I tested speed now.
Simple cycle case sensitive search for substring in string 1 000 000 times takes
about 2s. 
For 2 000 000 000 more than 1 hour. For such long run is necessary to show some
progress, make application react for user + read strings from list. In the final
it means about 3-4 hours of program run.

For case insensitive I see one possibility only - convert both files e.g. to
uppercase before search.
Convert strings inside cycle will cause several thousand times more conversion
and it will significantly slow down searching.

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