Alignment of the RP11-886P16 BAC clone and three deleted BAC subclones obtained during transferring of the GAP2 YAC/BAC TAR isolate from yeast into E. coli cells. BAC RP11-886P16 (AC136469) was identified by screening the genomic library; sequences of the deleted YAC/BACs, 3-17.1, 3-17.2, and 3.17.3, are in the Supplemental Material. Comparison of sequences revealed that each clone has overlapping deletions in the same region that is highly enriched by Alu repeats. The gap sequence was reconstructed using the sequences of the deleted BACs and additional PCR amplification of the sequence from YAC TAR isolate. The sequence obtained matched the sequence present in the BAC clone AC136469.
