We have explored the distributions of fully conserved ungapped blocks in 
genome-wide pair-wise alignments of recently completed species of Drosophila: D. 
melanogaster, D. yakuba, D. ananassae, D. pseudoobscura, D. virilis, and D. 
mojavensis. Based on these distributions we have found that nearly every 
functional sequence category possesses its own distinctive conservation pattern, 
sometimes independent of the overall sequence conservation level. In the coding 
and regulatory regions, the ungapped blocks were longer than in introns, UTRs, 
and nonfunctional sequences. At the same time, the blocks in the coding regions 
carried a 3N + 2 signature characteristic of synonymous substitutions in the 
third-codon position. Larger block sizes in transcription regulatory regions can 
be explained by the presence of conserved arrays of binding sites for 
transcription factors. We also have shown that the longest ungapped blocks, or 
"ultraconserved" sequences, are associated with specific gene groups, including 
those encoding ion channels and components of the cytoskeleton. We discuss how 
restraining conservation patterns may help in mapping functional sequence 
categories and improve genome annotation.