I am not sure I understand BLAST correctly.
When using BLAST in DNA and protein, they are different. There is a threshold T in protein "seeding" step, which means the seeding sequence is not perfectly matched. However, it seems there is no T in seeding step and we are looking for perfect match and extend them to neighbouring sequence.
So, if there is no word length 5 exact match between these 2 sequence, BLAST will fail.
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