msaConservationScore-methods: Computation of Conservation Scores from Multiple Alignment

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

This method computes a vector of conservation scores from a multiple alignment or a previously computed consensus matrix.

Usage

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## S4 method for signature 'matrix'
msaConservationScore(x, substitutionMatrix, gapVsGap=NULL,
    ...)
## S4 method for signature 'MultipleAlignment'
msaConservationScore(x, ...)

Arguments

x

an object of class MultipleAlignment (which includes objects of classes MsaAAMultipleAlignment, MsaDNAMultipleAlignment, and MsaRNAMultipleAlignment) or a previously computed consensus matrix (see details below).

substitutionMatrix

substitution matrix (see details below).

gapVsGap

score to use for aligning gaps versus gaps (see details below).

...

when the method is called for a MultipleAlignment object, the consensus matrix is computed and, including all further arguments, passed on to the msaConservationScore method with signature matrix. This method passes all further arguments on to the msaConsensusSequence method to customize the way the consensus sequence is computed.

Details

The method takes a MultipleAlignment object or a previously computed consensus matrix and computes the sum of pairwise scores for all positions of the alignment. For computing these scores, it is compulsory to specify a substitution/scoring matrix. This matrix must be provided as a matrix object. This can either be one of the ready-made matrices provided by the Biostrings package (e.g. BLOSUM62) or any other hand-crafted matrix. In the latter case, the following restrictions apply:

So, nucleotide substitution matrices created by nucleotideSubstitutionMatrix can be used for multiple alignments of nucleotide sequences, but must be completed with gap penalty rows and columns (see example below).

If the consensus matrix of a multiple alignment of nucleotide sequences contains rows labeled ‘+’ and/or ‘.’, these rows are ignored.

The parameter gapVsGap can be used to control how pairs of gaps are scored. If gapVsGap=NULL (default), the corresponding diagonal entry of the substitution matrix is used as is. In the BLOSUM matrices, this is usually a positive value, which may not make sense under all circumstances. Therefore, the parameter gapVsGap can be set to an alternative value, e.g. 0 for ignoring gap-gap pairs.

The method, in any case, returns a vector of scores that is as long as the alignment/consensus matrix has columns. The names of the vector entries are the corresponding positions of the consensus sequence of the alignment. How this consensus sequence is computed, can be controlled with additional arguments that are passed on to the msaConsensusSequence method.

Value

The function returns a vector as long as the alignment/consensus matrix has columns. The vector is named with the consensus sequence (see details above).

Author(s)

Ulrich Bodenhofer <[email protected]>

References

http://www.bioinf.jku.at/software/msa

U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.

See Also

msa, MsaAAMultipleAlignment, MsaDNAMultipleAlignment, MsaRNAMultipleAlignment, MsaMetaData, MultipleAlignment, msaConsensusSequence

Examples

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## read sequences
filepath <- system.file("examples", "HemoglobinAA.fasta", package="msa")
mySeqs <- readAAStringSet(filepath)

## perform multiple alignment
myAlignment <- msa(mySeqs)

## compute consensus scores using the BLOSUM62 matrix
data(BLOSUM62)
msaConservationScore(myAlignment, BLOSUM62)

## compute consensus scores using the BLOSUM62 matrix
## without scoring gap-gap pairs and using a different consensus sequence
msaConservationScore(myAlignment, BLOSUM62, gapVsGap=0,
                     type="upperlower")

## compute a consensus matrix first
conMat <- consensusMatrix(myAlignment)
data(PAM250)
msaConservationScore(conMat, PAM250, gapVsGap=0)


## DNA example
filepath <- system.file("examples", "exampleDNA.fasta", package="msa")
mySeqs <- readDNAStringSet(filepath)

## perform multiple alignment
myAlignment <- msa(mySeqs)

## create substitution matrix with gap penalty -8
mat <- nucleotideSubstitutionMatrix(4, -1)
mat <- cbind(rbind(mat, "-"=-8), "-"=-8)

## compute consensus scores using this matrix
msaConservationScore(myAlignment, mat, gapVsGap=0)

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

use default substitution matrix
   -    V    L    S    ?    A    D    K    ?    N    V    K    A    ?    W    G 
   5  681 1156  913  210  314 1605 1445  327  968 1052 1163  479  179 2854  376 
   K    ?    G    G    H    A    ?    E    Y    G    A    E    A    L    E    R 
1104  824  928  422 1625  606  353  745 1764 1181  637 1445  920 1156  547 1445 
   M    F    ?    S    F    P    T    T    K    T    Y    F    P    H    F    - 
 793 1540   11  434  976 2023  680 1445 1445 1445 2023 1734 1143 2022 1389  132 
   D    L    S    H    G    S    A    Q    V    K    G    H    G    K    K    V 
1605  760  842  722 1480 1156  625  965  960 1220  533 2053 1734 1028 1253 1096 
   A    D    A    L    T    ?    A    V    ?    H    ?    D    D    L    P    G 
 555  955 1156  976  506  126 1156  595  251 1625  610 1605 1434  744  745  514 
   A    L    S    A    L    S    D    L    H    A    H    K    L    R    V    D 
 792 1093 1060  446 1156 1156 1605 1156 2312 1156 1352 1109 1156 1349 1156 1734 
   P    V    N    F    K    L    L    S    H    C    L    L    V    T    L    A 
2023  626 1734 1734 1135  724 1156  637 1715 1298  778  873 1156  909  888 1060 
   ?    H    ?    P    A    ?    F    T    P    A    V    H    A    S    L    D 
  89 1956   90 1479  352  703 1366 1074 2023  481  792 1956  735  976  921 1734 
   K    F    L    A    ?    V    S    T    V    L    T    S    K    Y    R 
1445 1734  838  370  291  952  796  929 1028 1156 1165  937 1349 2023 1445 
   -    v    L    s    a    a    d    K    t    n    v    k    a    a    w    g 
-220  681 1156  913  210  314 1605 1445  327  968 1052 1163  479  179 2854  376 
   k    v    g    g    h    a    g    e    y    g    a    E    a    L    e    R 
1104  824  928  422 1625  606  353  745 1764 1181  637 1445  920 1156  547 1445 
   m    f    l    s    f    P    t    T    K    T    Y    F    p    h    f    - 
 793 1540   11  434  976 2023  680 1445 1445 1445 2023 1734 1143 2022 1389 -124 
   d    l    s    h    g    S    a    q    v    k    g    h    G    k    k    v 
1605  760  842  722 1480 1156  625  965  960 1220  533 2053 1734 1028 1253 1096 
   a    d    A    l    t    .    A    v    a    h    l    d    d    l    p    g 
 555  955 1156  976  506  126 1156  595  251 1625  610 1605 1434  744  745  514 
   a    l    s    a    L    S    d    L    H    A    h    k    L    r    V    D 
 792 1093 1060  446 1156 1156 1605 1156 2312 1156 1352 1109 1156 1349 1156 1734 
   P    v    N    F    k    l    L    s    h    c    l    l    V    t    l    a 
2023  626 1734 1734 1135  724 1156  637 1715 1298  778  873 1156  909  888 1060 
   .    h    h    p    a    d    f    t    P    a    v    h    a    s    l    D 
  89 1956   90 1479  352  703 1366 1074 2023  481  792 1956  735  976  921 1734 
   K    F    l    a    s    v    s    t    v    L    t    s    k    Y    R 
1445 1734  838  370  291  952  796  929 1028 1156 1165  937 1349 2023 1445 
   -    V    L    S    ?    A    D    K    ?    N    V    K    A    ?    W    G 
-456  760 1734  503  361  322 1124 1445  314  376 1172 1222  359   11 4361  522 
   K    ?    G    G    H    A    ?    E    Y    G    A    E    A    L    E    R 
1105  999  878  508 1305  493  530  649 2533 1019  468 1156  522 1734  519 1734 
   M    F    ?    S    F    P    T    T    K    T    Y    F    P    H    F    - 
1011 2374  -52  277 1514 1734  467  867 1445  867 2890 2601 1150 1572 2067 -254 
   D    L    S    H    G    S    A    Q    V    K    G    H    G    K    K    V 
1124 1266  498  756 1222  578  385  940 1119 1190  524 1636 1445 1026 1283 1160 
   A    D    A    L    T    ?    A    V    ?    H    ?    D    D    L    P    G 
 306  801  578 1486  410  100  578  549  335 1305  922 1124 1028 1146  806  533 
   A    L    S    A    L    S    D    L    H    A    H    K    L    R    V    D 
 402 1670  546  262 1734  578 1124 1734 1734  578  999 1165 1734 1637 1156 1156 
   P    V    N    F    K    L    L    S    H    C    L    L    V    T    L    A 
1734  715  578 2601 1135 1261 1734  412 1386 1710 1181 1325 1156  571 1290  546 
   ?    H    ?    P    A    ?    F    T    P    A    V    H    A    S    L    D 
 -70 1478  138 1370  299  728 2169  684 1734  348  848 1478  317  518 1430 1156 
   K    F    L    A    ?    V    S    T    V    L    T    S    K    Y    R 
1445 2601 1425  244  162 1045  471  535 1026 1734  741  486 1382 2890 1734 
use default substitution matrix
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   ?   G   T   C   C   ?   G   G   ?   C   ?   G   G   ?   G   -   ?   ? 
-28 -28 -26 -16 -16 -16 -16 -26 -16 -16 -26 -16 -26 -16 -16 -26 -16 -28 -26 -26 
  ?   G   G   ?   ?   ?   ?   ?   ?   C   ?   G   ?   ?   ?   ?   ?   ?   ?   C 
-26 -16 -16 -26 -26 -26 -26 -26 -26 -16 -26 -16 -26 -26 -26 -26 -26 -26 -26 -16 
  ?   ?   T   ?   ?   ?   C   T   ?   C   T   ?   C   G   T   C   A   G   G   ? 
-26 -26 -16 -26 -26 -26 -16 -16 -26 -16 -16 -26 -16 -16 -16 -16 -16 -16 -16 -26 
  C   A   A   ?   ?   C   C   -   C   ?   ?   ?   G   ?   G   ?   G   T   ?   A 
-16 -16 -16 -26 -26 -16 -16 -28 -16 -26 -26 -26 -16 -26 -16 -26 -16 -16 -26 -16 
  C   ?   ?   T   G   ?   ?   G   A   ?   -   T   G   C   A   -   -   -   -   G 
-16 -26 -26 -16 -16 -26 -26 -16 -16 -26 -28 -16 -16 -16 -16 -28 -28 -28 -28 -16 
  ?   ?   ?   G   A   G   A   C   A   C   C   C   T   T   ?   ?   ?   A   A   C 
-26 -26 -26 -16 -16 -16 -16 -16 -16 -16 -16 -16 -16 -16 -26 -26 -26 -16 -16 -16 
  -   T   C   T   C   ?   T   C   T   C   C   T   -   -   C   C   ?   ?   A   G 
-28 -16 -16 -16 -16 -26 -16 -16 -16 -16 -16 -16 -28 -28 -16 -16 -26 -26 -16 -16 
  ?   G   C   C   A   G   G   T   T   A   A   A   A   C   C   A   T   C   A   G 
-26 -16 -16  16  36  16  36  36  36  36  36  36  36  36  36  16  36  36  36  36 
  C   C   C   -   C   ?   C   A   T   C   C   T   G   A   G   T   G   C   A   A 
 36  36  36 -28  36   6  36  16  36  16  36  36  36  16  16  36  36  36  16  16 
  A   C   C   T   T   T   C   C   ?   A   A   C   C   C   -   -   -   -   C   G 
 36  36  16  36  16  16  36  16   6  16  36  36  36  16 -28 -28 -28 -28  16  16 
  C   T   G   C   T   A   A   G   C   T   A   G   A   C   A   C   C   T   C   A 
 36  36  16  16  16  36  36  36  36  16  36  36  36  16  36  36  36  36  36  36 
  C   T   C   A   C   T   G   A   G   A   G   C   C   A   G   C   A   T   G   G 
 36  36  16  16  36  16  36  16  36  36  36  36  36  36  36  36  36  36  36  16 
  C   A   G   C   T   G   T   T   G   T   C   C   T   G   G   A   G   A   A   C 
 36  16  16  36  36  36  16  16  36  36  36  36  36  36  36  36  16  36  36  16 
  G   G   A   G   T   C   C   T   G   A   G   C   A   G   A   A   A   A   C   T 
 16  16  36  36  16  36  16  36  36  16  36  36  36  36  16  36  36  36  36  36 
  C   T   C   A   G   A   C   T   T   T   G   G   G   C   A   G   G   A   A   A 
 36  36  36  16  36  36  36  36  36  36  36  36  16  36  36  36  36  36  36  36 
  C   A   A   G   C   T   A   T   A   T   T   G   A   A   G   A   C   A   A   C 
 36  36  36  36  16  36  36  16  36  36  16  36  36  36  36  36  36  36  36  36 
  T   C   C   A   A   T   C   A   A   A   A   T   G   G   T   G   C   C   A   T 
 36  16  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  16  16  36 
  A   T   C   T   C   T   G   A   T   A   T   T   C   T   C   A   C   T   C   A 
 36  36  36  16  36  36  36  36  36  16  36  36  36  36  36  36  36  36  36  36 
  A   A   G   A   G   G   A   A   G   T   T   G   G   T   G   C   C   C   T   G 
 36  36  36  36  16  36  36  36  36  36  36  36  36  36  36  36  16  16  36  16 
  G   C   C   A   A   G   G   T   C   C   T   G   C   G   C   T   T   A   T   T 
 36  36  36  36  36  16  36  36  16  16  36  36  36  36  36  36  36  36  36  36 
  T   G   A   G   G   A   G   A   A   T   G   A   T   A   T   C   A   A   C   C 
 36  36  36  36  36  36  36  36  36  16  36  36  16  16  36  16  36  36  36  36 
  T   G   A   C   A   C   A   C   A   T   T   G   A   A   T   C   C   A   G   A 
 36  36  36  36  16  36  36  36  36  36  36  36  36  36  36  36  16  36  36  36 
  C   C   T   T   C   T   C   G   T   T   T   A   A   A   C   A   A   A   G   A 
 36  36  36  36  36  16  36  36  36  36  36  36  36  36  16  36  36  36  36  36 
  T   G   A   G   T   A   T   G   A   G   T   T   T   T   T   C   A   C   C   T 
 36  36  36  36  36  36  36  36  36  16  36  36  16  36  36  36  36  36  16  16 
  A   T   C   T   G   G   A   T   A   A   G   C   G   T   A   G   C   A   A   G 
 36  36  16  36  36  36  36  36  36  36  16  36  36  36  36  36  36  16  16  16 
  C   C   T   G   T   T   C   T   G   G   G   C   A   G   C   A   T   C   A   T 
 36  36  16  36  16  16  36  36  36  16  16  16  36  16  36  36  36  36  36  36 
  C   A   A   G   A   G   C   C   T   G   A   G   G   A   A   T   G   A   C   A 
 36  36  36  36  36  16  36  16  36  36  36  36  36  16  36  16  36  36  36  36 
  T   T   G   G   T   G   C   C   A   C   T   G   T   C   C   A   T   G   A   G 
 36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  16  36  36  36 
  C   T   T   T   C   C   C   G   A   G   A   C   A   A   G   G   A   A   A   A 
 36  36  36  36  36  16  36  36  36  36  36  16  36  36  36  16  36  16  36  36 
  G   A   A   C   A   C   A   G   T   G   C   C   C   T   G   G   T   T   C   C 
 16  16  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36 
  C   A   A   G   G   A   C   C   A   T   T   C   A   G   G   A   G   C   T   G 
 36  36  36  36  16  36  36  36  36  36  36  36  36  16  36  36  36  16  36  36 
  G   A   C   A   G   A   T   T   C   G   C   C   A   A   T   C   A   G   A   T 
 36  36  36  16  36  36  36  36  16  36  36  36  36  36  36  36  36  36  36  36 
  T   C   T   C   A   G   C   T   A   T   G   G   A   G   C   C   G   A   A   C 
 36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  16  36  36  36  36 
  T   G   G   A   T   G   C   ?   G   A   C   C   A   C   C   C   A   G   G   C 
 36  36  36  36  36  36  36   6  36  36  36  36  36  36  36  36  16  36  36  16 
  T   T   T   A   A   A   G   A   T   C   C   T   G   T   G   T   A   C   C   G 
 36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36 
  G   G   C   G   A   G   A   C   G   A   A   A   G   C   A   G   T   T   T   G 
 16  36  36  16  36  36  36  36  36  16  36  36  36  36  36  36  36  36  36  36 
  C   T   G   A   C   A   T   T   G   C   C   T   A   C   A   A   C   T   A   C 
 36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36 
  C   G   C   C   A   T   G   G   G   C   A   G   C   C   C   A   T   C   C   C 
 36  36  36  36  36  36  36  36  16  36  36  36  36  36  36  36  36  16  36  36 
  T   C   G   G   G   T   G   G   A   A   T   A   C   A   C   A   G   A   G   G 
 36  36  36  16  36  36  36  36  36  36  36  36  36  36  16  16  36  36  36  36 
  A   A   G   A   G   A   A   G   A   A   G   A   C   C   T   G   G   G   G   A 
 36  16  36  36  16  36  16  36  16  36  16  36  36  16  36  36  36  36  36  16 
  A   C   G   G   T   G   T   T   C   A   G   G   A   C   T   C   T   G   A   A 
 36  36  16  36  36  36  36  36  36  36  16  36  36  36  16  16  36  36  36  36 
  G   G   C   C   T   T   G   T   A   T   A   A   A   A   C   A   C   A   T   G 
 36  16  36  36  36  36  36  36  36  36  36  36  36  36  36  16  36  36  36  36 
  C   C   T   G   C   T   A   C   G   A   G   C   A   C   A   A   C   C   A   C 
 36  16  36  36  36  36  36  16  36  36  36  16  36  36  36  36  16  36  36  36 
  A   T   T   T   T   C   C   C   A   C   T   T   C   T   G   G   A   A   A   A 
 36  36  16  36  36  16  36  36  16  36  36  36  36  36  16  36  36  36  36  36 
  G   T   A   C   T   G   C   G   G   T   T   T   C   C   G   T   G   A   A   G 
 36  36  36  36  36  36  16  36  36  16  36  36  36  36  16  36  36  36  36  36 
  A   C   A   A   C   A   T   T   C   C   ?   C   A   G   C   T   G   G   A   A 
 36  16  36  36  36  36  36  16  36  36   6  36  36  36  36  36  36  36  36  36 
  G   A   T   G   T   T   T   C   T   C   A   A   T   T   T   C   T   G   C   A 
 36  36  16  36  36  36  36  36  36  36  36  16  36  36  16  36  36  36  36  36 
  G   A   C   T   T   G   T   A   C   T   G   G   T   T   T   C   C   G   C   C 
 36  36  36  36  36  36  16  36  36  36  36  36  36  36  36  36  36  36  36  36 
  T   C   C   G   A   C   C   T   G   T   T   G   C   T   G   G   C   T   T   A 
 36  36  36  36  16  36  36  36  36  36  16  36  36  36  36  36  36  16  36  16 
  C   T   G   T   C   ?   T   C   T   C   G   A   G   A   T   T   T   C   T   T 
 36  36  16  36  36   6  36  36  36  36  36  16  36  36  36  36  36  36  36  36 
  G   G   G   T   G   G   C   C   T   G   G   C   C   T   T   C   C   G   A   G 
 36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36 
  T   C   T   T   C   C   A   C   T   G   C   A   C   A   C   A   G   T   A   C 
 36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36 
  A   T   T   A   G   G   C   A   T   G   G   A   T   C   ?   A   A   G   C   C 
 36  36  16  36  36  16  36  36  36  36  36  36  36  36   6  36  36  36  36  36 
  C   A   T   G   T   A   C   A   C   A   C   C   T   G   A   A   C   C   T   G 
 36  36  36  36  36  36  16  36  36  16  36  36  16  36  36  36  36  36  36  36 
  A   C   A   T   C   T   G   C   C   A   T   G   A   A   C   T   C   T   T   G 
 36  16  36  36  36  36  36  16  36  36  36  36  36  16  36  36  16  36  36  36 
  G   G   A   C   A   T   G   T   G   C   C   C   T   T   G   T   T   T   T   C 
 36  36  36  36  36  36  36  36  36  36  36  16  36  36  36  36  36  36  36  36 
  A   G   A   T   C   G   C   A   G   C   T   T   T   G   C   C   C   A   G   T 
 36  36  36  36  16  36  16  36  36  36  36  36  36  36  36  36  36  36  36  36 
  T   T   T   C   T   C   A   G   G   A   A   A   T   T   G   G   G   C   T   T 
 36  36  36  36  16  36  36  36  36  36  36  36  36  36  36  36  16  36  36  36 
  G   C   A   T   C   ?   C   T   G   G   G   G   G   C   A   C   C   T   G   A 
 36  36  16  36  36   6  36  36  36  36  36  16  36  36  36  36  36  36  36  36 
  T   G   A   G   T   A   C   A   T   T   G   A   G   A   A   A   C   T   G   G 
 36  36  36  16  36  36  36  36  36  36  36  36  16  36  36  16  36  36  16  36 
  C   C   A   C   A   A   T   T   T   A   C   T   G   G   T   T   T   A   C   T 
 36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36 
  G   T   G   G   A   G   T   T   T   G   G   G   C   T   T   T   G   C   A   A 
 36  36  36  36  36  36  36  36  36  36  36  36  36  36  16  36  36  36  36  36 
  G   G   A   A   G   G   A   G   A   T   T   C   T   A   T   A   A   A   G   G 
 16  16  36  36  36  36  36  36  36  16  36  36  16  36  36  36  36  36  36  36 
  C   A   T   A   T   G   G   T   G   C   T   G   G   G   C   T   C   T   T   G 
 36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  36  16  36  36 
  T   C   A   T   C   C   T   T   T   G   G   A   G   A   A   T   T   A   C   A 
 36  36  36  36  36  36  36  36  36  36  36  16  36  36  36  36  36  36  36  36 
  G   T   A   C   T   G   T   T   T   A   T   C   A   G   A   C   A   A   G   C 
 36  36  36  36  36  36  16  36  36  36  36  36  36  36  36  16  36  36  36  36 
  C   A   A   A   G   C   T   C   C   T   C   C   C   C   C   T   G   G   A   G 
 36  36  36  36  36  36  36  16  36  36  16  36  36  36  36  36  36  36  36  36 
  C   T   A   G   A   G   A   A   G   A   C   A   G   C   C   T   G   C   C   A 
 36  36  16  36  36  36  36  36  36  36  16  36  36  36  36  16  16  36  36  36 
  G   G   A   G   T   A   T   A   C   T   G   T   C   A   C   A   G   A   G   T 
 16  16  36  16  36  36  16  16  36  36  36  36  36  36  36  16  36  36  36  36 
  T   C   C   A   G   C   C   C   C   T   G   T   A   C   T   A   C   G   T   G 
 36  36  36  36  36  36  36  16  16  36  36  36  36  16  36  36  16  36  36  36 
  G   C   ?   G   A   G   A   G   T   T   T   C   A   A   T   G   A   T   G   C 
 36  36   6  36  36  36  36  36  36  36  36  16  36  16  36  36  36  36  36  36 
  C   A   A   G   G   A   G   A   A   A   G   T   G   A   G   G   A   C   T   T 
 36  36  36  36  36  36  36  36  36  36  36  36  16  36  36  36  36  16  16  36 
  T   T   G   C   T   G   C   C   A   C   A   A   T   C   C   C   T   C   G   G 
 36  36  36  36  36  36  36  36  36  36  16  36  36  16  36  36  16  36  36  36 
  C   C   C   T   T   C   T   C   ?   G   T   T   C   G   C   T   A   T   G   A 
 36  36  36  36  36  36  36  36   6  36  36  36  36  36  36  36  36  16  36  36 
  C   C   C   ?   T   A   C   A   C   T   C   A   A   A   G   G   G   T   T   G 
 36  36  36   6  36  36  36  36  36  16  36  36  36  36  36  36  16  36  36  36 
  A   G   G   T   C   C   T   G   G   A   C   A   A   T   A   C   T   C   A   G 
 36  36  36  36  36  16  36  36  36  36  36  36  36  36  36  36  16  36  36  36 
  C   A   G   T   T   G   A   A   G   A   T   T   T   T   A   G   C   T   G   A 
 36  36  36  16  36  16  36  36  36  36  36  36  36  36  16  36  36  36  36  36 
  C   T   C   C   A   T   T   A   A   T   A   G   T   G   A   G   G   T   T   G 
 16  36  36  36  36  36  36  36  36  16  36  36  36  36  36  16  16  36  16  36 
  G   A   A   T   C   C   T   T   T   G   C   A   A   T   G   C   C   C   T   G 
 36  36  36  36  36  36  36  36  36  36  36  16  16  36  36  36  36  36  36  16 
  C   A   G   A   A   A   A   T   A   A   A   G   T   C   ?   T   G   A   ?   C 
 36  36  36  36  36  16  36  36  36  36  36  36  36 -16 -26 -16 -16 -16 -26 -16 
  A   G   A   A   A   ?   T   G   A   C   G   T   C   A   T   G   G   A   C   A 
-16 -16 -16 -16 -16 -26 -16  16  36  16  36  16  36  36  36  16  36  16  36  36 
  G   A   A   C   T   T   A   G   G   A   G   G   T   C   A   A   C   C   A   ? 
 36  36  36  16  16  36  16  36  16  16  16  36  36  36  36  16  36  16  16   6 
  A   A   A   -   -   T   C   T   G   T   T   G   A   T   A   G   A   A   G   T 
 16  36  36 -28 -28  36  36  16  36  16  16  36  36  36  16  36  36  16  16  36 
  A   T   A   G   T   A   A   C   T   G   C   T   T   T   T   ?   T   T   ?   C 
 16  16  36  16  16  16  36  16  36  16  36  16  36  16  16 -26  36  16   6  16 
  C   C   T   G   A   -   -   -   -   -   A   G   A   A   G   A   A   A   A   G 
 16  16  16  16  36 -28 -28 -28 -28 -28  36  16  36  36  16  16  36  36  36  16 
  T   T   T   T   A   T   T   T   G   A   A   A   T   G   T   C   A   G   C   T 
 16  36  36  16  36  36  36  36  36  16  36  36  16  16  16  36  36  36  36  16 
  T   T   T   A   A   T   A   T   -   T   T   T   T   C   C   T   A   A   C   A 
 36  36  16  36  16  36 -16 -16 -28 -16 -16 -16  16  16  16  36  16  36  36  36 
  ?   A   G   T   G   G   A   G   ?   A   T   C   A   C   C   A   A   A   T   A 
  6  16  16  36  36  36  36  36   6  36  16  36  36  16  36  36  36  36  36  36 
  A   A   T   C   A   A   A   ?   T   T   C   T   C   T   G   A   A   A   T   G 
 36  16  36  36  36  36  16 -26  36  16  16  36  36  36  36  36  36  36  36  36 
  A   A   A   G   T   A   T   A   T   T   A   A   A   A   C   C   C   A   C   C 
 36  16  36  36  16  16  36  16  36  16  36  16  16  36  36  16  16  16  16  16 
  -   -   -   -   -   -   -   -   -   A   G   T   G   G   T   A   G   A   T   C 
-28 -28 -28 -28 -28 -28 -28 -28 -28  36  16  16  36  36  36  36  16  36  36  36 
  T   T   T   C   A   G   A   G   T   C   A   C   A   T   T   T   G   A   T   T 
 16  36  36  16  16  36  16  16  36  36  36  16  16  36  36  36  36  36  36  36 
  T   A   G   A   -   -   -   -   -   T   A   A   T   C   T   C   A   T   A   C 
 36  36  36  36 -28 -28 -28 -28 -28  36  36 -16  36  36  16  36  36  16  36  16 
  C   T   T   C   A   A   T   T   T   G   G   T   T   T   A   A   A   A   T   G 
 16  16  36  36  36  36  36  36  16  16  36  36  36  16  36  36  16  16  16  36 
  T   A   A   T   T   T   -   C   T   C   A   G   ?   T   C   T   C   A   T   C 
 36  36  36  36  16  36 -28  16  36  36  16  16   6  36  16  36  36  36  36  36 
  A   A   C   A   T   T   C   A   T   C   A   A   A   -   T   T   T   G   G   G 
 36  36  16  36  36  36  16  36  36  16  36  36  36 -28  36  36  36  36  36  36 
  A   C   T   T   G   T   ?   T   C   A   T   T   ?   G   G   G   C   T   T   C 
 16  36  16  16  16  16   6  36  36  36  36  36   6  16  16  36  36  36  16  16 
  A   T   C   T   G   T   T   C   A   T   T   T   T   T   A   A   C   C   T   C 
 16  36  16  16  16  36 -16 -16 -16 -16 -16 -16 -16 -16 -16  16  36  16  36  16 
  T   C   A   G   G   T   A   A   G   C   T   C   T   G   A   A   G   G   A   A 
 16  36  36  36  16  16  36  36  16  16  16  16  36  16  36  16  36  36  36  16 
  C   A   C   A   T   A   T   G   G   C   T   ?   A   G   T   G   T   A   A   A 
 16  36  16  36  36  16  16  16  36  36  36   6  36  16  36  36  36  36  36  36 
  A   T   G   T   A   A   G   A   C   T   G   T   C   A   T   C   A   G   G   A 
 36  16  16  16  16  36  36  36  36  36  36  16  36  36  36  16  16  36  16  16 
  A   T   G   A   A   T   T   A   T   T   C   C   G   T   T   C   A   G   T   A 
 16  16  16  36  36  36  16  36  36  36  16  16  16  16  36  16  36  16  36  36 
  C   A   G   A   T   T   G   T   A   A   T   C   T   A   C   A   A   A   G   ? 
 16  36  16  36  36  16  36  36  36  36  16  36  36  36  16  16  36  36  36   6 
  T   T   A   G   T   T   T   C   T   A   C   ?   T   T   C   G   T   T   C   A 
 16  36  36  16  36  36  36  16  16  36  16   6  36  36  16  16  36  36  16  36 
  T   T   A   T   G   G   C   T   C   T   G   A   G   A   A   C   T   A   C   T 
 16  36  36  36  36  16  16  36  36  16  16  36  16  16  36  36  36  16  36  36 
  T   T   G   T   T   A   G   C   C   T   G   C   T   T   A   C   A   T   A   A 
 36  36  36  36  36  36  16  16  16  36  16  36  16  36  36  16  16  36  36  36 
  A   T   ?   T   C   C   T   C   T   G   A   T   C   ?   A   A   G   A   C   C 
 36  36   6  36  16  36  16  16  36  16  16  16  16   6  16  16  16  36  16  16 
  C   T   A   T   T   A   A   G   A   T   A   G   T   T   A   C   A   A   G   C 
 36  16  36  36  36  36  36  16  36  36  36  36  36  36  36  36  36  36  36  36 
  A   A   T   A   A   A   G   T   T   ?   T   ?   ?   A   G   C   A   T   T   A 
 36  16  36  16  36  36  16 -16 -16 -26 -16 -26 -26 -16 -16  16  36  36  36  36 
  T   A   T   A   A   A   A   A   A   A   A   A   A   A   A   A   A   A   ?   ? 
 36  36  36  16  36  36  16  16  16  36  36  36  36  36  16  36  16  16 -26 -26 
  ?   ?   ?   A   ?   ?   ?   ?   ?   ?   -   -   -   -   -   -   -   -   -   - 
-26 -26 -26 -16 -26 -26 -26 -26 -26 -26 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 
  -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   - 
-28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 -28 

msa documentation built on Nov. 1, 2018, 2:58 a.m.