; 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/Marinobacter_adhaerens_HP15_uid162009/genome/Marinobacter_adhaerens_HP15_uid162009_stop_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Marinobacter_adhaerens_HP15_uid162009/genome/Marinobacter_adhaerens_HP15_uid162009_stop_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/Marinobacter_adhaerens_HP15_uid162009/genome/Marinobacter_adhaerens_HP15_uid162009_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Marinobacter_adhaerens_HP15_uid162009/genome/Marinobacter_adhaerens_HP15_uid162009_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 4411 ; 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 0.5552029018363 2449 taa taa 0.3037859895715 1340 tag tag 0.1407844026298 621 act act 0.0002267059624 1 ; Host name nic42 ; Job started 2012-05-05.030157 ; Job done 2012-05-05.030158 ; Seconds 0.18 ; user 0.18 ; system 0.08 ; cuser 0.16 ; csystem 0.1