Fig. 10

Forward and backward scores of LTR-retrotransposon(s). The y-axis shows the scores where positive values represent the forward scores and negative values represent the backward scores. The x-axis shows the genomic positions. Blue bars represent the LTRs of one LTR-retrotransposon and yellow bars represent the LTRs of another LTR-retrotransposon. a A single LTR-retrotransposon. The 5’ LTR (left bar) has a score of approximately 2600, meaning its match begins at approximately 2600 where the 3’ LTR (right bar) starts. b Two recently nested LTR-retrotransposons. The outer LTR-retrotransposon is colored blue (vertical hatch pattern) and the inner LTR-retrotransposon is colored yellow (horizontal hatch pattern). The forward scores and backward scores of the nested LTRs are clearly distinguished. The 5’ LTR of the inner element is at positions 400–500 and the 3’ LTR is at positions 900–1,000. However, the forward and the backward scores of the LTRs of the outer element have merged with the internal parts. The outer 5’ LTR and a slice of the internal parts are at positions 0–400 and the outer 3’ LTR and a slice of the internal parts are at positions 1,000–1,400. Note that the scores of the outer element are pointing to the inner element. The outer 5’ LTR and a slice of the internal parts point to positions 400–700, which include the inner 5’ LTR and a slice of the inner LTR-retrotransposon’s internal part. The outer 3’ LTR and a slice of the internal part point to positions 700–1,000, which include the inner 3’ LTR and a slice of the inner LTR-retrotransposon’s internal parts. It is important to understand that in a recently nested LTR-retrotransposon, the outer LTRs do not point to each other but rather to the inner element