In find_point() you pass in a reference to a hash, and then copy the hash from %$ref to %hash. If you're concerned about speed, dedreference the reference:

if( exists $ref->{$key} ) {
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Since the hashes are tiny, 2 to 7 members, copy it from the beginning, rather than passing in a referernce.

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TTTATCGGTCGTTATATAGATGTTTGCA