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BLAST module of the MLA course on Introduction to Molecular Biology Information Resources
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Scoring System for
Nucleotide Sequence Pairwise Alignments

The matrix used for BLASTn is an identity matrix: any substitutions result in a negative score at the changed position:
  • An identity results in a score of +1 at that position.
  • A mismatch results in a score of -3 at that position.
 
 

BLAST
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Revised 11/05/2007