This one gives me in 2 different files..

#!/usr/bin/perl
open FILE,"seq.txt";
open OUT1,">seq.out";
open OUT2,">num.out";
$seq = "";$num = "";
while(<FILE>) {
    if($_ =~ /^>/) {
        push(@seq,$seq) if $seq;
        $seq='';
        push(@seq,"\n$_");
    } else {
        $_ =~ s/\s*$//;
        $seq = $seq.$_;
    }
}
push(@seq,$seq);
close(FILE);
open FILE,"num.txt";
while(<FILE>) {
    if($_ =~ /^>/) {
        push(@num,$num) if $num;
        $num='';
        push(@num,"\n$_");
    } else {
        $_ =~ s/\s*$/ /;
        $num = $num."$_";
    }
}
push(@num,$num);
close(FILE);
while($_ = shift @seq) {
    my @marker;
    if( $_ =~ />/ ) {
        $shead = $_;
        $nhead = shift @num;
        $seq = shift @seq;
        $num = shift @num;
        #print $seq,"\n";
        #print $num,"\n";
        @s = split (//,$seq);
        @n = split (/ /,$num);
        $pre = "null";
        $cnt = 1;
        $arrcnt = -1;
        foreach(@s) {
            if($_ eq $pre) {
                $cnt++;
            }
            else {
                if ($cnt >= 3 && $n[$arrcnt] < 10) {
                    push(@marker,$arrcnt);
                }
                $cnt = 1;
            }
            $pre = $_;
            $arrcnt++;
        }
        $exp = 0;
        foreach(@marker) {
            $_ = $_ - $exp;
            splice(@n,$_,1);
            splice(@s,$_,1);
            $exp++;
        }
        $seq = join(" ",@s);
        $num = join(" ",@n);
                print OUT1 $shead;
                print OUT1 $seq,"\n";
                print OUT2 $shead;
                print OUT2 $num,"\n";
    } 
    else {
        print "give proper input file";
        exit;
    }
}
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THANK U ALL FOR THE HELP...Am learning a lot :)