Hello, We are working on creating a definition file for analyzing a mouse genomic array. We are using the probe sets for the Affymetrix GeneChip? Mouse Exon 1.0 ST Array and have megablasted the probes against a copy of the most current build of the mouse genome (NCBI). However, some of the contigs have very few matches and for 6 contigs, on the X chromosome, none at all. Has any one else experienced the same while using these Affymetrix probes? Any information or advice will be greatly appreciated. Thanks, Rick