We examined how letter position coding is achieved in a script (Arabic) in which the different letter forms (i.e., allographs) may vary depending on their position within the letter string (e.g., compare the same-ligation pair [see text] and [see text] vs. the different-ligation pair [see text] and [see text]. To that end, we conducted an experiment in Uyghur, an agglutinative language from the Turkic family that employs an Arabic-based script in which both consonants and vowels are explicitly written. Participants had to reproduce the correct word forms in rapid serial visual presentation sentences that either contained jumbled words (with the same ligation or different ligation) or were intact. The results revealed that readers had more difficulty correctly reporting the target words in the jumbled sentences when the letter transposition involved changes in the ligation pattern, thus demonstrating that position-dependent allography affects letter position coding. This finding poses constraints to a universal model of letter position encoding.