Overview

Microsatellite flanking regions are not necessarily unique sequences, but they may group into sequence families. This phenomenon seems to be widespread in Lepidoptera and also occurs in many other insect species (Meglécz et al. 2006). These microsatellites are likely to give multiple banding patterns during PCR amplifications, which can be very difficult to interpret. Therefore, identifying sequences that cluster together prior to primer design can save considerable time and money. MicroFamilyWIN is a program designed for identifying flanking region similarities between different microsatellite sequences obtained from screening partial genomic libraries (Meglécz, 2006). As a preparation for sequence comparison, sequences are edited by (i) replacing all characters other than ACGT by N (ii) by deleting the extremities if they contained more than two Ns in the ten most extreme base pairs, and (iii) by removing vector contamination if the sequence produced a BLAST hit against the UniVec vector base of NCB