Table 1. Summary of CPE Scans of 14,000 High-Confidence TSSs.

CPE	5′ CPE Start Positiona	Percentage of Sequencesb with CPEc	Percentage of Sequencesb Overlapping CPE Startd	Overlapped ROEe
GC box	−150	8.19,3.41,1.14*	62.76,39.59,19.4	No
CCAAT box	−75	16.1,NA,NA*	69,NA,NA	No
BREu	−38	11.06,6.08,1.99*	65.33,46.05,19.06	Yes
TATA box	−30	26.14,20.05,10.19*	71.88,57.35,29.07	Yes
BREd	−24	9.27,5.15,0.47*	70.1,45.62,3.9	Yes
Y-Patch	−13	32.09,24.16,3.98*	84.92,73.11,18.94	Yes
XCPE1	−8	10.18,4.61,0.89*	66.15,39.99,9.57	Yes
Inr	−2	8.34,7.19,1.6*	53.92,46.73,14.22	Yes
DCE	+6	14.59,8.41,2.15*	72.57,52.9,18.64	Yes
MTE	+18	13.61,8.05,1.23*	69.86,52.92,12.36	Yes
DPE	+28	9.13,4.17,0.81*	60.55,34.24,7.02	Yes
MED-1	+88	21.01,13.86,6.22*	74.32,58.04,32.07	No
Percentage of genes with no CPEf	0.01,0.2,17.35
Percentage of genes with no CPE around 5′ CPE startg	14.65,33.18,72.92

The asterisk indicates that each percentage was calculated using a threshold that held the false-positive rate at 0.001, 0.0005, and 0.0001 in the same order for each cell identified. This table compares observed positional enrichments for 12 traditionally identified CPEs in the genomic regions surrounding 14,000 high-confidence TSSs in wild-type Arabidopsis whole-root samples. CPE start position is the commonly listed location in the literature for each element with respect to the TSS; for each CPE, a point roughly in the middle of the various ranges reported (Bryne et al., 2008; Kadonaga, 2012; Kumari and Ware, 2013) was used. Region of enrichment (ROE) is the region with respect to TSS where the element was actually cumulatively observed to be enriched using log-likelihood scans over the Arabidopsis promoters. The overlapped ROE column highlights major differences (“No” entries) between expected locations of elements in the general literature and observed enrichment locations in Arabidopsis.

^aThe common midpoint used for each CPE, since most CPEs are reported as having a range of start positions.

^b14,000 genes were scanned 500 bp upstream and downstream of a high-confidence TSS identified by Cumbie et al. (2015a).

^cCPEs were found 50 bp up- and downstream of the 5′ start position.

^dCPEs were found anywhere within 500 bp of the TSS (see footnote b).

^eROE identified using an algorithm previously described (Morton et al., 2014) were found to overlap the region surrounding the CPE (see footnote c).

^fPercentage of genes where no CPE was found within 500 bp of the TSS (see footnote b).

^gPercentage of genes where no CPE was found around the preferred CPE start site (see footnote c).