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rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Scott Baker Dlp1.5-H/Oordlp4 Gene: D loop Length of Target: 350-390 get_seeds_local() minimum length: 245 get_seeds_local() maximum length: 495 blast_seeds() minimum length: 205 blast_seeds() maximum length: 455 max_to_blast: 100 Forward Sequence (5'-3'): TCACCCAAAGCTGRARTTCTA Reverse Sequence (5'-3'): GCGGGTTGCTGGTTTCACG Reference: Baker, C. S., Steel, D., Nieukirk, S., & Klinck, H. (2018). Environmental DNA (eDNA) from the wake of the whales: Droplet digital PCR for detection and species identification. Frontiers in Marine Science, 5, 133. https://doi.org/10.3389/fmars.2018.00133 We chose default rCRUX parameters for get_blast_seeds() 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'.
Metabarcoding, eDNA, Reference barcode database, Marine Mammals, NOAA, rCRUX, CalCOFI
Metabarcoding, eDNA, Reference barcode database, Marine Mammals, NOAA, rCRUX, CalCOFI
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