; 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_start_codons.wc -o $RSAT/public_html/data/genomes/Danaus_plexippus.DanPle_1.0.34/genome/Danaus_plexippus.DanPle_1.0.34_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/Danaus_plexippus.DanPle_1.0.34/genome/Danaus_plexippus.DanPle_1.0.34_start_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_start_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 atg atg 0.1977933570854 18931 gtg gtg 0.0534734774477 5118 gta gta 0.0407058749778 3896 gtt gtt 0.0402566058238 3853 ata ata 0.0319085580550 3054 gtc gtc 0.0315115295003 3016 gaa gaa 0.0288054664563 2757 att att 0.0277502063504 2656 aaa aaa 0.0220455329064 2110 gat gat 0.0214813344339 2056 atc atc 0.0209589284408 2006 gag gag 0.0207604141635 1987 aat aat 0.0177513556436 1699 ggt ggt 0.0174483601676 1670 gct gct 0.0159229346679 1524 gac gac 0.0153273918358 1467 gcg gcg 0.0153169437160 1466 gca gca 0.0151706700379 1452 aac aac 0.0142825798498 1367 gga gga 0.0135930039389 1301 aca aca 0.0135512114595 1297 aga aga 0.0128093949494 1226 ctg ctg 0.0120153378400 1150 ttg ttg 0.0116914461243 1119 acg acg 0.0115242762065 1103 ggc ggc 0.0109809739737 1051 agt agt 0.0109496296142 1048 caa caa 0.0107093228574 1025 ttt ttt 0.0106884266176 1023 tta tta 0.0104272236211 998 ttc ttc 0.0104167755012 997 agc agc 0.0103436386622 990 act act 0.0098212326692 940 gcc gcc 0.0095913740322 918 agg agg 0.0093824116350 898 tgt tgt 0.0090167274399 863 tat tat 0.0082226703305 787 tga tga 0.0081495334914 780 aag aag 0.0080555004127 771 tgg tgg 0.0078569861353 752 ctc ctc 0.0078047455360 747 cta cta 0.0076689199778 734 ctt ctt 0.0074390613409 712 tac tac 0.0069166553479 662 acc acc 0.0067703816698 648 cat cat 0.0065718673925 629 ggg ggg 0.0064046974747 613 tgc tgc 0.0060912538789 583 cgt cgt 0.0059136358412 566 cga cga 0.0058927396015 564 cca cca 0.0058718433618 562 cgg cgg 0.0057360178036 549 ccg ccg 0.0055479516461 531 tca tca 0.0054643666872 523 tct tct 0.0053389892489 511 tcg tcg 0.0052136118106 499 taa taa 0.0052031636907 498 cac cac 0.0051091306119 489 cct cct 0.0050986824921 488 tcc tcc 0.0043568659820 417 cgc cgc 0.0040016299067 383 ccc ccc 0.0036986344307 354 cag cag 0.0024866525269 238 tag tag 0.0009298826676 89 ; Host name n51 ; Job started 2017-04-15.091039 ; Job done 2017-04-15.091040 ; Seconds 1.08 ; user 1.08 ; system 0.02 ; cuser 0 ; csystem 0