; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Danio_rerio_GRCz10/genome/Danio_rerio_GRCz10_stop_codons.wc -o $RSAT/public_html/data/genomes/Danio_rerio_GRCz10/genome/Danio_rerio_GRCz10_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/Danio_rerio_GRCz10/genome/Danio_rerio_GRCz10_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Danio_rerio_GRCz10/genome/Danio_rerio_GRCz10_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 45335 ; Sum of sequence lengths 136005 ; discarded residues 25 (other letters than ACGT) ; discarded occurrences 9 (contain discarded residues) ; nb possible positions 45326 ; total oligo occurrences 45326 ; 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 0.2185500595685 9906 taa taa 0.1503772669108 6816 tag tag 0.0770859992058 3494 agg agg 0.0503022547765 2280 aga aga 0.0425142302431 1927 agc agc 0.0188854079336 856 agt agt 0.0174954772095 793 cag cag 0.0164144199797 744 aaa aaa 0.0147376781538 668 gag gag 0.0133256850373 604 aag aag 0.0131933106826 598 aca aca 0.0119136919208 540 gaa gaa 0.0112076953625 508 ttt ttt 0.0112076953625 508 ctg ctg 0.0108767594758 493 caa caa 0.0098177646384 445 tgg tgg 0.0097515774611 442 tgt tgt 0.0097295150686 441 tca tca 0.0096633278913 438 gga gga 0.0096192031064 436 cac cac 0.0092882672197 421 atg atg 0.0091558928650 415 cca cca 0.0089793937255 407 gtg gtg 0.0087587698010 397 tct tct 0.0086705202312 393 ctc ctc 0.0083175219521 377 gat gat 0.0082513347747 374 ttg ttg 0.0080527732427 365 aat aat 0.0076997749636 349 gca gca 0.0076556501787 347 act act 0.0075894630014 344 gct gct 0.0075232758240 341 att att 0.0074350262542 337 tgc tgc 0.0072364647222 328 ttc ttc 0.0071702775449 325 aac aac 0.0071261527600 323 cat cat 0.0069496536204 315 gtt gtt 0.0068834664431 312 ggt ggt 0.0067952168733 308 atc atc 0.0067952168733 308 gac gac 0.0067069673035 304 acc acc 0.0063980938093 290 cct cct 0.0063980938093 290 tcc tcc 0.0063760314168 289 ata ata 0.0060671579226 275 gcc gcc 0.0059127211755 268 ctt ctt 0.0058244716057 264 tat tat 0.0057803468208 262 ggc ggc 0.0056038476812 254 tta tta 0.0055817852888 253 ggg ggg 0.0055597228964 252 gtc gtc 0.0053390989719 242 ccc ccc 0.0049640383003 225 tac tac 0.0045889776287 208 cta cta 0.0042801041345 194 gta gta 0.0042580417420 193 acg acg 0.0041697921723 189 ccg ccg 0.0037064819309 168 cgg cgg 0.0035741075762 162 gcg gcg 0.0034196708291 155 cga cga 0.0033093588669 150 tcg tcg 0.0032211092971 146 cgt cgt 0.0030887349424 140 cgc cgc 0.0028681110180 130 ; Host name n77 ; Job started 2017-04-15.092830 ; Job done 2017-04-15.092831 ; Seconds 1.37 ; user 1.37 ; system 0.06 ; cuser 0 ; csystem 0