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Table 2 Default scoring parameters (can be arbitrarily weighted or changed by user defined settings).

From: Multiple sequence alignments of partially coding nucleic acid sequences

parameter default value
protein scores BLOSUM62 ×50
nucleic acid scores identity 1000, else 300
gap open penalty -1500
gap extension penalty -300
  1. Remark. The effect of the positive default score for nucleic acid mismatches is to reduce the influence of nucleic acid mismatches relative to the amino acid and gap scores.