When sending the cipher to Lewis, Jefferson wrote out the instructions, "suppose the keyword to be 'antipodes' write it thus.
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then copy out the ciphered line thus. uvyvqb&mgtsfrcsssnjemcuqitm." Jefferson then described the method, "look for the t. in the 1st vertical column, & a in the 1st horizontal one gives u."
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That is, use the letter you want to change and the letter above it in the keyword to plot the coded letter. For example, the first letter from Jefferson's example message is "t" and the first letter of the keyword is "a". With your left hand, locate the "t" the first column, and with your right hand, locate the "a" in the first row. Draw your fingers together down the column and along the row to get the coded letter "u." Write that underneath the "t" and move on to the next set of letters.
Deciphering is nearly the reverse. As an example find the second letter of the keyword, "n", in the top row. Then draw your finger down the column until you find the second cipher letter, which is "v" in this example. Then draw your finger left across this row to the first column to find the letter "h."
In another example (in which the key letters are read from the bottom row) Jefferson envisioned Lewis's first message to him:
"I am at the head of the Missouri. All is well, and the Indians so far friendly."
Or more securely (with the keyword of "artichoke"):
"jsfjwawpmfsxxiawprjjlxxzpwqxweudvsdmf&gmlibexpxu&izxpseer"
Lewis recognized the need for secrecy and said that gathering information was an undertaking best approached by "stealth." However, during the journey he never found the need to use the cipher.