; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Culex_quinquefasciatus.CpipJ2.34/genome/Culex_quinquefasciatus.CpipJ2.34_stop_codons.wc -o $RSAT/public_html/data/genomes/Culex_quinquefasciatus.CpipJ2.34/genome/Culex_quinquefasciatus.CpipJ2.34_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/Culex_quinquefasciatus.CpipJ2.34/genome/Culex_quinquefasciatus.CpipJ2.34_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Culex_quinquefasciatus.CpipJ2.34/genome/Culex_quinquefasciatus.CpipJ2.34_stop_codon_frequencies.tab
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	71281
; Sum of sequence lengths      	213843
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	71281
; total oligo occurrences      	71281
; 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	0.1004615535697	7161
cag	cag	0.0773417881343	5513
gag	gag	0.0622746594464	4439
atg	atg	0.0350303727501	2497
acg	acg	0.0296432429399	2113
aaa	aaa	0.0285489821972	2035
ttg	ttg	0.0285068952456	2032
caa	caa	0.0252241130175	1798
ctg	ctg	0.0252100840336	1797
tcg	tcg	0.0246348956945	1756
ccg	ccg	0.0228532147417	1629
tgg	tgg	0.0221237075799	1577
agg	agg	0.0220535626605	1572
gtg	gtg	0.0212959975309	1518
aat	aat	0.0207909541112	1482
gaa	gaa	0.0204262005303	1456
gcg	gcg	0.0201175628849	1434
gat	gat	0.0200053310139	1426
cgg	cgg	0.0188128673840	1341
aac	aac	0.0182376790449	1300
ggg	ggg	0.0148426649458	1058
ttt	ttt	0.0145901432359	1040
att	att	0.0136502013159	973
tag	tag	0.0134397665577	958
gtt	gtt	0.0118124044275	842
cac	cac	0.0115879406855	826
gac	gac	0.0114616798305	817
aga	aga	0.0113354189756	808
gct	gct	0.0110267813302	786
cga	cga	0.0105638248622	753
agt	agt	0.0100447524586	716
cat	cat	0.0100307234747	715
tac	tac	0.0099886365231	712
atc	atc	0.0098483466842	702
ttc	ttc	0.0097782017648	697
gga	gga	0.0087821439093	626
aca	aca	0.0085436511833	609
tgt	tgt	0.0085015642317	606
tat	tat	0.0085015642317	606
agc	agc	0.0081508396347	581
gca	gca	0.0080947236992	577
acc	acc	0.0080806947153	576
act	act	0.0080666657314	575
ggt	ggt	0.0078001150377	556
ctt	ctt	0.0067900281983	484
tgc	tgc	0.0067058542950	478
gcc	gcc	0.0066777963272	476
tct	tct	0.0062288688430	444
gtc	gtc	0.0062288688430	444
cca	cca	0.0061306659559	437
tcc	tcc	0.0061306659559	437
tca	tca	0.0061026079881	435
ggc	ggc	0.0060885790042	434
tga	tga	0.0058921732299	420
cgt	cgt	0.0058641152621	418
ctc	ctc	0.0054572747296	389
cct	cct	0.0051065501326	364
taa	taa	0.0050644631809	361
cgc	cgc	0.0047979124872	342
ata	ata	0.0045594197612	325
tta	tta	0.0042227241481	301
ccc	ccc	0.0039842314221	284
cta	cta	0.0031565213732	225
gta	gta	0.0026935649051	192
; Host name	n93
; Job started	2017-04-15.085644
; Job done	2017-04-15.085646
; Seconds	1.49
;	user	1.49
;	system	0.04
;	cuser	0
;	csystem	0