Ok this is what I came up with....it "looks" right to me. I do a Print " The ID is $rp1 and the Sequence is $invseq\n"; and the ID prints but the sequence has no value. I guess I messed up in the hash? Not really sure what I am doing wrong now.

if ($flag21 == 1) {
                        foreach $num(@number) {
                                if (($num) eq ($rp1)) {
                                        $invseq = $seqi{$rp1};
                                        $invseq = $invseq + 1;
                                        $seqi{$rp1} .= $invseq;
                                } else {
                                        $seqi{$rp1} .= 1;
                                        $invseq = $seqi{$rp1};
                                        push @number, $rp1;
                                }
                        }
                }
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I changed the first part to a 3 step add thinking I messed up somewhere there it was originally this (and didn't work)

if ($flag21 == 1) {
                        foreach $num(@number) {
                                if (($num) eq ($rp1)) {
                                $seqi{$rp1} += 1;
                                   $invseq = $seqi{$rp1};
                                } else { 
                    snipped the rest off as it was the same
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