Perles are those small bumps that are formed after you make the Buttohole stitch.
I have written on some of them on the diagram above.
Each line on the chart represents a fabric thread.
Buttonhole Stitch Diagram
The Perle is formed at step 4 as shown in the Buttonhole stitch diagram.
The perle is formed where the working thread crosses the loop. It is the same for the lace stitch shown below. It is also a buttonhole stitch.
The thread that formed the loop is being closed by pulling straight down on the working thread.