Each gene alignment ranged from 100 to 1,114 bp including indels.
The average identity of each alignment ranged from 69.9%70.8%.8% using BLASR, with little variation between datasets (Table 1) to 61.6-66.1% with LAST.
In the remaining five candidate genes, for which a contig was identified in the database, the number of sequences in each alignment ranged from two to five ESTs only (Table 2b) and was not sufficient to ensure authentic SNP detection.
The length of individual LCBs after DNA sequence alignment ranged from 645 bp to 129,020 bp and the number of genes per LCB ranged from zero to 30 and the mean was 6.07 genes per LCB for S. woodyi, for example.
There are 252 edges linking the ORs to the other Class A sequences, representing inter-group pairwise alignments ranging from E-values of 1×10−16 (24% identity across 305 residues) to 9×10−12 (31% identity over 121 residues).
Signal-to-noise ratios were computed for 6mer seeds (matches to position 2 7 of 5' miRNA sequences), 7mer seeds starting at position 1 (matches to position 1 7), 7mer seeds starting at position 2 (matches to position 2 8), 8mer seeds (matches to position 1 8) respectively, both in 5 species and 11 species alignments (ranging from human to dog/ tetraodon, respectively).
Sequence conservation in real data often varies dramatically along multiple sequence alignments ranging from constant sites to sequence positions that have effectively been randomized.
Specifically, we tested 14 shorter alignments ranging from 35,230 aa to 14,281 aa and reconstructed phylogenetic trees with LG and CAT models at each step to determine the support value for several nodes of interest.
The down-dip width of these hypocenter alignments ranges from 6 to 8 km, which is consistent with the typical rupture dimension of magnitude 6 earthquakes (Hanks, 1977).
Most alignments ranged from 70 82 amino acids.
