People used a cipher for a reason, to hide a message in plain sight. If you were dealing with a plain and simple straight forward Pig Pen cipher, it would be easy for you or most anybody else to decipher. To make things more difficult and to try to protect the message from those you didn't want to see it, another level of encoding such as "transpostion" was incorporated into the cipher. You may want to try and start the alpha-bit where the letter W or Y is located in the Pig Pen cipher, and if that doesn't work you may want to try something else. May be the W and Y are the initials of the person who wrote the cipher, like William Yates.
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