; 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_stop_codons.wc -o $RSAT/public_html/data/genomes/Manihot_esculenta.M.esculenta_v8.60/genome/Manihot_esculenta.M.esculenta_v8.60_stop_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_stop_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_stop_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
aag	aag	0.1803644247426	67053
cag	cag	0.1714367179178	63734
gag	gag	0.0982854714281	36539
atg	atg	0.0467796774298	17391
ctg	ctg	0.0358749098891	13337
ttg	ttg	0.0339247479584	12612
tag	tag	0.0230011512680	8551
caa	caa	0.0219063707083	8144
tgg	tgg	0.0195338978492	7262
aaa	aaa	0.0192380112114	7152
agg	agg	0.0175084193198	6509
aat	aat	0.0174035140573	6470
gtg	gtg	0.0168144306603	6251
gaa	gaa	0.0140599950506	5227
cat	cat	0.0126558784605	4705
gat	gat	0.0118569845386	4408
att	att	0.0106895772587	3974
tct	tct	0.0104555578270	3887
aga	aga	0.0101542914322	3775
acg	acg	0.0098395756448	3658
act	act	0.0098368857662	3657
gct	gct	0.0092827707901	3451
ttt	ttt	0.0088147319267	3277
ggg	ggg	0.0088012825341	3272
ctt	ctt	0.0087447950851	3251
tca	tca	0.0081019141176	3012
tcg	tcg	0.0079889392195	2970
tat	tat	0.0078490655362	2918
aca	aca	0.0076930525817	2860
cgg	cgg	0.0074267546078	2761
cct	cct	0.0072061845687	2679
ccg	ccg	0.0069963740437	2601
gca	gca	0.0068457408463	2545
cca	cca	0.0066520695925	2473
agt	agt	0.0063777019830	2371
gtt	gtt	0.0062539675708	2325
aac	aac	0.0061490623083	2286
gcg	gcg	0.0061114040090	2272
tgt	tgt	0.0054927319482	2042
ata	ata	0.0047664647465	1772
ttc	ttc	0.0044786477443	1665
tta	tta	0.0039648809460	1474
gga	gga	0.0038734250761	1440
ggt	ggt	0.0037227918787	1384
gac	gac	0.0036905133364	1372
cac	cac	0.0035909878310	1335
cta	cta	0.0034107659698	1268
agc	agc	0.0033811773060	1257
ctc	ctc	0.0033327594926	1239
atc	atc	0.0032036453234	1191
tac	tac	0.0031659870240	1177
tgc	tgc	0.0031498477529	1171
cga	cga	0.0031417781173	1168
tcc	tcc	0.0028243724513	1050
gta	gta	0.0026737392539	994
taa	taa	0.0025903530197	963
tga	tga	0.0025204161780	937
cgt	cgt	0.0025042769069	931
acc	acc	0.0024854477572	924
gcc	gcc	0.0022648777181	842
gtc	gtc	0.0019663012018	731
ggc	ggc	0.0019205732669	714
ccc	ccc	0.0018694655749	695
cgc	cgc	0.0010974704382	408
; Host name	baobab
; Job started	2024-11-28.152912
; Job done	2024-11-28.152920
; Seconds	7.82
;	user	7.82
;	system	0.12
;	cuser	0
;	csystem	0.01
