scoring-matrix.txt

// This is an example of a scoring matrix you would supply
//   to alnSeq. In this case the scoring matrix is set to
//   the default settings.

// This is a comment and needs to start at the start of a
//   line. It is ok to have stuff after the base
//   combination, since the read in step on looks at the
//   two base pairs and the provided number.  It does not
//   look past the number. However, starting a line with a
//   space is a good way to cause an error.

// A blank line will be ignored so long as it does not
//   have white space.

// Scoring matrix is EDNAFULL * 100. The * 100 allows for
//   an extension penalty of -1 to be -0.01. The aligners
//   will auto divide by 100 when printing out scores, so
//   it works out to a EDNAFULL matrix.
// I think I have the anonymous bases with the correct
//   scores.

// limit for score or gap penalty (not in matrix) is a
//   signed short, so roughly -300000to 30000

// Needleman-Wunsch alignment score matrix (non-anonymous)
A A 500      // Penalty for query A to reference A
A T -400     // Penalty for query A to reference T
A U -400     // Penalty for query A to reference T (RNA T)
A G -400     // Penalty for query A to reference G
A C -400     // Penalty for query A to reference C

T A -400     // Penalty for query T to reference A
T T 500      // Penalty for query T to reference T
T U 500      // Penalty for query T to reference U (RNA T)
T G -400     // Penalty for query T to reference G
T C -400     // Penalty for query T to reference C

U A -400     // Penalty for query U (RNA T) to reference A
U T 500      // Penalty for query U (RNA T) to reference T
U G -400     // Penalty for query U (RNA T) to reference G
U C -400     // Penalty for query U (RNA T) to reference C

G A -400     // Penalty for query G to reference A
G T -400     // Penalty for query G to reference T
G U -400     // Penalty for query G to reference T (RNA T)
G G 500      // Penalty for query G to reference G
G C -400     // Penalty for query G to reference C

C A -400     // Penalty for query C to reference A
C T -400     // Penalty for query C to reference T
C U -400     // Penalty for query C to reference T (RNA T)
C G -400     // Penalty for query C to reference G
C C 500      // Penalty for query C to reference C

// Needleman-Wunsch alignment scoring matrix anonymous (A)
A W 100      // Penalty for query A to reference W (AT)
A S -400     // Penalty for query A to reference S (CG)
A M 100      // Penalty for query A to reference M (AC)
A K -400     // Penalty for query A to reference K (GT)
A R 100      // Penalty for query A to reference R (AG)
A Y -400     // Penalty for query A to reference Y (CT)
A B -400     // Penalty for query A to reference B (CGT)
A D -100     // Penalty for query A to reference D (AGT)
A H -100     // Penalty for query A to reference H (ACT)
A V -100     // Penalty for query A to reference V (ACG)
A N -200     // Penalty for query A to reference N (ACGT)
A X -200     // Penalty for query A to reference X (ACGT)

W A 100      // Penalty for query W to reference A (AT)
S A -400     // Penalty for query S to reference A (CG)
M A 100      // Penalty for query M to reference A (AC)
K A -400     // Penalty for query K to reference A (GT)
R A 100      // Penalty for query R to reference A (AG)
Y A -400     // Penalty for query Y to reference A (CT)
B A -400     // Penalty for query B to reference A (CGT)
D A -100     // Penalty for query D to reference A (AGT)
H A -100     // Penalty for query H to reference A (ACT)
V A -100     // Penalty for query V to reference A (ACG)
N A -200     // Penalty for query N to reference A (ACGT)
X A -200     // Penalty for query X to reference A (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (C)
C W -400     // Penalty for query C to reference W (AT)
C S 100      // Penalty for query C to reference S (CG)
C M 100      // Penalty for query C to reference M (AC)
C K -400     // Penalty for query C to reference K (GT)
C R -400     // Penalty for query C to reference R (AG)
C Y 100      // Penalty for query C to reference Y (CT)
C B -100     // Penalty for query C to reference B (CGT)
C D -400     // Penalty for query C to reference D (AGT)
C H -100     // Penalty for query C to reference H (ACT)
C V -100     // Penalty for query C to reference V (ACG)
C N -200     // Penalty for query C to reference N (ACGT)
C X -200     // Penalty for query C to reference X (ACGT)

W C -400     // Penalty for query W to reference C (AT)
S C 100      // Penalty for query S to reference C (CG)
M C 100      // Penalty for query M to reference C (AC)
K C -400     // Penalty for query K to reference C (GT)
R C -400     // Penalty for query R to reference C (AG)
Y C 100      // Penalty for query Y to reference C (CT)
B C -100     // Penalty for query B to reference C (CGT)
D C -400     // Penalty for query D to reference C (AGT)
H C -100     // Penalty for query H to reference C (ACT)
V C -100     // Penalty for query V to reference C (ACG)
N C -200     // Penalty for query N to reference C (ACGT)
X C -200     // Penalty for query X to reference C (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (G)
G W -400     // Penalty for query G to reference W (AT)
G S 100      // Penalty for query G to reference S (CG)
G M -400     // Penalty for query G to reference M (AC)
G K 100      // Penalty for query G to reference K (GT)
G R 100      // Penalty for query G to reference R (AG)
G Y -400     // Penalty for query G to reference Y (CT)
G B -100     // Penalty for query G to reference B (CGT)
G D -100     // Penalty for query G to reference D (AGT)
G H -400     // Penalty for query G to reference H (ACT)
G V -100     // Penalty for query G to reference V (ACG)
G N -200     // Penalty for query G to reference N (ACGT)
G X -200     // Penalty for query G to reference X (ACGT)

W G -400     // Penalty for query G to reference W (AT)
S G 100      // Penalty for query G to reference S (CG)
M G -400     // Penalty for query G to reference M (AC)
K G 100      // Penalty for query G to reference K (GT)
R G 100      // Penalty for query G to reference R (AG)
Y G -400     // Penalty for query G to reference Y (CT)
B G -100     // Penalty for query G to reference B (CGT)
D G -100     // Penalty for query G to reference D (AGT)
H G -400     // Penalty for query G to reference H (ACT)
V G -100     // Penalty for query G to reference V (ACG)
N G -200     // Penalty for query G to reference N (ACGT)
X G -200     // Penalty for query G to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (T)
T W 100      // Penalty for query T to reference W (AT)
T S -400     // Penalty for query T to reference S (CG)
T M -400     // Penalty for query T to reference M (AC)
T K 100      // Penalty for query T to reference K (GT)
T R -400     // Penalty for query T to reference R (AG)
T Y 100      // Penalty for query T to reference Y (CT)
T B -100     // Penalty for query T to reference B (CGT)
T D -100     // Penalty for query T to reference D (AGT)
T H -100     // Penalty for query T to reference H (ACT)
T V -400     // Penalty for query T to reference V (ACG)
T N -200     // Penalty for query T to reference N (ACGT)
T X -200     // Penalty for query T to reference X (ACGT)

W T 100      // Penalty for query T to reference W (AT)
S T -400     // Penalty for query T to reference S (CG)
M T -400     // Penalty for query T to reference M (AC)
K T 100      // Penalty for query T to reference K (GT)
R T -400     // Penalty for query T to reference R (AG)
Y T -400     // Penalty for query T to reference Y (CT)
B T -100     // Penalty for query T to reference B (CGT)
D T -100     // Penalty for query T to reference D (AGT)
H T -100     // Penalty for query T to reference H (ACT)
V T -400     // Penalty for query T to reference V (ACG)
N T -200     // Penalty for query T to reference N (ACGT)
X T -200     // Penalty for query T to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (U)
U W 100      // Penalty for query U (RNA T) to ref W (AT)
U S -400     // Penalty for query U (RNA T) to ref S (CG)
U M -400     // Penalty for query U (RNA T) to ref M (AC)
U K 100      // Penalty for query U (RNA T) to ref K (GT)
U R -400     // Penalty for query U (RNA T) to ref R (AG)
U Y 100      // Penalty for query U (RNA T) to ref Y (CT)
U B -100     // Penalty for query U (RNA T) to ref B (CGT)
U D -100     // Penalty for query U (RNA T) to ref D (AGT)
U H -100     // Penalty for query U (RNA T) to ref H (ACT)
U V -400     // Penalty for query U (RNA T) to ref V (ACG)
U N -200     // Penalty for query U (RNA T) to ref N (ACGT)
U X -200     // Penalty for query U (RNA T) to ref X (ACGT)

W U 100      // Penalty for query U (RNA T) to ref W (AT)
S U -400     // Penalty for query U (RNA T) to ref S (CG)
M U -400     // Penalty for query U (RNA T) to ref M (AC)
K U 100      // Penalty for query U (RNA T) to ref K (GT)
R U -400     // Penalty for query U (RNA T) to ref R (AG)
Y U -400     // Penalty for query U (RNA T) to ref Y (CT)
B U -100     // Penalty for query U (RNA T) to ref B (CGT)
D U -100     // Penalty for query U (RNA T) to ref D (AGT)
H U -100     // Penalty for query U (RNA T) to ref H (ACT)
V U -400     // Penalty for query U (RNA T) to ref V (ACG)
N U -200     // Penalty for query U (RNA T) to ref N (ACGT)
X U -200     // Penalty for query U (RNA T) to ref X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (W)
W W -100     // Penalty for query W to reference W (AT)
W S -400     // Penalty for query W to reference S (CG)
W M -200     // Penalty for query W to reference M (AC)
W K -200     // Penalty for query W to reference K (GT)
W R -200     // Penalty for query W to reference R (AG)
W Y -200     // Penalty for query W to reference Y (CT)
W B -300     // Penalty for query W to reference B (CGT)
W D -100     // Penalty for query W to reference D (AGT)
W H -100     // Penalty for query W to reference H (ACT)
W V -300     // Penalty for query W to reference V (ACG)
W N -100     // Penalty for query W to reference N (ACGT)
W X -100     // Penalty for query W to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (S)
S W -400     // Penalty for query S to reference W (AT)
S S -100     // Penalty for query S to reference S (CG)
S M -200     // Penalty for query S to reference M (AC)
S K -200     // Penalty for query S to reference K (GT)
S R -200     // Penalty for query S to reference R (AG)
S Y -200     // Penalty for query S to reference Y (CT)
S B -100     // Penalty for query S to reference B (CGT)
S D -300     // Penalty for query S to reference D (AGT)
S H -300     // Penalty for query S to reference H (ACT)
S V -100     // Penalty for query S to reference V (ACG)
S N -100     // Penalty for query S to reference N (ACGT)
S X -100     // Penalty for query S to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (M)
M W -200     // Penalty for query M to reference W (AT)
M S -200     // Penalty for query M to reference S (CG)
M M -100     // Penalty for query M to reference M (AC)
M K -400     // Penalty for query M to reference K (GT)
M R -200     // Penalty for query M to reference R (AG)
M Y -200     // Penalty for query M to reference Y (CT)
M B -300     // Penalty for query M to reference B (CGT)
M D -300     // Penalty for query M to reference D (AGT)
M H -100     // Penalty for query M to reference H (ACT)
M V -100     // Penalty for query M to reference V (ACG)
M N -100     // Penalty for query M to reference N (ACGT)
M X -100     // Penalty for query M to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (K)
K W -200     // Penalty for query K to reference W (AT)
K S -200     // Penalty for query K to reference S (CG)
K M -400     // Penalty for query K to reference M (AC)
K K -100     // Penalty for query K to reference K (GT)
K R -200     // Penalty for query K to reference R (AG)
K Y -200     // Penalty for query K to reference Y (CT)
K B -100     // Penalty for query K to reference B (CGT)
K D -100     // Penalty for query K to reference D (AGT)
K H -300     // Penalty for query K to reference H (ACT)
K V -300     // Penalty for query K to reference V (ACG)
K N -100     // Penalty for query K to reference N (ACGT)
K X -100     // Penalty for query K to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (R)
R W -100     // Penalty for query R to reference W (AT)
R S -100     // Penalty for query R to reference S (CG)
R M -100     // Penalty for query R to reference M (AC)
R K -200     // Penalty for query R to reference K (GT)
R R -100     // Penalty for query R to reference R (AG)
R Y -400     // Penalty for query R to reference Y (CT)
R B -300     // Penalty for query R to reference B (CGT)
R D -100     // Penalty for query R to reference D (AGT)
R H -100     // Penalty for query R to reference H (ACT)
R V -300     // Penalty for query R to reference V (ACG)
R N -100     // Penalty for query R to reference N (ACGT)
R X -100     // Penalty for query R to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (Y)
Y W -200     // Penalty for query Y to reference W (AT)
Y S -200     // Penalty for query Y to reference S (CG)
Y M -200     // Penalty for query Y to reference M (AC)
Y K -200     // Penalty for query Y to reference K (GT)
Y R -400     // Penalty for query Y to reference R (AG)
Y Y -100     // Penalty for query Y to reference Y (CT)
Y B -200     // Penalty for query Y to reference B (CGT)
Y D -300     // Penalty for query Y to reference D (AGT)
Y H -100     // Penalty for query Y to reference H (ACT)
Y V -300     // Penalty for query Y to reference V (ACG)
Y N -100     // Penalty for query Y to reference N (ACGT)
Y X -100     // Penalty for query Y to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (B)
B W -300     // Penalty for query B to reference W (AT)
B S -100     // Penalty for query B to reference S (CG)
B M -300     // Penalty for query B to reference M (AC)
B K -100     // Penalty for query B to reference K (GT)
B R -300     // Penalty for query B to reference R (AG)
B Y -100     // Penalty for query B to reference Y (CT)
B B -100     // Penalty for query B to reference B (CGT)
B D -200     // Penalty for query B to reference D (AGT)
B H -200     // Penalty for query B to reference H (ACT)
B V -200     // Penalty for query B to reference V (ACG)
B N -100     // Penalty for query B to reference N (ACGT)
B X -100     // Penalty for query B to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (D)
D W -100     // Penalty for query D to reference W (AT)
D S -300     // Penalty for query D to reference S (CG)
D M -300     // Penalty for query D to reference M (AC)
D K -100     // Penalty for query D to reference K (GT)
D R -100     // Penalty for query D to reference R (AG)
D Y -300     // Penalty for query D to reference Y (CT)
D B -200     // Penalty for query D to reference B (CGT)
D D -100     // Penalty for query D to reference D (AGT)
D H -200     // Penalty for query D to reference H (ACT)
D V -200     // Penalty for query D to reference V (ACG)
D N -100     // Penalty for query D to reference N (ACGT)
D X -100     // Penalty for query D to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (H)
H W -100     // Penalty for query H to reference W (AT)
H S -300     // Penalty for query H to reference S (CG)
H M -100     // Penalty for query H to reference M (AC)
H K -300     // Penalty for query H to reference K (GT)
H R -300     // Penalty for query H to reference R (AG)
H Y -100     // Penalty for query H to reference Y (CT)
H B -200     // Penalty for query H to reference B (CGT)
H D -200     // Penalty for query H to reference D (AGT)
H H -100     // Penalty for query H to reference H (ACT)
H V -200     // Penalty for query H to reference V (ACG)
H N -100     // Penalty for query H to reference N (ACGT)
H X -100     // Penalty for query H to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (V)
V W -300     // Penalty for query V to reference W (AT)
V S -100     // Penalty for query V to reference S (CG)
V M -100     // Penalty for query V to reference M (AC)
V K -300     // Penalty for query V to reference K (GT)
V R -100     // Penalty for query V to reference R (AG)
V Y -300     // Penalty for query V to reference Y (CT)
V B -200     // Penalty for query V to reference B (CGT)
V D -200     // Penalty for query V to reference D (AGT)
V H -200     // Penalty for query V to reference H (ACT)
V V -100     // Penalty for query V to reference V (ACG)
V N -100     // Penalty for query V to reference N (ACGT)
V X -100     // Penalty for query V to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (N)
N W -200     // Penalty for query N to reference W (AT)
N S -200     // Penalty for query N to reference S (CG)
N M -200     // Penalty for query N to reference M (AC)
N K -200     // Penalty for query N to reference K (GT)
N R -200     // Penalty for query N to reference R (AG)
N Y -200     // Penalty for query N to reference Y (CT)
N B -200     // Penalty for query N to reference B (CGT)
N D -200     // Penalty for query N to reference D (AGT)
N H -200     // Penalty for query N to reference H (ACT)
N V -200     // Penalty for query N to reference V (ACG)
N N -100     // Penalty for query N to reference N (ACGT)
N X -100     // Penalty for query N to reference X (ACGT)

// Needleman-Wunsch alignment scoring matrix anonymous (X)
X W -100     // Penalty for query X to reference W (AT)
X S -100     // Penalty for query X to reference S (CG)
X M -100     // Penalty for query X to reference M (AC)
X K -100     // Penalty for query X to reference K (GT)
X R -100     // Penalty for query X to reference R (AG)
X Y -100     // Penalty for query X to reference Y (CT)
X B -100     // Penalty for query X to reference B (CGT)
X D -100     // Penalty for query X to reference D (AGT)
X H -100     // Penalty for query X to reference H (ACT)
X V -100     // Penalty for query X to reference V (ACG)
X N -100     // Penalty for query X to reference N (ACGT)
X X -100     // Penalty for query X to reference X (ACGT)