Try this: 
#!/usr/bin/perl 

use strict;
use warnings;
use Term::ANSIColor::Print

open READ, '<', '/root/Desktop/rna.dna';
my (@e) = <READ>;
my $a = join( " ", @e );
$a =~ s/\s+//gi;

my $s = 0;
my @c;
my $i; 
for ( $i = 0; $i < length($a); ++$i ) {
    my $d = substr( $a, $i, 6 );
    unless ( $d eq "AGGGGG" ) {
        my $print = Term::ANSIColor::Print->new();
        $print->bold_green($d);
        ++$s;
        push( @c, $i + 1 );
    }
}
print $a;
print "NUMBER OF SITES THE MOTIF (AGGGGG) IS PRESENT: $s";
print "AND THE POSITION IN THE STRING IS: \n",
  print join( ',', ( @c, "\n" ) ), "\n";

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In reply to Re: motif finding by Khen1950fx
in thread motif finding by devi

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