; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Ciona_intestinalis_KH/genome/Ciona_intestinalis_KH_start_codons.wc -o $RSAT/public_html/data/genomes/Ciona_intestinalis_KH/genome/Ciona_intestinalis_KH_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/Ciona_intestinalis_KH/genome/Ciona_intestinalis_KH_start_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Ciona_intestinalis_KH/genome/Ciona_intestinalis_KH_start_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 17299 ; Sum of sequence lengths 51897 ; discarded residues 27 (other letters than ACGT) ; discarded occurrences 12 (contain discarded residues) ; nb possible positions 17287 ; total oligo occurrences 17287 ; 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 0.4431653843929 7661 aaa aaa 0.0265517440852 459 ttt ttt 0.0219818360618 380 att att 0.0177590096604 307 aat aat 0.0176433157864 305 tta tta 0.0167756117314 290 ata ata 0.0153872852432 266 tat tat 0.0151558974952 262 ttg ttg 0.0150980505582 261 gtt gtt 0.0148666628102 257 aca aca 0.0137675710071 238 gaa gaa 0.0137097240701 237 caa caa 0.0134783363221 233 tgt tgt 0.0132469485741 229 aag aag 0.0130734077631 226 aac aac 0.0116272343379 201 aga aga 0.0109909180309 190 taa taa 0.0108173772199 187 tca tca 0.0105859894719 183 ctt ctt 0.0100075201018 173 gta gta 0.0098339792908 170 agt agt 0.0096025915428 166 tgg tgg 0.0091398160467 158 gat gat 0.0087927344247 152 ttc ttc 0.0085034997397 147 tga tga 0.0083878058657 145 cat cat 0.0083299589287 144 cca cca 0.0083299589287 144 tac tac 0.0080407242437 139 atc atc 0.0080407242437 139 gtg gtg 0.0079250303696 137 gct gct 0.0076357956846 132 ggt ggt 0.0076357956846 132 cag cag 0.0076357956846 132 gga gga 0.0075201018106 130 acc acc 0.0074622548736 129 gca gca 0.0074044079366 128 tct tct 0.0070573263146 122 agc agc 0.0068259385666 118 act act 0.0067680916295 117 tgc tgc 0.0067102446925 116 gac gac 0.0067102446925 116 agg agg 0.0065945508185 114 cac cac 0.0064210100075 111 ctg ctg 0.0061317753225 106 cgt cgt 0.0056111528895 97 cta cta 0.0054376120784 94 cct cct 0.0052640712674 91 gag gag 0.0050905304564 88 tcc tcc 0.0050905304564 88 acg acg 0.0050326835194 87 gtc gtc 0.0050326835194 87 tag tag 0.0048012957714 83 cga cga 0.0043963672124 76 tcg tcg 0.0043963672124 76 ggc ggc 0.0042228264013 73 ggg ggg 0.0041071325273 71 ccc ccc 0.0040492855903 70 gcc gcc 0.0039335917163 68 ctc ctc 0.0034708162203 60 cgc cgc 0.0030080407242 52 cgg cgg 0.0030080407242 52 gcg gcg 0.0028344999132 49 ccg ccg 0.0020824897322 36 ; Host name n79 ; Job started 2017-04-15.084021 ; Job done 2017-04-15.084021 ; Seconds 0.7 ; user 0.7 ; system 0.03 ; cuser 0 ; csystem 0