Fig. 4

Analysis of DNA-AA identity bias with respect to PQS distribution. A The scheme of non-LTR retrotransposon shows the average pairwise DNA and AA identity or similarity calculated as an average of each group with respect to functional regions of non-LTR retrotransposon. The charts above them show the difference of average DNA-AA identity and similarity as defined by BLOSUM62 for gag and pol genes for different telomeric retrotransposon groups. The distribution of PQS in functional regions is indicated by a pie chart. B Dissection of DNA-AA identity and similarity in gag gene that can be divided based on protein alignment to conserved area and the rest that shows little conserved motifs. The gag is divided by the conserved region to 5´fragment (N-terminal) and 3´fragment (see Additional file 1: Fig. S6; C-terminal; major homology region—MHR; zinc knuckle motifs—C2HC). As for A) the average DNA and AA pairwise similarities and identities derived from all elements are shown for corresponding regions as well as the DNA-AA difference for the transposon groups. The pie chart shows PQS distribution in the 3 gag regions, note that 5 PQS are on the border of the conserved region and the 5´fragment creating a difference of 10 between gag located PQS A) and sum of PQS in gag regions B). The difference is 10 since these 5 PQS were counted for both regions