Background: Tn3 is a bacterial transposon, which encodes transposase required for its transposition. Tn3 has terminal inverted repeat (IR) sequences of 38 bp in length, whose inner region, called the B domain, is bound by transposase. Tn3 confers transposition immunity, a phenomenon in which Tn3 transposes to a target replicon with Tn3 much less frequently than to a target replicon with no Tn3.