Also keep in mind that any gaps longer than one nucleotide or amino acid will be ignored, and that in the end you will only get one of each pairwise alignment.
Also, keep in mind that in MAFFT, the FFT algorithm produces more conservative results, and the L-INS-i method will produce more accurate results but will be less flexible in terms of computing time. The choice between the FFT-NS-1 or FFT-NS-2 will impact the 50e0806aeb leizeba