; 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_start_codons.wc -o $RSAT/public_html/data/genomes/Bos_taurus_UMD3.1/genome/Bos_taurus_UMD3.1_start_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_start_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Bos_taurus_UMD3.1/genome/Bos_taurus_UMD3.1_start_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 162 (other letters than ACGT) ; discarded occurrences 67 (contain discarded residues) ; nb possible positions 22051 ; total oligo occurrences 22051 ; 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 atg atg 0.4572128248152 10082 ctg ctg 0.0184572128248 407 cag cag 0.0167339349689 369 ggg ggg 0.0146932111922 324 gtg gtg 0.0144211146887 318 ccc ccc 0.0142850664369 315 gag gag 0.0136048251780 300 ggc ggc 0.0134687769262 297 gcc gcc 0.0132420298399 292 gga gga 0.0125617885810 277 agg agg 0.0120629449912 266 tgg tgg 0.0120629449912 266 gct gct 0.0116548002358 257 cct cct 0.0114734025668 253 ctc ctc 0.0111106072287 245 agc agc 0.0108385107251 239 tgc tgc 0.0107478118906 237 cca cca 0.0106117636388 234 aga aga 0.0104757153871 231 ttt ttt 0.0102943177180 227 tcc tcc 0.0102036188835 225 tct tct 0.0100675706317 222 aag aag 0.0100222212145 221 ctt ctt 0.0098408235454 217 aaa aaa 0.0095233776246 210 gaa gaa 0.0093419799556 206 cgg cgg 0.0092966305383 205 gcg gcg 0.0091152328693 201 ttc ttc 0.0088431363657 195 ttg ttg 0.0088431363657 195 gca gca 0.0083442927758 184 tca tca 0.0082082445241 181 acc acc 0.0079361480205 175 cgc cgc 0.0078907986032 174 tga tga 0.0078000997687 172 gac gac 0.0076640515169 169 ggt ggt 0.0076187020997 168 cac cac 0.0075733526824 167 ccg ccg 0.0075280032652 166 caa caa 0.0073012561789 161 act act 0.0073012561789 161 tgt tgt 0.0072105573443 159 agt agt 0.0069838102580 154 gtc gtc 0.0068477620063 151 aca aca 0.0066210149200 146 gtt gtt 0.0066210149200 146 att att 0.0063489184164 140 atc atc 0.0062128701646 137 tta tta 0.0059407736611 131 gat gat 0.0059407736611 131 aat aat 0.0057140265748 126 cat cat 0.0055326289057 122 ata ata 0.0052605324022 116 aac aac 0.0050791347331 112 gta gta 0.0048070382296 106 acg acg 0.0047163393950 104 tat tat 0.0042628452224 94 tcg tcg 0.0041267969707 91 cta cta 0.0039907487189 88 taa taa 0.0038093510498 84 tac tac 0.0037186522153 82 cga cga 0.0035826039635 79 cgt cgt 0.0032651580427 72 tag tag 0.0031291097909 69 ; Host name n85 ; Job started 2017-04-15.084943 ; Job done 2017-04-15.084944 ; Seconds 0.61 ; user 0.61 ; system 0.03 ; cuser 0 ; csystem 0