It looks like one of the elements of the array is undefined.

I'm also a little confused about what you're trying to print. For example: 

          SET: foreach $hit (@{$matches{$fastaseq}{$sitekey}}) {

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The foreach is iterating over the elements of the array, and $hit is the value of each element, not the index. This is important later. 

print "\$hit is: ",$hit,"\n";

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This line prints the value of $hit. The following line, however, 

print "\$hit is: ",$matches{$fastaseq}{$sitekey}[$hit],"\n";

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uses that value as an index. I don't know how you populated the array, but unless the values of $hit really are index values, you're accessing possibly undefined array elements. In your example above, $hit = 6906413. Do you really have that many elements in the array?

I suspect you may be having trouble with dereferencing, but I don't know enough about the data struct you have and what you're trying to get out to give you an example. Can you post a partial dump of %matches and an example of what you want to print?

Update: If you want to iterate over the array using indices instead of the values, you can use something like 

foreach my $index ( 0 .. $#array )

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If you want to simply skip undefined elements in the array, you can use 
next if( not defined $hit );

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In reply to Re: foreach in HoHoA problems by bobf
in thread foreach in HoHoA problems by mdunnbass

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