hi friend, Try out this one :)

open(FILE1,"file1.txt") or die $!;@file1=<FILE1>;close(FILE1);
open(FILE2,"file2.txt") or die $!;@file2=<FILE2>;close(FILE2);
foreach $file2(@file2){
        if($file2=~/(\w+)(_)(\w+)\s(\w+)(=)(\d+)/)
        {
                $id=$1;
                if($3 eq 'right'){$value=$6."r#";}
                if($3 eq 'left'){$value=$6."l";}
                push(@array,"$value");  push(@id,"$id");
        }
}
push(@newid,grep {!$ss{$_}++} @id);
@arraysplit=@array2=$ss=();
$ss=join('',@array); @arraysplit=split(/\s+|\n/,$ss);
@array2=split('#',$arraysplit[0]);
foreach $f1(0 .. $file1[$#fiel1])
{
        if($file1[$f1] =~/>/){  $firstline=$file1[$f1]; chomp($firstli
+ne);      }
        if($file1[$f1] =~/^>/)
        {
                $secondline=$file1[$f1+1];
                $secondlinej=join('',split(/\n/,$secondline));
                foreach $vv(0 .. scalar @array2)
                {
                        if($newid[$vv] eq substr($firstline,1,6))
                        {
                                ($left,$right)=split(/r|l/,$array2[$vv
+]);
                                print "\n".substr($firstline,0,7)."_le
+ft"." length=$left  \n";
                                @secondlinejj=split('\s',$secondlinej)
+;
                                for ($l=0;$l < $left;$l++){print "$sec
+ondlinejj[$l] ";}  print "\n";
                                print "\n".substr($firstline,0,7)."_ri
+ght"." length=$right \n";
                                $len=scalar @secondlinejj."\n";
                                $right=$len-$right;
                                for ($m=$right;$m <= scalar @secondlin
+ejj;$m++){print "$secondlinejj[$m] ";}print "\n"
                        }
                }
        }
}
[download]

Output will be like this

>AAAT3R_left length=6
40 40 40 40 40 40

>AAAT3R_right length=62
40 40 40 40 40 38 38 37 39 36 36 40 36 35 35 35 38 40 35 35 33 35 35 3
+5 40 40 40 40 37 37 38 38 38 40 40 40 40 40 40 40 40 40 40 40 40 40 4
+0 40 40 37 36 36 31 22 22 22 20 20 20 20 20 14

>AAA2OJ_left length=14
18 18 18 21 35 35 35 32 32 32 33 35 38 39

>AAA2OJ_right length=14
37 37 37 37 3737 33 32 32 30 20 17 17 17 0
[download]