Gradient Rectangle with mask cutouts

Sorry if this has been answered but i'm not sure how to search this. 

I'll try to explain. Please excuse my terminology.

I am trying to recreate the attached (blue) long rectangle . Sorry about the bad quality.

Imagine a long horizontal rectangle shape with a gradient on one end at 100% fill opacity and the other 0% opacity. Now, at points along the way i want to create uniform spaced out (Masks) which "cut out" sections of the rectangle. I have found ways to do this but the problem is when i follow the options i've found the gradient starts and stops with each and every mask cutout. I need the gradient to stay consistant from one end to the other and not be effected by the cutouts/masks.

I was able to get this to work using the transparency mask but i'm not sure how to do this and keep a identical size consistant distribution of cutout/masks (ex. a 1inch mask every other 1inch over a 5 inch length of the rectangle). 

I just added a Yellow gradient example (higher quality image)

The top version is what i made using a transparency mask but there is no way to create several cutouts with a set or evenly distributed distance between them. The bottom version is what i get when i use the shapebuilder tool and remove the overlapping section.

Thanks and sorry for any confusing descriptions.