; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_frik1996_ensembl_72_GCA_000267505.1/genome/Escherichia_coli_frik1996_ensembl_72_GCA_000267505.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_frik1996_ensembl_72_GCA_000267505.1/genome/Escherichia_coli_frik1996_ensembl_72_GCA_000267505.1_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_frik1996_ensembl_72_GCA_000267505.1/genome/Escherichia_coli_frik1996_ensembl_72_GCA_000267505.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_frik1996_ensembl_72_GCA_000267505.1/genome/Escherichia_coli_frik1996_ensembl_72_GCA_000267505.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	3308
; Sum of sequence lengths      	9924
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	3308
; total oligo occurrences      	3308
; 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	0.5238814993954	1733
tga	tga	0.3007859733978	995
tag	tag	0.0719467956469	238
cgg	cgg	0.0057436517533	19
ggg	ggg	0.0048367593712	16
ggc	ggc	0.0042321644498	14
acc	acc	0.0036275695284	12
tgt	tgt	0.0033252720677	11
agc	agc	0.0033252720677	11
ctg	ctg	0.0033252720677	11
cgc	cgc	0.0033252720677	11
ccg	ccg	0.0030229746070	10
aag	aag	0.0030229746070	10
atg	atg	0.0027206771463	9
gcg	gcg	0.0027206771463	9
ttt	ttt	0.0027206771463	9
tgc	tgc	0.0027206771463	9
acg	acg	0.0024183796856	8
tcc	tcc	0.0024183796856	8
aaa	aaa	0.0024183796856	8
agg	agg	0.0021160822249	7
tgg	tgg	0.0018137847642	6
cct	cct	0.0018137847642	6
gaa	gaa	0.0018137847642	6
aac	aac	0.0018137847642	6
gga	gga	0.0018137847642	6
gct	gct	0.0015114873035	5
aat	aat	0.0015114873035	5
cga	cga	0.0015114873035	5
gag	gag	0.0015114873035	5
gtc	gtc	0.0015114873035	5
gac	gac	0.0015114873035	5
gcc	gcc	0.0015114873035	5
caa	caa	0.0012091898428	4
gca	gca	0.0012091898428	4
ggt	ggt	0.0012091898428	4
atc	atc	0.0012091898428	4
gta	gta	0.0012091898428	4
ccc	ccc	0.0012091898428	4
ctc	ctc	0.0012091898428	4
ata	ata	0.0012091898428	4
gtt	gtt	0.0012091898428	4
agt	agt	0.0012091898428	4
ttc	ttc	0.0009068923821	3
ctt	ctt	0.0009068923821	3
cgt	cgt	0.0009068923821	3
tac	tac	0.0009068923821	3
aca	aca	0.0009068923821	3
act	act	0.0009068923821	3
cca	cca	0.0009068923821	3
cag	cag	0.0009068923821	3
tca	tca	0.0009068923821	3
att	att	0.0006045949214	2
tta	tta	0.0006045949214	2
ttg	ttg	0.0006045949214	2
gat	gat	0.0006045949214	2
tct	tct	0.0006045949214	2
cac	cac	0.0006045949214	2
cta	cta	0.0003022974607	1
tcg	tcg	0.0003022974607	1
cat	cat	0.0003022974607	1
gtg	gtg	0.0003022974607	1
aga	aga	0.0003022974607	1
tat	tat	0.0003022974607	1
; Host name	jolitorax
; Job started	2013-10-01.030403
; Job done	2013-10-01.030403
; Seconds	1.54
;	user	1.54
;	system	0.11
;	cuser	0
;	csystem	0