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FASTA format: the first line starts with >identifier, followed by the amino-acid sequence; only the 20 standard letters are allowed.
>test
YRQSMNQGSRSTGCRFGTCTMQKLAH...
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Matrix choice: BLOSUM62 is a general default; BLOSUM80 fits closer homologs, BLOSUM45 for distant ones; PAM matrices emphasize evolutionary distance modeling.
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Reading the output: focus on E-value, identities, gaps, and alignment length.