Figure 5

Chimeric alignments. This figure illustrates two examples of chimeric alignments of a human SNORA25 (small nucleolar RNA SNORA25, RF00402) on chromosome 7. a. Two pieces of sequences from two different scaffolds (dasNov1.scaffold 192792 and dasNov1.scaffold 7495, the two rows directly below the red rectangles) in armadillo are concatenated and aligned to the human ncRNA. However, when we extract a longer sequence from the genome at the position of the first fragment, dasNov1.scaffold 192792, the aligned fragment can be extended to a member of the small nucleolar RNA SNORA25 family. b. Two pieces of sequences from two different chromosomes in mouse (mm8.chr13 and mm8.chr6, the next two rows below armadillo) are aligned to the same human ncRNA. The first fragment, if extended, is also a member in the family. Note that neither armadillo nor mouse show a red rectangle, since these chimeric alignments score below the covariance model threshold. The thin horizontal lines show which regions of that species are included in the alignment.