Table 5.
RepeatMasker, STAR, Mreps, TRF and Sputnik detections between starting positions 532800 and 53500 in the human X chromosome.
| start | end | divergence | motif | sequence | |
| RepeatMasker | |||||
| 531688 | 531713 | 0 | AAT | AATAATAATAATAATAATAATAATAA | |
| 532355 | 532540 | 15.05 | TTCC | TTCCTTCCTCCCTTCCTTCCTTCCTTTCTTCTTTCTTTCTTTCCTTCCTTCCTGCTTTCCTTCCTTCC | |
| TTTCTTTTCTTTCTTTCCTTCCTTCCTTGCTTCCTTCCTTCCATCTTTCTCTTTCTCTTTTTCTTTCT | |||||
| TTCTCTCCTTCCTTCTTTCCTTCCTTCCTTCCCTTCCCTTCCTTCCTTCC | |||||
| 532704 | 532891 | 15.87 | TTCC | CCTTCCTTCCTTTCTTCTTTCTTTCCTTCCTTCCTTGCTTCCTTCCTTCCATCTTTCTTTCTTTCTTT | |
| CTTCCTCTCCTTCCTTCTTTCCTTCCTTCCTTCCCTTCCCTCCTTCCTTTTTCTTCTTCTCTTTCTTT | |||||
| CTTTCTCTTTCCTTCCTTCCTTCCTTCTTTCTCCTTCCTTCCTTCTTTCCTT | |||||
| STAR | |||||
| 531688 | 531713 | 0 | AAT | AATAATAATAATAATAATAATAATAA | |
| 532537 | 532731 | 25.38 | TTTTTC | TTCCTTTTTCTTCTTCTCTTTCTTTCTTTCTTTTTCTTTCCTTCCTTCCTTCTTTCTCCTTCCTTCCT | |
| TCCATTTTTCTTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTTTCTTTCTTTCTCTCTCTCTCTTCTTC | |||||
| CTTCCTTCCTTCCATTCTTCTTTCTTTCTTTCCTTCCTTCCTTTCTTCTTTCTTTCCTT | |||||
| Mreps | |||||
| 531688 | 531715 | 3.45 | AAT | AATAATAATAATAATAATAATAATAAAA | |
| 532330 | 532429 | 15.84 | TTCC | TTTCCTTCTTTCTTTCTTACTTTCTTTCCTTCCTCCCTTCCTTCCTTCCTTTCTTCTTTCTTTCTTTC | |
| CTTCCTTCCTGCTTTCCTTCCTTCCTTTCTTT | |||||
| 532428 | 532467 | 12.5 | TTCC | TTTCTTTCTTTCCTTCCTTCCTTGCTTCCTTCCTTCCATC | |
| 532466 | 532490 | 4 | TTTCTC | TCTTTCTCTTTCTCTTTTTCTTTCT | |
| 532491 | 532524 | 11.76 | TTCC | TTCTCTCCTTCCTTCTTTCCTTCCTTCCTTCCCT | |
| 532525 | 532542 | 5.56 | TTCC | TCCCTTCCTTCCTTCCTT | |
| 532551 | 532593 | 13.95 | TTTC | TCTCTTTCTTTCTTTCTTTTTCTTTCCTTCCTTCCTTCTTTCT | |
| 532593 | 532609 | 5.88 | TTCC | TCCTTCCTTCCTTCCAT | |
| 532609 | 532667 | 16.95 | TC | TTTTTCTTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTTTCTTTCTTTCTCTCTCTCTCT | |
| 532667 | 532689 | 8.7 | TTCC | TTCTTCCTTCCTTCCTTCCATTC | |
| 532690 | 532756 | 11.94 | TTCC | TTCTTTCTTTCTTTCCTTCCTTCCTTTCTTCTTTCTTTCCTTCCTTCCTTGCTTCCTTCCTTCCATC | |
| 532755 | 532777 | 4.35 | TTTC | TCTTTCTTTCTTTCTTTCTTCCT | |
| 532776 | 532820 | 8.89 | TTCC | CTCTCCTTCCTTCTTTCCTTCCTTCCTTCCCTTCCCTCCTTCCTT | |
| TRF {2,7,7;20} | |||||
| 531688 | 531713 | 0 | AAT | AATAATAATAATAATAATAATAATAA | |
| 532313 | 532330 | 5.26 | TTTTC | TTTTCTTTTCTTTCTTTT | |
| 532423 | 532438 | 5.88 | TTTTC | TTTCTTTTCTTTCTTT | |
| 532466 | 532490 | 4 | TTTCTC | TCTTTCTCTTTCTCTTTTTCTTTCT | |
| 532544 | 532553 | 0 | TTC | TTCTTCTTCT | |
| 532550 | 532576 | 13.79 | TTTCTC | TTCTCTTTCTTTCTTTCTTTTTCTTTC | |
| 532633 | 532667 | 8.57 | TC | TCTCTCTCTCTCTTTCTTTCTTTCTCTCTCTCTCT | |
| Sputnik {1,-6,7} | |||||
| 531568 | 531576 | 0 | ACC | ACCACCACC | |
| 531688 | 531711 | 0 | AAT | AATAATAATAATAATAATAATAAT | |
| 531849 | 531856 | 0 | TTGC | CTTGCTTG | |
| 531893 | 531900 | 0 | TG | TGTGTGTG | |
| 531927 | 531934 | 0 | ATGC | TGCATGCA | |
| 532078 | 532085 | 0 | AGGC | GCAGGCAG | |
| 532266 | 532273 | 0 | ATGC | TGCATGCA | |
| 532313 | 532322 | 0 | TTTTC | TTTTCTTTTC | |
| 532335 | 532354 | 5 | TTTC | TTCTTTCTTTCTTACTTTCT | |
| 532355 | 532422 | 10.29 | TTCC | TTCCTTCCTCCCTTCCTTCCTTCCTTTCTTCTTTCTTTCTTTCCTTCCTTCCTGCTTTCCTTCCTTCC | |
| 532423 | 532439 | 5.88 | TTTC | TTTCTTTTCTTTCTTTC | |
| 532440 | 532463 | 4.17 | TTCC | CTTCCTTCCTTGCTTCCTTCCTTC | |
| 532466 | 532489 | 4.17 | TTTCTC | TCTTTCTCTTTCTCTTTTTCTTTC | |
| 532500 | 532541 | 7.14 | TTCC | TCCTTCTTTCCTTCCTTCCTTCCCTTCCCTTCCTTCCTTCCT | |
| 532544 | 532552 | 0 | TTC | TTCTTCTTC | |
| 532553 | 532568 | 0 | TTTC | TCTTTCTTTCTTTCTT | |
| 532569 | 532576 | 0 | TTTC | TTTCTTTC | |
| 532577 | 532588 | 0 | TTCC | CTTCCTTCCTTC | |
| 532596 | 532607 | 0 | TTCC | TTCCTTCCTTCC | |
| 532615 | 532656 | 7.14 | TTTC | TTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTTTCTTTCTTTC | |
| 532657 | 532666 | 0 | TC | TCTCTCTCTC | |
| 532669 | 532684 | 0 | TTCC | CTTCCTTCCTTCCTTC | |
| 532687 | 532692 | 0 | TTC | TTCTTC | |
| 532693 | 532704 | 0 | TTTC | TTTCTTTCTTTC | |
| 532705 | 532752 | 8.33 | TTCC | CTTCCTTCCTTTCTTCTTTCTTTCCTTCCTTCCTTGCTTCCTTCCTTC | |
| 532755 | 532774 | 0 | TTTC | TCTTTCTTTCTTTCTTTCTT | |
| 532780 | 532820 | 7.32 | TTCC | CCTTCCTTCTTTCCTTCCTTCCTTCCCTTCCCTCCTTCCTT |
Resolution of Mreps was set to 1, threshold alignment score of TRF to 20 and alignment weights of TRF to {2,7,7}. Sputnik mismatch penalty and validation score were set to -6 and 7, respectively. The number of detections varies with algorithms (from 3 to 18). Moreover, the sequence information is dealt with in different ways; an example is the region of cryptic simplicity between positions 532815 and 533080. RepeatMasker and STAR decompose it into large, distant and highly imperfect detections, though not the same for the two algorithms. Mreps returns a succession of shorter detections, overlapping the whole region. TRF detects only short, not much divergent, subregions, which do not completely overlap with the whole region. Sputnik detections are very numerous, short and slightly divergent, but overlap the whole region. Detection of compound microsatellites by Mreps is illustrated at position 533706, where other algorithms detect only a perfect polyA strech. The detection at position 534186 is returned as two detections by Mreps, because the two consecutive errors (insertions of G and C) stop the detection when resolution is set to 1. Very short hexanucleotides (12 bp) are detected by both TRF and Sputnik at positions 533138 and 534112. Most detections of Sputnik are two-repeat tetranucleotides, or three-repeat trinucleotides, which cannot be detected by other algorithms.