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Multiple indels were also identified.
When multiple indels were present, half of the indel-bound region was ascribed to each flanking indel to avoid double-counting of polymorphisms.
Multiple indels were identified within SVSP alleles particularly in PEST domains and an amino acid alignment of the region of SVSP1 hyper-variable for indels and amino acid substitutions is shown in Figure 5.
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Because multiple insertion/deletion (indels) were common in SP14D, GNBP and defensin, direct sequencing was not possible.
For maximum parsimony trees, gaps were coded as a "fifth base", and multiple-base indels were down-weighted to single-base indels under the assumption that these represent single evolutionary changes.
To account for multiple allelic states, indels were analyzed as class explanatory variables in PROC MIXED.
In GSL1 multiple SNPs and indels were identified within the non-coding regions, with the greatest frequency occurring within the intron and the region from −2000 to −500 nucleotide positions relative to the 5'UTR.
Finally, Chen et al. (2009) have shown that approximately 10 Mb of the human genome contain multiple indels that were fixed under positive selection.
Sequences for all data sets were aligned using CLUSTAL W [ 37] with a gap-opening penalty of 10 and a gap-extension penalty of 1. Exonic indels were multiples of 3 bp and were adjusted by eye to reflect the open reading frame.
In addition, there were five "complex mutations", in which multiple SNMs, and often small indels, were in close proximity, giving a relative occurrence of ∼0.58% compared to SNMs.
The lengths of many indels were integral multiples of three bases, according to the indel length distribution (Fig. 6c).
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