how to match two sequences using arrays in perl -

when looping through 2 arrays, confused how move pointer through 1 loop keep constant in another. example:

• array 1: a t c g t c g g c g
• array 2: a c g t c c t g t c g

so in first array matches in second array move on next elements. since t doesn't match c in 2nd index, want program compare t next g in array 2 , on until finds matching t.

my ($array1ref, $array2ref) = @_;  @array1 = @$array1ref; @array2= @$array2ref; $count = 0;  foreach $element (@array1) {  foreach $element2 (@array2) {  if ($element eq $element2) {  $count++;   }else { ???????????   } 

you use while loop search matches. if find match, advance in both arrays. if don't, advance second array. @ end print remaining unmatched characters first array:

# [1, 2, 3] reference anonymous array (1, 2, 3) # qw(1, 2, 3) shorthand quoted-word ('1', '2', '3') $arr1 = [qw(a t c g t c g g c g)]; $arr2 = [qw(a c g t c c t g t c g)];  $idx1 = 0; $idx2 = 0;  # find matched characters # @$arr_ref size of array referenced $arr_ref while ($idx1 < @$arr1 && $idx2 < @$arr2) {     $char1 = $arr1->[$idx1];     $char2 = $arr2->[$idx2];     if ($char1 eq $char2) {         # matched character, advance arr1 , arr2         printf("%s %s  -- arr1[%d] matches arr2[%d]\n", $char1, $char2, $idx1, $idx2);         ++$idx1;         ++$idx2;     } else {         # unmatched character, advance arr2         printf(". %s  -- skipping arr2[%d]\n", $char2, $idx2);         ++$idx2;     } }  # remaining unmatched characters while ($idx1 < @$arr1) {     $char1 = $arr1->[$idx1];     printf("%s .  -- arr1[%d] beyond end of arr2\n", $char1, $idx1);     $idx1++; } 

the script prints:

a  -- arr1[0] matches arr2[0] . c  -- skipping arr2[1] . g  -- skipping arr2[2] t t  -- arr1[1] matches arr2[3] c c  -- arr1[2] matches arr2[4] . c  -- skipping arr2[5] . t  -- skipping arr2[6] g g  -- arr1[3] matches arr2[7] t t  -- arr1[4] matches arr2[8] c c  -- arr1[5] matches arr2[9] g g  -- arr1[6] matches arr2[10] .  -- arr1[7] beyond end of arr2 g .  -- arr1[8] beyond end of arr2 c .  -- arr1[9] beyond end of arr2 g .  -- arr1[10] beyond end of arr2