December 29 2007 8:41:02.786 PM PS_LG_ALIGN_PRB FORTRAN90 version Test PS_LG_ALIGN Profile/sequence local alignment, affine gap penalty. TEST01 PROFILE_SCORE_READ reads profile scoring information. PROFILE_SCORE_PRINT prints the information. Profile Score Print Number of positions in profile = ] Pos Cons Entropy Gap_Open Gap_Extend Percent Percent 0 100 100 1 Q 8 100 100 2 E 10 100 100 3 C 57 100 100 4 Y 19 100 100 5 H 9 100 100 6 G 22 100 100 7 N 12 100 100 8 D 12 1 1 9 R 11 100 1 10 G 37 100 99 11 Q 8 100 99 12 S 9 100 99 13 Y 44 100 100 14 R 23 100 100 15 G 37 100 100 16 T 12 99 99 17 Y 7 100 99 18 S 15 100 100 19 T 13 99 99 20 T 24 100 100 21 V 7 100 100 22 T 11 100 100 23 G 31 99 99 24 R 10 100 99 25 T 10 100 99 26 C 57 100 100 27 Q 25 100 100 28 A 7 100 100 29 W 61 100 100 30 S 12 100 100 31 S 15 100 100 32 M 12 100 100 33 T 7 100 100 34 P 23 100 100 35 H 23 100 100 36 W 6 70 70 37 H 7 56 26 38 G 6 75 1 39 H 15 99 1 40 S 9 100 42 41 H 26 100 98 42 S 6 100 99 43 R 9 100 99 44 T 10 97 96 45 P 17 100 99 46 E 12 99 99 47 Y 7 100 99 48 Y 14 100 100 49 P 16 98 98 50 N 8 99 99 51 A 8 99 98 52 G 18 100 99 53 L 23 100 100 54 I 5 100 100 55 M 11 99 99 56 H 44 17 17 57 N 35 100 100 58 Y 39 100 100 59 C 57 100 100 60 R 38 100 100 61 N 40 100 100 62 P 40 100 100 63 D 31 100 100 64 G 13 100 100 65 D 10 100 100 66 E 3 26 26 67 A 4 100 100 68 G 12 100 100 69 P 37 100 100 70 W 49 100 100 71 C 57 100 100 72 Y 35 100 100 73 T 26 100 100 74 M 8 100 100 75 D 17 99 99 76 N 4 3 2 77 G 6 100 18 78 P 19 100 99 79 G 5 100 99 80 V 10 100 99 81 R 15 99 99 82 W 25 100 99 83 E 19 100 100 84 Y 23 100 100 85 C 57 100 100 86 S 8 6 6 87 N 11 100 99 88 I 17 100 99 89 P 12 100 99 90 Q 7 100 100 91 C 57 100 100 92 S 7 100 100 93 D 6 100 100 Profile Position Scoring Matrix: Pos A B C D E F G H I K L M N P Q R S T V W X Y Z 1 5 -6 -21 -1 5 -24 -5 -2 -23 -1 -17 -18 -17 -18 30 4 -2 -5 -5 -23 -5 0 17 2 -14 14 -23 19 24 -28 -14 -16 -19 -9 -27 -12 3 -26 7 -5 -8 10 -15 -29 -9 -26 20 3 -51 -63 59 -66 -68 -59 -59 -63 -54 -64 -55 -54 -60 -65 -66 -65 -56 -53 -51 -55 -57 -59 -68 4 -11 -33 -23 -34 -32 6 -24 -15 3 -5 -5 21 -31 -36 -28 -27 -31 -27 -2 -14 -15 39 -31 5 -16 -7 -20 -10 1 -1 -22 38 -7 3 -9 3 -5 -13 6 2 -16 2 -6 6 -5 0 3 6 -23 2 24 7 -10 -36 33 -5 -36 -31 -38 -33 -12 -36 -33 -33 -13 -31 -35 -35 -21 -36 -14 7 -17 23 -21 9 -14 -26 -20 -13 -12 2 -16 -23 32 -27 10 3 -1 -2 -19 -28 -9 -10 -2 8 -10 25 -13 32 3 -16 -7 -4 -14 -5 -18 -15 4 -12 -5 -9 -6 -7 -16 -19 -7 -17 1 9 -8 -7 -12 -9 -5 -13 -12 0 -14 7 -11 -8 -5 -15 0 31 -9 -8 -12 -13 -6 -9 -3 10 -48 -53 -54 -55 -61 -62 38 -55 -64 -57 -66 -59 -51 -62 -60 -60 -53 -58 -62 -60 -52 -63 -61 11 -15 -11 -21 -11 15 -23 -14 4 -7 7 -13 -4 -12 -24 28 0 -9 -11 2 -22 -6 -8 20 12 -11 7 -16 0 -12 -7 6 -3 -24 -14 -19 -21 14 -25 -3 -14 25 6 -22 -27 -8 -14 -9 13 -47 -52 -43 -54 -51 -23 -52 -29 -43 -49 -43 -42 -50 -56 -48 -46 -30 -48 -43 -28 -42 49 -50 14 -24 -16 -28 -13 -10 -28 -21 -8 -29 -2 -22 -1 -21 -31 1 38 -25 -24 -21 -7 -16 -25 -5 15 -48 -53 -54 -55 -61 -62 38 -55 -64 -57 -66 -59 -51 -62 -60 -60 -53 -58 -62 -61 -52 -63 -61 16 -14 -4 -15 -14 -13 -24 -22 -9 -14 10 -16 -1 3 -6 -19 -9 -1 31 -10 -27 -9 -23 -14 17 4 -26 -17 -28 -26 4 -25 0 -1 -6 -2 13 -25 -30 -24 -9 1 -5 13 21 -7 26 -26 18 8 7 -21 1 -19 -2 -17 -23 -30 -24 -32 -27 13 -30 -25 -13 29 -19 -27 -33 -14 -28 -20 19 -15 -21 -17 -23 -18 -11 -25 2 -2 6 -12 -17 -20 -27 -15 1 -17 31 8 -27 -10 -14 -17 20 -8 -7 -23 -2 -31 -33 -31 -30 -8 -29 -30 -27 -17 -34 -31 -30 -5 37 -23 -36 -19 -33 -31 21 -5 -16 -16 -21 7 -19 -25 -4 2 2 -9 7 -12 -19 -19 3 -14 5 23 9 -6 -13 3 22 -4 -4 -16 -15 -22 -17 -8 -10 -22 -5 -15 -5 3 -26 -21 -15 20 26 -19 -29 -9 -25 -22 23 -29 -34 -36 -36 -41 -43 37 -36 -45 -25 -47 -40 -32 -43 -9 -16 -34 -39 -43 -42 -31 -44 -24 24 3 -22 -23 -27 -25 -24 -28 8 8 7 1 -19 -17 -32 -21 28 -13 -7 5 -30 -9 -25 -23 25 -9 -12 -20 -11 7 -28 -25 -21 -11 6 -26 -22 -14 18 8 -10 -5 25 -21 -29 -9 -27 7 26 -51 -63 59 -66 -68 -59 -59 -63 -54 -64 -55 -54 -60 -65 -66 -65 -56 -53 -51 -55 -57 -59 -68 27 -29 -27 -32 -28 -21 -33 -34 -10 -2 -21 4 -23 -27 -35 41 -22 -11 -15 -29 -31 -18 -31 23 28 20 -4 -17 -15 -6 -24 -15 3 -23 -2 -12 1 3 9 -19 14 8 -18 -20 -27 -6 -5 -9 29 -62 -66 -50 -67 -64 -42 -61 -55 -59 -63 -56 -55 -65 -66 -57 -61 -66 -63 -60 63 -58 -39 -62 30 3 17 -20 17 -16 -29 -12 -20 -28 -21 -25 -26 18 -28 -22 -6 24 -13 -16 -33 -11 -29 -18 31 7 -20 -18 -21 -8 -27 -20 0 -26 -7 -10 -23 -19 -27 -10 -12 30 -16 -18 -7 -11 -26 -9 32 -8 -5 -18 -15 -1 -18 -23 -2 -11 -12 -8 37 2 -7 23 -1 -6 -6 -12 -23 -7 -21 10 33 -1 -16 -14 -20 -3 2 -22 3 3 -15 -3 2 -13 -9 -10 -8 2 26 -8 -21 -4 6 -5 34 -13 -30 -27 -29 -13 -31 -31 -29 -27 -20 0 -27 -31 38 -19 -31 -29 -8 -4 -34 -17 -33 -14 35 -15 -5 -24 -6 -15 -12 -18 47 -9 -7 -6 -10 -5 -28 -16 -16 -15 -8 -24 -22 -12 1 -16 36 -1 -8 -17 -5 -1 -11 -8 -12 -9 7 -1 -14 -15 -15 18 20 -13 -4 -13 25 -4 -16 7 37 -13 -3 -16 -10 5 -14 -16 30 -16 15 0 -11 2 -19 7 11 -8 -14 -16 8 -5 -10 6 38 -4 -11 -5 -12 -16 -3 21 -10 0 -12 14 1 -10 -17 -14 -12 -10 -10 -3 -10 -4 -10 -15 39 -9 -2 -12 -6 -5 -5 -10 43 -15 -5 -14 -7 0 -15 -1 -2 -9 -10 -16 -8 -7 5 -4 40 -5 -6 -11 -7 -16 -20 -14 -15 -17 -4 -20 -3 -5 3 -16 -16 25 14 -2 -24 -7 -20 -16 41 -28 -20 -29 -19 -26 -21 -22 47 -32 -25 -32 -27 -21 7 -22 0 -2 -28 -33 -5 -18 20 -25 42 -17 7 -19 -4 -3 -25 -4 13 -5 6 -22 -21 16 -9 9 3 18 -2 -22 -28 -6 -23 1 43 0 -20 -21 -18 -23 21 -4 -2 0 3 -16 2 -22 -20 -19 25 -23 -17 -9 -18 -8 12 -21 44 -16 -9 -15 -15 -17 -1 -17 10 1 -18 -3 -15 -3 -17 -9 5 -2 29 -8 1 -7 -19 -14 45 -6 -17 -22 -23 -18 -12 -25 -21 -19 -18 -22 0 -12 36 -4 8 -8 -7 -24 1 -12 -26 -12 46 -5 -5 -24 -1 29 -29 -12 -19 -28 -10 -17 -25 -14 3 -15 -20 7 4 -25 -7 -10 -27 25 47 -15 14 -18 8 -9 0 -20 0 -16 6 -19 -19 20 -4 -5 0 -2 5 -16 -3 -5 25 -8 48 9 0 -20 -3 -20 21 -25 12 -21 -15 -21 -20 4 -21 -25 -17 -16 -24 -17 -12 -11 34 -21 49 -9 -13 -22 -16 -11 -12 -25 -22 0 -3 -5 -22 -9 35 -7 -4 -15 -22 -16 -28 -10 -27 -10 50 -3 19 23 5 -4 -24 1 -2 -23 -8 -13 -21 28 -18 1 0 -3 -4 -18 0 -6 -23 -2 51 22 -16 -17 -13 -6 -23 -2 -4 -19 15 6 -18 -22 -27 -9 -10 -5 -20 -7 1 -7 -24 -7 52 -14 11 -26 13 -26 -33 32 -24 -23 -6 -28 -30 9 -21 -12 -28 -24 -27 -32 -33 -16 -33 -21 53 -32 -31 -26 -41 -40 -2 -20 -35 -6 -37 31 -15 -23 -42 -21 -35 -40 -32 -20 -31 -23 -29 -32 54 -10 -1 -20 1 10 -23 12 -20 16 2 -20 -18 -7 -19 -1 2 -14 10 -4 -28 -5 -25 8 55 -14 4 -23 4 17 -23 -19 0 -20 11 -18 33 3 -19 -2 8 -18 -22 -21 -27 -9 -24 14 56 -33 -26 -36 -29 -29 -29 -33 54 -38 -29 -38 -31 -22 -38 -24 -25 -33 -34 -40 -32 -30 -18 -27 57 -12 31 -35 -23 -33 -41 -31 -25 -43 -31 -45 -40 43 -42 -32 -32 -22 -21 -42 -44 -29 -40 -33 58 -47 -53 -44 -54 -52 20 -52 -31 -42 -50 -42 -42 -50 -56 -49 -47 -51 -48 -43 -28 -42 46 -51 59 -51 -63 59 -66 -68 -59 -59 -63 -54 -64 -55 -54 -60 -65 -66 -65 -56 -53 -51 -55 -57 -59 -68 60 -46 -45 -50 -47 -42 -50 -50 -14 -51 -29 -49 -45 -42 -53 -37 42 -46 -45 -49 -50 -41 -47 -40 61 -46 32 -44 -32 -43 -51 -40 -33 -53 -40 -55 -49 44 -51 -41 -41 -27 -40 -51 -53 -40 -49 -42 62 -44 -47 -46 -46 -47 -53 -49 -47 -51 -44 -52 -51 -49 43 -47 -26 -47 -46 -49 -52 -43 -53 -47 63 -35 32 -38 40 -22 -41 -10 -29 -40 -21 -43 -40 -6 -37 -30 -11 -32 -33 -41 -44 -27 -42 -24 64 19 6 -23 -9 -29 -32 24 -25 -32 -26 -33 -29 15 -2 -28 -2 -5 -26 -28 -7 -14 -32 -29 65 -9 18 -24 25 12 -28 -15 -22 -19 -5 -26 -23 -6 -29 2 -9 2 -22 16 -32 -9 -29 10 66 3 -4 -9 -1 16 -15 -6 -10 0 -3 -12 0 -10 10 -1 -10 2 2 6 -18 -2 -15 12 67 15 -7 -18 -18 8 -24 -1 11 0 7 -14 -19 0 2 -5 4 -1 0 -15 -27 -3 -23 6 68 18 -26 -24 -28 -27 -32 20 -11 -31 5 -25 -27 -25 -32 -16 20 1 -26 -28 -33 -14 -31 -23 69 -16 -42 -40 -41 -41 -48 -43 -42 -45 -39 -46 -45 -44 42 -42 -44 -41 -40 -27 -47 -36 -47 -42 70 -51 -56 -41 -57 -54 -30 -52 -40 -47 -53 -45 -45 -54 -56 -48 -50 -55 -52 -49 59 -46 27 -52 71 -51 -63 59 -66 -68 -59 -59 -63 -54 -64 -55 -54 -60 -65 -66 -65 -56 -53 -51 -55 -57 -59 -68 72 -42 -47 -38 -49 -47 24 -47 4 -36 -44 -36 -36 -45 -51 -44 -42 -45 -43 -38 -24 -36 44 -46 73 -30 -34 -28 -36 -38 -36 -38 -36 -14 -35 -33 -30 -32 -40 -37 -36 -28 37 14 -41 -25 -19 -38 74 -8 -15 -17 -13 -22 -3 -12 -18 -4 -6 -1 23 -19 -27 1 17 -7 22 -12 1 -6 -21 -10 75 -26 28 -27 34 -16 -31 -14 -20 -12 5 -31 -14 15 -29 -14 -6 -12 -23 -8 -34 -14 -32 -16 76 12 10 -1 -2 -7 -11 -3 -2 -7 -5 -10 -6 18 -11 -6 -6 0 14 -4 -14 -2 -10 -7 77 16 7 -9 8 -12 -18 18 -10 -17 -10 -18 -14 5 -18 -1 3 1 -11 -13 -20 -5 -18 -8 78 -22 -12 -24 -9 -15 -30 -5 -24 -28 -13 -10 -27 -17 37 -7 2 -2 -24 -27 -30 -13 -17 -12 79 -11 6 0 0 3 -17 15 -8 -25 9 -16 -21 12 -6 2 8 8 -4 -24 -26 -5 -24 2 80 -19 -27 -16 -28 -20 1 -10 -24 7 6 0 -6 -26 -20 -2 -16 -25 0 27 -25 -8 -1 -13 81 -23 -11 -25 -7 -10 -8 -28 -18 -9 -5 -4 -21 -21 2 -12 34 -5 -2 -24 -28 -10 -25 -11 82 -20 -30 -18 -31 -22 15 -28 -10 -9 -26 -12 -5 -29 -33 -25 0 -10 -15 0 53 -14 8 -23 83 -13 8 -33 14 33 -36 -4 -22 -36 -21 -36 -31 -16 -32 7 -24 -27 -20 -34 -35 -18 -34 29 84 -29 -32 -26 -33 -1 19 -34 -7 -23 -31 -10 -23 -32 -23 -30 -29 -10 -30 -9 -13 -18 41 -5 85 -51 -63 59 -66 -68 -59 -59 -63 -54 -64 -55 -54 -60 -65 -66 -65 -56 -53 -51 -55 -57 -59 -68 86 -4 -8 -6 -10 -11 -4 -9 18 -14 -9 -15 -11 -5 -15 -9 -10 23 -4 -12 -8 -5 21 -10 87 -3 25 -22 20 -11 -28 -10 -15 -27 -9 -29 5 29 -6 3 -11 3 -11 -26 -30 -10 -28 -5 88 -32 -42 -27 -42 -43 -24 -43 -39 23 -39 22 -3 -42 -43 -40 -38 -40 -9 13 -36 -23 -32 -42 89 -11 -12 -20 -21 -13 -28 -24 0 -18 9 -22 -23 -4 27 -6 -5 -3 22 -21 -29 -10 -26 -11 90 -4 -4 -20 -3 -3 -16 -22 -13 -21 6 -19 -9 -6 -6 28 15 0 -6 0 -23 -5 -2 13 91 -51 -63 59 -66 -68 -59 -59 -63 -54 -64 -55 -54 -60 -65 -66 -65 -56 -53 -51 -55 -57 -59 -68 92 0 -1 -18 4 9 -27 0 -20 -19 -19 -16 -22 -17 1 -3 -8 23 3 -11 -29 -6 -26 7 93 -6 17 -20 24 12 -24 0 0 -19 -1 -17 -11 -10 -9 -1 -14 1 2 3 -27 -5 -15 9 * 544 0 936 660 626 231 965 404 255 444 462 215 808 934 532 881 904 1049 414 399 0 838 0 TEST02: PS_LG_FSQ - Forward score quadratic; PS_LG_FSL - Forward score linear; GAP_OPEN penalty = -10.0000 GAP_EXTEND penalty = -5.00000 Matching scores by PS_SCORE_12. Verify that the FSQ and FSL tables agree. I B 1 C 2 A 3 T 4 G 5 X 6 C 7 C 8 T 9 G 10 C 11 T 12 T Matching Scores: 0 1 2 3 4 5 6 7 8 9 10 11 12 C A T G X C C T G C T T 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 3.0 -1.0 -5.0 5.0-10.0 3.0 3.0 -5.0 5.0 3.0 -5.0 -5.0 2 0.0 5.0 -5.0 -1.0 3.0-10.0 5.0 5.0 -1.0 3.0 5.0 -1.0 -1.0 3 0.0 -1.0 3.0 5.0 -5.0-10.0 -1.0 -1.0 5.0 -5.0 -1.0 5.0 5.0 4 0.0 3.0 -1.0 -5.0 5.0-10.0 3.0 3.0 -5.0 5.0 3.0 -5.0 -5.0 5 0.0 -5.0 5.0 3.0 -1.0-10.0 -5.0 -5.0 3.0 -1.0 -5.0 3.0 3.0 6 0.0 -1.0 3.0 5.0 -5.0-10.0 -1.0 -1.0 5.0 -5.0 -1.0 5.0 5.0 7 0.0 -5.0 5.0 3.0 -1.0-10.0 -5.0 -5.0 3.0 -1.0 -5.0 3.0 3.0 8 0.0 -1.0 3.0 5.0 -5.0-10.0 -1.0 -1.0 5.0 -5.0 -1.0 5.0 5.0 9 0.0 -5.0 5.0 3.0 -1.0-10.0 -5.0 -5.0 3.0 -1.0 -5.0 3.0 3.0 10 0.0 3.0 -1.0 -5.0 5.0-10.0 3.0 3.0 -5.0 5.0 3.0 -5.0 -5.0 11 0.0 5.0 -5.0 -1.0 3.0-10.0 5.0 5.0 -1.0 3.0 5.0 -1.0 -1.0 12 0.0 -1.0 3.0 5.0 -5.0-10.0 -1.0 -1.0 5.0 -5.0 -1.0 5.0 5.0 PS_LG_FSQ: 0 1 2 3 4 5 6 7 8 9 10 11 12 SF: 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 3.0 0.0 0.0 5.0 0.0 3.0 3.0 0.0 5.0 3.0 0.0 0.0 2 0.0 5.0 0.0 0.0 3.0 0.0 5.0 8.0 2.0 3.0 10.0 2.0 0.0 3 0.0 0.0 8.0 5.0 0.0 0.0 0.0 4.0 13.0 1.5 2.0 15.0 7.0 4 0.0 3.0 0.0 3.0 10.0 1.0 3.0 3.0 1.5 18.0 9.0 6.0 10.0 5 0.0 0.0 8.0 3.0 2.0 0.0 0.0 0.0 6.0 9.0 13.0 12.0 9.0 6 0.0 0.0 3.0 13.0 6.5 4.0 1.5 0.0 5.0 6.5 8.0 18.0 17.0 7 0.0 0.0 5.0 6.5 12.0 5.5 3.0 0.5 3.0 4.0 4.0 11.5 21.0 8 0.0 0.0 3.0 10.0 5.5 2.0 4.5 2.0 5.5 1.5 3.0 9.0 16.5 9 0.0 0.0 5.0 6.0 9.0 0.8 0.0 0.0 5.0 4.5 0.0 6.0 12.0 10 0.0 3.0 0.0 0.0 11.0 0.0 3.8 3.0 0.0 10.0 7.5 0.8 6.3 11 0.0 5.0 0.0 0.0 3.0 1.0 5.0 8.8 2.0 3.0 15.0 6.5 1.8 12 0.0 0.0 8.0 5.0 0.0 0.0 0.0 4.0 13.8 0.0 2.0 20.0 11.5 EF: 0 0.0-15.0-20.0-25.0-30.0-35.0-40.0-45.0-50.0-55.0-60.0-65.0-70.0 1-25.0-14.0-11.0-14.0-14.0 -9.0-13.5-11.0-11.0-14.0 -9.0-11.0-14.0 2-29.5-13.5 -8.5-12.5-13.5-10.5-13.5 -8.5 -5.5 -9.5-10.5 -3.5 -7.5 3-33.5-11.5-11.5 -3.5 -6.5-10.0-11.5-11.5 -7.5 1.5 -2.0 -5.5 3.5 4-37.0 -9.0 -6.0 -9.0 -6.0 1.0 -2.0 -5.0 -6.0 -7.5 9.0 6.0 3.0 5-40.0 -6.5 -6.5 1.5 -1.0 -3.5 -6.0 -6.5 -6.5 -0.5 2.5 6.5 5.5 6-42.5 -6.5 -6.5 -3.5 6.5 4.0 1.5 -1.0 -3.5 -1.5 0.0 1.5 11.5 7-45.0 -6.5 -6.5 -1.5 0.0 5.5 3.0 0.5 -2.0 -3.5 -2.5 -2.5 5.0 8-47.5 -8.0 -8.0 -5.0 2.0 -2.0 -6.0 -3.5 -6.0 -2.5 -6.5 -5.0 1.0 9-51.5 -8.3 -8.3 -3.3 -2.3 0.8 -3.5 -7.8 -8.3 -3.3 -3.8 -8.0 -2.3 10-55.8-12.0 -9.0-12.0-12.0 -1.0 -5.5 -8.3 -9.0-12.0 -2.0 -4.5 -9.0 11-60.3-13.8 -8.8-13.5-13.8-10.8-12.8 -8.8 -5.0 -9.8-10.8 1.3 -3.5 12-65.0-15.0-15.0 -7.0-10.0-15.0-15.0-15.0-11.0 -1.3 -6.3-11.3 5.0 FF: 0 0.0-25.0-30.0-35.0-40.0-45.0-50.0-55.0-60.0-65.0-70.0-75.0-80.0 1-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0 2-19.5-11.0-14.0-14.0 -9.0-14.0-11.0-11.0-14.0 -9.0-11.0-14.0-14.0 3-23.5 -8.5-13.5-13.5-10.5-13.5 -8.5 -5.5-11.5-10.5 -3.5-11.5-13.5 4-27.0-11.5 -3.5 -6.5-11.5-11.5-11.5 -7.5 1.5-10.0 -7.0 3.5 -4.5 5-30.0 -6.0 -6.5 -6.0 1.0 -8.0 -6.0 -6.0 -1.5 9.0 0.0 0.5 1.0 6-32.5 -6.5 1.5 -3.5 -1.5 -6.5 -6.5 -6.5 -0.5 6.5 6.5 5.5 2.5 7-35.0 -6.5 -1.0 6.5 0.0 -2.5 -5.0 -6.5 -1.5 4.0 4.0 11.5 10.5 8-37.5 -6.5 -1.5 4.0 5.5 -1.0 -3.5 -6.0 -3.5 1.5 1.5 9.0 14.5 9-41.5 -8.0 -5.0 2.0 1.5 -5.0 -3.5 -6.0 -2.5 -2.5 -2.5 5.0 10.5 10-45.8 -8.3 -3.3 -2.3 0.8 -7.5 -7.8 -8.3 -3.3 -3.8 -6.8 0.8 6.3 11-50.3 -9.0 -7.8 -6.8 -1.0-12.0 -8.3 -9.0 -7.8 -2.0 -4.5 -3.8 1.8 12-55.0 -8.8-12.5-11.5 -5.8-12.8 -8.8 -5.0-11.8 -6.8 1.3 -7.3 -3.0 TF: 0 8 8 8 8 8 8 8 8 8 8 8 8 8 1 8 1 8 8 1 8 1 1 8 1 1 8 8 2 8 1 8 8 1 8 1 1 1 1 1 1 8 3 8 8 1 1 8 8 8 1 1 2 1 1 1 4 8 1 8 1 1 2 1 1 4 1 2 2 1 5 8 8 1 1 1 9 8 8 1 4 1 1 1 6 8 8 1 1 2 2 2 8 1 4 1 1 1 7 8 8 1 4 1 2 2 2 1 5 4 4 1 8 8 8 1 1 4 1 1 1 1 4 1 5 1 9 8 8 1 1 1 2 8 8 1 1 8 1 1 10 8 1 8 9 1 8 1 1 8 1 1 4 4 11 8 1 8 8 1 1 1 1 1 1 1 1 4 12 8 8 1 1 8 8 9 1 1 8 1 1 1 PS_LG_FSL: 0 1 2 3 4 5 6 7 8 9 10 11 12 SF: 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 3.0 0.0 0.0 5.0 0.0 3.0 3.0 0.0 5.0 3.0 0.0 0.0 2 0.0 5.0 0.0 0.0 3.0 0.0 5.0 8.0 2.0 3.0 10.0 2.0 0.0 3 0.0 0.0 8.0 5.0 0.0 0.0 0.0 4.0 13.0 1.5 2.0 15.0 7.0 4 0.0 3.0 0.0 3.0 10.0 1.0 3.0 3.0 1.5 18.0 9.0 6.0 10.0 5 0.0 0.0 8.0 3.0 2.0 0.0 0.0 0.0 6.0 9.0 13.0 12.0 9.0 6 0.0 0.0 3.0 13.0 6.5 4.0 1.5 0.0 5.0 6.5 8.0 18.0 17.0 7 0.0 0.0 5.0 6.5 12.0 5.5 3.0 0.5 3.0 4.0 4.0 11.5 21.0 8 0.0 0.0 3.0 10.0 5.5 2.0 4.5 2.0 5.5 1.5 3.0 9.0 16.5 9 0.0 0.0 5.0 6.0 9.0 0.8 0.0 0.0 5.0 4.5 0.0 6.0 12.0 10 0.0 3.0 0.0 0.0 11.0 0.0 3.8 3.0 0.0 10.0 7.5 0.8 6.3 11 0.0 5.0 0.0 0.0 3.0 1.0 5.0 8.8 2.0 3.0 15.0 6.5 1.8 12 0.0 0.0 8.0 5.0 0.0 0.0 0.0 4.0 13.8 0.0 2.0 20.0 11.5 EF: 0 0.0-15.0-20.0-25.0-30.0-35.0-40.0-45.0-50.0-55.0-60.0-65.0-70.0 1-25.0-14.0-11.0-14.0-14.0 -9.0-13.5-11.0-11.0-14.0 -9.0-11.0-14.0 2-29.5-13.5 -8.5-12.5-13.5-10.5-13.5 -8.5 -5.5 -9.5-10.5 -3.5 -7.5 3-33.5-11.5-11.5 -3.5 -6.5-10.0-11.5-11.5 -7.5 1.5 -2.0 -5.5 3.5 4-37.0 -9.0 -6.0 -9.0 -6.0 1.0 -2.0 -5.0 -6.0 -7.5 9.0 6.0 3.0 5-40.0 -6.5 -6.5 1.5 -1.0 -3.5 -6.0 -6.5 -6.5 -0.5 2.5 6.5 5.5 6-42.5 -6.5 -6.5 -3.5 6.5 4.0 1.5 -1.0 -3.5 -1.5 0.0 1.5 11.5 7-45.0 -6.5 -6.5 -1.5 0.0 5.5 3.0 0.5 -2.0 -3.5 -2.5 -2.5 5.0 8-47.5 -8.0 -8.0 -5.0 2.0 -2.0 -6.0 -3.5 -6.0 -2.5 -6.5 -5.0 1.0 9-51.5 -8.3 -8.3 -3.3 -2.3 0.8 -3.5 -7.8 -8.3 -3.3 -3.8 -8.0 -2.3 10-55.8-12.0 -9.0-12.0-12.0 -1.0 -5.5 -8.3 -9.0-12.0 -2.0 -4.5 -9.0 11-60.3-13.8 -8.8-13.5-13.8-10.8-12.8 -8.8 -5.0 -9.8-10.8 1.3 -3.5 12-65.0-15.0-15.0 -7.0-10.0-15.0-15.0-15.0-11.0 -1.3 -6.3-11.3 5.0 FF: 0 0.0-25.0-30.0-35.0-40.0-45.0-50.0-55.0-60.0-65.0-70.0-75.0-80.0 1-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0-15.0 2-19.5-11.0-14.0-14.0 -9.0-14.0-11.0-11.0-14.0 -9.0-11.0-14.0-14.0 3-23.5 -8.5-13.5-13.5-10.5-13.5 -8.5 -5.5-11.5-10.5 -3.5-11.5-13.5 4-27.0-11.5 -3.5 -6.5-11.5-11.5-11.5 -7.5 1.5-10.0 -7.0 3.5 -4.5 5-30.0 -6.0 -6.5 -6.0 1.0 -8.0 -6.0 -6.0 -1.5 9.0 0.0 0.5 1.0 6-32.5 -6.5 1.5 -3.5 -1.5 -6.5 -6.5 -6.5 -0.5 6.5 6.5 5.5 2.5 7-35.0 -6.5 -1.0 6.5 0.0 -2.5 -5.0 -6.5 -1.5 4.0 4.0 11.5 10.5 8-37.5 -6.5 -1.5 4.0 5.5 -1.0 -3.5 -6.0 -3.5 1.5 1.5 9.0 14.5 9-41.5 -8.0 -5.0 2.0 1.5 -5.0 -3.5 -6.0 -2.5 -2.5 -2.5 5.0 10.5 10-45.8 -8.3 -3.3 -2.3 0.8 -7.5 -7.8 -8.3 -3.3 -3.8 -6.8 0.8 6.3 11-50.3 -9.0 -7.8 -6.8 -1.0-12.0 -8.3 -9.0 -7.8 -2.0 -4.5 -3.8 1.8 12-55.0 -8.8-12.5-11.5 -5.8-12.8 -8.8 -5.0-11.8 -6.8 1.3 -7.3 -3.0 TF: 0 8 8 8 8 8 8 8 8 8 8 8 8 8 1 8 1 8 8 1 8 1 1 8 1 1 8 8 2 8 1 8 8 1 8 1 1 1 1 1 1 8 3 8 8 1 1 8 8 8 1 1 2 1 1 1 4 8 1 8 1 1 2 1 1 4 1 2 2 1 5 8 8 1 1 1 9 8 8 1 4 1 1 1 6 8 8 1 1 2 2 2 8 1 4 1 1 1 7 8 8 1 4 1 2 2 2 1 5 4 4 1 8 8 8 1 1 4 1 1 1 1 4 1 5 1 9 8 8 1 1 1 2 8 8 1 1 8 1 1 10 8 1 8 9 1 8 1 1 8 1 1 4 4 11 8 1 8 8 1 1 1 1 1 1 1 1 4 12 8 8 1 1 8 8 9 1 1 8 1 1 1 TEST03: PS_LG_BSQ - Backward score quadratic; PS_LG_BSL - Backward score linear; GAP_OPEN penalty = -10.0000 GAP_EXTEND penalty = -5.00000 Matching scores by PS_SCORE_12. Compare with the FSQ and FSL results. (The maxima of the SF and SB tables should agree.) Verify that the BSQ and BSL tables agree. I B 1 C 2 A 3 T 4 G 5 X 6 C 7 C 8 T 9 G 10 C 11 T 12 T Matching Scores: 0 1 2 3 4 5 6 7 8 9 10 11 12 C A T G X C C T G C T T 0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 3.0 -1.0 -5.0 5.0-10.0 3.0 3.0 -5.0 5.0 3.0 -5.0 -5.0 2 0.0 5.0 -5.0 -1.0 3.0-10.0 5.0 5.0 -1.0 3.0 5.0 -1.0 -1.0 3 0.0 -1.0 3.0 5.0 -5.0-10.0 -1.0 -1.0 5.0 -5.0 -1.0 5.0 5.0 4 0.0 3.0 -1.0 -5.0 5.0-10.0 3.0 3.0 -5.0 5.0 3.0 -5.0 -5.0 5 0.0 -5.0 5.0 3.0 -1.0-10.0 -5.0 -5.0 3.0 -1.0 -5.0 3.0 3.0 6 0.0 -1.0 3.0 5.0 -5.0-10.0 -1.0 -1.0 5.0 -5.0 -1.0 5.0 5.0 7 0.0 -5.0 5.0 3.0 -1.0-10.0 -5.0 -5.0 3.0 -1.0 -5.0 3.0 3.0 8 0.0 -1.0 3.0 5.0 -5.0-10.0 -1.0 -1.0 5.0 -5.0 -1.0 5.0 5.0 9 0.0 -5.0 5.0 3.0 -1.0-10.0 -5.0 -5.0 3.0 -1.0 -5.0 3.0 3.0 10 0.0 3.0 -1.0 -5.0 5.0-10.0 3.0 3.0 -5.0 5.0 3.0 -5.0 -5.0 11 0.0 5.0 -5.0 -1.0 3.0-10.0 5.0 5.0 -1.0 3.0 5.0 -1.0 -1.0 12 0.0 -1.0 3.0 5.0 -5.0-10.0 -1.0 -1.0 5.0 -5.0 -1.0 5.0 5.0 PS_LG_BSQ: 0 1 2 3 4 5 6 7 8 9 10 11 12 SB: 0 8.0 0.0 0.0 5.0 6.0 21.0 8.0 0.0 15.0 7.0 0.0 0.0 0.0 1 8.0 5.0 0.0 3.0 0.0 5.0 18.0 5.0 3.0 10.0 4.0 0.0 0.0 2 6.5 3.0 10.0 0.0 0.0 5.5 0.0 13.0 6.0 0.0 5.0 5.0 0.0 3 20.0 5.5 0.0 5.0 0.0 6.0 6.5 1.0 8.0 11.0 0.0 0.0 0.0 4 8.0 17.0 3.5 2.0 0.0 3.0 3.0 3.5 6.0 3.0 8.0 3.0 0.0 5 12.8 11.5 12.0 0.5 3.0 9.5 8.0 7.0 0.5 7.0 8.0 5.0 0.0 6 7.3 13.8 8.5 7.0 5.5 12.0 10.5 9.0 2.0 3.0 8.0 3.0 0.0 7 4.5 11.0 8.8 5.5 8.0 10.5 17.0 12.0 4.5 2.0 8.0 5.0 0.0 8 0.0 5.0 8.0 3.8 3.0 6.0 10.0 18.0 7.0 0.0 3.0 3.0 0.0 9 3.0 0.0 0.0 5.0 4.8 13.0 3.0 6.8 15.0 7.0 0.0 0.0 0.0 10 8.0 0.0 0.0 3.0 0.0 5.0 10.0 0.0 3.0 10.0 4.0 0.0 0.0 11 0.0 3.0 5.0 0.0 0.0 0.0 0.0 5.0 0.0 0.0 5.0 5.0 0.0 12 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 EB: 0-14.0 -9.0 -4.0 1.0 6.0 -7.0 -5.0 0.0 -8.0-15.0-15.0-15.0-65.0 1 -9.0-14.0 -9.5 -5.0 -0.5 4.0 -9.0 -8.5 -4.0-10.0-14.0-14.0-59.0 2 -7.5 -3.5-13.5-12.0 -8.0 -4.5 -0.5 -7.5-12.5 -8.5 -8.5-13.5-54.5 3 -6.0-10.0 -6.5 -9.0 -5.5 -5.0 -7.0 -3.5 -0.5-11.5-11.5-11.5-47.5 4 8.0 -5.5 -7.0 -9.0 -6.0 -6.0 -5.5 -3.0 -4.0 -1.0 -6.0 -9.0-40.0 5 5.0 5.5 -2.0 0.5 3.0 1.5 0.5 -2.0 0.5 1.5 -1.5 -6.5-33.0 6 7.3 2.0 0.5 3.0 5.5 4.0 2.5 -3.5 -1.0 1.5 -3.5 -6.5-30.5 7 4.5 2.3 3.0 5.5 8.0 10.5 5.5 -2.0 -1.0 1.5 -1.5 -6.5-28.0 8 -3.0 0.0 -4.3 -2.0 2.0 6.0 10.0 -1.0 -8.0 -5.0 -5.0 -8.0-25.5 9 -8.3 -7.5 -3.3 0.5 4.8 -1.8 2.5 6.8 -1.3 -8.3 -8.3 -8.3-21.5 10-12.0-12.0 -9.0-11.0 -6.5 -2.0-11.0 -6.5 -2.0 -8.0-12.0-12.0-24.3 11-10.8 -8.8-13.8-13.8-13.8-13.5 -8.8-13.8-13.5 -8.8 -8.8-13.8-22.8 12-70.0-65.0-60.0-55.0-50.0-45.0-40.0-35.0-30.0-25.0-20.0-15.0 0.0 FB: 0 -3.5-10.0 -9.5-12.0-15.0-10.0 3.0 -6.5-12.0 -5.0-11.0-14.5-55.0 1 2.0 -4.5 -4.0-13.0-14.0 -8.5-11.5 -1.0 -8.0 -7.0 -9.0 -9.0-49.0 2 6.5 0.0 -8.0 -8.5-13.5 -7.5 -7.0 -9.5 -5.5 -2.5 -9.0-13.5-44.5 3 -1.8 5.5 -2.5 -9.5-11.5 -5.0 -2.5 -4.0 -5.5 -7.5 -3.5 -8.5-37.5 4 3.8 2.5 3.0 -4.5 -6.0 0.5 3.0 1.5 -5.5 -2.0 -1.0 -4.0-30.0 5 0.8 7.3 2.0 0.5 -1.0 5.5 8.0 6.5 -0.5 -3.5 1.5 -3.5-23.0 6 -2.0 4.5 2.3 -1.0 1.5 4.0 10.5 9.0 2.0 -4.5 1.5 -1.5-20.5 7 -6.5 -1.5 1.5 -2.8 -3.5 2.5 3.5 11.5 4.5 -3.5 -3.5 -3.5-18.0 8 -4.3 -8.0 -8.0 -3.0 -3.3 5.0 -2.3 -1.3 7.0 -1.0 -8.0 -8.0-15.5 9 -0.3 -8.3 -7.8 -5.3 -8.3 -3.3 1.8 -7.8 -5.3 1.8 -4.3 -7.8-11.5 10-12.0 -9.0 -7.0-12.0-12.0-12.0-12.0 -7.0-12.0-12.0 -7.0 -7.0-14.3 11-13.8-13.8-13.8-13.8-13.8-13.8-13.8-13.8-13.8-13.8-13.8-13.8-12.8 12-80.0-75.0-70.0-65.0-60.0-55.0-50.0-45.0-40.0-35.0-30.0-25.0 0.0 TB: 0 1 8 8 1 2 1 1 10 1 1 8 8 8 1 1 1 8 1 8 1 1 1 1 1 1 8 8 2 4 1 1 8 8 1 9 1 1 8 1 1 8 3 1 4 8 1 8 1 1 1 1 1 8 8 8 4 2 1 1 1 8 1 4 1 1 1 1 1 8 5 1 1 1 7 2 1 5 1 2 1 1 1 8 6 2 1 1 1 2 1 4 4 4 1 1 1 8 7 2 1 1 2 2 2 1 1 4 1 1 1 8 8 8 1 1 1 1 2 2 1 4 8 1 1 8 9 1 8 8 1 2 1 1 2 1 1 8 8 8 10 1 9 8 1 8 1 1 8 1 1 1 8 8 11 8 1 1 8 8 8 8 1 8 8 1 1 8 12 8 8 8 8 8 8 8 8 8 8 8 8 8 PS_LG_BSL: 0 1 2 3 4 5 6 7 8 9 10 11 12 SB: 0 8.0 0.0 0.0 5.0 6.0 21.0 8.0 0.0 15.0 7.0 0.0 0.0 0.0 1 8.0 5.0 0.0 3.0 0.0 5.0 18.0 5.0 3.0 10.0 4.0 0.0 0.0 2 6.5 3.0 10.0 0.0 0.0 5.5 0.0 13.0 6.0 0.0 5.0 5.0 0.0 3 20.0 5.5 0.0 5.0 0.0 6.0 6.5 1.0 8.0 11.0 0.0 0.0 0.0 4 8.0 17.0 3.5 2.0 0.0 3.0 3.0 3.5 6.0 3.0 8.0 3.0 0.0 5 12.8 11.5 12.0 0.5 3.0 9.5 8.0 7.0 0.5 7.0 8.0 5.0 0.0 6 7.3 13.8 8.5 7.0 5.5 12.0 10.5 9.0 2.0 3.0 8.0 3.0 0.0 7 4.5 11.0 8.8 5.5 8.0 10.5 17.0 12.0 4.5 2.0 8.0 5.0 0.0 8 0.0 5.0 8.0 3.8 3.0 6.0 10.0 18.0 7.0 0.0 3.0 3.0 0.0 9 3.0 0.0 0.0 5.0 4.8 13.0 3.0 6.8 15.0 7.0 0.0 0.0 0.0 10 8.0 0.0 0.0 3.0 0.0 5.0 10.0 0.0 3.0 10.0 4.0 0.0 0.0 11 0.0 3.0 5.0 0.0 0.0 0.0 0.0 5.0 0.0 0.0 5.0 5.0 0.0 12 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 EB: 0-14.0 -9.0 -4.0 1.0 6.0 -7.0 -5.0 0.0 -8.0-15.0-15.0-15.0-65.0 1 -9.0-14.0 -9.5 -5.0 -0.5 4.0 -9.0 -8.5 -4.0-10.0-14.0-14.0-59.0 2 -7.5 -3.5-13.5-12.0 -8.0 -4.5 -0.5 -7.5-12.5 -8.5 -8.5-13.5-54.5 3 -6.0-10.0 -6.5 -9.0 -5.5 -5.0 -7.0 -3.5 -0.5-11.5-11.5-11.5-47.5 4 8.0 -5.5 -7.0 -9.0 -6.0 -6.0 -5.5 -3.0 -4.0 -1.0 -6.0 -9.0-40.0 5 5.0 5.5 -2.0 0.5 3.0 1.5 0.5 -2.0 0.5 1.5 -1.5 -6.5-33.0 6 7.3 2.0 0.5 3.0 5.5 4.0 2.5 -3.5 -1.0 1.5 -3.5 -6.5-30.5 7 4.5 2.3 3.0 5.5 8.0 10.5 5.5 -2.0 -1.0 1.5 -1.5 -6.5-28.0 8 -3.0 0.0 -4.3 -2.0 2.0 6.0 10.0 -1.0 -8.0 -5.0 -5.0 -8.0-25.5 9 -8.3 -7.5 -3.3 0.5 4.8 -1.8 2.5 6.8 -1.3 -8.3 -8.3 -8.3-21.5 10-12.0-12.0 -9.0-11.0 -6.5 -2.0-11.0 -6.5 -2.0 -8.0-12.0-12.0-24.3 11-10.8 -8.8-13.8-13.8-13.8-13.5 -8.8-13.8-13.5 -8.8 -8.8-13.8-22.8 12-70.0-65.0-60.0-55.0-50.0-45.0-40.0-35.0-30.0-25.0-20.0-15.0 0.0 FB: 0 -3.5-10.0 -9.5-12.0-15.0-10.0 3.0 -6.5-12.0 -5.0-11.0-14.5-55.0 1 2.0 -4.5 -4.0-13.0-14.0 -8.5-11.5 -1.0 -8.0 -7.0 -9.0 -9.0-49.0 2 6.5 0.0 -8.0 -8.5-13.5 -7.5 -7.0 -9.5 -5.5 -2.5 -9.0-13.5-44.5 3 -1.8 5.5 -2.5 -9.5-11.5 -5.0 -2.5 -4.0 -5.5 -7.5 -3.5 -8.5-37.5 4 3.8 2.5 3.0 -4.5 -6.0 0.5 3.0 1.5 -5.5 -2.0 -1.0 -4.0-30.0 5 0.8 7.3 2.0 0.5 -1.0 5.5 8.0 6.5 -0.5 -3.5 1.5 -3.5-23.0 6 -2.0 4.5 2.3 -1.0 1.5 4.0 10.5 9.0 2.0 -4.5 1.5 -1.5-20.5 7 -6.5 -1.5 1.5 -2.8 -3.5 2.5 3.5 11.5 4.5 -3.5 -3.5 -3.5-18.0 8 -4.3 -8.0 -8.0 -3.0 -3.3 5.0 -2.3 -1.3 7.0 -1.0 -8.0 -8.0-15.5 9 -0.3 -8.3 -7.8 -5.3 -8.3 -3.3 1.8 -7.8 -5.3 1.8 -4.3 -7.8-11.5 10-12.0 -9.0 -7.0-12.0-12.0-12.0-12.0 -7.0-12.0-12.0 -7.0 -7.0-14.3 11-13.8-13.8-13.8-13.8-13.8-13.8-13.8-13.8-13.8-13.8-13.8-13.8-12.8 12-80.0-75.0-70.0-65.0-60.0-55.0-50.0-45.0-40.0-35.0-30.0-25.0 0.0 TB: 0 1 8 8 1 2 1 1 10 1 1 8 8 8 1 1 1 8 1 8 1 1 1 1 1 1 8 8 2 4 1 1 8 8 1 9 1 1 8 1 1 8 3 1 4 8 1 8 1 1 1 1 1 8 8 8 4 2 1 1 1 8 1 4 1 1 1 1 1 8 5 1 1 1 7 2 1 5 1 2 1 1 1 8 6 2 1 1 1 2 1 4 4 4 1 1 1 8 7 2 1 1 2 2 2 1 1 4 1 1 1 8 8 8 1 1 1 1 2 2 1 4 8 1 1 8 9 1 8 8 1 2 1 1 2 1 1 8 8 8 10 1 9 8 1 8 1 1 8 1 1 1 8 8 11 8 1 1 8 8 8 8 1 8 8 1 1 8 12 8 8 8 8 8 8 8 8 8 8 8 8 8 TEST04: PS_LG_BPQ - Backward path quadratic; PS_LG_BSQ - Backward score quadratic; PS_LG_FPQ - Forward path quadratic; PS_LG_FSQ - Forward score quadratic; GAP_OPEN penalty = -10.0000 GAP_EXTEND penalty = -5.00000 Matching scores by PS_SCORE_12. Verify that the FSQ and BSQ paths agree. I B 1 C 2 A 3 T 4 G 5 X 6 C 7 C 8 T 9 G 10 C 11 T 12 T PS_LG_FSQ: Optimal score indices: 7 12 Optimal score: 21.0000 FSQ Matching path: 1 0 5 2 1 6 3 2 7 4 3 8 5 4 9 6 5 10 7 6 11 8 7 12 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 1 - C 6 3.00 3.00 2 - C 7 5.00 8.00 3 - T 8 5.00 13.00 4 - G 9 5.00 18.00 5 - C 10 -5.00 13.00 6 - T 11 5.00 18.00 7 - T 12 3.00 21.00 PS_LG_BSQ: Optimal score indices: 0 5 Optimal score: 21.0000 BSQ Matching path: 1 0 5 2 1 6 3 2 7 4 3 8 5 4 9 6 5 10 7 6 11 8 7 12 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 1 - C 6 3.00 3.00 2 - C 7 5.00 8.00 3 - T 8 5.00 13.00 4 - G 9 5.00 18.00 5 - C 10 -5.00 13.00 6 - T 11 5.00 18.00 7 - T 12 3.00 21.00 TEST05: PS_LG_CORNERS - identifies the endpoints of an optimal local alignment. PS_LG_RPL - Recursive path linear; GAP_OPEN penalty = -10.0000 GAP_EXTEND penalty = -5.00000 Matching scores by PS_SCORE_12. Verify that the path agrees with the FSQ and BSQ paths. I B 1 C 2 A 3 T 4 G 5 X 6 C 7 C 8 T 9 G 10 C 11 T 12 T PS_LG_CORNERS: Optimal alignment "corners" are: I1, J1 = 0 5 I2, J2 = 7 12 RPL Matching path: 1 0 5 2 1 6 3 2 7 4 3 8 5 4 9 6 5 10 7 6 11 8 7 12 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 1 - C 6 3.00 3.00 2 - C 7 5.00 8.00 3 - T 8 5.00 13.00 4 - G 9 5.00 18.00 5 - C 10 -5.00 13.00 6 - T 11 5.00 18.00 7 - T 12 3.00 21.00 TEST06: Forward algorithms using quadratic space: PS_LG_FSQ determines an alignment score; PS_LG_FPQ determines an alignment path. I B 1 A 2 C 3 G 4 C 5 T Matching Scores: 0 1 2 3 4 5 A C G C T 0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 -1.0 1.0 -1.0 -5.0 2 0.0 -1.0 4.0 -1.0 4.0 -5.0 3 0.0 4.0 -5.0 4.0 -5.0 -5.0 4 0.0 -1.0 -1.0 -1.0 -1.0 3.0 PS_LG_FSQ: 0 1 2 3 4 5 SF: 0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 2.8 2.4 2.0 1.6 2 0.0 2.8 9.0 7.2 6.8 6.5 3 0.0 4.0 7.2 13.0 11.8 11.6 4 0.0 2.8 7.0 11.8 12.0 14.8 EF: 0 0.0 -2.4 -2.9 -3.4 -3.9 -4.4 1 -2.4 -2.2 2.8 2.4 2.0 1.6 2 -2.8 -1.9 0.9 7.2 6.8 6.5 3 -3.2 -1.2 2.8 6.0 11.8 11.6 4 -3.4 -0.9 1.9 6.0 10.9 11.1 FF: 0 0.0 -4.3 -4.8 -5.3 -5.8 -6.3 1 -0.5 -2.4 -2.4 -2.4 -2.4 -2.4 2 -0.9 2.8 0.6 0.2 -0.2 -0.6 3 -1.3 2.5 7.2 5.3 5.0 4.6 4 -1.5 2.8 7.0 11.8 10.6 10.4 TF: 0 8 8 8 8 8 8 1 8 1 2 2 2 2 2 8 4 1 2 2 2 3 8 1 4 1 2 2 4 8 4 4 4 1 1 PS_LG_FSQ: Optimal score indices: 4 5 Optimal score: 14.8000 FSQ Matching path: 1 0 0 2 1 1 3 2 2 4 3 3 5 -1 4 6 4 5 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 1 - A 1 5.00 5.00 2 - C 2 4.00 9.00 3 - G 3 4.00 13.00 | C 4 -1.20 11.80 4 - T 5 3.00 14.80 TEST07: Backward algorithms using quadratic space: PS_LG_BSQ determines an alignment score; PS_LG_BPQ determines an alignment path. Verify that these results match those for PS_LG_FSQ/PS_GG_FPQ on the same data. I B 1 A 2 C 3 G 4 C 5 T Matching Scores: 0 1 2 3 4 5 A C G C T 0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 -1.0 1.0 -1.0 -5.0 2 0.0 -1.0 4.0 -1.0 4.0 -5.0 3 0.0 4.0 -5.0 4.0 -5.0 -5.0 4 0.0 -1.0 -1.0 -1.0 -1.0 3.0 PS_LG_BSQ: 0 1 2 3 4 5 SB: 0 14.8 7.4 6.2 2.8 0.0 0.0 1 7.6 9.8 3.6 5.2 0.5 0.0 2 5.4 4.0 5.8 0.0 1.1 0.0 3 1.2 1.4 1.6 1.8 3.0 0.0 4 0.0 0.0 0.0 0.0 0.0 0.0 EB: 0 5.0 3.8 0.4 -2.4 -2.4 -4.8 1 7.6 2.5 3.0 -1.7 -2.2 -4.1 2 3.6 4.0 -1.1 -0.7 -1.9 -3.1 3 1.2 1.4 1.6 1.8 -1.2 -1.7 4 -2.6 -2.2 -1.8 -1.4 -0.9 0.0 FB: 0 5.2 7.4 3.0 2.8 -0.1 -4.3 1 3.2 1.8 3.6 -0.8 0.5 -3.6 2 -0.7 -0.5 -0.3 -0.1 1.1 -2.6 3 -1.2 -1.2 -1.2 -1.2 -1.2 -1.2 4 -3.1 -2.7 -2.3 -1.8 -1.4 0.0 TB: 0 1 4 1 4 8 8 1 2 1 4 1 4 8 2 1 2 1 8 4 8 3 2 2 2 2 1 8 4 8 8 8 8 8 8 PS_LG_BSQ: Optimal score indices: 0 0 Optimal score: 14.8000 BSQ Matching path: 1 0 0 2 1 1 3 2 2 4 3 3 5 -1 4 6 4 5 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 1 - A 1 5.00 5.00 2 - C 2 4.00 9.00 3 - G 3 4.00 13.00 | C 4 -1.20 11.80 4 - T 5 3.00 14.80 TEST08: PS_LG_CORNERS determines determines the endpoints of an optimal local alignment; PS_LG_RPL determines an alignment path. Verify that these results match those for PS_LG_FSQ/PS_GG_FPQ and PS_GG_BSQ/PS_GG_BPQ on the same data. I B 1 A 2 C 3 G 4 C 5 T PS_LG_CORNERS: Optimal alignment "corners" are: I1, J1 = 0 0 I2, J2 = 4 5 RPL Matching path: 1 0 0 2 1 1 3 2 2 4 3 3 5 -1 4 6 4 5 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 1 - A 1 5.00 5.00 2 - C 2 4.00 9.00 3 - G 3 4.00 13.00 | C 4 -1.20 11.80 4 - T 5 3.00 14.80 TEST09: Backward algorithm using linear space: PS_LG_BSL determines an alignment score; Recursive algorithm using linear space: PS_LG_RPL determines an alignment path. Verify that these results match those for PS_LG_FSQ/PS_GG_FPQ, PS_GG_BSQ/PS_GG_BPQ and PS_LG_FSL/PS_GG_RPL on the same data. I B 1 A 2 C 3 G 4 C 5 T Matching Scores: 0 1 2 3 4 5 A C G C T 0 0.0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 -1.0 1.0 -1.0 -5.0 2 0.0 -1.0 4.0 -1.0 4.0 -5.0 3 0.0 4.0 -5.0 4.0 -5.0 -5.0 4 0.0 -1.0 -1.0 -1.0 -1.0 3.0 PS_LG_BSL: 0 1 2 3 4 5 SB: 0 14.8 7.4 6.2 2.8 0.0 0.0 1 7.6 9.8 3.6 5.2 0.5 0.0 2 5.4 4.0 5.8 0.0 1.1 0.0 3 1.2 1.4 1.6 1.8 3.0 0.0 4 0.0 0.0 0.0 0.0 0.0 0.0 EB: 0 5.0 3.8 0.4 -2.4 -2.4 -4.8 1 7.6 2.5 3.0 -1.7 -2.2 -4.1 2 3.6 4.0 -1.1 -0.7 -1.9 -3.1 3 1.2 1.4 1.6 1.8 -1.2 -1.7 4 -2.6 -2.2 -1.8 -1.4 -0.9 0.0 FB: 0 5.2 7.4 3.0 2.8 -0.1 -4.3 1 3.2 1.8 3.6 -0.8 0.5 -3.6 2 -0.7 -0.5 -0.3 -0.1 1.1 -2.6 3 -1.2 -1.2 -1.2 -1.2 -1.2 -1.2 4 -3.1 -2.7 -2.3 -1.8 -1.4 0.0 TB: 0 1 4 1 4 8 8 1 2 1 4 1 4 8 2 1 2 1 8 4 8 3 2 2 2 2 1 8 4 8 8 8 8 8 8 PS_LG_CORNERS: Optimal alignment "corners" are: I1, J1 = 0 0 I2, J2 = 4 5 RPL Matching path: 1 0 0 2 1 1 3 2 2 4 3 3 5 -1 4 6 4 5 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 1 - A 1 5.00 5.00 2 - C 2 4.00 9.00 3 - G 3 4.00 13.00 | C 4 -1.20 11.80 4 - T 5 3.00 14.80 TEST10: Forward algorithms using quadratic space: PS_LG_FSQ determines an alignment score; PS_LG_FPQ determines an alignment path. Sequence name: s00657 (chunk) Sequence: 1 N 2 G 3 Q 4 S 5 Y 6 R 7 G 8 T 9 Y 10 S 11 T 12 T 13 V 14 T 15 G 16 R 17 T 18 C 19 Q 20 A 21 W 22 S 23 S 24 M 25 T 26 P 27 H 28 S 29 H 30 S PS_LG_FSQ: Optimal score indices: 42 30 Optimal score: 1010.51 FSQ Matching path: 1 6 0 2 7 1 3 8 -1 4 9 -1 5 10 2 6 11 3 7 12 4 8 13 5 9 14 6 10 15 7 11 16 8 12 17 9 13 18 10 14 19 11 15 20 12 16 21 13 17 22 14 18 23 15 19 24 16 20 25 17 21 26 18 22 27 19 23 28 20 24 29 21 25 30 22 26 31 23 27 32 24 28 33 25 29 34 26 30 35 27 31 36 -1 32 37 -1 33 38 -1 34 39 -1 35 40 28 36 41 29 37 42 30 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 7 - N 1 32.00 32.00 8 | -2.50 29.50 9 | -0.00 29.50 10 - G 2 38.00 67.50 11 - Q 3 28.00 95.50 12 - S 4 25.00 120.50 13 - Y 5 49.00 169.49 14 - R 6 38.00 207.49 15 - G 7 38.00 245.49 16 - T 8 31.00 276.49 17 - Y 9 26.00 302.49 18 - S 10 29.00 331.49 19 - T 11 31.00 362.49 20 - T 12 37.00 399.49 21 - V 13 23.00 422.49 22 - T 14 26.00 448.49 23 - G 15 37.00 485.49 24 - R 16 28.00 513.49 25 - T 17 25.00 538.49 26 - C 18 59.00 597.49 27 - Q 19 41.00 638.49 28 - A 20 20.00 658.49 29 - W 21 63.00 721.49 30 - S 22 24.00 745.49 31 - S 23 30.00 775.49 32 - M 24 37.00 812.49 33 - T 25 26.00 838.49 34 - P 26 38.00 876.49 35 - H 27 47.00 923.49 36 | -2.50 920.99 37 | -0.35 920.65 38 | -0.13 920.52 39 | -0.00 920.51 40 - S 28 25.00 945.51 41 - H 29 47.00 992.51 42 - S 30 18.00 1010.51 Sequence name: c61545 (chunk) Sequence: 1 D 2 A 3 D 4 K 5 S 6 P 7 W 8 C 9 Y 10 T 11 T 12 D 13 P 14 R 15 V 16 R 17 W 18 E 19 F 20 C 21 N 22 L 23 K 24 K PS_LG_FSQ: Optimal score indices: 90 24 Optimal score: 717.515 FSQ Matching path: 1 62 0 2 63 1 3 64 2 4 65 3 5 66 -1 6 67 4 7 68 5 8 69 6 9 70 7 10 71 8 11 72 9 12 73 10 13 74 11 14 75 12 15 76 -1 16 77 -1 17 78 13 18 79 14 19 80 15 20 81 16 21 82 17 22 83 18 23 84 19 24 85 20 25 86 -1 26 87 21 27 88 22 28 89 23 29 90 24 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 63 - D 1 40.00 40.00 64 - A 2 19.00 59.00 65 - D 3 25.00 84.00 66 | -2.50 81.50 67 - K 4 7.00 88.50 68 - S 5 1.00 89.50 69 - P 6 42.00 131.50 70 - W 7 59.00 190.50 71 - C 8 59.00 249.50 72 - Y 9 44.00 293.50 73 - T 10 37.00 330.50 74 - T 11 22.00 352.50 75 - D 12 34.00 386.50 76 | -2.47 384.02 77 | -0.01 384.01 78 - P 13 37.00 421.01 79 - R 14 8.00 429.01 80 - V 15 27.00 456.01 81 - R 16 34.00 490.01 82 - W 17 53.00 543.02 83 - E 18 33.00 576.02 84 - F 19 19.00 595.02 85 - C 20 59.00 654.02 86 | -2.50 651.52 87 - N 21 29.00 680.52 88 - L 22 22.00 702.52 89 - K 23 9.00 711.52 90 - K 24 6.00 717.52 Sequence name: plhu-k (chunk) Sequence: 1 T 2 P 3 H 4 R 5 H 6 Q 7 K 8 T 9 P 10 E 11 N 12 Y 13 P 14 N 15 A 16 G 17 L 18 T 19 M 20 N 21 Y 22 C 23 R 24 N 25 P 26 D 27 A 28 D 29 K 30 G PS_LG_FSQ: Optimal score indices: 68 30 Optimal score: 912.650 FSQ Matching path: 1 19 0 2 20 1 3 21 -1 4 22 -1 5 23 -1 6 24 -1 7 25 -1 8 26 -1 9 27 -1 10 28 -1 11 29 -1 12 30 -1 13 31 -1 14 32 -1 15 33 -1 16 34 2 17 35 3 18 36 4 19 37 -1 20 38 -1 21 39 -1 22 40 -1 23 41 5 24 42 6 25 43 7 26 44 8 27 45 9 28 46 10 29 47 11 30 48 12 31 49 13 32 50 14 33 51 15 34 52 16 35 53 17 36 54 18 37 55 19 38 56 -1 39 57 20 40 58 21 41 59 22 42 60 23 43 61 24 44 62 25 45 63 26 46 64 27 47 65 28 48 66 -1 49 67 29 50 68 30 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 20 - T 1 37.00 37.00 21 | -2.50 34.50 22 | -0.50 34.00 23 | -0.50 33.50 24 | -0.50 33.01 25 | -0.50 32.51 26 | -0.50 32.02 27 | -0.50 31.52 28 | -0.50 31.02 29 | -0.50 30.52 30 | -0.50 30.02 31 | -0.50 29.52 32 | -0.50 29.02 33 | -0.50 28.52 34 - P 2 38.00 66.51 35 - H 3 47.00 113.51 36 - R 4 20.00 133.51 37 | -1.75 131.76 38 | -0.13 131.63 39 | -0.00 131.63 40 | -0.00 131.62 41 - H 5 47.00 178.62 42 - Q 6 9.00 187.62 43 - K 7 3.00 190.62 44 - T 8 29.00 219.62 45 - P 9 36.00 255.62 46 - E 10 29.00 284.63 47 - N 11 20.00 304.63 48 - Y 12 34.00 338.63 49 - P 13 35.00 373.63 50 - N 14 28.00 401.63 51 - A 15 22.00 423.63 52 - G 16 32.00 455.63 53 - L 17 31.00 486.63 54 - T 18 10.00 496.63 55 - M 19 33.00 529.63 56 | -2.47 527.15 57 - N 20 43.00 570.15 58 - Y 21 46.00 616.15 59 - C 22 59.00 675.15 60 - R 23 42.00 717.15 61 - N 24 44.00 761.15 62 - P 25 43.00 804.15 63 - D 26 40.00 844.15 64 - A 27 19.00 863.15 65 - D 28 25.00 888.15 66 | -2.50 885.65 67 - K 29 7.00 892.65 68 - G 30 20.00 912.65 Sequence name: Made-Up (chunk) Sequence: 1 W 2 S 3 S 4 M 5 T 6 P 7 H 8 R 9 H 10 Q 11 C 12 A 13 T 14 K 15 T 16 P 17 E 18 N 19 Y 20 P 21 N 22 A 23 G 24 L 25 T 26 M PS_LG_FSQ: Optimal score indices: 74 26 Optimal score: 684.710 FSQ Matching path: 1 28 0 2 29 1 3 30 2 4 31 3 5 32 4 6 33 5 7 34 6 8 35 7 9 36 8 10 37 -1 11 38 -1 12 39 9 13 -1 10 14 -1 11 15 -1 12 16 40 13 17 41 -1 18 42 14 19 43 -1 20 44 15 21 45 16 22 46 17 23 47 18 24 48 19 25 49 20 26 50 21 27 51 22 28 52 23 29 53 24 30 54 -1 31 55 -1 32 56 -1 33 57 -1 34 58 -1 35 59 -1 36 60 -1 37 61 -1 38 62 -1 39 63 -1 40 64 -1 41 65 -1 42 66 -1 43 67 -1 44 68 -1 45 69 -1 46 70 -1 47 71 -1 48 72 -1 49 73 25 50 74 26 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 29 - W 1 63.00 63.00 30 - S 2 24.00 87.00 31 - S 3 30.00 117.00 32 - M 4 37.00 154.00 33 - T 5 26.00 180.00 34 - P 6 38.00 218.00 35 - H 7 47.00 265.00 36 - R 8 20.00 285.00 37 | -1.75 283.25 38 | -0.13 283.12 39 - H 9 43.00 326.12 | Q 10 -1.99 324.14 | C 11 -0.00 324.13 | A 12 -0.00 324.13 40 - T 13 14.00 338.13 41 | -2.21 335.92 42 - K 14 6.00 341.92 43 | -2.49 339.42 44 - T 15 29.00 368.42 45 - P 16 36.00 404.42 46 - E 17 29.00 433.42 47 - N 18 20.00 453.42 48 - Y 19 34.00 487.42 49 - P 20 35.00 522.42 50 - N 21 28.00 550.42 51 - A 22 22.00 572.42 52 - G 23 32.00 604.42 53 - L 24 31.00 635.42 54 | -2.50 632.92 55 | -0.50 632.42 56 | -0.50 631.93 57 | -0.09 631.84 58 | -0.50 631.34 59 | -0.50 630.84 60 | -0.50 630.34 61 | -0.50 629.84 62 | -0.50 629.34 63 | -0.50 628.84 64 | -0.50 628.34 65 | -0.50 627.84 66 | -0.50 627.34 67 | -0.13 627.21 68 | -0.50 626.71 69 | -0.50 626.21 70 | -0.50 625.71 71 | -0.50 625.21 72 | -0.50 624.71 73 - T 25 37.00 661.71 74 - M 26 23.00 684.71 TEST11: Backward algorithms using quadratic space: PS_LG_BSQ determines an alignment score; PS_LG_BPQ determines an alignment path. Sequence name: s00657 (chunk) PS_LG_BSQ: Optimal score indices: 6 0 Optimal score: 1010.51 BSQ Matching path: 1 6 0 2 7 1 3 8 -1 4 9 -1 5 10 2 6 11 3 7 12 4 8 13 5 9 14 6 10 15 7 11 16 8 12 17 9 13 18 10 14 19 11 15 20 12 16 21 13 17 22 14 18 23 15 19 24 16 20 25 17 21 26 18 22 27 19 23 28 20 24 29 21 25 30 22 26 31 23 27 32 24 28 33 25 29 34 26 30 35 27 31 36 -1 32 37 -1 33 38 -1 34 39 -1 35 40 28 36 41 29 37 42 30 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 7 - N 1 32.00 32.00 8 | -2.50 29.50 9 | -0.00 29.50 10 - G 2 38.00 67.50 11 - Q 3 28.00 95.50 12 - S 4 25.00 120.50 13 - Y 5 49.00 169.49 14 - R 6 38.00 207.49 15 - G 7 38.00 245.49 16 - T 8 31.00 276.49 17 - Y 9 26.00 302.49 18 - S 10 29.00 331.49 19 - T 11 31.00 362.49 20 - T 12 37.00 399.49 21 - V 13 23.00 422.49 22 - T 14 26.00 448.49 23 - G 15 37.00 485.49 24 - R 16 28.00 513.49 25 - T 17 25.00 538.49 26 - C 18 59.00 597.49 27 - Q 19 41.00 638.49 28 - A 20 20.00 658.49 29 - W 21 63.00 721.49 30 - S 22 24.00 745.49 31 - S 23 30.00 775.49 32 - M 24 37.00 812.49 33 - T 25 26.00 838.49 34 - P 26 38.00 876.49 35 - H 27 47.00 923.49 36 | -2.50 920.99 37 | -0.35 920.65 38 | -0.13 920.52 39 | -0.00 920.51 40 - S 28 25.00 945.51 41 - H 29 47.00 992.51 42 - S 30 18.00 1010.51 Sequence name: c61545 (chunk) PS_LG_BSQ: Optimal score indices: 62 0 Optimal score: 717.515 BSQ Matching path: 1 62 0 2 63 1 3 64 2 4 65 3 5 66 -1 6 67 4 7 68 5 8 69 6 9 70 7 10 71 8 11 72 9 12 73 10 13 74 11 14 75 12 15 76 -1 16 77 -1 17 78 13 18 79 14 19 80 15 20 81 16 21 82 17 22 83 18 23 84 19 24 85 20 25 86 -1 26 87 21 27 88 22 28 89 23 29 90 24 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 63 - D 1 40.00 40.00 64 - A 2 19.00 59.00 65 - D 3 25.00 84.00 66 | -2.50 81.50 67 - K 4 7.00 88.50 68 - S 5 1.00 89.50 69 - P 6 42.00 131.50 70 - W 7 59.00 190.50 71 - C 8 59.00 249.50 72 - Y 9 44.00 293.50 73 - T 10 37.00 330.50 74 - T 11 22.00 352.50 75 - D 12 34.00 386.50 76 | -2.47 384.02 77 | -0.01 384.01 78 - P 13 37.00 421.01 79 - R 14 8.00 429.01 80 - V 15 27.00 456.01 81 - R 16 34.00 490.01 82 - W 17 53.00 543.02 83 - E 18 33.00 576.02 84 - F 19 19.00 595.02 85 - C 20 59.00 654.02 86 | -2.50 651.52 87 - N 21 29.00 680.52 88 - L 22 22.00 702.52 89 - K 23 9.00 711.52 90 - K 24 6.00 717.52 Sequence name: plhu-k (chunk) PS_LG_BSQ: Optimal score indices: 19 0 Optimal score: 912.650 BSQ Matching path: 1 19 0 2 20 1 3 21 -1 4 22 -1 5 23 -1 6 24 -1 7 25 -1 8 26 -1 9 27 -1 10 28 -1 11 29 -1 12 30 -1 13 31 -1 14 32 -1 15 33 -1 16 34 2 17 35 3 18 36 4 19 37 -1 20 38 -1 21 39 -1 22 40 -1 23 41 5 24 42 6 25 43 7 26 44 8 27 45 9 28 46 10 29 47 11 30 48 12 31 49 13 32 50 14 33 51 15 34 52 16 35 53 17 36 54 18 37 55 19 38 56 -1 39 57 20 40 58 21 41 59 22 42 60 23 43 61 24 44 62 25 45 63 26 46 64 27 47 65 28 48 66 -1 49 67 29 50 68 30 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 20 - T 1 37.00 37.00 21 | -2.50 34.50 22 | -0.50 34.00 23 | -0.50 33.50 24 | -0.50 33.01 25 | -0.50 32.51 26 | -0.50 32.02 27 | -0.50 31.52 28 | -0.50 31.02 29 | -0.50 30.52 30 | -0.50 30.02 31 | -0.50 29.52 32 | -0.50 29.02 33 | -0.50 28.52 34 - P 2 38.00 66.51 35 - H 3 47.00 113.51 36 - R 4 20.00 133.51 37 | -1.75 131.76 38 | -0.13 131.63 39 | -0.00 131.63 40 | -0.00 131.62 41 - H 5 47.00 178.62 42 - Q 6 9.00 187.62 43 - K 7 3.00 190.62 44 - T 8 29.00 219.62 45 - P 9 36.00 255.62 46 - E 10 29.00 284.63 47 - N 11 20.00 304.63 48 - Y 12 34.00 338.63 49 - P 13 35.00 373.63 50 - N 14 28.00 401.63 51 - A 15 22.00 423.63 52 - G 16 32.00 455.63 53 - L 17 31.00 486.63 54 - T 18 10.00 496.63 55 - M 19 33.00 529.63 56 | -2.47 527.15 57 - N 20 43.00 570.15 58 - Y 21 46.00 616.15 59 - C 22 59.00 675.15 60 - R 23 42.00 717.15 61 - N 24 44.00 761.15 62 - P 25 43.00 804.15 63 - D 26 40.00 844.15 64 - A 27 19.00 863.15 65 - D 28 25.00 888.15 66 | -2.50 885.65 67 - K 29 7.00 892.65 68 - G 30 20.00 912.65 Sequence name: Made-Up (chunk) PS_LG_BSQ: Optimal score indices: 28 0 Optimal score: 684.710 BSQ Matching path: 1 28 0 2 29 1 3 30 2 4 31 3 5 32 4 6 33 5 7 34 6 8 35 7 9 36 8 10 37 -1 11 38 -1 12 39 9 13 -1 10 14 -1 11 15 -1 12 16 40 13 17 41 -1 18 42 14 19 43 -1 20 44 15 21 45 16 22 46 17 23 47 18 24 48 19 25 49 20 26 50 21 27 51 22 28 52 23 29 53 24 30 54 -1 31 55 -1 32 56 -1 33 57 -1 34 58 -1 35 59 -1 36 60 -1 37 61 -1 38 62 -1 39 63 -1 40 64 -1 41 65 -1 42 66 -1 43 67 -1 44 68 -1 45 69 -1 46 70 -1 47 71 -1 48 72 -1 49 73 25 50 74 26 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 29 - W 1 63.00 63.00 30 - S 2 24.00 87.00 31 - S 3 30.00 117.00 32 - M 4 37.00 154.00 33 - T 5 26.00 180.00 34 - P 6 38.00 218.00 35 - H 7 47.00 265.00 36 - R 8 20.00 285.00 37 | -1.75 283.25 38 | -0.13 283.12 39 - H 9 43.00 326.12 | Q 10 -1.99 324.14 | C 11 -0.00 324.13 | A 12 -0.00 324.13 40 - T 13 14.00 338.13 41 | -2.21 335.92 42 - K 14 6.00 341.92 43 | -2.49 339.42 44 - T 15 29.00 368.42 45 - P 16 36.00 404.42 46 - E 17 29.00 433.42 47 - N 18 20.00 453.42 48 - Y 19 34.00 487.42 49 - P 20 35.00 522.42 50 - N 21 28.00 550.42 51 - A 22 22.00 572.42 52 - G 23 32.00 604.42 53 - L 24 31.00 635.42 54 | -2.50 632.92 55 | -0.50 632.42 56 | -0.50 631.93 57 | -0.09 631.84 58 | -0.50 631.34 59 | -0.50 630.84 60 | -0.50 630.34 61 | -0.50 629.84 62 | -0.50 629.34 63 | -0.50 628.84 64 | -0.50 628.34 65 | -0.50 627.84 66 | -0.50 627.34 67 | -0.13 627.21 68 | -0.50 626.71 69 | -0.50 626.21 70 | -0.50 625.71 71 | -0.50 625.21 72 | -0.50 624.71 73 - T 25 37.00 661.71 74 - M 26 23.00 684.71 TEST12: Linear space local alignment algorithms. PS_LG_CORNERS determines the "corners" of an alignment; PS_LG_RPL determines the path of an alignment. Sequence name: s00657 (chunk) PS_LG_CORNERS: Optimal alignment "corners" are: I1, J1 = 6 0 I2, J2 = 42 30 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 7 - N 1 32.00 32.00 8 | -2.50 29.50 9 | -0.00 29.50 10 - G 2 38.00 67.50 11 - Q 3 28.00 95.50 12 - S 4 25.00 120.50 13 - Y 5 49.00 169.49 14 - R 6 38.00 207.49 15 - G 7 38.00 245.49 16 - T 8 31.00 276.49 17 - Y 9 26.00 302.49 18 - S 10 29.00 331.49 19 - T 11 31.00 362.49 20 - T 12 37.00 399.49 21 - V 13 23.00 422.49 22 - T 14 26.00 448.49 23 - G 15 37.00 485.49 24 - R 16 28.00 513.49 25 - T 17 25.00 538.49 26 - C 18 59.00 597.49 27 - Q 19 41.00 638.49 28 - A 20 20.00 658.49 29 - W 21 63.00 721.49 30 - S 22 24.00 745.49 31 - S 23 30.00 775.49 32 - M 24 37.00 812.49 33 - T 25 26.00 838.49 34 - P 26 38.00 876.49 35 - H 27 47.00 923.49 36 | -2.50 920.99 37 | -0.35 920.65 38 | -0.13 920.52 39 | -0.00 920.51 40 - S 28 25.00 945.51 41 - H 29 47.00 992.51 42 - S 30 18.00 1010.51 Sequence name: c61545 (chunk) PS_LG_CORNERS: Optimal alignment "corners" are: I1, J1 = 62 0 I2, J2 = 90 24 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 63 - D 1 40.00 40.00 64 - A 2 19.00 59.00 65 - D 3 25.00 84.00 66 | -2.50 81.50 67 - K 4 7.00 88.50 68 - S 5 1.00 89.50 69 - P 6 42.00 131.50 70 - W 7 59.00 190.50 71 - C 8 59.00 249.50 72 - Y 9 44.00 293.50 73 - T 10 37.00 330.50 74 - T 11 22.00 352.50 75 - D 12 34.00 386.50 76 | -2.47 384.02 77 | -0.01 384.01 78 - P 13 37.00 421.01 79 - R 14 8.00 429.01 80 - V 15 27.00 456.01 81 - R 16 34.00 490.01 82 - W 17 53.00 543.02 83 - E 18 33.00 576.02 84 - F 19 19.00 595.02 85 - C 20 59.00 654.02 86 | -2.50 651.52 87 - N 21 29.00 680.52 88 - L 22 22.00 702.52 89 - K 23 9.00 711.52 90 - K 24 6.00 717.52 Sequence name: plhu-k (chunk) PS_LG_CORNERS: Optimal alignment "corners" are: I1, J1 = 19 0 I2, J2 = 68 30 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 20 - T 1 37.00 37.00 21 | -2.50 34.50 22 | -0.50 34.00 23 | -0.50 33.50 24 | -0.50 33.01 25 | -0.50 32.51 26 | -0.50 32.02 27 | -0.50 31.52 28 | -0.50 31.02 29 | -0.50 30.52 30 | -0.50 30.02 31 | -0.50 29.52 32 | -0.50 29.02 33 | -0.50 28.52 34 - P 2 38.00 66.51 35 - H 3 47.00 113.51 36 - R 4 20.00 133.51 37 | -1.75 131.76 38 | -0.13 131.63 39 | -0.00 131.63 40 | -0.00 131.62 41 - H 5 47.00 178.62 42 - Q 6 9.00 187.62 43 - K 7 3.00 190.62 44 - T 8 29.00 219.62 45 - P 9 36.00 255.62 46 - E 10 29.00 284.63 47 - N 11 20.00 304.63 48 - Y 12 34.00 338.63 49 - P 13 35.00 373.63 50 - N 14 28.00 401.63 51 - A 15 22.00 423.63 52 - G 16 32.00 455.63 53 - L 17 31.00 486.63 54 - T 18 10.00 496.63 55 - M 19 33.00 529.63 56 | -2.47 527.15 57 - N 20 43.00 570.15 58 - Y 21 46.00 616.15 59 - C 22 59.00 675.15 60 - R 23 42.00 717.15 61 - N 24 44.00 761.15 62 - P 25 43.00 804.15 63 - D 26 40.00 844.15 64 - A 27 19.00 863.15 65 - D 28 25.00 888.15 66 | -2.50 885.65 67 - K 29 7.00 892.65 68 - G 30 20.00 912.65 Sequence name: Made-Up (chunk) PS_LG_CORNERS: Optimal alignment "corners" are: I1, J1 = 28 0 I2, J2 = 74 26 Profile/sequence matching, Affine gap penalty: # B # Increm Score 0.00 29 - W 1 63.00 63.00 30 - S 2 24.00 87.00 31 - S 3 30.00 117.00 32 - M 4 37.00 154.00 33 - T 5 26.00 180.00 34 - P 6 38.00 218.00 35 - H 7 47.00 265.00 36 - R 8 20.00 285.00 37 | -1.75 283.25 38 | -0.13 283.12 39 - H 9 43.00 326.12 | Q 10 -1.99 324.14 | C 11 -0.00 324.13 | A 12 -0.00 324.13 40 - T 13 14.00 338.13 41 | -2.21 335.92 42 - K 14 6.00 341.92 43 | -2.49 339.42 44 - T 15 29.00 368.42 45 - P 16 36.00 404.42 46 - E 17 29.00 433.42 47 - N 18 20.00 453.42 48 - Y 19 34.00 487.42 49 - P 20 35.00 522.42 50 - N 21 28.00 550.42 51 - A 22 22.00 572.42 52 - G 23 32.00 604.42 53 - L 24 31.00 635.42 54 | -2.50 632.92 55 | -0.50 632.42 56 | -0.50 631.93 57 | -0.09 631.84 58 | -0.50 631.34 59 | -0.50 630.84 60 | -0.50 630.34 61 | -0.50 629.84 62 | -0.50 629.34 63 | -0.50 628.84 64 | -0.50 628.34 65 | -0.50 627.84 66 | -0.50 627.34 67 | -0.13 627.21 68 | -0.50 626.71 69 | -0.50 626.21 70 | -0.50 625.71 71 | -0.50 625.21 72 | -0.50 624.71 73 - T 25 37.00 661.71 74 - M 26 23.00 684.71 PS_LG_ALIGN_PRB Normal end of execution. December 29 2007 8:41:03.278 PM