I have reproduced your BLAST analysis using the NCBI web service, using your list of 10 positive strand ORF's for CoV_11241010.

I'm observing a classical number of hits (not 2 or 3 hits only as we observed in your results at the end of Class 3), for instance for your ORF4:21476:25201, I get 500 BLAST hits in RefSeq (ie the limit I chose in the BLAST parameters), with E-values ranging from 0.0 to 2e-08.

This confirms my suspicion that the results you showed me this morning resulted from a NCBI BLAST bug, could it be due to the fact that the computation was carrried out on a tablet rather than a laptop computer (maybe the tablet doesn't have sufficient hardware resources to deal with such complex web pages) ?

I did BLAST again after class, and I got the result that looks like what you showed. I agree with you. Thank you for reproducing my analysis.

I forgot to save annotation, so I did BLAST more again and I am now checking the result. In this result, the ORF that should be coding spike protein had only 2 hits. I did BLAST on laptop. Maybe it is the bug of BLAST, but I have no idea about the condition this bug happens.

In my BLAST result from your Spike (ORF4:21476:25201) I observe 89 hits, ranging from E-value 0-9.2. So indeed there seems to be a bug with the NCBI BLAST, but it is very concerning that we don't know what triggers the bug 🙀... If you get stuck with the NCBI BLAST, please use the Kyoto GenomeNet BLAST, it is very reliable, but you can't submit all ORFs at once as a multi FASTA, you need to open one BLAST submission page for each ORF.