; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_stop_codons.wc -o $RSAT/public_html/data/genomes/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_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/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Pristionchus_pacificus.P_pacificus-5.0.34/genome/Pristionchus_pacificus.P_pacificus-5.0.34_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 262888 ; Sum of sequence lengths 788664 ; discarded residues (other letters than ACGT) ; discarded occurrences (contain discarded residues) ; nb possible positions 262888 ; total oligo occurrences 262888 ; 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 0.1352172788412 35547 cag cag 0.1159353032470 30478 gag gag 0.1133676698822 29803 atg atg 0.0348779708469 9169 acg acg 0.0345698548431 9088 caa caa 0.0294193725084 7734 ctg ctg 0.0286890234625 7542 aaa aaa 0.0268973859590 7071 tcg tcg 0.0251704147774 6617 agg agg 0.0239113234533 6286 gaa gaa 0.0217735309333 5724 aat aat 0.0202025197042 5311 ccg ccg 0.0194303277441 5108 ttg ttg 0.0188901737622 4966 gat gat 0.0182587261495 4800 gtg gtg 0.0171175557652 4500 gcg gcg 0.0158166215270 4158 cgg cgg 0.0157215239950 4133 tgg tgg 0.0131881257418 3467 aga aga 0.0127392653906 3349 cat cat 0.0119100149113 3131 ggg ggg 0.0109780590974 2886 aac aac 0.0108753537628 2859 cga cga 0.0106319040808 2795 att att 0.0101412008156 2666 tag tag 0.0090723045556 2385 aca aca 0.0084674842518 2226 cac cac 0.0084066218314 2210 atc atc 0.0083761906211 2202 gac gac 0.0077143117982 2028 act act 0.0075925869572 1996 gga gga 0.0074328231034 1954 tat tat 0.0073681567816 1937 cca cca 0.0067443169715 1773 tca tca 0.0065465141049 1721 gct gct 0.0065198867959 1714 ctc ctc 0.0061775356806 1624 ttc ttc 0.0061204771614 1609 gca gca 0.0059759289127 1571 acc acc 0.0054966373513 1445 ata ata 0.0054738139436 1439 tac tac 0.0054281671282 1427 agt agt 0.0054205593256 1425 ctt ctt 0.0051390706308 1351 gtt gtt 0.0049755028757 1308 ttt ttt 0.0048423663309 1273 gtc gtc 0.0044277410913 1164 gcc gcc 0.0042908006451 1128 agc agc 0.0042071148170 1106 cct cct 0.0042033109157 1105 tga tga 0.0041728797054 1097 ccc ccc 0.0041386445939 1088 cta cta 0.0041348406926 1087 taa taa 0.0040435470619 1063 cgc cgc 0.0036593530325 962 tcc tcc 0.0035566476979 935 tgc tgc 0.0035300203889 928 tct tct 0.0034881774748 917 tgt tgt 0.0030925717416 813 cgt cgt 0.0030925717416 813 gta gta 0.0030659444326 806 tta tta 0.0030431210249 800 ggc ggc 0.0025866528712 680 ggt ggt 0.0022443017559 590 ; Host name n58 ; Job started 2017-04-15.085413 ; Job done 2017-04-15.085416 ; Seconds 2.8 ; user 2.8 ; system 0.04 ; cuser 0 ; csystem 0