The problem of musical query processing can be envisioned as a substring- matching problem when the melody is represented as a sequence of notes associated with a set of attributes. In comparison of two musical sequences, one of the important problems is to determine the weights of each operation. This paper presents an alternate weighting-scheme which is based on diatonic distinctions on melody perception. To achieve this, we run a cognitive experimentation applying Probe-Tone method. The results showed that perceptional hierarchy of pitches changes according to the interval distinction on melody, whether it has more disjunt interval than conjunct intervals, vice versa. Consequently, if the new weighting-scheme created in this study are used in sequenced- based melody comparison, melodies retrieved to user would have a more credible ranking. The details of experimentations and the results we reach are also presented in detail.