[Genome] Multiple alignment score

[Wen Huang]

Hello,

I have a question about the score in the MAF file formate:

In the first line of an alignment block (line starting with 'a'), for eample

a score=23262.0
s hg18.chr1.....................................

My question is how to interprete the score? For example, what does a score 
23262.0 mean compared to a score, say 13262.0, or even a negative score?

Thanks,
Wen Huang
Graduate Student, Dairy Science
University of Wisconsin-Madison