[Genome] question about output

[Tara Lauriat]

I have taken the human exons and flanking sequence for my gene of interest and done a BLAT against the mouse genome to look at conservation. Most of the exons had a nice conservation over the exon as one would expect. However, some like the attached file had strange profiles where part of the exon was not conserved. I was wondering if you know how to interpret this type of result.
Sincerely,
Tara Lauriat