April 2 2023 12:26:11.899 PM ss_lg_align_test(): FORTRAN90 version Test ss_lg_align(). TEST01: SS_LG_FSQ - Forward score quadratic; SS_LG_FSL - Forward score linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that the FSQ and FSL tables agree. Sequences A and B: 1 G C 2 C C 3 T G 4 G T 5 A G 6 T A 7 A T 8 T T 9 A A 10 G G 11 C C 12 T T Matching Scores: 0 1 2 3 4 5 6 7 8 9 10 11 12 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 -5.0 -5.0 5.0 -1.0 5.0 1.0 -1.0 -1.0 1.0 5.0 -5.0 -1.0 2 0.0 9.0 9.0 -5.0 -3.0 -5.0 -3.0 -3.0 -3.0 -3.0 -5.0 9.0 -3.0 3 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 4 0.0 -5.0 -5.0 5.0 -1.0 5.0 1.0 -1.0 -1.0 1.0 5.0 -5.0 -1.0 5 0.0 -3.0 -3.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 -3.0 1.0 6 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 7 0.0 -3.0 -3.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 -3.0 1.0 8 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 9 0.0 -3.0 -3.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 -3.0 1.0 10 0.0 -5.0 -5.0 5.0 -1.0 5.0 1.0 -1.0 -1.0 1.0 5.0 -5.0 -1.0 11 0.0 9.0 9.0 -5.0 -3.0 -5.0 -3.0 -3.0 -3.0 -3.0 -5.0 9.0 -3.0 12 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 SS_LG_FSQ: 0 1 2 3 4 5 6 7 8 9 10 11 12 SF: 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 0.0 0.0 5.0 2.5 5.0 2.5 2.0 1.5 1.0 5.0 2.5 2.0 2 0.0 9.0 9.0 6.5 6.0 5.5 5.0 4.5 4.0 3.5 3.0 14.0 11.5 3 0.0 6.5 6.5 8.0 10.5 8.0 7.5 9.0 8.5 6.0 5.5 11.5 18.0 4 0.0 6.0 6.0 11.5 9.0 15.5 13.0 12.5 12.0 11.5 11.0 11.0 15.5 5 0.0 5.5 5.5 9.0 12.5 13.0 18.5 16.0 15.5 15.0 14.5 14.0 15.0 6 0.0 5.0 5.0 8.5 13.0 12.5 16.0 22.5 20.0 19.5 19.0 18.5 18.0 7 0.0 4.5 4.5 8.0 10.5 14.0 15.5 20.0 23.5 23.0 20.5 20.0 19.5 8 0.0 4.0 4.0 7.5 12.0 11.5 15.0 19.5 24.0 24.5 22.0 21.5 24.0 9 0.0 3.5 3.5 7.0 9.5 13.0 14.5 19.0 21.5 27.0 25.5 24.0 23.5 10 0.0 3.0 3.0 8.5 9.0 14.5 14.0 18.5 21.0 24.5 32.0 29.5 29.0 11 0.0 9.0 12.0 9.5 9.0 12.0 13.5 18.0 20.5 24.0 29.5 41.0 38.5 12 0.0 6.5 9.5 11.0 13.5 11.5 13.0 17.5 22.0 23.5 29.0 38.5 45.0 EF: 0 0.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 -6.5 -7.0 -7.5 -8.0 1 -4.5 -2.5 -2.5 -2.5 2.5 2.0 2.5 2.0 1.5 1.0 0.5 2.5 2.0 2 -5.0 -2.5 6.5 6.5 6.0 5.5 5.0 4.5 4.0 3.5 3.0 2.5 11.5 3 -5.5 -2.5 4.0 4.0 5.5 8.0 7.5 7.0 6.5 6.0 5.5 5.0 9.0 4 -6.0 -2.5 3.5 3.5 9.0 8.5 13.0 12.5 12.0 11.5 11.0 10.5 10.0 5 -6.5 -2.5 3.0 3.0 6.5 10.0 10.5 16.0 15.5 15.0 14.5 14.0 13.5 6 -7.0 -2.5 2.5 2.5 6.0 10.5 10.0 13.5 20.0 19.5 19.0 18.5 18.0 7 -7.5 -2.5 2.0 2.0 5.5 8.0 11.5 13.0 17.5 21.0 20.5 20.0 19.5 8 -8.0 -2.5 1.5 1.5 5.0 9.5 9.0 12.5 17.0 21.5 22.0 21.5 21.0 9 -8.5 -2.5 1.0 1.0 4.5 7.0 10.5 12.0 16.5 19.0 24.5 24.0 23.5 10 -9.0 -2.5 0.5 0.5 6.0 6.5 12.0 11.5 16.0 18.5 22.0 29.5 29.0 11 -9.5 -2.5 6.5 9.5 9.0 8.5 9.5 11.0 15.5 18.0 21.5 27.0 38.5 12-10.0 -2.5 4.0 7.0 8.5 11.0 10.5 10.5 15.0 19.5 21.0 26.5 36.0 FF: 0 0.0 -4.5 -5.0 -5.5 -6.0 -6.5 -7.0 -7.5 -8.0 -8.5 -9.0 -9.5-10.0 1 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 2 -3.0 -2.5 -2.5 2.5 0.0 2.5 0.0 -0.5 -1.0 -1.5 2.5 0.0 -0.5 3 -3.5 6.5 6.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 2.0 11.5 9.0 4 -4.0 6.0 6.0 5.5 8.0 5.5 5.0 6.5 6.0 3.5 3.0 11.0 15.5 5 -4.5 5.5 5.5 9.0 7.5 13.0 10.5 10.0 9.5 9.0 8.5 10.5 15.0 6 -5.0 5.0 5.0 8.5 10.0 12.5 16.0 13.5 13.0 12.5 12.0 11.5 14.5 7 -5.5 4.5 4.5 8.0 10.5 12.0 15.5 20.0 17.5 17.0 16.5 16.0 15.5 8 -6.0 4.0 4.0 7.5 10.0 11.5 15.0 19.5 21.0 20.5 18.0 17.5 17.0 9 -6.5 3.5 3.5 7.0 9.5 11.0 14.5 19.0 21.5 22.0 19.5 19.0 21.5 10 -7.0 3.0 3.0 6.5 9.0 10.5 14.0 18.5 21.0 24.5 23.0 21.5 21.0 11 -7.5 2.5 2.5 6.0 8.5 12.0 13.5 18.0 20.5 24.0 29.5 27.0 26.5 12 -8.0 6.5 9.5 7.0 8.0 11.5 13.0 17.5 20.0 23.5 29.0 38.5 36.0 TF: 0 8 8 8 8 8 8 8 8 8 8 8 8 8 1 8 8 8 1 2 1 2 2 2 3 1 2 2 2 8 1 1 2 2 2 2 2 2 2 2 1 2 3 8 4 4 1 1 2 2 1 1 2 2 4 1 4 8 4 4 1 2 1 2 2 2 2 3 4 4 5 8 4 4 4 1 4 1 2 2 3 2 2 4 6 8 4 4 4 1 4 4 1 3 2 2 2 3 7 8 4 4 4 4 1 5 4 1 1 3 2 3 8 8 4 4 4 1 4 5 5 1 1 3 2 1 9 8 4 4 4 4 1 5 4 4 1 1 2 2 10 8 4 4 1 4 1 5 4 4 4 1 2 2 11 8 1 1 2 2 4 4 4 4 4 4 1 2 12 8 4 4 1 1 4 5 5 1 4 4 4 1 SS_LG_FSL: 0 1 2 3 4 5 6 7 8 9 10 11 12 SF: 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 0.0 0.0 5.0 2.5 5.0 2.5 2.0 1.5 1.0 5.0 2.5 2.0 2 0.0 9.0 9.0 6.5 6.0 5.5 5.0 4.5 4.0 3.5 3.0 14.0 11.5 3 0.0 6.5 6.5 8.0 10.5 8.0 7.5 9.0 8.5 6.0 5.5 11.5 18.0 4 0.0 6.0 6.0 11.5 9.0 15.5 13.0 12.5 12.0 11.5 11.0 11.0 15.5 5 0.0 5.5 5.5 9.0 12.5 13.0 18.5 16.0 15.5 15.0 14.5 14.0 15.0 6 0.0 5.0 5.0 8.5 13.0 12.5 16.0 22.5 20.0 19.5 19.0 18.5 18.0 7 0.0 4.5 4.5 8.0 10.5 14.0 15.5 20.0 23.5 23.0 20.5 20.0 19.5 8 0.0 4.0 4.0 7.5 12.0 11.5 15.0 19.5 24.0 24.5 22.0 21.5 24.0 9 0.0 3.5 3.5 7.0 9.5 13.0 14.5 19.0 21.5 27.0 25.5 24.0 23.5 10 0.0 3.0 3.0 8.5 9.0 14.5 14.0 18.5 21.0 24.5 32.0 29.5 29.0 11 0.0 9.0 12.0 9.5 9.0 12.0 13.5 18.0 20.5 24.0 29.5 41.0 38.5 12 0.0 6.5 9.5 11.0 13.5 11.5 13.0 17.5 22.0 23.5 29.0 38.5 45.0 EF: 12-10.0 -2.5 4.0 7.0 8.5 11.0 10.5 10.5 15.0 19.5 21.0 26.5 36.0 FF: 0 0.0 -4.5 -5.0 -5.5 -6.0 -6.5 -7.0 -7.5 -8.0 -8.5 -9.0 -9.5-10.0 1 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 2 -3.0 -2.5 -2.5 2.5 0.0 2.5 0.0 -0.5 -1.0 -1.5 2.5 0.0 -0.5 3 -3.5 6.5 6.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 2.0 11.5 9.0 4 -4.0 6.0 6.0 5.5 8.0 5.5 5.0 6.5 6.0 3.5 3.0 11.0 15.5 5 -4.5 5.5 5.5 9.0 7.5 13.0 10.5 10.0 9.5 9.0 8.5 10.5 15.0 6 -5.0 5.0 5.0 8.5 10.0 12.5 16.0 13.5 13.0 12.5 12.0 11.5 14.5 7 -5.5 4.5 4.5 8.0 10.5 12.0 15.5 20.0 17.5 17.0 16.5 16.0 15.5 8 -6.0 4.0 4.0 7.5 10.0 11.5 15.0 19.5 21.0 20.5 18.0 17.5 17.0 9 -6.5 3.5 3.5 7.0 9.5 11.0 14.5 19.0 21.5 22.0 19.5 19.0 21.5 10 -7.0 3.0 3.0 6.5 9.0 10.5 14.0 18.5 21.0 24.5 23.0 21.5 21.0 11 -7.5 2.5 2.5 6.0 8.5 12.0 13.5 18.0 20.5 24.0 29.5 27.0 26.5 12 -8.0 6.5 9.5 7.0 8.0 11.5 13.0 17.5 20.0 23.5 29.0 38.5 36.0 TF: 0 8 8 8 8 8 8 8 8 8 8 8 8 8 1 8 8 8 1 2 1 2 2 2 3 1 2 2 2 8 1 1 2 2 2 2 2 2 2 2 1 2 3 8 4 4 1 1 2 2 1 1 2 2 4 1 4 8 4 4 1 2 1 2 2 2 2 3 4 4 5 8 4 4 4 1 4 1 2 2 3 2 2 4 6 8 4 4 4 1 4 4 1 3 2 2 2 3 7 8 4 4 4 4 1 5 4 1 1 3 2 3 8 8 4 4 4 1 4 5 5 1 1 3 2 1 9 8 4 4 4 4 1 5 4 4 1 1 2 2 10 8 4 4 1 4 1 5 4 4 4 1 2 2 11 8 1 1 2 2 4 4 4 4 4 4 1 2 12 8 4 4 1 1 4 5 5 1 4 4 4 1 TEST02: SS_LG_BSQ - Backward score quadratic; SS_LG_BSL - Backward score linear. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that the BSQ and BSL tables agree. Sequences A and B: 1 G C 2 C C 3 T G 4 G T 5 A G 6 T A 7 A T 8 T T 9 A A 10 G G 11 C C 12 T T SS_LG_BSQ: 0 1 2 3 4 5 6 7 8 9 10 11 12 SB: 0 42.0 42.5 41.0 35.5 31.0 25.5 22.0 19.5 15.5 18.0 10.5 1.0 0.0 1 44.5 45.0 33.5 36.0 31.5 26.0 22.5 20.0 15.5 12.0 13.0 1.5 0.0 2 35.0 35.5 36.0 38.5 32.0 26.5 25.0 20.5 16.0 12.5 7.0 4.0 0.0 3 30.5 31.0 31.5 32.0 34.5 27.0 23.5 21.0 16.5 13.0 7.5 1.0 0.0 4 25.0 25.5 28.0 26.5 28.0 29.5 24.0 21.5 17.0 13.5 8.0 1.5 0.0 5 23.5 24.0 24.5 27.0 24.5 27.0 26.5 22.0 17.5 14.0 8.5 4.0 0.0 6 21.0 21.5 22.0 22.5 23.0 25.5 26.0 22.5 18.0 14.5 9.0 1.5 0.0 7 19.5 20.0 20.5 21.0 21.5 22.0 22.5 25.0 18.5 15.0 9.5 4.0 0.0 8 15.0 15.5 16.0 16.5 17.0 17.5 18.0 18.5 21.0 15.5 10.0 1.0 0.0 9 11.5 12.0 12.5 13.0 13.5 14.0 14.5 15.0 15.5 18.0 10.5 1.0 0.0 10 10.0 10.5 7.0 7.5 8.0 8.5 9.0 9.5 10.0 10.5 13.0 1.5 0.0 11 0.5 1.0 1.5 4.0 1.0 1.5 4.0 4.0 1.0 1.0 1.5 4.0 0.0 12 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 EB: 0 40.0 38.5 33.0 28.5 23.0 19.5 17.0 15.0 15.5 8.0 -1.5 -2.5-10.0 1 42.5 33.0 33.5 29.0 23.5 20.0 17.5 13.0 10.0 10.5 -1.0 -2.5 -9.5 2 35.0 35.5 36.0 29.5 24.0 22.5 18.0 13.5 10.0 4.5 1.5 -2.5 -9.0 3 30.5 31.0 31.5 32.0 24.5 21.0 18.5 14.0 10.5 5.0 -1.5 -2.5 -8.5 4 25.0 25.5 26.0 26.5 27.0 21.5 19.0 14.5 11.0 5.5 -1.0 -2.5 -8.0 5 23.5 24.0 24.5 24.0 24.5 24.0 19.5 15.0 11.5 6.0 1.5 -2.5 -7.5 6 21.0 21.5 22.0 22.5 23.0 23.5 20.0 15.5 12.0 6.5 -1.0 -2.5 -7.0 7 19.5 20.0 20.5 21.0 21.5 22.0 22.5 16.0 12.5 7.0 1.5 -2.5 -6.5 8 15.0 15.5 16.0 16.5 17.0 17.5 18.0 18.5 13.0 7.5 -1.5 -2.5 -6.0 9 11.5 12.0 12.5 13.0 13.5 14.0 14.5 15.0 15.5 8.0 -1.5 -2.5 -5.5 10 8.0 6.5 7.0 7.5 8.0 8.5 9.0 9.5 10.0 10.5 -1.0 -2.5 -5.0 11 0.5 1.0 1.5 0.5 1.0 1.5 1.5 0.0 0.5 1.0 1.5 -2.5 -4.5 12 -8.0 -7.5 -7.0 -6.5 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 0.0 FB: 0 42.0 42.5 33.0 35.5 31.0 25.5 22.0 19.5 15.0 11.5 10.5 1.0 -8.0 1 32.5 33.0 33.5 36.0 31.5 26.0 22.5 20.0 15.5 12.0 6.5 1.5 -7.5 2 28.0 28.5 29.0 29.5 32.0 26.5 23.0 20.5 16.0 12.5 7.0 0.5 -7.0 3 22.5 23.0 25.5 24.0 25.5 27.0 23.5 21.0 16.5 13.0 7.5 1.0 -6.5 4 21.0 21.5 22.0 24.5 22.0 24.5 24.0 21.5 17.0 13.5 8.0 1.5 -6.0 5 18.5 19.0 19.5 20.0 20.5 23.0 23.5 22.0 17.5 14.0 8.5 1.0 -5.5 6 17.0 17.5 18.0 18.5 19.0 19.5 20.0 22.5 18.0 14.5 9.0 1.5 -5.0 7 12.5 13.0 13.5 14.0 14.5 15.0 15.5 16.0 18.5 15.0 9.5 0.0 -4.5 8 9.0 9.5 10.0 10.5 11.0 11.5 12.0 12.5 13.0 15.5 10.0 0.5 -4.0 9 7.5 8.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0 10.5 1.0 -3.5 10 -2.0 -1.5 -1.0 1.5 -1.5 -1.0 1.5 1.5 -1.5 -1.5 -1.0 1.5 -3.0 11 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 12-10.0 -9.5 -9.0 -8.5 -8.0 -7.5 -7.0 -6.5 -6.0 -5.5 -5.0 -4.5 0.0 TB: 0 4 4 1 4 5 4 4 4 2 1 4 4 8 1 1 1 7 4 4 4 4 4 4 4 1 4 8 2 2 2 2 1 4 4 1 5 4 4 4 1 8 3 2 2 3 2 1 4 4 4 4 5 4 4 8 4 2 2 1 2 1 1 4 4 5 4 4 4 8 5 2 2 2 1 3 1 1 5 4 4 4 1 8 6 2 2 3 3 3 1 1 4 5 4 4 4 8 7 2 2 2 3 2 2 3 1 4 4 4 1 8 8 2 2 2 2 2 3 2 2 1 4 4 1 8 9 2 2 3 2 3 2 2 2 2 1 4 4 8 10 1 1 2 2 2 2 2 2 2 2 1 4 8 11 2 2 2 1 2 2 1 1 1 2 2 1 8 12 8 8 8 8 8 8 8 8 8 8 8 8 8 SS_LG_BSL: 0 1 2 3 4 5 6 7 8 9 10 11 12 SB: 0 42.0 42.5 41.0 35.5 31.0 25.5 22.0 19.5 15.5 18.0 10.5 1.0 0.0 1 44.5 45.0 33.5 36.0 31.5 26.0 22.5 20.0 15.5 12.0 13.0 1.5 0.0 2 35.0 35.5 36.0 38.5 32.0 26.5 25.0 20.5 16.0 12.5 7.0 4.0 0.0 3 30.5 31.0 31.5 32.0 34.5 27.0 23.5 21.0 16.5 13.0 7.5 1.0 0.0 4 25.0 25.5 28.0 26.5 28.0 29.5 24.0 21.5 17.0 13.5 8.0 1.5 0.0 5 23.5 24.0 24.5 27.0 24.5 27.0 26.5 22.0 17.5 14.0 8.5 4.0 0.0 6 21.0 21.5 22.0 22.5 23.0 25.5 26.0 22.5 18.0 14.5 9.0 1.5 0.0 7 19.5 20.0 20.5 21.0 21.5 22.0 22.5 25.0 18.5 15.0 9.5 4.0 0.0 8 15.0 15.5 16.0 16.5 17.0 17.5 18.0 18.5 21.0 15.5 10.0 1.0 0.0 9 11.5 12.0 12.5 13.0 13.5 14.0 14.5 15.0 15.5 18.0 10.5 1.0 0.0 10 10.0 10.5 7.0 7.5 8.0 8.5 9.0 9.5 10.0 10.5 13.0 1.5 0.0 11 0.5 1.0 1.5 4.0 1.0 1.5 4.0 4.0 1.0 1.0 1.5 4.0 0.0 12 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 EB: 0 40.0 38.5 33.0 28.5 23.0 19.5 17.0 15.0 15.5 8.0 -1.5 -2.5-10.0 1 42.5 33.0 33.5 29.0 23.5 20.0 17.5 13.0 10.0 10.5 -1.0 -2.5 -9.5 2 35.0 35.5 36.0 29.5 24.0 22.5 18.0 13.5 10.0 4.5 1.5 -2.5 -9.0 3 30.5 31.0 31.5 32.0 24.5 21.0 18.5 14.0 10.5 5.0 -1.5 -2.5 -8.5 4 25.0 25.5 26.0 26.5 27.0 21.5 19.0 14.5 11.0 5.5 -1.0 -2.5 -8.0 5 23.5 24.0 24.5 24.0 24.5 24.0 19.5 15.0 11.5 6.0 1.5 -2.5 -7.5 6 21.0 21.5 22.0 22.5 23.0 23.5 20.0 15.5 12.0 6.5 -1.0 -2.5 -7.0 7 19.5 20.0 20.5 21.0 21.5 22.0 22.5 16.0 12.5 7.0 1.5 -2.5 -6.5 8 15.0 15.5 16.0 16.5 17.0 17.5 18.0 18.5 13.0 7.5 -1.5 -2.5 -6.0 9 11.5 12.0 12.5 13.0 13.5 14.0 14.5 15.0 15.5 8.0 -1.5 -2.5 -5.5 10 8.0 6.5 7.0 7.5 8.0 8.5 9.0 9.5 10.0 10.5 -1.0 -2.5 -5.0 11 0.5 1.0 1.5 0.5 1.0 1.5 1.5 0.0 0.5 1.0 1.5 -2.5 -4.5 12 -8.0 -7.5 -7.0 -6.5 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 0.0 FB: 0 42.0 42.5 33.0 35.5 31.0 25.5 22.0 19.5 15.0 11.5 10.5 1.0 -8.0 1 32.5 33.0 33.5 36.0 31.5 26.0 22.5 20.0 15.5 12.0 6.5 1.5 -7.5 2 28.0 28.5 29.0 29.5 32.0 26.5 23.0 20.5 16.0 12.5 7.0 0.5 -7.0 3 22.5 23.0 25.5 24.0 25.5 27.0 23.5 21.0 16.5 13.0 7.5 1.0 -6.5 4 21.0 21.5 22.0 24.5 22.0 24.5 24.0 21.5 17.0 13.5 8.0 1.5 -6.0 5 18.5 19.0 19.5 20.0 20.5 23.0 23.5 22.0 17.5 14.0 8.5 1.0 -5.5 6 17.0 17.5 18.0 18.5 19.0 19.5 20.0 22.5 18.0 14.5 9.0 1.5 -5.0 7 12.5 13.0 13.5 14.0 14.5 15.0 15.5 16.0 18.5 15.0 9.5 0.0 -4.5 8 9.0 9.5 10.0 10.5 11.0 11.5 12.0 12.5 13.0 15.5 10.0 0.5 -4.0 9 7.5 8.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0 10.5 1.0 -3.5 10 -2.0 -1.5 -1.0 1.5 -1.5 -1.0 1.5 1.5 -1.5 -1.5 -1.0 1.5 -3.0 11 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 12-10.0 -9.5 -9.0 -8.5 -8.0 -7.5 -7.0 -6.5 -6.0 -5.5 -5.0 -4.5 0.0 TB: 0 4 4 1 4 5 4 4 4 2 1 4 4 8 1 1 1 7 4 4 4 4 4 4 4 1 4 8 2 2 2 2 1 4 4 1 5 4 4 4 1 8 3 2 2 3 2 1 4 4 4 4 5 4 4 8 4 2 2 1 2 1 1 4 4 5 4 4 4 8 5 2 2 2 1 3 1 1 5 4 4 4 1 8 6 2 2 3 3 3 1 1 4 5 4 4 4 8 7 2 2 2 3 2 2 3 1 4 4 4 1 8 8 2 2 2 2 2 3 2 2 1 4 4 1 8 9 2 2 3 2 3 2 2 2 2 1 4 4 8 10 1 1 2 2 2 2 2 2 2 2 1 4 8 11 2 2 2 1 2 2 1 1 1 2 2 1 8 12 8 8 8 8 8 8 8 8 8 8 8 8 8 TEST03: SS_LG_FSQ - Forward score quadratic; SS_LG_FSL - Forward score linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that the FSQ and FSL tables agree. Sequences A and B: 1 G G 2 C G 3 T G 4 T Matching Scores: 0 1 2 3 4 0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 5.0 5.0 -1.0 2 0.0 -5.0 -5.0 -5.0 -3.0 3 0.0 -1.0 -1.0 -1.0 4.0 SS_LG_FSQ: 0 1 2 3 4 SF: 0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 5.0 5.0 2.5 2 0.0 2.5 2.5 2.5 2.0 3 0.0 2.0 2.0 2.0 6.5 EF: 0 0.0 -2.5 -3.0 -3.5 -4.0 1 -4.5 -2.5 2.5 2.5 2.5 2 -5.0 -2.5 0.0 0.0 0.0 3 -5.5 -2.5 -0.5 -0.5 -0.5 FF: 0 0.0 -4.5 -5.0 -5.5 -6.0 1 -2.5 -2.5 -2.5 -2.5 -2.5 2 -3.0 2.5 2.5 2.5 0.0 3 -3.5 2.0 2.0 2.0 -0.5 TF: 0 8 8 8 8 8 1 8 1 1 1 2 2 8 4 4 4 1 3 8 4 4 4 1 SS_LG_FSL: 0 1 2 3 4 SF: 0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 5.0 5.0 2.5 2 0.0 2.5 2.5 2.5 2.0 3 0.0 2.0 2.0 2.0 6.5 EF: 0 0.0 -2.5 -3.0 -3.5 -4.0 1 -4.5 -2.5 2.5 2.5 2.5 2 -5.0 -2.5 0.0 0.0 0.0 3 -5.5 -2.5 -0.5 -0.5 -0.5 FF: 0 0.0 -4.5 -5.0 -5.5 -6.0 1 -2.5 -2.5 -2.5 -2.5 -2.5 2 -3.0 2.5 2.5 2.5 0.0 3 -3.5 2.0 2.0 2.0 -0.5 TF: 0 8 8 8 8 8 1 8 1 1 1 2 2 8 4 4 4 1 3 8 4 4 4 1 TEST04: SS_LG_BSQ - Backward score quadratic; SS_LG_BSL - Backward score linear. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that the BSQ and BSL tables agree. Sequences A and B: 1 G G 2 C G 3 T G 4 T SS_LG_BSQ: 0 1 2 3 4 SB: 0 5.0 5.0 6.5 1.0 0.0 1 0.0 0.0 0.0 1.5 0.0 2 0.5 1.0 1.5 4.0 0.0 3 0.0 0.0 0.0 0.0 0.0 EB: 0 3.5 4.0 -1.5 -2.5 -5.5 1 -2.0 -1.5 -1.0 -2.5 -5.0 2 0.5 1.0 1.5 -2.5 -4.5 3 -4.0 -3.5 -3.0 -2.5 0.0 FB: 0 -2.5 -2.0 -1.5 1.0 -3.5 1 -2.0 -1.5 -1.0 1.5 -3.0 2 -2.5 -2.5 -2.5 -2.5 -2.5 3 -6.0 -5.5 -5.0 -4.5 0.0 TB: 0 1 1 1 4 8 1 8 8 8 4 8 2 2 2 2 1 8 3 8 8 8 8 8 SS_LG_BSL: 0 1 2 3 4 SB: 0 5.0 5.0 6.5 1.0 0.0 1 0.0 0.0 0.0 1.5 0.0 2 0.5 1.0 1.5 4.0 0.0 3 0.0 0.0 0.0 0.0 0.0 EB: 0 3.5 4.0 -1.5 -2.5 -5.5 1 -2.0 -1.5 -1.0 -2.5 -5.0 2 0.5 1.0 1.5 -2.5 -4.5 3 -4.0 -3.5 -3.0 -2.5 0.0 FB: 0 -2.5 -2.0 -1.5 1.0 -3.5 1 -2.0 -1.5 -1.0 1.5 -3.0 2 -2.5 -2.5 -2.5 -2.5 -2.5 3 -6.0 -5.5 -5.0 -4.5 0.0 TB: 0 1 1 1 4 8 1 8 8 8 4 8 2 2 2 2 1 8 3 8 8 8 8 8 TEST05: SS_LG_BSQ - Backward score quadratic; SS_LG_FSQ - Forward score quadratic. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that the FSQ and (reversed) BSQ tables agree. Sequences A and B: 1 G G 2 C G 3 T G 4 T SS_LG_FSQ: 0 1 2 3 4 SF: 0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 5.0 5.0 2.5 2 0.0 2.5 2.5 2.5 2.0 3 0.0 2.0 2.0 2.0 6.5 EF: 0 0.0 -2.5 -3.0 -3.5 -4.0 1 -4.5 -2.5 2.5 2.5 2.5 2 -5.0 -2.5 0.0 0.0 0.0 3 -5.5 -2.5 -0.5 -0.5 -0.5 FF: 0 0.0 -4.5 -5.0 -5.5 -6.0 1 -2.5 -2.5 -2.5 -2.5 -2.5 2 -3.0 2.5 2.5 2.5 0.0 3 -3.5 2.0 2.0 2.0 -0.5 TF: 0 8 8 8 8 8 1 8 1 1 1 2 2 8 4 4 4 1 3 8 4 4 4 1 Reversed sequences A and B: 1 T T 2 C G 3 G G 4 G SS_LG_BSQ: (The tables are printed in reverse order) 4 3 2 1 0 SB: 3 0.0 0.0 0.0 0.0 0.0 2 0.0 5.0 5.0 5.0 2.5 1 0.0 2.5 2.5 2.5 2.0 0 0.0 2.0 2.0 2.0 6.5 EB: 3 0.0 -2.5 -3.0 -3.5 -4.0 2 -4.5 -2.5 2.5 2.5 2.5 1 -5.0 -2.5 0.0 0.0 0.0 0 -5.5 -2.5 -0.5 -0.5 -0.5 FB: 3 0.0 -4.5 -5.0 -5.5 -6.0 2 -2.5 -2.5 -2.5 -2.5 -2.5 1 -3.0 2.5 2.5 2.5 0.0 0 -3.5 2.0 2.0 2.0 -0.5 TB: 3 8 8 8 8 8 2 8 1 1 1 2 1 8 4 4 4 1 0 8 4 4 4 1 TEST055: SS_LG_FSQ - Forward quadratic; SS_LG_BSQ - Backward quadratic. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Do a score computation on a sub-block. Check that the highest entry in SF for FSQ agrees with the highest entry for SB BSQ. The paths prescribed from the highest entries in SF and SB should agree (although opposite in direction). Sequences A and B: 1 G C 2 C C 3 T G 4 G T 5 A G 6 T A 7 A T 8 T T 9 A A 10 G G 11 C C 12 T T Matching Scores: 0 1 2 3 4 5 6 7 8 9 10 11 12 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 -5.0 -5.0 5.0 -1.0 5.0 1.0 -1.0 -1.0 1.0 5.0 -5.0 -1.0 2 0.0 9.0 9.0 -5.0 -3.0 -5.0 -3.0 -3.0 -3.0 -3.0 -5.0 9.0 -3.0 3 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 4 0.0 -5.0 -5.0 5.0 -1.0 5.0 1.0 -1.0 -1.0 1.0 5.0 -5.0 -1.0 5 0.0 -3.0 -3.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 -3.0 1.0 6 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 7 0.0 -3.0 -3.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 -3.0 1.0 8 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 9 0.0 -3.0 -3.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 -3.0 1.0 10 0.0 -5.0 -5.0 5.0 -1.0 5.0 1.0 -1.0 -1.0 1.0 5.0 -5.0 -1.0 11 0.0 9.0 9.0 -5.0 -3.0 -5.0 -3.0 -3.0 -3.0 -3.0 -5.0 9.0 -3.0 12 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 SS_LG_FSQ: 3 4 5 6 7 8 9 SF: 4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 5 0.0 1.0 1.0 3.0 1.0 1.0 3.0 6 0.0 4.0 1.5 2.0 7.0 5.0 4.0 7 0.0 1.5 5.0 4.5 4.5 8.0 8.0 8 0.0 4.0 2.5 6.0 8.5 8.5 9.0 9 0.0 1.5 5.0 5.5 7.0 9.5 11.5 10 0.0 1.0 6.5 6.0 5.5 7.0 10.5 EF: 4 0.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 5 -4.5 -2.5 -1.5 -1.5 0.5 0.0 -0.5 6 -5.0 -2.5 1.5 1.0 0.5 4.5 4.0 7 -5.5 -2.5 -1.0 2.5 2.0 2.0 5.5 8 -6.0 -2.5 1.5 1.0 3.5 6.0 6.0 9 -6.5 -2.5 -1.0 2.5 3.0 4.5 7.0 10 -7.0 -2.5 -1.5 4.0 3.5 3.0 4.5 FF: 4 0.0 -4.5 -5.0 -5.5 -6.0 -6.5 -7.0 5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 6 -3.0 -1.5 -1.5 0.5 -1.5 -1.5 0.5 7 -3.5 1.5 -1.0 0.0 4.5 2.5 1.5 8 -4.0 1.0 2.5 2.0 4.0 5.5 5.5 9 -4.5 1.5 2.0 3.5 6.0 6.0 6.5 10 -5.0 1.0 2.5 3.0 5.5 7.0 9.0 TF: 4 8 8 8 8 8 8 8 5 8 1 1 1 1 1 1 6 8 1 2 1 1 1 2 7 8 4 1 1 4 1 1 8 8 1 4 1 1 1 1 9 8 4 1 1 1 1 1 10 8 4 1 1 4 4 1 SS_LG_FSQ: Optimal score indices: 9 9 Optimal score: 11.5000 Matching path: 1 4 5 2 5 6 3 6 7 4 7 -1 5 8 8 6 9 9 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 5 A = A 6 3.00 3.00 6 T = T 7 4.00 7.00 7 A | -2.50 4.50 8 T = T 8 4.00 8.50 9 A = A 9 3.00 11.50 SS_LG_BSQ: 3 4 5 6 7 8 9 SB: 4 9.0 10.0 11.5 8.0 4.5 3.0 0.0 5 10.5 8.0 9.0 8.5 7.0 1.0 0.0 6 6.0 6.5 9.0 8.0 4.5 3.0 0.0 7 6.5 3.5 4.0 6.0 7.0 1.0 0.0 8 6.0 2.5 3.0 1.0 2.0 3.0 0.0 9 2.5 5.0 1.0 0.0 0.0 1.0 0.0 10 0.0 0.0 0.0 0.0 0.0 0.0 0.0 EB: 4 8.5 9.0 5.5 2.0 0.5 -2.5 -7.0 5 6.0 6.5 6.0 4.5 -1.5 -2.5 -6.5 6 6.0 6.5 5.5 2.0 0.5 -2.5 -6.0 7 3.0 3.5 4.0 4.5 -1.5 -2.5 -5.5 8 0.0 0.5 -0.5 0.0 0.5 -2.5 -5.0 9 2.5 -1.5 -2.5 -2.0 -1.5 -2.5 -4.5 10 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 0.0 FB: 4 8.0 5.5 6.5 6.0 4.5 0.0 -5.0 5 3.5 4.0 6.5 5.5 4.0 0.5 -4.5 6 4.0 1.5 1.5 3.5 4.5 0.0 -4.0 7 3.5 2.0 0.5 -1.5 -0.5 0.5 -3.5 8 0.0 2.5 -1.5 -2.5 -2.5 -1.5 -3.0 9 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 -2.5 10 -7.0 -6.5 -6.0 -5.5 -5.0 -4.5 0.0 TB: 4 1 1 1 1 4 1 8 5 1 1 1 1 1 1 8 6 2 2 1 1 4 1 8 7 1 2 2 1 1 1 8 8 1 4 1 1 1 1 8 9 2 1 1 8 8 1 8 10 8 8 8 8 8 8 8 SS_LG_BSQ: Optimal score indices: 4 5 Optimal score: 11.5000 Matching path: 1 4 5 2 5 6 3 6 7 4 7 -1 5 8 8 6 9 9 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 5 A = A 6 3.00 3.00 6 T = T 7 4.00 7.00 7 A | -2.50 4.50 8 T = T 8 4.00 8.50 9 A = A 9 3.00 11.50 TEST06: SS_LG_FSL - Forward linear; SS_LG_BSL - Backward linear. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Do a score computation on a sub-block. Verify that the maximum entries for FSL and BSL are the same. Sequences A and B: 1 G C 2 C C 3 T G 4 G T 5 A G 6 T A 7 A T 8 T T 9 A A 10 G G 11 C C 12 T T Matching Scores: 0 1 2 3 4 5 6 7 8 9 10 11 12 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 -5.0 -5.0 5.0 -1.0 5.0 1.0 -1.0 -1.0 1.0 5.0 -5.0 -1.0 2 0.0 9.0 9.0 -5.0 -3.0 -5.0 -3.0 -3.0 -3.0 -3.0 -5.0 9.0 -3.0 3 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 4 0.0 -5.0 -5.0 5.0 -1.0 5.0 1.0 -1.0 -1.0 1.0 5.0 -5.0 -1.0 5 0.0 -3.0 -3.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 -3.0 1.0 6 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 7 0.0 -3.0 -3.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 -3.0 1.0 8 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 9 0.0 -3.0 -3.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 -3.0 1.0 10 0.0 -5.0 -5.0 5.0 -1.0 5.0 1.0 -1.0 -1.0 1.0 5.0 -5.0 -1.0 11 0.0 9.0 9.0 -5.0 -3.0 -5.0 -3.0 -3.0 -3.0 -3.0 -5.0 9.0 -3.0 12 0.0 -3.0 -3.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 SS_LG_FSL: 3 4 5 6 7 8 9 4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 5 0.0 1.0 1.0 3.0 1.0 1.0 3.0 6 0.0 4.0 1.5 2.0 7.0 5.0 4.0 7 0.0 1.5 5.0 4.5 4.5 8.0 8.0 8 0.0 4.0 2.5 6.0 8.5 8.5 9.0 9 0.0 1.5 5.0 5.5 7.0 9.5 11.5 10 0.0 1.0 6.5 6.0 5.5 7.0 10.5 SS_LG_BSL: 3 4 5 6 7 8 9 4 9.0 10.0 11.5 8.0 4.5 3.0 0.0 5 10.5 8.0 9.0 8.5 7.0 1.0 0.0 6 6.0 6.5 9.0 8.0 4.5 3.0 0.0 7 6.5 3.5 4.0 6.0 7.0 1.0 0.0 8 6.0 2.5 3.0 1.0 2.0 3.0 0.0 9 2.5 5.0 1.0 0.0 0.0 1.0 0.0 10 0.0 0.0 0.0 0.0 0.0 0.0 0.0 TEST07: SS_LG_FSQ - forward score quadratic SS_LG_FPQ - forward path quadratic GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Sequences A and B: 1 G C 2 C C 3 T G 4 G T 5 A G 6 T A 7 A T 8 T T 9 A A 10 G G 11 C C 12 T T SS_LG_FSQ reports optimal matching score is 45.0000 Matching path: 1 1 1 2 2 2 3 -1 3 4 3 4 5 4 5 6 5 6 7 6 7 8 7 -1 9 8 8 10 9 9 11 10 10 12 11 11 13 12 12 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 2 C = C 2 9.00 9.00 | G 3 -2.50 6.50 3 T = T 4 4.00 10.50 4 G = G 5 5.00 15.50 5 A = A 6 3.00 18.50 6 T = T 7 4.00 22.50 7 A | -2.50 20.00 8 T = T 8 4.00 24.00 9 A = A 9 3.00 27.00 10 G = G 10 5.00 32.00 11 C = C 11 9.00 41.00 12 T = T 12 4.00 45.00 TEST08: SS_LG_BSQ - backward score quadratic SS_LG_BPQ - backward path quadratic GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Compare path and score with FSQ/FPQ computation. Sequences A and B: 1 G C 2 C C 3 T G 4 G T 5 A G 6 T A 7 A T 8 T T 9 A A 10 G G 11 C C 12 T T SS_LG_BSQ reports optimal matching score is 45.0000 Matching path: 1 1 1 2 2 2 3 -1 3 4 3 4 5 4 5 6 5 6 7 6 7 8 7 -1 9 8 8 10 9 9 11 10 10 12 11 11 13 12 12 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 2 C = C 2 9.00 9.00 | G 3 -2.50 6.50 3 T = T 4 4.00 10.50 4 G = G 5 5.00 15.50 5 A = A 6 3.00 18.50 6 T = T 7 4.00 22.50 7 A | -2.50 20.00 8 T = T 8 4.00 24.00 9 A = A 9 3.00 27.00 10 G = G 10 5.00 32.00 11 C = C 11 9.00 41.00 12 T = T 12 4.00 45.00 TEST09: SS_LG_RPL - path routine; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that RPL agrees with FSQ/FPQ and BSQ/BPQ. Sequences A and B: 1 G C 2 C C 3 T G 4 G T 5 A G 6 T A 7 A T 8 T T 9 A A 10 G G 11 C C 12 T T SS_LG_CORNERS: (I1,J1) = 1 1 (I2,J2) = 12 12 Matching path: 1 1 1 2 2 2 3 -1 3 4 3 4 5 4 5 6 5 6 7 6 7 8 7 -1 9 8 8 10 9 9 11 10 10 12 11 11 13 12 12 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 2 C = C 2 9.00 9.00 | G 3 -2.50 6.50 3 T = T 4 4.00 10.50 4 G = G 5 5.00 15.50 5 A = A 6 3.00 18.50 6 T = T 7 4.00 22.50 7 A | -2.50 20.00 8 T = T 8 4.00 24.00 9 A = A 9 3.00 27.00 10 G = G 10 5.00 32.00 11 C = C 11 9.00 41.00 12 T = T 12 4.00 45.00 TEST12: SS_LG_FSQ - Forward score quadratic; SS_LG_FPQ - Forward path quadratic. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. SS_LG_FSQ reports optimal matching score is 249.500 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 M = M 1 8.00 8.00 2 M = M 2 8.00 16.00 3 A = A 3 3.00 19.00 4 A = A 4 3.00 22.00 5 E = E 5 5.00 27.00 6 A = A 6 3.00 30.00 7 G = G 7 5.00 35.00 8 G = G 8 5.00 40.00 9 E | -2.50 37.50 10 E | -0.50 37.00 11 G | -0.50 36.50 12 G | -0.50 36.00 13 P = P 9 6.00 42.00 14 V = V 10 5.00 47.00 15 T = T 11 4.00 51.00 16 A = A 12 3.00 54.00 17 G = G 13 5.00 59.00 18 A = A 14 3.00 62.00 19 A = A 15 3.00 65.00 20 G = G 16 5.00 70.00 21 G = G 17 5.00 75.00 22 G = G 18 5.00 80.00 23 A = A 19 3.00 83.00 24 A = A 20 3.00 86.00 | C 21 -2.50 83.50 | C 22 -0.50 83.00 | C 23 -0.50 82.50 25 A = A 24 3.00 85.50 26 A = A 25 3.00 88.50 27 S = S 26 3.00 91.50 28 G = G 27 5.00 96.50 29 A = A 28 3.00 99.50 30 Y = Y 29 8.00 107.50 31 P = P 30 6.00 113.50 32 A = A 31 3.00 116.50 33 V = V 32 5.00 121.50 34 C = C 33 9.00 130.50 35 R = R 34 6.00 136.50 36 V = V 35 5.00 141.50 37 K = K 36 5.00 146.50 38 I = I 37 6.00 152.50 39 P = P 38 6.00 158.50 40 A = A 39 3.00 161.50 41 A = A 40 3.00 164.50 42 L = L 41 5.00 169.50 43 P = P 42 6.00 175.50 44 V = V 43 5.00 180.50 45 A = A 44 3.00 183.50 46 A = A 45 3.00 186.50 47 A = A 46 3.00 189.50 48 A = A 47 3.00 192.50 49 P = P 48 6.00 198.50 50 F = F 49 8.00 206.50 51 P = P 50 6.00 212.50 52 G = G 51 5.00 217.50 53 L = L 52 5.00 222.50 54 A = A 53 3.00 225.50 55 E = E 54 5.00 230.50 56 A = A 55 3.00 233.50 57 G = G 56 5.00 238.50 58 V = V 57 5.00 243.50 59 A = A 58 3.00 246.50 60 A = A 59 3.00 249.50 TEST13: SS_LG_RPL - path routine; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Compare with FSQ/FPQ calculation. SS_LG_CORNERS: (I1,J1) = 0 0 (I2,J2) = 60 59 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 M = M 1 8.00 8.00 2 M = M 2 8.00 16.00 3 A = A 3 3.00 19.00 4 A = A 4 3.00 22.00 5 E = E 5 5.00 27.00 6 A = A 6 3.00 30.00 7 G | -2.50 27.50 8 G | -0.50 27.00 9 E | -0.50 26.50 10 E | -0.50 26.00 11 G = G 7 5.00 31.00 12 G = G 8 5.00 36.00 13 P = P 9 6.00 42.00 14 V = V 10 5.00 47.00 15 T = T 11 4.00 51.00 16 A = A 12 3.00 54.00 17 G = G 13 5.00 59.00 18 A = A 14 3.00 62.00 19 A = A 15 3.00 65.00 20 G = G 16 5.00 70.00 21 G = G 17 5.00 75.00 22 G = G 18 5.00 80.00 23 A = A 19 3.00 83.00 24 A = A 20 3.00 86.00 | C 21 -2.50 83.50 | C 22 -0.50 83.00 | C 23 -0.50 82.50 25 A = A 24 3.00 85.50 26 A = A 25 3.00 88.50 27 S = S 26 3.00 91.50 28 G = G 27 5.00 96.50 29 A = A 28 3.00 99.50 30 Y = Y 29 8.00 107.50 31 P = P 30 6.00 113.50 32 A = A 31 3.00 116.50 33 V = V 32 5.00 121.50 34 C = C 33 9.00 130.50 35 R = R 34 6.00 136.50 36 V = V 35 5.00 141.50 37 K = K 36 5.00 146.50 38 I = I 37 6.00 152.50 39 P = P 38 6.00 158.50 40 A = A 39 3.00 161.50 41 A = A 40 3.00 164.50 42 L = L 41 5.00 169.50 43 P = P 42 6.00 175.50 44 V = V 43 5.00 180.50 45 A = A 44 3.00 183.50 46 A = A 45 3.00 186.50 47 A = A 46 3.00 189.50 48 A = A 47 3.00 192.50 49 P = P 48 6.00 198.50 50 F = F 49 8.00 206.50 51 P = P 50 6.00 212.50 52 G = G 51 5.00 217.50 53 L = L 52 5.00 222.50 54 A = A 53 3.00 225.50 55 E = E 54 5.00 230.50 56 A = A 55 3.00 233.50 57 G = G 56 5.00 238.50 58 V = V 57 5.00 243.50 59 A = A 58 3.00 246.50 60 A = A 59 3.00 249.50 TEST14: SS_LG_FSQ - Forward score quadratic; SS_LG_FSL - Forward score linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Verify that FSQ agrees with Myers/Miller calculation. Verify that FSQ and FSL agree. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C Matching Scores: 0 1 2 3 0 0.0 0.0 0.0 0.0 1 0.0 1.0 1.0 -1.0 2 0.0 -1.0 -1.0 1.0 3 0.0 -1.0 -1.0 -1.0 4 0.0 1.0 1.0 -1.0 5 0.0 -1.0 -1.0 -1.0 SS_LG_FSQ: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 1.0 1.0 0.0 2 0.0 0.0 0.0 2.0 3 0.0 0.0 0.0 0.0 4 0.0 1.0 1.0 0.0 5 0.0 0.0 0.0 0.0 EF: 0 0.0 -2.5 -3.0 -3.5 1 -4.5 -2.5 -1.5 -1.5 2 -5.0 -2.5 -2.5 -2.5 3 -5.5 -2.5 -2.5 -2.5 4 -6.0 -2.5 -1.5 -1.5 5 -6.5 -2.5 -2.5 -2.5 FF: 0 0.0 -4.5 -5.0 -5.5 1 -2.5 -2.5 -2.5 -2.5 2 -3.0 -1.5 -1.5 -2.5 3 -3.5 -2.0 -2.0 -0.5 4 -4.0 -2.5 -2.5 -1.0 5 -4.5 -1.5 -1.5 -1.5 TF: 0 8 8 8 8 1 8 1 1 8 2 8 8 9 1 3 8 8 8 8 4 8 1 1 8 5 8 8 9 9 SS_LG_FSL: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 1.0 1.0 0.0 2 0.0 0.0 0.0 2.0 3 0.0 0.0 0.0 0.0 4 0.0 1.0 1.0 0.0 5 0.0 0.0 0.0 0.0 EF: 0 0.0 -2.5 -3.0 -3.5 1 -4.5 -2.5 -1.5 -1.5 2 -5.0 -2.5 -2.5 -2.5 3 -5.5 -2.5 -2.5 -2.5 4 -6.0 -2.5 -1.5 -1.5 5 -6.5 -2.5 -2.5 -2.5 FF: 0 0.0 -4.5 -5.0 -5.5 1 -2.5 -2.5 -2.5 -2.5 2 -3.0 -1.5 -1.5 -2.5 3 -3.5 -2.0 -2.0 -0.5 4 -4.0 -2.5 -2.5 -1.0 5 -4.5 -1.5 -1.5 -1.5 TF: 0 8 8 8 8 1 8 1 1 8 2 8 8 9 1 3 8 8 8 8 4 8 1 1 8 5 8 8 9 9 TEST15: SS_LG_BSQ - Backward score quadratic; SS_LG_BSL - Backward score linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Verify that BSQ agrees with Myers/Miller calculation. Compare BSQ and BSL results. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C SS_LG_BSQ: 0 1 2 3 SB: 0 1.0 2.0 0.0 0.0 1 0.0 0.0 1.0 0.0 2 0.0 0.0 0.0 0.0 3 1.0 1.0 0.0 0.0 4 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 EB: 0 -0.5 -2.5 -2.5 -6.5 1 -2.0 -1.5 -2.5 -6.0 2 -2.5 -2.5 -2.5 -5.5 3 -1.5 -2.5 -2.5 -5.0 4 -2.5 -2.5 -2.5 -4.5 5 -3.5 -3.0 -2.5 0.0 FB: 0 -2.5 -2.5 -1.5 -4.5 1 -2.0 -2.0 -2.5 -4.0 2 -1.5 -1.5 -2.5 -3.5 3 -2.5 -2.5 -2.5 -3.0 4 -2.5 -2.5 -2.5 -2.5 5 -5.5 -5.0 -4.5 0.0 TB: 0 1 1 8 8 1 8 8 1 8 2 9 8 8 8 3 1 1 8 8 4 8 8 8 8 5 8 8 8 8 SS_LG_BSL: 0 1 2 3 SB: 0 1.0 2.0 0.0 0.0 1 0.0 0.0 1.0 0.0 2 0.0 0.0 0.0 0.0 3 1.0 1.0 0.0 0.0 4 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 EB: 0 -0.5 -2.5 -2.5 -6.5 1 -2.0 -1.5 -2.5 -6.0 2 -2.5 -2.5 -2.5 -5.5 3 -1.5 -2.5 -2.5 -5.0 4 -2.5 -2.5 -2.5 -4.5 5 -3.5 -3.0 -2.5 0.0 FB: 0 -2.5 -2.5 -1.5 -4.5 1 -2.0 -2.0 -2.5 -4.0 2 -1.5 -1.5 -2.5 -3.5 3 -2.5 -2.5 -2.5 -3.0 4 -2.5 -2.5 -2.5 -2.5 5 -5.5 -5.0 -4.5 0.0 TB: 0 1 1 8 8 1 8 8 1 8 2 9 8 8 8 3 1 1 8 8 4 8 8 8 8 5 8 8 8 8 TEST16: SS_LG_FSQ - forward score quadratic SS_LG_FPQ - forward path quadratic GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Compare results with Myers/Miller calculation Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C Matching Scores: 0 1 2 3 0 0.0 0.0 0.0 0.0 1 0.0 1.0 1.0 -1.0 2 0.0 -1.0 -1.0 1.0 3 0.0 -1.0 -1.0 -1.0 4 0.0 1.0 1.0 -1.0 5 0.0 -1.0 -1.0 -1.0 SS_LG_FSQ: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 1.0 1.0 0.0 2 0.0 0.0 0.0 2.0 3 0.0 0.0 0.0 0.0 4 0.0 1.0 1.0 0.0 5 0.0 0.0 0.0 0.0 SS_LG_FSQ reports optimal matching score is 2.00000 Matching path: 1 0 1 2 1 2 3 2 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 A = A 2 1.00 1.00 2 G = G 3 1.00 2.00 TEST17: SS_LG_RPL - forward path linear GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Compare with FPQ results. Compare results with Myers/Miller calculation Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C SS_LG_CORNERS: (I1,J1) = 0 1 (I2,J2) = 2 3 Matching path: 1 0 1 2 1 2 3 2 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 A = A 2 1.00 1.00 2 G = G 3 1.00 2.00 TEST18: SS_LG_RPL - forward path linear GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. We simply switched the two sequences. Compare with unswitched results. Sequences A and B: 1 A A 2 A G 3 G T 4 A 5 C SS_LG_CORNERS: (I1,J1) = 1 0 (I2,J2) = 3 2 Matching path: 1 1 0 2 2 1 3 3 2 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 2 A = A 1 1.00 1.00 3 G = G 2 1.00 2.00 TEST19: SS_LG_BSQ - backward score quadratic SS_LG_BPQ - backward path quadratic GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Compare path and score with FSQ/FPQ computation. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C SS_LG_BSQ reports optimal matching score is 2.00000 Matching path: 1 0 1 2 1 2 3 2 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 A = A 2 1.00 1.00 2 G = G 3 1.00 2.00 TEST20: SS_LG_FSQ - Forward score quadratic; SS_LG_FPQ - Forward path quadratic; SS_LG_RPL - Recursive path linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Compare the score computed by FSQ/FPQ with the score associated with the path determined by RPL. If the scores don't match, the paths differ, and presumably, the RPL algorithm has failed. The test is carried out by comparing a fixed sequence with many "mutated" variations. Sample test number 10 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G = G 4 5.00 23.00 5 A = A 5 3.00 26.00 6 T | -2.50 23.50 7 A = A 6 3.00 26.50 8 T = T 7 4.00 30.50 9 A = A 8 3.00 33.50 10 G = G 9 5.00 38.50 11 C = C 10 9.00 47.50 12 T = T 11 4.00 51.50 Sample test number 20 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G = G 4 5.00 23.00 5 A - G 5 1.00 24.00 6 T = T 6 4.00 28.00 7 A = A 7 3.00 31.00 8 T = T 8 4.00 35.00 9 A = A 9 3.00 38.00 10 G = G 10 5.00 43.00 11 C = C 11 9.00 52.00 12 T = T 12 4.00 56.00 Sample test number 30 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G | -2.50 15.50 5 A = A 4 3.00 18.50 6 T = T 5 4.00 22.50 7 A = A 6 3.00 25.50 8 T | -2.50 23.00 9 A - G 7 1.00 24.00 10 G = G 8 5.00 29.00 11 C | -2.50 26.50 12 T = T 9 4.00 30.50 Sample test number 40 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G = G 4 5.00 23.00 5 A = A 5 3.00 26.00 6 T = T 6 4.00 30.00 7 A = A 7 3.00 33.00 8 T = T 8 4.00 37.00 9 A = A 9 3.00 40.00 10 G = G 10 5.00 45.00 11 C = C 11 9.00 54.00 12 T = T 12 4.00 58.00 Sample test number 50 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G = G 4 5.00 23.00 5 A = A 5 3.00 26.00 6 T = T 6 4.00 30.00 7 A = A 7 3.00 33.00 8 T = T 8 4.00 37.00 9 A = A 9 3.00 40.00 Sample test number 60 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 4 5.00 5.00 2 C = C 5 9.00 14.00 3 T = T 6 4.00 18.00 4 G = G 7 5.00 23.00 5 A = A 8 3.00 26.00 6 T = T 9 4.00 30.00 7 A = A 10 3.00 33.00 8 T = T 11 4.00 37.00 9 A - N 12 0.00 37.00 10 G = G 13 5.00 42.00 11 C = C 14 9.00 51.00 12 T = T 15 4.00 55.00 Sample test number 70 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G = G 4 5.00 23.00 5 A | -2.50 20.50 6 T | -0.50 20.00 7 A | -0.50 19.50 8 T | -0.50 19.00 9 A = A 5 3.00 22.00 10 G = G 6 5.00 27.00 11 C = C 7 9.00 36.00 12 T = T 8 4.00 40.00 Sample test number 80 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 | B 2 -2.50 2.50 2 C = C 3 9.00 11.50 3 T = T 4 4.00 15.50 | C 5 -2.50 13.00 4 G = G 6 5.00 18.00 5 A = A 7 3.00 21.00 6 T = T 8 4.00 25.00 7 A = A 9 3.00 28.00 8 T = T 10 4.00 32.00 9 A = A 11 3.00 35.00 10 G = G 12 5.00 40.00 11 C = C 13 9.00 49.00 12 T = T 14 4.00 53.00 Sample test number 90 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 4 G = G 1 5.00 5.00 5 A | -2.50 2.50 6 T | -0.50 2.00 7 A | -0.50 1.50 8 T | -0.50 1.00 9 A = A 2 3.00 4.00 10 G = G 3 5.00 9.00 11 C = C 4 9.00 18.00 12 T = T 5 4.00 22.00 Sample test number 100 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G = G 4 5.00 23.00 5 A = A 5 3.00 26.00 6 T = T 6 4.00 30.00 7 A = A 7 3.00 33.00 8 T = T 8 4.00 37.00 9 A = A 9 3.00 40.00 Number of score agreements = 100 Number of score disagreements = 0 TEST21: SS_LG_FSQ - Forward score quadratic; SS_LG_FPQ - Forward path quadratic. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. The second sequence is much shorter than the first. SS_LG_FSQ reports optimal matching score is 38.5000 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 27 S - T 3 2.00 2.00 28 G = G 4 5.00 7.00 29 A | -2.50 4.50 30 Y | -0.50 4.00 31 P = P 5 6.00 10.00 32 A = A 6 3.00 13.00 33 V = V 7 5.00 18.00 34 C | -2.50 15.50 35 R | -0.50 15.00 | L 8 -2.50 12.50 | G 9 -0.50 12.00 36 V = V 10 5.00 17.00 37 K = K 11 5.00 22.00 38 I = I 12 6.00 28.00 39 P = P 13 6.00 34.00 40 A = A 14 3.00 37.00 41 A - G 15 1.00 38.00 | T 16 -2.50 35.50 42 L - M 17 3.00 38.50 TEST22: SS_LG_RPL - path routine; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. The second sequence is much shorter than the first. Compare with FSQ/FPQ calculation. SS_LG_CORNERS: (I1,J1) = 26 2 (I2,J2) = 42 17 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 27 S - T 3 2.00 2.00 28 G = G 4 5.00 7.00 29 A | -2.50 4.50 30 Y | -0.50 4.00 31 P = P 5 6.00 10.00 32 A = A 6 3.00 13.00 33 V = V 7 5.00 18.00 34 C | -2.50 15.50 35 R | -0.50 15.00 | L 8 -2.50 12.50 | G 9 -0.50 12.00 36 V = V 10 5.00 17.00 37 K = K 11 5.00 22.00 38 I = I 12 6.00 28.00 39 P = P 13 6.00 34.00 40 A = A 14 3.00 37.00 41 A - G 15 1.00 38.00 | T 16 -2.50 35.50 42 L - M 17 3.00 38.50 TEST23: SS_LG_RPL - path routine; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Switch the sequences of the last example. The first sequence is much shorter than the second. Compare with previous and FSQ/FPQ calculations. SS_LG_CORNERS: (I1,J1) = 2 26 (I2,J2) = 17 42 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 3 T - S 27 2.00 2.00 4 G = G 28 5.00 7.00 | A 29 -2.50 4.50 | Y 30 -0.50 4.00 5 P = P 31 6.00 10.00 6 A = A 32 3.00 13.00 7 V = V 33 5.00 18.00 8 L | -2.50 15.50 9 G | -0.50 15.00 | C 34 -2.50 12.50 | R 35 -0.50 12.00 10 V = V 36 5.00 17.00 11 K = K 37 5.00 22.00 12 I = I 38 6.00 28.00 13 P = P 39 6.00 34.00 14 A = A 40 3.00 37.00 15 G | -2.50 34.50 16 T - A 41 1.00 35.50 17 M - L 42 3.00 38.50 ss_lg_align_test(): Normal end of execution. April 2 2023 12:26:11.923 PM