A degenerate motif defines SOX cut sites.

A position weight matrix (PWM) for nucleotide likelihood in the 20 nt surrounding the SOX cut sites was generated from the 129 sequences that contained SOX-specific sites with a confidence level of 99.999%. Sequences were scored using this matrix, after removing the 129 “parent” sequences where applicable. A) Frequency distribution histogram of log likelihood scores for the 20 nt surrounding the GFP- or SOX-specific cut sites. GFP: n = 61; SOX: n = 178. B) Frequency distribution histogram of log likelihood scores for the 20 nt surrounding all cut sites found in the two GFP and SOX samples. GFP rep1: n = 693; GFP rep2: n = 409; SOX rep1: n = 849; SOX rep2: n = 1160. C) All human and KSHV annotated transcripts were scored using the PWM. The frequency distribution histogram for the top scores for each transcript is plotted. D) Human transcripts were divided into coding and non-coding based on the annotation in ENSEMBL. The frequency distribution histogram for the top scores for each transcript in the two sets of human RNAs is shown. p value (Kolgorov-Smirnoff test) 7]. The frequency distribution histogram for the top scores for each transcript in the two sets is shown. p value (Kolgorov-Smirnoff test)