Number of aligned ancient DNA fragments and average sequence length. Properties of Mega BLAST alignments of ancient DNA sequences from a Neandertal fossil to genome sequences of increasing divergence. Left panel: number of reads with a best hit to the genome sequence and not to the GenBank nonredundant and environmental databases (yellow). Subset of reads with one unique best hit to the reference genome (light green). Subset of reads with one unique best hit to the reference genome that can be fully aligned with a positive alignment score (dark green). Right panel: Average length of best local alignments (yellow), average length of fragments with a unique best local alignment (red), average length of fragments with a positive score when fully aligned to reference genome (brown).