; 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_stop_codons.wc -o $RSAT/public_html/data/genomes/Ciona_intestinalis_KH/genome/Ciona_intestinalis_KH_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/Ciona_intestinalis_KH/genome/Ciona_intestinalis_KH_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Ciona_intestinalis_KH/genome/Ciona_intestinalis_KH_stop_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 40 (other letters than ACGT) ; discarded occurrences 14 (contain discarded residues) ; nb possible positions 17285 ; total oligo occurrences 17285 ; 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 taa taa 0.1847844952271 3194 tga tga 0.1217818918137 2105 tag tag 0.0624240671102 1079 agg agg 0.0366213479896 633 aga aga 0.0328030083888 567 aaa aaa 0.0268440844663 464 gaa gaa 0.0212901359560 368 agt agt 0.0182817471796 316 caa caa 0.0169511136824 293 agc agc 0.0152733584032 264 ttt ttt 0.0151576511426 262 aat aat 0.0146948221001 254 gtt gtt 0.0141162857969 244 aac aac 0.0134220422332 232 aag aag 0.0133641886028 231 aca aca 0.0130749204513 226 atg atg 0.0126699450391 219 att att 0.0123806768875 214 gat gat 0.0121492623662 210 ttg ttg 0.0116864333237 202 gag gag 0.0112236042812 194 tta tta 0.0109921897599 190 tgt tgt 0.0107029216083 185 ggt ggt 0.0106450679780 184 tca tca 0.0106450679780 184 ata ata 0.0106450679780 184 cca cca 0.0105293607174 182 tat tat 0.0097194098930 168 ttc ttc 0.0096615562627 167 ctt ctt 0.0093722881111 162 gtg gtg 0.0093722881111 162 act act 0.0091987272201 159 cag cag 0.0091408735898 158 gga gga 0.0087358981776 151 gta gta 0.0083887763957 145 atc atc 0.0083309227654 144 tac tac 0.0081573618745 141 cat cat 0.0080416546138 139 acc acc 0.0079259473532 137 gac gac 0.0079259473532 137 tct tct 0.0078680937229 136 gca gca 0.0076945328319 133 tgg tgg 0.0076366792016 132 ctg ctg 0.0075209719410 130 gct gct 0.0072317037894 125 tgc tgc 0.0067688747469 117 cct cct 0.0067110211166 116 cac cac 0.0065953138559 114 acg acg 0.0064217529650 111 tcc tcc 0.0064217529650 111 cga cga 0.0062481920741 108 ctc ctc 0.0062481920741 108 cgt cgt 0.0060746311831 105 cta cta 0.0059589239225 103 ggg ggg 0.0055539485103 96 gtc gtc 0.0051489730981 89 tcg tcg 0.0050332658374 87 cgg cgg 0.0048597049465 84 ggc ggc 0.0046861440555 81 ccc ccc 0.0045125831646 78 ccg ccg 0.0044547295343 77 gcg gcg 0.0043968759040 76 gcc gcc 0.0037604859705 65 cgc cgc 0.0030662424067 53 ; Host name n81 ; Job started 2017-04-15.083846 ; Job done 2017-04-15.083847 ; Seconds 1.3 ; user 1.3 ; system 0.08 ; cuser 0 ; csystem 0