Fig. 11

Connected components examples of LTR-retrotransposons. These connected components represent perfect-world scenarios; for simplicity, each edge represents two edges pointing in and out and the weights are not shown. For each example, there are two rows. The top rows contain forward nodes (representing LTR candidates found in the forward stretches) that point forward to a match further in the genome. The bottom rows contain backward nodes (representing LTR candidates found in the backward stretches) that point backwards. When nodes from the forward and backwards nodes overlap, they represent the same LTR. a A single LTR-retrotransposon with the 5’ LTR pointing to the 3’ LTR and vice versa. b An LTR-retrotransposon with a solo LTR. This connected component may represent one of three scenarios depending on which node represents the solo element, which can be the leftmost node, the rightmost node, or the middle node. c A recently nested LTR-retrotransposon. Note that the outermost LTRs merged with the internal part of the outer retrotransposon. Two nodes from the nested LTRs merged with the internal part of the nested retrotransposon. However, two nodes from the nested LTRs are not merged and are distinguishable. d A complex graph case where there are many LTRs right by each other