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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.

From: Multiple sequence alignment with user-defined anchor points

anchor nt positions in footprints
  total expanding new
none 1546 0 618
genes 1686 39 694
genes and BLASTZ hits 2433 39 841