; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_frik1999_ensembl_72_GCA_000303775.1/genome/Escherichia_coli_frik1999_ensembl_72_GCA_000303775.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_frik1999_ensembl_72_GCA_000303775.1/genome/Escherichia_coli_frik1999_ensembl_72_GCA_000303775.1_stop_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_frik1999_ensembl_72_GCA_000303775.1/genome/Escherichia_coli_frik1999_ensembl_72_GCA_000303775.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_frik1999_ensembl_72_GCA_000303775.1/genome/Escherichia_coli_frik1999_ensembl_72_GCA_000303775.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	2625
; Sum of sequence lengths      	7875
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	2625
; total oligo occurrences      	2625
; 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
taa	taa	0.5352380952381	1405
tga	tga	0.2979047619048	782
tag	tag	0.0758095238095	199
gga	gga	0.0057142857143	15
ggt	ggt	0.0041904761905	11
tgc	tgc	0.0034285714286	9
cgg	cgg	0.0034285714286	9
gcg	gcg	0.0030476190476	8
tgg	tgg	0.0030476190476	8
ctg	ctg	0.0026666666667	7
gct	gct	0.0026666666667	7
ggc	ggc	0.0026666666667	7
ggg	ggg	0.0026666666667	7
ccg	ccg	0.0026666666667	7
cag	cag	0.0026666666667	7
aaa	aaa	0.0026666666667	7
gaa	gaa	0.0022857142857	6
tcc	tcc	0.0022857142857	6
cac	cac	0.0022857142857	6
tgt	tgt	0.0019047619048	5
atg	atg	0.0019047619048	5
aac	aac	0.0019047619048	5
tac	tac	0.0019047619048	5
tcg	tcg	0.0019047619048	5
gtg	gtg	0.0019047619048	5
ttc	ttc	0.0015238095238	4
caa	caa	0.0015238095238	4
aca	aca	0.0015238095238	4
aag	aag	0.0015238095238	4
agc	agc	0.0015238095238	4
tat	tat	0.0015238095238	4
cca	cca	0.0011428571429	3
ctt	ctt	0.0011428571429	3
gat	gat	0.0011428571429	3
acg	acg	0.0011428571429	3
cga	cga	0.0011428571429	3
gac	gac	0.0011428571429	3
cct	cct	0.0011428571429	3
aga	aga	0.0011428571429	3
gtt	gtt	0.0011428571429	3
gcc	gcc	0.0011428571429	3
atc	atc	0.0011428571429	3
ttt	ttt	0.0007619047619	2
tct	tct	0.0007619047619	2
aat	aat	0.0007619047619	2
cgt	cgt	0.0007619047619	2
gag	gag	0.0007619047619	2
gtc	gtc	0.0007619047619	2
tca	tca	0.0007619047619	2
agt	agt	0.0007619047619	2
agg	agg	0.0003809523810	1
cgc	cgc	0.0003809523810	1
tta	tta	0.0003809523810	1
gta	gta	0.0003809523810	1
cta	cta	0.0003809523810	1
gca	gca	0.0003809523810	1
act	act	0.0003809523810	1
ctc	ctc	0.0003809523810	1
ttg	ttg	0.0003809523810	1
; Host name	jolitorax
; Job started	2013-10-01.031711
; Job done	2013-10-01.031712
; Seconds	1.48
;	user	1.48
;	system	0.09
;	cuser	0
;	csystem	0