It would be easier to diagnose if you provide a self-contained code sample that anyone can run. Regardless, my best guess is that 
    $Text =~ s/$Find$/$Link/g;

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should be: 
    $Text =~ s/$Find/$Link/;

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If LOC100282561 is not at the end of the $Text string, then the $ anchor prevents the substitution.

Update: with your updated code and my proposed fix, here is the output I get: 

<a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=LOC1002
+82561" target="_blank">LOC100282561</a>  [Source:RefSeq peptide;Acc:N
+P_001148941]

[download]
Is that what you expect?

In reply to Re: Matches but not substituting by toolic
in thread Matches but not substituting by seaver

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