Table 3. List of putative RNA Polymerase II binding motifs identified by PeakRegressor.

Pol II	Normalized coef.
T[AG]A[GC][TAG]CA[GCT]A[AC]AA	1.
A[GA]AA[AC][CA]AA[AC]AAA	0.78
C[ACT][GT][CG][CT][TA]CC[AGT]CC[TA]	0.76
C[CT][CG][AT]GGCTGG[AG]G	0.68
TTTCTGC[CT][CT]TT[GT]	0.67
T[TA]T[TC][CA]CAGACT[AT]	0.63
GGAGGGAGGC[AG]G	0.62
AC[AC][CA][AC][AT][AG]AGAAA	0.61
TTTGT[CT][TA]T[TG][AC][AT]T	0.54
AAA[AT][GC]AAA[AT]A[GA]A	0.54

The known Downstream Promoter Element and Initiator site motifs are shown in boldface.