Use Ruby Enumerable methods
Reformatted case

also removed commented out js debugging code, implemented default using else.
Simplified to_hash

This effectively creates one hash less, by filling up an empty hash instead of filling up a full hash, and then deleting just added content
Removed ruby’s own min method
Simplified averaging method
Removed modifying from re_match_all

Used position parameter of match. This ought to be faster, and removes the need to duplicate strings before passing them in
Use map to create an array, instead of each
Simplified method
Fixed whitespace
Simplified loop construction

Algorithm is the same, basically moved the if with break, to loop condition.
Fill up match_sequence from the other direction, instead of reversing at the end.
Simplified sequences code, and added support for overlapping sequences
Simplified some more
made check less expensive
Split up logic into methods
Extracted lambda to method
made logic a bit clearer
Simplified code

Removed temporary variables and unreachable debugger statement, used same syntax for adding to an array.
made syntax the same
Split up main scorer method, and made logic bit clearer