TIRs longer than Mites

[madelhorius]

TIRs longer than Mites

[juancresc]

Hello Marius,

The problem in this case is the way in which the TIR lenght is reported by the program. If you take that MITE sequence, reverse complement it and align against the original, you'll see that you have an overall a good alignment

https://mafft.cbrc.jp/alignment/server/spool/_ho.190311232414059YOWy7XQ0RMupr4mnehIlglsfnormal.html

This means that you have a very long TIR to work with. Next, the algorithm starts searching for valid TSDs (~findir.py:114). The reported TIR length in the output corresponds to the original TIR alignment, sometimes can be larger than the final MITE.

I'll evaluate making a re-calculation of the TIR lenght

[madelhorius]

I see, thanks for your explanation! Yes, it would be great to have re-calculated TIR length to work with.

[juancresc]

This is going to the backlog of the next release.