Hi everyone. I just finished writing a new app in C# that allows you to perform screen captures of the 1st and 2nd State designs, the dot plot and melt point graphs as well as just the dot plot. This app also has a function that applies a red dot overlay to the dot plot based on pairing probability.
The red dot overlay allows you to view dot plot at each intensity level from 0-255 (based on RGB intensity scale). At each intensity level the nucleotides dots that are the current intensity and all nucleotides with a lower intensity are viewed as red dots and all nucleotide dots with a higher intensity are viewed as black. The intensity levels correlate to the nucleotides pairing probabilty. The lower the intensity the higher the pairing probability and the higher the intensity the lower the pairing probability.
This app also has a google docs manual that should help you get started. If you have any questions please ask and I welcome all types of feedback. Hope you find this tool helpful.
Here is the application: ()
Here is the documentation: