; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Bos_taurus_UMD3.1/genome/Bos_taurus_UMD3.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Bos_taurus_UMD3.1/genome/Bos_taurus_UMD3.1_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/Bos_taurus_UMD3.1/genome/Bos_taurus_UMD3.1_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Bos_taurus_UMD3.1/genome/Bos_taurus_UMD3.1_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 22118 ; Sum of sequence lengths 66354 ; discarded residues 88 (other letters than ACGT) ; discarded occurrences 36 (contain discarded residues) ; nb possible positions 22082 ; total oligo occurrences 22082 ; 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 tga tga 0.2463997826284 5441 taa taa 0.1335476858980 2949 tag tag 0.1122633819400 2479 agg agg 0.0888053618332 1961 aga aga 0.0461461824110 1019 agc agc 0.0300244543067 663 agt agt 0.0226881623041 501 aag aag 0.0111855810162 247 aaa aaa 0.0106421519790 235 gag gag 0.0100987229418 223 ctg ctg 0.0096911511638 214 cca cca 0.0087854361018 194 cag cag 0.0085590073363 189 gcc gcc 0.0084684358301 187 gaa gaa 0.0083778643239 185 cct cct 0.0081514355584 180 gga gga 0.0081514355584 180 ccc ccc 0.0080155782991 177 tgg tgg 0.0079250067929 175 ggc ggc 0.0070645774839 156 gca gca 0.0065211484467 144 ggg ggg 0.0065211484467 144 ttt ttt 0.0063852911874 141 gat gat 0.0063400054343 140 tca tca 0.0062947196812 139 tct tct 0.0062494339281 138 aca aca 0.0061588624219 136 atg atg 0.0060230051626 133 ctc ctc 0.0059777194095 132 gtg gtg 0.0059324336564 131 ctt ctt 0.0058871479033 130 gct gct 0.0058871479033 130 caa caa 0.0058871479033 130 aat aat 0.0057965763971 128 tcc tcc 0.0057965763971 128 cac cac 0.0055701476316 123 ggt ggt 0.0053890046191 119 gac gac 0.0053890046191 119 att att 0.0052531473598 116 ttg ttg 0.0052531473598 116 aac aac 0.0052078616067 115 tgt tgt 0.0051625758536 114 tgc tgc 0.0049814328412 110 acc acc 0.0048455755819 107 act act 0.0048455755819 107 atc atc 0.0046644325695 103 cat cat 0.0046191468164 102 ttc ttc 0.0042568607916 94 gtc gtc 0.0038945747668 86 tta tta 0.0036681460013 81 gtt gtt 0.0036681460013 81 gta gta 0.0034417172358 76 cgg cgg 0.0033964314827 75 ccg ccg 0.0033511457296 74 ata ata 0.0033511457296 74 tat tat 0.0033058599765 73 tac tac 0.0030794312109 68 acg acg 0.0029888597047 66 cta cta 0.0027171451861 60 cgc cgc 0.0024454306675 54 gcg gcg 0.0024001449144 53 cgt cgt 0.0021284303958 47 cga cga 0.0020831446427 46 tcg tcg 0.0019925731365 44 ; Host name n89 ; Job started 2017-04-15.090124 ; Job done 2017-04-15.090125 ; Seconds 0.61 ; user 0.61 ; system 0.05 ; cuser 0 ; csystem 0