hi, thank you very much for your advice. As you said, i tried a different method to solve the problem and succeeded in it, its very fast too :) here is how i did it !!!

#!/usr/bin/perl -w
use strict;
use warnings;

open(FH1,$ARGV[0]) or die "can not open\n";
open(FH2,$ARGV[1]) or die "can not open\n";

my @indx;

while(<FH1>){
    my ($id,$seq)=split("\t",$_);
    push(@indx, $id,$seq);
}

my %hashseq=@indx;

while(<FH2>){
    if($_=~m/^clus/){
        my $clushead=$_;
        print "$clushead";
    }
    else{
        $_=~s/\t//g;$_=~s/\n//g;
        my $tes=$_;
        print $tes,"\t",$hashseq{"$tes"};
    }
}
[download]

Thank you very much once again :) (p.s: sorry for posting twice. forgot to login previously.)