You can use repeated letters in a columnar transposition key. The important part is deciding which repeated letter comes first. CipherSteps reads tied columns from left to right in their original positions, so both sender and solver can follow the same order.

Put the BALLOON columns in order

Original positionKey letterRead order
1B2
2A1
3L3
4L4
5O6
6O7
7N5

Read columns 2, 1, 3, 4, 7, 5, 6. The first L stays before the second L, and the first O stays before the second O. Swapping either pair would change the ciphertext, so keep this tie rule with your puzzle instructions.

Repeated letters and a short final row

InputMEETATNOON
SettingsKey BALLOON; stable tie order; no padding
Expected resultEOMOENTNAT
Try this method

Find column lengths before sorting

MEETATNOON has ten letters and BALLOON has seven. After one full row, three letters remain. That makes original columns 1, 2, and 3 two letters long, while columns 4–7 hold one letter each. Keep these lengths attached to the original columns when you sort them.

Read positionOriginal columnLengthCiphertext slice
122EO
212MO
332EN
441T
571N
651A
761T

Put the columns back

Place each slice back into its original column, reading down from the top. Then read across the rows to recover MEETATNOON. The extra letters belong to the first three columns in the original grid, not the first three columns after sorting.

Try a smaller tied key

Use key BABA and message ABCDE. Which columns are read first, and which column is longest?

Columnar transposition toolDecode a short final columnar rowScytale cipher tool