Score refers to the BLAST (Basic Local Alignment Search Tool) score.  BLAST is a Registered Trademark of the National Library of Medicine.  BLAST finds regions of similarity between nucleotide or protein sequences and is used to search sequence databases for optimal local alignments to a query sequence. Compare BLAST results by sorting by both Score and Mismatches.  Per NCBI's definition page, the raw score of BLAST is the score of an alignment, calculated as the sum of substitution and gap scores.