Table 1  Effect of different anchors in the Fugu example of Figure 2. We consider aligned sequence positions in intergenic regions (i.e., outside the coding regions and introns) only. Column 2 gives the number of sequence positions for which DIALIGN added at least one additional sequence that was not represented in original TRACKER footprint. Column 3 lists the total number of nucleotides in footprints that were not detected by tracker but were aligned by anchored DIALIGN.
anchor  nt positions in footprints
total  expanding  new
none  1546  0  618
genes  1686  39  694
genes and BLASTZ hits  2433  39  841