; 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_immitis_RMSCC_2394_MO/genome/Coccidioides_immitis_RMSCC_2394_MO_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Coccidioides_immitis_RMSCC_2394_MO/genome/Coccidioides_immitis_RMSCC_2394_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/Coccidioides_immitis_RMSCC_2394_MO/genome/Coccidioides_immitis_RMSCC_2394_MO_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Coccidioides_immitis_RMSCC_2394_MO/genome/Coccidioides_immitis_RMSCC_2394_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      	10407
; 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	0.5630825405977	5860
ctc	ctc	0.0220044201019	229
ctt	ctt	0.0196982800038	205
caa	caa	0.0172960507351	180
cga	cga	0.0169116940521	176
atc	atc	0.0159508023446	166
cgc	cgc	0.0144133756126	150
ctg	ctg	0.0122994138561	128
cag	cag	0.0111463438071	116
gga	gga	0.0108580762948	113
ttt	ttt	0.0104737196118	109
att	att	0.0103776304410	108
aaa	aaa	0.0102815412703	107
ccc	ccc	0.0100893629288	105
gtc	gtc	0.0095128279043	99
cac	cac	0.0095128279043	99
cct	cct	0.0091284712213	95
gtt	gtt	0.0088402037090	92
ggc	ggc	0.0082636686845	86
cgg	cgg	0.0081675795138	85
cca	cca	0.0080714903430	84
gaa	gaa	0.0079754011723	83
ccg	ccg	0.0075910444893	79
cat	cat	0.0073988661478	77
gat	gat	0.0070145094648	73
gac	gac	0.0067262419525	70
tga	tga	0.0067262419525	70
ttc	ttc	0.0065340636110	68
tgc	tgc	0.0062457960988	65
gcc	gcc	0.0062457960988	65
gca	gca	0.0060536177573	63
agc	agc	0.0059575285865	62
tct	tct	0.0059575285865	62
gag	gag	0.0056692610743	59
cgt	cgt	0.0054770827328	57
cta	cta	0.0053809935620	56
aga	aga	0.0053809935620	56
gtg	gtg	0.0049966368790	52
aac	aac	0.0049966368790	52
gct	gct	0.0049005477083	51
tcc	tcc	0.0049005477083	51
ggg	ggg	0.0049005477083	51
aat	aat	0.0045161910253	47
tcg	tcg	0.0045161910253	47
ttg	ttg	0.0044201018545	46
tca	tca	0.0044201018545	46
ata	ata	0.0043240126838	45
ggt	ggt	0.0039396560008	41
aca	aca	0.0034592101470	36
gcg	gcg	0.0033631209763	35
acc	acc	0.0033631209763	35
tgt	tgt	0.0032670318055	34
gta	gta	0.0030748534640	32
aag	aag	0.0030748534640	32
acg	acg	0.0029787642933	31
tat	tat	0.0029787642933	31
tgg	tgg	0.0024983184395	26
act	act	0.0024983184395	26
taa	taa	0.0022100509273	23
tac	tac	0.0021139617565	22
tta	tta	0.0018256942443	19
agg	agg	0.0015374267320	16
agt	agt	0.0012491592198	13
tag	tag	0.0009608917075	10
; Host name	nic47
; Job started	2011_11_26.223249
; Job done	2011_11_26.223249
; Seconds	0.16