use warnings;
use strict;

my $fh;

while (<DATA>) {
    chomp;
    if (/(XLOC_\d+$)/) {
        open $fh, '>', "$1.txt" or die $!;
        print $fh $_, $/;
    }
    else {
        print $fh $_, $/;
    }
}

__DATA__
XLOC_000039
>chr1:983051-985037
CATGACTTTGTCGGAATTATGTTACTGCTCATTATCAATTCCACCATTAGCTTCATAGAG
GAAAACAATGCCGGGAATGCTGCTGCTGCGCTTATGGCCCGCCTCGCACCAAAATCCAAG
GTAAGCCCCACACCCTACTTACCACTCCTTTTTCTTCTCAATACTGCTTTTCATCATGTT
ACACTCATTTTCTAGGTTTTACGTGATGGAACCTGGAGTGAAATGGACGCATCTTTGTTG
GTGCCCGGTGACATAATCAGCATTAAACTTGGAGACATCATTCCGGCAGATGCGCGTCTT
CTCGAGGGAGATCCGCTGAAAATTGACCAGGTCTTTCTTGTGTCTCAATCATAGTGTTCT
TGGTAGAGCGGAAAAAAAAATATTCTGATATGAAAATTACATGAGACACTAAAACACATA

XLOC_000456
>chr1:12600284-12601781
CAACAATCTCTGATGATGCGGCAGGGCCTTGCTCGCGGGGCGTGGTGCTACCTCGAGGAT
GAGTTCCTTGGCCAAAGGGAATCCCGGGCGCTTCTACTTGAGACAAAATTCCGCAACTTC
CGCCAAGAGTCCTTGAGCATCACTGACTACTGCCGCCAGCTTGAGTCAATGGCGGCATCC
CTTGCCGGTTTCGGCGATCCCATCGGCGATAGGCAGATGGTGCTCACGCTCCTTCGTGGC
CTCGGCGGCAAGTTCCGTCACATGGTGTCCATCCTCAAGATGCACCAGCCGTTCCCCACG
TTCGCAGAGGCTCGTGCGCACCTGCTGTTGGAGGAGCTGGAAATCGACGCACGACCTCCA
TCACCGCCATCGGCACTTGTTGCTGCAGCGCCGCGGCATGCGACTCCGGGGGCCCCAGTA