; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Oreochromis_niloticus_Orenil1.0/genome/Oreochromis_niloticus_Orenil1.0_stop_codons.wc -o $RSAT/public_html/data/genomes/Oreochromis_niloticus_Orenil1.0/genome/Oreochromis_niloticus_Orenil1.0_stop_codon_frequencies ; 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/Oreochromis_niloticus_Orenil1.0/genome/Oreochromis_niloticus_Orenil1.0_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Oreochromis_niloticus_Orenil1.0/genome/Oreochromis_niloticus_Orenil1.0_stop_codon_frequencies ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 26757 ; Sum of sequence lengths 80271 ; discarded residues 181 (other letters than ACGT) ; discarded occurrences 72 (contain discarded residues) ; nb possible positions 26685 ; total oligo occurrences 26685 ; 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 tga tga 0.2005995877834 5353 agg agg 0.1193554431328 3185 taa taa 0.1162450815065 3102 tag tag 0.0791830616451 2113 aga aga 0.0698894510024 1865 agc agc 0.0422334644932 1127 agt agt 0.0348885141465 931 aaa aaa 0.0139404159640 372 gag gag 0.0122915495597 328 cag cag 0.0103054150272 275 aag aag 0.0102679407907 274 ctg ctg 0.0101180438449 270 aca aca 0.0095934045344 256 tgt tgt 0.0094060333521 251 gaa gaa 0.0087689713322 234 tgg tgg 0.0083192804947 222 ttt ttt 0.0081693835488 218 atg atg 0.0079820123665 213 tca tca 0.0079070638936 211 gtg gtg 0.0074948472925 200 aat aat 0.0073074761102 195 tct tct 0.0071950534008 192 aac aac 0.0071575791643 191 gga gga 0.0071575791643 191 tgc tgc 0.0069702079820 186 caa caa 0.0068203110362 182 act act 0.0068203110362 182 cca cca 0.0067078883268 179 gct gct 0.0066329398539 177 gac gac 0.0066329398539 177 cct cct 0.0063706201986 170 gat gat 0.0061832490163 165 att att 0.0060333520705 161 atc atc 0.0059958778340 160 acc acc 0.0058834551246 157 ctc ctc 0.0058834551246 157 tcc tcc 0.0058459808881 156 gca gca 0.0058085066517 155 ttc ttc 0.0056960839423 152 cac cac 0.0052089188683 139 ttg ttg 0.0050215476860 134 ctt ctt 0.0049840734495 133 ggt ggt 0.0049840734495 133 ccc ccc 0.0046842795578 125 tta tta 0.0043095371932 115 cat cat 0.0043095371932 115 gtt gtt 0.0042720629567 114 ata ata 0.0042345887203 113 gcc gcc 0.0041971144838 112 tat tat 0.0040472175379 108 ggc ggc 0.0039722690650 106 ggg ggg 0.0039347948286 105 gtc gtc 0.0038223721192 102 tac tac 0.0035225782275 94 gta gta 0.0035225782275 94 cta cta 0.0030354131535 81 acg acg 0.0028480419711 76 cgt cgt 0.0025857223159 69 cgc cgc 0.0025107738430 67 cga cga 0.0023983511336 64 ccg ccg 0.0021735057148 58 gcg gcg 0.0020985572419 56 cgg cgg 0.0016863406408 45 tcg tcg 0.0015739179314 42 ; Host name biow ; Job started 2015-09-04.063742 ; Job done 2015-09-04.063742 ; Seconds 0.68 ; user 0.69 ; system 0.01 ; cuser 0 ; csystem 0