Difference between NCBI and mega 6 software based nucleotide sequence alignments

I tried to align two nucleotide sequences using NCBI “blast” with “Align two or more sequences” program and Mega 6 software . The results of the two alignment programs are different. The NCBI alignment starts at 57 nucleotides whereas using Mega 6 software, it starts at nucleotide one.

Is there any explanation for this?