; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Amphimedon_queenslandica.Aqu1.34/genome/Amphimedon_queenslandica.Aqu1.34_start_codons.wc -o $RSAT/public_html/data/genomes/Amphimedon_queenslandica.Aqu1.34/genome/Amphimedon_queenslandica.Aqu1.34_start_codon_frequencies.tab
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. 
; Program version              	1.169
; Slow counting mode           
; Oligomer length              	3
; Input file                   	$RSAT/public_html/data/genomes/Amphimedon_queenslandica.Aqu1.34/genome/Amphimedon_queenslandica.Aqu1.34_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Amphimedon_queenslandica.Aqu1.34/genome/Amphimedon_queenslandica.Aqu1.34_start_codon_frequencies.tab
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	166733
; Sum of sequence lengths      	500199
; discarded residues           	17	 (other letters than ACGT)
; discarded occurrences        	6	 (contain discarded residues)
; nb possible positions        	166727
; total oligo occurrences      	166727
; alphabet size                	4
; nb possible oligomers        	64
; oligomers tested for significance	0
;
; 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	0.1726894864059	28792
gtt	gtt	0.0485584218513	8096
gta	gta	0.0395496830147	6594
gtg	gtg	0.0351652701722	5863
gat	gat	0.0328081234593	5470
ata	ata	0.0307808573296	5132
att	att	0.0293113892771	4887
gaa	gaa	0.0272061513732	4536
gag	gag	0.0239493303424	3993
gtc	gtc	0.0233735387790	3897
ttt	ttt	0.0226418036671	3775
gct	gct	0.0221139947339	3687
ttg	ttg	0.0214662292250	3579
tta	tta	0.0208304593737	3473
ggt	ggt	0.0205965440511	3434
aat	aat	0.0200447438027	3342
aaa	aaa	0.0186772388395	3114
tat	tat	0.0172497555885	2876
gca	gca	0.0162481181812	2709
gga	gga	0.0153664373497	2562
atc	atc	0.0149885741362	2499
agt	agt	0.0145567304636	2427
ttc	ttc	0.0144367738879	2407
aga	aga	0.0133811560215	2231
act	act	0.0131412428701	2191
ctg	ctg	0.0130992580686	2184
gac	gac	0.0124814817036	2081
tgt	tgt	0.0122115794083	2036
tct	tct	0.0118697031675	1979
aca	aca	0.0111139767404	1853
ctc	ctc	0.0110420027950	1841
ctt	ctt	0.0109700288496	1829
tca	tca	0.0109160483905	1820
cta	cta	0.0102262980801	1705
tga	tga	0.0101843132786	1698
tac	tac	0.0090627192956	1511
cat	cat	0.0088168083154	1470
agg	agg	0.0086188799655	1437
caa	caa	0.0084689342458	1412
agc	agc	0.0083009950398	1384
aag	aag	0.0082050297792	1368
tgg	tgg	0.0081810384641	1364
aac	aac	0.0079351274839	1323
taa	taa	0.0078331643945	1306
ggc	ggc	0.0077072099900	1285
gcc	gcc	0.0072513750022	1209
cct	cct	0.0069394879054	1157
tgc	tgc	0.0063217115404	1054
tcc	tcc	0.0058538808951	976
ggg	ggg	0.0057819069497	964
acc	acc	0.0056439568876	941
cca	cca	0.0050981544681	850
gcg	gcg	0.0041684910063	695
cac	cac	0.0041085127184	685
acg	acg	0.0036706712170	612
tcg	tcg	0.0035747059564	596
cgt	cgt	0.0033108014899	552
ccc	ccc	0.0027530034128	459
cag	cag	0.0021112357327	352
tag	tag	0.0018173421222	303
cga	cga	0.0016973855464	283
ccg	ccg	0.0016853898889	281
cgg	cgg	0.0010136330648	169
cgc	cgc	0.0008217025437	137
; Host name	n55
; Job started	2017-04-15.090442
; Job done	2017-04-15.090444
; Seconds	1.74
;	user	1.74
;	system	0.04
;	cuser	0
;	csystem	0