An IR is a maximal sequence of alignment columns having at least one gap character each and flanked by gapless columns.
We represent one alignment A between two proteins as a sequence of alignment states, where L is the alignment length and is the alignment state at position i.
The sequence of alignment of R. pseudochrysanthum s.l. had 585 bp, including 41 polymorphic sites, of which 15 were parsimony-informative.
Sequence logos of alignments were generated with WebLogo [ 72].
In order to ensure that sequences of alignment are representative and diverse, we collected the homologue sequences by using seventeen different sequences as initial query sequences.
The primers used for the qPCR were designed based on the consensus sequence of each alignment.
Consensus sequences of the alignments were then aligned with the corresponding transposon from M. murinus.
Nucleotide sequences of these alignments were then aligned codon by codon, using the PAL2NAL script [ 49].
Genedoc [32] was used for manual editing of sequence alignments and shading of conserved residues.
We provide FASTA files of concatenated sequence alignments of the above filtered loci datasets.
The number of sequences of an alignment does not influence prediction performance significantly.
