Impact of sequence length differences, ambiguous bases or missing data on K2P distance and the output of the BLAST algorithm (Percentage Identity and Bit-Score).

seq_ok is a 368 bp long sequence without missing data or ambiguous bases. It is compared to that same sequence with slight modifications representative of the limits of sequencing techniques: seq_N has three “N” within the sequence (internal missing data), seq_Y has three “C” or “T” bases replaced by a “Y” (ambiguous bases), seq_short is 14 bp shorter (missing data at each end). K2P: K2P distance obtained with the PAUP software. PI (Percentage Identity) and Bit-Score result from a BLAST analysis obtained with the BLASTCLUST software. % Bit-Score max. is the percentage of the Bit-Score obtained compared to the maximum Bit-Score (when seq_ok is blasted on itself).