Figure 1.

Description of RepeatExplorer cluster output. (A) Short tandem repeats, including many satellite sequences, form characteristic “star burst”-type clusters. Because they are tandem, and such repeats are of similar size or shorter than the length of an individual sequence read, a very high percentage of reads within the cluster meet the RepeatExplorer-defined criteria for pair formation. This results in each read successfully pairing with a very high percentage of the other reads assigned to the cluster. Because nearly all of the reads within the cluster are paired with nearly all of the other reads within this same cluster, a compact network of very short edges forms between reads. This in turn generates a very dense cluster with a core of paired reads possessing nearly identical sequences. If of sufficient length for assay design, the consensus sequences for these clusters make ideal diagnostic targets, as they contain the greatest number of repeats per read. (B) Long tandem repeats characteristically result in “doughnut”-like clusters. In such clusters, neighboring reads within the underlying scaffold meet the criteria for pair formation. However, because the length of the repeat monomers generating these clusters is longer, reads may be significantly shorter than the monomer itself. This results in many reads within the cluster that do not meet the criteria for pair formation as they map to different regions of the same monomer unit. Yet because they are tandemly arranged, reads spanning a repeat-repeat junction will meet the pair formation criteria, closing the sequence “loop” and resulting in a “doughnut”-shaped cluster. (C) Long interspersed repeats, such as transposable elements form characteristic “line”-type clusters. While reads neighboring each other in the underlying scaffold meet the criteria for pair formation, the extended length of a repeat monomer means that distant reads within a single monomer will not meet this threshold. This results in similar pairings to those seen in clusters generated from long tandem repeats. However, because these elements are interspersed, reads do not span repeat-repeat junctions, so a “loop” is not formed, and clusters attain a linear appearance.