I am trying to actually iterate through my different nucleotide sequences searching for a query pattern to determine how many of these patterns I can find that are identical matches and which ones are slight mismatches. Here is my beginning. Say I am searching TGTGTGTGTGTG for all sequences matching the search TX Basically, if the program checks from left to right, the $x means that there will be 9 chances to check through this 10nt seequence. If my search was TXXX, then there would be 7 different sequences to check. 
while (my ($key,$value) = each(%o)) {
my $i;
my $j;
my $x = (length($value)-(length($search)-1));# x = the length of value
+ minus (the length of search minus 1) AKA how many times to iterate..
+.
for (i=0; $x; $i++) {
  $l_seq = substr($value, $i, length($search))
    for (j=0; j<(length($search)); $j++) {
      $match += substr($l_seq, $j, 1) eq substr($search,$j,1)
    }
      $mis_match (??)

[download]
It ends abruptly; I am not sure how to proceed in order to allow for mis-matching. Thanks, ER

In reply to Pattern searching allowing for mis-matches... by MaroonBalloon

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