccg	0.0027352297593	30
acc	acc	0.0026440554340	29
ttc	ttc	0.0024617067834	27
cgt	cgt	0.0024617067834	27
gac	gac	0.0024617067834	27
att	att	0.0023705324581	26
cta	cta	0.0023705324581	26
gca	gca	0.0022793581327	25
gaa	gaa	0.0020970094821	23
ttt	ttt	0.0020970094821	23
acg	acg	0.0020058351568	22
ggt	ggt	0.0018234865062	20
tct	tct	0.0018234865062	20
gga	gga	0.0017323121809	19
ggc	ggc	0.0015499635303	17
aac	aac	0.0015499635303	17
aaa	aaa	0.0015499635303	17
gcg	gcg	0.0014587892050	16
tcc	tcc	0.0013676148796	15
aca	aca	0.0012764405543	14
aat	aat	0.0011852662290	13
tac	tac	0.0011852662290	13
tcg	tcg	0.0011852662290	13
act	act	0.0011852662290	13
gtg	gtg	0.0010940919037	12
gta	gta	0.0010029175784	11
aga	aga	0.0010029175784	11
tta	tta	0.0009117432531	10
gag	gag	0.0009117432531	10
tgc	tgc	0.0009117432531	10
aag	aag	0.0009117432531	10
tga	tga	0.0009117432531	10
agc	agc	0.0008205689278	9
tgg	tgg	0.0007293946025	8
cgg	cgg	0.0007293946025	8
agg	agg	0.0006382202772	7
gat	gat	0.0006382202772	7
ggg	ggg	0.0006382202772	7
ttg	ttg	0.0005470459519	6
taa	taa	0.0005470459519	6
tca	tca	0.0005470459519	6
agt	agt	0.0005470459519	6
tag	tag	0.0003646973012	4
ata	ata	0.0002735229759	3
tgt	tgt	0.0001823486506	2
tat	tat	0.0000911743253	1
; Host name	nic54
; Job started	2011_11_26.230458
; Job done	2011_11_26.230458
; Seconds	0.15