Hi Esther, The Tandem Repeats Finder (TRF) only works on the reference genome sequence, it has no concept of the population.
TRF can find tandem repeats that are not perfect copies. "Percentage Match" and "Percentage Indel" are measures of divergence of the actual repetitive sequence from a perfectly regular repeat sequence. I hope that clarifies the issue for you. If you have further questions, please email the list: [email protected] Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Leshinsky, Silver EsterDr <[email protected]> Date: Mon, May 14, 2012 at 11:22 PM Subject: [Genome] question To: [email protected] In the tandem repeat browser, the Insert/Delete Percentage means the population percentage? Can I conclude that if it has a value of 22%, means that 22% heterozygosity index? Dr. Esther Leshinsky-Silver Director, Molecular-Genetic Laboratory Wolfson Medical Center, Holon Israel, 58100 Tel:972-3-502-8692 <Tel:972-3-502-8692> Fax:972-3-502-8543 Emails: [email protected], Additional emails: [email protected], [email protected] _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
