; 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_start_codons.wc -o $RSAT/public_html/data/genomes/Drosophila_sechellia.dsec_caf1.34/genome/Drosophila_sechellia.dsec_caf1.34_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/Drosophila_sechellia.dsec_caf1.34/genome/Drosophila_sechellia.dsec_caf1.34_start_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Drosophila_sechellia.dsec_caf1.34/genome/Drosophila_sechellia.dsec_caf1.34_start_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 58017 ; Sum of sequence lengths 174051 ; discarded residues 47 (other letters than ACGT) ; discarded occurrences 19 (contain discarded residues) ; nb possible positions 57998 ; total oligo occurrences 57998 ; 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 0.3017173005966 17499 gtg gtg 0.0277250939688 1608 atc atc 0.0251387978896 1458 att att 0.0238801337977 1385 aaa aaa 0.0209662402152 1216 ctg ctg 0.0201041415221 1166 ata ata 0.0195523983586 1134 gtc gtc 0.0195006724370 1131 gtt gtt 0.0191385909859 1110 gaa gaa 0.0183109762406 1062 gca gca 0.0170178282010 987 ctc ctc 0.0163281492465 947 aac aac 0.0161212455602 935 aat aat 0.0145867098865 846 gac gac 0.0144660160695 839 gct gct 0.0138453050105 803 caa caa 0.0138108210628 801 gta gta 0.0136901272458 794 gat gat 0.0135349494810 785 gcc gcc 0.0135349494810 785 ctt ctt 0.0132590778992 769 agc agc 0.0126211248664 732 ttc ttc 0.0123969792062 719 ttt ttt 0.0116555743301 676 gag gag 0.0115176385393 668 act act 0.0115176385393 668 ggc ggc 0.0114314286700 663 cca cca 0.0111555570882 647 ttg ttg 0.0110865891927 643 tgc tgc 0.0110865891927 643 cta cta 0.0110348632711 640 gcg gcg 0.0108452015587 629 aca aca 0.0106210558985 616 acc acc 0.0104141522121 604 cac cac 0.0102589744474 595 gga gga 0.0097934411531 568 tgg tgg 0.0093106658850 540 cat cat 0.0092244560157 535 ggt ggt 0.0085175350874 494 cct cct 0.0082416635056 478 ccc ccc 0.0081899375841 475 acg acg 0.0078968240284 458 cgc cgc 0.0078623400807 456 aga aga 0.0078623400807 456 agt agt 0.0075864684989 440 tac tac 0.0073795648126 428 tta tta 0.0071726611262 416 tga tga 0.0071554191524 415 cga cga 0.0069485154661 403 ccg ccg 0.0067588537536 392 aag aag 0.0064140142764 372 tca tca 0.0062415945377 362 agg agg 0.0061726266423 358 tcc tcc 0.0060174488775 349 tgt tgt 0.0057933032174 336 tct tct 0.0052243180799 303 tat tat 0.0051036242629 296 tcg tcg 0.0049829304459 289 cgg cgg 0.0048622366288 282 cgt cgt 0.0045173971516 262 cag cag 0.0037415083279 217 ggg ggg 0.0035863305631 208 taa taa 0.0030173454257 175 tag tag 0.0005517431636 32 ; Host name n79 ; Job started 2017-04-15.090813 ; Job done 2017-04-15.090815 ; Seconds 1.69 ; user 1.69 ; system 0.04 ; cuser 0 ; csystem 0