; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Danio_rerio_GRCz10/genome/Danio_rerio_GRCz10_start_codons.wc -o $RSAT/public_html/data/genomes/Danio_rerio_GRCz10/genome/Danio_rerio_GRCz10_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/Danio_rerio_GRCz10/genome/Danio_rerio_GRCz10_start_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Danio_rerio_GRCz10/genome/Danio_rerio_GRCz10_start_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 45335 ; Sum of sequence lengths 136005 ; discarded residues 39 (other letters than ACGT) ; discarded occurrences 14 (contain discarded residues) ; nb possible positions 45321 ; total oligo occurrences 45321 ; 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 0.4517773217714 20475 ttt ttt 0.0182696763090 828 aaa aaa 0.0150040819929 680 cag cag 0.0138567110170 628 ctg ctg 0.0132609607025 601 tgt tgt 0.0127534696940 578 aca aca 0.0124224972971 563 tga tga 0.0122901083383 557 aga aga 0.0122239138589 554 gtg gtg 0.0118488118091 537 gtt gtt 0.0116060987180 526 att att 0.0114737097593 520 tca tca 0.0111206725359 504 gaa gaa 0.0110544780565 501 tta tta 0.0107014408332 485 ttg ttg 0.0107014408332 485 gga gga 0.0105690518744 479 tct tct 0.0104807925686 475 gag gag 0.0104366629156 473 aac aac 0.0101498201717 460 aag aag 0.0099512367335 451 ttc ttc 0.0098850422541 448 cat cat 0.0096864588160 439 act act 0.0096864588160 439 gat gat 0.0095099402043 431 ata ata 0.0095099402043 431 aat aat 0.0094437457249 428 ctc ctc 0.0093334215926 423 taa taa 0.0092672271133 420 caa caa 0.0092230974603 418 tat tat 0.0092010326339 417 agt agt 0.0091348381545 414 tgg tgg 0.0091127733280 413 cac cac 0.0089803843693 407 gca gca 0.0088479954105 401 agg agg 0.0086935416253 394 ctt ctt 0.0085611526665 388 atc atc 0.0085390878401 387 agc agc 0.0084949581872 385 gct gct 0.0083625692284 379 tgc tgc 0.0083184395755 377 cca cca 0.0077226892610 350 gac gac 0.0075903003023 344 ggt ggt 0.0073917168641 335 gtc gtc 0.0072593279054 329 tcc tcc 0.0068621610291 311 cct cct 0.0066635775910 302 ggc ggc 0.0060898921030 276 gta gta 0.0060457624501 274 acc acc 0.0056706604003 257 tac tac 0.0054500121357 247 gcc gcc 0.0054500121357 247 ggg ggg 0.0054058824827 245 gcg gcg 0.0052072990446 236 cgg cgg 0.0049204563006 223 ccc ccc 0.0048542618212 220 cta cta 0.0046777432095 212 cgc cgc 0.0045894839037 208 cgt cgt 0.0042805763333 194 tag tag 0.0042585115068 193 cga cga 0.0042143818539 191 ccg ccg 0.0040819928951 185 tcg tcg 0.0038392798041 174 acg acg 0.0037289556718 169 ; Host name n43 ; Job started 2017-04-15.092547 ; Job done 2017-04-15.092547 ; Seconds 0.58 ; user 0.58 ; system 0.02 ; cuser 0 ; csystem 0