Black dots are displayed inside the weaving wherever a thread has a turning point. You now have the ability to leave holes unthreaded. This is very easily done. Go to the design screen, set a used thread width to 0, change the weft color if necessary, go back to weaving and switch to weft display mode. Read up on the palette for details.
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See the manual . The program can handle more than 32 harnesses and 36 treadles.