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men12265-sup-0001-FigS1a.pdfapplication/PDF423K 
men12265-sup-0002-FigS1b.pdfapplication/PDF466KFig. S1 Drosophila melanogaster 16S ribosomal DNA (a) and cytochrome oxidase c subunit I (COI) sequence (b) showing primer-binding sites for newly designed and existing metabarcoding markers, as well as standard Sanger sequencing primers (Folmer et al. 1994; Simon et al. 1994).
men12265-sup-0003-FigS2.docWord document602KFig. S2 Percentage of mismatches for each nucleotide within metabarcoding primer-binding sites for insect taxa with complete mitochondrial genomes available.
men12265-sup-0004-TableS1-3.docxWord document67K

Table S1 Taxonomic coverage and resolution (species level) of insect metabarcodes estimated by in silico PCR against a database of complete Anopheles mitochondrial genomes.

Table S2 In vitro PCR amplification success using newly developed insect metabarcodes with insect and potential contaminant DNA.

Table S3 Number of HTS reads for each combination of metabarcoding marker and thermal cycling protocol at each stage of read processing.

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