; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Salmo_salar.Ssal_v3.1.108/genome/Salmo_salar.Ssal_v3.1.108_stop_codons.wc -o $RSAT/public_html/data/genomes/Salmo_salar.Ssal_v3.1.108/genome/Salmo_salar.Ssal_v3.1.108_stop_codon_frequencies.tab ; 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/Salmo_salar.Ssal_v3.1.108/genome/Salmo_salar.Ssal_v3.1.108_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Salmo_salar.Ssal_v3.1.108/genome/Salmo_salar.Ssal_v3.1.108_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 1852893 ; Sum of sequence lengths 5558679 ; discarded residues (other letters than ACGT) ; discarded occurrences (contain discarded residues) ; nb possible positions 1852893 ; total oligo occurrences 1852893 ; 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 cag cag 0.2007072183877 371889 aag aag 0.1549042497327 287021 gag gag 0.0976240937820 180887 ctg ctg 0.0389196785783 72114 atg atg 0.0358471859951 66421 agg agg 0.0314902155710 58348 tgg tgg 0.0235609935382 43656 acg acg 0.0217508512364 40302 caa caa 0.0212019798229 39285 gtg gtg 0.0171278104024 31736 tag tag 0.0165125563106 30596 ttg ttg 0.0156344699883 28969 aaa aaa 0.0154892916105 28700 aca aca 0.0137028959578 25390 ggg ggg 0.0131599612066 24384 ccg ccg 0.0118409427851 21940 aga aga 0.0116229053701 21536 tcg tcg 0.0114027091689 21128 cca cca 0.0107070402878 19839 aat aat 0.0106881509078 19804 cgg cgg 0.0103691902339 19213 cat cat 0.0100836907474 18684 gaa gaa 0.0098629548495 18275 cct cct 0.0098143821581 18185 act act 0.0095974241362 17783 tct tct 0.0087344493179 16184 gat gat 0.0086167954653 15966 tca tca 0.0083491059656 15470 aac aac 0.0080776385900 14967 cac cac 0.0075401008045 13971 gct gct 0.0072497440489 13433 gac gac 0.0072227592203 13383 tgt tgt 0.0068314792058 12658 agt agt 0.0064806764341 12008 gcg gcg 0.0064720412889 11992 gca gca 0.0061913990716 11472 ttt ttt 0.0050191781177 9300 acc acc 0.0047795528398 8856 att att 0.0046915822986 8693 tat tat 0.0046732326152 8659 tga tga 0.0045982147917 8520 gga gga 0.0045507214934 8432 tac tac 0.0042976038012 7963 agc agc 0.0040142631010 7438 ctc ctc 0.0039198162009 7263 cta cta 0.0038917519792 7211 ccc ccc 0.0036985406065 6853 ata ata 0.0035787279676 6631 ctt ctt 0.0035614576773 6599 tcc tcc 0.0034583756321 6408 atc atc 0.0034313908035 6358 gcc gcc 0.0031901464359 5911 ttc ttc 0.0030681750106 5685 taa taa 0.0030676353141 5684 tgc tgc 0.0027875327933 5165 ggt ggt 0.0027724212893 5137 gtt gtt 0.0027470555504 5090 gtc gtc 0.0026634025818 4935 cga cga 0.0025009539137 4634 tta tta 0.0023903161165 4429 gta gta 0.0023735855227 4398 ggc ggc 0.0020254812339 3753 cgt cgt 0.0015386749262 2851 cgc cgc 0.0013211772078 2448 ; Host name clust-rsat ; Job started 2024-05-22.081720 ; Job done 2024-05-22.081734 ; Seconds 13.62 ; user 13.62 ; system 0.19 ; cuser 0 ; csystem 0.01