; 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/Staphylococcus_saprophyticus_ATCC_15305_uid58411/genome/Staphylococcus_saprophyticus_ATCC_15305_uid58411_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Staphylococcus_saprophyticus_ATCC_15305_uid58411/genome/Staphylococcus_saprophyticus_ATCC_15305_uid58411_start_codon_frequencies ; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. ; Program version 1.165 ; Quick counting mode ; Oligomer length 3 ; Input file $RSAT/public_html/data/genomes/Staphylococcus_saprophyticus_ATCC_15305_uid58411/genome/Staphylococcus_saprophyticus_ATCC_15305_uid58411_start_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Staphylococcus_saprophyticus_ATCC_15305_uid58411/genome/Staphylococcus_saprophyticus_ATCC_15305_uid58411_start_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 2515 ; 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 atg atg 0.8318091451292 2092 ttg ttg 0.0994035785288 250 gtg gtg 0.0679920477137 171 atc atc 0.0003976143141 1 tcc tcc 0.0003976143141 1 ; Host name nic28 ; Job started 2012-05-05.044151 ; Job done 2012-05-05.044152 ; Seconds 0.4 ; user 0.4 ; system 0.05 ; cuser 0.38 ; csystem 0.07