Why doesn Primaclade find any primers at the far end of my alignment?
Most likely because of the length of your alignment. Primaclade asks the Primer3 program to return 20 primers per sequence and it stores both the forward and reverse primers that are returned. In the normal course of events this will usually cover the entire sequence. If there are highly conserved regions at the far end of your alignment or if you suspect that there primers that should exist near the ends, try running Primaclade again and use the “Exclude Regions” function to block out the beginning of the alignment.
