Table 1.
SSR-clouds recovery of Tandem Repeats Finder (TRF) loci
| Highest Cloud Stringency of Locus | FDR ≤ %5 | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Perfect Repeats | Mid-stringency | Low Stringency | |||||||
| Loci | bp | Loci | bp | Loci | bp | Loci | bp | ||
| Poly-A | SSR-Clouds TRF Intersection | 453,128 | 11,518,426 | 615,893 | 16,085,955 | 665,794 | 17,373,114 | 660,469 | 17,272,038 |
| Total SSR-Cloud Recovery of TRF | 67.73% | 62.37% | 92.06% | 87.10% | 99.52% | 94.07% | 98.72% | 93.52% | |
| Novel Clouds | 244,269 | 13,490,320 | 889,630 | 36,272,378 | 2,282,559 | 65,260,452 | 1,552,401 | 53,363,205 | |
| (AC)n | SSR-Clouds TRF Intersection | 120,498 | 4,813,795 | 143,941 | 5,989,636 | 148,027 | 6,301,466 | 148,027 | 6,301,466 |
| Total SSR-Cloud Recovery of TRF | 81.09% | 65.02% | 96.86% | 80.90% | 99.61% | 85.11% | 99.61% | 85.11% | |
| Novel Clouds | 28,365 | 3,444,295 | 724,496 | 25,393,739 | 1,621,096 | 44,746,021 | 1,621,096 | 44,746,021 | |
| All Motifs | SSR-Clouds TRF Intersection | 1,741,873 | 59,642,996 | 1,965,320 | 67,616,136 | 2,119,405 | 71,906,834 | 1,946,410 | 68,221,956 |
| Total SSR-Cloud Recovery of TRF | 78.73% | 67.40% | 88.83% | 76.41% | 95.80% | 81.26% | 87.98% | 77.10% | |
| Novel Clouds | 2,046,914 | 58,749,285 | 2,690,429 | 75,993,192 | 6,702,981 | 149,673,223 | 2,008,354 | 70,732,930 | |
SSR-clouds loci with a merge distance of 5 bp were divided into 3 nested sets based on the most stringent oligo used to annotate each locus and compared to TRF loci. Comparisons were also made for SSR-clouds loci with FDR ≤ 5%. Cells in the table report the number of loci that overlap TRF loci and the number of bp within overlapping loci. We also report the number of novel SSR-clouds loci and bp. Recovery percentages are reported relative to the total number of TRF loci in each comparison category (Poly-A: 669,020; (AC)n: 148,607; All Motifs: 2,212,424) and total length in bp of the TRF loci (Poly-A: 18,468,468; (AC)n: 7,403,867; All Motifs: 88,485,889)