Final answer:
Finding protein matches upstream of the first methionine in a BLASTX search suggests alternative or extended open reading frames in the cloned DNA that could result in different protein isoforms.
Step-by-step explanation:
If a BLASTX search shows matches to proteins in the database upstream of the first M (methionine) in your clone, it suggests that there may be additional coding sequences in your cloned DNA that precede the expected start codon.
This could indicate that your cloned sequence contains a different or extended open reading frame (ORF) that encodes a longer or different protein than initially anticipated.
The upstream region could also contain alternative start codons that lead to the production of different protein isoforms.