This script can be used for coloring regions of an alignment to better visualize the location of features. For instance, if the sequences being aligned are transcripts, then the coding regions can be displayed in red - this helps to see if the coding regions align with each other or not. The format for specifying the color of the features and their location in the sequences is shown in the colored box. For more details on how to represent possibly overlapping features etc. please check the FAQ
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