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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