Hello and welcome, aseee.

You posted a rather large amount of code for a broad question. If you can show expected output and tell where exactly you are having trouble it will be much easier to provide a helpful answer. Also, I'd suggest having a look through perlintro and perlstyle. Cleaning up your code a bit will go a long way towards helping us help you. Not to mention, a strong understanding of the basics will better equip you to answer your own questions in the future.

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**UPDATE**

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Since you didn't exactly point out where your problem lies, I'm going to guess it is most likely in the maze of single char variable names and unformatted loops. I would suggest cleaning up your algorithm subs. The added clarity in conjunction with a slow review may yield the solution to your problem. Also, the Knuth-Morris-Pratt algorithm is covered on page 370 in Mastering Algorithms with Perl by Jarkko Hietaniemi, John Macdonald, and Jon Orwant. There is a link to view this material online in this node Knuth-Morris-Pratt Vs. Perl. I suggest you contemplate rewriting your code using this material as a guide, and implore you to research more thoroughly before asking for help. Finding your own answers is infinitely more rewarding ( I myself learned what the KMP algorithm is and how it works by researching Your question tonight ;).

I took a stab at cleaning up some of your code. Some notes to keep in mind:

Incremented for loops i.e. for ($i = 0; $i <10; $i++) { ... } are easily changed to for (0..9) { ... }

White space can be key in clarity. Try to keep a consistent indentation theme. i.e:

for (0..9) {
    print "line1\n";
    print "line2\n";
    if ($cond =~ /pattern/i) {
        do something;
    }
}
[download]

Here is a revised (UNTESTED) sample of your opening for loop.

my @tt=($T_one,$Ta,$rr);

foreach my $string (@tt) {  
    @loc=();
    @text=();

    my $strLength = length($string); 
    my @stringArr = split //, $string;
 
    print "<\br>";  
    print "Length of Gene Sequence Array:    $strLength\n";
            
    foreach my $pattern (@patterns){
        print knuth_morris_pratt($string, $pattern), "\n";
    }
                
    @loc = sort {$a <=> $b} @loc;

    print "</br>";
    print "@loc";
    print "</br>";

    my $i=0;
    foreach my $k (0 .. ($strLength-1)) {
        print $i;
        if ($k == $loc[$i]){ 
            print "<span style=background-color:red;>$text[$k]</span>"
+;
            $i++;
        } else { 
            print $text[$k];
        }
    }
    
    print "</br>";

}
[download]

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