; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Escherichia_coli_dec1b_ensembl_72_GCA_000249075.2/genome/Escherichia_coli_dec1b_ensembl_72_GCA_000249075.2_stop_codons.wc -o $RSAT/public_html/data/genomes/Escherichia_coli_dec1b_ensembl_72_GCA_000249075.2/genome/Escherichia_coli_dec1b_ensembl_72_GCA_000249075.2_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_dec1b_ensembl_72_GCA_000249075.2/genome/Escherichia_coli_dec1b_ensembl_72_GCA_000249075.2_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Escherichia_coli_dec1b_ensembl_72_GCA_000249075.2/genome/Escherichia_coli_dec1b_ensembl_72_GCA_000249075.2_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	5332
; Sum of sequence lengths      	15996
; discarded residues           		 (other letters than ACGT)
; discarded occurrences        		 (contain discarded residues)
; nb possible positions        	5332
; total oligo occurrences      	5332
; 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	0.5843960990248	3116
tga	tga	0.3270817704426	1744
tag	tag	0.0802700675169	428
att	att	0.0005626406602	3
caa	caa	0.0005626406602	3
ggc	ggc	0.0005626406602	3
ccg	ccg	0.0005626406602	3
cac	cac	0.0005626406602	3
tgc	tgc	0.0003750937734	2
acc	acc	0.0003750937734	2
cgg	cgg	0.0003750937734	2
gga	gga	0.0003750937734	2
tat	tat	0.0003750937734	2
ttt	ttt	0.0001875468867	1
gat	gat	0.0001875468867	1
cgc	cgc	0.0001875468867	1
atg	atg	0.0001875468867	1
tta	tta	0.0001875468867	1
aat	aat	0.0001875468867	1
acg	acg	0.0001875468867	1
tac	tac	0.0001875468867	1
gac	gac	0.0001875468867	1
tcg	tcg	0.0001875468867	1
gag	gag	0.0001875468867	1
aaa	aaa	0.0001875468867	1
gtc	gtc	0.0001875468867	1
aag	aag	0.0001875468867	1
tcc	tcc	0.0001875468867	1
gtg	gtg	0.0001875468867	1
gtt	gtt	0.0001875468867	1
agc	agc	0.0001875468867	1
gcc	gcc	0.0001875468867	1
; Host name	jolitorax
; Job started	2013-09-30.151632
; Job done	2013-09-30.151632
; Seconds	0.36
;	user	0.36
;	system	0.02
;	cuser	0
;	csystem	0