The sequences to be screened for should be similar in length and each stored in a plain text file i.e. sequence only, records <81 characters. Establish the cutoff score by trial and error! Tailor the individual files to suit i.e. their sequence and the number required. At present repe is set to handle up to 2000 individual files totalling 100,000 characters. If it is necessary to screen for several families, treat them separately, each with their own file of file names. At present it always writes tags of type ALUS. Contact us if you want this to string to be selectable.