Distinct characteristics of loop sequences of twoDrosophilafoldback transposable elements

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Abstract
A few foldback (FB) transposable elements have, between their long terminal inverted repeats, central loop sequences which have been shown to be different from FB inverted repeat sequences. We have investigated loop sequences from two such FB elements by analyzing their genomic distribution and sequence conservation and, in particular, by determining if they are normally associated with FE elements. One of these FB loop sequences seems to be present in a few conserved copies found adjacent to FB inverted repeat sequences, suggesting that it represents an integral component of some FB elements. The other loop sequence is less well-conserved and not usually associated with FR inverted repeats. This sequence is a member of another famtly of transposable elements, the HR family, and was found inserted in an FB element only by chance. We compare the complete DNA sequences of two HE elements and examine the ends of four HB elements.