A misalignment between two identical sets of repeating units of nucleotides within two copies of the same chromosome (one set of repeating units per copy of the chromosome), where repeating unit "A" from one set is inappropriately aligned with repeating unit "B" on the other set, so that "ABABAB" on one set would be aligned with "BABABA" on the other set instead of the correct "ABABAB" with "ABABAB".