Running AutoDimer



1. Prepare an input file containing at least two sequences following the input file format.

          Note: You must use an input file.  Sequences cannot be entered manually in the blue text box.

2. Open file from “File” menu.

3. Confirm that the proper number of sequences have been read in by reviewing the “# of Sequences box”.

4. If desired, vary the parameters for Score, [Na+] or total DNA strand concentration (CT).

5.Click either “Primer Dimer Checker” or “Hairpin Checker” the meter will indicate progress.

6. Potential structures are displayed in the text box in the lower portion of the program screen.

7. If you wish to save the screening results go to “File” and “SaveAs”.  The information can be opened later in Word, Excel, Notebook etc.

8. The results can also be printed directly from the AutoDimer program.


Possible run time errors:

As the algorithm runs, AutoDimer saves temp files to your “C” (C:\) drive.  It erases these files when you exit the program.  However, if you load the program onto a D, E (non C) drive or if your “C” drive is full then you will have problems running the program.