Figure 5.

RepeatMasker MIR transposon element at hg18 chr10:364, 241-364, 409. Pairwise alignment created by RepeatMasker [12] using Crossmatch [15]. The top line of each block is the segment of human genome (version 18) found to be a "hit" to the MIR transposon family consensus sequence, shown on the bottom line of each block. The middle line shows exact matches (spaces), gaps (dashes) and mismatches ("i" for transitions and "v" for transversions). This is an element for which a mouse analogue was not found by RepeatMasker, but was known to exist by human-mouse homology. The mouse analogue was found using a profile HMM.

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