I have used the Geneiuos tool to BLAST my sequence and obtained a %pairwise identity and the query coverage of my sequence.
However, if I take the same sequence and run a BLAST in the NCBI website directly, the query covery changes from 84.3% (geneious) to 100% (NCBI).
So I wonder what's the differences between those two results.
My guess is the two programs may be using a different database you're searching against, or different algorithm settings. First check if the two sequences BLAST returned are the same in the part of the sequence they overlap. If not, it's likely the databases (also check the sequence IDs), if yes, it could be the algorithm or its settings.
This is a helpful article regarding tools for pairwise comparisons.
http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0108277&type=printable
Thanks Matej for your answer
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