my @new = split ('>', $joi1);
...
my @new;
..
foreach (@new) {

##</code><code>##

use warnings;
use strict;

my $seq = <<DATA;
>s1
AGCTTTTCGGGCAAT
>s2
GCTGCCCCCCATCTT
>s3
TCGTAGCTGAAAATC
DATA
my $num = <<DATA;
>s1
23 43 45 65 76 54 3 34 54 65 7 45 56 87 56
>s2
23 43 23 45 65 45 76 78 34 8 12 32 65 23 25
>s3
12 23 34 45 56 54 43 32 65 43 12 34 75 76 45
DATA

open FH1, '<', \$seq;
open FH2, '<', \$num;
my @arr1    = <FH1>;
my @arr2    = <FH2>;
my $joi1    = join (' ', @arr1);
my $joi2    = join (' ', @arr2);
my @new     = grep length, split ('>', $joi1);
my @numbers = grep length, split ('>', $joi2);
my @seqid;
my @alp;

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

my @num;
my @numid;
foreach (@numbers) {
    my ($num_id, $numb) = split (/\n/, $_);
    push (@num, split (' ', $numb));
    push (
        @numid, $num_id
        );
}
my @keep =
    grep {$_ < 1 || $num[$_] >= 10 || $alp[$_ - 1] ne $alp[$_ - 0]} 0 .. $#num;
print (join ('  ', @alp[@keep]), "\n");
print (join (' ', map {sprintf '%2d', $_} @num[@keep]), "\n");

##</code><code>##

A  G  C  T  T  T  C  G  G  C  A  A  T  G  C  T  G  C  C  C  C  C  A  T  C  T  T  T  C  G  T  A  G  C  T  G  A  A  A  A  T  C
23 43 45 65 76 54 34 54 65 45 56 87 56 23 43 23 45 65 45 76 78 34 12 32 65 23 25 12 23 34 45 56 54 43 32 65 43 12 34 75 76 45