N.P.
Yes, it probably is mold. I just discovered this problem in my own tubing this week!
The good news is that the boiling will have killed it, but it won't remove the discoloration. So, it is probably just fine. I noticed a recommendation somewhere to inject alcohol down the tubing after you clean it to dry it out - I'm planning on giving it a try!
Though this also will likely not remove the color (bleach would, but seems like a bad idea!)
N.