rCRUX Generated 18S v9 Reference Database

rCRUX generated reference database using NCBI mitochondrial and nt blast databases downloaded in December 2022, and the EMBL std rel 143 (fun, inv, mam, pln, pro, vrt).

Primer Name:  18S V9
Gene:   18S V9
Length of Target:    87 - 186
get_seeds_local() minimum length:    50
get_seeds_local() maximum length:    300
blast_seeds() minimum length:    50   
blast_seeds() maximum length:    300
max_to_blast:  100
Forward Sequence (5'-3'):   TTGTACACACCGCCC   

Reverse Sequence (5'-3'):    CCTTCYGCAGGTTCACCTAC

Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W. & Huse, S. M. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA Genes. PLoS ONE 4, (2009).

We chose default rCRUX parameters for get_seeds_local() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for blast_seeds() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'. 
We used a blast formatted EMBL database for get_seeds_local() and the NCBI mitochondrial and nt blast database for blast_seeds().