We identified network motifs in the simplified network as described in [20], which generates random networks in tandem and counts the number of motifs in the random network to make assessments of the likelihood of the observed number of motifs.
Repetitive DNA can be divided into two categories: interspersed repeats, which are individual repeat units that are distributed around the genome in an apparently random fashion, and tandem repeated DNA, whose repeat units are placed next to each other in an array.
By self-ligation of small sized DNAs, circular small sized DNA templates were prepared for error-prone rolling circle amplification using multiply-primed random hexamers to create tandem repeats of small sized DNAs and simultaneous introduction of random point mutations into those tandem repeats of small sized DNAs.
Whereas the number of DBL and CIDR domains vary between PfEMP1, PfEMP1 domain architecture is not random in that certain tandem domain associations — such as DBLαCIDRα, DBLδCIDRβ, and DBLβC2 — are preferentially observed.
The tandem duplication random deletion model was proposed when more than one gene was involved and/or non-coding sequence was found between the genes involved.
Three different modes leading to a change in gene order were assumed: (1) tandem duplication random deletion events [ 52], (2) inversions, and (3) transposition of single tRNAs.
This is a further hint towards a tandem duplication random deletion event, although there are no apparent sequence homologies to any of the lost genes.
Metastriata (Parasitiformes: Ixodidae) show a derived gene order probably caused by a tandem duplication random deletion event and an additional tRNA translocation (Rhipicephalus [ 42], Haemaphysalis [ 53], Amblyomma, [GenBank: NC_005963]).
However, further studies are necessary to confirm this observation and reveal the mode of the cassette integration (tandem or random, out of site), as integration of higher number of copies is rather surprising in the strain Po1g-pYLSC1 system.
Lastly, apply tandem duplication "random loss" (TDRL) to the C. azureus mitogenome, the "loss" events, from the duplicated genome to the C. azureus type, shared very peculiar characteristic: only the L-strand coding gene including ND6 and tRNA of P, E, S, Y, C, A and Q was translocated and grouped together.
