Progress in mammalian genome sequencing demands development of efficient, high-throughput methods for functional annotation of megabase-scale regions. We report the first complete sequence of a tumor amplicon that is associated with aggressive tumor behavior and occurs in a wide range of tumors. The overwhelming amount of data generated for this region by traditional analysis tools (such as GenScan, BLAST and RepeatMasker) required development of efficient annotation methods. For a comprehensive biological annotation of the amplicon we developed Genome Cryptographer. This tool integrates information on distribution and type of repetitive elements, results of database searches, comparative sequence data, expression data, array comparative genomic hybridization copy number data and information on CpG dinucleotide distribution. Genome Cryptographer revealed an uneven distribution of genes and repetitive elements in the 1-megabase region. The proximal amplicon peak as defined by array comparative genomic hybridization is composed of 60% repetitive sequence and encodes one protein-coding gene, ZNF217. A 14-kb duplicon was identified close to the 5′ end of ZNF217; it is 97% homologous to a 14-kb element on chromosome 22q13; contains one of three identified CpG islands, a conserved putative RNA gene and a single repetitive element; and is present at the murine ZNF217 locus. The distal amplicon peak contains two genes, CYP24 and PFDN4. Breakpoints for both amplicon peaks are located in regions of local repeat maxima. We have also developed software to create digital expression profiles of multi-megabase regions. This allowed us to confirm that ZNF217 has the highest relative expression in tumors and to identify three additional putative cancer-related genes.