; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Bos_taurus_UMD3.1/genome/Bos_taurus_UMD3.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Bos_taurus_UMD3.1/genome/Bos_taurus_UMD3.1_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/Bos_taurus_UMD3.1/genome/Bos_taurus_UMD3.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Bos_taurus_UMD3.1/genome/Bos_taurus_UMD3.1_stop_codon_frequencies.tab
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	22118
; Sum of sequence lengths      	66354
; discarded residues           	88	 (other letters than ACGT)
; discarded occurrences        	36	 (contain discarded residues)
; nb possible positions        	22082
; total oligo occurrences      	22082
; 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	0.2463997826284	5441
taa	taa	0.1335476858980	2949
tag	tag	0.1122633819400	2479
agg	agg	0.0888053618332	1961
aga	aga	0.0461461824110	1019
agc	agc	0.0300244543067	663
agt	agt	0.0226881623041	501
aag	aag	0.0111855810162	247
aaa	aaa	0.0106421519790	235
gag	gag	0.0100987229418	223
ctg	ctg	0.0096911511638	214
cca	cca	0.0087854361018	194
cag	cag	0.0085590073363	189
gcc	gcc	0.0084684358301	187
gaa	gaa	0.0083778643239	185
cct	cct	0.0081514355584	180
gga	gga	0.0081514355584	180
ccc	ccc	0.0080155782991	177
tgg	tgg	0.0079250067929	175
ggc	ggc	0.0070645774839	156
gca	gca	0.0065211484467	144
ggg	ggg	0.0065211484467	144
ttt	ttt	0.0063852911874	141
gat	gat	0.0063400054343	140
tca	tca	0.0062947196812	139
tct	tct	0.0062494339281	138
aca	aca	0.0061588624219	136
atg	atg	0.0060230051626	133
ctc	ctc	0.0059777194095	132
gtg	gtg	0.0059324336564	131
ctt	ctt	0.0058871479033	130
gct	gct	0.0058871479033	130
caa	caa	0.0058871479033	130
aat	aat	0.0057965763971	128
tcc	tcc	0.0057965763971	128
cac	cac	0.0055701476316	123
ggt	ggt	0.0053890046191	119
gac	gac	0.0053890046191	119
att	att	0.0052531473598	116
ttg	ttg	0.0052531473598	116
aac	aac	0.0052078616067	115
tgt	tgt	0.0051625758536	114
tgc	tgc	0.0049814328412	110
acc	acc	0.0048455755819	107
act	act	0.0048455755819	107
atc	atc	0.0046644325695	103
cat	cat	0.0046191468164	102
ttc	ttc	0.0042568607916	94
gtc	gtc	0.0038945747668	86
tta	tta	0.0036681460013	81
gtt	gtt	0.0036681460013	81
gta	gta	0.0034417172358	76
cgg	cgg	0.0033964314827	75
ccg	ccg	0.0033511457296	74
ata	ata	0.0033511457296	74
tat	tat	0.0033058599765	73
tac	tac	0.0030794312109	68
acg	acg	0.0029888597047	66
cta	cta	0.0027171451861	60
cgc	cgc	0.0024454306675	54
gcg	gcg	0.0024001449144	53
cgt	cgt	0.0021284303958	47
cga	cga	0.0020831446427	46
tcg	tcg	0.0019925731365	44
; Host name	n89
; Job started	2017-04-15.090124
; Job done	2017-04-15.090125
; Seconds	0.61
;	user	0.61
;	system	0.05
;	cuser	0
;	csystem	0