; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Manihot_esculenta.M.esculenta_v8.60/genome/Manihot_esculenta.M.esculenta_v8.60_start_codons.wc -o $RSAT/public_html/data/genomes/Manihot_esculenta.M.esculenta_v8.60/genome/Manihot_esculenta.M.esculenta_v8.60_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/Manihot_esculenta.M.esculenta_v8.60/genome/Manihot_esculenta.M.esculenta_v8.60_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Manihot_esculenta.M.esculenta_v8.60/genome/Manihot_esculenta.M.esculenta_v8.60_start_codon_frequencies.tab
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	371764
; Sum of sequence lengths      	1115292
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	371764
; total oligo occurrences      	371764
; 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	0.1842136409120	68484
gtt	gtt	0.0737726084290	27426
gtg	gtg	0.0490176563626	18223
gaa	gaa	0.0430676450651	16011
gta	gta	0.0405149503448	15062
gat	gat	0.0356973779064	13271
att	att	0.0320633520190	11920
gga	gga	0.0291421439408	10834
gca	gca	0.0291179350341	10825
gct	gct	0.0264630249298	9838
ata	ata	0.0249459334416	9274
gtc	gtc	0.0243245715024	9043
gag	gag	0.0235445067301	8753
ggt	ggt	0.0219251998580	8151
aaa	aaa	0.0179011415844	6655
ctt	ctt	0.0156443335019	5816
aat	aat	0.0151762946385	5642
atc	atc	0.0146033505127	5429
ggg	ggg	0.0134655318966	5006
ttg	ttg	0.0133337278489	4957
ttt	ttt	0.0132180630723	4914
aga	aga	0.0126101505256	4688
gac	gac	0.0125724922263	4674
gcc	gcc	0.0103506525645	3848
ggc	ggc	0.0102538169376	3812
caa	caa	0.0099821392066	3711
tgg	tgg	0.0097266007467	3616
ctg	ctg	0.0094414736231	3510
aca	aca	0.0094253343519	3504
tta	tta	0.0093822962955	3488
cat	cat	0.0093607772673	3480
agg	agg	0.0088981181610	3308
agt	agt	0.0083709019701	3112
ttc	ttc	0.0082686865861	3074
cta	cta	0.0078383060221	2914
tat	tat	0.0073487481305	2732
aag	aag	0.0073191594668	2721
act	act	0.0072922606815	2711
tga	tga	0.0071712161479	2666
tgt	tgt	0.0071039691848	2641
aac	aac	0.0068591902390	2550
cct	cct	0.0062405181782	2320
cca	cca	0.0060683659526	2256
agc	agc	0.0059284922693	2204
ctc	ctc	0.0057751691934	2147
tca	tca	0.0056890930806	2115
gcg	gcg	0.0055384598832	2059
tgc	tgc	0.0054765926771	2036
tct	tct	0.0051080793191	1899
cag	cag	0.0037658299351	1400
acc	acc	0.0036125068592	1343
cac	cac	0.0035129813538	1306
tac	tac	0.0031848161737	1184
tcc	tcc	0.0024854477572	924
taa	taa	0.0023644032236	879
acg	acg	0.0019474720522	724
ccc	ccc	0.0018640858179	693
ccg	ccg	0.0018613959394	692
cga	cga	0.0018291173971	680
cgt	cgt	0.0017376615272	646
tcg	tcg	0.0017000032279	632
cgg	cgg	0.0014283254968	531
cgc	cgc	0.0012023757007	447
tag	tag	0.0009495271194	353
; Host name	baobab
; Job started	2024-11-28.152827
; Job done	2024-11-28.152834
; Seconds	7.37
;	user	7.37
;	system	0.11
;	cuser	0
;	csystem	0.01
