The parse program requires two inputs:

1. Paste into the left box a list of cDTs in the form name-CCATAT, for example.

2. Paste into the right box a list of cDT-cataloger motifs copy-pasted from the second column of the cDT-cataloger table titled 'Motif'.

To get a complete recording of the frequency of each cDT, make sure you run both forward and reverse complemented CDTs in the cDT-cataloger. The output of cDT-counter is displayed in the first window and consists of a list of the cDTs with the number of repeat hits from obtained the cDT-cataloger, for example name05-CCATAT if there were five hits of that sequence in the cDT-cataloger. Make sure the sequences in the two windows are of equal length (hexamer for example).