It is better if you use a text editor to modify the heading of the combined list so that the annotation in the list correctly reflects what you have done. Remember to delete the text heading from the second file so that it does not occur in the middle of the list. You can also put comments into a list anywhere on a line by placing an exclamation point before the comment. You cannot assume that a text pattern search is exhaustive. The text you choose may not have been used by the data collectors.
Hyphenation is particularly prone to inconsistent usage.
Using a nonspecific pattern such as pseudo to find sequences of pseudogenes will result in many false matches. It's usually better to use a less-specific search pattern and then edit the resulting list file to remove entries that you aren't interested in. The conclusion is that a search with StringSearch can only tell you what is available and not what is not available. The complete annotation search takes a lot of computing, but the search includes a lot of information, such as author and journal names, that is not found in the sequence definitions. Batch Queue StringSearch is one of the few programs in the Wisconsin Package that can take more than a few minutes to run.