; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Callithrix_jacchus_C_jacchus3.2.1/genome/Callithrix_jacchus_C_jacchus3.2.1_stop_codons.wc -o $RSAT/public_html/data/genomes/Callithrix_jacchus_C_jacchus3.2.1/genome/Callithrix_jacchus_C_jacchus3.2.1_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/Callithrix_jacchus_C_jacchus3.2.1/genome/Callithrix_jacchus_C_jacchus3.2.1_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Callithrix_jacchus_C_jacchus3.2.1/genome/Callithrix_jacchus_C_jacchus3.2.1_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 43771 ; Sum of sequence lengths 131313 ; discarded residues 170 (other letters than ACGT) ; discarded occurrences 69 (contain discarded residues) ; nb possible positions 43702 ; total oligo occurrences 43702 ; 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 0.2209281039769 9655 taa taa 0.1317788659558 5759 tag tag 0.0974554940277 4259 agg agg 0.0666559882843 2913 aga aga 0.0395176422132 1727 agc agc 0.0256281177063 1120 agt agt 0.0202736716855 886 cag cag 0.0135234085397 591 aag aag 0.0126767653654 554 aaa aaa 0.0122648849023 536 ctg ctg 0.0115784174637 506 gag gag 0.0113495949842 496 tgg tgg 0.0107775387854 471 cca cca 0.0106631275457 466 gaa gaa 0.0105258340579 460 cct cct 0.0102512470825 448 gga gga 0.0100224246030 438 gcc gcc 0.0091757814288 401 ttt ttt 0.0091528991808 400 atg atg 0.0087867832136 384 gtg gtg 0.0087410187177 382 ccc ccc 0.0085350784861 373 caa caa 0.0081460802709 356 tgc tgc 0.0080545512791 352 aca aca 0.0079172577914 346 ggg ggg 0.0078028465516 341 gct gct 0.0077799643037 340 tcc tcc 0.0076884353119 336 ttc ttc 0.0076655530639 335 ggc ggc 0.0074824950803 327 tgt tgt 0.0073909660885 323 ctc ctc 0.0072765548487 318 acc acc 0.0071850258569 314 tca tca 0.0071621436090 313 tct tct 0.0070934968651 310 gca gca 0.0070477323692 308 aac aac 0.0069790856254 305 ggt ggt 0.0068646743856 300 aat aat 0.0066129696581 289 gac gac 0.0066129696581 289 ctt ctt 0.0064985584184 284 cat cat 0.0064070294266 280 cac cac 0.0063155004348 276 gat gat 0.0059493844675 260 att att 0.0057892087319 253 act act 0.0057663264839 252 ttg ttg 0.0057205619880 250 atc atc 0.0054002105167 236 tat tat 0.0053086815249 232 gtt gtt 0.0048281543179 211 gta gta 0.0047595075740 208 gtc gtc 0.0047137430781 206 tta tta 0.0046450963343 203 ata ata 0.0045306850945 198 cta cta 0.0041645691273 182 tac tac 0.0039586288957 173 cgg cgg 0.0037526886641 164 cga cga 0.0035009839367 153 ccg ccg 0.0029975744817 131 acg acg 0.0029289277379 128 cgc cgc 0.0026543407624 116 gcg gcg 0.0024255182829 106 cgt cgt 0.0020136378198 88 tcg tcg 0.0019449910759 85 ; Host name n95 ; Job started 2017-04-15.091026 ; Job done 2017-04-15.091027 ; Seconds 1.02 ; user 1.02 ; system 0.03 ; cuser 0 ; csystem 0