The left and right PDF documents are displayed in two different colors. What you see on the screen is a merged result from both PDF documents. By default, red and cyan are used as the pair of colors to represent the left and right documents. You are allowed to change the colors, if you like other colors.
In the drop down list on the right of 'Ways to mark difference', you can find all the available options.
Red stands for Red and Cyan colors to display the contents of the left and right PDF document.
Green stands for Green and Magenta to display the contents of the left and right PDF document.
Blue stands for Blue and Yellow to display the contents of the left and right PDF document.
Other options are filtered designed for users with intended needs.
