If the sequester occurs, agencies like NASA will have to cut each program (but with wiggle room to move cuts around) by 5% relative to their Fiscal Year 2012 spending. Since half of the current fiscal year has passed (the fiscal year starts October 1), the cut to the remainder of the year spending will be 9%. (Some agencies have been under spending so far this year to bank money in case the sequester occurs; I don't know if NASA has been one of them.)
NASA has now sent Congress a letter giving examples of how the sequester will impact each of its programs. Because its Science program absorbed a 3.2% budget cut in FY13 compared to FY12, the program would have to absorb just(!) an additional 1.8% cut to the FY13 budget. (NASA's letter says the additional cut would be $51.1M. My spreadsheet says it would be $91.1M, so either the letter has a typo or more probably the budget summary I work from doesn't have the complete picture.)
NASA's Planetary Science program absorbed a 20.5% cut from FY13 to FY12, so in theory it might be spared any sequester cuts. However, NASA has some discretion to move cuts from higher priority programs such as the James Webb Space Telescope (with a 20% FY13 budget increase) to programs it considers lower priority. The Planetary Science program might see some sequester cuts, if the sequester occurs, but perhaps less than the 5%. The two specific examples of programs provided by NASA for the Science program shows that the amount of cuts is flexible between programs. The low cost Earth Science and Astrophysics mission programs would have a 10-15% cut while the research and analysis program that supports individual scientists would have a 2% cut.
Still not good news -- the Science program already is hurting from the FY13 cut and paying for the cost overruns on the James Webb Space Telescope. However, the addition sequester cuts to the Planetary Science program -- if they happen -- may not be as bad as I had feared. I also still have some hope that in the end, the two political parties will blink and either cancel the sequester (everyone agrees that blanket cuts are terrible policy) or substitute it with a more thoughtful approach to reducing the deficit.