; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Drosophila_pseudoobscura.Dpse_3.0.34/genome/Drosophila_pseudoobscura.Dpse_3.0.34_stop_codons.wc -o $RSAT/public_html/data/genomes/Drosophila_pseudoobscura.Dpse_3.0.34/genome/Drosophila_pseudoobscura.Dpse_3.0.34_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/Drosophila_pseudoobscura.Dpse_3.0.34/genome/Drosophila_pseudoobscura.Dpse_3.0.34_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Drosophila_pseudoobscura.Dpse_3.0.34/genome/Drosophila_pseudoobscura.Dpse_3.0.34_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 64201 ; Sum of sequence lengths 192603 ; discarded residues (other letters than ACGT) ; discarded occurrences (contain discarded residues) ; nb possible positions 64201 ; total oligo occurrences 64201 ; 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 0.1036899736764 6657 cag cag 0.0945468139126 6070 gag gag 0.0564477188829 3624 atg atg 0.0378966059719 2433 caa caa 0.0336754879207 2162 aaa aaa 0.0291740004050 1873 tgg tgg 0.0279123378141 1792 ttg ttg 0.0246102085637 1580 gcg gcg 0.0245323281569 1575 aat aat 0.0241740782854 1552 acg acg 0.0237846762511 1527 agg agg 0.0233641220542 1500 ctg ctg 0.0230681765082 1481 tcg tcg 0.0203267861871 1305 cgg cgg 0.0193766452236 1244 gat gat 0.0183174716905 1176 gaa gaa 0.0177567327612 1140 gtg gtg 0.0174452111338 1120 aac aac 0.0165262223330 1061 cat cat 0.0139873210698 898 tag tag 0.0135823429542 872 att att 0.0132085170013 848 ccg ccg 0.0125075933397 803 aga aga 0.0120558869800 774 ggg ggg 0.0118378218408 760 gac gac 0.0117132131898 752 tac tac 0.0109188330400 701 aca aca 0.0108565287145 697 gca gca 0.0105450070871 677 cac cac 0.0103425180293 664 gcc gcc 0.0103269419479 663 ttc ttc 0.0101088768088 649 ttt ttt 0.0097506269373 626 tat tat 0.0096571704491 620 atc atc 0.0093923770658 603 agc agc 0.0093144966589 598 gct gct 0.0092054640893 591 act act 0.0090029750315 578 cca cca 0.0081462905562 523 cga cga 0.0080684101494 518 agt agt 0.0078191928475 502 ggc ggc 0.0075543994642 485 gtc gtc 0.0072273017554 464 tct tct 0.0070092366163 450 gga gga 0.0068534758026 440 cgc cgc 0.0068223236398 438 ctc ctc 0.0067600193143 434 tca tca 0.0066509867448 427 tgt tgt 0.0063394651174 407 gtt gtt 0.0062304325478 400 acc acc 0.0061681282223 396 tgc tgc 0.0060279434900 387 ata ata 0.0059656391645 383 tcc tcc 0.0057164218626 367 ctt ctt 0.0057008457812 366 ccc ccc 0.0052491394215 337 tga tga 0.0051868350960 333 taa taa 0.0050310742823 323 cct cct 0.0046416722481 298 cgt cgt 0.0045949440040 295 ggt ggt 0.0044080310276 283 tta tta 0.0042055419698 270 cta cta 0.0038472920983 247 gta gta 0.0028348468092 182 ; Host name n43 ; Job started 2017-04-15.083715 ; Job done 2017-04-15.083716 ; Seconds 0.75 ; user 0.75 ; system 0.01 ; cuser 0 ; csystem 0