The net file format is used to describe the axtNet data that underlie the net alignment annotations in the Genome Browser. For a detailed description of the methods used to generate these data, refer to the Genome Browser description pages that accompany the -downloadable net alignment tracks. +downloadable net alignment tracks. You can find a detailed example how nets are constructed on our wiki.
At the beginning of each target species chromosome, a "net" line appears with the format:
net chromName chromSizechromName is the target species chromosome name, and chromSize is the chromosome size. For example:
net chr2L 23011544Each target chromosome section in the file starts with a net line. The net line is followed by a set of "fill" and "gap" lines.