**1.5 Potential Cre-mediated cross-recombination of loxP & lox511 sites does not occur in our method**

The 34 bp sequence in the mutant lox site, lox511, differs by one nucleotide in the spacer region from that of loxP [see references (24, 32), for actual sequence of lox511]. Varying degrees of promiscuity in recombining different mutant *lox* sites, including the lox511 mutant, with wild type loxP have been reported in previous studies; using both partially purified Cre-extracts *in vitro* (32-36), or Cre over-expressed in cells (36-38). For example, cross recombination between loxP and lox511 has been reported to occur at efficiencies ranging from 5 to 100 % under those experimental conditions that express Cre constitutively (33, 35-38). We have not observed such cross-recombination, and high levels of stringency *in vivo* in recombining identical *lox* sites (21, 24), or *lox* sites with at least identical spacers (39), have been achieved with Cre protein expressed from its native source namely, a phage P1 infection (21, 24, 39). Depending on whether a loxP or a lox511 transposon is used, truncations from the corresponding lox- end can be made readily and exclusively with high stringency [shown schematically in Figure 4]. Thus truncations of genomic DNA from either end are not only efficient, but are highly specific for that end.
