CRISPR differences in statistics txt file

[ireneortega]

I observed difference for the CRISPR: line in the statistics txt file between two genomes that harbor the same 3 /product="putative CRISPR-associated protein" (equal protein sequence). The unique difference is at the end of one of these proteins in which the length of a protein in a genome is 3 aa larger. I am checking the presence of a CRISPR system in each genome based on the info written to the statistics txt file, but I realised that no information regarding CRISPR system appeared for one of these two genomes in that file, despite it has cas1, cas2 and cas9 proteins. Moreover the log file for this genome says:

Searching for CRISPR repeats
Found 0 CRISPRs

What can be the reason? Therefore I can not trust on that file to check the presence of CRISPR system in my genomes.