Flowchart of the de novo strategy. Input genomic sequences (black lines on top) contain a family of repeats with three copies (i.e., elements); two full length (blue and red boxes) and one partially deleted (green box). These elements, unknown at this point, will yield three alignments in an all versus all pairwise comparison of the genomic sequences. The aligned fragments (i.e., images), colored as their corresponding elements for clarity, are sorted to their corresponding genomic region, and those coming from the same element (i.e., syntopic images) can be grouped together according to their overlaps. On the basis of the syntopic sets, elements can be defined. These defined elements are then clustered into one family because they are all similar to each other.