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while(<IN1>)        {
chomp;    
...
    push @lengths, length($_);
        }
}

while (<IN1>)
{
    chomp;
    push @lengths, length $_ unless />/;
}

while(<IN2>)        {
chomp;    
...
    push @source, $_;
        }
}

chomp, push @source, $_ while <IN2>;