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++;
        }

[download]

Aside: perltidy is nice.

In reply to Re: Creating a column of frequency for the unique entries of another column by toolic
in thread Creating a column of frequency for the unique entries of another column by bluray

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