You could use zsh with its expression-as-a-glob-qualifier to select files that only have nine such symbols:
$ hasnine() { [[ $(greptr -cdc '>' < "$REPLY" | wc -c) -eq 9 ]]; } $ mv *.fna(+hasnine) location/ The first line defines a function whose purpose is to create a true/false filter for files that have exactly nine lines with > symbols in them. The greptr command acts on its input, expected in the REPLY variable, deleting anything that is not a >, then asks wc to count the number of resulting characters, and then compares thethat output to 9.
The second line executes the mv command for matching *.fna files to the (example) location directory. Matching *.fna files also have to pass the expression qualifier, which is the given as the name of the function we defined.