While running this the first two $orf with $count values ge 4 do not enter the "for" loop (it does print the newline contained in "if" statement). However all subsequent values of $count ge 4 do.

$input = 'YAVSNCKFNIEDYNNIFKVMENIRKHSNKNLNDQDELNIYLGVQSSNAKR';
$l = length ($input) - 1;

###     P(a), P(b), P(turn), f(i), f(i+1), f(i+2), f(i+3)     ###
%aa = (
    A => [1.42,.83,.66,0.060,0.076,0.035,0.058],
    R => [.98,.93,.95,0.070,0.106,0.099,0.085],
    N => [.67,.89,1.56,0.161,0.083,0.191,0.091],
    D => [1.01,.54,1.46,0.147,0.110,0.179,0.081],
    C => [.70,1.19,1.19,0.149,0.050,0.117,0.128],
    E => [1.51,.37,.74,0.056,0.060,0.077,0.064],
    Q => [1.11,1.10,.98,0.074,0.098,0.037,0.098],
    G => [.57,.75,1.56,0.102,0.085,0.190,0.152],
    H => [1.00,.87,.95,0.140,0.047,0.093,0.054],
    I => [1.08,1.60,.47,0.043,0.034,0.013,0.056],
    L => [1.21,1.30,.59,0.061,0.025,0.036,0.070],
    K => [1.14,.74,1.01,0.055,0.115,0.072,0.095],
    M => [1.45,1.05,.60,0.068,0.082,0.014,0.055],
    F => [1.13,1.38,.60,0.059,0.041,0.065,0.065],
    P => [.57,.55,1.52,0.102,0.301,0.034,0.068],
    S => [.77,.75,1.43,0.120,0.139,0.125,0.106],
    T => [.83,1.19,.96,0.086,0.108,0.065,0.079],
    W => [1.08,1.37,.96,0.077,0.013,0.064,0.167],
    Y => [.69,1.47,1.14,0.082,0.065,0.114,0.125],
    V => [1.06,1.70,.50,0.062,0.048,0.028,0.053],);
    

for(my $i=0; $i < $l - 4; $i++) { 
    my $col = 0; # reference to hashmap column 1, P(a)
    $orf = substr($input,$i,6); 
    @fra = split('', $orf), "\t";
    $count = count(@fra), "\t";  #characters ge 1
    print $orf, " ", $count, "\n";
    if ($count ge 4) {
        for (my $j=$i+3; $j le $l - 3; $j++) { 
            print my $frame = substr($input, $j, 4);#
            print " ";
            print my $alpha4 = average ($frame, $col), "\n";
            if ($alpha4 lt 1.00) {$j = $l};
        }; 
        print "\n";
    }
}

exit;

sub count {
    my $c = 0;
    foreach (@_) {
        my $p = $aa{$_}[0];
        if ($p ge 1.00) {$c++};
    }
    return $c;
}
    
    
sub average {
    my ($frame, $col) = @_;
    my $a = 0;
    @seq = split ('', $frame);
    foreach $_ (@seq) {
        $a += $aa{$_}[$col];
    }
    return $a/(length($frame));
}
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