Figure 7.

Transitive alignment comparing the new MIR element found in mouse using a profile HMM and the MIR element found in human by RepeatMasker. Generated by removing the genome lines from the transitive pileup multiple alignment depicted in Figure 6, and adding the usual pairwise lines depicting matches, gaps, transitions, and transversions. Lowercase characters represent regions of one element that could not possibly align transitively because the genome-genome alignment contains a gap there. Gap symbols at such positions are represented as dots "." rather than as dashes "-". Note that the statistics at the bottom are computed after removing all such positions of the alignment. The matches and transitions from transitive alignments are used to compare the profile HMM parameterization algorithms.

Edlefsen and Liu BMC Genomics 2010 11(Suppl 1):S10   doi:10.1186/1471-2164-11-S1-S10