Then just peek back.

use strict;
use warnings;

my @alphas = split ' ', 'A G C T G G G G A C T T T A G C';
my @nums   = split ' ', '34 23 43 45 34 43 45 7 45 43 12 34 32 56 43 6
+7';

my @keep = grep {  $_ < 1
                || $nums[$_] >= 10
                || $alphas[$_-1] ne $alphas[$_-0]
                }
           0..$#nums;

print( join( ' ', @alphas[ @keep ] ), "\n" );
print( join( ' ', @nums  [ @keep ] ), "\n" );
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thanks for the program... but then, i m not able to remove the duplicate values even after nulling the array... where should i do it? my input file is:

read.txt
>s1
A G C T G G G G A C T T T A G C
>s2
A G C T G G G G A C T T T A G C
>s3
A G C T G G G G A C T T T A G C


and

num.txt is
>s1
34 23 43 45 34 43 45 7 45 43 12 34 32 56 43
>s2
34 23 43 45 34 43 45 7 45 43 12 34 32 56 43
>s3
34 23 43 45 34 43 45 7 45 43 12 34 32 56 43
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i have just given the same values as example. my program follows:

#!/usr/bin/perl
open(FH1,"read.txt");
open(FH2,"num.txt");
@arr1=<FH1>;
@arr2=<FH2>;
$joi1=join('',@arr1);
$joi2=join('',@arr2);
@new=split('>',$joi1);
@numbers=split('>',$joi2);

foreach(@new){
        ($seq_id,$seq)=split(/\n/,$_);
        push(@alp,split('',$seq));
        push(@seqid,$seq_id);
}

foreach(@numbers){
        ($num_id,$numb)=split(/\n/,$_);
        push(@num,split(' ',$numb));
        push(@numid,$num_id)
}

#my @alp=split(' ','A G G G G T C A A A T C');
#my @num=split(' ','23 34 54 23 2 43 54 56 23 5 76 34'); 
my @keep= grep {$_ < 1 || $num[$_]>=10 || $alp[$_-1] ne $alp[$_-0]} 0.
+.$#num;

foreach(@seqid){
print "$_\n";
print (join(' ',@alp[@keep]),"\n");
}

foreach(@numid){
print "$_\n";
print (join(' ',@num[@keep]),"\n");
}
[download]

Start with use warnings;, and you're doing yourself a big disfavour by not using use strict; either.