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Table 3 Ancestral repeats - Second-order root distribution estimates

From: Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences

YX

Ï€ YX|A

Ï€ YX|C

Ï€ YX|G

Ï€ YX|T

AA

0.3492

[0.3398; 0.3586]

0.1539

[0.1466; 0.1613]

0.2132

[0.2050; 0.2215]

0.2837

[0.2747; 0.2928]

CA

0.2453

[0.2355; 0.2552]

0.2036

[0.1942; 0.2133]

0.2639

[0.2536; 0.2742]

0.2872

[0.2767; 0.2981]

GA

0.3308

[0.3192; 0.3426]

0.1588

[0.1495; 0.1682]

0.2737

[0.2626; 0.2848]

0.2367

[0.2261; 0.2473]

TA

0.3134

[0.3031; 0.3237]

0.1698

[0.1613; 0.1788]

0.1977

[0.1888; 0.2068]

0.3191

[0.3083; 0.3298]

AC

0.3824

[0.3684; 0.3960]

0.2331

[0.2215; 0.2451]

0.0462

[0.0380; 0.0551]

0.3384

[0.3252; 0.3516]

CC

0.3579

[0.3447; 0.3715]

0.2379

[0.2259; 0.2497]

0.0406

[0.0331; 0.0486]

0.3636

[0.3501; 0.3772]

GC

0.3597

[0.3443; 0.3752]

0.2585

[0.2448; 0.2724]

0.0291

[0.0218; 0.0372]

0.3527

[0.3375; 0.3678]

TC

0.3344

[0.3228; 0.3458]

0.2587

[0.2480; 0.2695]

0.0290

[0.0236; 0.0347]

0.3779

[0.3661; 0.3896]

AG

0.3160

[0.3052; 0.3265]

0.1941

[0.1851; 0.2036]

0.2492

[0.2394; 0.2594]

0.2407

[0.2309; 0.2506]

CG

0.2122

[0.1726; 0.2542]

0.1598

[0.1237; 0.1990]

0.2467

[0.2025; 0.2934]

0.3813

[0.3310; 0.4327]

GG

0.3053

[0.2927; 0.3181]

0.2070

[0.1959; 0.2185]

0.2429

[0.2312; 0.2546]

0.2448

[0.2331; 0.2569]

TG

0.2842

[0.2741; 0.2945]

0.1857

[0.1771; 0.1946]

0.2499

[0.2402; 0.2598]

0.2802

[0.2699; 0.2904]

AT

0.2643

[0.2550; 0.2736]

0.1683

[0.1606; 0.1762]

0.2378

[0.2285; 0.2471]

0.3296

[0.3198; 0.3394]

CT

0.2025

[0.1934; 0.2117]

0.2247

[0.2152; 0.2342]

0.2514

[0.2416; 0.2614]

0.3214

[0.3112; 0.3320]

GT

0.2387

[0.2271; 0.2501]

0.1944

[0.1837; 0.2048]

0.2727

[0.2608; 0.2846]

0.2942

[0.2823; 0.3067]

TT

0.2295

[0.2216; 0.2372]

0.2106

[0.2030; 0.2183]

0.2051

[0.1974; 0.2126]

0.3548

[0.3460; 0.3637]

  1. Estimates (mean and accompanying 95% credibility interval) for the sixteen sets of base frequencies at the ancestral root sequence under the context-dependent model with context-dependent model frequencies. The probabilities are grouped by the identity of the immediately preceding site.
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