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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〉

From: Accelerating the Smith-Waterman algorithm with interpair pruning and band optimization for the all-pairs comparison of base sequences

Pair Initial lower bound L Score # of mismatches # of gaps Similar region
      [x, y] [z, w]
〈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]