This is one the example:

# Both strings and candidate are always
# the same length 
 
$str        = '[TCG]TTCG[AT]';
$candidate1 = '  T  TTCG G';   # I manually aligned this 

# The number of mismatch of those string would be: 1
# Namely the only last position gives a mismatch,
# The first position it is considered a match.
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