; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Danio_rerio_EnsEMBL/genome/Danio_rerio_EnsEMBL_stop_codons.wc -o $RSAT/public_html/data/genomes/Danio_rerio_EnsEMBL/genome/Danio_rerio_EnsEMBL_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_EnsEMBL/genome/Danio_rerio_EnsEMBL_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Danio_rerio_EnsEMBL/genome/Danio_rerio_EnsEMBL_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 29304 ; Sum of sequence lengths 87912 ; discarded residues 1 (other letters than ACGT) ; discarded occurrences 1 (contain discarded residues) ; nb possible positions 29303 ; total oligo occurrences 29303 ; 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 0.2941337064464 8619 taa taa 0.2071460260042 6070 tag tag 0.1120363102754 3283 aaa aaa 0.0196908166399 577 aag aag 0.0172678565335 506 gag gag 0.0159369347848 467 cag cag 0.0136846056718 401 gaa gaa 0.0120806743337 354 aca aca 0.0113640241613 333 ctg ctg 0.0102378596048 300 ttt ttt 0.0092823260417 272 aga aga 0.0090434426509 265 gac gac 0.0087363068628 256 aac aac 0.0083609186773 245 caa caa 0.0081561614852 239 aat aat 0.0078490256970 230 cca cca 0.0078490256970 230 gtg gtg 0.0076101423062 223 ttc ttc 0.0075418899089 221 tca tca 0.0073712589155 216 gat gat 0.0073030065181 214 ggt ggt 0.0072006279221 211 atg atg 0.0070641231273 207 agt agt 0.0067228611405 197 tgt tgt 0.0066204825444 194 gta gta 0.0064839777497 190 att att 0.0064498515510 189 ata ata 0.0064498515510 189 cac cac 0.0063815991537 187 atc atc 0.0058697061734 172 tct tct 0.0057332013787 168 tta tta 0.0056649489813 166 tac tac 0.0055966965840 164 agc agc 0.0055966965840 164 cct cct 0.0055625703853 163 cat cat 0.0055284441866 162 agg agg 0.0054943179879 161 ctc ctc 0.0054260655906 159 ttg ttg 0.0053578131932 157 act act 0.0052213083985 153 ctt ctt 0.0050848036037 149 gtc gtc 0.0050848036037 149 gga gga 0.0049824250077 146 tat tat 0.0049482988090 145 gtt gtt 0.0049141726103 144 tgc tgc 0.0048459202129 142 gct gct 0.0046070368222 135 gca gca 0.0046070368222 135 tcc tcc 0.0045046582261 132 ccc ccc 0.0041292700406 121 acc acc 0.0039586390472 116 gcc gcc 0.0037880080538 111 tgg tgg 0.0035491246630 104 cta cta 0.0029007268880 85 ggc ggc 0.0029007268880 85 acg acg 0.0022864553117 67 cgg cgg 0.0022182029144 65 cgc cgc 0.0021840767157 64 cga cga 0.0020816981196 61 ggg ggg 0.0020816981196 61 ccg ccg 0.0020475719210 60 cgt cgt 0.0018086885302 53 tcg tcg 0.0018086885302 53 gcg gcg 0.0015698051394 46 ; Host name n44 ; Job started 2017-04-15.090943 ; Job done 2017-04-15.090943 ; Seconds 0.42 ; user 0.42 ; system 0.02 ; cuser 0 ; csystem 0