I have a sequence with 620 bases that I blast against Chromosome 3.
Over the web, from both NCBI and Goldenpath site, I gets an exact match for 620 bases in Chromosome 3 ( 176403446-176404065).
When I blast locally against Chromosome 3 which we downloaded from Goldenpath, it finds exact match on the first 164 bases. Then it skips 16 bases and finds exact match again starting at base 181.
But the strange thing is that the segment of Ch3 in our local fasta file, the whole 620 bases are exactly the same as my sequence. So why doesn't the local blast result return 100% match for 620 bases, instead it chops the segment off into two regions and skips some bases in between?
The local blast is done by megablast v2.2.2. The local databases is human genome build 28, the same as the build over the web.