; 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_start_codons.wc -o $RSAT/public_html/data/genomes/Oreochromis_niloticus_Orenil1.0/genome/Oreochromis_niloticus_Orenil1.0_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/Oreochromis_niloticus_Orenil1.0/genome/Oreochromis_niloticus_Orenil1.0_start_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Oreochromis_niloticus_Orenil1.0/genome/Oreochromis_niloticus_Orenil1.0_start_codon_frequencies.tab ; 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 199 (other letters than ACGT) ; discarded occurrences 83 (contain discarded residues) ; nb possible positions 26674 ; total oligo occurrences 26674 ; 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 0.3706605683437 9887 ttt ttt 0.0212941441104 568 aaa aaa 0.0197570668066 527 ctg ctg 0.0193821699033 517 cag cag 0.0182949688836 488 gag gag 0.0147334483017 393 gtg gtg 0.0141336132564 377 tgt tgt 0.0134213091400 358 aga aga 0.0132713503786 354 aag aag 0.0131588813076 351 ctt ctt 0.0128964534753 344 aca aca 0.0128589637850 343 gaa gaa 0.0125965359526 336 agc agc 0.0124840668816 333 ctc ctc 0.0122966184299 328 att att 0.0122591287396 327 tct tct 0.0121091699783 323 tta tta 0.0116218040039 310 ttc ttc 0.0115093349329 307 ttg ttg 0.0114343555522 305 agt agt 0.0114343555522 305 gct gct 0.0113593761716 303 tgg tgg 0.0113593761716 303 gga gga 0.0111344380295 297 tca tca 0.0109469895779 292 gtt gtt 0.0109469895779 292 agg agg 0.0104596236035 279 aat aat 0.0104596236035 279 act act 0.0101597060808 271 atc atc 0.0098972782485 264 tga tga 0.0098972782485 264 aac aac 0.0097473194871 260 caa caa 0.0097098297968 259 cac cac 0.0097098297968 259 gca gca 0.0096723401065 258 cct cct 0.0096723401065 258 tgc tgc 0.0095973607258 256 cca cca 0.0093724225838 250 gtc gtc 0.0093349328935 249 cat cat 0.0089600359901 239 acc acc 0.0087350978481 233 tat tat 0.0086226287771 230 gat gat 0.0085476493964 228 tcc tcc 0.0085101597061 227 gac gac 0.0084351803254 225 ata ata 0.0083602009447 223 ggt ggt 0.0081352628027 217 taa taa 0.0076853865187 205 gcc gcc 0.0076853865187 205 ggc ggc 0.0074604483767 199 gta gta 0.0069730824023 186 ggg ggg 0.0068231236410 182 cta cta 0.0067106545700 179 ccc ccc 0.0066731648797 178 tac tac 0.0061108195246 163 acg acg 0.0058483916923 156 gcg gcg 0.0048361700532 129 cgg cgg 0.0045737422209 122 cga cga 0.0044987628402 120 tag tag 0.0044612731499 119 cgt cgt 0.0044237834595 118 cgc cgc 0.0043488040789 116 ccg ccg 0.0042363350079 113 tcg tcg 0.0032990927495 88 ; Host name n42 ; Job started 2017-04-15.090504 ; Job done 2017-04-15.090504 ; Seconds 0.38 ; user 0.38 ; system 0.02 ; cuser 0 ; csystem 0