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Table 2 Ancestral repeats - Second-order root sequence distribution

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

 

Root

YX

Ï€ YX|A

Ï€ YX|C

Ï€ YX|G

Ï€ YX|T

AA

0.3496

[0.3404; 0.3587]

0.1518

[0.1449; 0.1588]

0.2160

[0.2080; 0.2241]

0.2826

[0.2737; 0.2916]

CA

0.2437

[0.2343; 0.2533]

0.1987

[0.1899; 0.2074]

0.2648

[0.2554; 0.2748]

0.2928

[0.2831; 0.3028]

GA

0.3326

[0.3212; 0.3442]

0.1553

[0.1461; 0.1647]

0.2753

[0.2644; 0.2864]

0.2367

[0.2261; 0.2473]

TA

0.3148

[0.3044; 0.3253]

0.1679

[0.1594; 0.1766]

0.1983

[0.1894; 0.2075]

0.3190

[0.3083; 0.3298]

AC

0.4062

[0.3929; 0.4199]

0.2295

[0.2177; 0.2406]

0.0092

[0.0064; 0.0124]

0.3551

[0.3422; 0.3681]

CC

0.3791

[0.3661; 0.3922]

0.2357

[0.2242; 0.2473]

0.0057

[0.0036; 0.0083]

0.3795

[0.3665; 0.3927]

GC

0.3763

[0.3614; 0.3916]

0.2541

[0.2407; 0.2679]

0.0040

[0.0020; 0.0065]

0.3656

[0.3503; 0.3803]

TC

0.3487

[0.3373; 0.3603]

0.2554

[0.2448; 0.2664]

0.0083

[0.0060; 0.0109]

0.3875

[0.3757; 0.3994]

AG

0.3153

[0.3051; 0.3260]

0.1941

[0.1853; 0.2032]

0.2464

[0.2368; 0.2562]

0.2441

[0.2343; 0.2537]

CG

0.2557

[0.1796; 0.3398]

0.1960

[0.1272; 0.2723]

0.2617

[0.1887; 0.3433]

0.2866

[0.2044; 0.3719]

GG

0.3081

[0.2955; 0.3212]

0.2049

[0.1939; 0.2163]

0.2400

[0.2281; 0.2517]

0.2471

[0.2353; 0.2592]

TG

0.2844

[0.2747; 0.2944]

0.1839

[0.1754; 0.1926]

0.2462

[0.2368; 0.2556]

0.2855

[0.2757; 0.2953]

AT

0.2575

[0.2484; 0.2668]

0.1657

[0.1582; 0.1735]

0.2495

[0.2405; 0.2586]

0.3272

[0.3175; 0.3368]

CT

0.1968

[0.1879; 0.2059]

0.2200

[0.2111; 0.2290]

0.2630

[0.2533; 0.2725]

0.3202

[0.3100; 0.3307]

GT

0.2322

[0.2208; 0.2437]

0.1919

[0.1812; 0.2025]

0.2814

[0.2694; 0.2938]

0.2945

[0.2824; 0.3069]

TT

0.2256

[0.2179; 0.2334]

0.2077

[0.2000; 0.2153]

0.2110

[0.2036; 0.2187]

0.3558

[0.3472; 0.3646]

 

Rest of the tree

 

Ï€ A

Ï€ C

Ï€ G

Ï€ T

 

0.3114

[0.3016; 0.3211]

0.1681

[0.1617; 0.1746]

0.1721

[0.1658; 0.1785]

0.3484

[0.3385; 0.3589]

  1. Estimates (mean and accompanying 95% credibility interval) for the sixteen sets of base frequencies at the ancestral root sequence and the set of base frequencies used in the remainder of the tree, for the context-dependent model with independent model frequencies and a second-order Markov chain at the ancestral root. The probabilities are grouped by the identity of the immediate preceding site. Note that the base frequencies used throughout the remainder of the tree are similar to those when assuming a first order Markov chain at the ancestral root sequence.
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BMC Ecology and Evolution

ISSN: 2730-7182

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