May 9 2025 9:45:51.095 PM ss_qg_align_test(): FORTRAN90 version Test ss_qg_align(). TEST01: SS_QG_FSQ - Forward score quadratic; SS_QG_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 T 2 C A 3 T G 4 A 5 G 6 T 7 A 8 T 9 A 10 G 11 C 12 T Matching Scores: 0 0.0 0.0 0.0 0.0 1 0.0 -1.0 1.0 5.0 2 0.0 -3.0 -3.0 -5.0 3 0.0 4.0 1.0 -1.0 4 0.0 1.0 3.0 1.0 5 0.0 -1.0 1.0 5.0 6 0.0 4.0 1.0 -1.0 7 0.0 1.0 3.0 1.0 8 0.0 4.0 1.0 -1.0 9 0.0 1.0 3.0 1.0 10 0.0 -1.0 1.0 5.0 11 0.0 -3.0 -3.0 -5.0 12 0.0 4.0 1.0 -1.0 SS_QG_FSQ: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 -1.0 1.0 5.0 2 0.0 -2.5 -1.5 2.5 3 0.0 4.0 1.5 2.0 4 0.0 1.5 7.0 4.5 5 0.0 1.0 4.5 12.0 6 0.0 4.0 4.0 9.5 7 0.0 1.5 7.0 9.0 8 0.0 4.0 4.5 8.5 9 0.0 1.5 7.0 8.0 10 0.0 1.0 4.5 12.0 11 0.0 0.5 4.0 9.5 12 0.0 4.0 3.5 9.0 EF: 0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 -3.0 -1.5 2 -2.0 -2.5 -3.0 -3.5 3 -2.0 -2.5 1.5 1.0 4 -2.0 -2.5 -1.0 4.5 5 -2.0 -2.5 -1.5 2.0 6 -2.0 -2.5 1.5 1.5 7 -2.0 -2.5 -1.0 4.5 8 -2.0 -2.5 1.5 2.0 9 -2.0 -2.5 -1.0 4.5 10 -2.0 -2.5 -1.5 2.0 11 -2.0 -2.5 -2.0 1.5 12 -2.0 -2.5 1.5 1.0 FF: 0 0.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 2 0.0 -3.0 -1.5 2.5 3 0.0 -3.5 -2.0 2.0 4 0.0 1.5 -1.0 1.5 5 0.0 1.0 4.5 2.0 6 0.0 0.5 4.0 9.5 7 0.0 1.5 3.5 9.0 8 0.0 1.0 4.5 8.5 9 0.0 1.5 4.0 8.0 10 0.0 1.0 4.5 7.5 11 0.0 0.5 4.0 9.5 12 0.0 0.0 3.5 9.0 TF: 0 8 8 8 8 1 8 1 1 1 2 8 2 4 4 3 8 1 2 4 4 8 4 1 2 5 8 4 4 1 6 8 1 4 4 7 8 4 1 4 8 8 1 4 4 9 8 4 1 4 10 8 4 4 1 11 8 4 4 4 12 8 1 4 4 SS_QG_FSL: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 -1.0 1.0 5.0 2 0.0 -2.5 -1.5 2.5 3 0.0 4.0 1.5 2.0 4 0.0 1.5 7.0 4.5 5 0.0 1.0 4.5 12.0 6 0.0 4.0 4.0 9.5 7 0.0 1.5 7.0 9.0 8 0.0 4.0 4.5 8.5 9 0.0 1.5 7.0 8.0 10 0.0 1.0 4.5 12.0 11 0.0 0.5 4.0 9.5 12 0.0 4.0 3.5 9.0 EF: 0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 -3.0 -1.5 2 -2.0 -2.5 -3.0 -3.5 3 -2.0 -2.5 1.5 1.0 4 -2.0 -2.5 -1.0 4.5 5 -2.0 -2.5 -1.5 2.0 6 -2.0 -2.5 1.5 1.5 7 -2.0 -2.5 -1.0 4.5 8 -2.0 -2.5 1.5 2.0 9 -2.0 -2.5 -1.0 4.5 10 -2.0 -2.5 -1.5 2.0 11 -2.0 -2.5 -2.0 1.5 12 -2.0 -2.5 1.5 1.0 FF: 0 0.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 2 0.0 -3.0 -1.5 2.5 3 0.0 -3.5 -2.0 2.0 4 0.0 1.5 -1.0 1.5 5 0.0 1.0 4.5 2.0 6 0.0 0.5 4.0 9.5 7 0.0 1.5 3.5 9.0 8 0.0 1.0 4.5 8.5 9 0.0 1.5 4.0 8.0 10 0.0 1.0 4.5 7.5 11 0.0 0.5 4.0 9.5 12 0.0 0.0 3.5 9.0 TF: 0 8 8 8 8 1 8 1 1 1 2 8 2 4 4 3 8 1 2 4 4 8 4 1 2 5 8 4 4 1 6 8 1 4 4 7 8 4 1 4 8 8 1 4 4 9 8 4 1 4 10 8 4 4 1 11 8 4 4 4 12 8 1 4 4 TEST02: SS_QG_BSQ - Backward score quadratic; SS_QG_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 T 2 C A 3 T G 4 A 5 G 6 T 7 A 8 T 9 A 10 G 11 C 12 T SS_QG_BSQ: 0 1 2 3 SB: 0 9.0 4.5 5.0 0.0 1 9.5 5.0 1.5 0.0 2 12.0 5.5 2.0 0.0 3 8.0 8.0 2.5 0.0 4 8.5 4.0 5.0 0.0 5 9.0 4.5 1.0 0.0 6 9.5 5.0 1.5 0.0 7 12.0 5.5 2.0 0.0 8 5.5 8.0 2.5 0.0 9 2.0 2.5 5.0 0.0 10 1.5 -1.5 -2.5 0.0 11 4.0 1.0 -1.0 0.0 12 0.0 0.0 0.0 0.0 EB: 0 2.0 2.5 -2.5 -2.0 1 2.5 -1.0 -2.5 -2.0 2 3.0 -0.5 -2.5 -2.0 3 5.5 0.0 -2.5 -2.0 4 2.0 2.5 -2.5 -2.0 5 2.0 -1.5 -2.5 -2.0 6 2.5 -1.0 -2.5 -2.0 7 3.0 -0.5 -2.5 -2.0 8 5.5 0.0 -2.5 -2.0 9 2.0 2.5 -2.5 -2.0 10 -3.5 -3.0 -2.5 -2.0 11 -1.5 -3.0 -2.5 -2.0 12 0.0 0.0 0.0 0.0 FB: 0 9.0 4.5 1.0 0.0 1 9.5 5.0 1.5 0.0 2 7.5 5.5 2.0 0.0 3 8.0 3.5 2.5 0.0 4 8.5 4.0 0.5 0.0 5 9.0 4.5 1.0 0.0 6 9.5 5.0 1.5 0.0 7 3.0 5.5 2.0 0.0 8 0.5 0.0 2.5 0.0 9 1.0 -2.0 -3.5 0.0 10 1.5 -1.5 -3.0 0.0 11 -2.5 -2.5 -2.5 0.0 12 -2.0 -2.0 -2.0 0.0 TB: 0 4 4 1 8 1 4 4 4 8 2 1 4 4 8 3 4 1 4 8 4 4 4 1 8 5 5 4 4 8 6 4 5 4 8 7 1 4 4 8 8 2 1 4 8 9 2 2 1 8 10 4 4 2 8 11 1 1 1 8 12 8 8 8 8 SS_QG_BSL: 0 1 2 3 SB: 0 9.0 4.5 5.0 0.0 1 9.5 5.0 1.5 0.0 2 12.0 5.5 2.0 0.0 3 8.0 8.0 2.5 0.0 4 8.5 4.0 5.0 0.0 5 9.0 4.5 1.0 0.0 6 9.5 5.0 1.5 0.0 7 12.0 5.5 2.0 0.0 8 5.5 8.0 2.5 0.0 9 2.0 2.5 5.0 0.0 10 1.5 -1.5 -2.5 0.0 11 4.0 1.0 -1.0 0.0 12 0.0 0.0 0.0 0.0 EB: 0 2.0 2.5 -2.5 -2.0 1 2.5 -1.0 -2.5 -2.0 2 3.0 -0.5 -2.5 -2.0 3 5.5 0.0 -2.5 -2.0 4 2.0 2.5 -2.5 -2.0 5 2.0 -1.5 -2.5 -2.0 6 2.5 -1.0 -2.5 -2.0 7 3.0 -0.5 -2.5 -2.0 8 5.5 0.0 -2.5 -2.0 9 2.0 2.5 -2.5 -2.0 10 -3.5 -3.0 -2.5 -2.0 11 -1.5 -3.0 -2.5 -2.0 12 0.0 0.0 0.0 0.0 FB: 0 9.0 4.5 1.0 0.0 1 9.5 5.0 1.5 0.0 2 7.5 5.5 2.0 0.0 3 8.0 3.5 2.5 0.0 4 8.5 4.0 0.5 0.0 5 9.0 4.5 1.0 0.0 6 9.5 5.0 1.5 0.0 7 3.0 5.5 2.0 0.0 8 0.5 0.0 2.5 0.0 9 1.0 -2.0 -3.5 0.0 10 1.5 -1.5 -3.0 0.0 11 -2.5 -2.5 -2.5 0.0 12 -2.0 -2.0 -2.0 0.0 TB: 0 4 4 1 8 1 4 4 4 8 2 1 4 4 8 3 4 1 4 8 4 4 4 1 8 5 5 4 4 8 6 4 5 4 8 7 1 4 4 8 8 2 1 4 8 9 2 2 1 8 10 4 4 2 8 11 1 1 1 8 12 8 8 8 8 TEST03: SS_QG_FSQ - Forward score quadratic; SS_QG_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 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_QG_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 0.0 0.0 0.0 0.0 1 -2.0 -2.5 2.5 2.5 2.5 2 -2.0 -2.5 0.0 0.0 0.0 3 -2.0 -2.5 -0.5 -0.5 -0.5 FF: 0 0.0 -2.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 -2.5 2 0.0 2.5 2.5 2.5 0.0 3 0.0 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_QG_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 0.0 0.0 0.0 0.0 1 -2.0 -2.5 2.5 2.5 2.5 2 -2.0 -2.5 0.0 0.0 0.0 3 -2.0 -2.5 -0.5 -0.5 -0.5 FF: 0 0.0 -2.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 -2.5 2 0.0 2.5 2.5 2.5 0.0 3 0.0 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_QG_BSQ - Backward score quadratic; SS_QG_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_QG_BSQ: 0 1 2 3 4 SB: 0 3.5 4.0 6.5 1.0 0.0 1 -2.0 -1.5 -1.0 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 -2.0 1 -2.0 -1.5 -1.0 -2.5 -2.0 2 0.5 1.0 1.5 -2.5 -2.0 3 0.0 0.0 0.0 0.0 0.0 FB: 0 -2.5 -2.0 -1.5 1.0 0.0 1 -2.0 -1.5 -1.0 1.5 0.0 2 -2.5 -2.5 -2.5 -2.5 0.0 3 -2.0 -2.0 -2.0 -2.0 0.0 TB: 0 3 3 1 4 8 1 6 6 7 4 8 2 2 2 2 1 8 3 8 8 8 8 8 SS_QG_BSL: 0 1 2 3 4 SB: 0 3.5 4.0 6.5 1.0 0.0 1 -2.0 -1.5 -1.0 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 -2.0 1 -2.0 -1.5 -1.0 -2.5 -2.0 2 0.5 1.0 1.5 -2.5 -2.0 3 0.0 0.0 0.0 0.0 0.0 FB: 0 -2.5 -2.0 -1.5 1.0 0.0 1 -2.0 -1.5 -1.0 1.5 0.0 2 -2.5 -2.5 -2.5 -2.5 0.0 3 -2.0 -2.0 -2.0 -2.0 0.0 TB: 0 3 3 1 4 8 1 6 6 7 4 8 2 2 2 2 1 8 3 8 8 8 8 8 TEST05: SS_QG_BSQ - Backward score quadratic; SS_QG_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_QG_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 0.0 0.0 0.0 0.0 1 -2.0 -2.5 2.5 2.5 2.5 2 -2.0 -2.5 0.0 0.0 0.0 3 -2.0 -2.5 -0.5 -0.5 -0.5 FF: 0 0.0 -2.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 -2.5 2 0.0 2.5 2.5 2.5 0.0 3 0.0 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_QG_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 0.0 0.0 0.0 0.0 2 -2.0 -2.5 2.5 2.5 2.5 1 -2.0 -2.5 0.0 0.0 0.0 0 -2.0 -2.5 -0.5 -0.5 -0.5 FB: 3 0.0 -2.0 -2.0 -2.0 -2.0 2 0.0 -2.5 -2.5 -2.5 -2.5 1 0.0 2.5 2.5 2.5 0.0 0 0.0 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 TEST07: SS_QG_FSQ - forward score quadratic SS_QG_FOQ - forward optimal score quadratic SS_QG_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 T 2 C A 3 T G 4 A 5 G 6 T 7 A 8 T 9 A 10 G 11 C 12 T SS_QG_FOQ reports optimal matching score is 12.0000 I2 = 10 J2 = 3 Matching path: 1 7 0 2 8 1 3 9 2 4 10 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 8 T = T 1 4.00 4.00 9 A = A 2 3.00 7.00 10 G = G 3 5.00 12.00 TEST08: SS_QG_BSQ - backward score quadratic SS_QG_BOQ - backward optimal score quadratic SS_QG_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 T 2 C A 3 T G 4 A 5 G 6 T 7 A 8 T 9 A 10 G 11 C 12 T SS_QG_BOQ reports optimal matching score is 12.0000 I1 = 7 J1 = 0 Matching path: 1 7 0 2 8 1 3 9 2 4 10 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 8 T = T 1 4.00 4.00 9 A = A 2 3.00 7.00 10 G = G 3 5.00 12.00 TEST09: SS_QG_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 T 2 C A 3 T G 4 A 5 G 6 T 7 A 8 T 9 A 10 G 11 C 12 T Matching path: 1 2 0 2 3 1 3 4 2 4 5 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 3 T = T 1 4.00 4.00 4 A = A 2 3.00 7.00 5 G = G 3 5.00 12.00 TEST12: SS_QG_FSQ - forward score quadratic; SS_QG_FOQ - forward optimal score quadratic SS_QG_FPQ - Forward path quadratic. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. SS_QG_FOQ reports optimal matching score is 249.500 I2 = 60 J2 = 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 = 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_QG_RPL - path routine; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Compare with FSQ/FPQ calculation. 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_QG_FSQ - forward score quadratic; SS_QG_FOQ - forward optimal score quadratic SS_QG_FSL - Forward score linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. 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 0.0 0.0 0.0 0.0 1 0.0 2.0 2.0 -1.0 2 0.0 -1.0 -1.0 2.0 3 0.0 -1.0 -1.0 -1.0 4 0.0 2.0 2.0 -1.0 5 0.0 -1.0 -1.0 -1.0 SS_QG_FSQ: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 2.0 2.0 -0.5 2 0.0 -0.5 1.0 4.0 3 0.0 -1.0 -1.0 1.5 4 0.0 2.0 1.0 1.0 5 0.0 -0.5 1.0 0.5 EF: 0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 -0.5 -0.5 2 -2.0 -2.5 -3.0 -1.5 3 -2.0 -2.5 -3.0 -3.5 4 -2.0 -2.5 -0.5 -1.0 5 -2.0 -2.5 -3.0 -1.5 FF: 0 0.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 2 0.0 -0.5 -0.5 -3.0 3 0.0 -1.0 -1.0 1.5 4 0.0 -1.5 -1.5 1.0 5 0.0 -0.5 -1.5 0.5 TF: 0 8 8 8 8 1 8 1 1 2 2 8 4 1 1 3 8 5 4 4 4 8 1 1 4 5 8 4 1 4 SS_QG_FSL: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 2.0 2.0 -0.5 2 0.0 -0.5 1.0 4.0 3 0.0 -1.0 -1.0 1.5 4 0.0 2.0 1.0 1.0 5 0.0 -0.5 1.0 0.5 EF: 0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 -0.5 -0.5 2 -2.0 -2.5 -3.0 -1.5 3 -2.0 -2.5 -3.0 -3.5 4 -2.0 -2.5 -0.5 -1.0 5 -2.0 -2.5 -3.0 -1.5 FF: 0 0.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 2 0.0 -0.5 -0.5 -3.0 3 0.0 -1.0 -1.0 1.5 4 0.0 -1.5 -1.5 1.0 5 0.0 -0.5 -1.5 0.5 TF: 0 8 8 8 8 1 8 1 1 2 2 8 4 1 1 3 8 5 4 4 4 8 1 1 4 5 8 4 1 4 TEST15: SS_QG_BSQ - Backward score quadratic; SS_QG_BSL - Backward score linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Compare BSQ and BSL results. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C SS_QG_BSQ: 0 1 2 3 SF: 0 1.5 4.0 -0.5 0.0 1 -1.0 -0.5 2.0 0.0 2 0.0 -1.5 -1.0 0.0 3 1.0 1.0 -1.0 0.0 4 -1.0 -1.0 -1.0 0.0 5 0.0 0.0 0.0 0.0 EF: 0 1.5 -3.0 -2.5 -2.0 1 -1.0 -0.5 -2.5 -2.0 2 -3.5 -3.0 -2.5 -2.0 3 -1.5 -3.0 -2.5 -2.0 4 -3.5 -3.0 -2.5 -2.0 5 0.0 0.0 0.0 0.0 FF: 0 -2.5 -2.5 -0.5 0.0 1 -2.0 -2.0 -3.5 0.0 2 -1.5 -1.5 -3.5 0.0 3 -3.0 -3.0 -3.0 0.0 4 -2.5 -2.5 -2.5 0.0 5 -2.0 -2.0 -2.0 0.0 TF: 0 3 1 4 8 1 2 2 1 8 2 1 4 1 8 3 1 1 1 8 4 1 1 1 8 5 8 8 8 8 SS_QG_BSL: 0 1 2 3 SF: 0 1.5 4.0 -0.5 0.0 1 -1.0 -0.5 2.0 0.0 2 0.0 -1.5 -1.0 0.0 3 1.0 1.0 -1.0 0.0 4 -1.0 -1.0 -1.0 0.0 5 0.0 0.0 0.0 0.0 EF: 0 1.5 -3.0 -2.5 -2.0 1 -1.0 -0.5 -2.5 -2.0 2 -3.5 -3.0 -2.5 -2.0 3 -1.5 -3.0 -2.5 -2.0 4 -3.5 -3.0 -2.5 -2.0 5 0.0 0.0 0.0 0.0 FF: 0 -2.5 -2.5 -0.5 0.0 1 -2.0 -2.0 -3.5 0.0 2 -1.5 -1.5 -3.5 0.0 3 -3.0 -3.0 -3.0 0.0 4 -2.5 -2.5 -2.5 0.0 5 -2.0 -2.0 -2.0 0.0 TF: 0 3 1 4 8 1 2 2 1 8 2 1 4 1 8 3 1 1 1 8 4 1 1 1 8 5 8 8 8 8 TEST16: SS_QG_FSQ - forward score quadratic SS_QG_FOQ - forward optimal score quadratic SS_QG_FPQ - forward path quadratic GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C SS_QG_FSQ: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 2.0 2.0 -0.5 2 0.0 -0.5 1.0 4.0 3 0.0 -1.0 -1.0 1.5 4 0.0 2.0 1.0 1.0 5 0.0 -0.5 1.0 0.5 EF: 0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 -0.5 -0.5 2 -2.0 -2.5 -3.0 -1.5 3 -2.0 -2.5 -3.0 -3.5 4 -2.0 -2.5 -0.5 -1.0 5 -2.0 -2.5 -3.0 -1.5 FF: 0 0.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 2 0.0 -0.5 -0.5 -3.0 3 0.0 -1.0 -1.0 1.5 4 0.0 -1.5 -1.5 1.0 5 0.0 -0.5 -1.5 0.5 TF: 0 8 8 8 8 1 8 1 1 2 2 8 4 1 1 3 8 5 4 4 4 8 1 1 4 5 8 4 1 4 SS_QG_FOQ reports optimal matching score is 4.00000 I2 = 2 J2 = 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 2.00 2.00 2 G = G 3 2.00 4.00 TEST165: SS_QG_BSQ - backward score quadratic SS_QG_BOQ - backward optimal score quadratic SS_QG_BPQ - backward path quadratic GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C SS_QG_BSQ: 0 1 2 3 SB: 0 1.5 4.0 -0.5 0.0 1 -1.0 -0.5 2.0 0.0 2 0.0 -1.5 -1.0 0.0 3 1.0 1.0 -1.0 0.0 4 -1.0 -1.0 -1.0 0.0 5 0.0 0.0 0.0 0.0 EB: 0 1.5 -3.0 -2.5 -2.0 1 -1.0 -0.5 -2.5 -2.0 2 -3.5 -3.0 -2.5 -2.0 3 -1.5 -3.0 -2.5 -2.0 4 -3.5 -3.0 -2.5 -2.0 5 0.0 0.0 0.0 0.0 FB: 0 -2.5 -2.5 -0.5 0.0 1 -2.0 -2.0 -3.5 0.0 2 -1.5 -1.5 -3.5 0.0 3 -3.0 -3.0 -3.0 0.0 4 -2.5 -2.5 -2.5 0.0 5 -2.0 -2.0 -2.0 0.0 TB: 0 3 1 4 8 1 2 2 1 8 2 1 4 1 8 3 1 1 1 8 4 1 1 1 8 5 8 8 8 8 SS_QG_BOQ reports optimal matching score is 4.00000 I1 = 0 J1 = 1 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 2.00 2.00 2 G = G 3 2.00 4.00 TEST17: SS_QG_RPL - recursive path linear GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Compare with FPQ results. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C 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 2.00 2.00 2 G = G 3 2.00 4.00 TEST18: SS_QG_RPL - recursive 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 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 2.00 2.00 3 G = G 2 2.00 4.00 TEST20: SS_QG_FSQ - forward score quadratic; SS_QG_FOQ - forward optimal score quadratic SS_QG_FPQ - forward path quadratic; SS_QG_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. Using a random number seed of ISEED = 1169506082 Test Quadratic Linear 1 27.5000 27.5000 2 54.0000 54.0000 3 48.0000 48.0000 4 55.0000 55.0000 5 47.5000 47.5000 6 49.0000 49.0000 7 26.0000 26.0000 8 49.0000 49.0000 9 36.0000 36.0000 10 55.0000 55.0000 Details for 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 | D 4 -2.50 15.50 | Y 5 -0.50 15.00 4 G = G 6 5.00 20.00 5 A = A 7 3.00 23.00 6 T = T 8 4.00 27.00 7 A = A 9 3.00 30.00 8 T = T 10 4.00 34.00 9 A = A 11 3.00 37.00 10 G = G 12 5.00 42.00 11 C = C 13 9.00 51.00 12 T = T 14 4.00 55.00 11 53.0000 53.0000 12 53.0000 53.0000 13 14.0000 14.0000 14 51.0000 51.0000 15 47.5000 47.5000 16 55.0000 55.0000 17 45.5000 45.5000 18 42.5000 42.5000 19 52.5000 52.5000 20 48.0000 48.0000 Details for 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 | -2.50 20.50 6 T | -0.50 20.00 7 A = A 5 3.00 23.00 8 T = T 6 4.00 27.00 9 A = A 7 3.00 30.00 10 G = G 8 5.00 35.00 11 C = C 9 9.00 44.00 12 T = T 10 4.00 48.00 21 51.0000 51.0000 22 33.0000 33.0000 23 32.0000 32.0000 24 40.0000 40.0000 25 46.0000 46.0000 26 41.5000 41.5000 27 34.0000 34.0000 28 41.5000 41.5000 29 30.5000 30.5000 30 40.0000 40.0000 Details for sample test number 30 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 3 5.00 5.00 2 C = C 4 9.00 14.00 3 T | -2.50 11.50 4 G | -0.50 11.00 5 A = A 5 3.00 14.00 6 T = T 6 4.00 18.00 7 A = A 7 3.00 21.00 8 T = T 8 4.00 25.00 9 A = A 9 3.00 28.00 10 G - T 10 -1.00 27.00 11 C = C 11 9.00 36.00 12 T = T 12 4.00 40.00 31 34.5000 34.5000 32 35.0000 35.0000 33 55.0000 55.0000 34 26.0000 26.0000 35 53.0000 53.0000 36 46.5000 46.5000 37 49.0000 49.0000 38 53.0000 53.0000 39 43.0000 43.0000 40 43.0000 43.0000 Details for 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 | -2.50 37.50 | Y 10 -2.50 35.00 11 C = C 11 9.00 44.00 12 T - P 12 -1.00 43.00 41 51.0000 51.0000 42 58.0000 58.0000 43 55.0000 55.0000 44 18.5000 18.5000 45 58.0000 58.0000 46 40.0000 40.0000 47 55.5000 55.5000 48 31.0000 31.0000 49 34.5000 34.5000 50 47.5000 47.5000 Details for 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 | -2.50 34.50 10 G = G 9 5.00 39.50 11 C = C 10 9.00 48.50 12 T - D 11 -1.00 47.50 51 39.0000 39.0000 52 31.5000 31.5000 53 38.0000 38.0000 54 42.5000 42.5000 55 58.0000 58.0000 56 34.0000 34.0000 57 50.5000 50.5000 58 19.0000 19.0000 59 38.0000 38.0000 60 44.5000 44.5000 Details for sample test number 60 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 - T 6 1.00 23.50 8 T = T 7 4.00 27.50 9 A = A 8 3.00 30.50 10 G = G 9 5.00 35.50 | H 10 -2.50 33.00 | P 11 -0.50 32.50 | M 12 -0.50 32.00 | N 13 -0.50 31.50 11 C = C 14 9.00 40.50 12 T = T 15 4.00 44.50 61 40.0000 40.0000 62 35.0000 35.0000 63 34.5000 34.5000 64 48.0000 48.0000 65 42.0000 42.0000 66 42.5000 42.5000 67 47.0000 47.0000 68 32.0000 32.0000 69 49.0000 49.0000 70 44.0000 44.0000 Details for 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 - K 4 -3.00 15.00 5 A - B 5 0.00 15.00 6 T = T 6 4.00 19.00 7 A = A 7 3.00 22.00 8 T = T 8 4.00 26.00 9 A = A 9 3.00 29.00 10 G = G 10 5.00 34.00 | E 11 -2.50 31.50 | A 12 -0.50 31.00 11 C = C 13 9.00 40.00 12 T = T 14 4.00 44.00 71 37.0000 37.0000 72 47.0000 47.0000 73 47.0000 47.0000 74 34.5000 34.5000 75 44.5000 44.5000 76 58.0000 58.0000 77 41.0000 41.0000 78 55.0000 55.0000 79 53.0000 53.0000 80 41.5000 41.5000 Details for sample test number 80 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 | -2.50 11.50 4 G | -0.50 11.00 5 A = A 3 3.00 14.00 6 T = T 4 4.00 18.00 7 A - G 5 1.00 19.00 | F 6 -2.50 16.50 8 T = T 7 4.00 20.50 9 A = A 8 3.00 23.50 10 G = G 9 5.00 28.50 11 C = C 10 9.00 37.50 12 T = T 11 4.00 41.50 81 50.5000 50.5000 82 38.0000 38.0000 83 39.0000 39.0000 84 51.0000 51.0000 85 49.0000 49.0000 86 55.0000 55.0000 87 37.0000 37.0000 88 37.5000 37.5000 89 33.0000 33.0000 90 40.0000 40.0000 Details for sample test number 90 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C | -2.50 2.50 | L 2 -2.50 0.00 3 T = T 3 4.00 4.00 4 G = G 4 5.00 9.00 5 A = A 5 3.00 12.00 6 T = T 6 4.00 16.00 7 A = A 7 3.00 19.00 8 T = T 8 4.00 23.00 9 A - Q 9 -1.00 22.00 10 G = G 10 5.00 27.00 11 C = C 11 9.00 36.00 12 T = T 12 4.00 40.00 91 30.0000 30.0000 92 30.5000 30.5000 93 42.5000 42.5000 94 27.5000 27.5000 95 47.0000 47.0000 96 42.5000 42.5000 97 52.5000 52.5000 98 48.0000 48.0000 99 31.5000 31.5000 100 46.5000 46.5000 Details for sample test number 100 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 2 5.00 5.00 2 C | -2.50 2.50 3 T = T 3 4.00 6.50 4 G = G 4 5.00 11.50 5 A = A 5 3.00 14.50 6 T = T 6 4.00 18.50 7 A = A 7 3.00 21.50 8 T = T 8 4.00 25.50 9 A = A 9 3.00 28.50 10 G = G 10 5.00 33.50 11 C = C 11 9.00 42.50 12 T = T 12 4.00 46.50 Number of score agreements = 100 Number of score disagreements = 0 ss_qg_align_test(): Normal end of execution. May 9 2025 9:45:51.101 PM