March 28 2023 6:56:04.118 PM ss_gd_align_test(): FORTRAN90 version Test SS_GD_ALIGN(). TEST01: Sequence-Sequence Global Distance Forward/backward score Quadratic/Linear alignment routines: SS_GD_FSQ - Forward quadratic; SS_GD_FSL - Forward linear; SS_GD_BSQ - Backward quadratic; SS_GD_BSL - Backward linear. Gap extend penalty = -0.500000 Sequences A and B: 1 G G 2 C G 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 TEST01 Scoring Matrix: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 1 -1.0 0.0 0.0 0.0 -1.0 0.0 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 -1.0 2 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 3 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 -1.0 0.0 0.0 -1.0 -1.0 -1.0 0.0 4 -1.0 0.0 0.0 0.0 -1.0 0.0 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 -1.0 5 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 -1.0 0.0 -1.0 -1.0 -1.0 6 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 -1.0 0.0 0.0 -1.0 -1.0 -1.0 0.0 7 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 -1.0 0.0 -1.0 -1.0 -1.0 8 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 -1.0 0.0 0.0 -1.0 -1.0 -1.0 0.0 9 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 -1.0 0.0 -1.0 -1.0 -1.0 10 -1.0 0.0 0.0 0.0 -1.0 0.0 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 -1.0 11 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 12 -1.0 -1.0 -1.0 -1.0 0.0 -1.0 -1.0 0.0 0.0 -1.0 -1.0 -1.0 0.0 SS_GD_FSQ: 0 1 2 3 4 5 6 7 8 9 10 11 12 SF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 2 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -4.5 -5.0 3 -1.5 -1.0 -1.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -4.5 4 -2.0 -1.5 -1.0 -1.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 5 -2.5 -2.0 -1.5 -2.0 -2.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 6 -3.0 -2.5 -2.0 -2.5 -2.0 -2.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 7 -3.5 -3.0 -2.5 -3.0 -2.5 -3.0 -2.5 -2.0 -2.5 -2.0 -2.5 -3.0 -3.5 8 -4.0 -3.5 -3.0 -3.5 -3.0 -3.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 -3.0 9 -4.5 -4.0 -3.5 -4.0 -3.5 -4.0 -3.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 10 -5.0 -4.5 -4.0 -3.5 -4.0 -3.5 -4.0 -3.5 -3.0 -2.5 -2.0 -2.5 -3.0 11 -5.5 -5.0 -4.5 -4.0 -4.5 -4.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -2.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -4.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 EF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 2 -1.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -5.0 3 -1.5 -2.0 -1.5 -2.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 4 -2.0 -2.5 -2.0 -1.5 -2.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 5 -2.5 -3.0 -2.5 -2.0 -2.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 6 -3.0 -3.5 -3.0 -2.5 -3.0 -2.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 7 -3.5 -4.0 -3.5 -3.0 -3.5 -3.0 -3.5 -3.0 -2.5 -3.0 -2.5 -3.0 -3.5 8 -4.0 -4.5 -4.0 -3.5 -4.0 -3.5 -4.0 -3.5 -3.0 -2.5 -3.0 -3.5 -4.0 9 -4.5 -5.0 -4.5 -4.0 -4.5 -4.0 -4.5 -4.0 -3.5 -3.0 -2.5 -3.0 -3.5 10 -5.0 -5.5 -5.0 -4.5 -4.0 -4.5 -4.0 -4.5 -4.0 -3.5 -3.0 -2.5 -3.0 11 -5.5 -6.0 -5.5 -5.0 -4.5 -5.0 -4.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 12 -6.0 -6.5 -6.0 -5.5 -5.0 -4.5 -5.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 FF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 -6.5 2 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 3 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -5.0 -5.5 4 -2.0 -1.5 -2.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -5.0 5 -2.5 -2.0 -1.5 -2.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 6 -3.0 -2.5 -2.0 -2.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 7 -3.5 -3.0 -2.5 -3.0 -2.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 8 -4.0 -3.5 -3.0 -3.5 -3.0 -3.5 -3.0 -2.5 -3.0 -2.5 -3.0 -3.5 -4.0 9 -4.5 -4.0 -3.5 -4.0 -3.5 -4.0 -3.5 -3.0 -2.5 -3.0 -3.5 -4.0 -3.5 10 -5.0 -4.5 -4.0 -4.5 -4.0 -4.5 -4.0 -3.5 -3.0 -2.5 -3.0 -3.5 -4.0 11 -5.5 -5.0 -4.5 -4.0 -4.5 -4.0 -4.5 -4.0 -3.5 -3.0 -2.5 -3.0 -3.5 12 -6.0 -5.5 -5.0 -4.5 -5.0 -4.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -3.0 TF: 0 0 2 2 2 2 2 2 2 2 2 2 2 2 1 4 1 3 3 2 3 2 2 2 2 3 2 2 2 4 4 7 7 7 7 7 7 7 7 7 1 2 3 4 4 7 7 1 2 2 3 3 2 2 6 1 4 4 5 1 3 6 1 2 2 2 2 3 2 6 5 4 4 4 7 7 4 1 2 2 3 2 2 2 6 4 4 4 7 1 6 4 1 3 2 2 2 3 7 4 4 4 7 4 7 5 4 7 1 2 2 2 8 4 4 4 7 5 7 4 5 1 6 7 7 1 9 4 4 4 7 4 7 5 4 4 1 2 2 6 10 4 5 5 1 6 1 6 4 4 4 1 2 2 11 4 4 4 4 7 4 7 4 4 4 4 1 2 12 4 4 4 4 1 6 7 5 5 4 4 4 1 SS_GD_FSL: 0 1 2 3 4 5 6 7 8 9 10 11 12 SF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 2 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -4.5 -5.0 3 -1.5 -1.0 -1.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -4.5 4 -2.0 -1.5 -1.0 -1.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 5 -2.5 -2.0 -1.5 -2.0 -2.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 6 -3.0 -2.5 -2.0 -2.5 -2.0 -2.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 7 -3.5 -3.0 -2.5 -3.0 -2.5 -3.0 -2.5 -2.0 -2.5 -2.0 -2.5 -3.0 -3.5 8 -4.0 -3.5 -3.0 -3.5 -3.0 -3.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 -3.0 9 -4.5 -4.0 -3.5 -4.0 -3.5 -4.0 -3.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 10 -5.0 -4.5 -4.0 -3.5 -4.0 -3.5 -4.0 -3.5 -3.0 -2.5 -2.0 -2.5 -3.0 11 -5.5 -5.0 -4.5 -4.0 -4.5 -4.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -2.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -4.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 EF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 2 -1.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -5.0 3 -1.5 -2.0 -1.5 -2.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 4 -2.0 -2.5 -2.0 -1.5 -2.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 5 -2.5 -3.0 -2.5 -2.0 -2.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 6 -3.0 -3.5 -3.0 -2.5 -3.0 -2.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 7 -3.5 -4.0 -3.5 -3.0 -3.5 -3.0 -3.5 -3.0 -2.5 -3.0 -2.5 -3.0 -3.5 8 -4.0 -4.5 -4.0 -3.5 -4.0 -3.5 -4.0 -3.5 -3.0 -2.5 -3.0 -3.5 -4.0 9 -4.5 -5.0 -4.5 -4.0 -4.5 -4.0 -4.5 -4.0 -3.5 -3.0 -2.5 -3.0 -3.5 10 -5.0 -5.5 -5.0 -4.5 -4.0 -4.5 -4.0 -4.5 -4.0 -3.5 -3.0 -2.5 -3.0 11 -5.5 -6.0 -5.5 -5.0 -4.5 -5.0 -4.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 12 -6.0 -6.5 -6.0 -5.5 -5.0 -4.5 -5.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 FF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 -6.5 2 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 3 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -5.0 -5.5 4 -2.0 -1.5 -2.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -5.0 5 -2.5 -2.0 -1.5 -2.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 6 -3.0 -2.5 -2.0 -2.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 7 -3.5 -3.0 -2.5 -3.0 -2.5 -3.0 -2.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 8 -4.0 -3.5 -3.0 -3.5 -3.0 -3.5 -3.0 -2.5 -3.0 -2.5 -3.0 -3.5 -4.0 9 -4.5 -4.0 -3.5 -4.0 -3.5 -4.0 -3.5 -3.0 -2.5 -3.0 -3.5 -4.0 -3.5 10 -5.0 -4.5 -4.0 -4.5 -4.0 -4.5 -4.0 -3.5 -3.0 -2.5 -3.0 -3.5 -4.0 11 -5.5 -5.0 -4.5 -4.0 -4.5 -4.0 -4.5 -4.0 -3.5 -3.0 -2.5 -3.0 -3.5 12 -6.0 -5.5 -5.0 -4.5 -5.0 -4.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -3.0 TF: 0 0 2 2 2 2 2 2 2 2 2 2 2 2 1 4 1 3 3 2 3 2 2 2 2 3 2 2 2 4 4 7 7 7 7 7 7 7 7 7 1 2 3 4 4 7 7 1 2 2 3 3 2 2 6 1 4 4 5 1 3 6 1 2 2 2 2 3 2 6 5 4 4 4 7 7 4 1 2 2 3 2 2 2 6 4 4 4 7 1 6 4 1 3 2 2 2 3 7 4 4 4 7 4 7 5 4 7 1 2 2 2 8 4 4 4 7 5 7 4 5 1 6 7 7 1 9 4 4 4 7 4 7 5 4 4 1 2 2 6 10 4 5 5 1 6 1 6 4 4 4 1 2 2 11 4 4 4 4 7 4 7 4 4 4 4 1 2 12 4 4 4 4 1 6 7 5 5 4 4 4 1 SS_GD_BSQ: 0 1 2 3 4 5 6 7 8 9 10 11 12 SB: 0 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 2 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 3 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 4 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 5 -2.5 -2.0 -1.5 -1.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 6 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 7 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 8 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 -0.5 -1.0 -1.5 -2.0 9 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 -0.5 -1.0 -1.5 10 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 -0.5 -1.0 11 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 EB: 0 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 -6.5 -6.0 1 -2.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 -5.5 2 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -5.0 3 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -4.5 4 -3.0 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -4.0 5 -2.5 -2.0 -1.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -3.5 6 -3.0 -2.5 -2.0 -1.5 -1.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -3.0 7 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -2.5 8 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -2.0 9 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -1.5 10 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -1.0 11 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 FB: 0 -3.0 -2.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 2 -3.0 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 3 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 4 -3.0 -2.5 -2.0 -1.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 5 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 6 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 7 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 8 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 9 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 10 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 11 -6.5 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 TB: 0 3 3 1 4 5 4 4 4 4 5 4 4 4 1 7 7 7 4 4 4 4 4 4 4 5 4 4 2 2 2 2 1 4 4 5 5 4 4 4 5 4 3 3 3 3 2 1 4 4 4 4 5 4 4 4 4 7 7 7 6 2 1 4 4 5 4 4 4 4 5 2 2 2 1 7 6 1 5 4 4 4 5 4 6 2 2 2 2 2 1 7 4 5 4 4 4 4 7 2 2 2 3 2 2 3 1 4 4 4 5 4 8 2 2 2 2 2 3 2 2 1 4 4 4 4 9 3 3 3 2 3 2 2 2 2 1 4 4 4 10 2 2 2 2 2 2 2 2 2 2 1 4 4 11 2 2 2 3 2 2 3 3 2 2 2 1 4 12 2 2 2 2 2 2 2 2 2 2 2 2 0 SS_GD_BSL: 0 1 2 3 4 5 6 7 8 9 10 11 12 SB: 0 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 2 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 3 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 4 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 5 -2.5 -2.0 -1.5 -1.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 6 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 7 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 8 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 -0.5 -1.0 -1.5 -2.0 9 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 -0.5 -1.0 -1.5 10 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 -0.5 -1.0 11 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 EB: 0 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 -6.5 -6.0 1 -2.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 -5.5 2 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -5.0 3 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -4.5 4 -3.0 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -4.0 5 -2.5 -2.0 -1.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -3.5 6 -3.0 -2.5 -2.0 -1.5 -1.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -3.0 7 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -2.5 8 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -2.0 9 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -1.5 10 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -1.0 11 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 FB: 0 -3.0 -2.5 -2.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 2 -3.0 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 3 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 4 -3.0 -2.5 -2.0 -1.5 -2.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 5 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -1.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 6 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 7 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 -2.5 8 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 -2.0 9 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 -1.5 10 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 -1.0 11 -6.5 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 TB: 0 3 3 1 4 5 4 4 4 4 5 4 4 4 1 7 7 7 4 4 4 4 4 4 4 5 4 4 2 2 2 2 1 4 4 5 5 4 4 4 5 4 3 3 3 3 2 1 4 4 4 4 5 4 4 4 4 7 7 7 6 2 1 4 4 5 4 4 4 4 5 2 2 2 1 7 6 1 5 4 4 4 5 4 6 2 2 2 2 2 1 7 4 5 4 4 4 4 7 2 2 2 3 2 2 3 1 4 4 4 5 4 8 2 2 2 2 2 3 2 2 1 4 4 4 4 9 3 3 3 2 3 2 2 2 2 1 4 4 4 10 2 2 2 2 2 2 2 2 2 2 1 4 4 11 2 2 2 3 2 2 3 3 2 2 2 1 4 12 2 2 2 2 2 2 2 2 2 2 2 2 0 TEST02: Sequence-Sequence Global Distance Forward/backward score Quadratic/Linear alignment routines: SS_GD_FSQ - Forward quadratic; SS_GD_FSL - Forward linear; SS_GD_BSQ - Backward quadratic; SS_GD_BSL - Backward linear. Gap extend penalty = -0.500000 Sequences A and B: 1 G G 2 C G 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 TEST015 Scoring Matrix: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 -2.0 -2.0 -2.0 -2.0 -2.0 -2.0 -2.0 -2.0 -2.0 -2.0 -2.0 -2.0 -2.0 1 -2.0 1.0 1.0 1.0 -1.0 1.0 -1.0 -1.0 -1.0 -1.0 1.0 -1.0 -1.0 2 -2.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 1.0 -1.0 3 -2.0 -1.0 -1.0 -1.0 1.0 -1.0 -1.0 1.0 1.0 -1.0 -1.0 -1.0 1.0 4 -2.0 1.0 1.0 1.0 -1.0 1.0 -1.0 -1.0 -1.0 -1.0 1.0 -1.0 -1.0 5 -2.0 -1.0 -1.0 -1.0 -1.0 -1.0 1.0 -1.0 -1.0 1.0 -1.0 -1.0 -1.0 6 -2.0 -1.0 -1.0 -1.0 1.0 -1.0 -1.0 1.0 1.0 -1.0 -1.0 -1.0 1.0 7 -2.0 -1.0 -1.0 -1.0 -1.0 -1.0 1.0 -1.0 -1.0 1.0 -1.0 -1.0 -1.0 8 -2.0 -1.0 -1.0 -1.0 1.0 -1.0 -1.0 1.0 1.0 -1.0 -1.0 -1.0 1.0 9 -2.0 -1.0 -1.0 -1.0 -1.0 -1.0 1.0 -1.0 -1.0 1.0 -1.0 -1.0 -1.0 10 -2.0 1.0 1.0 1.0 -1.0 1.0 -1.0 -1.0 -1.0 -1.0 1.0 -1.0 -1.0 11 -2.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 1.0 -1.0 12 -2.0 -1.0 -1.0 -1.0 1.0 -1.0 -1.0 1.0 1.0 -1.0 -1.0 -1.0 1.0 SS_GD_FSQ: 0 1 2 3 4 5 6 7 8 9 10 11 12 SF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 2 -1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -2.5 -3.0 3 -1.5 0.0 -0.5 -1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -1.5 4 -2.0 -0.5 1.0 0.5 0.0 1.5 1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 5 -2.5 -1.0 0.5 0.0 -0.5 1.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 6 -3.0 -1.5 0.0 -0.5 1.0 0.5 2.0 3.5 3.0 2.5 2.0 1.5 1.0 7 -3.5 -2.0 -0.5 -1.0 0.5 0.0 1.5 3.0 2.5 4.0 3.5 3.0 2.5 8 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 4.0 3.5 3.0 2.5 4.0 9 -4.5 -3.0 -1.5 -2.0 -0.5 -1.0 0.5 2.0 3.5 5.0 4.5 4.0 3.5 10 -5.0 -3.5 -2.0 -0.5 -1.0 0.5 0.0 1.5 3.0 4.5 6.0 5.5 5.0 11 -5.5 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 4.0 5.5 7.0 6.5 12 -6.0 -4.5 -3.0 -1.5 0.0 -0.5 -1.0 0.5 2.0 3.5 5.0 6.5 8.0 EF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 2 -1.0 -1.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -3.0 3 -1.5 -2.0 -0.5 -1.0 -1.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 4 -2.0 -2.5 -1.0 0.5 0.0 -0.5 1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 5 -2.5 -3.0 -1.5 0.0 -0.5 -1.0 0.5 2.0 1.5 1.0 0.5 0.0 -0.5 6 -3.0 -3.5 -2.0 -0.5 -1.0 0.5 0.0 1.5 3.0 2.5 2.0 1.5 1.0 7 -3.5 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 2.0 3.5 3.0 2.5 8 -4.0 -4.5 -3.0 -1.5 -2.0 -0.5 -1.0 0.5 2.0 3.5 3.0 2.5 2.0 9 -4.5 -5.0 -3.5 -2.0 -2.5 -1.0 -1.5 0.0 1.5 3.0 4.5 4.0 3.5 10 -5.0 -5.5 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 4.0 5.5 5.0 11 -5.5 -6.0 -4.5 -3.0 -1.5 -2.0 -0.5 -1.0 0.5 2.0 3.5 5.0 6.5 12 -6.0 -6.5 -5.0 -3.5 -2.0 -0.5 -1.0 -1.5 0.0 1.5 3.0 4.5 6.0 FF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 -6.5 2 -1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 3 -1.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -3.0 -3.5 4 -2.0 -0.5 -1.0 -1.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -2.0 5 -2.5 -1.0 0.5 0.0 -0.5 1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 6 -3.0 -1.5 0.0 -0.5 -1.0 0.5 2.0 1.5 1.0 0.5 0.0 -0.5 -1.0 7 -3.5 -2.0 -0.5 -1.0 0.5 0.0 1.5 3.0 2.5 2.0 1.5 1.0 0.5 8 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 2.0 3.5 3.0 2.5 2.0 9 -4.5 -3.0 -1.5 -2.0 -0.5 -1.0 0.5 2.0 3.5 3.0 2.5 2.0 3.5 10 -5.0 -3.5 -2.0 -2.5 -1.0 -1.5 0.0 1.5 3.0 4.5 4.0 3.5 3.0 11 -5.5 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 4.0 5.5 5.0 4.5 12 -6.0 -4.5 -3.0 -1.5 -2.0 -0.5 -1.0 0.5 2.0 3.5 5.0 6.5 6.0 TF: 0 0 2 2 2 2 2 2 2 2 2 2 2 2 1 4 1 3 3 2 3 2 2 2 2 3 2 2 2 4 4 7 7 7 7 7 7 7 7 7 1 2 3 4 4 7 7 1 2 2 3 3 2 2 6 1 4 4 5 1 3 6 1 2 2 2 2 3 2 6 5 4 4 4 7 7 4 1 2 2 3 2 2 2 6 4 4 4 7 1 6 4 1 3 2 2 2 3 7 4 4 4 7 4 7 5 4 7 1 2 2 2 8 4 4 4 7 5 7 4 5 1 6 7 7 1 9 4 4 4 7 4 7 5 4 4 1 2 2 6 10 4 5 5 1 6 1 6 4 4 4 1 2 2 11 4 4 4 4 7 4 7 4 4 4 4 1 2 12 4 4 4 4 1 6 7 5 5 4 4 4 1 SS_GD_FSL: 0 1 2 3 4 5 6 7 8 9 10 11 12 SF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 2 -1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -2.5 -3.0 3 -1.5 0.0 -0.5 -1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -1.5 4 -2.0 -0.5 1.0 0.5 0.0 1.5 1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 5 -2.5 -1.0 0.5 0.0 -0.5 1.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 6 -3.0 -1.5 0.0 -0.5 1.0 0.5 2.0 3.5 3.0 2.5 2.0 1.5 1.0 7 -3.5 -2.0 -0.5 -1.0 0.5 0.0 1.5 3.0 2.5 4.0 3.5 3.0 2.5 8 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 4.0 3.5 3.0 2.5 4.0 9 -4.5 -3.0 -1.5 -2.0 -0.5 -1.0 0.5 2.0 3.5 5.0 4.5 4.0 3.5 10 -5.0 -3.5 -2.0 -0.5 -1.0 0.5 0.0 1.5 3.0 4.5 6.0 5.5 5.0 11 -5.5 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 4.0 5.5 7.0 6.5 12 -6.0 -4.5 -3.0 -1.5 0.0 -0.5 -1.0 0.5 2.0 3.5 5.0 6.5 8.0 EF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 2 -1.0 -1.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -3.0 3 -1.5 -2.0 -0.5 -1.0 -1.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 4 -2.0 -2.5 -1.0 0.5 0.0 -0.5 1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 5 -2.5 -3.0 -1.5 0.0 -0.5 -1.0 0.5 2.0 1.5 1.0 0.5 0.0 -0.5 6 -3.0 -3.5 -2.0 -0.5 -1.0 0.5 0.0 1.5 3.0 2.5 2.0 1.5 1.0 7 -3.5 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 2.0 3.5 3.0 2.5 8 -4.0 -4.5 -3.0 -1.5 -2.0 -0.5 -1.0 0.5 2.0 3.5 3.0 2.5 2.0 9 -4.5 -5.0 -3.5 -2.0 -2.5 -1.0 -1.5 0.0 1.5 3.0 4.5 4.0 3.5 10 -5.0 -5.5 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 4.0 5.5 5.0 11 -5.5 -6.0 -4.5 -3.0 -1.5 -2.0 -0.5 -1.0 0.5 2.0 3.5 5.0 6.5 12 -6.0 -6.5 -5.0 -3.5 -2.0 -0.5 -1.0 -1.5 0.0 1.5 3.0 4.5 6.0 FF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 -6.5 2 -1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 3 -1.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -3.0 -3.5 4 -2.0 -0.5 -1.0 -1.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -2.0 5 -2.5 -1.0 0.5 0.0 -0.5 1.0 0.5 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 6 -3.0 -1.5 0.0 -0.5 -1.0 0.5 2.0 1.5 1.0 0.5 0.0 -0.5 -1.0 7 -3.5 -2.0 -0.5 -1.0 0.5 0.0 1.5 3.0 2.5 2.0 1.5 1.0 0.5 8 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 2.0 3.5 3.0 2.5 2.0 9 -4.5 -3.0 -1.5 -2.0 -0.5 -1.0 0.5 2.0 3.5 3.0 2.5 2.0 3.5 10 -5.0 -3.5 -2.0 -2.5 -1.0 -1.5 0.0 1.5 3.0 4.5 4.0 3.5 3.0 11 -5.5 -4.0 -2.5 -1.0 -1.5 0.0 -0.5 1.0 2.5 4.0 5.5 5.0 4.5 12 -6.0 -4.5 -3.0 -1.5 -2.0 -0.5 -1.0 0.5 2.0 3.5 5.0 6.5 6.0 TF: 0 0 2 2 2 2 2 2 2 2 2 2 2 2 1 4 1 3 3 2 3 2 2 2 2 3 2 2 2 4 4 7 7 7 7 7 7 7 7 7 1 2 3 4 4 7 7 1 2 2 3 3 2 2 6 1 4 4 5 1 3 6 1 2 2 2 2 3 2 6 5 4 4 4 7 7 4 1 2 2 3 2 2 2 6 4 4 4 7 1 6 4 1 3 2 2 2 3 7 4 4 4 7 4 7 5 4 7 1 2 2 2 8 4 4 4 7 5 7 4 5 1 6 7 7 1 9 4 4 4 7 4 7 5 4 4 1 2 2 6 10 4 5 5 1 6 1 6 4 4 4 1 2 2 11 4 4 4 4 7 4 7 4 4 4 4 1 2 12 4 4 4 4 1 6 7 5 5 4 4 4 1 SS_GD_BSQ: 0 1 2 3 4 5 6 7 8 9 10 11 12 SB: 0 8.0 8.5 9.0 7.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 -6.0 1 6.5 7.0 7.5 8.0 6.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 -5.5 2 7.0 7.5 8.0 8.5 7.0 5.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 -5.0 3 5.5 6.0 6.5 7.0 7.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 4 4.0 4.5 5.0 5.5 6.0 6.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 5 4.5 5.0 5.5 6.0 4.5 5.0 5.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 6 3.0 3.5 4.0 4.5 5.0 5.5 4.0 4.5 3.0 1.5 0.0 -1.5 -3.0 7 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 3.5 2.0 0.5 -1.0 -2.5 8 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 2.5 1.0 -0.5 -2.0 9 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 1.5 0.0 -1.5 10 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 0.5 -1.0 11 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 EB: 0 8.0 8.5 7.0 5.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 -5.0 -6.5 -6.0 1 6.5 7.0 7.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 -6.0 -5.5 2 7.0 7.5 8.0 6.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 -5.5 -5.0 3 5.5 6.0 6.5 7.0 5.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 -5.0 -4.5 4 4.0 4.5 5.0 5.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 -4.0 5 4.5 5.0 5.5 4.0 4.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 -3.5 6 3.0 3.5 4.0 4.5 5.0 3.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 -3.0 7 1.5 2.0 2.5 3.0 3.5 4.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -2.5 8 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 2.0 0.5 -1.0 -2.5 -2.0 9 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 1.0 -0.5 -2.0 -1.5 10 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 0.0 -1.5 -1.0 11 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 FB: 0 6.0 6.5 7.0 7.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 -6.0 1 6.5 7.0 7.5 8.0 6.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 -5.5 2 5.0 5.5 6.0 6.5 7.0 5.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 -5.0 3 3.5 4.0 4.5 5.0 5.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 4 4.0 4.5 5.0 5.5 4.0 4.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 5 2.5 3.0 3.5 4.0 4.5 5.0 3.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 6 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 3.0 1.5 0.0 -1.5 -3.0 7 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 2.0 0.5 -1.0 -2.5 8 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 1.0 -0.5 -2.0 9 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 0.0 -1.5 10 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 -1.0 11 -6.5 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 TB: 0 3 3 1 4 5 4 4 4 4 5 4 4 4 1 7 7 7 4 4 4 4 4 4 4 5 4 4 2 2 2 2 1 4 4 5 5 4 4 4 5 4 3 3 3 3 2 1 4 4 4 4 5 4 4 4 4 7 7 7 6 2 1 4 4 5 4 4 4 4 5 2 2 2 1 7 6 1 5 4 4 4 5 4 6 2 2 2 2 2 1 7 4 5 4 4 4 4 7 2 2 2 3 2 2 3 1 4 4 4 5 4 8 2 2 2 2 2 3 2 2 1 4 4 4 4 9 3 3 3 2 3 2 2 2 2 1 4 4 4 10 2 2 2 2 2 2 2 2 2 2 1 4 4 11 2 2 2 3 2 2 3 3 2 2 2 1 4 12 2 2 2 2 2 2 2 2 2 2 2 2 0 SS_GD_BSL: 0 1 2 3 4 5 6 7 8 9 10 11 12 SB: 0 8.0 8.5 9.0 7.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 -6.0 1 6.5 7.0 7.5 8.0 6.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 -5.5 2 7.0 7.5 8.0 8.5 7.0 5.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 -5.0 3 5.5 6.0 6.5 7.0 7.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 4 4.0 4.5 5.0 5.5 6.0 6.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 5 4.5 5.0 5.5 6.0 4.5 5.0 5.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 6 3.0 3.5 4.0 4.5 5.0 5.5 4.0 4.5 3.0 1.5 0.0 -1.5 -3.0 7 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 3.5 2.0 0.5 -1.0 -2.5 8 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 2.5 1.0 -0.5 -2.0 9 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 1.5 0.0 -1.5 10 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 0.5 -1.0 11 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 EB: 0 8.0 8.5 7.0 5.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 -5.0 -6.5 -6.0 1 6.5 7.0 7.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 -6.0 -5.5 2 7.0 7.5 8.0 6.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 -5.5 -5.0 3 5.5 6.0 6.5 7.0 5.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 -5.0 -4.5 4 4.0 4.5 5.0 5.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 -4.0 5 4.5 5.0 5.5 4.0 4.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 -3.5 6 3.0 3.5 4.0 4.5 5.0 3.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 -3.0 7 1.5 2.0 2.5 3.0 3.5 4.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -2.5 8 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 2.0 0.5 -1.0 -2.5 -2.0 9 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 1.0 -0.5 -2.0 -1.5 10 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 0.0 -1.5 -1.0 11 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 FB: 0 6.0 6.5 7.0 7.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 -6.0 1 6.5 7.0 7.5 8.0 6.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 -5.5 2 5.0 5.5 6.0 6.5 7.0 5.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 -5.0 3 3.5 4.0 4.5 5.0 5.5 6.0 4.5 3.0 1.5 0.0 -1.5 -3.0 -4.5 4 4.0 4.5 5.0 5.5 4.0 4.5 5.0 3.5 2.0 0.5 -1.0 -2.5 -4.0 5 2.5 3.0 3.5 4.0 4.5 5.0 3.5 4.0 2.5 1.0 -0.5 -2.0 -3.5 6 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 3.0 1.5 0.0 -1.5 -3.0 7 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 2.0 0.5 -1.0 -2.5 8 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 1.0 -0.5 -2.0 9 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 0.0 -1.5 10 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 -1.0 11 -6.5 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 TB: 0 3 3 1 4 5 4 4 4 4 5 4 4 4 1 7 7 7 4 4 4 4 4 4 4 5 4 4 2 2 2 2 1 4 4 5 5 4 4 4 5 4 3 3 3 3 2 1 4 4 4 4 5 4 4 4 4 7 7 7 6 2 1 4 4 5 4 4 4 4 5 2 2 2 1 7 6 1 5 4 4 4 5 4 6 2 2 2 2 2 1 7 4 5 4 4 4 4 7 2 2 2 3 2 2 3 1 4 4 4 5 4 8 2 2 2 2 2 3 2 2 1 4 4 4 4 9 3 3 3 2 3 2 2 2 2 1 4 4 4 10 2 2 2 2 2 2 2 2 2 2 1 4 4 11 2 2 2 3 2 2 3 3 2 2 2 1 4 12 2 2 2 2 2 2 2 2 2 2 2 2 0 TEST04: Sequence-Sequence Global Distance Forward score and path quadratic alignment routines: SS_GD_FSQ - score routine; SS_GD_FPQ - path routine. Gap extend penalty = -0.500000 Sequences A and B: 1 G G 2 C G 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 path: 1 0 0 2 1 1 3 2 -1 4 -1 2 5 -1 3 6 3 4 7 4 5 8 5 6 9 6 7 10 7 -1 11 8 8 12 9 9 13 10 10 14 11 11 15 12 12 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0 0 0.00 1 G = G 1 1.00 1.00 2 C | -0.50 0.50 | G 2 -0.50 0.00 | G 3 -0.50 -0.50 3 T = T 4 1.00 0.50 4 G = G 5 1.00 1.50 5 A = A 6 1.00 2.50 6 T = T 7 1.00 3.50 7 A | -0.50 3.00 8 T = T 8 1.00 4.00 9 A = A 9 1.00 5.00 10 G = G 10 1.00 6.00 11 C = C 11 1.00 7.00 12 T = T 12 1.00 8.00 TEST05: Sequence-Sequence Global Distance Recursive Path Linear alignment routine: SS_GD_RPL - path routine; Gap extend penalty = -0.500000 Sequences A and B: 1 G G 2 C G 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 path: 1 0 0 2 1 1 3 2 -1 4 -1 2 5 -1 3 6 3 4 7 4 5 8 5 6 9 6 7 10 7 -1 11 8 8 12 9 9 13 10 10 14 11 11 15 12 12 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0 0 0.00 1 G = G 1 1.00 1.00 2 C | -0.50 0.50 | G 2 -0.50 0.00 | G 3 -0.50 -0.50 3 T = T 4 1.00 0.50 4 G = G 5 1.00 1.50 5 A = A 6 1.00 2.50 6 T = T 7 1.00 3.50 7 A | -0.50 3.00 8 T = T 8 1.00 4.00 9 A = A 9 1.00 5.00 10 G = G 10 1.00 6.00 11 C = C 11 1.00 7.00 12 T = T 12 1.00 8.00 TEST06: Using PAM120 scoring matrix. Sequence-Sequence Global Distance Forward Score Quadratic/Linear alignment routines: SS_GD_FSQ - Forward quadratic; SS_GD_FSL - Forward linear; SS_GD_BSQ - Backward quadratic; SS_GD_BSL - Backward linear. Gap extend penalty = -0.500000 Sequences A and B: 1 G G 2 C G 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 PAM120 Scoring Matrix: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 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 -5.0 -5.0 -5.0 -3.0 -5.0 -3.0 -3.0 -3.0 -3.0 -5.0 9.0 -3.0 3 0.0 -1.0 -1.0 -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 1.0 1.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 -3.0 1.0 6 0.0 -1.0 -1.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 7 0.0 1.0 1.0 1.0 1.0 1.0 3.0 1.0 1.0 3.0 1.0 -3.0 1.0 8 0.0 -1.0 -1.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 9 0.0 1.0 1.0 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 -5.0 -5.0 -5.0 -3.0 -5.0 -3.0 -3.0 -3.0 -3.0 -5.0 9.0 -3.0 12 0.0 -1.0 -1.0 -1.0 4.0 -1.0 1.0 4.0 4.0 1.0 -1.0 -3.0 4.0 SS_GD_FSQ: 0 1 2 3 4 5 6 7 8 9 10 11 12 SF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 5.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 2 -1.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 9.5 9.0 3 -1.5 4.0 3.5 3.0 7.5 7.0 6.5 6.0 5.5 5.0 4.5 9.0 13.5 4 -2.0 3.5 9.0 8.5 8.0 12.5 12.0 11.5 11.0 10.5 10.0 9.5 13.0 5 -2.5 3.0 8.5 10.0 9.5 12.0 15.5 15.0 14.5 14.0 13.5 13.0 12.5 6 -3.0 2.5 8.0 9.5 14.0 13.5 15.0 19.5 19.0 18.5 18.0 17.5 17.0 7 -3.5 2.0 7.5 9.0 13.5 15.0 16.5 19.0 20.5 22.0 21.5 21.0 20.5 8 -4.0 1.5 7.0 8.5 13.0 14.5 16.0 20.5 23.0 22.5 22.0 21.5 25.0 9 -4.5 1.0 6.5 8.0 12.5 14.0 17.5 20.0 22.5 26.0 25.5 25.0 24.5 10 -5.0 0.5 6.0 11.5 12.0 17.5 17.0 19.5 22.0 25.5 31.0 30.5 30.0 11 -5.5 0.0 5.5 11.0 11.5 17.0 16.5 19.0 21.5 25.0 30.5 40.0 39.5 12 -6.0 -0.5 5.0 10.5 15.0 16.5 18.0 20.5 23.0 24.5 30.0 39.5 44.0 EF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 2 -1.0 -1.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 9.0 3 -1.5 -2.0 3.5 3.0 2.5 7.0 6.5 6.0 5.5 5.0 4.5 4.0 8.5 4 -2.0 -2.5 3.0 8.5 8.0 7.5 12.0 11.5 11.0 10.5 10.0 9.5 9.0 5 -2.5 -3.0 2.5 8.0 9.5 9.0 11.5 15.0 14.5 14.0 13.5 13.0 12.5 6 -3.0 -3.5 2.0 7.5 9.0 13.5 13.0 14.5 19.0 18.5 18.0 17.5 17.0 7 -3.5 -4.0 1.5 7.0 8.5 13.0 14.5 16.0 18.5 20.0 21.5 21.0 20.5 8 -4.0 -4.5 1.0 6.5 8.0 12.5 14.0 15.5 20.0 22.5 22.0 21.5 21.0 9 -4.5 -5.0 0.5 6.0 7.5 12.0 13.5 17.0 19.5 22.0 25.5 25.0 24.5 10 -5.0 -5.5 0.0 5.5 11.0 11.5 17.0 16.5 19.0 21.5 25.0 30.5 30.0 11 -5.5 -6.0 -0.5 5.0 10.5 11.0 16.5 16.0 18.5 21.0 24.5 30.0 39.5 12 -6.0 -6.5 -1.0 4.5 10.0 14.5 16.0 17.5 20.0 22.5 24.0 29.5 39.0 FF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 -6.5 2 -1.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 -1.0 3 -1.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 9.0 8.5 4 -2.0 3.5 3.0 2.5 7.0 6.5 6.0 5.5 5.0 4.5 4.0 8.5 13.0 5 -2.5 3.0 8.5 8.0 7.5 12.0 11.5 11.0 10.5 10.0 9.5 9.0 12.5 6 -3.0 2.5 8.0 9.5 9.0 11.5 15.0 14.5 14.0 13.5 13.0 12.5 12.0 7 -3.5 2.0 7.5 9.0 13.5 13.0 14.5 19.0 18.5 18.0 17.5 17.0 16.5 8 -4.0 1.5 7.0 8.5 13.0 14.5 16.0 18.5 20.0 21.5 21.0 20.5 20.0 9 -4.5 1.0 6.5 8.0 12.5 14.0 15.5 20.0 22.5 22.0 21.5 21.0 24.5 10 -5.0 0.5 6.0 7.5 12.0 13.5 17.0 19.5 22.0 25.5 25.0 24.5 24.0 11 -5.5 0.0 5.5 11.0 11.5 17.0 16.5 19.0 21.5 25.0 30.5 30.0 29.5 12 -6.0 -0.5 5.0 10.5 11.0 16.5 16.0 18.5 21.0 24.5 30.0 39.5 39.0 TF: 0 0 2 2 2 2 2 2 2 2 2 2 2 2 1 4 1 3 3 2 3 2 2 2 2 3 2 2 2 4 4 6 6 6 6 6 6 6 6 6 1 2 3 4 4 7 7 1 2 2 3 3 2 2 4 1 4 4 5 1 3 2 1 2 2 2 2 3 2 4 5 4 4 4 1 3 4 1 2 2 3 2 2 6 6 4 4 4 4 1 2 4 1 3 2 2 2 3 7 4 4 4 5 4 1 1 4 1 1 2 2 2 8 4 4 4 4 5 4 5 1 1 2 2 2 1 9 4 4 4 5 4 5 1 4 4 1 2 2 6 10 4 5 5 1 4 1 6 4 4 4 1 2 2 11 4 4 4 4 4 4 6 4 4 4 4 1 2 12 4 4 4 4 1 4 1 1 1 4 4 4 1 SS_GD_FSL: 0 1 2 3 4 5 6 7 8 9 10 11 12 SF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 5.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 2 -1.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 9.5 9.0 3 -1.5 4.0 3.5 3.0 7.5 7.0 6.5 6.0 5.5 5.0 4.5 9.0 13.5 4 -2.0 3.5 9.0 8.5 8.0 12.5 12.0 11.5 11.0 10.5 10.0 9.5 13.0 5 -2.5 3.0 8.5 10.0 9.5 12.0 15.5 15.0 14.5 14.0 13.5 13.0 12.5 6 -3.0 2.5 8.0 9.5 14.0 13.5 15.0 19.5 19.0 18.5 18.0 17.5 17.0 7 -3.5 2.0 7.5 9.0 13.5 15.0 16.5 19.0 20.5 22.0 21.5 21.0 20.5 8 -4.0 1.5 7.0 8.5 13.0 14.5 16.0 20.5 23.0 22.5 22.0 21.5 25.0 9 -4.5 1.0 6.5 8.0 12.5 14.0 17.5 20.0 22.5 26.0 25.5 25.0 24.5 10 -5.0 0.5 6.0 11.5 12.0 17.5 17.0 19.5 22.0 25.5 31.0 30.5 30.0 11 -5.5 0.0 5.5 11.0 11.5 17.0 16.5 19.0 21.5 25.0 30.5 40.0 39.5 12 -6.0 -0.5 5.0 10.5 15.0 16.5 18.0 20.5 23.0 24.5 30.0 39.5 44.0 EF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 2 -1.0 -1.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 9.0 3 -1.5 -2.0 3.5 3.0 2.5 7.0 6.5 6.0 5.5 5.0 4.5 4.0 8.5 4 -2.0 -2.5 3.0 8.5 8.0 7.5 12.0 11.5 11.0 10.5 10.0 9.5 9.0 5 -2.5 -3.0 2.5 8.0 9.5 9.0 11.5 15.0 14.5 14.0 13.5 13.0 12.5 6 -3.0 -3.5 2.0 7.5 9.0 13.5 13.0 14.5 19.0 18.5 18.0 17.5 17.0 7 -3.5 -4.0 1.5 7.0 8.5 13.0 14.5 16.0 18.5 20.0 21.5 21.0 20.5 8 -4.0 -4.5 1.0 6.5 8.0 12.5 14.0 15.5 20.0 22.5 22.0 21.5 21.0 9 -4.5 -5.0 0.5 6.0 7.5 12.0 13.5 17.0 19.5 22.0 25.5 25.0 24.5 10 -5.0 -5.5 0.0 5.5 11.0 11.5 17.0 16.5 19.0 21.5 25.0 30.5 30.0 11 -5.5 -6.0 -0.5 5.0 10.5 11.0 16.5 16.0 18.5 21.0 24.5 30.0 39.5 12 -6.0 -6.5 -1.0 4.5 10.0 14.5 16.0 17.5 20.0 22.5 24.0 29.5 39.0 FF: 0 0.0 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 1 -0.5 -1.0 -1.5 -2.0 -2.5 -3.0 -3.5 -4.0 -4.5 -5.0 -5.5 -6.0 -6.5 2 -1.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 -1.0 3 -1.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0 -0.5 9.0 8.5 4 -2.0 3.5 3.0 2.5 7.0 6.5 6.0 5.5 5.0 4.5 4.0 8.5 13.0 5 -2.5 3.0 8.5 8.0 7.5 12.0 11.5 11.0 10.5 10.0 9.5 9.0 12.5 6 -3.0 2.5 8.0 9.5 9.0 11.5 15.0 14.5 14.0 13.5 13.0 12.5 12.0 7 -3.5 2.0 7.5 9.0 13.5 13.0 14.5 19.0 18.5 18.0 17.5 17.0 16.5 8 -4.0 1.5 7.0 8.5 13.0 14.5 16.0 18.5 20.0 21.5 21.0 20.5 20.0 9 -4.5 1.0 6.5 8.0 12.5 14.0 15.5 20.0 22.5 22.0 21.5 21.0 24.5 10 -5.0 0.5 6.0 7.5 12.0 13.5 17.0 19.5 22.0 25.5 25.0 24.5 24.0 11 -5.5 0.0 5.5 11.0 11.5 17.0 16.5 19.0 21.5 25.0 30.5 30.0 29.5 12 -6.0 -0.5 5.0 10.5 11.0 16.5 16.0 18.5 21.0 24.5 30.0 39.5 39.0 TF: 0 0 2 2 2 2 2 2 2 2 2 2 2 2 1 4 1 3 3 2 3 2 2 2 2 3 2 2 2 4 4 6 6 6 6 6 6 6 6 6 1 2 3 4 4 7 7 1 2 2 3 3 2 2 4 1 4 4 5 1 3 2 1 2 2 2 2 3 2 4 5 4 4 4 1 3 4 1 2 2 3 2 2 6 6 4 4 4 4 1 2 4 1 3 2 2 2 3 7 4 4 4 5 4 1 1 4 1 1 2 2 2 8 4 4 4 4 5 4 5 1 1 2 2 2 1 9 4 4 4 5 4 5 1 4 4 1 2 2 6 10 4 5 5 1 4 1 6 4 4 4 1 2 2 11 4 4 4 4 4 4 6 4 4 4 4 1 2 12 4 4 4 4 1 4 1 1 1 4 4 4 1 SS_GD_BSQ: 0 1 2 3 4 5 6 7 8 9 10 11 12 SB: 0 44.0 44.5 45.0 39.5 35.0 29.5 26.0 21.5 17.0 13.5 8.0 -1.5 -6.0 1 38.5 39.0 39.5 40.0 35.5 30.0 26.5 22.0 17.5 14.0 8.5 -1.0 -5.5 2 39.0 39.5 40.0 40.5 36.0 30.5 27.0 22.5 18.0 14.5 9.0 -0.5 -5.0 3 36.5 37.0 35.5 36.0 36.5 31.0 27.5 23.0 18.5 15.0 9.5 0.0 -4.5 4 31.0 31.5 32.0 30.5 31.0 31.5 28.0 23.5 19.0 15.5 10.0 0.5 -4.0 5 29.5 30.0 30.5 31.0 27.5 28.0 28.5 24.0 19.5 16.0 10.5 1.0 -3.5 6 25.0 25.5 26.0 26.5 27.0 27.5 26.0 24.5 20.0 16.5 11.0 1.5 -3.0 7 21.5 22.0 22.5 23.0 23.5 24.0 24.5 25.0 20.5 17.0 11.5 2.0 -2.5 8 17.0 17.5 18.0 18.5 19.0 19.5 20.0 20.5 21.0 17.5 12.0 2.5 -2.0 9 13.5 14.0 14.5 15.0 15.5 16.0 16.5 17.0 17.5 18.0 12.5 3.0 -1.5 10 8.0 8.5 9.0 9.5 10.0 10.5 11.0 11.5 12.0 12.5 13.0 3.5 -1.0 11 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 EB: 0 44.0 44.5 39.0 34.5 29.0 25.5 21.0 16.5 13.0 7.5 -2.0 -6.5 -6.0 1 38.5 39.0 39.5 35.0 29.5 26.0 21.5 17.0 13.5 8.0 -1.5 -6.0 -5.5 2 39.0 39.5 40.0 35.5 30.0 26.5 22.0 17.5 14.0 8.5 -1.0 -5.5 -5.0 3 36.5 35.0 35.5 36.0 30.5 27.0 22.5 18.0 14.5 9.0 -0.5 -5.0 -4.5 4 31.0 31.5 30.0 30.5 31.0 27.5 23.0 18.5 15.0 9.5 0.0 -4.5 -4.0 5 29.5 30.0 30.5 27.0 27.5 28.0 23.5 19.0 15.5 10.0 0.5 -4.0 -3.5 6 25.0 25.5 26.0 26.5 27.0 25.5 24.0 19.5 16.0 10.5 1.0 -3.5 -3.0 7 21.5 22.0 22.5 23.0 23.5 24.0 24.5 20.0 16.5 11.0 1.5 -3.0 -2.5 8 17.0 17.5 18.0 18.5 19.0 19.5 20.0 20.5 17.0 11.5 2.0 -2.5 -2.0 9 13.5 14.0 14.5 15.0 15.5 16.0 16.5 17.0 17.5 12.0 2.5 -2.0 -1.5 10 8.0 8.5 9.0 9.5 10.0 10.5 11.0 11.5 12.0 12.5 3.0 -1.5 -1.0 11 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 FB: 0 38.0 38.5 39.0 39.5 35.0 29.5 26.0 21.5 17.0 13.5 8.0 -1.5 -6.0 1 38.5 39.0 39.5 40.0 35.5 30.0 26.5 22.0 17.5 14.0 8.5 -1.0 -5.5 2 36.0 36.5 35.0 35.5 36.0 30.5 27.0 22.5 18.0 14.5 9.0 -0.5 -5.0 3 30.5 31.0 31.5 30.0 30.5 31.0 27.5 23.0 18.5 15.0 9.5 0.0 -4.5 4 29.0 29.5 30.0 30.5 27.0 27.5 28.0 23.5 19.0 15.5 10.0 0.5 -4.0 5 24.5 25.0 25.5 26.0 26.5 27.0 25.5 24.0 19.5 16.0 10.5 1.0 -3.5 6 21.0 21.5 22.0 22.5 23.0 23.5 24.0 24.5 20.0 16.5 11.0 1.5 -3.0 7 16.5 17.0 17.5 18.0 18.5 19.0 19.5 20.0 20.5 17.0 11.5 2.0 -2.5 8 13.0 13.5 14.0 14.5 15.0 15.5 16.0 16.5 17.0 17.5 12.0 2.5 -2.0 9 7.5 8.0 8.5 9.0 9.5 10.0 10.5 11.0 11.5 12.0 12.5 3.0 -1.5 10 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 -1.0 11 -6.5 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 TB: 0 3 3 1 4 5 4 4 4 4 5 4 4 4 1 6 6 6 4 4 4 4 4 4 4 5 4 4 2 2 2 2 1 4 4 5 5 4 4 4 5 4 3 3 1 3 2 1 4 4 4 4 5 4 4 4 4 3 3 1 6 2 1 4 4 5 4 4 4 4 5 2 2 2 1 2 2 1 5 4 4 4 5 4 6 2 2 2 2 2 1 1 4 5 4 4 4 4 7 2 2 2 3 2 2 3 1 4 4 4 5 4 8 2 2 2 2 2 3 2 2 1 4 4 4 4 9 3 3 3 2 3 2 2 2 2 1 4 4 4 10 2 2 2 2 2 2 2 2 2 2 1 4 4 11 2 2 2 3 2 2 3 3 2 2 2 1 4 12 2 2 2 2 2 2 2 2 2 2 2 2 0 SS_GD_BSL: 0 1 2 3 4 5 6 7 8 9 10 11 12 SB: 0 44.0 44.5 45.0 39.5 35.0 29.5 26.0 21.5 17.0 13.5 8.0 -1.5 -6.0 1 38.5 39.0 39.5 40.0 35.5 30.0 26.5 22.0 17.5 14.0 8.5 -1.0 -5.5 2 39.0 39.5 40.0 40.5 36.0 30.5 27.0 22.5 18.0 14.5 9.0 -0.5 -5.0 3 36.5 37.0 35.5 36.0 36.5 31.0 27.5 23.0 18.5 15.0 9.5 0.0 -4.5 4 31.0 31.5 32.0 30.5 31.0 31.5 28.0 23.5 19.0 15.5 10.0 0.5 -4.0 5 29.5 30.0 30.5 31.0 27.5 28.0 28.5 24.0 19.5 16.0 10.5 1.0 -3.5 6 25.0 25.5 26.0 26.5 27.0 27.5 26.0 24.5 20.0 16.5 11.0 1.5 -3.0 7 21.5 22.0 22.5 23.0 23.5 24.0 24.5 25.0 20.5 17.0 11.5 2.0 -2.5 8 17.0 17.5 18.0 18.5 19.0 19.5 20.0 20.5 21.0 17.5 12.0 2.5 -2.0 9 13.5 14.0 14.5 15.0 15.5 16.0 16.5 17.0 17.5 18.0 12.5 3.0 -1.5 10 8.0 8.5 9.0 9.5 10.0 10.5 11.0 11.5 12.0 12.5 13.0 3.5 -1.0 11 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 EB: 0 44.0 44.5 39.0 34.5 29.0 25.5 21.0 16.5 13.0 7.5 -2.0 -6.5 -6.0 1 38.5 39.0 39.5 35.0 29.5 26.0 21.5 17.0 13.5 8.0 -1.5 -6.0 -5.5 2 39.0 39.5 40.0 35.5 30.0 26.5 22.0 17.5 14.0 8.5 -1.0 -5.5 -5.0 3 36.5 35.0 35.5 36.0 30.5 27.0 22.5 18.0 14.5 9.0 -0.5 -5.0 -4.5 4 31.0 31.5 30.0 30.5 31.0 27.5 23.0 18.5 15.0 9.5 0.0 -4.5 -4.0 5 29.5 30.0 30.5 27.0 27.5 28.0 23.5 19.0 15.5 10.0 0.5 -4.0 -3.5 6 25.0 25.5 26.0 26.5 27.0 25.5 24.0 19.5 16.0 10.5 1.0 -3.5 -3.0 7 21.5 22.0 22.5 23.0 23.5 24.0 24.5 20.0 16.5 11.0 1.5 -3.0 -2.5 8 17.0 17.5 18.0 18.5 19.0 19.5 20.0 20.5 17.0 11.5 2.0 -2.5 -2.0 9 13.5 14.0 14.5 15.0 15.5 16.0 16.5 17.0 17.5 12.0 2.5 -2.0 -1.5 10 8.0 8.5 9.0 9.5 10.0 10.5 11.0 11.5 12.0 12.5 3.0 -1.5 -1.0 11 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 FB: 0 38.0 38.5 39.0 39.5 35.0 29.5 26.0 21.5 17.0 13.5 8.0 -1.5 -6.0 1 38.5 39.0 39.5 40.0 35.5 30.0 26.5 22.0 17.5 14.0 8.5 -1.0 -5.5 2 36.0 36.5 35.0 35.5 36.0 30.5 27.0 22.5 18.0 14.5 9.0 -0.5 -5.0 3 30.5 31.0 31.5 30.0 30.5 31.0 27.5 23.0 18.5 15.0 9.5 0.0 -4.5 4 29.0 29.5 30.0 30.5 27.0 27.5 28.0 23.5 19.0 15.5 10.0 0.5 -4.0 5 24.5 25.0 25.5 26.0 26.5 27.0 25.5 24.0 19.5 16.0 10.5 1.0 -3.5 6 21.0 21.5 22.0 22.5 23.0 23.5 24.0 24.5 20.0 16.5 11.0 1.5 -3.0 7 16.5 17.0 17.5 18.0 18.5 19.0 19.5 20.0 20.5 17.0 11.5 2.0 -2.5 8 13.0 13.5 14.0 14.5 15.0 15.5 16.0 16.5 17.0 17.5 12.0 2.5 -2.0 9 7.5 8.0 8.5 9.0 9.5 10.0 10.5 11.0 11.5 12.0 12.5 3.0 -1.5 10 -2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 -1.0 11 -6.5 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 12 -6.0 -5.5 -5.0 -4.5 -4.0 -3.5 -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 TB: 0 3 3 1 4 5 4 4 4 4 5 4 4 4 1 6 6 6 4 4 4 4 4 4 4 5 4 4 2 2 2 2 1 4 4 5 5 4 4 4 5 4 3 3 1 3 2 1 4 4 4 4 5 4 4 4 4 3 3 1 6 2 1 4 4 5 4 4 4 4 5 2 2 2 1 2 2 1 5 4 4 4 5 4 6 2 2 2 2 2 1 1 4 5 4 4 4 4 7 2 2 2 3 2 2 3 1 4 4 4 5 4 8 2 2 2 2 2 3 2 2 1 4 4 4 4 9 3 3 3 2 3 2 2 2 2 1 4 4 4 10 2 2 2 2 2 2 2 2 2 2 1 4 4 11 2 2 2 3 2 2 3 3 2 2 2 1 4 12 2 2 2 2 2 2 2 2 2 2 2 2 0 TEST07: Using PAM120 scoring matrix. Sequence-Sequence Global Distance forward score and path quadratic alignment routines: SS_GD_FSQ - score routine; SS_GD_FPQ - path routine. Gap extend penalty = -0.500000 Sequences A and B: 1 G G 2 C G 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 path: 1 0 0 2 1 1 3 2 -1 4 -1 2 5 -1 3 6 3 4 7 4 5 8 5 6 9 6 7 10 7 -1 11 8 8 12 9 9 13 10 10 14 11 11 15 12 12 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0 0 0.00 1 G = G 1 5.00 5.00 2 C | -0.50 4.50 | G 2 -0.50 4.00 | G 3 -0.50 3.50 3 T = T 4 4.00 7.50 4 G = G 5 5.00 12.50 5 A = A 6 3.00 15.50 6 T = T 7 4.00 19.50 7 A | -0.50 19.00 8 T = T 8 4.00 23.00 9 A = A 9 3.00 26.00 10 G = G 10 5.00 31.00 11 C = C 11 9.00 40.00 12 T = T 12 4.00 44.00 TEST08: Using PAM120 scoring matrix. Sequence-sequence Global Distance Recursive Path Linear alignment routine: SS_GG_RPL - path routine; Gap extend penalty = -0.500000 Sequences A and B: 1 G G 2 C G 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 path: 1 0 0 2 1 1 3 2 -1 4 -1 2 5 -1 3 6 3 4 7 4 5 8 5 6 9 6 7 10 7 -1 11 8 8 12 9 9 13 10 10 14 11 11 15 12 12 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0 0 0.00 1 G = G 1 5.00 5.00 2 C | -0.50 4.50 | G 2 -0.50 4.00 | G 3 -0.50 3.50 3 T = T 4 4.00 7.50 4 G = G 5 5.00 12.50 5 A = A 6 3.00 15.50 6 T = T 7 4.00 19.50 7 A | -0.50 19.00 8 T = T 8 4.00 23.00 9 A = A 9 3.00 26.00 10 G = G 10 5.00 31.00 11 C = C 11 9.00 40.00 12 T = T 12 4.00 44.00 TEST09: Using PAM120 scoring matrix. Sequence-sequence Global Distance Recursive Path Linear alignment routines: SS_GD_RPL - path routine; Gap extend penalty = -0.500000 Sequences A and B: 1 M M 2 M M 3 A A 4 A A 5 E E 6 A A 7 G G 8 G G 9 E P 10 E V 11 G T 12 G A 13 P G 14 V A 15 T A 16 A G 17 G G 18 A G 19 A A 20 G A 21 G C 22 G C 23 A C 24 A A 25 A A 26 A S 27 S G 28 G A 29 A Y 30 Y P 31 P A 32 A V 33 V C 34 C R 35 R V 36 V K 37 K I 38 I P 39 P A 40 A A 41 A L 42 L P 43 P V 44 V A 45 A A 46 A A 47 A A 48 A P 49 P F 50 F P 51 P G 52 G L 53 L A 54 A E 55 E A 56 A G 57 G V 58 V A 59 A A 60 A Matching path: 1 0 0 2 1 1 3 2 2 4 3 3 5 4 4 6 5 5 7 6 6 8 7 -1 9 8 -1 10 9 -1 11 10 -1 12 11 7 13 12 8 14 13 9 15 14 10 16 15 11 17 16 12 18 17 13 19 18 14 20 19 15 21 20 16 22 21 17 23 22 18 24 23 19 25 24 20 26 -1 21 27 -1 22 28 -1 23 29 25 24 30 26 25 31 27 26 32 28 27 33 29 28 34 30 29 35 31 30 36 32 31 37 33 32 38 34 33 39 35 34 40 36 35 41 37 36 42 38 37 43 39 38 44 40 39 45 41 40 46 42 41 47 43 42 48 44 43 49 45 44 50 46 45 51 47 46 52 48 47 53 49 48 54 50 49 55 51 50 56 52 51 57 53 52 58 54 53 59 55 54 60 56 55 61 57 56 62 58 57 63 59 58 64 60 59 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0 0 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 | -0.50 29.50 8 G | -0.50 29.00 9 E | -0.50 28.50 10 E | -0.50 28.00 11 G = G 7 5.00 33.00 12 G = G 8 5.00 38.00 13 P = P 9 6.00 44.00 14 V = V 10 5.00 49.00 15 T = T 11 4.00 53.00 16 A = A 12 3.00 56.00 17 G = G 13 5.00 61.00 18 A = A 14 3.00 64.00 19 A = A 15 3.00 67.00 20 G = G 16 5.00 72.00 21 G = G 17 5.00 77.00 22 G = G 18 5.00 82.00 23 A = A 19 3.00 85.00 24 A = A 20 3.00 88.00 | C 21 -0.50 87.50 | C 22 -0.50 87.00 | C 23 -0.50 86.50 25 A = A 24 3.00 89.50 26 A = A 25 3.00 92.50 27 S = S 26 3.00 95.50 28 G = G 27 5.00 100.50 29 A = A 28 3.00 103.50 30 Y = Y 29 8.00 111.50 31 P = P 30 6.00 117.50 32 A = A 31 3.00 120.50 33 V = V 32 5.00 125.50 34 C = C 33 9.00 134.50 35 R = R 34 6.00 140.50 36 V = V 35 5.00 145.50 37 K = K 36 5.00 150.50 38 I = I 37 6.00 156.50 39 P = P 38 6.00 162.50 40 A = A 39 3.00 165.50 41 A = A 40 3.00 168.50 42 L = L 41 5.00 173.50 43 P = P 42 6.00 179.50 44 V = V 43 5.00 184.50 45 A = A 44 3.00 187.50 46 A = A 45 3.00 190.50 47 A = A 46 3.00 193.50 48 A = A 47 3.00 196.50 49 P = P 48 6.00 202.50 50 F = F 49 8.00 210.50 51 P = P 50 6.00 216.50 52 G = G 51 5.00 221.50 53 L = L 52 5.00 226.50 54 A = A 53 3.00 229.50 55 E = E 54 5.00 234.50 56 A = A 55 3.00 237.50 57 G = G 56 5.00 242.50 58 V = V 57 5.00 247.50 59 A = A 58 3.00 250.50 60 A = A 59 3.00 253.50 TEST10: Using PAM200 scoring matrix. Sequence-sequence Global Distance Recursive Score and Path Linear alignment routines: SS_GD_FSQ - score routine; SS_GD_FPQ - path routine. Gap extend penalty = -0.500000 Sequences A and B: 1 G G 2 C G 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 path: 1 0 0 2 1 1 3 2 -1 4 -1 2 5 -1 3 6 3 4 7 4 5 8 5 6 9 6 7 10 7 -1 11 8 8 12 9 9 13 10 10 14 11 11 15 12 12 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0 0 0.00 1 G = G 1 4.00 4.00 2 C | -0.50 3.50 | G 2 -0.50 3.00 | G 3 -0.50 2.50 3 T = T 4 3.00 5.50 4 G = G 5 4.00 9.50 5 A = A 6 2.00 11.50 6 T = T 7 3.00 14.50 7 A | -0.50 14.00 8 T = T 8 3.00 17.00 9 A = A 9 2.00 19.00 10 G = G 10 4.00 23.00 11 C = C 11 8.00 31.00 12 T = T 12 3.00 34.00 TEST11: Using PAM200 scoring matrix. Sequence-sequence Global Distance Recursive Path Linear alignment routines: SS_GD_RPL - path routine; Gap extend penalty = -0.500000 Compare with SS_GD_FSQ/SS_GD_FPQ on same data. Sequences A and B: 1 G G 2 C G 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 path: 1 0 0 2 1 1 3 2 -1 4 -1 2 5 -1 3 6 3 4 7 4 5 8 5 6 9 6 7 10 7 -1 11 8 8 12 9 9 13 10 10 14 11 11 15 12 12 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0 0 0.00 1 G = G 1 4.00 4.00 2 C | -0.50 3.50 | G 2 -0.50 3.00 | G 3 -0.50 2.50 3 T = T 4 3.00 5.50 4 G = G 5 4.00 9.50 5 A = A 6 2.00 11.50 6 T = T 7 3.00 14.50 7 A | -0.50 14.00 8 T = T 8 3.00 17.00 9 A = A 9 2.00 19.00 10 G = G 10 4.00 23.00 11 C = C 11 8.00 31.00 12 T = T 12 3.00 34.00 ss_gd_test(): Normal end of execution. March 28 2023 6:56:04.122 PM