If -nastout is specified, then the search database must be a multiple alignment in FASTA format.
Hits are written to the -nastout file as follows. Only the query sequence is written; if you need to know the target sequence or label, you can use one of the other standard output files and match up the query labels. Gaps are added as needed to align to that target sequence. Insertions relative to that target are deleted, so that the resulting sequence has exactly the same number of columns as the database multiple alignment. The deleted insertions are noted by appending an "ins=" annotation to the label, as in the following example:
The ins= annotation is a comma-separated list of insertions. Each insertion gives the deleted sequence and column number in the multiple alignment. So, for example, TT/3972 means that two TTs were deleted following the letter in the query sequence that appears in column 3972 in the multiple alignment.
-usearch_global reads.fastq -db gg_13_5_ssualign.fasta -strand both -id 0.95 \
-blast6out hits.b6 -nastout reads.nast