I am working with a string consisting of characters A-Z and four characters A,C,G,and T are of particular interest. I am trying to extract substrings from the string that qualifies the following conditions:

1] Distance between A,C,G, or T to any other A,C.G, or T should be 0 to 8 characters.

for example: string: AGRTGAXWXX

substrings: AG, AGRT, AGRTGA, GRT, GRTG, GRTGA, TG, TGA, GA

2] I want the maximum length substring possible, in above example,

string: AGRTGAXWXX

I would just want the substring: AGRTGA

as all the other substrings are part of this longest substring and this has the maximum distance between A and A within the distance allowed.

I have this so far: can anyone help please?

#!/usr/bin/perl
use strict;
use warnings;


my %uniq=();
my $string = 'ACRMGAHKMAHGTXX';

      substr($string, $_, 10 ) =~ m[([AGTC].{0,8}[AGTC])]
      and ++$uniq{ $1 }
      for 0 .. length( $string )-1;

for my $key (keys %uniq){
    print $key, "\n";
}


#above code outputs the following:
GAHKMAHG
CRMGAHKMA
AHGT
AHKMAHGT
GT
GAHKMAHGT
ACRMGAHKMA

#and I only want the following:
ACRMGAHKMA
GAHKMAHGT

[download]

Anyone has any suggestions? Thanks!

In reply to substring selection from a string on certain qualifying conditions by BhariD

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