; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Amphimedon_queenslandica.Aqu1.34/genome/Amphimedon_queenslandica.Aqu1.34_stop_codons.wc -o $RSAT/public_html/data/genomes/Amphimedon_queenslandica.Aqu1.34/genome/Amphimedon_queenslandica.Aqu1.34_stop_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/Amphimedon_queenslandica.Aqu1.34/genome/Amphimedon_queenslandica.Aqu1.34_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Amphimedon_queenslandica.Aqu1.34/genome/Amphimedon_queenslandica.Aqu1.34_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 166733 ; Sum of sequence lengths 500199 ; discarded residues 31 (other letters than ACGT) ; discarded occurrences 14 (contain discarded residues) ; nb possible positions 166719 ; total oligo occurrences 166719 ; 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 aag aag 0.1240230567602 20677 cag cag 0.0891919937140 14870 aaa aaa 0.0832058733558 13872 gag gag 0.0611567967658 10196 caa caa 0.0580977573042 9686 atg atg 0.0469652529106 7830 gaa gaa 0.0373982569473 6235 ctg ctg 0.0329476544365 5493 tag tag 0.0273154229572 4554 ttg ttg 0.0260138316569 4337 aat aat 0.0254380124641 4241 aca aca 0.0197218073525 3288 aga aga 0.0166027867250 2768 taa taa 0.0155951031376 2600 gat gat 0.0151272500435 2522 gtg gtg 0.0150192839448 2504 cat cat 0.0142395287880 2374 att att 0.0141315626893 2356 tca tca 0.0136037284293 2268 agg agg 0.0132798301333 2214 ata ata 0.0128539638553 2143 tgg tgg 0.0123681164114 2062 act act 0.0123441239451 2058 tat tat 0.0115343782052 1923 cca cca 0.0107306305820 1789 aac aac 0.0098069206269 1635 ttt ttt 0.0094410355148 1574 tta tta 0.0093270712996 1555 cta cta 0.0092370995507 1540 ctt ctt 0.0081754329141 1363 acg acg 0.0078935214343 1316 tga tga 0.0078275421518 1305 tct tct 0.0077075798199 1285 gca gca 0.0077015817033 1284 gct gct 0.0075936156047 1266 agt agt 0.0068978340801 1150 gac gac 0.0066938981160 1116 cct cct 0.0065199527348 1087 gga gga 0.0064179847528 1070 cac cac 0.0057581919277 960 gtt gtt 0.0056382295959 940 tac tac 0.0050684085197 845 gta gta 0.0050024292372 834 ggg ggg 0.0049244537215 821 tcg tcg 0.0043246420624 721 ccg ccg 0.0042946514794 716 tgt tgt 0.0041926834974 699 atc atc 0.0037188322867 620 agc agc 0.0034849057396 581 acc acc 0.0034609132732 577 cga cga 0.0034069302239 568 ctc ctc 0.0030290488787 505 cgg cgg 0.0028910921971 482 ttc ttc 0.0028431072643 474 gcg gcg 0.0022372974886 373 gtc gtc 0.0021593219729 360 ggt ggt 0.0020873445738 348 tgc tgc 0.0020633521074 344 tcc tcc 0.0019313935424 322 gcc gcc 0.0019133991927 319 cgt cgt 0.0015715065469 262 ccc ccc 0.0015715065469 262 ggc ggc 0.0013735686994 229 cgc cgc 0.0009057156053 151 ; Host name n44 ; Job started 2017-04-15.091230 ; Job done 2017-04-15.091231 ; Seconds 1.74 ; user 1.74 ; system 0.04 ; cuser 0 ; csystem 0