; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Melitaea_cinxia.MelCinx1.0.34/genome/Melitaea_cinxia.MelCinx1.0.34_stop_codons.wc -o $RSAT/public_html/data/genomes/Melitaea_cinxia.MelCinx1.0.34/genome/Melitaea_cinxia.MelCinx1.0.34_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/Melitaea_cinxia.MelCinx1.0.34/genome/Melitaea_cinxia.MelCinx1.0.34_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Melitaea_cinxia.MelCinx1.0.34/genome/Melitaea_cinxia.MelCinx1.0.34_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 96573 ; Sum of sequence lengths 289719 ; discarded residues 27 (other letters than ACGT) ; discarded occurrences 9 (contain discarded residues) ; nb possible positions 96564 ; total oligo occurrences 96564 ; 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 aag aag 0.1072035126962 10352 cag cag 0.0844310509092 8153 gag gag 0.0501636220538 4844 aaa aaa 0.0499150822253 4820 atg atg 0.0331904229319 3205 tag tag 0.0328176131892 3169 caa caa 0.0327244107535 3160 aat aat 0.0291723623711 2817 ttg ttg 0.0278778840976 2692 gaa gaa 0.0244501056294 2361 acg acg 0.0207944989851 2008 ctg ctg 0.0204424008947 1974 tat tat 0.0181123400025 1749 agg agg 0.0172942297336 1670 att att 0.0171388923408 1655 tgg tgg 0.0169214199909 1634 aac aac 0.0167764384243 1620 gat gat 0.0158651257197 1532 tcg tcg 0.0157304999793 1519 taa taa 0.0152748436270 1475 aca aca 0.0148916780581 1438 ata ata 0.0147674081438 1426 gtg gtg 0.0134832856965 1302 cat cat 0.0133383041299 1288 ttt ttt 0.0131415434323 1269 aga aga 0.0125616171658 1213 tac tac 0.0123545006421 1193 tta tta 0.0120748933350 1166 ccg ccg 0.0119195559422 1151 cac cac 0.0110289548900 1065 gcg gcg 0.0105318752330 1017 act act 0.0102419120997 989 gac gac 0.0100037280974 966 tca tca 0.0099415931403 960 cgg cgg 0.0096205625285 929 ctt ctt 0.0087713847811 847 atc atc 0.0086574706930 836 cga cga 0.0079946978170 772 cta cta 0.0079843419908 771 agt agt 0.0077047346837 744 cca cca 0.0076322439004 737 gtt gtt 0.0076218880742 736 gct gct 0.0072490783315 700 ttc ttc 0.0071662317220 692 ggg ggg 0.0071351642434 689 tct tct 0.0070005385030 676 gca gca 0.0068555569363 662 gta gta 0.0062756306698 606 cct cct 0.0061824282341 597 ctc ctc 0.0061099374508 590 gga gga 0.0060892257984 588 tga tga 0.0058096184914 561 tgt tgt 0.0057474835342 555 agc agc 0.0056749927509 548 acc acc 0.0055610786629 537 gtc gtc 0.0052193363987 504 tgc tgc 0.0041423304751 400 cgt cgt 0.0038316556895 370 gcc gcc 0.0038316556895 370 tcc tcc 0.0038212998633 369 cgc cgc 0.0037384532538 361 ggt ggt 0.0035416925562 342 ggc ggc 0.0033345760325 322 ccc ccc 0.0031171036825 301 ; Host name n79 ; Job started 2017-04-15.091749 ; Job done 2017-04-15.091752 ; Seconds 2.65 ; user 2.65 ; system 0.05 ; cuser 0 ; csystem 0