; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_ars4_2123_ensembl_72_GCA_000304095.1/genome/Escherichia_coli_ars4_2123_ensembl_72_GCA_000304095.1_start_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_ars4_2123_ensembl_72_GCA_000304095.1/genome/Escherichia_coli_ars4_2123_ensembl_72_GCA_000304095.1_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/Escherichia_coli_ars4_2123_ensembl_72_GCA_000304095.1/genome/Escherichia_coli_ars4_2123_ensembl_72_GCA_000304095.1_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_ars4_2123_ensembl_72_GCA_000304095.1/genome/Escherichia_coli_ars4_2123_ensembl_72_GCA_000304095.1_start_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4107
; Sum of sequence lengths      	12321
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4107
; total oligo occurrences      	4107
; 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	0.8390552714877	3446
gtg	gtg	0.0981251521792	403
ttg	ttg	0.0528366204042	217
ggt	ggt	0.0009739469199	4
acc	acc	0.0007304601899	3
aat	aat	0.0007304601899	3
gtt	gtt	0.0007304601899	3
tgg	tgg	0.0004869734599	2
gat	gat	0.0004869734599	2
gca	gca	0.0004869734599	2
cgc	cgc	0.0004869734599	2
aaa	aaa	0.0004869734599	2
gaa	gaa	0.0002434867300	1
ggg	ggg	0.0002434867300	1
att	att	0.0002434867300	1
ctt	ctt	0.0002434867300	1
ccg	ccg	0.0002434867300	1
ctg	ctg	0.0002434867300	1
aac	aac	0.0002434867300	1
gct	gct	0.0002434867300	1
gtc	gtc	0.0002434867300	1
ctc	ctc	0.0002434867300	1
aag	aag	0.0002434867300	1
caa	caa	0.0002434867300	1
aga	aga	0.0002434867300	1
acg	acg	0.0002434867300	1
gta	gta	0.0002434867300	1
gcc	gcc	0.0002434867300	1
atc	atc	0.0002434867300	1
agt	agt	0.0002434867300	1
; Host name	jolitorax
; Job started	2013-09-30.092133
; Job done	2013-09-30.092133
; Seconds	1.65
;	user	1.65
;	system	0.06
;	cuser	0
;	csystem	0