removing sequences with ambiguous seq

I am analysing data for Sanger sequencing and am following the Esophageal community analysis example.
When doing the multiple sample analysis and trying to run make.shared(list=ks.an.list, group=ks.groups) mothur tells me: Your group file contains 3240 sequences and list file contains 3059 sequences. Please correct.
What am I doing wrong? What do I need to do?
TIA,
Kathrin

do you use the remove.seqs command to remove accons from your list file? if you have do so, you need to do the same command again to your groups file in order to maintain the same size of your groups file and list file. Hope could help you in someway.