Should I trust the sequence of the transposons in Release 1 and 2?
No. As a result of the whole genome shotgun assembly, the sequence of each transposon in Releases 1 and 2 is a composite derived from a number of elements of that transposon type. The extent of the composite varies among the transposons depending on the length of the traces that run from unique sequence into the transposon. The sequence is most often not the actual sequence of the particular transposon at that location. Users are warned not to base too much on any analysis of these transposable element sequences. As we finish the sequence to high quality, we are replacing these composite sequences with the actual sequences present at each location in the y; cn bw sp strain. The BAC sequence submitted to GenBank and Release 3 contain transposons that have been resequenced and the sequence relects the sequence of the transposon at that location.
