; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Mus_musculus_GRCm38/genome/Mus_musculus_GRCm38_stop_codons.wc -o $RSAT/public_html/data/genomes/Mus_musculus_GRCm38/genome/Mus_musculus_GRCm38_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/Mus_musculus_GRCm38/genome/Mus_musculus_GRCm38_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Mus_musculus_GRCm38/genome/Mus_musculus_GRCm38_stop_codon_frequencies.tab
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	57410
; Sum of sequence lengths      	172230
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	57410
; total oligo occurrences      	57410
; 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
tga	tga	0.2376937815712	13646
taa	taa	0.1301167044069	7470
tag	tag	0.1070545201184	6146
agg	agg	0.0444521860303	2552
aga	aga	0.0307437728619	1765
agc	agc	0.0209719561052	1204
cag	cag	0.0143006444870	821
ctg	ctg	0.0140916216687	809
agt	agt	0.0140045288277	804
aag	aag	0.0120362306218	691
gga	gga	0.0119665563491	687
tgg	tgg	0.0114788364396	659
gaa	gaa	0.0110956279394	637
gag	gag	0.0109214422574	627
cct	cct	0.0106427451663	611
atg	atg	0.0099111653022	569
cca	cca	0.0098414910294	565
aaa	aaa	0.0096847239157	556
ccc	ccc	0.0095279568020	547
ctc	ctc	0.0094408639610	542
tgc	tgc	0.0093537711200	537
gct	gct	0.0093189339836	535
gtg	gtg	0.0091273297335	524
gcc	gcc	0.0089008883470	511
tcc	tcc	0.0088312140742	507
ggc	ggc	0.0081344713465	467
caa	caa	0.0080125413691	460
aca	aca	0.0079951228009	459
gca	gca	0.0078906113917	453
ttg	ttg	0.0078731928235	452
ctt	ctt	0.0078209371190	449
tct	tct	0.0077860999826	447
tgt	tgt	0.0077512628462	445
ttc	ttc	0.0076815885734	441
tca	tca	0.0075770771643	435
ttt	ttt	0.0074551471869	428
ggg	ggg	0.0074028914823	425
gac	gac	0.0073506357777	422
acc	acc	0.0070719386866	406
aac	aac	0.0069674272775	400
act	act	0.0067758230273	389
cac	cac	0.0066887301864	384
gat	gat	0.0066190559136	380
ggt	ggt	0.0060094060268	345
cat	cat	0.0058874760495	338
aat	aat	0.0056261975266	323
atc	atc	0.0056087789584	322
att	att	0.0054694304128	314
gtc	gtc	0.0053823375719	309
cta	cta	0.0049991290716	287
tac	tac	0.0046159205713	265
gtt	gtt	0.0045288277304	260
tta	tta	0.0045288277304	260
ata	ata	0.0042675492075	245
tat	tat	0.0040759449573	234
gta	gta	0.0040759449573	234
cgg	cgg	0.0037798292980	217
ccg	ccg	0.0036578993207	210
gcg	gcg	0.0034488765024	198
cga	cga	0.0030830865703	177
cgc	cgc	0.0028566451838	164
tcg	tcg	0.0026998780700	155
acg	acg	0.0025431109563	146
cgt	cgt	0.0024908552517	143
; Host name	clust-rsat
; Job started	2024-05-20.222947
; Job done	2024-05-20.222948
; Seconds	0.63
;	user	0.63
;	system	0.02
;	cuser	0
;	csystem	0