I extracted a genomic DNA from a plant leaf and proceeded with determining polymorphisms in SSR markers. I used commercial primers specific in amplifiying repetitive motifs in a specific locus for my given plant. The primers did amplify the expected size variation (e.g. around 220 to 260 bp) and the number of expected alleles per loci, however, it did also amplify bright bands of very high molecular weight (around 1000bp). An error that I've realized was that I did not optimize the primers first (since I believe it's already optimized given that they were commercial and based on a journal) and I do not have any positive controls.

Nonetheless, I do want to know what the high molecular bands indicates. Is it correct to say that bands represent other loci of the allele with longer repetitive motif? or it's just that primers or PCR conditions were not optimized hence the non-specific amplification?