These were subsequently aligned to the BAC-derived O and P' genome specific coding sequences of genes encoding dehydration responsive element binding protein (DREB3) and acyl-coA oxidase respectively (alignments are shown in Additional file 5).
Number of total bases multiplied by the mean identity yields weighted BLASR and LAST (respectively) alignments for the A) E. coli, B) vaccinia-Lister, C) vaccinia-MVA, and D) cowpox data sets.
Therefore, given two sequence template pairs (S, T) and (X, Y), as long as S and T have the same lengths as X and Y, respectively, the alignment space (i.e. the set of all possible alignments) for S and T is the same as that for X and Y.
Briefly, matched and mismatched nucleotides received rewards of +4 and -3, respectively, in alignment.
Library sizes were of 32, 46, and 57 million unique reads, respectively, with alignment rate of 92% in each case.
For 1,439 and 642 of these, respectively, the alignment extended for more than 80% of the length of the FL sequence.
CfdefORF142 and HycuORF148 were identified as genes unique to CfDEFNPV and HycuNPV, respectively, but alignment of Anpe143 to Cfdef142 and Anpe3 to Hycu148 revealed high conservation (34% and 62% amino acid identity, respectively).
Both the PacBio and Illumina reads covered the majority of the P. micrantha chloroplast genome, with 100%andd 99.6% of the genome covered by PacBio and Illumina respectively following alignment of all reads from each dataset to the assembled chloroplast consensus sequence using BLAT.
To avoid bias PCR duplicates were removed and each unique read-alignment location was considered only once, resulting in 9,658 (3,410, 2,765, and 3,483, in repeats 1, 2, and 3, respectively) read-alignment sites.
The B. mori Lep1 Helitrons with an 87- or 335-bp region H3 were subsequently called Bm Lep1_87 and Bm Lep1_335 variants, respectively, and alignments showed no discernable homology (Fig. 3).
