Table 3.

Comparison of genomic and transcriptomic SSRs developed in Glycine. The number of reads, total number of bases, reads containing an SSR, reads containing a potentially amplifiable locus (PAL), unique PALs, mean number of PALs in a coding region, and percentage of PALs found in a coding region are presented for both data sets. The analyses to determine which loci were in translated regions were run on both forward and reverse loci, and the results were averaged. Thus, some of the counts of motifs in coding regions are not integers.

Statistic of data set	Genomic	Transcriptomic
Reads	717,309 (raw 454 reads)	364,755 (Illumina assembly scaffolds)
Total bases	84,930,732	133,872,643
Reads/scaffolds with SSR	7368	13,667
Reads/scaffolds with primers (PALs)	624	8456
Total unique PALs	532	7186
Dinucleotides, total	286	2893
Trinucleotides, total	212	4050
Tetranucleotides, total	24	174
Pentanucleotides, total	9	39
Hexanucleotides, total	1	30
Dinucleotides, % of total	53.8	40.3
Trinucleotides, % of total	39.8	56.4
Tetranucleotides, % of total	4.5	2.4
Pentanucleotides, % of total	1.7	0.5
Hexanucleotides, % of total	0.2	0.4
Mean PALs in coding region	65	2552
% of PALs in coding region	12.2	35.5
Dinucleotides, in coding region	17.5	643
Trinucleotides, in coding region	46	1838
Tetranucleotides, in coding region	1.5	48
Pentanucleotides, in coding region	0	7.5
Hexanucleotides, in coding region	0	15
Dinucleotides, % of total in coding region	26.9	25.2
Trinucleotides, % of total in coding region	70.8	72.0
Tetranucleotides, % of total in coding region	2.3	1.9
Pentanucleotides, % of total in coding region	0.0	0.3
Hexanucleotides, % of total in coding region	0.0	0.6
Dinucleotides, % in coding relative to total dinucleotides	6.1	22.2
Trinucleotides, % in coding relative to total trinucleotides	21.7	45.4
Tetranucleotides, % in coding relative to total tetranucleotides	6.3	27.6
Pentanucleotides, % in coding relative to total pentanucleotides	0.0	19.2
Hexanucleotides, % in coding relative to total hexanucleotides	0.0	50.0