Phylogenetic tree based on alignments of LTRs from Ty elements of <i>S</i>. <i>cerevisiae</i> S288C.

<p>LTRs longer than 200 nucleotides were retrieved and a multiple alignment was performed at <a href="http://www.ebi.ac.uk/Tools/msa/clustalw2" target="_blank">www.ebi.ac.uk/Tools/msa/clustalw2</a>. A) A phylogenetic tree was created using the maximum likelihood method for tree building provided by the software MEGA6. The main cluster for each Ty family is highlighted blue (Ty1), green (Ty2), light pink (Ty3) or dark pink (Ty4). Five consensus sequences—Ty1Cons1, Ty1Cons2, Ty2Cons, Ty3Cons, and Ty4Cons—are specified in bold letters. B) Per Ty consensus sequence, the number of genome sequences sharing >0.95, >0.97 or >0.98 level of identity is reported. C) Pair-wise comparison of identity levels between consensus sequences.