Padded position in Consensus sequence

[Jayaprakash Rudraraju]

Hi,

I have written a small subroutine to as part of the program to tag primers
in Consed. The following subroutine gives padded position on the consensus
sequence, given its position on reference sequence.

#!perl -w
my $consensus = "AGG*TGAC**TA***AGTCCT*T";
print map { "$_\t". padded_position($_) ."\n"} (1..16);

sub padded_position {
my ($unpad, $pads) = (@_, 0);
$pads++ until $unpad == substr($consensus, 0, $unpad+$pads) =~ tr/ACGT//;
$unpad+$pads;
}

can you suggest me some more efficient or elegant solutions. Eventhough I
have condensed it as much as I can, I am looking for a simpler logic.

Prakash.