Accounting for background binding dramatically improves motif finding from PAR-CLIP data. A) Percent change in motif enrichment after background correction for full Pum motif (UGUAHAUA) and half Pum motif (UGUA). Blue bars indicate improvement for Pum library after background correction. HuR (red bars) and Total (green bars) are controls that do not specifically associate with Pum motifs. B) Matched-pair analysis of 7mers from uncorrected Caprin1 sites versus 7mers from background corrected Caprin1 sites (normalized for library size). Motif 1 and Motif 2 are enriched by background correction and both are A-rich with motif 1 containing poly (A) signal sequences. Motif 3 is U-rich and moderately depleted by background correction while Motif 4 is G-rich and dramatically depleted.