Simple sequence repeats (SSRs) were identified within the transcript assembly (PUT) sequences that are part of BFGR. All SSR motifs from singlets to hexanucleotide that have a total length greater than 10 bp have been identified. Additionally, candidate primers to amplify identified SSRs were identified using Primer3.

Motif: selects SSRs made of a particular motif.

Min Length: selects SSRs that are at least this long.

Max Length: selects SSRs that are at most this long.

Single nucleotide polymorphisms were predicted within PUT transcript assemblies. Multiple sequence alignments from PlantGDB PUT assemblies were examined for positions that had a minimum of 4 overlapping transcript sequences and at least 2 bases at that position that differed from the consensus base call.

Minimum depth: The minimum number of sequences in the multiple sequence alignment at the SNP position (minimum 4).

Minimum SNP prevalence percentage: The percentage of sequences that have the alternate base (default 25%).

*SNPs are not available for Triticum aestivum because the multiple sequence alignments for T. aestivum PUTs have not been made available by PlantGDB. For Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Sorghum bicolor and Vitis vinifera, official gene models for those species are used within BFGR, and transcript assemblies for those species were not analyzed.