; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Callithrix_jacchus_C_jacchus3.2.1/genome/Callithrix_jacchus_C_jacchus3.2.1_start_codons.wc -o $RSAT/public_html/data/genomes/Callithrix_jacchus_C_jacchus3.2.1/genome/Callithrix_jacchus_C_jacchus3.2.1_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/Callithrix_jacchus_C_jacchus3.2.1/genome/Callithrix_jacchus_C_jacchus3.2.1_start_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Callithrix_jacchus_C_jacchus3.2.1/genome/Callithrix_jacchus_C_jacchus3.2.1_start_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 43771 ; Sum of sequence lengths 131313 ; discarded residues 563 (other letters than ACGT) ; discarded occurrences 231 (contain discarded residues) ; nb possible positions 43540 ; total oligo occurrences 43540 ; 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 0.4168121267800 18148 cag cag 0.0183509416628 799 ctg ctg 0.0181672025723 791 gtg gtg 0.0166743224621 726 agg agg 0.0163757464401 713 ggg ggg 0.0148139641709 645 ggc ggc 0.0145153881488 632 gag gag 0.0144464859899 629 gcc gcc 0.0144005512173 627 ttt ttt 0.0136655948553 595 ccc ccc 0.0135048231511 588 gga gga 0.0129765732660 565 tgg tgg 0.0125401929260 546 gaa gaa 0.0121038125861 527 aag aag 0.0120808451998 526 aga aga 0.0112310519063 489 gct gct 0.0111621497474 486 ctc ctc 0.0109095084979 475 cca cca 0.0108865411116 474 cct cct 0.0108176389527 471 tcc tcc 0.0105879650896 461 aaa aaa 0.0102664216812 447 ctt ctt 0.0101975195223 444 tct tct 0.0099678456592 434 gca gca 0.0098530087276 429 agc agc 0.0098530087276 429 tgc tgc 0.0097611391824 425 ttc ttc 0.0095084979329 414 ttg ttg 0.0095084979329 414 aca aca 0.0093477262288 407 tgt tgt 0.0091869545246 400 tca tca 0.0088194763436 384 gcg gcg 0.0087735415710 382 ggt ggt 0.0083371612311 363 gtt gtt 0.0081993569132 357 tga tga 0.0079696830501 347 ccg ccg 0.0079237482774 345 att att 0.0078778135048 343 acc acc 0.0077629765733 338 agt agt 0.0077400091870 337 cgc cgc 0.0077170418006 336 cat cat 0.0076711070280 334 gat gat 0.0076022048691 331 cac cac 0.0076022048691 331 cgg cgg 0.0075562700965 329 gac gac 0.0074414331649 324 gtc gtc 0.0073725310060 321 caa caa 0.0072347266881 315 acg acg 0.0069591180524 303 atc atc 0.0066835094166 291 act act 0.0066146072577 288 ata ata 0.0063619660083 277 aat aat 0.0063160312356 275 tta tta 0.0060633899862 264 aac aac 0.0057418465779 250 gta gta 0.0054203031695 236 cta cta 0.0048461185117 211 tat tat 0.0047312815802 206 taa taa 0.0046394120349 202 tac tac 0.0044786403307 195 tcg tcg 0.0036058796509 157 tag tag 0.0034451079467 150 cga cga 0.0032613688562 142 cgt cgt 0.0027560863574 120 ; Host name n85 ; Job started 2017-04-15.091026 ; Job done 2017-04-15.091027 ; Seconds 0.99 ; user 0.99 ; system 0.04 ; cuser 0 ; csystem 0