Additional file 16: of Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

(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)