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The individual DNA-division sequences overlap each other but run independently.
For the caspases, 24% of the sequences overlap with the small Pfam set; 28% overlap with the large set.
Twenty other species showed deep intraspecific splits (see below), but these never lead to misidentifications, because none of the sequences overlap with those in any other species.
Comparison of α-subunit and β-subunit sequences revealed a surprisingly limited set of sites where the sequences overlap in a clear manner, with many regions aligning very poorly (Figs. 2A and S2D).
Out of 421 residues where at least two sequences overlap, 51 residues (12.1%) are common to all sequences and a further 91 (21.6%) are found in 9 of the 11 species considered.
Initial analysis of the sequences flanking the breakpoints involved searches in 20, 40, 200 and 500 bp flanking sequences (up- and downstream) for regions of >10 bp sequence identity, carried out for 18 out of 20 deletions (excluding the 15 bp and 25 bp deletions for which the flanking sequences overlap).
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Analyzed sequences overlapped those amplified in the qPCR assay.
The remaining 419 sequences included vertebrate MS4A gene sequences overlapping with those found in the earlier searches, as well as sequences from several invertebrate species, including B. floridae.
Sequences overlapping with other URs were excluded from flanks.
If RefSeq mRNA sequences overlapped, only the longest was considered.
Therefore, all of the sequences overlapped by at least 300 bases.
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