We are performing CRISPR on a gene from a strain of Aspergillus niger and then sequencing the results by Sanger. When we compare the gene sequence with the resulting sequence we observe in the reverse readout that it matches plus/minus (as it should), but also plus/minus. The dot plot is attached

It only occurs in the reverse read of 2 of the 30 mutants we sequenced. Does anyone have any clues as to what might be going on here? It looks like the sequence is slightly palindromic, but we don't know the reason. Maybe it has to do with some kind of primer dimer during PCR, or some nonspecific primer binding site? Has anyone who has done CRISPR had these results? Could these be mutants? It is odd that it only occurs in a small subset of reverse reads. It happened to us previously with the same strains and another set of primers, but it also happens with the new primers. Thanks in advance.