; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_ec96038_ensembl_72_GCA_000304035.1/genome/Escherichia_coli_ec96038_ensembl_72_GCA_000304035.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_ec96038_ensembl_72_GCA_000304035.1/genome/Escherichia_coli_ec96038_ensembl_72_GCA_000304035.1_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_ec96038_ensembl_72_GCA_000304035.1/genome/Escherichia_coli_ec96038_ensembl_72_GCA_000304035.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_ec96038_ensembl_72_GCA_000304035.1/genome/Escherichia_coli_ec96038_ensembl_72_GCA_000304035.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	4227
; Sum of sequence lengths      	12681
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	4227
; total oligo occurrences      	4227
; 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	0.5613910574876	2373
tga	tga	0.2933522592855	1240
tag	tag	0.0828010409274	350
gat	gat	0.0030754672344	13
ggg	ggg	0.0030754672344	13
gac	gac	0.0028388928318	12
gaa	gaa	0.0026023184291	11
acc	acc	0.0023657440265	10
ctg	ctg	0.0018925952212	8
ggc	ggc	0.0018925952212	8
ttc	ttc	0.0016560208185	7
tgc	tgc	0.0016560208185	7
gca	gca	0.0016560208185	7
ccg	ccg	0.0016560208185	7
cgc	cgc	0.0014194464159	6
atg	atg	0.0014194464159	6
aac	aac	0.0014194464159	6
tgg	tgg	0.0014194464159	6
ggt	ggt	0.0014194464159	6
gag	gag	0.0014194464159	6
gcc	gcc	0.0014194464159	6
att	att	0.0011828720132	5
agg	agg	0.0011828720132	5
gcg	gcg	0.0011828720132	5
acg	acg	0.0011828720132	5
aca	aca	0.0011828720132	5
cag	cag	0.0011828720132	5
aaa	aaa	0.0011828720132	5
aag	aag	0.0011828720132	5
cct	cct	0.0011828720132	5
gtg	gtg	0.0011828720132	5
ata	ata	0.0011828720132	5
atc	atc	0.0011828720132	5
cgt	cgt	0.0009462976106	4
gtc	gtc	0.0009462976106	4
tat	tat	0.0009462976106	4
gct	gct	0.0007097232079	3
aat	aat	0.0007097232079	3
tac	tac	0.0007097232079	3
cat	cat	0.0007097232079	3
aga	aga	0.0007097232079	3
gga	gga	0.0007097232079	3
gtt	gtt	0.0007097232079	3
cca	cca	0.0004731488053	2
ttt	ttt	0.0004731488053	2
tta	tta	0.0004731488053	2
tcc	tcc	0.0004731488053	2
act	act	0.0004731488053	2
ttg	ttg	0.0004731488053	2
tca	tca	0.0004731488053	2
cac	cac	0.0004731488053	2
agc	agc	0.0004731488053	2
tgt	tgt	0.0002365744026	1
ctt	ctt	0.0002365744026	1
cta	cta	0.0002365744026	1
cga	cga	0.0002365744026	1
ccc	ccc	0.0002365744026	1
tcg	tcg	0.0002365744026	1
cgg	cgg	0.0002365744026	1
agt	agt	0.0002365744026	1
; Host name	jolitorax
; Job started	2013-10-01.012203
; Job done	2013-10-01.012204
; Seconds	1.71
;	user	1.71
;	system	0.08
;	cuser	0
;	csystem	0