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Gene Runner saves the information on Amino Acids in tables and this data is also be used with the 'Protein Analysis' functions, the 'Suppressor' and the 'Translation Tables'. This is required as Gene Runner will send an error message if the used Amino Acid is not defined in the said tables. In addition, all information concerning these elements is editable, so users can fully adjust their values. With the 'Oligo Analysis' function, users can select a small section, of twenty to thirty bases, click on the 'Oligo' button and obtain a detailed description of it, including all its properties.

The 'Sequencing and Hybridization Analysis' feature allows users to display the primer characteristics of the selected DNA portion, or discard certain types of primers.