On 8/13/2009 3:37 PM, Robert Levis wrote: I am attaching a table of sequence locations for the collection at the Bloomington Stock Center of P-element insertions described by Staudt et al. (2005) (FBrf0191391). These locations are based on the flanking sequence tags deposited by the authors in GenBank. The sequences were retrieved from GenBank by Joseph Carlson, who aligned them with the D. melanogaster reference genomic sequence (Release 5) using software he developed for his work on the Gene Disruption Project. In some cases, I selected the best alignment from a table of several alternative alignments in his database. For almost all of the lines in the table, the flanking sequence clearly aligned at a single site in the genomic sequence. There is a "1" in the right column of the table for these unique alignments. However, there are three lines for which the flanking sequence aligned equally well at two genomic sites a few kilobases apart. There is one line for which the flanking sequence aligned equally well at two genomic sites on different chromosomes. For these four lines for which the flanking sequence maps to two sites, each site is listed on a separate line in the table and there is a "2" in the right column. The GenBank records do not specify the position of the insertion within the flanking sequence. However, the flanking sequences are relatively short (approximately 50 bp or less) and so the ambiguity in the insertion position is fairly small. The location specified in the attached table is that of the nucleotide of the genomic sequence that aligns with the 5' end of the flanking sequence. In addition, I was not able to determine a map location from the GenBank sequence for the following lines. Either the sequence was never submitted to GenBank, the sequence aligns equally well to multiple sites in the genome, or I can't find any credible alignment of the flanking sequence to genomic sequence. DP00384 45/47 match to TE 1360 consensus HP36889 aligns at multiple sites HP35104 no credible alignment HP32367 no credible alignment HP31858 no credible alignment HP21974 nts 16-50 align with TE hobo HP20255 no credible alignment HP11042 no credible alignment HP10995 no credible alignment HP10973 no credible alignment DP01487 46/47 match to TE 1360 consensus, 47/47 match to multiple sites DP01433 46/47 match to multiple sites DP01393 19 bp flank, no 19/19 hits DP00102 no credible alignment
