Summary of alignment improvement for V19 candidate sequences using the blastn, Gotoh, or Needleman-Wunsch pairwise alignment algorithms when the best template was selected for each candidate sequence. ^a

aData for the other regions and comparisons to region specific template sequences are provided in Tables S3 and S4. bThe average percentage difference in similarity between the template sequence and the SILVA aligned candidate sequence and the difference in similarity between the template sequence and the candidate sequence aligned by the different implementations. Positive values indicate the candidate alignment is more similar to the template sequence and negative values are less similar. Values in parentheses indicate the standard deviation. bblastn does not permit these gap penalties when using a match reward and mismatch penalty of 1 and the Needleman-Wunsch algorithm only takes one gap penalty parameter.