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Table 2 Analysis of short and long tandem repeats in three assemblies of rice

From: Hybrid assembly with long and short reads improves discovery of gene family expansions

A Category ALLPATHS PBJelly Alpaca
Unit > =2Kbp One scaffold 2.4% 6.9% 51.6%
Two scaffolds 4.2% 25.3% 36.5%
Underrepresented 93.4% 67.8% 11.8%
Total 4734 4734 4734
Unit < 2Kbp One scaffold 71.3% 81.8% 80.1%
Two scaffolds 12.8% 12.0% 6.7%
Underrepresented 15.9% 6.2% 13.2%
Total 61,140 61,140 61,140
B Category ALLPATHS PBJelly Alpaca
Unit > =2Kbp One chromosome 43.9% 32.1% 61.3%
Two chromosomes 0.9% 1.1% 4.7%
Underrepresented 55.3% 66.8% 33.9%
Total 114 184 548
Unit < 2Kbp One chromosome 61.6% 58.1% 73.3%
Two chromosomes 4.1% 4.2% 1.9%
Underrepresented 34.3% 37.7% 24.7%
Total 8079 8034 9368
  1. A. Repeat pairs on reference chromosomes were classified by whether both repeated units were 50% covered by alignments to one scaffold, two scaffolds, or were “underrepresented”, in each of three assemblies. B. Conversely, repeat pairs on assembled scaffolds were classified by whether they were 50% covered by alignments to chromosomes in the reference. There are fewer total repeats in (B) because the number of same-scaffold repeats is lower in each assembly than the number of same-chromosome repeats in the reference