Please help.
You will likely receive substantially more help if you take the time to enclose each datafile and program in its own pair of <code> tags. See Markup in the Monastery for more help on that.
Even without that, code which looks like this sets alarm bells ringing:
if($aa =~/A/ig){ $A++; } if($aa=~/C/ig){ $C++; } if($aa=~/D/ig){ $D++;
+ } if($aa=~/E/ig){ $E++; } if($aa=~/F/ig){ $F++; } if($aa=~/G/ig){ $G
+++; } if($aa=~/H/ig){ $H++; } if($aa=~/I/ig){ $I++; } if($aa=~/K/ig){
+ $K++; } if($aa=~/L/ig){ $L++; } if($aa=~/M/ig){ $M++; } if($aa=~/N/i
+g){ $N++; } if($aa=~/P/ig){ $P++; } if($aa=~/Q/ig){ $Q++; } if($aa=~/
+R/ig){ $R++; } if($aa=~/S/ig){ $S++; } if($aa=~/T/ig){ $T++; } if($aa
+=~/V/ig){ $V++; } if($aa=~/W/ig){ $W++; } if($aa=~/Y/ig){ $Y++; }
Why not use a hash instead?