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Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

Figure 3

Two alignments of assemblies to the finished sequence of BAC GMEZ.

The original Atlas assembly created a single scaffold. The UMD+Atlas assembly of GMEZ assembled a 26 Kb section from the middle of the bigger scaffold into a separate Scaffold 1. Note that the large scaffold gap in the Scaffold 2 is estimated correctly. This UMD+Atlas assembly used reliable overlaps. This was the BAC that gave UMD+Atlas the most trouble and the only case where UMD+Atas assembly had two scaffolds.

Figure 3