; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Danaus_plexippus.DanPle_1.0.34/genome/Danaus_plexippus.DanPle_1.0.34_stop_codons.wc -o $RSAT/public_html/data/genomes/Danaus_plexippus.DanPle_1.0.34/genome/Danaus_plexippus.DanPle_1.0.34_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/Danaus_plexippus.DanPle_1.0.34/genome/Danaus_plexippus.DanPle_1.0.34_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Danaus_plexippus.DanPle_1.0.34/genome/Danaus_plexippus.DanPle_1.0.34_stop_codon_frequencies.tab
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	95711
; Sum of sequence lengths      	287133
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	95711
; total oligo occurrences      	95711
; 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	0.1368494739372	13098
cag	cag	0.1324403673559	12676
gag	gag	0.0742756840906	7109
atg	atg	0.0339563895477	3250
aaa	aaa	0.0320234873734	3065
tag	tag	0.0311249490654	2979
caa	caa	0.0289517401344	2771
acg	acg	0.0273218334361	2615
ttg	ttg	0.0266949462444	2555
ctg	ctg	0.0258904410151	2478
agg	agg	0.0198723239753	1902
tcg	tcg	0.0197887390164	1894
gaa	gaa	0.0192140924241	1839
tgg	tgg	0.0190260262666	1821
ccg	ccg	0.0184618277941	1767
aat	aat	0.0183155541160	1753
gtg	gtg	0.0152542549968	1460
gat	gat	0.0141572024114	1355
cgg	cgg	0.0132900084630	1272
gcg	gcg	0.0128093949494	1226
aga	aga	0.0108764927751	1041
aca	aca	0.0108138040560	1035
aac	aac	0.0107824596964	1032
tat	tat	0.0106570822580	1020
att	att	0.0104794642204	1003
cat	cat	0.0103854311417	994
taa	taa	0.0091630011179	877
act	act	0.0090898642789	870
ttt	ttt	0.0089749349605	859
ggg	ggg	0.0088913500016	851
gac	gac	0.0086092507653	824
ata	ata	0.0083271515291	797
cac	cac	0.0077002643374	737
tca	tca	0.0076480237381	732
gct	gct	0.0074913019402	717
cca	cca	0.0070002403068	670
tta	tta	0.0068957591081	660
tac	tac	0.0068330703890	654
gtt	gtt	0.0067912779095	650
tct	tct	0.0067285891904	644
agt	agt	0.0067181410705	643
cga	cga	0.0060599095193	580
ctt	ctt	0.0059972208001	574
ttc	ttc	0.0056733290844	543
cct	cct	0.0052554042900	503
gca	gca	0.0051718193311	495
gga	gga	0.0051404749715	492
tgt	tgt	0.0051195787318	490
ctc	ctc	0.0050046494133	479
cta	cta	0.0048270313757	462
atc	atc	0.0047643426565	456
acc	acc	0.0046703095778	447
agc	agc	0.0043255216224	414
tga	tga	0.0040329742663	386
gta	gta	0.0037404269102	358
gcc	gcc	0.0036881863109	353
ggt	ggt	0.0036568419513	350
tcc	tcc	0.0036359457116	348
gtc	gtc	0.0034478795541	330
cgt	cgt	0.0033851908349	324
ccc	ccc	0.0033225021157	318
cgc	cgc	0.0029045773213	278
ggc	ggc	0.0028418886021	272
tgc	tgc	0.0027583036433	264
; Host name	n88
; Job started	2017-04-15.091147
; Job done	2017-04-15.091149
; Seconds	1.98
;	user	1.98
;	system	0.05
;	cuser	0
;	csystem	0