Figure 2

Smoothed entropy. The three panels show the smoothed entropy for the Greengenes, RDP and SILVA alignments covering the same 12362 sequences in this study. Positions with less than 30 bases have no entropy here, hence the ’holes’ at some positions. Notice the difference in the number of positions, Greengenes being the shortest and SILVA the longest alignment. The nine variable regions V1,..., V9 are indicated for each alignment. Five examples of primers (27F, 536F, 928F, U2 and 1492R) used for PCR amplification of 16S are also marked along the position axis, indicating where they frequently match.