; oligo-analysis  -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i /bio/rsa-tools/data/genomes/Saccharomyces_cerevisiae/genome/Saccharomyces_cerevisiae_stop_codons.wc -o /bio/rsa-tools/data/genomes/Saccharomyces_cerevisiae/genome/Saccharomyces_cerevisiae_stop_codon_frequencies
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. 
; Oligomer length              	3
; Input file                   	/bio/rsa-tools/data/genomes/Saccharomyces_cerevisiae/genome/Saccharomyces_cerevisiae_stop_codons.wc
; Input format                 	wc
; Output file                  	/bio/rsa-tools/data/genomes/Saccharomyces_cerevisiae/genome/Saccharomyces_cerevisiae_stop_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Method                       	
; Sequence type                	DNA
; Nb of sequences              	5869
; Sum of sequence lengths      	17607
; discarded residues           	0	 (other letters than ACGT)
; discarded occurrences        	0	 (contain discarded residues)
; nb possible positions        	5869
; total oligo occurrences      	5869
; alphabet size                	4
; nb possible oligomers        	64
; oligomers tested for significance	0
; Threshold values
;	Parameter      	Lower	Upper
;	occ_P          	none	1
;
; column headers
;	1	seq            	oligomer sequence
;	2	id             	oligomer identifier
;	3	observed_freq  	observed relative frequency
;	4	occ            	observed occurrences
;	5	test           	over- or under-representation test
;seq	id	observed_freq	occ	test
taa	taa	0.4755494973590	2791	
tga	tga	0.2956210598058	1735	
tag	tag	0.2288294428352	1343	
; Job started 2006_09_29.171454
; Job done    2006_09_29.171454