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Direct Repeats


Direct repeats
Two identical (or nearly identical) nucleotide sequences sometimes separated by a sequence of non-repeated DNA. For example, 3' TAGT . . . TAGT 5'
5' ATCA . . . ATCA 3' ...
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Direct Repeats: Identical or related sequences present in two or more copies in the same orientation in the same molecule of DNA; they are not necessarily adjacent.
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Comparison revealed that the inverted terminal repeats were in each case flanked externally by direct repeats of the same length, but of different sequence (asterisks in the above alignment).
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Like DNA transposons, retrotransposons generate direct repeats at their new sites of insertion. In fact, it is the presence of these direct repeats that often is the clue that the intervening stretch of DNA arrived there by retrotransposition.
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Alu repeats integrate into AT rich regions of the genome, are flanked by short intact direct repeats (formed from the preintegration site) and also contain a characteristic 3' oligo-dA rich tail.
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