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#usr/bin/perl
use strict;
...
        print "$query does not appear in the sequence with ID $id\n"; 
+   
    }
}

>chr1
AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC
...
CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA
AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT
GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAANAATTTCCACC

Insert query:
tatt
TATT does not appear in the sequence with ID chr1
TATT    compare 5 volte  in posizione 20 55 152 155 177 with ID chrM