Homologous IESs at non-homologous sites in the genome.

A BLASTN internal comparison of all IESs, carried out with an E-value cutoff of 1e-10, was filtered for HSP coverage of at least 85% of the longest IES and for the absence of significant homology between 500 nt of MAC flanking sequence. The IESs were than transitively clustered and aligned using MUSCLE (Text S2). Some clusters were eliminated because of low complexity of the IES sequences. BLASTN homology searches at NCBI and against known Paramecium transposons ([34] and the present manuscript) were carried out using each IES in the clusters as query. Thon is a Tc1/mariner-like transposon. BLASTX similarity searches against the non-redundant protein database at NCBI did not yield any significant hits at an E-value cutoff of 0.001. The location of the IES, if in a coding sequence, is provided as a ParameciumDB accession number.