April 3 2023 8:06:51.607 AM 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 = 810292943 Test Quadratic Linear 1 42.5000 42.5000 2 54.5000 54.5000 3 48.0000 48.0000 4 53.0000 53.0000 5 48.0000 48.0000 6 26.5000 26.5000 7 5.50000 5.50000 8 54.5000 54.5000 9 34.5000 34.5000 10 50.5000 50.5000 Details for sample test number 10 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G | -2.50 -2.50 2 C = C 2 9.00 6.50 3 T = T 3 4.00 10.50 4 G = G 4 5.00 15.50 5 A = A 5 3.00 18.50 6 T = T 6 4.00 22.50 7 A = A 7 3.00 25.50 8 T = T 8 4.00 29.50 9 A = A 9 3.00 32.50 10 G = G 10 5.00 37.50 11 C = C 11 9.00 46.50 12 T = T 12 4.00 50.50 11 39.0000 39.0000 12 51.0000 51.0000 13 35.0000 35.0000 14 54.5000 54.5000 15 55.0000 55.0000 16 45.0000 45.0000 17 42.5000 42.5000 18 41.0000 41.0000 19 58.0000 58.0000 20 54.5000 54.5000 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 = 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 | S 11 -2.50 42.50 | C 12 -0.50 42.00 | X 13 -0.50 41.50 11 C = C 14 9.00 50.50 12 T = T 15 4.00 54.50 21 50.0000 50.0000 22 55.5000 55.5000 23 50.5000 50.5000 24 55.5000 55.5000 25 42.0000 42.0000 26 51.0000 51.0000 27 27.0000 27.0000 28 52.5000 52.5000 29 55.0000 55.0000 30 46.0000 46.0000 Details for 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 | X 4 -2.50 15.50 | E 5 -0.50 15.00 4 G = G 6 5.00 20.00 5 A - I 7 -1.00 19.00 6 T = T 8 4.00 23.00 7 A = A 9 3.00 26.00 8 T = T 10 4.00 30.00 9 A = A 11 3.00 33.00 10 G - N 12 0.00 33.00 11 C = C 13 9.00 42.00 12 T = T 14 4.00 46.00 31 49.5000 49.5000 32 50.5000 50.5000 33 48.5000 48.5000 34 49.0000 49.0000 35 54.5000 54.5000 36 45.0000 45.0000 37 36.0000 36.0000 38 37.0000 37.0000 39 31.5000 31.5000 40 35.0000 35.0000 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 | -2.50 23.50 | W 6 -2.50 21.00 7 A = A 7 3.00 24.00 8 T = T 8 4.00 28.00 9 A = A 9 3.00 31.00 10 G = G 10 5.00 36.00 11 C | -2.50 33.50 | M 11 -2.50 31.00 12 T = T 12 4.00 35.00 41 52.0000 52.0000 42 53.0000 53.0000 43 7.00000 7.00000 44 56.0000 56.0000 45 52.5000 52.5000 46 43.5000 43.5000 47 43.5000 43.5000 48 33.0000 33.0000 49 39.0000 39.0000 50 24.5000 24.5000 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 | -2.50 20.50 6 T = T 5 4.00 24.50 51 27.5000 27.5000 52 30.5000 30.5000 53 46.5000 46.5000 54 48.0000 48.0000 55 53.0000 53.0000 56 52.5000 52.5000 57 34.0000 34.0000 58 54.5000 54.5000 59 39.0000 39.0000 60 55.0000 55.0000 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 = G 4 5.00 23.00 5 A = A 5 3.00 26.00 6 T = T 6 4.00 30.00 | L 7 -2.50 27.50 | Y 8 -0.50 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 61 39.0000 39.0000 62 36.0000 36.0000 63 47.5000 47.5000 64 55.0000 55.0000 65 32.0000 32.0000 66 16.5000 16.5000 67 48.0000 48.0000 68 48.0000 48.0000 69 50.5000 50.5000 70 56.0000 56.0000 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 = 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 - T 9 1.00 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 71 17.5000 17.5000 72 44.0000 44.0000 73 24.0000 24.0000 74 52.0000 52.0000 75 55.0000 55.0000 76 31.0000 31.0000 77 49.0000 49.0000 78 40.0000 40.0000 79 42.0000 42.0000 80 43.0000 43.0000 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 = 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 - D 10 -1.00 43.00 81 40.5000 40.5000 82 25.5000 25.5000 83 41.5000 41.5000 84 40.0000 40.0000 85 55.0000 55.0000 86 21.5000 21.5000 87 34.0000 34.0000 88 35.5000 35.5000 89 52.5000 52.5000 90 46.0000 46.0000 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 = 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 = A 5 3.00 21.00 8 T = T 6 4.00 25.00 9 A = A 7 3.00 28.00 10 G = G 8 5.00 33.00 11 C = C 9 9.00 42.00 12 T = T 10 4.00 46.00 91 47.5000 47.5000 92 34.5000 34.5000 93 36.5000 36.5000 94 42.0000 42.0000 95 30.0000 30.0000 96 54.5000 54.5000 97 49.5000 49.5000 98 41.0000 41.0000 99 53.0000 53.0000 100 42.5000 42.5000 Details for 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 - M 4 -4.00 14.00 5 A = A 5 3.00 17.00 6 T = T 6 4.00 21.00 7 A = A 7 3.00 24.00 8 T = T 8 4.00 28.00 9 A = A 9 3.00 31.00 10 G = G 10 5.00 36.00 11 C = C 11 9.00 45.00 | C 12 -2.50 42.50 Number of score agreements = 100 Number of score disagreements = 0 ss_qg_align_test(): Normal end of execution. April 3 2023 8:06:51.614 AM