Please show us your perl1.pl script inside <code> and </code> tags so we can see where you are going wrong. As for working on a multi-line file, calculate the offsets, open your file then do something like

while ( <$inputFH> )
{
    foreach my $offset ( reverse @cums[ 1 .. $#cums ] )
    }
        substr $_, $offset, 0, q{-};
    }
    print;
}
[download]

I hope this moves you forward.

Update: Code modified to replace for statement modifier with an explicit loop, thanks choroba.