The Last Straw

Yesterday, Rosie kindly ran her Perl script over the USS construct I designed. The final thing I was worried about was whether or not my design had any USS or USS-like sequences in it, other than the one it's supposed to have. I'd checked the construct for any core USS motifs (5'-AAGTGCGGT-3'), but since we think that the motif is more complex than this, it was important to make sure that there were no extra sequences that got high scores using the USS position-weight matrix.
Fortunately, the construct looks good, so I can go ahead and order the control oligos and have high expectations that they'll work...

Here's how every 32 base pair window over the 199mer looks when scored with the USS PWM:
There's a single prominent high-scoring site right where it should be, and all of the surrounding area scores near background. The USS in the construct has a score (~10^-8) more than 10 orders of magnitude better than the next best sites. There's a slight increase for windows immediately adjacent to the USS, presumably because the AT-tracts in the USS are still contained in those windows. The rest of the construct only has scores at background.

Just to show that these other sites really do represent background levels of USS score, Rosie also ran a randomized version of the sequence:
Nothing better than 10^-18. Excellent.