Sorry guys...thanks for your code...I am still trying to see if it is applicable...done some initial testing with it and I think that I might not have explained myself well enough.
In one of my user prompts I ask for a string (it is actually a short protein sequence that they can put in)...lets say they input 20 letters (they represent the proteins sequence). I want to take these 20 letters and initiate a search into the file of their choice...
What I would like to happen is for the program to take the first letter (1/20) and search with it...if this letter is found in their file, the program will add onto the first letter, the second letter (2/20), and now search with both 1&2/20. If these two letters are found in the file in succession then the third letter will be added to the search string and so on. What may happen in reality is that it won't be until letter 8/20 before there is an initial match...letters 9, 10, 11, 12 when added one at a time will eventually make a search string of 8,9,10,11,12/20. Letter 13 will not match and then the program must end.
Here is my latest modification...

while (<MOTIF>) {@motif = <MOTIF>};

for ($i=0;$i<=length($blocks);$i++) {
$pattern = substr($blocks, 0, $i);
if (/$pattern/) 
{push(@array, $&);
[download]

not sure...
Again, thank-you for your help,
dr_jgbn

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