Another way to do it - avoid all that fiddly substr stuff:

use strict;
use warnings;

print comNucCount('acgtacgtacgtacgt', 'aaaaccccggggtttt'), "\n";

sub comNucCount {
    my @str1 = split '', lc shift;
    my @str2 = split '', lc shift;
    my %counts = (a => 0, c => 0, g => 0, t => 0);
    
    for (@str1) {
        last if ! @str2; # Length mismatch - done
        $counts{$_}++ if $_ eq shift @str2;
    }

    return "A=$counts{'a'}, C=$counts{'c'}, G=$counts{'g'}, T=$counts{
+'t'}";
  }
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Prints:

A=1, C=1, G=1, T=1
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