Overlap between query and subject sequences was scored only when the alignment encompassed up to the last nucleotide at the 5' or 3' end of the sequences.
The sequence alignment encompassed >97% of the chameleon mtDNA (∼17,000 bp).
The final alignment encompassed 20 taxa and 13, 184 nucleotide sites, of which 3, 882 sites were parsimony informative.
At the nucleotide level the final alignments encompassed respectively for the Ig2, Ig3 and Ig7 exons, 106, 290 and 219 sequences; 197, 147 and 328 alignment patterns; and 22%, 18% and 21% gaps and completely undetermined positions (Additional files 16, 17 and17).
In this case, at the nucleotide level the final alignments encompassed respectively for the Ig2, Ig3 and Ig7 exons, 25, 99 and 66 sequences; 148, 128 and 296 alignment patterns; and 6.8%, 8.9% and 0.6% gaps and completely undetermined positions (Additional files 19, 20 and 21).
Multiple alignment encompassing database and PCR sequences were trimmed at the same length before phylogenetic analysis.
They also provided alignments encompassing LTRs of most of beta-, gamma- and lentiretroviruslike LTRs, presenting further insight into the common LTR structure of these genera.
A threshold of E<10-80yielded E<10-80yieldeds encompassing a total of 1.2414bp from ealignmentss, whencompassingshold of E<10-20 yielded 2820 alignmentotalcofpassing a total of 1.25 Mbp.
Most of the recombination breakpoints per sequence were single and thus involved recombination of sequences encompassing one of the two halves of the alignment.
Based on the alignment of sequences of the bont/B gene (3876 bp) present in the GenBank database, the region encompassing nucleotides 920 to 3727 was selected for PCR amplification because it has shown a certain degree of nucleotide polymorphism.
