Rain Rot sucks. Nelson has it on his hind legs due to the tall grass while being out in pasture.
You first, need to scrub the infected area well with a gelly curry comb or something to that effect. Then scrub the area well with warm water and betadine or iodine shampoo/wash. Then cover it with MTG or a fungus spray that you can get from TSC.
You have to do this on a daily basis to get it under wraps - or it will spread.
Cutter had it on the back of his hind legs too, but not that bad, so I just took a jelly scrubber and warm water and a gentle shampoo and scrubbed the areas and then dried it well and dabbed on betadine with a cotton swab. This was a couple days ago and I litterally just got back from the barn and its all gone!
Who told you your horse has rain rot?
It's a fungal scab like stuff that has a yellow tint to it, usually found along the withers and back.
Take a Anti-Fungal lotion (MTG works great) and gently rub in circles until the scab comes loose. Don't just peel them off and that doesn't feel to great to the horse.
If you rub with your fingertips until it becomes loose, you'll know when it's ready to come off.
Continue using the MTG until the condition clears up. Your hands work just as good as any comb, even better because you can feel what you're doing. :)
This is the Jelly Curry Comb. Nelson's is in baby blue.
I use the smaller bristle side and scrub his legs so the scabs all come off as instructed to me by my vet. Feel around with your free hand to find the scabby bumps, then scrub the area's as best as you can.
My horses had rain rot too, from all the rain we got. MTG works great, my horses did not like me putting the MTG on them after the scabs fell off, it seemed to bother them, but it cleared them all up and yes you have to do it everyday.
We use Tinactin spray for athletels foot and it is amazing. You can get it at any pharmacy. Works for all different kinds of fungus! If it is a very sticky case and gets worse, you can ask your vet about oral meds such as Omeprazole and Fulvison. The first is a paste amd the second is a powder that can be drenched or mixed in feed. Both are great options and not too expensive.
Oh, be carefull to keep your brushes and equipment separate and only use them for your horse. Wash regularly and dry thoroughly. It might be a more contagious fungus like ring worm or something similar. You never know.