How to get the sequence differences between multiple bacterial genomes

I am working on some closely related bacterial species (complete genomes from NCBI). I would like to extract the sequence differences between them. To be more specific, I want to find unique sequences (50 -100 nts) in each of the bacterial species (n=6) under my study.
I found many other related posts suggesting tools like Mauve, Mummer, Artemis ACT etc.. and I tried all of them. Mauve gave pretty good results, but when I extracted the sequences in the range as suggested to be different from other genomes under comparison, and performed blast, I got multiple hits to other bacterial species.

Thanks in advance.

Here’s one solution with unikmer, for limited number of input files.
for loop can be replaced with parallel for saving time.

1. Generating k-mers.

   for f in *.fa.gz; do
       unikmer count -k 31 -K -s -o $f.k31 $f;
   done
   

2. Computing k-mers shared by two or more strains. (updated here)

   unikmer common -n 2 *.k31.unik -o shared
   
   # method 2, faster
   unikmer sort  *.k31.unik --repeated -o shared
   

3. Removing k-mers shared by two or more strainss, left are unique k-mers.

   for f in *.k31.unik; do 
       unikmer diff $f shared.unik -s -o $f.uniq;
   done
   

4. Retrieving unique sequences from genome with unique k-mers.
   Output format can be in BED (default) or FASTA (-a),
   minimum lengths (-m) are configurable.

   for f in *.fa.gz; do
       unikmer uniqs -g $f $f.k31.unik.uniq.unik -M -m 50 -a -o $f.uniq.fa;
   done
   

5. Stats of result.

   unikmer stats *.uniq.unik -a 
   file                                            k  canonical  hashed  scaled  include-taxid  global-taxid  sorted  compact  gzipped  version  number
   1773-GCA_000706665.1.fa.gz.k31.unik.uniq.unik  31          ✓       ✕       ✕              ✕                     ✓        ✕        ✓     v4.1  16,217
   1773-GCA_000738445.1.fa.gz.k31.unik.uniq.unik  31          ✓       ✕       ✕              ✕                     ✓        ✕        ✓     v4.1  11,939
   1773-GCA_000738475.1.fa.gz.k31.unik.uniq.unik  31          ✓       ✕       ✕              ✕                     ✓        ✕        ✓     v4.1   7,074
   1773-GCA_000756525.1.fa.gz.k31.unik.uniq.unik  31          ✓       ✕       ✕              ✕                     ✓        ✕        ✓     v4.1   9,679
   1773-GCA_000756545.1.fa.gz.k31.unik.uniq.unik  31          ✓       ✕       ✕              ✕                     ✓        ✕        ✓     v4.1  72,867
   1773-GCA_000934585.1.fa.gz.k31.unik.uniq.unik  31          ✓       ✕       ✕              ✕                     ✓        ✕        ✓     v4.1  20,135
   
   seqkit stats *.uniq.fa
   file                                format  type  num_seqs  sum_len  min_len  avg_len  max_len
   1773-GCA_000706665.1.fa.gz.uniq.fa  FASTA   DNA        358   28,030       50     78.3    1,005
   1773-GCA_000738445.1.fa.gz.uniq.fa  FASTA   DNA        379   23,088       50     60.9       89
   1773-GCA_000738475.1.fa.gz.uniq.fa  FASTA   DNA        220   13,486       50     61.3       99
   1773-GCA_000756525.1.fa.gz.uniq.fa  FASTA   DNA        239   16,306       50     68.2      354
   1773-GCA_000756545.1.fa.gz.uniq.fa  FASTA   DNA      1,888  129,254       50     68.5    6,865
   1773-GCA_000934585.1.fa.gz.uniq.fa  FASTA   DNA        479  211,054       50    440.6    9,400