Figure 4.

Complications because of sequence similarity between related families. (A) The schematic structure of Tc1 and Tc7, two related DNA transposons that are similar at the end of their terminal inverted repeats (black and grey blocks) but not in the rest of the sequences (Plasterk and von Luenen 1997). (B) A Tc1 element and its images. (C) Images in B are filtered, and only those ends labeled with closed circles will be collected to determine whether the element should be split. Open circles in Box b mark the misleading ends. Dashed lines link the pairs of images formed with the same copy of Tc7 and represent the unalignable sequences between a Tc1 and a Tc7. Although not shown in the figure, the two TIRs of Tc1 also form alignments in the opposite strands, and images from these alignments are also filtered.