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If the user chooses to set AutoPenalty=False, this will set the penalty for the alignment.

  • If user set an integer value >= 1, the penalty will be maximal allowed # mismatches + gap penalty.
  • If user set a value between 0 and 1 (cannot be 1), the penalty will be treated as proportion. If user sets 0.1, then (maximal allowed # mismatches + gap penalty) is ReadLength*0.1.