These are the references to the Nature Genetics articles that describe:

The generation of the collection:

Thibault, et al.     PubMed ID: 14981521

and how it was used to generate deficiencies:

Parks, et al.         PubMed ID: 14981519

In regards to the sequences flanking the insertion sites that are found in Supplementary Table 3 in Thibault, et al., the keys to reading these entries are the following:

The first two letters refer to the element type. (XP, PB, RB or WH)
The second entry is the stock number. (one letter followed by five digits)
The third entry indicates the number of flanking sequences are associated with that particular stock.  In some cases this represents multiple inserts per stock, in others this may represent erroneously assigned sequence files (more on this later).
The fourth entry is the R3 coordinate of the insertion site.
The fifth entry is the chromosome arm.  U is unknown.
The sixth entry is the orientation of the element in the chromosome.
Finally, the flanking sequence data completes the set of data.  As a general rule, the first 200 nt precede the transposon while the remaining 201 nt are 3' to the insertion site.

All of this data is in the process of being refined.  Insertion sites should be considered approximate.  In the case of multiple flanking sequences for a given line, one should assume the existence of multiple inserts until proven otherwise.