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Table 6 Values of the six criteria for the ambiguFS dataset

From: Aligning coding sequences with frameshift extension penalties

fs_open_ cost

fs_extend_cost (# CDS pairs)

Method

Identity_ NT

Identity_ AA

Gap_ init

Gap_ length

FS_init (avg)

FS_ length

−10

−1 (2127)

fse0 (862)

1095102

1737105

24489

908218

1111 (1.28 ± 0.54)

42730

fse

1086546

1719774

23483

906540

0

0

macse_p (2076)

1124316

1790199

45335

936002

12436 (5.99 \(\pm\,4.96\))

216772

needleprot

1085007

1723950

25288

916518

0

0

−0.5 (1953)

fse0 (688)

1008514

1597605

22984

854021

855 (1.24 \(\pm\,0.53\) )

31172

fse (2)

1003293

1587258

22102

853793

2 (1.0 \(\pm\,0\) )

80

macse_p (1902)

1036768

1649604

42619

880399

11562 (6.07 \(\pm\,4.91\))

197772

needleprot

1001957

1591134

23790

863199

0

0

−0.2 (1720)

fse0 (455)

890042

1420569

20050

764510

532 (1.16 \(\pm\,0.48\))

19568

fse (3)

887372

1415403

19465

764162

3 (1.0 \(\pm\,0\))

92

macse_p (1669)

915754

1468305

37472

789220

9975 (5.97 \(\pm\,4.75\))

167484

needleprot

886178

1418748

20955

772272

0

0

−20

−1 (409)

fse0 (100)

219277

358554

3633

153487

120 (1.2 \(\pm\,0.40\))

6937

fse

216936

353586

3619

152391

0

0

macse_p (403)

225976

374391

6509

158165

1348 (3.34 \(\pm\,3.00\))

36179

needleprot

216842

355656

4172

153957

0

0

−0.5 (381)

fse0 (72)

195615

311757

3545

144317

91 (1.26 \(\pm\,0.44\))

5108

fse

194048

308448

3505

144045

0

0

macse_p (375)

202374

327711

6380

148909

1311 (3.49 \(\pm\,3.05\))

34322

needleprot

193980

310632

4051

145563

0

0

−0.2 (354)

fse0 (45)

181185

284787

3371

138419

63 (1.4 \(\pm\,0.49\))

3407

fse (1)

180151

282693

3344

138217

1 (1.0 \(\pm\,0\))

40

macse_p (348)

187895

300777

6157

143035

1265 (3.63 \(\pm\,3.11\))

32301

needleprot

180116

284946

3883

139731

0

0

−30

−1 (200)

fse0 (119)

151090

289617

805

42437

120 (1.01 \(\pm\,0.09\))

6818

fse

147590

282018

852

40221

0

0

macse_p (200)

152626

292254

1309

43043

378 (1.89 \(\pm\,2.16\))

14515

needleprot

147228

281472

933

40455

0

0

−0.5 (117)

fse0 (36)

77603

143115

590

30765

37 (1.02 \(\pm\,0.16\))

2109

fse

76678

141108

626

29913

0

0

macse_p (117)

79224

146046

990

31321

284 (2.42 \(\pm\,2.65\))

9731

needleprot

76561

141036

703

30099

0

0

−0.2 (93)

fse0 (12)

60710

109842

510

22691

12 (1.0 \(\pm\,0\))

668

fse

60407

109170

518

22491

0

0

macse_p (93)

62387

112872

878

23181

252 (2.70 \(\pm\,2.89\))

8262

needleprot

60270

109122

581

22677

0

0

  1. For varying values of the parameters fs_open_cost and fs_extend_cost, and for each method, the number of CDS pairs displaying a FS translation is given. The values of the criteria for each method are indicated. For each method, the average number of FS_init per alignment, with corresponding standard error values are also indicated