; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Rattus_norvegicus_Rnor_5.0/genome/Rattus_norvegicus_Rnor_5.0_start_codons.wc -o $RSAT/public_html/data/genomes/Rattus_norvegicus_Rnor_5.0/genome/Rattus_norvegicus_Rnor_5.0_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/Rattus_norvegicus_Rnor_5.0/genome/Rattus_norvegicus_Rnor_5.0_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Rattus_norvegicus_Rnor_5.0/genome/Rattus_norvegicus_Rnor_5.0_start_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	26153
; Sum of sequence lengths      	78459
; discarded residues           	102	 (other letters than ACGT)
; discarded occurrences        	48	 (contain discarded residues)
; nb possible positions        	26105
; total oligo occurrences      	26105
; 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	0.4936602183490	12887
ctg	ctg	0.0142501436506	372
gtg	gtg	0.0139436889485	364
cag	cag	0.0137521547596	359
ggg	ggg	0.0129477111664	338
agg	agg	0.0127944838154	334
gag	gag	0.0120283470600	314
ggc	ggc	0.0116835855200	305
cct	cct	0.0116835855200	305
aga	aga	0.0115303581689	301
gga	gga	0.0113005171423	295
aag	aag	0.0111089829535	290
tct	tct	0.0106876077380	279
ctc	ctc	0.0102279256847	267
tgg	tgg	0.0101513120092	265
ccc	ccc	0.0098448573070	257
gct	gct	0.0098065504693	256
gcc	gcc	0.0096916299559	253
gaa	gaa	0.0095767094426	250
tgc	tgc	0.0095384026049	249
cca	cca	0.0094617889293	247
ctt	ctt	0.0093085615782	243
ttt	ttt	0.0092702547405	242
tcc	tcc	0.0091553342272	239
agc	agc	0.0090787205516	237
ttc	ttc	0.0090404137138	236
tgt	tgt	0.0090021068761	235
gca	gca	0.0084658111473	221
ggt	ggt	0.0083508906340	218
gat	gat	0.0083508906340	218
aca	aca	0.0082359701207	215
ttg	ttg	0.0079295154185	207
cac	cac	0.0078145949052	204
gtt	gtt	0.0077762880674	203
aaa	aaa	0.0076996743919	201
ccg	ccg	0.0076613675541	200
agt	agt	0.0075464470408	197
gac	gac	0.0073166060142	191
cgg	cgg	0.0073166060142	191
gcg	gcg	0.0071250718253	186
acc	acc	0.0070867649876	185
tga	tga	0.0070484581498	184
tca	tca	0.0068569239609	179
cat	cat	0.0067420034476	176
caa	caa	0.0065887760965	172
att	att	0.0063972419077	167
gtc	gtc	0.0063972419077	167
atc	atc	0.0060141735300	157
aat	aat	0.0057843325034	151
aac	aac	0.0057460256656	150
act	act	0.0056694119900	148
cta	cta	0.0054778778012	143
gta	gta	0.0050181957479	131
ata	ata	0.0048266615591	126
tat	tat	0.0047883547213	125
tta	tta	0.0047117410458	123
cgc	cgc	0.0046351273702	121
acg	acg	0.0039456042904	103
taa	taa	0.0038306837771	100
tac	tac	0.0037157632637	97
tag	tag	0.0036008427504	94
tcg	tcg	0.0033710017238	88
cga	cga	0.0030262401839	79
cgt	cgt	0.0026048649684	68
; Host name	biow
; Job started	2015-04-23.072024
; Job done	2015-04-23.072024
; Seconds	0.66
;	user	0.66
;	system	0.03
;	cuser	0
;	csystem	0