I have a small clarification to clear out for the gaps present in the sequence alignment. When i did the sequence alignment using targeted sequence (original sequence) and template, there is gaps present in the first 50 position of template sequence. The similarity results is 85%, is it fine to keep the gaps in the sequence itself or should i remove the gaps?
I don't know the objective of the alignment in your case. However, it is just a way to find how similar the 2 sequences in question are. When you use gapped alignment, gaps will be introduced to get what we call the "optimal" alignment. DNA sequences do not of course have gaps. But when two or more sequences are aligned they may fit together best when gaps are introduced for instance these seqs:
match almost everywhere if we write them like this: