The most common pixel order in displays is rgb (red on the left) (you can check your pixel order here ). When you rotate 90 clockwise, you get red on the top, which is called vrgb. For abbreviations, see this file.
This answer to a different questions gives the helpful command
gsettings set org.gnome.settings-daemon.plugins.xsettings rgba-order 'vrgb'
It seems to help, even though I run unity. For the terminal. For firefox and chrome, it does not work. So, in the end, I gave up, turned my monitor into landscape mode, and started to work.
For the setup with several monitors---thus, one monitor with rgb, another monitor with vrgb---see the answer https://askubuntu.com/a/708725/41363.
UPDATE two years later: I tried again, and it seems to affect both chrome and in terminal. However, it is still so-so.