; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_start_codons.wc -o $RSAT/public_html/data/genomes/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_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/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_start_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_start_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 262888 ; Sum of sequence lengths 788664 ; discarded residues (other letters than ACGT) ; discarded occurrences (contain discarded residues) ; nb possible positions 262888 ; total oligo occurrences 262888 ; 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 0.1404742704117 36929 gtg gtg 0.0493898542345 12984 atc atc 0.0373923495937 9830 gaa gaa 0.0330292748243 8683 gtc gtc 0.0320402604912 8423 att att 0.0305186999787 8023 gtt gtt 0.0288411795137 7582 gag gag 0.0271864824564 7147 gac gac 0.0229413286266 6031 gcg gcg 0.0228386232920 6004 gca gca 0.0222490185935 5849 gat gat 0.0216822373026 5700 gta gta 0.0206627917592 5432 aaa aaa 0.0195938954992 5151 ata ata 0.0188102918353 4945 aat aat 0.0186239006725 4896 gcc gcc 0.0178136696996 4683 aag aag 0.0168855177870 4439 acg acg 0.0164404613371 4322 gga gga 0.0161551687411 4247 ttc ttc 0.0160562673078 4221 gct gct 0.0158698761450 4172 aac aac 0.0154818782143 4070 ttg ttg 0.0147819603786 3886 ggc ggc 0.0139527098993 3668 aca aca 0.0134353793250 3532 aga aga 0.0129256565534 3398 act act 0.0128914214418 3389 ggt ggt 0.0124844040047 3282 ctc ctc 0.0118757797998 3122 acc acc 0.0114573506588 3012 agt agt 0.0108715498615 2858 agc agc 0.0104226895104 2740 tcg tcg 0.0102401022489 2692 caa caa 0.0100917500989 2653 ctg ctg 0.0100841422963 2651 tgc tgc 0.0093994400657 2471 ttt ttt 0.0088745016889 2333 ccg ccg 0.0087147378351 2291 ccc ccc 0.0087109339338 2290 tct tct 0.0086310520069 2269 tac tac 0.0085968168954 2260 tcc tcc 0.0084370530416 2218 tga tga 0.0084028179301 2209 tgg tgg 0.0079007029610 2077 tgt tgt 0.0076039986610 1999 tca tca 0.0073187060649 1924 tat tat 0.0072274124342 1900 agg agg 0.0070258056663 1847 cac cac 0.0069497276407 1827 cca cca 0.0069231003317 1820 cct cct 0.0062878488177 1653 tta tta 0.0062422020024 1641 ctt ctt 0.0061547122729 1618 cga cga 0.0057476948358 1511 cat cat 0.0056107543897 1475 cgc cgc 0.0050629926052 1331 cta cta 0.0048119351207 1265 cgt cgt 0.0045456620310 1195 ggg ggg 0.0044924074130 1181 cag cag 0.0044924074130 1181 taa taa 0.0042831928426 1126 cgg cgg 0.0031724536685 834 tag tag 0.0018867350355 496 ; Host name n55 ; Job started 2017-04-15.084734 ; Job done 2017-04-15.084738 ; Seconds 2.69 ; user 2.7 ; system 0.05 ; cuser 0 ; csystem 0