Summary of the in silico Analysis of the CENP-A-Binding Region of the 20p12 Neocentromere
| Sequence motifs | CENP-A- binding region | Nonbinding region | P value | Genome average | AT-rich average (>64%) | |
| Base composition | AT, % | 61.1 | 60.7 | >0.05 | 58.0 | n/a |
| Repeats | Tandem repeats, % | 2.11 | 2.20 | >0.05 | n/a | n/a |
| Satellites , % | 0 | 0 | 1 | n/a | n/a | |
| LINEs, % | 15.1 | 17.3 | >0.05 | 16.6 | 23.1 | |
| L1, % | 11.6 | 14.1 | >0.05 | 13.1 | 20.0 | |
| SINEs, % | 5.49 | 7.23 | <0.05 | 14.9 | 6.5 | |
| Alus, % | 3.99 | 5.67 | <0.05 | 12.5 | 6.0 | |
| MIRs, % | 1.50 | 1.47 | >0.05 | n/a | n/a | |
| LTRs, % | 6.94 | 9.13 | <0.05 | 7.4 | 7.4 | |
| DNA elements, % | 2.54 | 3.40 | >0.05 | n/a | n/a | |
| Protein binding motifs | HMG1 | 17.6 | 19.3 | >0.05 | 17.7 | n/a |
| Topo II | 0.07 | 0.06 | >0.05 | n/a | n/a | |
| CENP-B | 0 | 0 | 1 | n/a | n/a | |
| pJα | 0.01 | 0.02 | >0.05 | n/a | n/a |
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To facilitate statistical analysis of differences between the two regions, the 460-kb CENP-A-binding region was split into three equal segments of 125 kb and one 87 kb segment, which were analyzed separately. Similarly, the nonbinding regions were split into 31 segments of 125 kb and two of 144 kb and 142 kb. Results are averages for each region unless otherwise stated, and P values fromt-tests comparing both regions are also given. Where known, values for average genomic sequences and genomic AT-rich sequences are quoted in the final two columns.
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↵ Smit 1999.
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↵Tandem repeats were classed as being ≥2 copies of any repeat of unit length ≥2 bp.
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↵Satellite repeats (with % homology to consensus): α-satellite (80%); β-satellite (100%); γ-satellite (100%); 48-bp repeat (100%); classical satellites Ia and Ib (100%); classical satellite III (100%, ≥2 copies in tandem).
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↵per kb.
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↵100% homology to consensus.
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↵From Barry et al. (1999).
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↵Number of matches.
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n/a, not applicable/attempted.
