Table 1.

Overlap between conserved genomic regions as identified by BLSSpeller and experimentally profiled open chromatin regions in rice and transcription factor binding sites inferred through protein-binding microarrays in rice and maize

Overlap with experimentally profiled open chromatin regions (OCR) in O.sativa
BLSSpeller	No. of conserved	No. of OCR regions	No. of conserved regions	No. of rand. conserved regions	enrichment
thresholds	regions		within OCR regions	within OCR regions	fold
BLS $\ge$ 15%, $C\ge$ 0.9, $F\ge$20	754 205	77 247	121 026	40 277	3.005
BLS $\ge$ 95%, $C\hspace{0.17em}\ge$ 0.9, $F\hspace{0.17em}\ge$20	464 229	77 247	98 681	25 996	3.796

Overlap with experimentally profiled TF binding sites (TBS) in O.sativa
BLSSpeller	No. of conserved	No. of TBS regions	No. of TBS regions within	No. of TBS regions within	enrichment
thresholds	regions		conserved regions	rand. conserved regions	fold
BLS $\ge$ 15%, $C\ge$ 0.9, $F\hspace{0.17em}\ge$20	754 205	442 506	159 542	42 522	3.752
BLS $\ge$ 95%, $C\ge$ 0.9, $F\ge$20	464 229	442 506	37 093	5 689	6.520

Overlap with experimentally profiled TF binding sites (TBS) in Z.mays
BLSSpeller	No. of conserved	No. of TBS regions	No. of TBS regions within	No. of TBS regions within	enrichment
thresholds	regions		conserved regions	rand. conserved regions	fold
BLS $\ge$ 15%, $C\ge$ 0.9, $F\ge$20	828 400	482 317	156 929	66 564	2.358
BLS $\ge$ 95%, $C\ge$ 0.9, $F\ge$20	454 221	482 317	35 710	10 755	3.320

Regions are required to fully overlap in order to be scored.