Find if items in a list of list matches to another list
Extract this into functions

You are doing one well defined thing (finding fuzzy matches), so this should be at least one function, but I suggest more because you are returning two results.

Write automatic tests

Re-factoring is very hard without tests, re-running and checking the input manually is very time consuming, an automatic test runs in milliseconds.

Use the list comprehensions and zip

You are basically checking the single-dimensional list (xs) against each row of the two-dimensional list (matrix) and seeing which elements are contained and which are not. This can be expressed very easily in code.

def fuzzy_matches(xs, matrix):
    """
    &gt;&gt;&gt; list(fuzzy_matches(["a","b","c"], [["a", "b43", "x"], ["w", "b", "5cfg"]]))
    [[True, True, False], [False, True, True]]
    """
    return ([i in j for i, j in zip(xs, line)] for line in matrix)