You're going to have to give us some more context than that for us to be able to answer correctly.

My guess is that you have something like this:

while (<>) {
    if ( /__END__/ ) {
        # condition 1
    }
    if ( /(.)/ ) {
        # condition 2
    }
}
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Condition 1 matches a line with the literal text "__END__" on it somewhere. The second condition matches any line that has anything on it (not blank lines), and it puts whatever one character it matches into $1 (see perlvar).