Figure 5

Conserved and variable regions in MSG genes. A) The 73 core MSG sequences were aligned. The DNA alignment was partitioned into regions containing 16 bp and average p-distances were calculated for each region using MEGA4 software [117]. The horizontal lines labeled HV1 etc, demarcate five hypervariable regions. The horizontal lines labeled CR, C1 and C2, demarcate constant regions CRJE, C1 and C2. B) A depiction of the majority and minority sequences observed. The height of a letter is proportionate to the frequency at which the base it represents was observed in the 73 aligned sequences. Thin vertical lines represent positions where INDELS occurred in the alignment. Each of the 12 blocks of sequence contains two of the twenty-four 16-base segments analyzed in panel A. The limits of each 16-base segment are indicated by the black and gray horizontal bars. The leftmost pairs of numbers correspond to the region-numbers in panel A. For example, the first block of 32 bases contains regions 1 and 2. Region 1 is covered by the black bar. Region 2 is covered by the gray bar.