We analyze minisatellites derived from Alu fragments corresponding approximately 
to the first 44 bases of human Alu consensus sequences from different 
subfamilies. The origin of Alu-derived minisatellites appears to have been 
mediated by short flanking repeats, as first proposed by Haber and Louis [Haber, 
J.E., Louis, E.J., 1998. Minisatellite origins in yeast and humans. Genomics 48, 
132-135.]. We also present evidence for base substitutions and deletions 
introduced to minisatellites by gene conversion with partially similar but 
unrelated flanking regions. Segments flanked by short direct repeats are 
relatively common in different regions of Alu and other repetitive sequences. 
Our analysis shows that they can be effectively used in comparative studies of 
the overall sequence context which may contribute to instability of DNA segments 
flanked by short direct repeats.