; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Drosophila_sechellia.dsec_caf1.34/genome/Drosophila_sechellia.dsec_caf1.34_stop_codons.wc -o $RSAT/public_html/data/genomes/Drosophila_sechellia.dsec_caf1.34/genome/Drosophila_sechellia.dsec_caf1.34_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/Drosophila_sechellia.dsec_caf1.34/genome/Drosophila_sechellia.dsec_caf1.34_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Drosophila_sechellia.dsec_caf1.34/genome/Drosophila_sechellia.dsec_caf1.34_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 58017 ; Sum of sequence lengths 174051 ; discarded residues 33 (other letters than ACGT) ; discarded occurrences 16 (contain discarded residues) ; nb possible positions 58001 ; total oligo occurrences 58001 ; 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 aag aag 0.1024637506250 5943 cag cag 0.0927397803486 5379 gag gag 0.0555852485302 3224 atg atg 0.0362235133877 2101 caa caa 0.0317235909726 1840 aaa aaa 0.0304822330649 1768 tgg tgg 0.0265857485216 1542 ttg ttg 0.0238961397217 1386 ctg ctg 0.0237237289012 1376 acg acg 0.0236202824089 1370 agg agg 0.0235858002448 1368 aat aat 0.0228789158808 1327 gcg gcg 0.0218099687936 1265 tcg tcg 0.0192065654040 1114 gtg gtg 0.0185858864502 1078 cgg cgg 0.0183445113015 1064 gat gat 0.0180341718246 1046 aac aac 0.0179479664144 1041 gaa gaa 0.0176376269375 1023 tag tag 0.0147583662351 856 ccg ccg 0.0140169997069 813 att att 0.0130859812762 759 cat cat 0.0128273650454 744 ggg ggg 0.0121549628455 705 gcc gcc 0.0120687574352 700 gac gac 0.0119480698609 693 aga aga 0.0116377303840 675 cac cac 0.0112929087430 655 aca aca 0.0108791227737 631 gct gct 0.0107584351994 624 tac tac 0.0107411941173 623 ttt ttt 0.0106894708712 620 tat tat 0.0099653454251 578 atc atc 0.0095343183738 553 ttc ttc 0.0095170772918 552 agc agc 0.0091032913226 528 agt agt 0.0091032913226 528 gca gca 0.0090515680764 525 act act 0.0089136394200 517 gga gga 0.0081722728918 474 cga cga 0.0078619334149 456 cca cca 0.0078274512508 454 gtc gtc 0.0076033171842 441 tgc tgc 0.0073964241996 429 tcc tcc 0.0070688436406 410 ggt ggt 0.0069309149842 402 ctt ctt 0.0066550576714 386 tct tct 0.0066550576714 386 ggc ggc 0.0065688522612 381 tca tca 0.0064481646868 374 gtt gtt 0.0063619592766 369 tgt tgt 0.0062412717022 362 acc acc 0.0062412717022 362 ata ata 0.0061895484561 359 cgc cgc 0.0058964500612 342 ctc ctc 0.0058447268151 339 taa taa 0.0058274857330 338 cct cct 0.0057240392407 332 tga tga 0.0052412889433 304 ccc ccc 0.0046033689074 267 tta tta 0.0045861278254 266 cta cta 0.0043102705126 250 cgt cgt 0.0042240651023 245 gta gta 0.0023965104050 139 ; Host name n81 ; Job started 2017-04-15.085142 ; Job done 2017-04-15.085144 ; Seconds 3.14 ; user 3.14 ; system 0.07 ; cuser 0 ; csystem 0