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Table 2 Seeds optimized for the CHK, DOG, MUS, ZFS comparisons, for weight W = 10..16, using hill-climbing. For large weights (e.g., W ≥ 16), the fixed span k = 22 may significantly constrain the range of seeds, and therefore the seeds produced under this model may not be optimal in practice.

From: Universal seeds for cDNA-to-genome comparison

Comparison

n 1

n 0

n x

W

Sensitivity

Seed

CHK

9

11

2

10

0.9033819146

1x11011011x11000000000

CHK

9

9

4

11

0.8373594847

1xx1011011011xx1000000

CHK

10

8

4

12

0.7617553847

1xx1011011011xx1100000

CHK

11

7

4

13

0.6781533749

11x1101101x011xx110000

CHK

12

6

4

14

0.5907201266

11x11011011011xxx11000

CHK

12

4

6

15

0.5096393921

11x110xxx1011011011xx1

CHK

14

4

4

16

0.4328248093

11x110xx11011011011x11

DOG

8

10

4

10

0.9991951771

11xx1101x011x100000000

DOG

9

9

4

11

0.9976354479

11x110110x0x1x11000000

DOG

10

8

4

12

0.9943213958

11x110x1011x1x11000000

DOG

10

6

6

13

0.9882916262

11x1101x1x0xx011x11000

DOG

11

5

6

14

0.9790689537

11xx11011x0x0x1011x110

DOG

12

4

6

15

0.9652197277

11x110x1x010x1011x1x11

DOG

13

3

6

16

0.9461146848

11x110x1x01xx1011x1111

MUS

8

10

4

10

0.9946391036

1xx1011011xx1100000000

MUS

9

9

4

11

0.9868058410

11x1101x011xx110000000

MUS

9

7

6

12

0.9737371393

1x1101x010x1x011xx1000

MUS

10

6

6

13

0.9538071885

1x1101xx10x1x011x11000

MUS

11

5

6

14

0.9260863280

11xx110x1x010x1011x110

MUS

11

3

8

15

0.8901430490

11x110x1x01xx1011x1xx1

MUS

13

3

6

16

0.8445827211

11x1101xxx011x11011x11

ZFS

9

11

2

10

0.7113928043

1x11011011x11000000000

ZFS

10

10

2

11

0.6041894577

11x11011011x1100000000

ZFS

10

8

4

12

0.4894026703

x1x11011011011xx100000

ZFS

12

8

2

13

0.3972876500

11x11011011011x1100000

ZFS

12

6

4

14

0.3090795416

1xx110110x1011011x1100

ZFS

13

5

4

15

0.2419994803

11x1101101xx11011x1100

ZFS

14

4

4

16

0.1863098023

11xx11011011x11011x110