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Table 6 Substitution and gap probabilities and scores inferred from genome alignments

From: Split-alignment of genomes finds orthologies more accurately

Genomes

Probabilities

t

Scores

  
 

a c g t

 

a c g t

  
 

a.29.00053.0022.00044

 

a 77 -300 -212 -337

  

human-chimp

c.00053.2.00054.0022

63.495

c -300 100 -275 -212

  
 

g.0022.00054.2.00053

 

g -212 -275 100 -300

  
 

t.00044.0022.00053.29

 

t -337 -212 -300 77

  
 

gap existence probability: 0.00077

 

gap existence cost: 495

  
 

gap extension probability: 0.65

 

gap extension cost: 27

  
 

a c g t

 

a c g t

  
 

a.29.0013.0055.001

 

a 77 -248 -154 -287

  

human-orangutan

c.0013.2.0013.0055

64.4704

c -248 100 -222 -154

  
 

g.0055.0013.2.0013

 

g -154 -222 100 -248

  
 

t.001.0055.0013.29

 

t -287 -154 -248 77

  
 

gap existence probability: 0.0018

 

gap existence cost: 448

  
 

gap extension probability: 0.65

 

gap extension cost: 28

  
 

a c g t

 

a c g t

  
 

a.24.012.037.013

 

a 77 -126 -38 -154

  

human-dog

c.012.14.0087.037

79.0646

c -126 100 -121 -38

  
 

g.037.0087.14.012

 

g -38 -121 100 -126

  
 

t.013.037.012.24

 

t -154 -38 -126 77

  
 

gap existence probability: 0.012

 

gap existence cost: 429

  
 

gap extension probability: 0.73

 

gap extension cost: 25

  
 

a c g t

 

a c g t

  
 

a.22.016.044.018

 

a 79 -114 -27 -136

  

human-mouse

c.016.13.011.044

86.9541

c -114 100 -115 -27

  
 

g.044.011.13.016

 

g -27 -115 100 -114

  
 

t.018.044.016.22

 

t -136 -27 -114 79

  
 

gap existence probability: 0.015

 

gap existence cost: 451

  
 

gap extension probability: 0.73

 

gap extension cost: 27

  
 

a c g t

 

a c g t

  
 

a.21.015. 031.014

 

a 92 -123 -59 -139

  

Dro.mel-Dro.pse

c.015.17.014.031

86.2603

c -123 100 -117 -59

  
 

g.031.014.17.015

 

g -59 -117 100 -123

  
 

t.014.031.015.21

 

t -139 -59 -123 92

  
 

gap existence probability: 0.016

 

gap existence cost: 445

  
 

gap extension probability: 0.73

 

gap extension cost: 27

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