Table 3 Summary of the alignment results. With respect to the genomes of Bacillus anthracis, the best and worst speedups on a single GPU were obtained for pairs 〈3,6〉 and 〈2,5〉, respectively. Because our method estimates a lower bound from aligned pairs, early-processed pairs such as 〈1,2〉, 〈1,5〉, 〈7,8〉, 〈7,9〉, 〈10,11〉, and 〈10,12〉 use L=0. In contrast, our method fails to increase the initial lower bound for pair 〈11,12〉

〈2,3〉

5,054,849

5,226,806

19

134

[101, 5,227,293]

[1, 5,227,319]

〈2,6〉

1,360,803

1,439,963

234

1,991

[3,781,820, 5,227,293]

[3,783,219, 5,229,989]

〈3,6〉

1,433,837

1,440,080

231

1,990

[3,781,847, 5,227,419]

[3,783,219, 5,230,089]

〈1,2〉

0

5,179,709

628

15,972

[1, 5,218,947]

[1, 5,227,293]

〈1,5〉

0

5,183,765

657

14,578

[1, 5,218,946]

[2, 5,228,663]

〈2,5〉

5,061,056

5,220,960

165

2,430

[1, 5,227,292]

[2, 5,228,663]

〈7,8〉

0

31,073,252

178,471

425,571

[570,587, 33,483,523]

[13,789,327, 46,683,588]

〈7,9〉

0

30,779,997

168,946

472,978

[799,132, 33,483,523]

[14,990,367, 47,664,260]

〈8,9〉

26,801,979

32,682,564

113,078

238,057

[12,915,809, 46,709,983]

[13,921,377, 47,690,666]

〈10,11〉

0

6,268,702

3,664,543

3,655,628

[27,961,827, 58,340,489]

[25,036,812, 55,918,720]

〈10,12〉

0

14,383,541

1,626,256

3,780,342

[27,437,780, 58,535,035]

[32,521,523, 63,596,428]

〈11,12〉

0

3,113,889

636,188

1,032,735

[25,014,281, 33,464,562]

[33,028,220, 41,362,068]