HMM logos representing pneumococcal interspersed repeat sequences. These images describe the HMMs used for sequence searches. Each column corresponds to a nucleotide in the repeat element. The total height of bases in each column represents how informative that position is in describing the element; the relative heights of the different bases indicate their respective emission probabilities in the model. Red shaded columns show positions where base insertions occur: the total width of these columns represents the expected number of inserted bases, whilst the dark shaded component indicates the probability that an insertion occurs. The repeats displayed are a) i) boxA, ii) boxB, iii) boxC, b) RUP and c) SPRITE.