One copy of the type II stem-loop structure is located within a ~300 bp segment that is devoid of any discernable repeat units, but close to the high and low GC regions noted earlier.
For example, to discriminate between a M. ulcerans and a M. marinum isolate, there is a 2,688 bp segment that is present in all M. ulcerans isolates and absent from all other M. marinum isolates.
At the breakpoints of the 1.2-Mb inversion, we find in mat A a short duplication of a 50-bp segment that is unique in the N. tetrasperma mat a genome.
After comparison, the SOAP-denovo program was most effective for the assembly of 25-bp segments that are randomly clipped from the reads obtained in long parts with the help of the de Bruijn graph algorithm and was then used for de novo assembly of our PE reads and generation of non-redundant unique sequences.
pMC1103 contains a NheI site between the two PstI sites, in the 661 bp sequence segment that was inserted, and this site conflicts with subsequent cloning strategies.
We independently sequenced the complete mt genome of three C. hongkongensis individuals, all of which were 18,622 bp and contained the segment that was missing in Yu et al.'s sequence.
The deletion was likely to have occurred by nonallelic homologous recombination (NAHR [ 93- 96]), as it is flanked by 679-bp duplicated segments that are 92.1% similar to each other.
In general, the segments involved in such recombination events are fairly large (700 to 2500 bp), and the segments that are exchanged in exons of 3FTxs are probably much too small.
Ultra-conserved regions (UCRs) are by definition DNA segments that are at least 200 bp in length and that are 100% conserved between human, rat and mouse genomes.
Furthermore, Cedric's haplotype also lacks two other long segments that are present in Spirit's, one (~12230 bp) lying between the pseudogene and Saha-UB, and the other (~16970 bp) between Saha-UB and Saha-UC.
