Sequence logo is a well-accepted scientific method to visualize the conservation characteristics of biological sequence motifs. Previous studies found that using sequence logo graphical representation for scientific evidence reports or arguments could seriously cause biases and misinterpretation by users. This study investigates on the visual attributes performance of a sequence logo in helping users to perceive and interpret the information based on preattentive theories and Gestalt principles of perception. A survey was conducted to gather users' opinion after being presented with several alternative design details to perform selected tasks on motif analysis. Analysis of results showed that there are improvements needed on the use of colour, negative space, size, and arrangement of the nucleotides, richness of information and interactivity aspect in a sequence logo visualization. These improvements can alleviate biases and misinterpretation of the results in sequence logo visualization.