The USPTO has published a final rulemaking to implement the new fee structure. See the rules description here. There is a discussion of new section 1.52(f)(1).
Section 1.52: Section 1.52(f)(1) is added to provide that any sequence listing in an electronic medium in compliance with ?? 1.52(e) and 1.821(c) or (e), and any computer program listing filed in an electronic medium in compliance with ?? 1.52(e) and 1.96, will be excluded when determining the application size fee required by ? 1.16(s) or ? 1.492(j). See 35 U.S.C. 41(a)(1)(G) (which provides that a sequence listing or a computer program listing is excluded if filed in an electronic medium as prescribed by the Director).
This is a welcome relief for anyone who was pondering whether or not sequence listings submitted on CD-ROM in lieu of paper copy would count towards your page fee. Since sequence listings can (and often are) thousands if not tens of thousands of pages, the cost of a provisional could have been an added $5000 per 1000 pages of sequence listing submitted. Not exactly the $200 originally.
