; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_ec4421_ensembl_72_GCA_000267385.1/genome/Escherichia_coli_ec4421_ensembl_72_GCA_000267385.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_ec4421_ensembl_72_GCA_000267385.1/genome/Escherichia_coli_ec4421_ensembl_72_GCA_000267385.1_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_ec4421_ensembl_72_GCA_000267385.1/genome/Escherichia_coli_ec4421_ensembl_72_GCA_000267385.1_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_ec4421_ensembl_72_GCA_000267385.1/genome/Escherichia_coli_ec4421_ensembl_72_GCA_000267385.1_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	2648
; Sum of sequence lengths      	7944
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	2648
; total oligo occurrences      	2648
; 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	0.5294561933535	1402
tga	tga	0.3043806646526	806
tag	tag	0.0777945619335	206
ccg	ccg	0.0049093655589	13
ctg	ctg	0.0045317220544	12
tgc	tgc	0.0033987915408	9
ggg	ggg	0.0033987915408	9
acc	acc	0.0033987915408	9
gaa	gaa	0.0030211480363	8
aaa	aaa	0.0030211480363	8
atg	atg	0.0026435045317	7
cag	cag	0.0026435045317	7
agc	agc	0.0026435045317	7
gat	gat	0.0022658610272	6
aac	aac	0.0022658610272	6
gac	gac	0.0022658610272	6
tgg	tgg	0.0022658610272	6
ttc	ttc	0.0018882175227	5
tct	tct	0.0018882175227	5
aat	aat	0.0018882175227	5
cgt	cgt	0.0018882175227	5
ggc	ggc	0.0018882175227	5
gca	gca	0.0018882175227	5
aag	aag	0.0018882175227	5
cgg	cgg	0.0018882175227	5
cac	cac	0.0018882175227	5
att	att	0.0015105740181	4
cca	cca	0.0015105740181	4
agg	agg	0.0015105740181	4
gct	gct	0.0015105740181	4
acg	acg	0.0015105740181	4
ggt	ggt	0.0015105740181	4
gcc	gcc	0.0015105740181	4
tat	tat	0.0015105740181	4
ttt	ttt	0.0011329305136	3
tcg	tcg	0.0011329305136	3
cat	cat	0.0011329305136	3
ctc	ctc	0.0011329305136	3
tgt	tgt	0.0007552870091	2
gcg	gcg	0.0007552870091	2
tac	tac	0.0007552870091	2
gta	gta	0.0007552870091	2
cga	cga	0.0007552870091	2
ccc	ccc	0.0007552870091	2
gag	gag	0.0007552870091	2
gtc	gtc	0.0007552870091	2
act	act	0.0007552870091	2
aga	aga	0.0007552870091	2
gtg	gtg	0.0007552870091	2
ata	ata	0.0007552870091	2
cgc	cgc	0.0003776435045	1
caa	caa	0.0003776435045	1
cta	cta	0.0003776435045	1
aca	aca	0.0003776435045	1
cct	cct	0.0003776435045	1
ttg	ttg	0.0003776435045	1
gga	gga	0.0003776435045	1
atc	atc	0.0003776435045	1
; Host name	jolitorax
; Job started	2013-10-01.003528
; Job done	2013-10-01.003528
; Seconds	1.47
;	user	1.47
;	system	0.08
;	cuser	0
;	csystem	0