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use Bio::SeqIO;

# Setting minimum length to 250
...
        $seqio_out->write_seq($seq);
    }
}

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>NM_030643.4 Homo sapiens apolipoprotein L4 (APOL4) 
GAGGTGCTGGGGAGCAGCGTGTTTGCTGTGCTTGATTGTGAGCTGCTGGGAAGTTGTGAC
TTTCATTTTACCTTTCGAATTCCTGGGTATATCTTGGGGGCTGGAGGACGTGTCTGGTTA
...
ATCTCAGCTCACTGCAACCTCTGCTGCCCAGGTTCAAGGGATTCTCCTGCCTCAGCCTCC
CAAGTAGCTGGTATTACAGGCACCTGCCACCGCGCCTGGCTAATTTTTTTTTTTTTTTTT
TTTTGTATTT