SSR were identified using the MISA MicroSatellite identification tool (http://pgrc.ipk-gatersleben.de/misa/), defining a minimum repeat length criteria of six repeated units for dinucleotides, five repeated units for tri, tetra, penta and hexanucleotides.
We then extracted di-, tetra-,etra-, and penta-nucleotide repeats with a minimum repeat length of six, respectively.
We used this program to find matching sequences of a minimum repeat length of 100 bp and a minimum consensus of 95%.
Using the program Sputnik [ 22], we identified 552 di-, tetra-,etra-, and penta-nucleotide repeats with a minimum repeat length of six, respectively (Additional file 3).
(B ) To identify both perfect (100% sequence identity) and degenerate genomic tandem repeats, we used XSTREAM (Newman and Cooper, 2007 ), with a minimum repeat length of 20 bp, minimum word match of 0.8, and otherwise default parameters.
It should be noted that RIP mutation requires a minimum repeat length and we would not expect it to occur in repeats less than 400 bp in length [ 20, 21].
It is hypothesised that repeat expansions can increase in size through a human lifetime resulting in significant somatic heterogeneity [ 73] and therefore, perhaps the minimum repeat length in the CNS is more reflective of the germline repeat number.
Our search for repeat motifs revealed 521 sequences containing some such motif from the total set of 52,053 sequences (using a minimum repeat length of seven, Additional file 2).
The unassembled sequences were screened for di-, tetra-,etra-, and pentanucleotide microsatellites using MSATCOMMANDER 1.0.2 alpha (Rozen and Skaletsky, 1999; Faircloth, 2008), ensuring a minimum repeat length of 8 bp for dinucleotides and 6 bp for all others.
For perfect TRs this is the minimum repeat length or its associated alignment score, which in TR search programs is often defined as a function of the unit size.
