Aligning short sequences to alignment

A short oligonucleotide sequence should be aligned to a single location of an alignment. This is useful in a scenario when there is an alignment of similar nucleotide sequences and primers are chosen for doing PCR.

MAFFT, used to do the alignment task, sometimes tear such sequences apart. Try, for example, align the attached "primer.fa" to "COI.aln".

An additional step should be added for the "Align sequence to this alignment" action, executed in case the MAFFT tool was used for a nucleotide alignment. It should check if the aligned sequence is short (assume that "short" means <= 50 bp). And if it so, and it has been aligned to several locations, remove the intermediate gaps (see the attached "COI_with_primer" file).

If the step is executed, add the corresponding "INFO" entry to the log, also remove message like "Saving document C:/Users/username/AppData/Local/Temp/ugene_tmp/p492/add_to_alignment/d_0/UnSAUJXEGapdN492_add.fa" from the "INFO" category. Thus, you should have smth like this:

[INFO]Align sequences to an existing alignment by MAFFT started
[INFO]MAFFT alignment successfully finished
[INFO]Additional enhancement of short sequences alignment performed