... PDF doc] An automatic annotation of a sequence is based on statistics assembled from the result of the homology search, that is for a prediction description elements (DEL) of the given sequence. ... The desired percent of coinciding (from the maximum in the case of complete similarity) "one-color" pair-patterns on the selected shift (in 1/100 of 1) (0.02 for protein and 0.08 for nucleotide query sequence). ... Title: Amino acid substitution matrices from protein blocks. ...