We provide both theoretical and simulation results on the progress of an STS mapping project in the presence of clone length inhomogeneity. For an example in which the genome comprises alternating regions of clones with short and long average length, the main conclusion is that the efficiency of the project is clearly decreased in the presence of such inhomogeneity. The case of deterministic clone length gives the worst progress. The general simulation algorithm we propose shows that strategies that space the anchors as regularly as possible do best: fewer contigs of larger average length are expected. The simulation algorithm can be used to study many statistical properties of the progress of any anchoring project