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$VAR1 = '<html><title>GAL7</title>
<body bgcolor=white>
...
ATGCAGAGCATCAACATGATAAAAAAAAACAGTTGAATATTCCCTCAAAA
ATGACTGCTGAAGAATTTGATTTTTCTAGCCATTCCCATAGACGTTACAA
';

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my $new_output = '
>YBR018C  GAL7  275433  275933        #this fasta marker line is to be
+ kept
...
ATGCAGAGCATCAACATGATAAAAAAAAACAGTTGAATATTCCCTCAAAA
ATGACTGCTGAAGAATTTGATTTTTCTAGCCATTCCCATAGACGTTACAA
';