LOC_Os01g01010.1 3017 : PAS [2993,3017] : AGTAAA AAATGGAGGAATTCTGCCA LOC_Os01g01010.2 2218 : uORF [7,129] : ATG AAGAAGACGAGACGACGACTTCCCCACTAGGAAACACGACGGAGGCGGAGATGATC #### LOC_Os01g01010.1 : PS51373 HIPIP High potential iron-sulfur proteins family profile. 2139 - 2208 AATGATTTATCATGTGAGGTGAAAGA-----AGAGCACCGGGTGAACAGTTACACAAGAA L=-1 GAAAGTCCAAAAGCA LOC_Os01g01010.2 : PS00022 EGF_1 EGF-like domain signature 1. 298 - 309 CtCccTtcGTtC L=(-1) #### #!/usr/bin/perl use strict; use warnings; open(FH, "outputps_scan_chr1_.out") or die "Can't Open File1\n"; my @array1=; close(FH); open(BH, "chr1_1.txt") or die "Can't Open File2\n"; my @array2=; close(BH); my $pattern='/^LOC_Os0[1-7]g[0-9]*.[0-9]\s'; foreach my $line1(@array1) { foreach my $line2(@array2) if { $line1=~ /^$pattern/; $line2=~ /^$pattern/; $line1==$line2; { print $line1; } } else print "nothing to print\n"; }