Transitive pileup multiple alignment depicting the new element in the context of the mouse-human homology, with the human MIR element found by RepeatMasker. The first line depicts the complemented MIRc element found via profile HMM on chromosome 13 of the mouse genome. The second line is the corresponding region of the mouse genome. The second and third lines together depict the relevant fragment of the mouse-human alignment (from UCSC's chain/net alignments). The bottom line is the MIR hit found by RM on hg18. This is an excerpt; the mm9 element extends further on both ends.
Edlefsen and Liu BMC Genomics 2010 11(Suppl 1):S10 doi:10.1186/1471-2164-11-S1-S10