Figure 1

Skittle user interface. This shows the first 28,670 nucleotides of the Human Y chromosome. A) The Annotation Display is a single bar that shows annotation entries alongside the Nucleotide Display. The two annotations shown here are user notes created using Skittle. B) The Skittle Nucleotide View, with black = A, red = C, green = G, and blue = T. Unsequenced gaps (represented by "N" in the data file) are in gray. A high copy repeat of length 61 can be seen in the lower portion. Since the width of the nucleotide display is set to 122, two repeats appear on each line. C) The Skittle Repeat Map uses each row of the Nucleotide Display as a search string. The vertical red bar is a reference to the Width setting in the Nucleotide View in this case, width 122. The Repeat Map allows the user to see other repeats that are not currently aligned, such as the C-rich (red) repeat in the middle of the view window.