How to edit your DNA sequence
You can either use your raw DNA sequence to perform your blast search against all sequences of your organism in PAMDB or you can first cut your raw sequence to the correct size by aligning your sequence with a sequence of the same locus downloaded from PAMDB and then cutting of the unaligned regions. To do this, you will need specialized DNA software like Lasergene, Sequencher, or DNA workbench. There is also a free program you can download: EMBOSS.