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    Genebank identifiers of the nucleotide sequences of atpA, pheS and rpoA genes, used for the phylogenetic analyses. Table S2. NCBI Refseq/Genbank assembly accession numbers for the comparative genomic analysis of Leuconostoc species (29.09.2015). Table S3. L. gelidum subsp. gasicomitatum draft genomes statistics. Figure S1. Phylogenetic tree showing the relationship of L. citreum 1300_LCIT, L. gelidum subsp. gasicomitatum 1301_LGAS and L. inhae LMG 22919 genomes to other Leuconostoc species. (PDF 406 kb

    Community composition

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    Relative abundance of different taxa in 40 day serial transfer microcosm experimen

    Fungi OTUs

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    FASTA file. Fungi ITS2 region sequenced with 454 and clustered at 99% similarity threshold. Homopolymers of 454 reads converted into monomers. Cluster size included in FASTA ID of each OTU

    The principle of ligation detection reaction.

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    <p>The discriminating probe (DP) and the common probe (CP) are designed to hybridize adjacently on the template DNA and are joined by ligase in the presence of a matching template (HPV PCR product). The discriminating 3′ base can be A, C, T or G. The reaction is thermally cycled and ligation products addressed on microarray spots by the unique ZipCode sequences flanking each CP. Hybridization control probe carries a different label (6-Fam) than the DP (Cy3).</p

    Specificity of HPV LDR probe pool.

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    <p>The HPV LDR probe pool was tested against individual plasmid templates. The horizontal axis shows the probes by ZipCodes and corresponding HPV types. The vertical axis shows plasmid templates by HPV type. The signals are medians over spot replicates on 1–3 microarrays. The majority of the probes give a high hybridization signal only for their specific target plasmids. For HPV 11, 42 and 43, there are no functional probes. HPVs 39, 56 and 68 have only one functional probe each. The probe A85 (HPV 73 ) shows a strong nonspecific hybridization signal to HPV 44 template. Minor nonspecific hybridisation signals are evident in probes A59, A110, A57 and A56.</p

    Comparison of the PGMY-t and the original PGMY multiplex PCR primer mixes as measured by HPV LDR signals on microarray.

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    <p>Both primer mixes at 0.2 µM primer concentration amplify all five HPV types from 1 ng of template (A) & (B) and from 1 pg of template (C) & (D). With the original PGMY mix at 1 ng template concentration, HPV 59 gives a false positive signal (B). HPV 33 signal is also relatively weak with the original PGMY at 1 pg template concentrations (D). Data are presented as means±SD from two independent microarrays. Y-axis shows signal intensity in arbitrary units. Asterisk (*) indicates the target HPV types present in the experiment.</p