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Intuitively, t1 describes the proportion of unaligned residues higher values imply longer stretches of unaligned residues and fewer model segments overall, and the converse, lower values favor fewer unaligned residues and more frequent matches.
For PG prealignments were made with Dialign [22] (with the parameter T = 2 to avoid long unaligned regions obtained with higher values of T).
If paralogous non-coding regions could be aligned, nucleotide identity was calculated from the alignment; if not, a nominal value was calculated from unaligned sequences.
We set the fraction of reads that do not derive from any known transcript at the mean value of the proportion of unaligned reads observed in the real data (θ0 = 0.018).
The orthologous sequence data may be multiply aligned, unaligned, or a combination of aligned and unaligned.
Secondly, read pairs where one mate is aligned to the genome reference uniquely (i.e. with high read mapping quality value, or MQ) and the other mate is either soft-clipped or unaligned, are collected as the starting material for SR mapping.
Unaligned voters everywhere!
The unaligned Greens would demand concessions on oil exploration.
Those responsible included Jabhat al-Nusra and unaligned foreign fighters, Syrians were few among them.
Some big donors who remain unaligned are waiting for former Vice President Joseph R. Biden Jr.
"He had an unaligned quality that made him useful," Mr. Strick van Linschoten said.
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