These microsatellites were bounded at least 50 nucleotides upstream and downstream, respectively, so that primers can be designed conveniently.
Among the di-nucleotide repeats there were approximately three times more AG motif microsatellites (124) than AC motif microsatellites (48), and only a few AT microsatellites were found (24).
Dinucleotide microsatellites were located preferentially at the beginning (5'part) of the cDNA (50% of the total were located before the 100th nucleotide) and in the UTR (75%).
In terms of other di-nucleotide motifs, the lack of GC microsatellites has been observed before within the bean genome [ 6, 31], while AT-rich microsatellites were not expected to be found in genic sequences neither as di-nucleotides nor tri-nucleotides such as those studied by Blair et al. [ 23].
On a simulated genealogy from two subspecies with the shared ancestral population [ 42], random mutations were placed and the changes of repeat numbers at microsatellites were simulated.
In addition, when the chimpanzee and human datasets were merged, all chimpanzee genotypes at select microsatellites were adjusted by the same amount to account for primer differences among the constituent datasets [ 66].
Non-STR length differences at some microsatellites were appreciable, contributing up to an additional 28 nucleotides to the chimpanzee ePCR fragment and 32 nucleotides to the human ePCR fragment.
The third comparison was made between microsatellites that were at least 30 bp long and had <3 or ≥3 mismatches (note that microsatellites <30 bp canno't have more than three mismatches as per our search conditions).
We only examined microsatellites that were at least 5,000 bp from the canonical transcription start site, as provided by GREAT, for a total of 38,432 loci.
The melon chloroplast genome was screened for simple sequence repeats (SSRs), which resulted in the identification of 69 microsatellites that were at least 10 nt in length (1 to 2 nt repeats) or contained at least four tandem repeat units (3 to 6 nt repeats).
