; oligo-analysis  -quick -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Mycobacterium_avium_paratuberculosis_K_10_uid57699/genome/Mycobacterium_avium_paratuberculosis_K_10_uid57699_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Mycobacterium_avium_paratuberculosis_K_10_uid57699/genome/Mycobacterium_avium_paratuberculosis_K_10_uid57699_stop_codon_frequencies
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. 
; Program version              	1.163
; Quick counting mode          
; Oligomer length              	3
; Input file                   	$RSAT/public_html/data/genomes/Mycobacterium_avium_paratuberculosis_K_10_uid57699/genome/Mycobacterium_avium_paratuberculosis_K_10_uid57699_stop_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Mycobacterium_avium_paratuberculosis_K_10_uid57699/genome/Mycobacterium_avium_paratuberculosis_K_10_uid57699_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	0
; Sum of sequence lengths      	0
; discarded residues           	NA (quick mode)	 (other letters than ACGT)
; discarded occurrences        	NA (quick mode)	 (contain discarded residues)
; nb possible positions        	NA (quick mode)
; total oligo occurrences      	4351
; alphabet size                	4
; nb possible oligomers        	64
; oligomers tested for significance	0
; Threshold values
;	Parameter      	Lower	Upper
;	ms_P           	none	1
;	occ_P          	none	1
; Sequences:
;
; 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
tga	tga	0.6329579407033	2754
tag	tag	0.2613192369570	1137
taa	taa	0.1054929901172	459
act	act	0.0002298322225	1
; Host name	nic58
; Job started	2011_11_21.115708
; Job done	2011_11_21.115708
; Seconds	0.16