; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Danaus_plexippus.DanPle_1.0.34/genome/Danaus_plexippus.DanPle_1.0.34_stop_codons.wc -o $RSAT/public_html/data/genomes/Danaus_plexippus.DanPle_1.0.34/genome/Danaus_plexippus.DanPle_1.0.34_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/Danaus_plexippus.DanPle_1.0.34/genome/Danaus_plexippus.DanPle_1.0.34_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Danaus_plexippus.DanPle_1.0.34/genome/Danaus_plexippus.DanPle_1.0.34_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 95711 ; Sum of sequence lengths 287133 ; discarded residues (other letters than ACGT) ; discarded occurrences (contain discarded residues) ; nb possible positions 95711 ; total oligo occurrences 95711 ; 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 0.1368494739372 13098 cag cag 0.1324403673559 12676 gag gag 0.0742756840906 7109 atg atg 0.0339563895477 3250 aaa aaa 0.0320234873734 3065 tag tag 0.0311249490654 2979 caa caa 0.0289517401344 2771 acg acg 0.0273218334361 2615 ttg ttg 0.0266949462444 2555 ctg ctg 0.0258904410151 2478 agg agg 0.0198723239753 1902 tcg tcg 0.0197887390164 1894 gaa gaa 0.0192140924241 1839 tgg tgg 0.0190260262666 1821 ccg ccg 0.0184618277941 1767 aat aat 0.0183155541160 1753 gtg gtg 0.0152542549968 1460 gat gat 0.0141572024114 1355 cgg cgg 0.0132900084630 1272 gcg gcg 0.0128093949494 1226 aga aga 0.0108764927751 1041 aca aca 0.0108138040560 1035 aac aac 0.0107824596964 1032 tat tat 0.0106570822580 1020 att att 0.0104794642204 1003 cat cat 0.0103854311417 994 taa taa 0.0091630011179 877 act act 0.0090898642789 870 ttt ttt 0.0089749349605 859 ggg ggg 0.0088913500016 851 gac gac 0.0086092507653 824 ata ata 0.0083271515291 797 cac cac 0.0077002643374 737 tca tca 0.0076480237381 732 gct gct 0.0074913019402 717 cca cca 0.0070002403068 670 tta tta 0.0068957591081 660 tac tac 0.0068330703890 654 gtt gtt 0.0067912779095 650 tct tct 0.0067285891904 644 agt agt 0.0067181410705 643 cga cga 0.0060599095193 580 ctt ctt 0.0059972208001 574 ttc ttc 0.0056733290844 543 cct cct 0.0052554042900 503 gca gca 0.0051718193311 495 gga gga 0.0051404749715 492 tgt tgt 0.0051195787318 490 ctc ctc 0.0050046494133 479 cta cta 0.0048270313757 462 atc atc 0.0047643426565 456 acc acc 0.0046703095778 447 agc agc 0.0043255216224 414 tga tga 0.0040329742663 386 gta gta 0.0037404269102 358 gcc gcc 0.0036881863109 353 ggt ggt 0.0036568419513 350 tcc tcc 0.0036359457116 348 gtc gtc 0.0034478795541 330 cgt cgt 0.0033851908349 324 ccc ccc 0.0033225021157 318 cgc cgc 0.0029045773213 278 ggc ggc 0.0028418886021 272 tgc tgc 0.0027583036433 264 ; Host name n88 ; Job started 2017-04-15.091147 ; Job done 2017-04-15.091149 ; Seconds 1.98 ; user 1.98 ; system 0.05 ; cuser 0 ; csystem 0