array1 contains gene accession numbers of this format: X65a293846,X65a030294,X65a129385 array2 contains much more information that looks like this: 37483919..36271893 - 0 0 - X65a293846 - - DAR 42948502..38291239 - 0 0 - X65a030294 - - DAR Both arrays are read in from a file like this:

my $file = "gene.txt";
open(FH, "< $file") or die "Can't open $file for read";
while(<FH>){
    push(@array1, $_);
    }
close(FH);
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The strange thing is that before this, I manually entered them into an array and it worked fine. Only now is it having problems.

Oops, replied to the wrong node... should've been to andybshaker

Tip #3 from the Basic debugging checklist: chomp

Hero

Sorry, your description of the second array is unintelligible. Use <c> tags. Better still, I would suggest using the debugger to inspect the arrays immediately prior to your logic to make sure they contain what you expect. I suspect toolic's tip about chomp is also relevant.

Dum Spiro Spero