Additional file 16: of Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters DalleryJean-Félix LapaluNicolas ZampounisAntonios PignéSandrine LuytenIsabelle AmselemJoëlle WittenbergAlexander ZhouShiguo de QueirozMarisa RobinGuillaume AugerAnnie HainautMatthieu HenrissatBernard KimKi-Tae LeeYong-Hwan LespinetOlivier SchwartzDavid ThonMichael O’ConnellRichard 2017 (A) Dinucleotide mutation bias among TE copies belonging to different TE orders. Mutation rates were calculated using RIPCAL by comparing each TE copy with a Ti/Tv > 1.5 to the TE consensus sequence. Y-axis: percentage relative to the total number of copies used in RIPCAL analysis. Coloured bars indicate the percentage of copies with expected RIP (Ti/Tv > 1.5) and dinucleotide preferentially used (>1/3) in CN- > TN and (cNG - > cNA) mutations. Black bar: percentage of copies without expected RIP (Ti/Tv > 1.5). Gray bar: percentage of copies with expected RIP (Ti/Tv > 1.5) but no evidence of dinucleotide bias. (B) Plot showing the sequence divergence of TE copies belonging to different TE orders relative to their respective consensus sequences. (PDF 466 kb)