; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_start_codons.wc -o $RSAT/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_start_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/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_start_codon_frequencies.tab
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	33960
; Sum of sequence lengths      	101880
; discarded residues           	1	 (other letters than ACGT)
; discarded occurrences        	1	 (contain discarded residues)
; nb possible positions        	33959
; total oligo occurrences      	33959
; 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
atg	atg	0.3945934803734	13400
aaa	aaa	0.0461438793840	1567
att	att	0.0436997555876	1484
ata	ata	0.0411672899673	1398
aat	aat	0.0375747224594	1276
gaa	gaa	0.0279160163727	948
ttt	ttt	0.0236756088224	804
gtt	gtt	0.0224682705616	763
tta	tta	0.0222326923643	755
gat	gat	0.0215848523219	733
gta	gta	0.0171383138491	582
tat	tat	0.0156070555670	530
aca	aca	0.0131629317707	447
aga	aga	0.0127506699255	433
aag	aag	0.0119261462352	405
atc	atc	0.0116316734886	395
gtg	gtg	0.0107777025236	366
ctt	ctt	0.0106893606997	363
agt	agt	0.0106304661504	361
taa	taa	0.0104243352278	354
gca	gca	0.0102770988545	349
ttg	ttg	0.0101004152066	343
aac	aac	0.0096587060868	328
gga	gga	0.0092464442416	314
caa	caa	0.0088930769457	302
cat	cat	0.0080980005301	275
act	act	0.0074501604876	253
gct	gct	0.0073323713890	249
tca	tca	0.0072734768397	247
tgt	tgt	0.0072440295651	246
gag	gag	0.0072145822904	245
ttc	ttc	0.0068906622692	234
tga	tga	0.0065078476987	221
ggt	ggt	0.0064195058747	218
cta	cta	0.0058894549309	200
ctg	ctg	0.0052710621632	179
tct	tct	0.0052121676139	177
tac	tac	0.0050943785153	173
gtc	gtc	0.0050354839660	171
gac	gac	0.0046232221208	157
tgg	tgg	0.0044759857475	152
agg	agg	0.0041815130010	142
cca	cca	0.0033569893106	114
agc	agc	0.0033275420360	113
cct	cct	0.0031508583881	107
cac	cac	0.0030330692894	103
tag	tag	0.0029447274655	100
tgc	tgc	0.0027974910922	95
tcc	tcc	0.0026797019936	91
ctc	ctc	0.0026797019936	91
acg	acg	0.0020613092258	70
acc	acc	0.0020318619512	69
cag	cag	0.0020024146765	68
gcc	gcc	0.0018551783032	63
ggg	ggg	0.0017962837539	61
cgt	cgt	0.0016196001060	55
ggc	ggc	0.0014429164581	49
gcg	gcg	0.0011189964369	38
cga	cga	0.0010306546129	35
tcg	tcg	0.0007950764157	27
ccc	ccc	0.0006183927677	21
cgg	cgg	0.0005300509438	18
ccg	ccg	0.0005006036691	17
cgc	cgc	0.0004417091198	15
; Host name	n83
; Job started	2017-04-15.082832
; Job done	2017-04-15.082833
; Seconds	1.99
;	user	1.99
;	system	0.06
;	cuser	0
;	csystem	0