In the presence module, the sequence identity of the contig sequence overlapping the TE sequence is now take into account to define the presence of a TE insertion. By default, the min sequence identity is 70%.
The information if the identity, number of mismatches and matches are returned in the "Tresult" file.
Minor changes:
The number of strains in which a TE is defined as absent is now reported in the "Tfreq" file.
Fix the combRes option.
Improve the alignment output.