Figure 1

Interpretation of RepeatMasker outfiles and TinT information. Schematic representation of the nested insertion of an AluSq element (coordinates in red) into an AluJb element (coordinates in blue). The framed area of the RepeatMasker outfile contains the information analyzed by the TinT application and the default parameters. The five characteristics used for extracting unambiguous nested clusters are as follows: (1) fragmented/inserted elements must be located at the same query sequence, (2) for stringent conditions, the element indices for the two parts of the fragmented element must be identical and the index for the nested element must be higher than this; for relaxed conditions the same class of fragmented element parts is sufficient, (3) the minimum size of all elements (starting/ending coordinates) must be 20 nt or more, (4) the fragmented parts of the host element must both be in the same orientation, and (5) the non-overlapping host elements should preferably be larger than 50 nt, but at least ≥ 19 nt with an overlap of no more than 35 nt (starting/end-position consensus).