Why do I see different hits when I use BLAT or BLAST from Ensembl, UCSC, and NCBI?
The parameters that Ensembl uses for BLAT are the same as those used by UCSC. BLAT results can differ across these resources if there are discrepancies in the underlying genome assembly, or if sequence repeats are masked using different methods. BLAST can give various results when comparing resources depending on parameters used, and underlying sequence and repeat differences.
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