Fig. 1

Overview of possible ambiguities, when comparing two annotations of CSEs (benchmark and predicted CSEs). Black lines depict query sequences, blue lines indicate benchmark CSEs, red and orange lines represent predicted CSEs. a Multiple true positive sites (left) and a single false positiv site (right). b A true positive matches to multiple, overlapping benchmark sites (left) or to a single benchmark site (right). c The overlap between a predicted site and a benchmark site may be large (left), minimal (center) or one predicted site may patch multiple benchmark sites (right). d An excessively large predicted site overlaps with a short benchmark site. e Two predictors have one true positive and one false negative; the matching benchmark site may be short (left) or long (right). f A predictor finds a benchmark site in either a long sequence (top) or a short sequence (bottom). For more details, see Main Text