ProDesign generates four output files:

     - one containing all the determined probe sets
     - one containing the sequence cluster specifications
     - one containing all the determined probe sets with probes grouped based on their melting temperature
     - and finally one file that has the optimal probe set

The file containing all the probe candidates has the first line with a leading with *, with the second number being the total number of clusters. The lines starting with > are descriptive: the first number is cluster ID, the second number is the size of the cluster, the third number is the number of probe candidates found by ProDesign.

The optimal probe set file looks like:

The optimal probe set
The melting temperature is 54.67
The coverage of this set is 118/155

ID_cluster probe_sequences
0 GAACGGCCAAAGGAACTGCAACTGC AGCGGCAGGTACTACCACTTGACGCC
1 TCTGCTAGACGAAGCCAAGGTCCCA
2 GCTAGTACCTGCCGCTTTGCGAACT TTGCGAACTTGGCTAGTTCTAGCAGA
3 GCGGGGTCATGAGCTAGTACCTGCCGCTTTGGGAG

where the first three lines describe the melting temperature and coverage. Then cluster IDs and related probes are listed, one line per cluster

If the run is succesful ProDesign displays four buttons:

These buttons are enabled/disabled depending on the type of run, and they are used to save all the above files in ASCII format.