#!/usr/bin/perl   
use strict;   
use warnings;   
use Bio::SeqIO;   
  
my $in  = Bio::SeqIO->new( -file   => "input1.txt" ,   
                           -format => 'fasta');   
  
while ( my $seq = $in->next_seq() ) {   
	my $fasta = $seq->seq;   
	while ($fasta =~ /AATT/ig) {   
		print pos($fasta), ' ', $seq->id, "\n";	   
	}   
}   
  
__END__   
*** contents of input1.txt   
>chr1   
AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC   
CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT   
TTTATCTTTAGGCGGTATGCACTTTTAACAAAAAANNNNNNNNNNNNNNN   
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN   
GCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAAC   
CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCNNNN   
>chrM   
GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT   
TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG   
GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT   
CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA   
AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT   
GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAANAATTTCCACC   
>GJKKTUG01DYDGC   
GGGTATTCCTTCTCCACCTTGCAGCTAACATCAGTGTTTCGTCTACTCAAGCACGCCAAC   
ACGCCCTAGAGCGCCCTGTCCAGGGGATGGCAACCAACTCTGACCCTGCAAGTGCAGCAG   
ACATGAGGAATACAAACTACAATCTTTTACTTGATGATGCAATGCCGGACAAACTCTAGA   
>F0Z7V0F01EDB3V   
AAGGCGAGNGGTATCACGCAGTAAGTTACGGTTTTCGGGTAACGCGTCNGNGGNACTAAC   
CCACGGNGGGTAACCCGTCNCTACCGGTATAGGACTAAGGTTACCGGAACGTCGTGGGGT   
ACCCCCCGGACGGGGACCGTCCCCTCATANAGTCAACNGTNTGAGATGGACTAACTCAAA   
CCTAGTTTCAAGTACTATTTAACTTACTTACGTTACCCGTAATTTCGGCGTTTAGAGGCG

  C:\Old_Data\perlp>perl t33.pl   
101 chr1   
213 chrM   
217 chrM   
246 chrM   
294 chrM   
224 F0Z7V0F01EDB3V