Short by-products are generated during piRNA-directed targeting. (A) Contour-plot of the frequency distribution of (piRNA length, by-product length) values. Cleavage products always have the 3' end located opposite position 11 of the guide piRNA. On the x-axis is the length of the cleavage product and on the y-axis the length of the guide sequence. (B) A 3 kb long region from chromosome 15 is shown (positions 59'105'450 to 59'108'450 on the mouse mm9 genome assembly). On the top, the log2 densities of unique mapping reads to the plus and minus strand within a 10 base window are shown in red and blue respectively. Below is the density of P9 patterns as well as P28 sites where the 19-mer is located at the plus and minus strand. (C) The Markov model with transition probabilities between P28T (T) and P28B (B) sites is shown.