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Colors are used to divide sections of the graph and on the trace nodes displayed in the Map View. The color is determined by the ping time to that node, taken from a range determined in this section of the Options Dialog.
You may choose a default range of times by pressing the Default Fast or Default Slow buttons (low latency and high latency). If you are using a modem you should use the slow settings, most other users should use the fast settings. This has no effect on anything other than the colors used in the graph and on the map nodes.
Once you are familiar with the characteristics of your connection you may want to set your own custom color bands.
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