kcount: K-mer counting.
In kmer: Fast K-Mer Counting and Clustering for Biological Sequence Analysis
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
Description
Count all k-letter words in a sequence or set of sequences
with a sliding window of length k.
Usage
1
2
Arguments
x
a matrix of aligned sequences, a list of unaligned sequences,
or a vector representing a single sequence.
Accepted modes are "character" and "raw" (the latter being applicable
for "DNAbin" and "AAbin" objects).
k
integer representing the k-mer size. Defaults to 5.
Note that high values of k may be slow to compute and use a lot of
memory due to the large numbers of calculations required,
particularly when the residue alphabet is also large.
residues
either NULL (default; the residue alphabet is automatically
detected from the sequences), a case sensitive character vector
specifying the residue alphabet, or one of the character strings
"RNA", "DNA", "AA", "AMINO". Note that the default option can be slow for
large lists of character vectors. Specifying the residue alphabet is therefore
recommended unless x is a "DNAbin" or "AAbin" object.
gap
the character used to represent gaps in the alignment matrix
(if applicable). Ignored for "DNAbin" and "AAbin" objects.
Defaults to "-" otherwise.
named
logical. Should the k-mers be returned as column names in
the returned matrix? Defaults to TRUE.
compress
logical indicating whether to compress AAbin sequences
using the Dayhoff(6) alphabet for k-mer sizes exceeding 4.
Defaults to TRUE to avoid memory overflow and excessive computation time.
encode
logical indicating if the resulting matrix should be encoded
in raw bytes (output matrix can be decoded with kmer:::.decodekc()).
Note that the output will be rounded and have maximum k-mer count of 15.
Details
This function computes a vector or matrix of k-mer counts
from a sequence or set of sequences using a sliding a window of length k.
DNA and amino acid sequences can be passed to the function either as
a list of non-aligned sequences or a matrix of aligned sequences,
preferably in the "DNAbin" or "AAbin" raw-byte format
(Paradis et al 2004, 2012; see the ape package
documentation for more information on these S3 classes).
Character sequences are supported; however ambiguity codes may
not be recognized or treated appropriately, since raw ambiguity
codes are counted according to their underlying residue frequencies
(e.g. the 5-mer "ACRGT" would contribute 0.5 to the tally for "ACAGT"
and 0.5 to that of "ACGGT").
To minimize computation time when counting longer k-mers (k > 3),
amino acid sequences in the raw "AAbin" format are automatically
compressed using the Dayhoff-6 alphabet as detailed in Edgar (2004).
Note that amino acid sequences will not be compressed if they
are supplied as a list of character vectors rather than an "AAbin"
object, in which case the k-mer length should be reduced
(k < 4) to avoid excessive memory use and computation time.
Value
Returns a matrix of k-mer counts with one row for each sequence
and n^k columns (where n is the size of the
residue alphabet and k is the k-mer size)
Author(s)
Shaun Wilkinson
References
Edgar RC (2004) Local homology recognition and distance measures in
linear time using compressed amino acid alphabets.
Nucleic Acids Research, 32, 380-385.
Paradis E, Claude J, Strimmer K, (2004) APE: analyses of phylogenetics
and evolution in R language. Bioinformatics 20, 289-290.
Paradis E (2012) Analysis of Phylogenetics and Evolution with R
(Second Edition). Springer, New York.
See Also
kdistance for k-mer distance matrix computation.
Examples
1
2
3
4
5
6
7
8
9
10
11
## compute a matrix of k-mer counts for the woodmouse
## data (ape package) using a k-mer size of 3
library(ape)
data(woodmouse)
x <- kcount(woodmouse, k = 3)
x
## 64 columns for nucleotide 3-mers AAA, AAC, ... TTT
## convert to AAbin object and repeat the operation
y <- kcount(ape::trans(woodmouse, 2), k = 2)
y
## 400 columns for amino acid 2-mers AA, AB, ... , YY
Example output
AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC
No305 21 21 2 31 30 15 8 22 10 12 13 12 26 21 13 34 18 20
No304 23 23 2 33 28 16 8 22 9 12 13 10 26 20 14 35 20 18
No306 23 22 2 34 29 15 8 22 9 12 13 9 27 23 14 35 20 18
No0906S 23 21 2 35 29 14 8 21 9 12 13 9 27 26 14 36 20 18
No0908S 23 22 2 33 28 15 8 22 9 11 13 10 27 24 13 35 20 18
No0909S 23 22 2 32 29 15 8 24 9 12 13 10 26 26 13 30 20 19
No0910S 22 22 2 32 29 15 8 21 10 12 13 10 26 25 13 36 19 18
No0912S 23 22 2 33 30 15 8 21 9 12 12 10 25 25 13 34 20 18
No0913S 23 23 2 33 28 16 8 22 9 12 13 9 25 23 15 35 20 18
No1103S 23 22 2 33 29 15 8 21 9 12 13 10 26 24 13 35 19 18
No1007S 23 21 2 33 29 15 8 23 9 12 13 10 26 26 13 31 20 19
No1114S 16 21 2 30 27 14 8 17 9 11 14 11 28 19 12 34 19 14
No1202S 22 22 2 32 29 15 8 21 10 12 13 10 26 25 13 36 19 18
No1206S 23 22 2 33 29 14 8 21 9 12 13 10 26 24 13 36 20 18
No1208S 23 22 2 32 29 15 8 24 9 12 13 10 26 26 13 29 20 19
CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT
No305 17 30 23 16 4 28 7 6 7 2 30 12 7 25 9 13 11 9
No304 15 30 22 16 4 28 6 6 8 2 30 13 7 26 11 12 9 8
No306 15 30 22 16 4 27 6 6 8 2 31 11 6 26 11 12 9 9
No0906S 15 31 21 15 4 27 7 6 7 2 30 12 6 25 10 11 10 12
No0908S 15 29 22 19 4 27 7 6 7 2 30 13 6 24 10 12 9 10
No0909S 15 28 21 16 4 29 7 6 7 2 32 13 6 28 9 13 10 10
No0910S 16 30 20 16 4 26 7 6 7 3 30 12 6 25 10 11 10 13
No0912S 15 31 22 16 4 28 6 6 8 2 30 13 6 26 10 13 9 9
No0913S 15 30 22 16 4 27 6 6 8 3 31 13 6 25 11 12 9 10
No1103S 15 30 21 16 4 28 7 6 7 2 30 13 6 26 10 12 10 10
No1007S 15 28 21 16 5 29 7 6 7 2 31 13 6 28 9 13 10 10
No1114S 15 29 19 15 5 28 5 6 8 2 28 13 6 24 9 12 11 8
No1202S 16 30 21 16 5 27 7 6 7 3 30 12 6 25 10 11 10 13
No1206S 15 30 21 16 4 27 7 6 7 2 30 13 6 25 10 11 10 11
No1208S 15 28 21 17 5 29 7 6 7 2 32 14 6 27 9 13 10 10
GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC
No305 8 15 1 7 13 5 1 5 10 8 5 4 27 21 17 24 24 25
No304 8 14 1 8 13 5 1 5 11 6 3 5 27 21 18 23 25 24
No306 8 14 1 8 13 5 1 5 10 5 4 5 27 22 17 25 24 24
No0906S 8 14 1 8 14 5 0 3 11 3 3 4 28 23 16 24 26 24
No0908S 8 15 1 7 12 6 3 4 10 4 5 5 27 21 17 26 24 24
No0909S 8 14 1 8 13 5 2 4 10 4 5 5 27 22 17 24 24 26
No0910S 9 14 2 8 14 6 0 2 10 3 4 5 27 22 17 24 25 22
No0912S 8 14 1 8 13 5 3 4 10 4 5 5 27 21 17 23 24 26
No0913S 9 14 2 8 14 6 0 3 10 4 3 5 27 21 17 24 24 24
No1103S 8 14 1 8 13 5 1 4 10 4 5 5 28 21 17 24 24 25
No1007S 8 15 1 8 13 5 2 4 10 3 5 5 27 22 17 24 24 26
No1114S 8 14 1 9 14 6 0 5 8 6 5 5 25 19 17 25 23 25
No1202S 8 15 2 8 14 6 0 2 10 2 4 5 27 22 17 24 25 24
No1206S 9 15 1 8 13 5 1 4 10 4 6 4 27 21 17 24 24 24
No1208S 8 15 1 8 13 5 2 4 10 3 5 5 27 22 17 24 24 26
TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT
No305 9 17 12 8 3 8 24 34 6 34
No304 9 18 12 8 2 9 22 37 7 33
No306 9 17 13 8 2 8 24 35 7 34
No0906S 9 17 13 8 2 7 23 35 7 35
No0908S 9 17 13 8 2 8 24 33 7 34
No0909S 9 18 13 8 2 8 22 34 7 30
No0910S 9 18 13 9 2 7 24 34 8 36
No0912S 9 18 13 8 2 8 23 35 7 32
No0913S 9 18 13 9 2 7 23 35 7 33
No1103S 9 18 13 8 2 8 24 35 7 33
No1007S 8 18 13 9 2 7 23 34 7 30
No1114S 7 17 12 9 3 6 22 34 7 32
No1202S 8 17 13 9 2 6 24 35 7 35
No1206S 9 18 13 10 2 8 23 34 8 33
No1208S 7 18 13 9 2 7 22 32 7 30
Warning message:
In ape::trans(woodmouse, 2) :
sequence length not a multiple of 3: 2 nucleotides dropped
AA AC AD AE AF AG AH AI AK AL AM AN AP AQ AR AS AT AV AW AY CA CC CD CE
No305 1 0 1 0 3 0 0 3 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No304 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No306 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0906S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0908S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0909S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0910S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0912S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0913S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No1103S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No1007S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No1114S 1 0 1 0 3 0 0 2 0 3 2 2 1 0 0 1 2 1 0 1 0 0 0 0
No1202S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No1206S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No1208S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
CF CG CH CI CK CL CM CN CP CQ CR CS CT CV CW CY DA DC DD DE DF DG DH DI
No305 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No304 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No306 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0906S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0908S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0909S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0910S 0 0 0 0 1 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0912S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0913S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1103S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1007S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1114S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1202S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1206S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1208S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
DK DL DM DN DP DQ DR DS DT DV DW DY EA EC ED EE EF EG EH EI EK EL EM EN
No305 2 2 0 1 1 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No304 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No306 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0906S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0908S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0909S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0910S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0912S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0913S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1103S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1007S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1114S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1202S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1206S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1208S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
EP EQ ER ES ET EV EW EY FA FC FD FE FF FG FH FI FK FL FM FN FP FQ FR FS
No305 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No304 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No306 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0906S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0908S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0909S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0910S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0912S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0913S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No1103S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No1007S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No1114S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 3 0 7 1 0 1 0 2 2
No1202S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No1206S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No1208S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
FT FV FW FY GA GC GD GE GF GG GH GI GK GL GM GN GP GQ GR GS GT GV GW GY
No305 0 0 1 0 2 0 1 0 1 2 0 0 0 2 1 0 0 1 1 3 1 4 1 1
No304 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No306 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No0906S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 2 0 0 1 1 3 1 2 1 1
No0908S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No0909S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No0910S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No0912S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No0913S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No1103S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No1007S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No1114S 0 0 1 0 2 0 1 0 1 3 0 0 0 2 1 0 0 2 1 3 1 4 1 1
No1202S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No1206S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No1208S 0 0 0 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
HA HC HD HE HF HG HH HI HK HL HM HN HP HQ HR HS HT HV HW HY IA IC ID IE
No305 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 2 1 0
No304 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No306 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0906S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0908S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0909S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0910S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0912S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0913S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No1103S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No1007S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No1114S 1 0 0 1 1 0 0 3 0 1 0 0 1 0 0 0 1 1 0 1 1 2 1 0
No1202S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No1206S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No1208S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
IF IG IH II IK IL IM IN IP IQ IR IS IT IV IW IY KA KC KD KE KF KG KH KI
No305 1 2 0 1 2 7 0 0 3 1 1 2 2 1 1 0 2 0 1 0 0 0 0 1
No304 1 2 0 2 3 7 0 1 3 1 2 1 1 1 1 0 1 0 1 0 0 0 0 2
No306 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No0906S 1 2 0 2 2 8 0 1 3 1 2 2 2 1 1 0 1 0 1 0 0 0 0 2
No0908S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No0909S 0 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No0910S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No0912S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No0913S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No1103S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No1007S 0 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No1114S 1 2 0 1 2 8 0 0 3 1 1 1 2 1 2 0 1 0 1 0 0 0 0 1
No1202S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No1206S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No1208S 0 2 0 2 2 8 0 1 3 1 1 1 2 1 1 0 1 0 1 0 0 0 0 2
KK KL KM KN KP KQ KR KS KT KV KW KY LA LC LD LE LF LG LH LI LK LL LM LN
No305 0 2 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No304 0 1 0 1 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No306 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0906S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0908S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0909S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0910S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0912S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0913S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No1103S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No1007S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No1114S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 0 5 5 2
No1202S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No1206S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No1208S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
LP LQ LR LS LT LV LW LY MA MC MD ME MF MG MH MI MK ML MM MN MP MQ MR MS
No305 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No304 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No306 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No0906S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 3 0 0 1 0 1 0 1 1
No0908S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No0909S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No0910S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No0912S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No0913S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No1103S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No1007S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No1114S 4 0 1 2 2 3 0 0 0 0 0 1 2 1 2 1 0 0 1 0 2 0 0 1
No1202S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No1206S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No1208S 4 0 1 2 2 3 1 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 1 1
MT MV MW MY NA NC ND NE NF NG NH NI NK NL NM NN NP NQ NR NS NT NV NW NY
No305 2 1 0 1 0 0 0 0 1 1 0 2 1 0 0 1 2 0 0 1 1 0 0 2
No304 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No306 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0906S 2 0 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0908S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0909S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0910S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0912S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0913S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No1103S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No1007S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No1114S 2 2 0 1 0 0 0 0 2 1 0 2 1 0 0 1 2 0 0 1 1 0 0 2
No1202S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No1206S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No1208S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
PA PC PD PE PF PG PH PI PK PL PM PN PP PQ PR PS PT PV PW PY QA QC QD QE
No305 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No304 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No306 2 0 2 1 3 0 0 1 0 2 0 1 0 0 0 1 1 0 1 3 0 0 0 0
No0906S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No0908S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No0909S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No0910S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No0912S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No0913S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No1103S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No1007S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No1114S 2 0 2 1 3 0 1 1 0 1 0 1 1 0 0 1 1 1 1 2 1 0 0 0
No1202S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No1206S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No1208S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
QF QG QH QI QK QL QM QN QP QQ QR QS QT QV QW QY RA RC RD RE RF RG RH RI
No305 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No304 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No306 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No0906S 0 0 0 1 0 0 2 0 0 0 1 0 0 0 0 0 0 0 1 0 1 1 0 0
No0908S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No0909S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No0910S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No0912S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No0913S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No1103S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No1007S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No1114S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 1 0
No1202S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No1206S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No1208S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
RK RL RM RN RP RQ RR RS RT RV RW RY SA SC SD SE SF SG SH SI SK SL SM SN
No305 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 1 2 1 2 1 2
No304 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No306 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No0906S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No0908S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No0909S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No0910S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 0 2 1 2
No0912S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No0913S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No1103S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No1007S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No1114S 0 0 0 0 1 0 0 2 0 0 1 1 1 0 2 0 2 0 0 2 2 2 1 2
No1202S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No1206S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No1208S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 2 0 0 2 1 3 1 2
SP SQ SR SS ST SV SW SY TA TC TD TE TF TG TH TI TK TL TM TN TP TQ TR TS
No305 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 1 4 1 0 1 1 1 2
No304 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 4 1 0 1 1 1 2
No306 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 4 1 1 1 1 1 2
No0906S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 3 1 1 1 1 1 2
No0908S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 2 0 3 1 1 1 1 1 2
No0909S 0 0 0 2 0 2 1 1 2 0 0 1 1 3 2 1 0 3 1 1 1 1 1 2
No0910S 0 0 0 2 0 2 1 1 2 1 0 0 0 3 2 1 0 3 1 1 1 1 1 1
No0912S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 2 0 3 1 1 1 1 1 2
No0913S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 3 1 1 1 1 2 2
No1103S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 3 1 1 1 1 2 2
No1007S 0 0 0 2 0 2 1 1 2 0 0 0 1 3 2 1 0 3 1 1 1 1 1 2
No1114S 0 0 0 2 0 1 1 1 2 0 0 1 0 3 1 1 0 3 1 1 1 1 1 2
No1202S 0 0 0 2 0 2 1 1 3 0 0 0 0 3 2 1 0 3 1 1 1 1 1 2
No1206S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 3 1 1 1 1 1 2
No1208S 0 0 0 2 0 2 1 1 2 0 0 0 1 3 2 1 0 3 1 1 1 1 1 2
TT TV TW TY VA VC VD VE VF VG VH VI VK VL VM VN VP VQ VR VS VT VV VW VY
No305 1 1 1 0 0 1 1 1 0 1 1 2 0 5 1 1 0 0 0 1 1 1 0 0
No304 1 1 1 0 0 0 1 1 0 1 1 2 0 5 1 1 0 0 0 1 1 1 0 0
No306 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No0906S 1 1 1 0 0 0 1 1 0 1 1 2 0 4 1 1 0 0 0 0 1 0 0 0
No0908S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No0909S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No0910S 1 1 1 1 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No0912S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No0913S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No1103S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No1007S 2 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No1114S 1 1 1 0 0 1 1 1 0 1 1 3 0 5 1 1 0 0 0 1 1 1 0 0
No1202S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No1206S 1 1 2 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No1208S 1 1 1 1 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
WA WC WD WE WF WG WH WI WK WL WM WN WP WQ WR WS WT WV WW WY YA YC YD YE
No305 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No304 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No306 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0906S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0908S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0909S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0910S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0912S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0913S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No1103S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No1007S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No1114S 0 0 0 0 0 3 0 2 0 1 0 2 0 0 1 0 0 0 1 1 1 0 0 0
No1202S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No1206S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No1208S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
YF YG YH YI YK YL YM YN YP YQ YR YS YT YV YW YY
No305 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No304 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No306 1 2 1 2 0 0 2 0 0 0 0 0 2 1 0 2
No0906S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No0908S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No0909S 1 2 0 1 0 0 2 0 0 0 0 0 3 1 0 2
No0910S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No0912S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No0913S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No1103S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No1007S 1 2 0 1 0 0 2 0 0 0 0 0 3 1 0 2
No1114S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No1202S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No1206S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No1208S 1 2 0 1 0 0 2 0 0 0 0 0 3 1 0 2
kmer documentation built on May 20, 2019, 9:02 a.m.
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Description Usage Arguments Details Value Author(s) References See Also Examples
Description
Count all k-letter words in a sequence or set of sequences with a sliding window of length k.
Usage
1 2 |
Arguments
x |
a matrix of aligned sequences, a list of unaligned sequences, or a vector representing a single sequence. Accepted modes are "character" and "raw" (the latter being applicable for "DNAbin" and "AAbin" objects). |
k |
integer representing the k-mer size. Defaults to 5. Note that high values of k may be slow to compute and use a lot of memory due to the large numbers of calculations required, particularly when the residue alphabet is also large. |
residues |
either NULL (default; the residue alphabet is automatically detected from the sequences), a case sensitive character vector specifying the residue alphabet, or one of the character strings "RNA", "DNA", "AA", "AMINO". Note that the default option can be slow for large lists of character vectors. Specifying the residue alphabet is therefore recommended unless x is a "DNAbin" or "AAbin" object. |
gap |
the character used to represent gaps in the alignment matrix
(if applicable). Ignored for |
named |
logical. Should the k-mers be returned as column names in the returned matrix? Defaults to TRUE. |
compress |
logical indicating whether to compress AAbin sequences using the Dayhoff(6) alphabet for k-mer sizes exceeding 4. Defaults to TRUE to avoid memory overflow and excessive computation time. |
encode |
logical indicating if the resulting matrix should be encoded
in raw bytes (output matrix can be decoded with |
Details
This function computes a vector or matrix of k-mer counts
from a sequence or set of sequences using a sliding a window of length k.
DNA and amino acid sequences can be passed to the function either as
a list of non-aligned sequences or a matrix of aligned sequences,
preferably in the "DNAbin" or "AAbin" raw-byte format
(Paradis et al 2004, 2012; see the ape package
documentation for more information on these S3 classes).
Character sequences are supported; however ambiguity codes may
not be recognized or treated appropriately, since raw ambiguity
codes are counted according to their underlying residue frequencies
(e.g. the 5-mer "ACRGT" would contribute 0.5 to the tally for "ACAGT"
and 0.5 to that of "ACGGT").
To minimize computation time when counting longer k-mers (k > 3), amino acid sequences in the raw "AAbin" format are automatically compressed using the Dayhoff-6 alphabet as detailed in Edgar (2004). Note that amino acid sequences will not be compressed if they are supplied as a list of character vectors rather than an "AAbin" object, in which case the k-mer length should be reduced (k < 4) to avoid excessive memory use and computation time.
Value
Returns a matrix of k-mer counts with one row for each sequence and n^k columns (where n is the size of the residue alphabet and k is the k-mer size)
Author(s)
Shaun Wilkinson
References
Edgar RC (2004) Local homology recognition and distance measures in linear time using compressed amino acid alphabets. Nucleic Acids Research, 32, 380-385.
Paradis E, Claude J, Strimmer K, (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289-290.
Paradis E (2012) Analysis of Phylogenetics and Evolution with R (Second Edition). Springer, New York.
See Also
kdistance for k-mer distance matrix computation.
Examples
1 2 3 4 5 6 7 8 9 10 11 | ## compute a matrix of k-mer counts for the woodmouse
## data (ape package) using a k-mer size of 3
library(ape)
data(woodmouse)
x <- kcount(woodmouse, k = 3)
x
## 64 columns for nucleotide 3-mers AAA, AAC, ... TTT
## convert to AAbin object and repeat the operation
y <- kcount(ape::trans(woodmouse, 2), k = 2)
y
## 400 columns for amino acid 2-mers AA, AB, ... , YY
|
Example output
AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC
No305 21 21 2 31 30 15 8 22 10 12 13 12 26 21 13 34 18 20
No304 23 23 2 33 28 16 8 22 9 12 13 10 26 20 14 35 20 18
No306 23 22 2 34 29 15 8 22 9 12 13 9 27 23 14 35 20 18
No0906S 23 21 2 35 29 14 8 21 9 12 13 9 27 26 14 36 20 18
No0908S 23 22 2 33 28 15 8 22 9 11 13 10 27 24 13 35 20 18
No0909S 23 22 2 32 29 15 8 24 9 12 13 10 26 26 13 30 20 19
No0910S 22 22 2 32 29 15 8 21 10 12 13 10 26 25 13 36 19 18
No0912S 23 22 2 33 30 15 8 21 9 12 12 10 25 25 13 34 20 18
No0913S 23 23 2 33 28 16 8 22 9 12 13 9 25 23 15 35 20 18
No1103S 23 22 2 33 29 15 8 21 9 12 13 10 26 24 13 35 19 18
No1007S 23 21 2 33 29 15 8 23 9 12 13 10 26 26 13 31 20 19
No1114S 16 21 2 30 27 14 8 17 9 11 14 11 28 19 12 34 19 14
No1202S 22 22 2 32 29 15 8 21 10 12 13 10 26 25 13 36 19 18
No1206S 23 22 2 33 29 14 8 21 9 12 13 10 26 24 13 36 20 18
No1208S 23 22 2 32 29 15 8 24 9 12 13 10 26 26 13 29 20 19
CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT
No305 17 30 23 16 4 28 7 6 7 2 30 12 7 25 9 13 11 9
No304 15 30 22 16 4 28 6 6 8 2 30 13 7 26 11 12 9 8
No306 15 30 22 16 4 27 6 6 8 2 31 11 6 26 11 12 9 9
No0906S 15 31 21 15 4 27 7 6 7 2 30 12 6 25 10 11 10 12
No0908S 15 29 22 19 4 27 7 6 7 2 30 13 6 24 10 12 9 10
No0909S 15 28 21 16 4 29 7 6 7 2 32 13 6 28 9 13 10 10
No0910S 16 30 20 16 4 26 7 6 7 3 30 12 6 25 10 11 10 13
No0912S 15 31 22 16 4 28 6 6 8 2 30 13 6 26 10 13 9 9
No0913S 15 30 22 16 4 27 6 6 8 3 31 13 6 25 11 12 9 10
No1103S 15 30 21 16 4 28 7 6 7 2 30 13 6 26 10 12 10 10
No1007S 15 28 21 16 5 29 7 6 7 2 31 13 6 28 9 13 10 10
No1114S 15 29 19 15 5 28 5 6 8 2 28 13 6 24 9 12 11 8
No1202S 16 30 21 16 5 27 7 6 7 3 30 12 6 25 10 11 10 13
No1206S 15 30 21 16 4 27 7 6 7 2 30 13 6 25 10 11 10 11
No1208S 15 28 21 17 5 29 7 6 7 2 32 14 6 27 9 13 10 10
GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC
No305 8 15 1 7 13 5 1 5 10 8 5 4 27 21 17 24 24 25
No304 8 14 1 8 13 5 1 5 11 6 3 5 27 21 18 23 25 24
No306 8 14 1 8 13 5 1 5 10 5 4 5 27 22 17 25 24 24
No0906S 8 14 1 8 14 5 0 3 11 3 3 4 28 23 16 24 26 24
No0908S 8 15 1 7 12 6 3 4 10 4 5 5 27 21 17 26 24 24
No0909S 8 14 1 8 13 5 2 4 10 4 5 5 27 22 17 24 24 26
No0910S 9 14 2 8 14 6 0 2 10 3 4 5 27 22 17 24 25 22
No0912S 8 14 1 8 13 5 3 4 10 4 5 5 27 21 17 23 24 26
No0913S 9 14 2 8 14 6 0 3 10 4 3 5 27 21 17 24 24 24
No1103S 8 14 1 8 13 5 1 4 10 4 5 5 28 21 17 24 24 25
No1007S 8 15 1 8 13 5 2 4 10 3 5 5 27 22 17 24 24 26
No1114S 8 14 1 9 14 6 0 5 8 6 5 5 25 19 17 25 23 25
No1202S 8 15 2 8 14 6 0 2 10 2 4 5 27 22 17 24 25 24
No1206S 9 15 1 8 13 5 1 4 10 4 6 4 27 21 17 24 24 24
No1208S 8 15 1 8 13 5 2 4 10 3 5 5 27 22 17 24 24 26
TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT
No305 9 17 12 8 3 8 24 34 6 34
No304 9 18 12 8 2 9 22 37 7 33
No306 9 17 13 8 2 8 24 35 7 34
No0906S 9 17 13 8 2 7 23 35 7 35
No0908S 9 17 13 8 2 8 24 33 7 34
No0909S 9 18 13 8 2 8 22 34 7 30
No0910S 9 18 13 9 2 7 24 34 8 36
No0912S 9 18 13 8 2 8 23 35 7 32
No0913S 9 18 13 9 2 7 23 35 7 33
No1103S 9 18 13 8 2 8 24 35 7 33
No1007S 8 18 13 9 2 7 23 34 7 30
No1114S 7 17 12 9 3 6 22 34 7 32
No1202S 8 17 13 9 2 6 24 35 7 35
No1206S 9 18 13 10 2 8 23 34 8 33
No1208S 7 18 13 9 2 7 22 32 7 30
Warning message:
In ape::trans(woodmouse, 2) :
sequence length not a multiple of 3: 2 nucleotides dropped
AA AC AD AE AF AG AH AI AK AL AM AN AP AQ AR AS AT AV AW AY CA CC CD CE
No305 1 0 1 0 3 0 0 3 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No304 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No306 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0906S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0908S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0909S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0910S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0912S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No0913S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No1103S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No1007S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No1114S 1 0 1 0 3 0 0 2 0 3 2 2 1 0 0 1 2 1 0 1 0 0 0 0
No1202S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No1206S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
No1208S 1 0 1 0 3 0 0 2 0 3 1 2 1 0 0 1 3 1 0 1 0 0 0 0
CF CG CH CI CK CL CM CN CP CQ CR CS CT CV CW CY DA DC DD DE DF DG DH DI
No305 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No304 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No306 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0906S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0908S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0909S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0910S 0 0 0 0 1 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0912S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No0913S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1103S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1007S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1114S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1202S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1206S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
No1208S 0 0 0 0 0 2 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1
DK DL DM DN DP DQ DR DS DT DV DW DY EA EC ED EE EF EG EH EI EK EL EM EN
No305 2 2 0 1 1 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No304 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No306 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0906S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0908S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0909S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0910S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0912S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No0913S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1103S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1007S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1114S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1202S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1206S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
No1208S 2 2 0 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
EP EQ ER ES ET EV EW EY FA FC FD FE FF FG FH FI FK FL FM FN FP FQ FR FS
No305 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No304 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No306 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0906S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0908S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0909S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0910S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0912S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No0913S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No1103S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No1007S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No1114S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 3 0 7 1 0 1 0 2 2
No1202S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No1206S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
No1208S 0 0 0 0 2 0 2 0 3 0 0 0 3 1 2 4 0 6 2 0 1 0 1 2
FT FV FW FY GA GC GD GE GF GG GH GI GK GL GM GN GP GQ GR GS GT GV GW GY
No305 0 0 1 0 2 0 1 0 1 2 0 0 0 2 1 0 0 1 1 3 1 4 1 1
No304 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No306 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No0906S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 2 0 0 1 1 3 1 2 1 1
No0908S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No0909S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No0910S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No0912S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No0913S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No1103S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No1007S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No1114S 0 0 1 0 2 0 1 0 1 3 0 0 0 2 1 0 0 2 1 3 1 4 1 1
No1202S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No1206S 0 0 1 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
No1208S 0 0 0 0 2 0 1 0 1 2 0 1 0 2 1 0 0 1 1 3 1 3 1 1
HA HC HD HE HF HG HH HI HK HL HM HN HP HQ HR HS HT HV HW HY IA IC ID IE
No305 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 2 1 0
No304 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No306 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0906S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0908S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0909S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0910S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0912S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No0913S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No1103S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No1007S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No1114S 1 0 0 1 1 0 0 3 0 1 0 0 1 0 0 0 1 1 0 1 1 2 1 0
No1202S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No1206S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
No1208S 1 0 0 1 1 0 0 2 0 1 0 0 2 0 0 1 1 1 0 1 1 3 1 0
IF IG IH II IK IL IM IN IP IQ IR IS IT IV IW IY KA KC KD KE KF KG KH KI
No305 1 2 0 1 2 7 0 0 3 1 1 2 2 1 1 0 2 0 1 0 0 0 0 1
No304 1 2 0 2 3 7 0 1 3 1 2 1 1 1 1 0 1 0 1 0 0 0 0 2
No306 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No0906S 1 2 0 2 2 8 0 1 3 1 2 2 2 1 1 0 1 0 1 0 0 0 0 2
No0908S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No0909S 0 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No0910S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No0912S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No0913S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No1103S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No1007S 0 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No1114S 1 2 0 1 2 8 0 0 3 1 1 1 2 1 2 0 1 0 1 0 0 0 0 1
No1202S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No1206S 1 2 0 2 2 8 0 1 3 1 2 1 2 1 1 0 1 0 1 0 0 0 0 2
No1208S 0 2 0 2 2 8 0 1 3 1 1 1 2 1 1 0 1 0 1 0 0 0 0 2
KK KL KM KN KP KQ KR KS KT KV KW KY LA LC LD LE LF LG LH LI LK LL LM LN
No305 0 2 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No304 0 1 0 1 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No306 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0906S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0908S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0909S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0910S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0912S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No0913S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No1103S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No1007S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No1114S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 0 5 5 2
No1202S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No1206S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
No1208S 0 1 0 0 1 1 0 0 1 0 0 0 3 0 0 0 6 4 3 3 1 7 4 2
LP LQ LR LS LT LV LW LY MA MC MD ME MF MG MH MI MK ML MM MN MP MQ MR MS
No305 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No304 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No306 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No0906S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 3 0 0 1 0 1 0 1 1
No0908S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No0909S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No0910S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No0912S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No0913S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No1103S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No1007S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No1114S 4 0 1 2 2 3 0 0 0 0 0 1 2 1 2 1 0 0 1 0 2 0 0 1
No1202S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No1206S 4 0 1 2 2 3 0 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 0 1
No1208S 4 0 1 2 2 3 1 0 1 0 0 1 2 1 2 1 0 0 1 0 1 0 1 1
MT MV MW MY NA NC ND NE NF NG NH NI NK NL NM NN NP NQ NR NS NT NV NW NY
No305 2 1 0 1 0 0 0 0 1 1 0 2 1 0 0 1 2 0 0 1 1 0 0 2
No304 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No306 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0906S 2 0 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0908S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0909S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0910S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0912S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No0913S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No1103S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No1007S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No1114S 2 2 0 1 0 0 0 0 2 1 0 2 1 0 0 1 2 0 0 1 1 0 0 2
No1202S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No1206S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
No1208S 2 1 0 1 0 0 0 0 1 1 1 2 1 1 0 1 2 0 0 1 1 0 0 2
PA PC PD PE PF PG PH PI PK PL PM PN PP PQ PR PS PT PV PW PY QA QC QD QE
No305 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No304 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No306 2 0 2 1 3 0 0 1 0 2 0 1 0 0 0 1 1 0 1 3 0 0 0 0
No0906S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No0908S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No0909S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No0910S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No0912S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No0913S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No1103S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No1007S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No1114S 2 0 2 1 3 0 1 1 0 1 0 1 1 0 0 1 1 1 1 2 1 0 0 0
No1202S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No1206S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
No1208S 2 0 2 1 3 0 1 1 0 2 0 1 1 0 0 1 1 0 1 2 0 0 0 0
QF QG QH QI QK QL QM QN QP QQ QR QS QT QV QW QY RA RC RD RE RF RG RH RI
No305 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No304 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No306 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No0906S 0 0 0 1 0 0 2 0 0 0 1 0 0 0 0 0 0 0 1 0 1 1 0 0
No0908S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No0909S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No0910S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No0912S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No0913S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No1103S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No1007S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No1114S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 1 0
No1202S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No1206S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
No1208S 0 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0
RK RL RM RN RP RQ RR RS RT RV RW RY SA SC SD SE SF SG SH SI SK SL SM SN
No305 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 1 2 1 2 1 2
No304 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No306 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No0906S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No0908S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No0909S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No0910S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 0 2 1 2
No0912S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No0913S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No1103S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No1007S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No1114S 0 0 0 0 1 0 0 2 0 0 1 1 1 0 2 0 2 0 0 2 2 2 1 2
No1202S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No1206S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 3 0 0 2 1 2 1 2
No1208S 1 0 0 0 1 0 0 2 0 0 0 1 1 0 2 0 2 0 0 2 1 3 1 2
SP SQ SR SS ST SV SW SY TA TC TD TE TF TG TH TI TK TL TM TN TP TQ TR TS
No305 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 1 4 1 0 1 1 1 2
No304 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 4 1 0 1 1 1 2
No306 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 4 1 1 1 1 1 2
No0906S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 3 1 1 1 1 1 2
No0908S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 2 0 3 1 1 1 1 1 2
No0909S 0 0 0 2 0 2 1 1 2 0 0 1 1 3 2 1 0 3 1 1 1 1 1 2
No0910S 0 0 0 2 0 2 1 1 2 1 0 0 0 3 2 1 0 3 1 1 1 1 1 1
No0912S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 2 0 3 1 1 1 1 1 2
No0913S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 3 1 1 1 1 2 2
No1103S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 3 1 1 1 1 2 2
No1007S 0 0 0 2 0 2 1 1 2 0 0 0 1 3 2 1 0 3 1 1 1 1 1 2
No1114S 0 0 0 2 0 1 1 1 2 0 0 1 0 3 1 1 0 3 1 1 1 1 1 2
No1202S 0 0 0 2 0 2 1 1 3 0 0 0 0 3 2 1 0 3 1 1 1 1 1 2
No1206S 0 0 0 2 0 2 1 1 2 0 0 0 0 3 2 1 0 3 1 1 1 1 1 2
No1208S 0 0 0 2 0 2 1 1 2 0 0 0 1 3 2 1 0 3 1 1 1 1 1 2
TT TV TW TY VA VC VD VE VF VG VH VI VK VL VM VN VP VQ VR VS VT VV VW VY
No305 1 1 1 0 0 1 1 1 0 1 1 2 0 5 1 1 0 0 0 1 1 1 0 0
No304 1 1 1 0 0 0 1 1 0 1 1 2 0 5 1 1 0 0 0 1 1 1 0 0
No306 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No0906S 1 1 1 0 0 0 1 1 0 1 1 2 0 4 1 1 0 0 0 0 1 0 0 0
No0908S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No0909S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No0910S 1 1 1 1 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No0912S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No0913S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No1103S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No1007S 2 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No1114S 1 1 1 0 0 1 1 1 0 1 1 3 0 5 1 1 0 0 0 1 1 1 0 0
No1202S 1 1 1 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No1206S 1 1 2 0 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
No1208S 1 1 1 1 0 0 1 1 0 1 1 3 0 4 1 1 0 0 0 1 1 0 0 0
WA WC WD WE WF WG WH WI WK WL WM WN WP WQ WR WS WT WV WW WY YA YC YD YE
No305 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No304 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No306 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0906S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0908S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0909S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0910S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0912S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No0913S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No1103S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No1007S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No1114S 0 0 0 0 0 3 0 2 0 1 0 2 0 0 1 0 0 0 1 1 1 0 0 0
No1202S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No1206S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
No1208S 0 0 0 0 0 3 0 1 0 1 0 2 0 0 0 0 0 0 1 1 1 0 0 0
YF YG YH YI YK YL YM YN YP YQ YR YS YT YV YW YY
No305 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No304 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No306 1 2 1 2 0 0 2 0 0 0 0 0 2 1 0 2
No0906S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No0908S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No0909S 1 2 0 1 0 0 2 0 0 0 0 0 3 1 0 2
No0910S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No0912S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No0913S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No1103S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No1007S 1 2 0 1 0 0 2 0 0 0 0 0 3 1 0 2
No1114S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No1202S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No1206S 1 2 0 2 0 0 2 0 0 0 0 0 2 1 0 2
No1208S 1 2 0 1 0 0 2 0 0 0 0 0 3 1 0 2
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