It is not unlikely that you want to use your own reference sequence, but are not (yet) willing to submit your sequence data to GenBank.
Mutalyzer has an option for you to submit your own reference sequence files.
Mutalyzer will generate a unique identifier, which you can use from then on.

Please insert the GenBank record below:
The file needs to be a text file in GenBank format. The name of the file should not contain any spaces! You can choose to upload your file from your local computer or from a remote location.

Options My GenBank is a local file
I have an URL on the Internet where my GenBank file can be found
I want to fetch the reference genome for a (HGNC) gene symbol
I want to fetch a range of a chromosome
 
Input Please select a GenBank file

Please enter a GenBank file location (including http://)

Please enter a Gene symbol and organism name without spaces and specify the flanking sequences
Gene symbol
Organism name
# of 5' flanking nucleotides
# of 3' flanking nucleotides
Please enter a NC accession number and the range of the chromosome you want to upload.
Chromosome Accession Number

Start Position

Stop Position