The subdirectories contain predictions of AUGUSTUS on the 44 ENCODE regions.
The coordinates in the files in encode_coords start with 1 while the coordinates in the files in chr_coords are the positions 
on the chromosome in build hg17=ncbi35.
The predictions are from 4 different caterogies in the EGASP 2005 gene prediction assessment (see http://www1.imim.es/gencode/workshop2005.html).
The categories with AUGUSTUS predictions are

1. methods using any type of available information to reproduce the HAVANA-ENCODE annotation 
2. ab initio single-genome methods 
3. EST-, mRNA-, and protein-based methods 
4. dual- or multiple- genome based methods 

The files are in gtf format. Only the coding sequence (CDS) is annotated. The stop codon is excluded from the CDS. Only one transcript per gene.