is there any easy way to count the letters between each time it finds the substring

Perhaps this will give you some ideas on how to do that:

$ perl -le'
$_ = "GAGAGACCCCGATCGAGAGACCCGATCFGAGAVCTGATCCCC";
my $substring = "GATC";

print "length of string is ", length;
my $start = 0;
while ( /$substring/g ) {                                             
+                     
    print qq/"$substring" found at $-[0] to $+[0], distance from last 
+is /, $-[0] - $start;
    $start = $+[0];
    }                                            
print "distance from end is ", length() - $start;
'
length of string is 42
"GATC" found at 10 to 14, distance from last is 10
"GATC" found at 23 to 27, distance from last is 9
"GATC" found at 35 to 39, distance from last is 8
distance from end is 3
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