I think you want to print headings only outside your foreach loop:

        print OUTPUT "\n", $headings;
        foreach ( $line =~ m/$sequence/i ) {
            if ( $line =~ m/$sequence(.{11})(.{11})$sequence/ ) {
                print OUTPUT "\n", $1, "\n", $2;
            }
            $local_count++;
        }
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Aside: perltidy is nice.