; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_stop_codons.wc -o $RSAT/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_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/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34/genome/Strongyloides_ratti.S_ratti_ED321_v5_0_4.34_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 33960 ; Sum of sequence lengths 101880 ; discarded residues 2 (other letters than ACGT) ; discarded occurrences 1 (contain discarded residues) ; nb possible positions 33959 ; total oligo occurrences 33959 ; 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 0.0965870608675 3280 aaa aaa 0.0903442386407 3068 aat aat 0.0639300332754 2171 cag cag 0.0527400689066 1791 atg atg 0.0437292028623 1485 ttt ttt 0.0366618569451 1245 att att 0.0363084896493 1233 gag gag 0.0341882858741 1161 gaa gaa 0.0314202420566 1067 caa caa 0.0310079802114 1053 tat tat 0.0293589328308 997 ttg ttg 0.0292705910068 994 gat gat 0.0256780234989 872 tta tta 0.0253541034777 861 tag tag 0.0252363143791 857 ata ata 0.0220854559910 750 gtt gtt 0.0165788156306 563 cat cat 0.0158131864896 537 aga aga 0.0154303719191 524 tgt tgt 0.0128979062988 438 aca aca 0.0128095644748 435 tca tca 0.0123678553550 420 agt agt 0.0123384080803 419 aac aac 0.0119850407845 407 ctt ctt 0.0116316734886 395 tct tct 0.0113077534674 384 act act 0.0111605170941 379 tgg tgg 0.0105715716010 359 ctg ctg 0.0098353897347 334 taa taa 0.0096587060868 328 gct gct 0.0092464442416 314 gta gta 0.0091875496923 312 gtg gtg 0.0088341823964 300 agg agg 0.0086280514738 293 acg acg 0.0083924732766 285 gga gga 0.0071851350158 244 atc atc 0.0065667422480 223 tac tac 0.0065078476987 221 ggt ggt 0.0062722695015 213 ttc ttc 0.0058894549309 200 cgt cgt 0.0057422185577 195 cca cca 0.0056538767337 192 tcg tcg 0.0055066403604 187 gca gca 0.0051827203392 176 cct cct 0.0047999057687 163 cta cta 0.0045054330222 153 tga tga 0.0042404075503 144 gac gac 0.0042109602756 143 cac cac 0.0039753820784 135 ccg ccg 0.0029741747401 101 tgc tgc 0.0028858329162 98 acc acc 0.0027385965429 93 tcc tcc 0.0027091492682 92 ggg ggg 0.0025913601696 88 gtc gtc 0.0023852292470 81 cga cga 0.0022968874231 78 gcg gcg 0.0022379928738 76 cgg cgg 0.0022379928738 76 ctc ctc 0.0021790983245 74 agc agc 0.0021496510498 73 gcc gcc 0.0016196001060 55 ggc ggc 0.0010012073383 34 cgc cgc 0.0006772873171 23 ccc ccc 0.0005006036691 17 ; Host name n80 ; Job started 2017-04-15.082828 ; Job done 2017-04-15.082829 ; Seconds 1.98 ; user 1.98 ; system 0.07 ; cuser 0 ; csystem 0