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foreach my $line1(@array1)
{ 
...
                        {  print $line1;    }
}

#!/usr/bin/perl
use strict;
...
}
close(FH);
close(BH);

LOC_Os01g01010.1 3017 : PAS 2993,3017 : AGTAAA AAATGGAGGAATTCTGCCA
LOC_Os01g01010.2 2218 : uORF 7,129 : ATG AAGAAGACGAGACGACGACTTCCCCACTA
+GGAAACACGACGGAGGCGGAGATGATC

LOC_Os01g01010.1 : PS51373 HIPIP High potential iron-sulfur proteins f
+amily profile. 2139 - 2208 AATGATTTATCATGTGAGGTGAAAGA-----AGAGCACCGGG
+TGAACAGTTACACAAGAA L=-1 GAAAGTCCAAAAGCA
LOC_Os01g01010.2 : PS00022 EGF_1 EGF-like domain signature 1. 298 - 30
+9 CtCccTtcGTtC L=(-1
LOC_Os01g01010.2 2218 : uORF 7,129 : ATG AAGAAGACGAGACGACGACTTCCCCACTA
+GGAAACACGACGGAGGCGGAGATGATC