; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_stop_codons.wc -o $RSAT/public_html/data/genomes/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_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/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_stop_codon_frequencies.tab
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	262888
; Sum of sequence lengths      	788664
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	262888
; total oligo occurrences      	262888
; 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	0.1352172788412	35547
cag	cag	0.1159353032470	30478
gag	gag	0.1133676698822	29803
atg	atg	0.0348779708469	9169
acg	acg	0.0345698548431	9088
caa	caa	0.0294193725084	7734
ctg	ctg	0.0286890234625	7542
aaa	aaa	0.0268973859590	7071
tcg	tcg	0.0251704147774	6617
agg	agg	0.0239113234533	6286
gaa	gaa	0.0217735309333	5724
aat	aat	0.0202025197042	5311
ccg	ccg	0.0194303277441	5108
ttg	ttg	0.0188901737622	4966
gat	gat	0.0182587261495	4800
gtg	gtg	0.0171175557652	4500
gcg	gcg	0.0158166215270	4158
cgg	cgg	0.0157215239950	4133
tgg	tgg	0.0131881257418	3467
aga	aga	0.0127392653906	3349
cat	cat	0.0119100149113	3131
ggg	ggg	0.0109780590974	2886
aac	aac	0.0108753537628	2859
cga	cga	0.0106319040808	2795
att	att	0.0101412008156	2666
tag	tag	0.0090723045556	2385
aca	aca	0.0084674842518	2226
cac	cac	0.0084066218314	2210
atc	atc	0.0083761906211	2202
gac	gac	0.0077143117982	2028
act	act	0.0075925869572	1996
gga	gga	0.0074328231034	1954
tat	tat	0.0073681567816	1937
cca	cca	0.0067443169715	1773
tca	tca	0.0065465141049	1721
gct	gct	0.0065198867959	1714
ctc	ctc	0.0061775356806	1624
ttc	ttc	0.0061204771614	1609
gca	gca	0.0059759289127	1571
acc	acc	0.0054966373513	1445
ata	ata	0.0054738139436	1439
tac	tac	0.0054281671282	1427
agt	agt	0.0054205593256	1425
ctt	ctt	0.0051390706308	1351
gtt	gtt	0.0049755028757	1308
ttt	ttt	0.0048423663309	1273
gtc	gtc	0.0044277410913	1164
gcc	gcc	0.0042908006451	1128
agc	agc	0.0042071148170	1106
cct	cct	0.0042033109157	1105
tga	tga	0.0041728797054	1097
ccc	ccc	0.0041386445939	1088
cta	cta	0.0041348406926	1087
taa	taa	0.0040435470619	1063
cgc	cgc	0.0036593530325	962
tcc	tcc	0.0035566476979	935
tgc	tgc	0.0035300203889	928
tct	tct	0.0034881774748	917
tgt	tgt	0.0030925717416	813
cgt	cgt	0.0030925717416	813
gta	gta	0.0030659444326	806
tta	tta	0.0030431210249	800
ggc	ggc	0.0025866528712	680
ggt	ggt	0.0022443017559	590
; Host name	n58
; Job started	2017-04-15.085413
; Job done	2017-04-15.085416
; Seconds	2.8
;	user	2.8
;	system	0.04
;	cuser	0
;	csystem	0