; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Oreochromis_niloticus_Orenil1.0/genome/Oreochromis_niloticus_Orenil1.0_start_codons.wc -o $RSAT/public_html/data/genomes/Oreochromis_niloticus_Orenil1.0/genome/Oreochromis_niloticus_Orenil1.0_start_codon_frequencies
; 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/Oreochromis_niloticus_Orenil1.0/genome/Oreochromis_niloticus_Orenil1.0_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Oreochromis_niloticus_Orenil1.0/genome/Oreochromis_niloticus_Orenil1.0_start_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	26757
; Sum of sequence lengths      	80271
; discarded residues           	199	 (other letters than ACGT)
; discarded occurrences        	83	 (contain discarded residues)
; nb possible positions        	26674
; total oligo occurrences      	26674
; 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	0.3706605683437	9887
ttt	ttt	0.0212941441104	568
aaa	aaa	0.0197570668066	527
ctg	ctg	0.0193821699033	517
cag	cag	0.0182949688836	488
gag	gag	0.0147334483017	393
gtg	gtg	0.0141336132564	377
tgt	tgt	0.0134213091400	358
aga	aga	0.0132713503786	354
aag	aag	0.0131588813076	351
ctt	ctt	0.0128964534753	344
aca	aca	0.0128589637850	343
gaa	gaa	0.0125965359526	336
agc	agc	0.0124840668816	333
ctc	ctc	0.0122966184299	328
att	att	0.0122591287396	327
tct	tct	0.0121091699783	323
tta	tta	0.0116218040039	310
ttc	ttc	0.0115093349329	307
ttg	ttg	0.0114343555522	305
agt	agt	0.0114343555522	305
gct	gct	0.0113593761716	303
tgg	tgg	0.0113593761716	303
gga	gga	0.0111344380295	297
tca	tca	0.0109469895779	292
gtt	gtt	0.0109469895779	292
agg	agg	0.0104596236035	279
aat	aat	0.0104596236035	279
act	act	0.0101597060808	271
atc	atc	0.0098972782485	264
tga	tga	0.0098972782485	264
aac	aac	0.0097473194871	260
caa	caa	0.0097098297968	259
cac	cac	0.0097098297968	259
gca	gca	0.0096723401065	258
cct	cct	0.0096723401065	258
tgc	tgc	0.0095973607258	256
cca	cca	0.0093724225838	250
gtc	gtc	0.0093349328935	249
cat	cat	0.0089600359901	239
acc	acc	0.0087350978481	233
tat	tat	0.0086226287771	230
gat	gat	0.0085476493964	228
tcc	tcc	0.0085101597061	227
gac	gac	0.0084351803254	225
ata	ata	0.0083602009447	223
ggt	ggt	0.0081352628027	217
taa	taa	0.0076853865187	205
gcc	gcc	0.0076853865187	205
ggc	ggc	0.0074604483767	199
gta	gta	0.0069730824023	186
ggg	ggg	0.0068231236410	182
cta	cta	0.0067106545700	179
ccc	ccc	0.0066731648797	178
tac	tac	0.0061108195246	163
acg	acg	0.0058483916923	156
gcg	gcg	0.0048361700532	129
cgg	cgg	0.0045737422209	122
cga	cga	0.0044987628402	120
tag	tag	0.0044612731499	119
cgt	cgt	0.0044237834595	118
cgc	cgc	0.0043488040789	116
ccg	ccg	0.0042363350079	113
tcg	tcg	0.0032990927495	88
; Host name	biow
; Job started	2015-09-04.063738
; Job done	2015-09-04.063738
; Seconds	0.67
;	user	0.67
;	system	0.01
;	cuser	0
;	csystem	0