The used options are listed in Table 1 in column 'value D. mel.'. Column 'Predictions' gives the number of predicted and column 'References' the number of annotated 'full length' LTR retrotransposons for each chromosome. A prediction is classified as true positive (TP), if the maximum allowed distance between 5' and 3' coordinates of the prediction and the reference is at most 20 nucleotides. If only one of the two predicted boundary coordinates lies within the allowed distance of 20 nucleotides, the prediction is categorised as a half true positive (hTP). All other predictions are labelled false positive (FP). LTR retrotransposons that are missing in the prediction are labelled false negative (FN).