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From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese:

Homologous recombination. All cellular organisms have molecular functions dedicated to recognizing and recombining DNA molecules that have extensive sequence similarity at the region of cross-over, usually greater than 200 base pairs. The principle molecule involved in homologous recombination belongs to the family of RecA/Rad51 DNA binding enzymes that catalyse post-replicative strand exchange during meiotic/mitotic recombination or repair of DNA double-strand breaks. These enzymes show some sequence preferences (Raja et al., 2006) and require minimally efficient processing segments of 20–30 base pairs to initiate strand exchange (Majewski and Cohan, 1999).

I'm not sure of the meaning of "greater than 200 base pairs". Does that relate to "sequence similarity"? Is similarity somehow measured in base pairs?

Or does that relate to "the region of cross-over"? Is the meaning "the region of cross-over is usually greater than 200 base pairs"?

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No, similarity is not measured in base pairs. They are talking of regions of cross-over being marked by at least 200bp of highly similar sequence between the two strands involved in exchange.

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