NOTE - before you begin, make sure your WORKING DIRECTORY is set to the location of the .vcf file being used.
All of this material will appear on the exam. Take notes on the workflow, functions, and concepts.
getwd() and
list.files(pattern = ...)extract.gt() command doesna.omit() on SNPsWe need just one package for this lesson, vcfR.
# install.packages("vcfR")
library(vcfR)## Warning: package 'vcfR' was built under R version 4.2.2##
## ***** *** vcfR *** *****
## This is vcfR 1.13.0
## browseVignettes('vcfR') # Documentation
## citation('vcfR') # Citation
## ***** ***** ***** *****In this lesson you will be using a .vcf file called
“all_loci.vcf”.
You must make sure that R has its working directory set to where this file is located.
The easiest way to do this is
Check the location of your working directory with
getwd()
# run getwd()
getwd() # todo## [1] "C:/Users/Fatsn/OneDrive/CBioFinal"Check for the presence of the “all_loci.vcf” file in the working
directory with list.files()
# run list.files()
# todo
list.files()## [1] "all_loci.vcf" "transpose_VCF_data.Rmd"If you have lots of files in the working directory, you can search for the file specifically with list.files(pattern = “vcf”)
# Run list.files() with pattern = "vcf
list.files(pattern = "vcf") # todo## [1] "all_loci.vcf"SNP data is often stored in Variant Call Format (VCF) files that are organized differently than normal R data. When SNP data is analyzed in R, such as by doing PCA or cluster analysis, the SNPs are usually the features (variables) and each row is a sample (such as a person, or other organism). VCF files, however, are organized with SNPs in rows and samples in columns.
Changing how data is arranged is called reshaping. Reshaping can take different forms. In this case we need to flip the orientation of the data so that the rows, SNPS, become the columns.
In R we can flip the orientation of matrix or dataframe using
t() operation, which stands for transpose.
The transpose of a dataset takes each row and makes it into a column.
For vcf data, this means that the SNPs in rows can be made into
columns.
The example below will illustrate the general principle of transposition of data. First, let’s make two vectors of data in vcf-like format, with genotypes expressed as “A|A”.
# Add the c() function to make
## vectors containing SNP genotypes
SNP01 <- c("A|A","A|A","A|A","A|A") # TODO
SNP02 <- c("G|G","G|G","G|G","G|G")Now let’s make a matrix with rbind()
# add the rbind() function
## to combine the vectors into a dataframe
my_matrix <- rbind(SNP01, SNP02) # TODOSince this is representing a vcf file, the rows will be SNPS and the
columns will be samples. I’ll name the columns with
colnames().
# add the colnames() function around
## the my_matrix object to
## rename it
colnames(my_matrix) <- c("sample1", # TODO
"sample2",
"sample3",
"sample4")We now have a matrix in the general form of a vcf file
# add the my_matrix object to the chunk so
## its contents are shown
my_matrix## sample1 sample2 sample3 sample4
## SNP01 "A|A" "A|A" "A|A" "A|A"
## SNP02 "G|G" "G|G" "G|G" "G|G" # TODOThe t() function will re-orient our matrix for us so
that SNPs are in columns and samples are in rows.
# add the t() function to transpose
## the matrix
t(my_matrix) # TODO## SNP01 SNP02
## sample1 "A|A" "G|G"
## sample2 "A|A" "G|G"
## sample3 "A|A" "G|G"
## sample4 "A|A" "G|G"We can save the transposed output to a new matrix.
# add the t() function and assign
## the output to an object called
## my_matrix_t
my_matrix_t <- t(my_matrix) # TODOWe can do this in R with dataframes also:
# add the data.frame() function to
## turn my_matrix into a dataframe
## and assign it to an object called my_df
my_df <- data.frame(my_matrix) # TODOAgain, t() flips the dataframe for us:
# add the t() function to show the flipped
## dataframe
t(my_df) # TODO## SNP01 SNP02
## sample1 "A|A" "G|G"
## sample2 "A|A" "G|G"
## sample3 "A|A" "G|G"
## sample4 "A|A" "G|G"A typical VCF file can be found in the file
all_loci.vcf. (Note that this file is NOT compressed and so
has an extension of .vcf, not .vcf.gz). Load
the data into an object called bird_snps using the function
vcfR::read.vcfR().
NOTE - before you begin, make sure your WORKING DIRECTORY is set to the location of the .vcf file being used.
# Load the data with vcfR::read.vcfR()
# into an object called bird_snps
bird_snps <- vcfR::read.vcfR("all_loci.vcf",
convertNA = T) #TODO## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 1929
## column count: 81
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 1929
## Character matrix gt cols: 81
## skip: 0
## nrows: 1929
## row_num: 0
##
Processed variant 1000
Processed variant: 1929
## All variants processedwarning("If this didn't work, you may not have set your working directory to the location of the vcf file")## Warning: If this didn't work, you may not have set your working directory to the
## location of the vcf fileMake sure that at the bottom of the output in the console it says “Processed variant: 1929”.
Call head on the bird_snps object. You should be able to identify the metadata (at the top) and be able to see how samples are organized in rows.
# run head() on bird_snps
head(bird_snps) # TODO## [1] "***** Object of class 'vcfR' *****"
## [1] "***** Meta section *****"
## [1] "##fileformat=VCFv4.0"
## [1] "##fileDate=20160506"
## [1] "##source=\"Stacks v1.20\""
## [1] "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">"
## [1] "##INFO=<ID=AF,Number=.,Type=Float,Description=\"Allele Frequency\">"
## [1] "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">"
## [1] "First 6 rows."
## [1]
## [1] "***** Fixed section *****"
## CHROM POS ID REF ALT QUAL FILTER
## [1,] "un" "1478" "17" "C" "A" NA "PASS"
## [2,] "un" "1479" "17" "A" "G" NA "PASS"
## [3,] "un" "1723" "20" "C" "T" NA "PASS"
## [4,] "un" "1948" "22" "C" "A" NA "PASS"
## [5,] "un" "1972" "22" "C" "T" NA "PASS"
## [6,] "un" "2299" "26" "C" "T" NA "PASS"
## [1]
## [1] "***** Genotype section *****"
## FORMAT sample_ACAAA_Nel3 sample_ACAGTG_Nel5
## [1,] "GT:DP:GL" "1/0:344:.,-359.6,." "1/0:265:.,-273.8,."
## [2,] "GT:DP:GL" "0/1:344:.,-359.6,." "0/1:265:.,-273.8,."
## [3,] "GT:DP:GL" "0/0:254:.,352.119,." "0/0:267:.,370.141,."
## [4,] "GT:DP:GL" "0/0:332:.,460.25,." "0/0:339:.,469.954,."
## [5,] "GT:DP:GL" "0/0:332:.,431.419,." "0/0:339:.,454.108,."
## [6,] "GT:DP:GL" "0/0:421:.,553.847,." "0/0:412:.,540.081,."
## sample_AGCAT_Nel8 sample_ATGAAAC_Nel10 sample_ATGAAAC_Nel15
## [1,] "0/0:252:.,349.346,." "0/0:253:.,350.732,." "0/0:260:.,360.437,."
## [2,] "0/0:252:.,349.346,." "0/0:253:.,350.732,." "0/0:260:.,360.437,."
## [3,] "0/0:373:.,517.088,." "0/0:222:.,307.757,." "0/0:298:.,413.116,."
## [4,] "0/0:288:.,399.253,." "0/0:232:.,321.62,." "0/0:342:.,474.113,."
## [5,] "0/0:288:.,399.253,." "0/0:232:.,321.62,." "0/0:342:.,474.113,."
## [6,] "0/0:444:.,615.515,." "0/0:377:.,522.633,." "0/0:379:.,525.406,."
## [1] "First 6 columns only."
## [1]
## [1] "Unique GT formats:"
## [1] "GT:DP:GL"
## [1]We can view just the meta data like this:
bird_snps@meta## [1] "##fileformat=VCFv4.0"
## [2] "##fileDate=20160506"
## [3] "##source=\"Stacks v1.20\""
## [4] "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">"
## [5] "##INFO=<ID=AF,Number=.,Type=Float,Description=\"Allele Frequency\">"
## [6] "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">"
## [7] "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">"
## [8] "##FORMAT=<ID=GL,Number=.,Type=Float,Description=\"Genotype Likelihood\">"(Don’t worry about what the “at” symbol is using - this is a somewhat less common R syntax).
We can get a snapshot of the samples like this:
bird_snps@gt[1:10, 1:3]## FORMAT sample_ACAAA_Nel3 sample_ACAGTG_Nel5
## [1,] "GT:DP:GL" "1/0:344:.,-359.6,." "1/0:265:.,-273.8,."
## [2,] "GT:DP:GL" "0/1:344:.,-359.6,." "0/1:265:.,-273.8,."
## [3,] "GT:DP:GL" "0/0:254:.,352.119,." "0/0:267:.,370.141,."
## [4,] "GT:DP:GL" "0/0:332:.,460.25,." "0/0:339:.,469.954,."
## [5,] "GT:DP:GL" "0/0:332:.,431.419,." "0/0:339:.,454.108,."
## [6,] "GT:DP:GL" "0/0:421:.,553.847,." "0/0:412:.,540.081,."
## [7,] "GT:DP:GL" "0/0:421:.,583.63,." "0/0:412:.,571.153,."
## [8,] "GT:DP:GL" "0/0:421:.,583.63,." "0/0:412:.,571.153,."
## [9,] "GT:DP:GL" "0/0:528:.,731.963,." "0/0:301:.,417.275,."
## [10,] "GT:DP:GL" "0/0:253:.,350.732,." "0/0:248:.,343.801,."Each row is a SNP and each column is a sample (a bird in this case.)
We extract genotype scores using vcfR::extract.gt(). You
need to be familiar with this command, but I’ll give you the code to do
this on an exam.
# Add vcfR::extract.gt() to extract the
## numeric scores
bird_snps_num <- vcfR::extract.gt(bird_snps, # TODO
element = "GT",
IDtoRowNames = F,
as.numeric = T,
convertNA = T)We now have just the numeric data that would go into an analysis such as PCA.
The sample names are REALLY long so its hard to display in a compact
way. The code below will make this a a little easier to see using the
regular expression gsub().
colnames(bird_snps_num) <- gsub("sample_", "",
colnames(bird_snps_num))
colnames(bird_snps_num) <- gsub("_", "",
colnames(bird_snps_num))We can see that the matrix just contains numeric genotype scores of 0, 1 or 2.
Here’s a small view of data:
bird_snps_num[1:10, 1:4]## ACAAANel3 ACAGTGNel5 AGCATNel8 ATGAAACNel10
## [1,] 1 1 0 0
## [2,] 0 0 0 0
## [3,] 0 0 0 0
## [4,] 0 0 0 0
## [5,] 0 0 0 0
## [6,] 0 0 0 0
## [7,] 0 0 0 0
## [8,] 0 0 0 0
## [9,] 0 0 0 0
## [10,] 0 0 0 0We can call summary of a bit of the data like this:
summary(bird_snps_num[, 1:5])## ACAAANel3 ACAGTGNel5 AGCATNel8 ATGAAACNel10
## Min. :0.00000 Min. :0.00000 Min. :0.00000 Min. :0.00000
## 1st Qu.:0.00000 1st Qu.:0.00000 1st Qu.:0.00000 1st Qu.:0.00000
## Median :0.00000 Median :0.00000 Median :0.00000 Median :0.00000
## Mean :0.08574 Mean :0.07962 Mean :0.08259 Mean :0.07192
## 3rd Qu.:0.00000 3rd Qu.:0.00000 3rd Qu.:0.00000 3rd Qu.:0.00000
## Max. :1.00000 Max. :1.00000 Max. :1.00000 Max. :1.00000
## NA's :28 NA's :20 NA's :28 NA's :24
## ATGAAACNel15
## Min. :0.0000
## 1st Qu.:0.0000
## Median :0.0000
## Mean :0.0766
## 3rd Qu.:0.0000
## Max. :1.0000
## NA's :23The data are formatted as genotype scores but SNPs are in columns and
samples in row. We can reformat them using the transpose function
t().
# run t() on bird_snps_num and
## save the output to bird_snps_num_t
bird_snps_num_t <- t(bird_snps_num) # TODOWe can look at the output like this:
bird_snps_num_t[1:10, 1:4]## [,1] [,2] [,3] [,4]
## ACAAANel3 1 0 0 0
## ACAGTGNel5 1 0 0 0
## AGCATNel8 0 0 0 0
## ATGAAACNel10 0 0 0 0
## ATGAAACNel15 0 0 0 0
## CGATGTNel4 0 0 0 0
## CTAGCNel7 0 0 0 0
## CTGTANel12 0 0 0 0
## CTGTANel9 0 0 0 0
## CTTGANel2 0 0 0 0These data have a lot of NAs. If we just call na.omit() on them, what
happens? Call na.omit() on the bird_snps_num_t
object, then check the dimensions.
# Call na.omit() on bird_snps_num_t
## and assign the output to no_NAs
no_NAs <- (bird_snps_num_t) # TODO
# what is the remaining size of the data?
# why
(no_NAs) # TODO## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
## ACAAANel3 1 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 1 0 0 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0 0 0 0
## GGACCTANel13 1 0 0 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 1 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 1 0 0 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 1 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 1 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 1 0 0 0 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 1 0 0 0 0 0 0 0 0 0 0 1
## AAAAGTTSub15 NA NA 0 0 0 0 0 0 NA 0 NA NA
## ACAAASub1 0 0 0 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 NA NA 0 0 0 0 0 0 0
## CGATGTSub6 NA NA 0 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA 0 0 0 0 NA 0 0
## CTTGCTTSub14 0 0 0 0 0 0 0 0 NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA 0 0 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 0 0 0 0 0 0 0 NA NA
## TGACCASub2 0 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA NA 0 0 1 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 1 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 1 0 0 0 0 1 0 0
## ACTATCau9 0 0 0 0 1 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 1 0 0 0 0 0 0 0
## ATGAAACCau12 NA NA 0 0 1 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 1 0 0 0 0 NA 0 0
## [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23]
## ACAAANel3 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 NA 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 1 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0 0 NA
## GGACCTANel11 0 0 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 NA 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 0 0 NA 0 0 NA NA
## ACAAASub1 0 0 0 0 0 0 NA 1 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 NA 0 0 NA 0 0 0 0
## CGATGTSub6 0 NA 0 0 0 0 0 0 0 NA 0
## CTAGCSub3 0 NA 0 NA 0 NA NA 0 NA NA NA
## CTTGCTTSub14 0 NA 0 NA 0 0 NA 1 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA 0 NA NA NA 0 NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 NA 0 NA 0 0 0 NA 0
## TGACCASub2 0 1 0 0 0 0 0 1 0 0 0
## ACAGTGCau2 0 0 0 NA 1 NA 1 1 NA 1 0
## ACAGTGCau3 0 0 0 0 1 0 1 1 0 NA 0
## ACTATCau11 0 0 0 0 1 0 1 1 0 1 0
## ACTATCau9 0 0 0 0 1 0 1 1 0 1 0
## AGCCCCau7 0 0 0 0 1 0 1 1 0 NA 0
## ATGAAACCau12 0 0 0 0 1 0 NA NA 0 NA NA
## CTAGCCau5 0 0 0 0 1 0 1 1 0 1 0
## [,24] [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34]
## ACAAANel3 0 0 0 0 0 1 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 1 1 0 0 0
## AGCATNel8 0 0 0 0 0 1 0 1 0 1 0
## ATGAAACNel10 0 0 0 0 0 0 0 1 1 1 0
## ATGAAACNel15 0 0 0 0 0 1 0 1 0 1 0
## CGATGTNel4 0 0 0 0 0 0 1 1 0 0 0
## CTAGCNel7 0 0 0 0 0 1 0 1 0 0 0
## CTGTANel12 0 0 0 0 0 1 0 1 0 1 0
## CTGTANel9 0 0 0 0 0 0 0 1 0 0 0
## CTTGANel2 NA NA NA NA 0 1 0 1 0 1 0
## GGACCTANel11 0 0 1 0 0 1 0 1 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 1 0 1 0
## GTATTNel14 0 0 0 0 0 1 0 1 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 1 1 1 0
## TGACCANel1 0 0 0 0 0 0 0 1 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 1 0 1 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 1 0 1 0 0 0
## ATCACGAlt5 0 0 0 0 0 1 0 1 0 0 0
## ATCACGAlt7 0 0 0 0 0 1 0 1 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 1 0 1 0
## CTGTAAlt14 0 0 0 0 0 1 0 1 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 1 0 1 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 1 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA 0 0 NA NA NA NA NA
## ACAAASub1 NA NA NA NA 0 0 0 NA NA NA NA
## ACTATSub7 0 0 0 0 0 0 0 1 1 1 0
## AGCATSub13 0 0 0 0 0 0 0 1 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 NA NA NA NA 0
## CTAGCSub3 NA NA NA NA NA 0 0 1 0 0 NA
## CTTGCTTSub14 0 0 0 0 0 0 NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA 0 NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 1 0 1 0 0 0
## GTATTSub12 0 0 0 0 0 0 NA 1 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 1 0 0 0
## ACAGTGCau2 0 0 0 0 NA 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 1 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 NA NA NA NA 0 0 0 0 0 0 NA
## CTAGCCau5 0 0 0 0 0 0 0 0 0 0 0
## [,35] [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45]
## ACAAANel3 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0 0 1
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 1 0 0 0 0 0 0 0 1 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 NA 0 0 NA NA 0 NA 0 0
## ACAAASub1 NA 1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 NA 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA 0 0 NA 0 NA 0 0 0
## CTTGCTTSub14 0 0 0 0 0 NA 0 NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 NA NA 0 NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 0 NA 0 NA 0 NA NA
## TGACCASub2 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 NA 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 1 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 1 1 0 0 0 0 0
## ACTATCau9 0 0 0 0 1 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 NA 0 0 0 0 0 0
## ATGAAACCau12 NA 0 0 0 NA NA 0 0 0 0 0
## CTAGCCau5 0 0 0 0 1 0 0 0 0 0 0
## [,46] [,47] [,48] [,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56]
## ACAAANel3 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 NA 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 NA 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 1 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 1 0 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 1 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 1 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 NA 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 NA 0 0 NA 0 0 0
## ACAAASub1 0 0 0 0 NA 0 0 NA 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 1 0 0 0 0 0 0
## AGCCCSub11 0 NA NA 0 0 0 0 0 0 0 0
## CGATGTSub6 NA 0 0 0 0 0 0 0 0 0 0
## CTAGCSub3 0 NA NA 0 NA 0 0 NA NA NA NA
## CTTGCTTSub14 0 NA NA 0 0 0 0 NA 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 0 NA NA NA NA 0 NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 NA NA 0 0 0 0 NA NA
## TGACCASub2 0 1 0 NA 0 0 0 NA 0 0 0
## ACAGTGCau2 0 1 0 0 0 NA NA 0 1 NA NA
## ACAGTGCau3 0 1 0 0 0 0 1 0 0 NA 0
## ACTATCau11 0 1 0 0 0 0 1 0 1 0 0
## ACTATCau9 0 1 0 0 0 0 1 0 0 0 0
## AGCCCCau7 0 NA NA 0 0 0 1 0 0 0 0
## ATGAAACCau12 0 1 0 0 0 NA NA NA 0 0 0
## CTAGCCau5 0 1 0 0 0 0 1 0 0 0 0
## [,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64] [,65] [,66] [,67]
## ACAAANel3 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 1 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 1 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 1 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 1 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 NA 0 0 0 0 NA NA 0
## ACAAASub1 0 0 0 0 0 0 NA 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 NA NA 0
## CTAGCSub3 0 NA 0 NA 0 NA NA 0 NA NA NA
## CTTGCTTSub14 0 NA 0 0 0 0 NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 NA 0 0 NA 0 NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 NA 0 NA NA 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0 NA NA 0
## ACAGTGCau2 0 NA NA 0 0 0 NA 0 0 1 NA
## ACAGTGCau3 0 NA 0 0 0 0 0 0 0 1 NA
## ACTATCau11 0 0 0 0 0 0 0 0 0 1 1
## ACTATCau9 0 0 0 0 0 0 0 0 0 1 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0 1 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0 1 1
## CTAGCCau5 0 0 0 0 0 0 0 0 0 1 1
## [,68] [,69] [,70] [,71] [,72] [,73] [,74] [,75] [,76] [,77] [,78]
## ACAAANel3 1 0 0 0 1 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 1 1 0 0 0 0 0 0
## AGCATNel8 1 0 0 0 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 1 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 NA 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 1 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 1 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 1 0 0 0 0 0 0
## GGACCTANel13 1 0 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0 0 0
## TGACCANel1 1 0 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 1 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 1 0 0 0 0 0 0
## ACAGTGAlt3 1 0 0 0 1 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 1 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 1 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 1 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 1 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 1 1 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA NA NA NA NA
## ACAAASub1 0 0 0 NA NA NA 0 0 0 NA 0
## ACTATSub7 1 0 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 NA 0 0 0 0
## CGATGTSub6 NA 0 NA NA NA 0 0 NA NA 0 NA
## CTAGCSub3 NA NA NA NA NA NA NA NA NA NA NA
## CTTGCTTSub14 NA 0 0 0 0 0 0 0 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 NA 1 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA 1 0 0 0 NA NA NA 0
## TGACCASub2 0 0 0 0 1 0 0 NA NA 0 0
## ACAGTGCau2 NA 0 1 0 0 0 0 NA NA NA 1
## ACAGTGCau3 0 1 0 0 0 0 1 0 0 0 1
## ACTATCau11 0 0 0 0 0 0 NA 0 0 0 1
## ACTATCau9 0 0 1 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 1 0 0 0 0 0 0 0 1
## ATGAAACCau12 0 0 1 0 0 0 NA NA NA 0 1
## CTAGCCau5 0 0 1 0 0 0 0 0 0 0 1
## [,79] [,80] [,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88] [,89]
## ACAAANel3 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 1 0 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 1 0 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0 1 0
## TCACCNel6 1 0 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 NA 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 NA 0 0 0 NA NA 0 0
## ACAAASub1 0 0 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 NA NA 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 NA NA 0 0 0 0 0
## CTAGCSub3 NA 0 NA NA 0 0 0 NA NA NA NA
## CTTGCTTSub14 0 0 NA 0 NA NA 0 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 NA NA 0 0 NA NA NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 NA 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 NA 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 1 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 NA 0 NA NA 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0 0 0
## [,90] [,91] [,92] [,93] [,94] [,95] [,96] [,97] [,98] [,99] [,100]
## ACAAANel3 0 0 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0 0 0
## AGCATNel8 1 0 1 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0 0 0
## CGATGTNel4 1 0 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 1 0 0 0 0 0 0 0 0
## CTGTANel12 1 0 1 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 1 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 1 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 1 0 0 0 0 0 0 0 0
## GGACCTANel13 1 0 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 1 0 0 1 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 1 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 1 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 1 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 1 0 0 0 0 1 0 0
## AGCCCAlt13 0 0 1 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 1 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 1 0 1
## CTGTAAlt14 0 0 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 1 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 1 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA NA 0 0 0 0 0 0 0
## ACAAASub1 1 NA 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 1 0 0 0 0 0 0 0 0
## AGCATSub13 1 0 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 1 0 0 0 0
## CGATGTSub6 0 0 1 NA 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA 0 0 0 NA NA NA 0 0
## CTTGCTTSub14 NA NA 0 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA NA 0 0 0 0 0 NA 0 0
## GGACCTASub10 1 0 0 0 0 0 0 0 0 0 0
## GTATTSub12 1 NA 0 0 0 0 0 0 0 0 0
## TGACCASub2 1 0 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 1 NA 0 0 0 0 1 0 0 1 0
## ACAGTGCau3 1 1 NA 0 0 0 1 0 0 1 0
## ACTATCau11 1 1 0 0 0 0 1 0 0 1 0
## ACTATCau9 1 1 1 0 0 0 1 0 0 1 0
## AGCCCCau7 1 1 0 0 0 0 1 0 0 1 0
## ATGAAACCau12 1 NA NA 0 0 0 1 0 0 1 0
## CTAGCCau5 1 1 0 0 0 0 1 0 0 1 0
## [,101] [,102] [,103] [,104] [,105] [,106] [,107] [,108] [,109]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 1 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 0 1 0 0 1
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 NA NA
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 NA NA
## ATCACGAlt5 0 0 0 0 0 1 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 1
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 NA NA NA NA 1 0
## ACAAASub1 0 0 0 NA NA NA 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 NA NA
## AGCCCSub11 0 0 0 0 0 0 NA NA NA
## CGATGTSub6 NA 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 0 NA NA NA 0 0
## CTTGCTTSub14 0 1 0 0 0 0 NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 1 0
## GTATTSub12 0 NA 0 NA NA NA 0 0 0
## TGACCASub2 0 NA 0 0 0 0 0 1 0
## ACAGTGCau2 0 0 0 0 0 0 NA 0 0
## ACAGTGCau3 NA 0 0 0 0 0 0 NA NA
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 NA 0 0 0 NA NA
## ATGAAACCau12 0 0 0 0 0 0 NA 0 0
## CTAGCCau5 0 0 0 1 0 0 0 NA NA
## [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117] [,118]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 NA NA NA NA NA
## CTGTANel12 0 0 0 0 1 0 0 0 0
## CTGTANel9 0 0 0 1 0 0 0 0 0
## CTTGANel2 0 0 0 0 1 0 0 0 0
## GGACCTANel11 0 0 1 0 0 0 0 1 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 1 0 0 0 0
## TCACCNel6 NA NA NA NA 0 0 0 0 0
## TGACCANel1 0 0 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 1 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 NA NA NA NA NA
## ACAGTGAlt3 0 1 0 0 0 0 0 0 0
## AGCCCAlt13 NA NA NA NA 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 NA NA NA NA NA
## CTTGAAlt10 0 0 0 1 0 0 0 1 0
## GAATTCAAlt15 0 0 0 0 1 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 1 0 0 0 1 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 NA NA NA NA 0 0 0 0 0
## AGCCCSub11 NA NA NA NA 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 0 0 0 0 0 0 0 0 0
## CTTGCTTSub14 0 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 0 0 0 0 0 0
## GGACCTASub10 0 1 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0 0
## ACAGTGCau3 NA NA NA NA 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 NA NA NA NA 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 NA NA NA NA 0 0 0 0 0
## [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 1
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 1 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA 0 0 0
## ACAAASub1 NA NA NA NA 0 NA 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 1 NA 0 0 0
## CGATGTSub6 NA NA NA NA 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA 0 0 0
## CTTGCTTSub14 0 0 0 0 NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA NA NA 0 0 0
## TGACCASub2 0 0 0 0 NA 0 0 0 0
## ACAGTGCau2 NA NA NA NA NA 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 1 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 NA NA NA NA
## ATGAAACCau12 NA NA NA NA NA 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 NA 0 0 0 0 1
## ATGAAACNel10 0 0 0 0 0 1 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 NA 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 NA 0 0 0 1
## CTGTANel9 0 0 0 0 0 0 0 0 1
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 NA 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 1
## ACAGTGAlt3 0 0 0 0 0 0 0 0 1
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 NA 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 NA 0 0 0 1
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 NA 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0 1
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 0 NA 0 0 0 NA
## ACAAASub1 0 0 0 NA 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 1 0 1
## AGCATSub13 0 0 NA 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 1 0 NA
## CGATGTSub6 0 0 0 0 NA 0 0 0 0
## CTAGCSub3 0 0 NA NA NA 0 0 0 NA
## CTTGCTTSub14 0 0 NA 0 0 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 NA 0 0 0 0 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA 0 NA 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 NA 0 0 0 1 0 0
## ACAGTGCau3 0 0 0 0 0 0 1 0 0
## ACTATCau11 0 0 0 0 0 0 1 0 0
## ACTATCau9 0 0 0 0 1 0 1 0 0
## AGCCCCau7 0 0 0 0 0 0 1 0 0
## ATGAAACCau12 0 0 0 0 0 0 1 0 0
## CTAGCCau5 0 0 0 0 0 0 1 0 0
## [,137] [,138] [,139] [,140] [,141] [,142] [,143] [,144] [,145]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 1 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 1 0 0 0 0 0
## CTGTANel12 0 0 0 1 0 0 0 0 0
## CTGTANel9 0 0 0 1 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 1 0 1 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 1 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 1 0 0
## GCCAATAlt4 0 0 0 1 0 0 0 0 0
## GCCAATAlt9 0 0 0 1 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 NA NA 0 0 NA
## ACAAASub1 0 0 0 0 0 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 1
## AGCCCSub11 0 NA 0 0 0 0 0 0 NA
## CGATGTSub6 NA 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 0 NA 0 NA 0 0
## CTTGCTTSub14 0 NA 0 0 0 0 NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 0 NA NA NA 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0 NA
## GTATTSub12 NA NA 0 0 0 0 NA 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA NA 0 0 0 0 NA 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 NA
## ATGAAACCau12 0 0 0 0 0 0 NA 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,146] [,147] [,148] [,149] [,150] [,151] [,152] [,153] [,154]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 1 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 1 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 1 1 0 0 0 0 0 0 0
## AAAAGTTAlt12 1 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 1 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 NA NA
## ACAAASub1 0 0 0 0 0 0 0 NA NA
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 0 NA 0 0 0 0 NA NA NA
## CTTGCTTSub14 0 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 0 0 NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 NA 0 0
## TGACCASub2 0 0 0 0 0 0 0 NA NA
## ACAGTGCau2 NA 0 0 0 0 0 NA 0 0
## ACAGTGCau3 1 0 0 0 0 0 0 0 0
## ACTATCau11 1 0 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 0 0 0 0 0 0
## AGCCCCau7 1 0 0 0 0 0 0 0 0
## ATGAAACCau12 1 0 0 0 0 0 NA NA NA
## CTAGCCau5 1 0 0 0 0 0 0 0 0
## [,155] [,156] [,157] [,158] [,159] [,160] [,161] [,162] [,163]
## ACAAANel3 0 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 0 0 0 1 0 0 0
## AGCATNel8 0 0 0 0 0 1 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 1 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 1 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 1 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 1 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 1 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 NA NA NA NA 0 NA NA
## ACAAASub1 0 0 0 0 0 0 0 NA NA
## ACTATSub7 0 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 NA NA
## CGATGTSub6 0 0 NA NA NA NA 0 0 0
## CTAGCSub3 0 0 0 0 0 0 NA NA NA
## CTTGCTTSub14 0 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 1 0
## GTATTSub12 0 0 NA NA NA NA 0 NA NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 1 0 NA NA
## ACAGTGCau3 0 0 NA NA NA NA 0 0 1
## ACTATCau11 0 0 1 0 0 1 0 1 0
## ACTATCau9 0 0 0 0 0 1 0 1 0
## AGCCCCau7 0 0 0 0 0 1 0 1 0
## ATGAAACCau12 0 1 0 0 0 1 0 NA NA
## CTAGCCau5 0 0 1 0 0 1 0 1 0
## [,164] [,165] [,166] [,167] [,168] [,169] [,170] [,171] [,172]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 1
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 1
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 1 0 0 0 0 0 0 0 1
## CTTGANel2 0 0 0 0 0 0 0 0 1
## GGACCTANel11 0 0 0 0 0 0 0 0 1
## GGACCTANel13 0 0 0 1 0 0 0 0 1
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 1
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 NA 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA NA NA NA NA 0 NA
## ACAAASub1 0 NA NA 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 1 0 0 0
## AGCATSub13 0 0 0 0 0 1 0 0 0
## AGCCCSub11 0 0 0 NA NA NA 0 0 NA
## CGATGTSub6 0 NA NA 0 0 0 0 NA NA
## CTAGCSub3 0 NA NA NA NA NA 0 NA NA
## CTTGCTTSub14 0 0 0 NA NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA 0 0 0 0 0 0
## TGACCASub2 0 0 0 NA NA NA 0 0 0
## ACAGTGCau2 0 1 0 NA NA NA 0 0 0
## ACAGTGCau3 0 NA NA 0 0 1 0 0 1
## ACTATCau11 0 1 0 0 0 1 0 0 1
## ACTATCau9 0 1 0 NA NA NA 0 0 0
## AGCCCCau7 0 1 0 NA NA NA 0 NA NA
## ATGAAACCau12 0 NA NA 0 0 1 0 0 0
## CTAGCCau5 0 0 0 0 0 1 0 0 1
## [,173] [,174] [,175] [,176] [,177] [,178] [,179] [,180] [,181]
## ACAAANel3 1 0 0 0 0 0 0 0 0
## ACAGTGNel5 1 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 1 0 0 0 0 0 NA NA 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 NA NA 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 1 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 NA NA 0
## GTATTNel14 0 0 1 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 1 0 0 0 0 0 0
## ACAAAAlt11 1 0 1 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 1 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 1 0 0 0 0 0 0
## TTAGGCAlt2 1 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 0 0 0 NA NA 0
## ACAAASub1 0 NA 0 0 0 0 NA NA 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 NA 0 0 0 0 0 NA NA 0
## CGATGTSub6 NA 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA 0
## CTTGCTTSub14 0 0 NA 0 NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA 0 NA NA 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA NA 0 0 0 0 0 0
## TGACCASub2 0 0 NA 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 1 0 NA
## ACAGTGCau3 0 NA 0 0 0 0 0 0 1
## ACTATCau11 0 0 0 0 0 0 0 0 1
## ACTATCau9 0 NA 0 0 0 0 0 0 1
## AGCCCCau7 NA NA 0 0 0 0 NA NA 1
## ATGAAACCau12 0 0 0 0 0 0 NA NA 1
## CTAGCCau5 0 NA 0 0 0 0 0 0 1
## [,182] [,183] [,184] [,185] [,186] [,187] [,188] [,189] [,190]
## ACAAANel3 0 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 0 0 0 0 1 0 0
## AGCATNel8 0 0 1 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 1 0 0
## CTAGCNel7 0 0 1 0 1 0 1 1 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 1 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 1 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 1 0 0
## TCACCNel6 0 0 0 0 0 0 1 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 1 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0 0
## TTAGGCAlt8 0 0 0 0 0 0 1 0 0
## AAAAGTTSub15 0 NA NA NA NA NA NA 0 0
## ACAAASub1 0 NA NA NA NA NA 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 NA NA NA NA NA 0 0 0
## CTAGCSub3 0 NA NA NA NA NA 0 NA NA
## CTTGCTTSub14 0 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0 0
## GCCAATSub4 NA 0 0 0 0 0 0 NA NA
## GGACCTASub10 1 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA NA NA NA NA 0 NA NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 1 NA NA NA NA NA 0 NA NA
## ACAGTGCau3 1 0 0 0 0 0 0 0 1
## ACTATCau11 0 0 0 0 0 0 0 0 1
## ACTATCau9 1 0 0 0 0 0 0 0 1
## AGCCCCau7 1 0 0 0 0 0 0 0 1
## ATGAAACCau12 NA NA NA NA NA NA 0 NA NA
## CTAGCCau5 1 0 0 0 0 0 0 0 1
## [,191] [,192] [,193] [,194] [,195] [,196] [,197] [,198] [,199]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 1 0 0 0 0 0
## AGCATNel8 0 1 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 1 0 0 0 0 0
## CTAGCNel7 0 1 0 1 0 0 0 0 0
## CTGTANel12 0 0 0 1 0 0 0 0 0
## CTGTANel9 0 1 0 0 0 0 0 0 0
## CTTGANel2 0 1 0 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 0 0 0 0 0
## GGACCTANel13 0 1 0 1 0 0 0 0 0
## GTATTNel14 0 1 NA 1 0 0 0 0 0
## TCACCNel6 0 1 NA 1 0 0 0 0 0
## TGACCANel1 0 0 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 1 0 0 0 0 0
## ACAAAAlt11 0 0 NA 1 0 0 0 0 0
## ACAGTGAlt3 0 0 0 1 0 0 0 0 0
## AGCCCAlt13 0 0 NA 0 1 0 0 0 0
## ATCACGAlt5 0 0 0 1 0 0 0 0 0
## ATCACGAlt7 0 0 0 1 1 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 1 0 1 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 1 0 1 0 0 0 0 0
## GCCAATAlt9 0 1 NA 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 1 0 0 1 0 0
## TTAGGCAlt6 0 1 0 1 0 0 0 0 0
## TTAGGCAlt8 0 0 0 1 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA 0 NA 0
## ACAAASub1 NA NA 0 NA NA 0 0 NA 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 1 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 NA NA NA NA 0 0 0
## CTAGCSub3 NA NA NA NA NA NA 0 NA NA
## CTTGCTTSub14 NA NA 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA 0 NA 0
## GGACCTASub10 0 1 0 1 0 0 0 0 1
## GTATTSub12 NA NA NA 1 0 NA 0 0 0
## TGACCASub2 0 1 0 1 0 0 0 0 0
## ACAGTGCau2 0 0 0 NA NA NA 0 0 1
## ACAGTGCau3 0 0 NA 0 0 1 0 0 1
## ACTATCau11 0 0 0 0 0 1 0 0 1
## ACTATCau9 0 0 0 0 0 0 0 0 1
## AGCCCCau7 0 0 0 0 0 NA 0 0 1
## ATGAAACCau12 0 0 0 0 0 NA 0 0 1
## CTAGCCau5 0 0 0 0 0 1 0 0 1
## [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207] [,208]
## ACAAANel3 0 0 0 0 1 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 1 0 NA 0
## AGCATNel8 0 0 0 0 0 0 0 NA 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 1 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 1 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 NA 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 NA 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 NA 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 NA NA 0 0 NA 0 0
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 NA 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA 0 NA NA 0 NA NA 0 0
## CTTGCTTSub14 0 0 0 0 0 0 NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA 0 NA
## GAATTCASub9 0 0 0 0 0 0 0 NA 0
## GCCAATSub4 0 0 NA NA 0 0 NA 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 NA 0 0
## TGACCASub2 0 0 0 0 0 0 NA 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 1 0
## ACAGTGCau3 0 0 0 0 0 0 0 1 0
## ACTATCau11 0 1 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 0 1 0
## AGCCCCau7 0 0 0 0 0 1 0 1 0
## ATGAAACCau12 0 0 NA NA 0 0 NA 1 0
## CTAGCCau5 0 0 0 0 0 0 0 1 0
## [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217]
## ACAAANel3 0 0 0 1 0 0 0 0 1
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 1 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 1
## CGATGTNel4 0 0 0 0 0 0 0 0 1
## CTAGCNel7 1 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 1 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 1 0 0 0 0 1
## GTATTNel14 0 1 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 1 0 0 0 0 1
## TGACCANel1 0 0 0 0 0 0 0 0 1
## AAAAGTTAlt12 0 0 0 1 0 0 0 0 0
## ACAAAAlt11 0 0 0 1 0 0 0 0 0
## ACAGTGAlt3 0 0 0 1 0 0 0 0 1
## AGCCCAlt13 0 0 0 1 0 0 0 0 1
## ATCACGAlt5 0 0 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 0 0 0 0 0 0 1
## CGATGTAlt1 0 1 0 0 0 0 0 0 1
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 1 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 1 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0 1
## TTAGGCAlt8 0 0 0 0 0 0 0 0 1
## AAAAGTTSub15 NA NA 0 0 0 0 NA NA 0
## ACAAASub1 NA 0 0 0 0 0 0 0 NA
## ACTATSub7 1 0 0 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 0 NA
## CGATGTSub6 1 0 0 0 0 0 0 0 0
## CTAGCSub3 NA 0 0 0 0 NA 0 0 NA
## CTTGCTTSub14 NA 0 0 0 0 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 1
## GCCAATSub4 NA 0 0 0 0 0 NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0 1
## GTATTSub12 NA 0 0 0 0 0 0 0 0
## TGACCASub2 1 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 1 0 0
## ACAGTGCau3 0 0 0 0 0 0 1 0 0
## ACTATCau11 0 0 NA NA NA 0 1 0 0
## ACTATCau9 0 0 1 0 1 0 1 0 0
## AGCCCCau7 0 0 0 0 0 0 1 0 0
## ATGAAACCau12 0 0 0 0 0 0 1 0 0
## CTAGCCau5 0 0 0 0 0 0 1 0 0
## [,218] [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226]
## ACAAANel3 0 0 0 0 0 0 0 1 0
## ACAGTGNel5 0 0 0 0 0 1 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 1 0 0 1 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 1 0
## CTGTANel9 0 0 0 0 0 1 0 0 0
## CTTGANel2 0 0 0 0 1 0 0 0 0
## GGACCTANel11 0 0 0 0 0 1 0 0 0
## GGACCTANel13 0 0 0 0 0 1 0 1 0
## GTATTNel14 0 0 0 0 0 1 0 1 0
## TCACCNel6 0 0 0 0 0 1 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 1 0 0 0
## ACAAAAlt11 0 0 0 1 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 1 0 0 0 0
## AGCCCAlt13 0 0 0 0 1 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 1 0 0 0
## ATCACGAlt7 0 0 0 0 1 0 0 0 0
## CGATGTAlt1 0 0 0 1 1 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 1 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 1 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 1 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 NA 0 1 0 0 0 NA
## ACAAASub1 0 0 0 0 1 0 0 0 0
## ACTATSub7 0 0 0 0 0 1 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 0 1
## CGATGTSub6 0 0 0 0 0 1 0 0 NA
## CTAGCSub3 NA NA 0 0 0 1 0 0 NA
## CTTGCTTSub14 0 NA NA 0 1 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0 0
## GCCAATSub4 0 NA NA 0 0 0 0 0 NA
## GGACCTASub10 0 0 0 0 0 1 0 0 0
## GTATTSub12 0 0 0 0 1 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 NA NA 0 0 0 0 0 NA
## ACAGTGCau3 0 0 1 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 NA 0 0 0 NA NA 0
## ATGAAACCau12 0 0 0 0 0 0 NA NA 0
## CTAGCCau5 0 0 1 0 0 0 1 0 0
## [,227] [,228] [,229] [,230] [,231] [,232] [,233] [,234] [,235]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 1 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 1
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 1 0 0 1
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 0 0 0 1 0 0 0
## CGATGTAlt1 0 0 0 0 0 1 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 1
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 1 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 NA NA 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 NA NA NA 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 0 0 0 0 0 NA NA 0 0
## CTTGCTTSub14 NA NA NA 0 0 NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 0 0 NA NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA 0 0 NA NA 0 0
## TGACCASub2 NA NA NA 0 0 NA 0 0 0
## ACAGTGCau2 1 0 0 0 1 NA NA 0 0
## ACAGTGCau3 1 0 0 0 1 0 1 0 0
## ACTATCau11 1 0 0 0 1 0 1 0 0
## ACTATCau9 1 0 0 0 1 0 1 0 0
## AGCCCCau7 1 0 0 0 1 0 NA NA 0
## ATGAAACCau12 1 0 0 0 1 NA 1 0 0
## CTAGCCau5 1 0 0 0 1 0 1 0 0
## [,236] [,237] [,238] [,239] [,240] [,241] [,242] [,243] [,244]
## ACAAANel3 0 0 0 0 1 1 1 1 0
## ACAGTGNel5 0 0 0 0 0 0 1 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 1 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 1 1 1 1 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 1
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 1 0 0
## CTGTAAlt14 0 0 0 0 1 1 1 1 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 NA NA NA NA NA 0
## ACAAASub1 0 0 0 NA NA NA NA NA 0
## ACTATSub7 0 0 0 1 0 0 0 0 0
## AGCATSub13 0 0 0 1 0 0 0 0 0
## AGCCCSub11 0 0 0 NA NA NA NA NA 0
## CGATGTSub6 NA NA NA NA NA NA NA NA 0
## CTAGCSub3 NA NA NA 0 0 0 0 0 0
## CTTGCTTSub14 NA NA NA 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA 0
## GGACCTASub10 1 0 0 1 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0 0
## TGACCASub2 NA NA NA 0 0 0 0 0 0
## ACAGTGCau2 NA NA NA 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,245] [,246] [,247] [,248] [,249] [,250] [,251] [,252] [,253]
## ACAAANel3 0 1 0 0 1 0 0 0 0
## ACAGTGNel5 0 0 0 0 1 0 0 0 0
## AGCATNel8 0 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 1 0 0 1 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 1 0 0 0 0
## CTAGCNel7 0 1 0 0 1 1 0 0 0
## CTGTANel12 0 1 0 0 0 0 0 1 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 1 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 1 0 0 1 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 1 0 0 0 1
## TGACCANel1 0 1 0 0 1 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 1 0 0 1 0 0 0 0
## CTTGAAlt10 0 1 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 1 0
## GCCAATAlt4 0 0 0 0 0 0 0 1 0
## GCCAATAlt9 1 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 1 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA 0 0 0 NA NA NA
## ACAAASub1 0 0 0 0 1 0 NA NA 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 1 0 0 1 0
## AGCCCSub11 0 0 0 0 1 0 0 0 0
## CGATGTSub6 0 NA NA NA NA 0 0 0 NA
## CTAGCSub3 0 NA NA NA NA 0 0 0 NA
## CTTGCTTSub14 0 0 0 0 1 0 NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA NA 0 1 0 NA NA NA
## GGACCTASub10 0 1 0 0 0 0 0 0 0
## GTATTSub12 0 1 0 0 1 0 NA NA 0
## TGACCASub2 0 0 0 0 1 1 0 0 0
## ACAGTGCau2 0 0 0 0 0 1 0 0 0
## ACAGTGCau3 0 0 0 0 0 1 0 0 0
## ACTATCau11 0 0 0 0 0 1 0 0 0
## ACTATCau9 0 0 0 0 0 1 0 0 0
## AGCCCCau7 0 0 0 0 0 1 NA NA 0
## ATGAAACCau12 0 0 0 0 0 1 0 0 NA
## CTAGCCau5 0 0 0 0 0 1 0 0 0
## [,254] [,255] [,256] [,257] [,258] [,259] [,260] [,261] [,262]
## ACAAANel3 0 0 1 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 1 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 1 0
## CTAGCNel7 0 0 1 1 0 1 1 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 1 0
## CTTGANel2 0 1 0 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 0 0 0 0 0
## GGACCTANel13 0 0 1 0 0 0 0 1 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 1 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 1 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 1 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 1 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA NA NA
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 NA 0 0 0 0 0 0 0 NA
## CTAGCSub3 NA 0 0 0 0 0 0 0 NA
## CTTGCTTSub14 NA 0 0 0 0 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA 0 NA
## GGACCTASub10 0 0 1 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0 NA
## ACAGTGCau3 0 0 0 0 0 0 0 0 NA
## ACTATCau11 0 0 0 0 0 0 0 NA 1
## ACTATCau9 0 0 0 0 0 0 0 0 NA
## AGCCCCau7 0 0 0 0 0 0 0 NA 1
## ATGAAACCau12 NA 0 0 0 0 0 0 NA 1
## CTAGCCau5 0 0 0 0 0 0 0 0 1
## [,263] [,264] [,265] [,266] [,267] [,268] [,269] [,270] [,271]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 NA NA 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 1 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 NA NA NA 0 0 NA NA
## ACAAASub1 NA NA 0 0 0 0 NA 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 1 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 NA NA
## CGATGTSub6 NA NA NA 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA 0 NA 0 0
## CTTGCTTSub14 NA NA NA NA NA 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA 0 NA NA NA
## GGACCTASub10 0 0 0 1 0 0 0 0 0
## GTATTSub12 NA NA NA NA NA 0 NA 0 0
## TGACCASub2 0 0 0 NA NA 0 NA 0 0
## ACAGTGCau2 0 0 NA NA NA 0 NA 0 0
## ACAGTGCau3 0 0 NA 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 1 0 0 0 0 0 0
## ATGAAACCau12 0 0 1 NA NA 0 0 NA NA
## CTAGCCau5 0 0 1 0 0 0 0 0 0
## [,272] [,273] [,274] [,275] [,276] [,277] [,278] [,279] [,280]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 1 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 1 0 0
## ATGAAACNel10 0 0 0 0 0 0 1 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 1 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 1 0 0
## CTGTANel9 0 0 0 0 0 1 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 1 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 1 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 1 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 1 0 0
## GCCAATAlt4 0 0 0 0 0 0 1 0 0
## GCCAATAlt9 0 0 0 0 0 0 1 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 1 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0 0
## ACAAASub1 NA NA NA 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 NA NA NA
## CGATGTSub6 NA NA NA 0 0 0 0 0 0
## CTAGCSub3 0 0 0 0 0 0 NA NA NA
## CTTGCTTSub14 0 0 0 0 0 0 NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA 0 NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 NA NA NA
## ACAGTGCau3 0 1 0 0 0 0 0 1 1
## ACTATCau11 0 0 0 0 0 0 0 0 1
## ACTATCau9 0 0 0 0 0 0 0 1 1
## AGCCCCau7 0 0 0 0 0 0 0 0 1
## ATGAAACCau12 0 0 0 0 0 0 0 0 1
## CTAGCCau5 0 0 0 0 0 0 0 0 1
## [,281] [,282] [,283] [,284] [,285] [,286] [,287] [,288] [,289]
## ACAAANel3 1 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 NA
## ATGAAACNel15 1 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 1 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 NA
## GGACCTANel13 0 0 0 0 0 0 0 0 NA
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 NA
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 NA
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA NA NA
## ACAAASub1 0 0 0 NA NA NA 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 1 0
## AGCCCSub11 0 0 0 0 1 0 0 0 NA
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 0 NA NA 0 0 0 0 0 NA
## CTTGCTTSub14 0 0 0 0 0 0 NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA 0 0 0 NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 NA
## ACAGTGCau2 0 0 1 0 1 0 0 0 NA
## ACAGTGCau3 0 0 1 0 1 0 0 0 1
## ACTATCau11 0 0 1 0 1 0 0 0 1
## ACTATCau9 0 0 1 0 1 0 0 0 1
## AGCCCCau7 0 0 1 0 1 0 0 0 1
## ATGAAACCau12 0 0 1 0 1 0 0 0 NA
## CTAGCCau5 0 0 1 0 1 0 0 0 1
## [,290] [,291] [,292] [,293] [,294] [,295] [,296] [,297] [,298]
## ACAAANel3 1 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 1 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 1 0 0 0
## CTGTANel12 1 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 0 0 0 0 0
## GGACCTANel13 0 1 0 0 0 0 1 0 0
## GTATTNel14 0 1 0 0 0 0 0 0 0
## TCACCNel6 1 1 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 1 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 1 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 1 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 1 0 0 0 0 0 0 1 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 1 0
## AAAAGTTSub15 NA 0 0 NA NA NA NA NA NA
## ACAAASub1 NA 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 1
## AGCATSub13 1 0 0 0 0 0 0 0 0
## AGCCCSub11 1 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 NA NA NA NA NA 0
## CTAGCSub3 NA NA 0 NA NA NA NA NA NA
## CTTGCTTSub14 NA NA 0 0 0 NA NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 1
## GCCAATSub4 NA 0 0 NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 0 0 NA NA NA NA
## TGACCASub2 1 1 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 NA NA NA NA NA 0
## ACAGTGCau3 0 0 0 0 0 NA NA NA 0
## ACTATCau11 0 0 0 0 0 0 1 0 0
## ACTATCau9 0 0 0 0 0 0 1 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 NA NA NA 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,299] [,300] [,301] [,302] [,303] [,304] [,305] [,306] [,307]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 1
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 1
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 NA
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 1 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 1 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 NA NA 0
## ACAAASub1 0 0 0 0 0 0 NA NA 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 NA
## CGATGTSub6 0 0 0 0 0 0 0 0 1
## CTAGCSub3 0 0 0 0 0 0 NA NA 1
## CTTGCTTSub14 0 0 0 0 0 0 NA 0 0
## CTTGCTTSub8 NA 0 0 0 0 NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 NA 0
## ACAGTGCau2 0 0 0 0 0 NA 0 NA 0
## ACAGTGCau3 0 0 0 0 0 0 1 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,308] [,309] [,310] [,311] [,312] [,313] [,314] [,315] [,316]
## ACAAANel3 0 0 0 0 1 0 0 0 1
## ACAGTGNel5 0 0 0 0 0 0 0 0 1
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 1
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 1
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 1
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 1
## GTATTNel14 0 0 0 0 0 0 0 0 1
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 1
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 1 0 0 0 0
## ACAGTGAlt3 NA 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 1 1 0 0 1 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 1 0 0 1 1
## CTGTAAlt14 0 0 1 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 1
## GAATTCAAlt15 0 0 0 0 0 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 1
## AAAAGTTSub15 0 NA NA NA 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0 1
## ACTATSub7 0 0 0 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 0 0 0 0 1
## AGCCCSub11 NA 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 1 0 0 0 0
## CTAGCSub3 0 0 0 0 0 0 0 0 0
## CTTGCTTSub14 0 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 NA NA NA NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0 1
## GTATTSub12 NA NA NA NA NA NA NA NA 0
## TGACCASub2 0 0 0 0 1 0 0 0 1
## ACAGTGCau2 0 0 0 0 0 1 0 0 0
## ACAGTGCau3 0 0 0 0 0 1 0 0 0
## ACTATCau11 0 0 0 0 0 1 0 0 1
## ACTATCau9 0 0 0 0 0 1 0 0 1
## AGCCCCau7 0 0 0 0 0 1 0 0 0
## ATGAAACCau12 0 0 0 0 0 1 0 0 NA
## CTAGCCau5 0 0 0 0 0 1 0 0 1
## [,317] [,318] [,319] [,320] [,321] [,322] [,323] [,324] [,325]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 1 0 0 0 0 0 0 0 0
## AGCATNel8 0 1 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 1 0 1 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 1 0 1 0 0 0 0 0
## CTGTANel9 0 1 0 1 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 1 0 1 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 1 0 1 0 1 0 0 0
## TGACCANel1 0 1 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 1 0 1 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 1 0 0 0 0 0
## ATCACGAlt5 0 NA NA NA NA 0 0 0 NA
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 1 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 1 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0 NA
## ACAAASub1 NA 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 1 0 1 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 1 0 1 0 0 0 0 0
## CTAGCSub3 NA 0 0 0 0 0 0 NA NA
## CTTGCTTSub14 0 NA NA NA NA 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA 0 0 NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 1 0 1 0 0 0 NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 1 0 0 0 0 0 0 0 NA
## TGACCASub2 NA 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 NA 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 1 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 NA 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 1 0
## [,326] [,327] [,328] [,329] [,330] [,331] [,332] [,333] [,334]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 1 0 1 0 0 0 0
## AGCATNel8 0 1 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 1 0 0
## CGATGTNel4 0 0 0 0 1 0 0 0 0
## CTAGCNel7 0 0 0 1 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 1 0 1 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 1 0 0 0 0 0
## TCACCNel6 0 0 0 0 1 0 0 0 0
## TGACCANel1 0 1 1 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 NA 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 1 1 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 1 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 1 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 1 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA 0 0 NA
## ACAAASub1 0 0 0 0 0 0 0 0 NA
## ACTATSub7 0 0 0 0 1 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 1 0 0 0 0
## CGATGTSub6 0 NA NA 0 0 0 0 0 NA
## CTAGCSub3 NA NA NA NA NA NA 0 NA NA
## CTTGCTTSub14 NA 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 1 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA 0 NA
## GGACCTASub10 0 0 0 0 1 0 0 0 0
## GTATTSub12 NA 0 0 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 1 0 0 0 0 0 0 NA
## ACAGTGCau3 0 1 0 0 0 0 0 0 0
## ACTATCau11 0 1 0 0 0 0 0 0 NA
## ACTATCau9 0 1 0 0 0 0 0 0 0
## AGCCCCau7 0 1 0 0 0 0 0 0 0
## ATGAAACCau12 0 1 0 0 0 1 NA 0 NA
## CTAGCCau5 0 1 0 0 0 0 0 0 0
## [,335] [,336] [,337] [,338] [,339] [,340] [,341] [,342] [,343]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 1 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 1 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 1
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 1 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA NA NA
## ACAAASub1 NA NA 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 NA NA 0 0 0 0 NA 0 0
## CTAGCSub3 NA NA NA NA 0 0 0 0 0
## CTTGCTTSub14 0 0 NA NA 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA 0 0 NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA 0 0 0 0 0
## TGACCASub2 0 1 0 0 0 0 0 1 0
## ACAGTGCau2 NA NA 0 0 NA NA 0 0 0
## ACAGTGCau3 1 0 0 0 NA NA 0 0 0
## ACTATCau11 NA NA 0 0 1 0 1 0 0
## ACTATCau9 1 0 0 0 1 0 0 0 0
## AGCCCCau7 1 0 0 0 NA 0 0 0 0
## ATGAAACCau12 NA NA 0 0 NA NA NA 0 0
## CTAGCCau5 1 0 0 0 1 0 0 0 0
## [,344] [,345] [,346] [,347] [,348] [,349] [,350] [,351] [,352]
## ACAAANel3 0 1 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 1 0 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 1 0 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 0 0 0 0 0
## GGACCTANel13 0 1 0 0 0 0 0 0 0
## GTATTNel14 0 0 1 0 0 0 0 0 0
## TCACCNel6 0 1 0 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 1 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 1 1 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 1 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA NA 0 0 NA NA 0
## ACAAASub1 0 1 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 1 0 0 0 0 0 0 0
## CGATGTSub6 0 1 0 0 0 0 0 0 0
## CTAGCSub3 0 1 NA NA 0 NA 0 0 0
## CTTGCTTSub14 0 1 0 0 0 0 NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 0 0
## GCCAATSub4 0 0 NA NA 0 0 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA NA 0 0 0 0 0
## TGACCASub2 0 1 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 1 0 0
## ACAGTGCau3 0 0 0 0 0 0 1 0 0
## ACTATCau11 0 0 0 0 0 0 1 0 0
## ACTATCau9 0 0 0 0 0 0 1 0 0
## AGCCCCau7 0 0 0 0 0 0 1 0 0
## ATGAAACCau12 0 0 0 0 0 0 1 0 0
## CTAGCCau5 0 0 0 0 0 0 1 0 0
## [,353] [,354] [,355] [,356] [,357] [,358] [,359] [,360] [,361]
## ACAAANel3 0 0 0 0 0 1 0 1 0
## ACAGTGNel5 0 0 0 0 1 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 1 1 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 1 0 0 0
## CTTGANel2 0 0 0 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 1 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 1 1 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 1 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 1 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 1 0 0 0
## GAATTCAAlt15 0 0 0 0 0 1 0 0 0
## GCCAATAlt4 0 0 0 0 1 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA 1 NA 0 NA
## ACAAASub1 NA NA NA NA NA 1 0 0 0
## ACTATSub7 0 0 0 0 0 1 0 1 0
## AGCATSub13 0 0 0 0 0 1 0 0 0
## AGCCCSub11 0 0 0 0 0 1 0 0 0
## CGATGTSub6 0 0 0 0 0 1 0 0 0
## CTAGCSub3 NA NA NA 0 0 NA 0 NA 0
## CTTGCTTSub14 NA NA NA 0 0 1 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA 0 0 NA NA NA 0
## GGACCTASub10 0 0 0 0 0 1 0 0 0
## GTATTSub12 NA NA NA 0 0 NA 0 NA NA
## TGACCASub2 0 0 0 0 0 1 0 0 0
## ACAGTGCau2 0 NA NA 1 0 NA 1 NA 0
## ACAGTGCau3 0 NA NA 1 0 0 1 0 0
## ACTATCau11 0 0 0 1 0 0 1 0 0
## ACTATCau9 0 0 0 1 0 0 1 0 0
## AGCCCCau7 0 0 1 NA NA 0 1 0 0
## ATGAAACCau12 0 NA NA NA NA 0 1 NA 0
## CTAGCCau5 0 0 0 0 0 0 1 0 0
## [,362] [,363] [,364] [,365] [,366] [,367] [,368] [,369] [,370]
## ACAAANel3 0 0 0 0 1 0 0 1 0
## ACAGTGNel5 0 0 0 0 1 0 0 0 0
## AGCATNel8 0 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 0 0 0 1 0 0 0 0
## ATGAAACNel15 0 0 0 NA 1 0 0 0 0
## CGATGTNel4 0 0 0 NA 1 0 0 0 0
## CTAGCNel7 0 0 0 0 1 0 0 0 0
## CTGTANel12 0 0 0 0 1 0 0 1 0
## CTGTANel9 1 1 0 0 1 0 0 1 0
## CTTGANel2 0 0 0 0 1 0 0 1 0
## GGACCTANel11 0 0 0 1 1 0 0 1 0
## GGACCTANel13 0 0 0 0 0 1 0 1 0
## GTATTNel14 0 0 0 NA 1 0 0 1 0
## TCACCNel6 0 0 0 NA 1 0 0 1 0
## TGACCANel1 0 0 0 0 1 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 0 1 0 0 1 0
## ACAGTGAlt3 0 0 0 0 NA NA 0 0 0
## AGCCCAlt13 0 0 0 NA 1 0 0 0 0
## ATCACGAlt5 0 0 0 NA 1 0 0 1 0
## ATCACGAlt7 0 0 0 0 1 0 0 0 0
## CGATGTAlt1 0 0 0 0 1 0 0 0 0
## CTGTAAlt14 0 0 0 0 1 0 0 0 0
## CTTGAAlt10 0 0 0 NA 1 0 0 1 0
## GAATTCAAlt15 0 0 0 0 1 0 0 1 0
## GCCAATAlt4 0 0 0 0 1 0 0 1 0
## GCCAATAlt9 0 0 0 0 1 0 0 0 0
## TTAGGCAlt2 0 0 0 0 1 0 0 1 0
## TTAGGCAlt6 0 0 0 0 1 0 0 0 0
## TTAGGCAlt8 0 0 0 0 1 0 0 1 0
## AAAAGTTSub15 NA NA NA NA 0 1 NA NA NA
## ACAAASub1 0 0 NA 0 NA NA NA NA 0
## ACTATSub7 0 0 0 0 1 0 0 0 0
## AGCATSub13 0 0 0 0 1 0 0 0 0
## AGCCCSub11 1 1 1 NA 0 1 NA NA 0
## CGATGTSub6 0 0 NA NA NA NA NA NA 0
## CTAGCSub3 1 1 NA 0 NA NA 0 1 0
## CTTGCTTSub14 1 1 NA NA 1 0 NA NA 0
## CTTGCTTSub8 NA NA NA 0 NA NA NA NA NA
## GAATTCASub9 0 0 1 0 1 0 0 0 0
## GCCAATSub4 0 0 NA NA NA NA NA NA 0
## GGACCTASub10 0 0 0 0 1 0 0 1 0
## GTATTSub12 NA NA 0 NA NA NA 0 1 0
## TGACCASub2 0 0 0 0 NA NA 0 1 0
## ACAGTGCau2 0 0 NA 0 NA NA 0 0 0
## ACAGTGCau3 0 0 0 0 0 1 0 0 0
## ACTATCau11 0 0 0 0 0 1 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 1 0 0
## ATGAAACCau12 0 0 0 NA 0 1 0 0 0
## CTAGCCau5 0 0 0 0 0 1 0 0 0
## [,371] [,372] [,373] [,374] [,375] [,376] [,377] [,378] [,379]
## ACAAANel3 0 1 0 0 0 0 1 0 0
## ACAGTGNel5 0 1 0 0 0 0 1 0 0
## AGCATNel8 0 1 0 0 0 0 1 0 0
## ATGAAACNel10 0 0 0 0 0 0 1 0 0
## ATGAAACNel15 0 1 0 0 0 0 1 0 0
## CGATGTNel4 0 0 0 0 0 1 1 0 0
## CTAGCNel7 0 0 0 0 0 0 NA NA 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 1 0 0 0 1 0 0 0
## CTTGANel2 0 0 0 0 0 0 1 0 0
## GGACCTANel11 0 0 0 0 0 0 1 0 0
## GGACCTANel13 0 1 0 0 0 0 1 0 0
## GTATTNel14 0 1 0 0 0 1 1 0 0
## TCACCNel6 0 1 0 0 0 1 1 0 0
## TGACCANel1 0 1 0 0 0 0 1 0 0
## AAAAGTTAlt12 0 1 0 0 1 0 1 0 0
## ACAAAAlt11 0 0 0 0 0 0 1 0 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0 0
## AGCCCAlt13 0 0 0 0 0 0 1 0 0
## ATCACGAlt5 0 1 0 0 0 1 1 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 0 0 0 0 0 0
## CTGTAAlt14 0 1 0 0 1 0 1 0 0
## CTTGAAlt10 0 1 0 0 0 0 1 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 1 0 0
## GCCAATAlt9 0 0 0 0 0 0 1 0 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0 0
## TTAGGCAlt8 0 0 0 0 0 1 1 0 0
## AAAAGTTSub15 0 NA NA NA 0 0 1 0 0
## ACAAASub1 0 0 0 0 1 0 NA NA 0
## ACTATSub7 0 0 0 0 1 0 1 0 1
## AGCATSub13 0 0 0 0 0 0 1 0 0
## AGCCCSub11 NA NA 0 0 0 0 1 0 NA
## CGATGTSub6 0 0 0 0 NA 0 1 0 0
## CTAGCSub3 0 NA 0 0 NA 0 1 0 NA
## CTTGCTTSub14 NA 0 0 0 NA 0 NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 1 0 0
## GCCAATSub4 NA NA 0 0 NA 0 1 0 NA
## GGACCTASub10 0 0 0 0 0 0 1 0 0
## GTATTSub12 NA NA 0 0 NA 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 NA
## ACAGTGCau2 0 0 0 0 NA 0 0 0 NA
## ACAGTGCau3 0 0 0 0 0 0 0 1 1
## ACTATCau11 0 0 0 0 0 0 0 1 1
## ACTATCau9 0 0 0 0 0 0 0 1 1
## AGCCCCau7 0 0 0 0 0 0 0 0 1
## ATGAAACCau12 0 0 0 0 0 0 NA NA NA
## CTAGCCau5 0 0 0 0 0 0 0 0 1
## [,380] [,381] [,382] [,383] [,384] [,385] [,386] [,387] [,388]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 1 1 0 0 1 0 0 1
## AGCATNel8 0 0 0 0 0 1 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 1 0 1
## CTAGCNel7 0 0 0 0 0 0 0 0 1
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 1 0 0 0
## CTTGANel2 0 1 0 0 0 0 0 0 1
## GGACCTANel11 0 0 0 0 0 0 0 0 1
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 1 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 1 0 0 0
## ATCACGAlt5 0 0 0 0 1 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 1 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 1 0 0 1
## GCCAATAlt4 0 0 0 0 0 1 0 0 0
## GCCAATAlt9 0 0 0 0 0 1 0 0 0
## TTAGGCAlt2 0 1 0 0 0 1 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 NA NA NA 0 NA 0
## ACAAASub1 NA 0 0 0 NA 1 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 NA 0 1 0 0 0
## CGATGTSub6 0 NA NA 0 0 0 NA 0 0
## CTAGCSub3 NA NA NA 0 NA 0 0 NA 0
## CTTGCTTSub14 NA 0 0 0 0 1 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 1 0 0 0
## GCCAATSub4 NA NA NA NA NA 1 0 NA NA
## GGACCTASub10 0 0 0 0 0 1 1 0 0
## GTATTSub12 0 0 0 0 NA 1 0 NA NA
## TGACCASub2 0 0 0 0 0 1 0 0 0
## ACAGTGCau2 1 1 0 1 0 1 1 0 NA
## ACAGTGCau3 0 1 0 1 0 1 1 0 0
## ACTATCau11 1 1 0 1 0 1 1 0 0
## ACTATCau9 1 1 0 1 0 1 1 0 0
## AGCCCCau7 0 1 0 1 0 1 1 0 0
## ATGAAACCau12 0 1 0 1 NA 1 1 NA 0
## CTAGCCau5 1 1 0 1 0 1 1 NA 0
## [,389] [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397]
## ACAAANel3 0 0 1 1 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 1 0 1 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 1 0 1 0 0 0 0
## CTGTANel12 0 0 1 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 1 0 0 NA 0 0 0
## GGACCTANel11 0 0 1 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 1 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 NA 0 0 0
## AAAAGTTAlt12 0 0 1 0 0 0 0 0 0
## ACAAAAlt11 0 0 1 0 0 0 0 0 0
## ACAGTGAlt3 0 0 1 0 0 0 0 0 0
## AGCCCAlt13 0 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 0 1 0 0 0 0 0 0
## ATCACGAlt7 0 0 1 1 0 0 0 0 0
## CGATGTAlt1 0 0 0 1 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 1 0 0 0 0 0 0
## GAATTCAAlt15 0 0 1 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 1 1 0 0 0 0 0
## TTAGGCAlt6 0 0 1 1 1 0 0 0 0
## TTAGGCAlt8 0 0 1 1 0 0 0 0 0
## AAAAGTTSub15 0 NA 0 1 NA NA 0 NA NA
## ACAAASub1 0 NA NA NA NA NA 0 0 0
## ACTATSub7 0 0 1 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 NA 0 NA NA 0 0 0 NA NA
## CGATGTSub6 0 0 NA NA 0 0 0 0 0
## CTAGCSub3 NA NA 0 1 NA NA NA NA NA
## CTTGCTTSub14 NA NA 0 0 NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 1 0 0 0 0 0 0
## GTATTSub12 NA 0 NA NA 0 NA 0 0 0
## TGACCASub2 0 NA 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 NA 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 NA NA 0 0 0 NA 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,398] [,399] [,400] [,401] [,402] [,403] [,404] [,405] [,406]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 1 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 1 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 1 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 1 0 0 0
## GCCAATAlt4 0 0 0 0 0 1 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 0 0 0 0 0 0
## ACAAASub1 1 0 0 0 0 NA NA 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 NA NA 0 0
## CGATGTSub6 NA NA 0 0 0 0 0 NA 0
## CTAGCSub3 NA NA NA NA NA NA NA 0 0
## CTTGCTTSub14 0 0 0 0 0 0 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 1 0 0 0
## GTATTSub12 NA NA 0 0 0 NA NA 0 0
## TGACCASub2 NA NA 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 NA NA 0 0
## ACAGTGCau3 0 0 1 0 0 0 1 0 0
## ACTATCau11 0 0 0 0 0 0 1 0 1
## ACTATCau9 0 0 0 0 0 0 1 0 0
## AGCCCCau7 0 0 0 0 0 NA NA 0 0
## ATGAAACCau12 0 0 1 0 0 NA NA 0 0
## CTAGCCau5 0 0 0 0 0 0 1 0 1
## [,407] [,408] [,409] [,410] [,411] [,412] [,413] [,414] [,415]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 1 0 0 0 1 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 1 0 0 0
## CTAGCNel7 0 0 0 0 0 1 0 0 0
## CTGTANel12 0 0 0 0 0 0 1 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 1 0 0 0
## GGACCTANel13 0 1 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 1 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 1 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 1 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 1 0 0 0 0 0 1 0
## TTAGGCAlt6 0 1 0 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA 0 0 0 NA NA NA
## ACAAASub1 0 NA 0 0 0 0 0 0 0
## ACTATSub7 0 1 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 1 0 0 0 0 0 0 0
## CGATGTSub6 0 0 NA 0 0 0 0 0 0
## CTAGCSub3 0 NA NA NA NA NA 0 NA NA
## CTTGCTTSub14 0 NA NA 0 0 0 NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA 0 NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA 0 0 0 0 0 0 NA
## TGACCASub2 0 1 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 NA 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 NA
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,416] [,417] [,418] [,419] [,420] [,421] [,422] [,423] [,424]
## ACAAANel3 0 0 1 0 0 0 0 0 0
## ACAGTGNel5 0 0 1 0 0 0 1 0 0
## AGCATNel8 0 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 0 1 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 1 0 0 0 0
## CGATGTNel4 0 0 1 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 1 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 1 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 1 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 1 0 0 0 0 0 1
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 1 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 1 0
## CTTGAAlt10 0 0 0 0 1 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 1 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 1 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 NA NA NA 0 0
## ACAAASub1 0 0 0 0 1 1 0 0 0
## ACTATSub7 0 0 1 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 1 0 0 0 0
## CGATGTSub6 0 NA NA NA 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA 0 0
## CTTGCTTSub14 0 0 0 0 NA NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 0 0 0 0 0 0
## GCCAATSub4 0 0 1 0 NA NA NA 0 0
## GGACCTASub10 0 0 1 0 0 0 0 0 0
## GTATTSub12 0 0 1 0 NA NA NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 NA NA
## ACAGTGCau2 0 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,425] [,426] [,427] [,428] [,429] [,430] [,431] [,432] [,433]
## ACAAANel3 0 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 0 0 0 0 1 0 0
## AGCATNel8 0 0 0 0 0 0 1 0 0
## ATGAAACNel10 1 0 0 0 0 0 1 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 1 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 1 0 0
## CTTGANel2 0 0 0 0 0 0 1 0 0
## GGACCTANel11 0 0 0 0 0 0 1 0 0
## GGACCTANel13 0 0 0 0 0 0 1 0 0
## GTATTNel14 0 0 0 0 0 0 1 0 0
## TCACCNel6 0 0 0 0 0 0 1 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 1 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 1 0 0 0 0 0 1 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 0 1 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 1 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 1 0 0
## GCCAATAlt9 0 0 0 0 0 0 1 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA NA NA 0 NA NA NA
## ACAAASub1 1 NA NA NA NA 0 NA NA NA
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 1 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 NA NA NA NA 0 NA 0 0
## CTAGCSub3 0 0 0 0 0 NA 1 0 0
## CTTGCTTSub14 0 0 0 0 0 0 NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 1 0 0
## GCCAATSub4 0 0 0 0 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 1 0 0
## GTATTSub12 NA NA NA NA NA 0 NA 0 0
## TGACCASub2 NA 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 1 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,434] [,435] [,436] [,437] [,438] [,439] [,440] [,441] [,442]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 NA 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 1 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA 0 0 0
## ACAAASub1 NA NA 0 0 NA 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 NA NA 0 0 NA NA NA
## CTAGCSub3 0 0 NA NA NA 0 0 0 0
## CTTGCTTSub14 0 0 0 0 0 0 NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 NA NA NA
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 NA NA NA
## GTATTSub12 0 0 0 NA 0 NA 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 NA 0 1 0 0 0
## ACAGTGCau3 0 0 0 0 0 NA 0 0 0
## ACTATCau11 0 0 0 0 0 1 0 0 0
## ACTATCau9 0 0 0 0 0 1 0 0 0
## AGCCCCau7 0 0 0 0 0 1 0 0 0
## ATGAAACCau12 0 0 0 0 0 1 0 0 0
## CTAGCCau5 0 0 0 0 0 1 0 0 0
## [,443] [,444] [,445] [,446] [,447] [,448] [,449] [,450] [,451]
## ACAAANel3 0 1 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 1 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 1 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 1 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 1 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 1 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 NA 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 NA 0 0 0 0 0
## CTAGCSub3 0 NA 0 0 NA 0 0 0 0
## CTTGCTTSub14 0 0 0 0 NA NA NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 NA NA NA 0 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 NA NA 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 NA NA NA NA NA
## ACAGTGCau3 0 0 0 0 1 0 0 0 0
## ACTATCau11 0 0 0 0 1 0 0 0 0
## ACTATCau9 0 0 0 0 1 0 0 0 0
## AGCCCCau7 0 0 0 0 1 0 0 0 0
## ATGAAACCau12 0 0 0 0 1 0 0 0 0
## CTAGCCau5 0 0 0 0 1 0 0 0 0
## [,452] [,453] [,454] [,455] [,456] [,457] [,458] [,459] [,460]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 1 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 NA NA NA NA NA NA NA NA 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 1 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA NA 0
## ACAAASub1 0 1 1 0 0 0 0 0 0
## ACTATSub7 NA NA NA NA NA NA NA NA 0
## AGCATSub13 NA NA NA NA NA NA NA NA 0
## AGCCCSub11 0 NA 1 0 0 0 0 0 0
## CGATGTSub6 0 1 1 0 0 0 0 0 0
## CTAGCSub3 0 1 1 0 0 0 0 0 0
## CTTGCTTSub14 0 1 1 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 1 1 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 1 1 0 0 0 0 0 0
## ACAGTGCau3 0 1 1 0 1 0 1 0 0
## ACTATCau11 0 0 1 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 1 1 0 0 0 0 0 0
## ATGAAACCau12 NA NA NA NA NA NA NA NA 0
## CTAGCCau5 0 0 1 0 0 0 0 0 0
## [,461] [,462] [,463] [,464] [,465] [,466] [,467] [,468] [,469]
## ACAAANel3 0 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 0 0 0 0 1 0 0
## AGCATNel8 0 0 0 0 0 0 1 0 0
## ATGAAACNel10 0 0 0 0 0 1 1 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 1 0
## CGATGTNel4 0 0 0 0 0 0 1 0 0
## CTAGCNel7 0 0 0 0 0 0 1 0 0
## CTGTANel12 0 0 0 0 0 0 1 0 0
## CTGTANel9 0 0 0 0 0 0 1 1 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 1 0 0
## GGACCTANel13 0 0 0 0 0 0 1 0 0
## GTATTNel14 0 0 0 0 0 1 1 0 0
## TCACCNel6 0 0 0 0 0 1 1 0 0
## TGACCANel1 0 0 0 0 0 0 1 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 1 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 1 0
## ATCACGAlt5 0 0 0 0 0 0 1 0 0
## ATCACGAlt7 0 0 0 0 0 0 1 1 0
## CGATGTAlt1 0 0 0 0 0 1 1 0 0
## CTGTAAlt14 0 0 0 0 0 0 1 0 0
## CTTGAAlt10 0 0 0 0 0 0 1 0 0
## GAATTCAAlt15 0 0 0 0 0 0 1 1 0
## GCCAATAlt4 0 0 0 0 0 0 1 1 0
## GCCAATAlt9 0 0 0 0 0 0 1 0 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0 0
## TTAGGCAlt8 0 0 0 0 0 0 1 0 0
## AAAAGTTSub15 0 NA NA NA NA NA NA NA NA
## ACAAASub1 0 0 0 0 0 NA NA 0 0
## ACTATSub7 0 0 0 0 0 0 1 0 0
## AGCATSub13 0 0 0 0 0 0 1 1 0
## AGCCCSub11 0 0 0 0 0 NA NA 0 0
## CGATGTSub6 0 0 0 0 0 NA NA 0 0
## CTAGCSub3 0 NA NA NA 0 NA NA NA NA
## CTTGCTTSub14 0 NA NA NA 0 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA NA NA 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 1 0 0
## GTATTSub12 NA NA NA NA 0 0 1 0 NA
## TGACCASub2 0 0 0 0 0 0 1 0 0
## ACAGTGCau2 0 NA NA NA 0 0 0 0 NA
## ACAGTGCau3 0 1 0 0 0 0 0 0 1
## ACTATCau11 0 1 0 0 0 0 0 0 0
## ACTATCau9 0 1 0 0 0 0 0 0 0
## AGCCCCau7 0 1 0 0 0 0 0 0 0
## ATGAAACCau12 0 NA NA NA 0 0 0 0 0
## CTAGCCau5 0 1 0 0 0 0 0 NA 0
## [,470] [,471] [,472] [,473] [,474] [,475] [,476] [,477] [,478]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 0 0
## CTAGCNel7 0 1 0 0 1 0 1 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 1 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 1 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 1 0 0
## GCCAATAlt4 0 0 1 0 0 0 0 0 0
## GCCAATAlt9 0 0 1 0 0 0 1 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA 0 0 0 NA NA 0
## ACAAASub1 0 0 1 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 NA NA 0 0 0 0 0 0
## CGATGTSub6 0 NA NA 0 0 0 0 0 0
## CTAGCSub3 NA NA NA 0 0 0 NA NA 0
## CTTGCTTSub14 NA 0 0 0 0 0 NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA 0 0 0 NA 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA NA 0 0 0 0 0 0 0
## ACAGTGCau3 0 1 0 0 0 0 0 0 0
## ACTATCau11 0 1 0 0 0 0 0 0 0
## ACTATCau9 0 1 0 0 0 0 0 0 0
## AGCCCCau7 0 1 0 0 0 0 NA 0 0
## ATGAAACCau12 0 1 0 0 0 0 NA 0 0
## CTAGCCau5 0 1 0 0 0 0 0 0 0
## [,479] [,480] [,481] [,482] [,483] [,484] [,485] [,486] [,487]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 1 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 1 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 1 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 1 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 1 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 1 0 0 0
## AAAAGTTSub15 0 0 0 1 0 NA NA NA NA
## ACAAASub1 0 0 0 NA 0 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 NA 0 0 0 0 0
## CGATGTSub6 0 0 0 1 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA 0 NA NA NA
## CTTGCTTSub14 0 0 0 NA 0 0 NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 1 0 0 0 0 0
## GTATTSub12 0 0 0 1 NA 0 NA NA 0
## TGACCASub2 0 0 0 NA 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 NA 0 NA NA 0
## ACAGTGCau3 0 0 0 0 NA 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 NA
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 NA NA 0
## [,488] [,489] [,490] [,491] [,492] [,493] [,494] [,495] [,496]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 1
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 1
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 NA 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 1
## AAAAGTTSub15 NA 0 0 0 NA NA 0 0 0
## ACAAASub1 0 0 0 0 0 NA 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 NA 0 0 0 0
## CTAGCSub3 NA NA 0 0 NA NA 0 0 0
## CTTGCTTSub14 NA 0 0 0 NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 NA NA 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 1 0 0 NA 0 0 0 NA
## ACAGTGCau3 0 1 0 0 0 0 0 0 0
## ACTATCau11 0 1 0 0 1 0 0 0 0
## ACTATCau9 0 1 0 0 0 0 0 0 0
## AGCCCCau7 0 NA 0 0 0 0 0 0 0
## ATGAAACCau12 0 1 0 0 NA NA 0 0 0
## CTAGCCau5 0 1 0 0 0 0 0 0 0
## [,497] [,498] [,499] [,500] [,501] [,502] [,503] [,504] [,505]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 1 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 1 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 1 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 1 0 0
## AAAAGTTAlt12 0 0 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 1 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 1 0 0
## ATCACGAlt7 0 0 0 0 1 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 1 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0 NA
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 NA
## CTAGCSub3 0 0 0 0 0 NA NA NA NA
## CTTGCTTSub14 0 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 0 NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 1 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 1 0 0 0 0 0
## AGCCCCau7 0 0 0 1 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,506] [,507] [,508] [,509] [,510] [,511] [,512] [,513] [,514]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 1 0 0 0 0 0 0 0
## AGCATNel8 1 0 0 0 0 0 0 1 0
## ATGAAACNel10 0 1 0 0 0 1 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 1 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 1 0 0 0 0 0 1 0
## CTGTANel9 0 0 0 0 0 0 0 1 0
## CTTGANel2 0 1 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 1 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 1 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 1 0 0 0 0 0 0 0
## ACAGTGAlt3 0 1 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 1 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 1 0 0 1 0
## CGATGTAlt1 0 1 0 0 0 0 0 1 0
## CTGTAAlt14 0 0 0 0 0 0 0 1 0
## CTTGAAlt10 0 1 0 0 0 0 0 1 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0 0
## GCCAATAlt4 0 1 0 0 0 0 0 0 0
## GCCAATAlt9 0 1 0 0 0 0 0 0 0
## TTAGGCAlt2 0 1 0 0 1 0 0 1 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 NA 0 0 0 0
## ACAAASub1 NA 0 0 0 0 0 NA NA NA
## ACTATSub7 0 1 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 NA NA NA
## CGATGTSub6 NA 0 0 0 0 0 NA NA NA
## CTAGCSub3 0 NA NA 0 0 0 NA NA NA
## CTTGCTTSub14 NA 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA 0 NA 0 NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 NA 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 NA NA NA
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 NA 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,515] [,516] [,517] [,518] [,519] [,520] [,521] [,522] [,523]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 1 0 0 0 0 0 0
## AGCATNel8 0 0 1 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 1
## CGATGTNel4 0 0 1 0 0 0 0 0 1
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 1 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 1 0 0 0 0 1 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 1 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 1 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0 0
## ATCACGAlt5 0 1 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 0 0 0 0 0 1
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 1 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0 0
## GCCAATAlt4 0 1 0 0 0 0 0 0 0
## GCCAATAlt9 0 1 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 1 0 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0 0
## AAAAGTTSub15 0 1 0 0 NA NA NA 0 0
## ACAAASub1 0 1 0 0 NA 0 0 0 0
## ACTATSub7 0 1 0 0 0 0 0 0 0
## AGCATSub13 0 1 0 0 0 0 0 0 0
## AGCCCSub11 0 1 0 0 0 0 0 0 0
## CGATGTSub6 0 1 0 0 0 0 0 0 1
## CTAGCSub3 0 1 0 0 0 NA NA 0 0
## CTTGCTTSub14 0 1 0 0 NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 0 0
## GCCAATSub4 0 1 0 0 NA NA NA 0 0
## GGACCTASub10 0 1 0 0 0 0 0 0 0
## GTATTSub12 0 1 0 0 NA 0 NA 0 0
## TGACCASub2 0 1 0 0 0 0 NA 0 0
## ACAGTGCau2 0 0 0 0 0 0 NA 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 NA 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,524] [,525] [,526] [,527] [,528] [,529] [,530] [,531] [,532]
## ACAAANel3 0 0 0 1 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 1 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 1 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 1 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 1 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 1 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 1 0 0
## TCACCNel6 0 0 0 0 1 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 1 0 0 0 0 0
## ACAAAAlt11 0 0 0 1 0 0 0 0 0
## ACAGTGAlt3 0 0 0 1 0 0 0 0 0
## AGCCCAlt13 0 0 0 1 0 0 0 0 0
## ATCACGAlt5 0 0 0 1 0 0 0 0 0
## ATCACGAlt7 0 0 0 1 0 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 1 0 0 0 0 0
## CTTGAAlt10 0 0 0 1 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 1 0 0 0 0 0
## GCCAATAlt9 0 0 0 1 0 0 0 0 0
## TTAGGCAlt2 0 0 0 1 0 0 0 0 0
## TTAGGCAlt6 0 0 0 1 0 0 0 0 0
## TTAGGCAlt8 0 0 0 1 0 0 0 0 0
## AAAAGTTSub15 0 0 NA NA 0 0 NA 0 0
## ACAAASub1 0 0 0 1 0 0 NA 0 0
## ACTATSub7 0 0 0 1 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 NA NA 0 0 NA 0 0
## CGATGTSub6 0 0 0 1 0 0 0 0 0
## CTAGCSub3 0 0 NA NA NA NA NA 0 0
## CTTGCTTSub14 0 0 NA NA NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA 0 1 0 0 NA 0 0
## TGACCASub2 0 0 0 1 NA NA 0 0 0
## ACAGTGCau2 0 NA 1 0 0 0 0 0 0
## ACAGTGCau3 0 1 1 0 0 1 0 0 0
## ACTATCau11 0 0 1 0 0 1 0 0 0
## ACTATCau9 0 0 1 0 0 1 0 0 0
## AGCCCCau7 0 0 1 0 0 1 NA 0 0
## ATGAAACCau12 0 0 1 0 0 0 0 0 0
## CTAGCCau5 0 0 1 0 0 1 0 0 0
## [,533] [,534] [,535] [,536] [,537] [,538] [,539] [,540] [,541]
## ACAAANel3 0 0 0 0 0 0 0 0 1
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 1 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 NA 0 0 0
## CTTGANel2 0 0 1 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 1 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 1 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA 0 NA NA NA 0 NA NA
## ACAAASub1 0 NA 0 0 0 NA 0 NA 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 NA
## CGATGTSub6 0 NA 0 0 0 NA 0 0 NA
## CTAGCSub3 0 NA 0 0 0 NA NA NA 0
## CTTGCTTSub14 0 0 0 NA NA 0 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 0 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA 0 0 0 NA NA NA NA
## TGACCASub2 0 0 0 0 1 0 0 0 NA
## ACAGTGCau2 0 NA 0 1 1 0 0 NA 0
## ACAGTGCau3 0 0 0 1 1 1 0 0 NA
## ACTATCau11 0 0 0 1 1 NA 0 0 0
## ACTATCau9 0 0 0 1 1 1 0 0 0
## AGCCCCau7 0 0 0 1 1 NA 0 0 0
## ATGAAACCau12 0 0 0 1 1 NA 0 NA 0
## CTAGCCau5 0 0 0 1 1 1 0 0 0
## [,542] [,543] [,544] [,545] [,546] [,547] [,548] [,549] [,550]
## ACAAANel3 0 0 0 0 1 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 1 0 0
## AGCATNel8 0 0 0 0 1 0 1 0 1
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 1
## CGATGTNel4 0 0 0 0 1 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 1 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 1 0 0 0 1
## TCACCNel6 0 0 0 0 0 0 1 0 0
## TGACCANel1 0 0 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 1 0 0 0 0 0 0 0 1
## ACAGTGAlt3 0 0 0 0 1 0 1 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 1 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 1 0 1 0 0
## CTTGAAlt10 0 0 0 0 1 0 0 0 0
## GAATTCAAlt15 1 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 1 0 0 0 0
## GCCAATAlt9 0 0 0 0 1 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 1 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 NA NA NA NA NA NA
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 1 0 0 0 0
## AGCATSub13 0 0 0 0 1 0 0 0 0
## AGCCCSub11 NA 0 0 NA NA 0 0 0 0
## CGATGTSub6 NA 0 0 0 0 0 0 0 0
## CTAGCSub3 0 NA 0 NA NA 0 0 0 NA
## CTTGCTTSub14 0 NA NA NA NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 NA NA NA NA 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 NA NA 0 0 0 NA
## TGACCASub2 NA 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 NA NA 0 0 0 NA
## ACAGTGCau3 NA 0 0 1 0 0 0 0 0
## ACTATCau11 0 0 1 1 0 0 0 0 0
## ACTATCau9 1 0 0 1 0 0 0 0 0
## AGCCCCau7 0 0 0 1 0 0 0 0 0
## ATGAAACCau12 0 0 0 1 0 NA NA 0 0
## CTAGCCau5 1 0 0 1 0 0 0 0 0
## [,551] [,552] [,553] [,554] [,555] [,556] [,557] [,558] [,559]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 1
## ATGAAACNel15 0 0 0 0 0 0 0 0 1
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 1
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 1 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 1 0 0 1 1
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 1 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 1
## AAAAGTTSub15 NA NA NA NA NA NA NA NA NA
## ACAAASub1 0 0 0 0 0 0 0 0 1
## ACTATSub7 0 0 0 0 1 0 0 0 1
## AGCATSub13 0 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 1
## CTAGCSub3 NA NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 0 0 0 0 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 1
## GTATTSub12 NA NA NA NA NA NA NA 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 1
## ACAGTGCau2 NA NA NA NA 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 1 1 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 NA NA NA 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,560] [,561] [,562] [,563] [,564] [,565] [,566] [,567] [,568]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA 0 0 NA NA
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 NA 0 0 0
## CGATGTSub6 0 0 0 0 NA 0 0 NA NA
## CTAGCSub3 NA NA NA NA NA 0 0 NA NA
## CTTGCTTSub14 NA NA NA NA 0 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA 0 0 NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 NA 0 0 NA NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 1 0 0 1 NA 0 NA NA
## ACAGTGCau3 0 1 1 0 NA 1 0 0 0
## ACTATCau11 0 1 0 0 1 1 0 0 0
## ACTATCau9 0 0 1 0 0 1 0 0 0
## AGCCCCau7 0 1 0 0 0 0 0 0 0
## ATGAAACCau12 0 1 0 0 NA NA 0 0 0
## CTAGCCau5 0 1 0 0 1 1 0 0 0
## [,569] [,570] [,571] [,572] [,573] [,574] [,575] [,576] [,577]
## ACAAANel3 0 0 0 0 0 0 0 1 1
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 1 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 1
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 1 0
## GGACCTANel11 0 0 0 0 0 0 0 1 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 1
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 1
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 NA NA NA NA NA 0 0 0
## CTGTAAlt14 0 0 1 0 1 1 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 1
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 1 0 1 1 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 1 1
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0 1
## ACTATSub7 0 0 0 0 0 0 0 0 NA
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 NA NA NA NA NA NA 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA NA
## CTTGCTTSub14 NA NA NA NA NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA 0 0 0 0 0 NA NA 0
## ACAGTGCau3 0 NA NA NA NA NA 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,578] [,579] [,580] [,581] [,582] [,583] [,584] [,585] [,586]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 NA NA
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 NA NA
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 NA NA
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 NA NA
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 NA NA
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 NA NA
## TTAGGCAlt6 0 1 0 0 1 0 0 NA NA
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 NA 0 0
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 NA NA NA NA NA NA 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA 0 0
## CTTGCTTSub14 0 0 0 0 0 0 NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA 0 0
## GAATTCASub9 0 1 0 0 1 0 0 0 0
## GCCAATSub4 0 0 0 0 0 0 NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA NA NA NA 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 1 0 0 1 0 1 0 0 0
## ACAGTGCau3 1 0 0 1 0 1 0 0 0
## ACTATCau11 1 0 0 1 0 1 0 0 0
## ACTATCau9 1 0 0 1 0 1 0 0 0
## AGCCCCau7 1 0 0 1 0 1 0 0 0
## ATGAAACCau12 1 0 0 1 0 1 0 0 0
## CTAGCCau5 1 0 0 1 0 1 0 0 0
## [,587] [,588] [,589] [,590] [,591] [,592] [,593] [,594] [,595]
## ACAAANel3 0 0 0 1 0 0 0 1 1
## ACAGTGNel5 0 0 0 1 0 0 0 0 1
## AGCATNel8 0 0 1 0 0 0 0 0 0
## ATGAAACNel10 0 1 0 0 0 0 0 1 0
## ATGAAACNel15 0 1 0 1 0 0 1 1 1
## CGATGTNel4 0 0 1 1 0 0 0 1 0
## CTAGCNel7 0 0 0 0 0 0 0 0 1
## CTGTANel12 0 0 0 0 1 0 0 0 1
## CTGTANel9 0 1 0 1 1 0 1 1 1
## CTTGANel2 0 0 0 0 0 0 0 1 0
## GGACCTANel11 0 0 0 0 1 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 1 0
## GTATTNel14 0 1 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 1 0 0 0 1 1
## TGACCANel1 0 0 0 0 0 0 0 1 1
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 0 0 0 1 1
## ACAGTGAlt3 0 0 0 1 0 0 0 1 1
## AGCCCAlt13 0 0 1 0 0 0 0 1 0
## ATCACGAlt5 0 1 1 0 0 0 0 0 0
## ATCACGAlt7 0 1 1 0 0 0 0 1 1
## CGATGTAlt1 0 0 1 0 1 0 0 1 0
## CTGTAAlt14 0 0 0 1 0 0 0 1 1
## CTTGAAlt10 0 0 0 0 0 0 0 1 1
## GAATTCAAlt15 0 1 0 0 0 1 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 1 0
## GCCAATAlt9 0 0 0 0 0 0 0 1 1
## TTAGGCAlt2 0 0 1 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 1 1 0 0 0 1
## TTAGGCAlt8 0 0 0 1 1 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA 0 NA 0 1
## ACAAASub1 0 0 NA NA 0 0 NA NA NA
## ACTATSub7 0 0 0 1 0 0 0 1 1
## AGCATSub13 0 0 0 1 1 0 0 1 1
## AGCCCSub11 0 0 0 1 0 0 0 NA NA
## CGATGTSub6 0 0 0 0 NA 0 0 1 0
## CTAGCSub3 NA NA 0 1 NA 0 0 1 NA
## CTTGCTTSub14 0 0 NA NA 0 0 0 NA 1
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 1 1
## GCCAATSub4 NA NA NA NA NA 0 NA NA NA
## GGACCTASub10 0 0 0 1 0 0 0 1 0
## GTATTSub12 NA NA NA NA NA 0 NA NA 0
## TGACCASub2 0 0 0 1 NA 0 0 0 1
## ACAGTGCau2 0 0 1 0 NA 0 0 0 0
## ACAGTGCau3 1 0 1 0 0 0 0 0 0
## ACTATCau11 0 0 1 0 0 0 0 0 0
## ACTATCau9 0 0 1 0 0 0 0 0 0
## AGCCCCau7 0 0 NA NA 0 0 NA 0 0
## ATGAAACCau12 NA NA 1 0 0 0 0 0 0
## CTAGCCau5 0 0 1 0 0 0 1 0 0
## [,596] [,597] [,598] [,599] [,600] [,601] [,602] [,603] [,604]
## ACAAANel3 0 0 0 1 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 1
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 NA NA 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 1 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 0 NA NA NA 0 0 NA 0 0
## CTTGCTTSub14 NA 0 0 0 0 0 NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 0 0 NA 0 1
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 1 NA 0 0
## ACAGTGCau3 0 0 0 0 0 1 0 0 0
## ACTATCau11 0 0 0 0 0 1 0 0 0
## ACTATCau9 0 0 0 0 0 1 0 0 0
## AGCCCCau7 0 0 0 0 0 1 0 0 0
## ATGAAACCau12 0 0 0 0 0 1 0 0 0
## CTAGCCau5 0 0 0 0 0 1 0 0 0
## [,605] [,606] [,607] [,608] [,609] [,610] [,611] [,612] [,613]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 1 0 1 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 1 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 1 0 0 0 0 0 0 1 0
## GCCAATAlt9 0 0 0 0 0 0 0 1 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 1 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 0 0 0 0 0 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA NA NA NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 NA 0
## ACAGTGCau2 0 0 0 0 0 0 0 0 1
## ACAGTGCau3 0 0 0 0 0 0 0 0 1
## ACTATCau11 0 0 0 0 0 0 0 0 1
## ACTATCau9 0 0 0 0 0 0 0 0 1
## AGCCCCau7 0 0 0 0 0 0 0 0 1
## ATGAAACCau12 0 0 0 0 0 0 0 0 1
## CTAGCCau5 0 0 0 0 0 0 0 0 1
## [,614] [,615] [,616] [,617] [,618] [,619] [,620] [,621] [,622]
## ACAAANel3 1 0 1 0 0 0 0 0 0
## ACAGTGNel5 1 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 1 0 0 0 1 0 0
## ATGAAACNel10 0 0 1 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 1 0 1 0 0 0 0 0 0
## CTAGCNel7 0 0 1 0 0 0 0 0 0
## CTGTANel12 1 0 0 0 0 0 1 0 0
## CTGTANel9 0 0 1 0 0 0 0 1 0
## CTTGANel2 0 0 1 0 0 0 0 0 0
## GGACCTANel11 0 0 1 0 0 0 0 0 0
## GGACCTANel13 1 0 0 0 0 0 0 0 0
## GTATTNel14 1 0 1 0 0 0 0 0 0
## TCACCNel6 0 0 1 0 0 0 0 0 0
## TGACCANel1 0 0 1 0 0 0 0 0 0
## AAAAGTTAlt12 1 0 1 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 0 1 0 0 0 0 0 0
## ATCACGAlt7 0 0 1 0 0 0 0 0 0
## CGATGTAlt1 0 0 1 0 0 0 0 0 0
## CTGTAAlt14 1 0 1 0 0 0 0 0 1
## CTTGAAlt10 0 0 1 0 0 0 0 0 0
## GAATTCAAlt15 0 0 1 0 0 0 0 0 0
## GCCAATAlt4 1 0 0 0 0 0 0 0 1
## GCCAATAlt9 1 0 1 0 0 0 1 0 0
## TTAGGCAlt2 1 0 1 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 1 0 1 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA NA 0 0 NA NA NA
## ACAAASub1 0 0 0 0 0 0 NA NA NA
## ACTATSub7 0 0 1 0 0 0 0 0 0
## AGCATSub13 0 0 1 0 0 0 0 0 0
## AGCCCSub11 1 0 0 0 0 0 0 0 0
## CGATGTSub6 NA 0 NA 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 NA NA NA NA NA 0
## CTTGCTTSub14 0 NA 0 NA 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 NA NA NA NA NA NA
## GGACCTASub10 0 0 1 0 0 0 0 0 0
## GTATTSub12 0 0 0 NA 0 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 NA 0 NA 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 NA
## ATGAAACCau12 0 0 0 NA 0 0 NA NA 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,623] [,624] [,625] [,626] [,627] [,628] [,629] [,630] [,631]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 1 0 1 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 1 0
## CTAGCNel7 0 0 0 0 0 0 0 1 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 1 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 1 0
## GGACCTANel13 0 0 0 0 1 0 0 1 0
## GTATTNel14 0 0 0 0 0 0 0 1 0
## TCACCNel6 0 0 0 0 0 0 0 1 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 1 0
## ACAAAAlt11 0 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 1 0 0 1 0
## ATCACGAlt5 0 0 0 0 0 0 0 1 0
## ATCACGAlt7 0 0 0 0 0 0 0 1 0
## CGATGTAlt1 0 0 0 0 0 0 0 1 0
## CTGTAAlt14 0 0 0 0 0 0 0 1 0
## CTTGAAlt10 0 1 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 1 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 1 0 0 1 0
## TTAGGCAlt8 0 0 0 1 0 1 0 0 0
## AAAAGTTSub15 NA NA NA 0 0 NA 0 NA 1
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 NA 0 0 0 0 0 0
## CTAGCSub3 NA NA NA 0 0 0 0 0 1
## CTTGCTTSub14 NA NA NA 0 0 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA 0 0 0 0 NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA 0 0 0 NA 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 NA 0 0 NA 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 1 0 0 0 0 0 0
## ACTATCau9 0 0 NA 0 0 0 0 0 0
## AGCCCCau7 NA NA 0 0 0 NA 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,632] [,633] [,634] [,635] [,636] [,637] [,638] [,639] [,640]
## ACAAANel3 1 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 0 0 0 0 1 0 0
## AGCATNel8 0 0 0 0 0 0 1 0 0
## ATGAAACNel10 0 0 0 0 0 0 1 0 0
## ATGAAACNel15 1 0 0 0 0 0 1 0 0
## CGATGTNel4 0 0 0 0 0 0 1 0 0
## CTAGCNel7 0 0 0 0 0 0 1 0 0
## CTGTANel12 0 0 0 0 0 0 1 0 0
## CTGTANel9 0 0 0 0 0 0 1 0 0
## CTTGANel2 0 0 0 0 0 0 1 0 0
## GGACCTANel11 0 0 0 0 0 0 1 0 0
## GGACCTANel13 0 0 0 0 0 0 1 0 0
## GTATTNel14 0 0 0 0 0 0 1 0 0
## TCACCNel6 1 0 0 0 0 0 1 0 0
## TGACCANel1 0 0 0 0 0 0 1 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 1 0 0
## ACAAAAlt11 0 0 0 0 0 0 1 0 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0 0
## AGCCCAlt13 0 0 0 0 0 0 1 0 0
## ATCACGAlt5 0 0 0 0 0 0 1 0 0
## ATCACGAlt7 0 0 0 0 0 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 0 1 0 0
## CTGTAAlt14 0 0 0 0 0 0 1 0 0
## CTTGAAlt10 0 0 0 0 0 0 1 0 0
## GAATTCAAlt15 1 0 0 0 0 0 1 0 0
## GCCAATAlt4 0 0 0 0 0 0 1 0 0
## GCCAATAlt9 0 0 0 0 NA NA 1 0 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0 0
## TTAGGCAlt8 0 0 0 0 0 0 1 0 0
## AAAAGTTSub15 1 0 NA 0 0 0 1 NA NA
## ACAAASub1 0 0 NA 0 0 0 1 0 0
## ACTATSub7 0 0 0 0 0 0 1 0 0
## AGCATSub13 1 0 0 0 0 0 1 0 0
## AGCCCSub11 1 0 NA 0 0 0 1 0 0
## CGATGTSub6 0 0 0 0 0 0 1 0 0
## CTAGCSub3 1 NA NA 0 NA NA 1 0 NA
## CTTGCTTSub14 NA 0 NA 0 0 0 1 0 NA
## CTTGCTTSub8 NA NA NA 0 NA NA 1 NA NA
## GAATTCASub9 1 0 0 0 0 0 1 0 0
## GCCAATSub4 0 NA NA 0 NA NA 1 NA NA
## GGACCTASub10 0 0 0 0 0 0 1 0 0
## GTATTSub12 NA NA 0 0 NA NA 1 0 NA
## TGACCASub2 0 0 0 0 NA NA 1 0 0
## ACAGTGCau2 0 NA NA 0 NA NA 1 0 NA
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 1 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 1 0 0
## ATGAAACCau12 0 NA NA NA 0 0 1 0 NA
## CTAGCCau5 0 0 0 0 0 0 1 0 0
## [,641] [,642] [,643] [,644] [,645] [,646] [,647] [,648] [,649]
## ACAAANel3 1 1 0 0 0 1 1 0 0
## ACAGTGNel5 0 1 0 0 0 0 0 0 0
## AGCATNel8 0 1 0 0 0 0 0 0 0
## ATGAAACNel10 0 1 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 1 0 0 0 0 0 0 0
## CTGTANel12 0 1 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 1 0 0 0 0 0 0 0
## GGACCTANel11 1 0 0 0 0 0 0 0 0
## GGACCTANel13 0 1 0 0 0 0 0 0 0
## GTATTNel14 0 1 0 0 0 0 0 0 0
## TCACCNel6 0 1 0 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 1 0 0 0 0 0 0 0
## ACAGTGAlt3 0 1 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0 0
## ATCACGAlt5 1 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 0 0 1 1 0 0
## CTGTAAlt14 0 1 0 0 0 1 1 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 1 0 0 0 0 0 0 0
## GCCAATAlt9 0 1 0 0 0 0 0 0 0
## TTAGGCAlt2 0 1 0 0 0 0 0 0 0
## TTAGGCAlt6 1 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 1 1 0 0
## AAAAGTTSub15 0 NA NA NA NA NA NA 0 0
## ACAAASub1 0 0 0 NA 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 1 1 0 0
## AGCATSub13 0 0 0 0 0 1 1 0 0
## AGCCCSub11 0 0 0 0 0 0 0 NA NA
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA 0 0 NA NA NA NA
## CTTGCTTSub14 0 NA NA 0 0 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA 0 0 0 NA NA
## GGACCTASub10 0 0 1 0 0 1 1 0 0
## GTATTSub12 0 NA NA NA 0 0 0 NA NA
## TGACCASub2 0 NA NA 0 0 0 0 NA NA
## ACAGTGCau2 0 NA NA 0 0 0 0 NA NA
## ACAGTGCau3 0 0 1 0 0 0 0 1 1
## ACTATCau11 0 0 1 0 0 0 0 1 1
## ACTATCau9 0 0 1 0 0 0 0 NA NA
## AGCCCCau7 0 NA NA 0 0 0 0 1 0
## ATGAAACCau12 0 0 1 0 0 0 0 NA NA
## CTAGCCau5 0 0 0 0 0 0 0 1 1
## [,650] [,651] [,652] [,653] [,654] [,655] [,656] [,657] [,658]
## ACAAANel3 0 1 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 1 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 NA 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 NA NA NA 0 0
## ACAAASub1 0 0 0 0 NA NA 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 NA 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 NA 0 0 0 NA 0 0
## CTAGCSub3 NA 0 0 0 NA NA NA 0 0
## CTTGCTTSub14 NA 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 NA NA 0 0 0
## TGACCASub2 NA 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA 0 1 0 0 1 NA 0 0
## ACAGTGCau3 0 NA 1 0 0 1 0 0 0
## ACTATCau11 0 0 1 0 0 1 0 0 0
## ACTATCau9 0 NA 1 0 0 1 0 0 0
## AGCCCCau7 0 0 1 0 NA NA 0 0 0
## ATGAAACCau12 NA 0 1 0 NA NA 1 0 0
## CTAGCCau5 0 0 1 0 0 1 0 0 0
## [,659] [,660] [,661] [,662] [,663] [,664] [,665] [,666] [,667]
## ACAAANel3 0 0 0 0 0 NA NA NA NA
## ACAGTGNel5 0 1 0 0 0 0 0 0 0
## AGCATNel8 0 1 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 NA 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 0 0
## CTAGCNel7 0 1 0 1 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 1 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 1 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 NA NA NA NA
## ATCACGAlt5 0 1 0 0 0 0 0 0 0
## ATCACGAlt7 1 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 NA NA NA NA NA
## CTGTAAlt14 1 1 0 0 0 0 0 0 0
## CTTGAAlt10 1 1 0 0 NA 0 0 0 0
## GAATTCAAlt15 0 1 0 0 NA 0 0 0 0
## GCCAATAlt4 0 1 0 0 0 NA NA NA NA
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 1 0 0 0 NA NA NA NA
## TTAGGCAlt6 0 1 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 NA 0 0 0 0
## AAAAGTTSub15 NA NA 0 NA 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 1 1
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 1 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 NA 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 NA 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 NA 0 NA 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 NA NA NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 NA 0
## ACAGTGCau2 0 0 0 0 NA NA NA NA NA
## ACAGTGCau3 0 0 0 0 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 0 1 1
## ACTATCau9 0 0 0 0 1 0 0 1 0
## AGCCCCau7 0 0 0 0 1 0 0 0 0
## ATGAAACCau12 0 0 0 0 NA 0 NA 1 0
## CTAGCCau5 0 0 0 0 0 0 0 1 1
## [,668] [,669] [,670] [,671] [,672] [,673] [,674] [,675] [,676]
## ACAAANel3 NA NA 1 0 1 1 0 0 0
## ACAGTGNel5 0 0 0 0 0 1 0 0 0
## AGCATNel8 0 0 1 1 0 1 0 0 0
## ATGAAACNel10 0 0 0 0 1 1 0 0 0
## ATGAAACNel15 0 0 1 0 0 1 0 0 0
## CGATGTNel4 0 0 0 NA NA NA NA NA NA
## CTAGCNel7 0 0 0 0 0 1 0 0 0
## CTGTANel12 0 0 1 1 0 0 0 0 0
## CTGTANel9 0 0 1 0 0 1 0 0 0
## CTTGANel2 0 0 1 0 0 1 0 0 0
## GGACCTANel11 0 0 1 NA NA NA NA NA NA
## GGACCTANel13 0 0 0 0 0 1 0 0 0
## GTATTNel14 0 0 0 1 0 1 0 0 0
## TCACCNel6 0 0 1 1 0 1 0 0 0
## TGACCANel1 0 0 1 NA NA NA NA NA NA
## AAAAGTTAlt12 0 0 1 0 0 1 0 0 0
## ACAAAAlt11 0 0 1 1 0 1 0 0 0
## ACAGTGAlt3 0 0 0 NA NA NA NA NA NA
## AGCCCAlt13 NA NA 1 0 0 1 0 0 0
## ATCACGAlt5 0 0 1 0 0 1 0 0 0
## ATCACGAlt7 0 0 1 1 0 0 0 0 0
## CGATGTAlt1 NA NA 1 0 0 1 0 0 0
## CTGTAAlt14 0 0 1 1 0 1 0 0 0
## CTTGAAlt10 0 0 0 1 0 1 0 0 0
## GAATTCAAlt15 0 0 0 0 1 1 0 0 0
## GCCAATAlt4 NA NA 1 0 0 1 0 0 0
## GCCAATAlt9 0 0 1 1 0 1 0 0 0
## TTAGGCAlt2 NA NA 1 0 0 1 0 0 0
## TTAGGCAlt6 0 0 1 NA NA NA NA NA NA
## TTAGGCAlt8 0 0 1 0 0 1 0 0 0
## AAAAGTTSub15 0 0 NA NA NA NA NA NA NA
## ACAAASub1 0 0 1 NA NA NA NA NA NA
## ACTATSub7 0 0 1 0 0 1 0 0 0
## AGCATSub13 0 0 NA 0 1 1 0 0 0
## AGCCCSub11 0 0 1 1 0 0 0 0 0
## CGATGTSub6 0 0 1 1 0 1 0 0 0
## CTAGCSub3 NA NA 1 NA NA NA NA NA NA
## CTTGCTTSub14 0 0 1 1 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 0 0 1 0 0 0
## GCCAATSub4 NA NA 1 NA NA NA NA NA NA
## GGACCTASub10 0 0 1 1 0 1 0 0 0
## GTATTSub12 NA NA 1 NA NA NA NA NA NA
## TGACCASub2 NA 0 1 1 0 0 0 0 0
## ACAGTGCau2 NA NA 1 NA NA NA NA NA NA
## ACAGTGCau3 0 0 1 1 0 0 0 0 0
## ACTATCau11 0 0 1 0 0 0 0 0 0
## ACTATCau9 0 0 1 1 0 0 0 0 0
## AGCCCCau7 0 0 1 1 0 0 0 0 0
## ATGAAACCau12 0 0 1 1 0 0 0 0 0
## CTAGCCau5 0 0 1 NA NA NA NA NA NA
## [,677] [,678] [,679] [,680] [,681] [,682] [,683] [,684] [,685]
## ACAAANel3 0 0 0 0 0 0 0 0 1
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 1 0 0 1
## ATGAAACNel10 1 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 1 0 0 0
## CGATGTNel4 0 0 0 0 0 1 0 0 0
## CTAGCNel7 0 1 0 0 0 1 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 1
## CTGTANel9 0 0 0 0 0 1 0 0 1
## CTTGANel2 0 0 0 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 0 1 0 0 0
## GGACCTANel13 1 0 0 0 0 1 0 0 0
## GTATTNel14 0 0 0 0 0 1 0 0 1
## TCACCNel6 0 0 0 0 0 1 0 0 1
## TGACCANel1 0 0 0 0 0 1 0 0 0
## AAAAGTTAlt12 1 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 NA NA NA NA 1 0 0 0
## ACAGTGAlt3 0 NA NA NA NA 1 0 0 1
## AGCCCAlt13 1 0 0 0 0 1 0 0 0
## ATCACGAlt5 0 0 0 0 0 1 0 0 1
## ATCACGAlt7 1 0 0 0 0 1 0 0 1
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 NA NA NA NA 1 0 0 1
## CTTGAAlt10 0 0 0 0 0 1 0 0 0
## GAATTCAAlt15 0 0 1 0 0 1 0 0 0
## GCCAATAlt4 0 0 0 0 0 1 0 0 1
## GCCAATAlt9 0 NA NA NA NA 1 0 0 0
## TTAGGCAlt2 1 0 0 0 0 1 0 0 0
## TTAGGCAlt6 0 NA NA NA NA 1 0 0 0
## TTAGGCAlt8 1 0 1 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA 0 0 NA NA
## ACAAASub1 1 NA NA NA NA 0 0 0 1
## ACTATSub7 0 0 0 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 NA NA NA NA NA 0 0 NA NA
## CGATGTSub6 1 0 0 0 0 0 0 0 1
## CTAGCSub3 NA NA NA NA NA 0 0 NA NA
## CTTGCTTSub14 NA NA NA NA NA 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 0 0 0 1 0 0 1
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 1
## GTATTSub12 0 0 0 0 0 0 0 NA NA
## TGACCASub2 NA 0 0 0 0 1 0 0 1
## ACAGTGCau2 0 0 0 0 1 0 0 NA NA
## ACAGTGCau3 0 0 0 1 1 0 0 0 0
## ACTATCau11 0 0 0 1 1 0 0 1 0
## ACTATCau9 0 0 0 0 1 0 0 1 0
## AGCCCCau7 0 NA NA NA NA 0 0 1 0
## ATGAAACCau12 0 NA NA NA NA 0 0 1 0
## CTAGCCau5 NA 0 0 1 1 0 0 NA NA
## [,686] [,687] [,688] [,689] [,690] [,691] [,692] [,693] [,694]
## ACAAANel3 0 0 0 0 0 1 0 NA 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 NA
## AGCATNel8 0 0 0 0 0 1 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 1 0 0 0
## CGATGTNel4 0 0 0 0 0 1 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 NA 0
## CTGTANel12 0 0 0 0 0 1 0 NA 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 NA NA 0
## TGACCANel1 0 0 0 0 0 1 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 NA 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 1 0 0 0
## GAATTCAAlt15 0 0 0 0 0 1 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 NA 0
## AAAAGTTSub15 NA NA NA NA NA NA 0 0 NA
## ACAAASub1 0 0 NA 0 0 0 0 NA 0
## ACTATSub7 0 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 NA 0
## CGATGTSub6 NA 0 0 0 0 0 0 0 0
## CTAGCSub3 0 0 NA 0 0 NA 0 0 NA
## CTTGCTTSub14 NA 0 NA 0 0 0 NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0 0
## GCCAATSub4 NA NA NA NA NA NA 0 NA NA
## GGACCTASub10 0 0 0 0 0 1 0 0 0
## GTATTSub12 NA NA NA 0 0 NA 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 NA 0
## ACAGTGCau2 0 1 0 0 0 0 1 0 NA
## ACAGTGCau3 0 0 0 1 0 0 NA 0 1
## ACTATCau11 0 1 0 0 0 0 0 0 1
## ACTATCau9 0 1 0 0 0 0 0 0 1
## AGCCCCau7 0 NA 0 0 0 0 0 0 NA
## ATGAAACCau12 0 0 0 0 0 0 1 NA NA
## CTAGCCau5 0 1 0 0 0 0 1 NA 1
## [,695] [,696] [,697] [,698] [,699] [,700] [,701] [,702] [,703]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 NA 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 1 0 0 0 1 0 0 0 0
## CGATGTNel4 0 0 0 0 0 1 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 1 0 0 0 1 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 1 0 0 0
## GTATTNel14 1 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 1 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 1 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 1 0 0 0 0 1 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 1 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 0 NA NA NA NA NA
## ACAAASub1 0 0 0 0 NA 0 NA NA 0
## ACTATSub7 1 0 0 0 1 0 0 1 0
## AGCATSub13 1 0 0 0 0 0 0 1 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 NA 0 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 0 NA NA 0 1 0
## CTTGCTTSub14 0 NA 0 0 NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 1 0
## GCCAATSub4 NA NA 0 0 NA NA 0 0 NA
## GGACCTASub10 1 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 0 NA NA 0 1 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA NA 0 0 0 0 0 0 0
## ACAGTGCau3 0 NA 0 0 0 0 0 0 0
## ACTATCau11 0 1 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 NA 1 0 0 0 0 0 0 0
## ATGAAACCau12 NA NA 0 0 NA 0 0 0 0
## CTAGCCau5 0 1 0 0 0 0 0 0 0
## [,704] [,705] [,706] [,707] [,708] [,709] [,710] [,711] [,712]
## ACAAANel3 0 0 1 1 0 0 0 0 1
## ACAGTGNel5 0 0 0 1 0 1 0 0 1
## AGCATNel8 0 0 0 1 0 0 0 0 1
## ATGAAACNel10 0 0 1 1 0 0 0 0 0
## ATGAAACNel15 0 0 1 0 0 1 0 0 1
## CGATGTNel4 0 0 0 0 0 0 0 0 1
## CTAGCNel7 0 0 0 1 1 0 0 0 1
## CTGTANel12 0 0 0 0 0 1 0 0 1
## CTGTANel9 0 0 1 0 0 1 0 0 1
## CTTGANel2 0 0 1 1 0 0 0 0 1
## GGACCTANel11 0 0 0 1 0 0 0 0 1
## GGACCTANel13 0 0 1 1 0 0 0 0 1
## GTATTNel14 0 0 1 1 0 0 0 0 1
## TCACCNel6 0 0 0 0 0 1 0 0 1
## TGACCANel1 0 0 0 1 1 0 0 0 1
## AAAAGTTAlt12 0 0 0 1 0 0 0 0 1
## ACAAAAlt11 0 0 0 1 1 0 0 0 1
## ACAGTGAlt3 0 0 0 0 0 1 0 0 1
## AGCCCAlt13 0 0 0 1 1 0 0 0 1
## ATCACGAlt5 0 0 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 1 1 0 0 0 0 1
## CGATGTAlt1 1 0 0 1 0 1 0 0 1
## CTGTAAlt14 0 0 0 0 0 1 0 0 1
## CTTGAAlt10 0 0 0 0 0 1 0 0 1
## GAATTCAAlt15 0 0 1 0 0 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 1 0 0 1
## GCCAATAlt9 0 0 1 0 0 1 0 0 0
## TTAGGCAlt2 0 0 1 1 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0 1
## TTAGGCAlt8 0 0 0 1 0 1 0 0 1
## AAAAGTTSub15 0 0 NA NA NA NA NA NA NA
## ACAAASub1 NA NA 1 NA NA NA NA NA NA
## ACTATSub7 0 0 1 1 0 0 0 0 1
## AGCATSub13 0 0 0 1 0 1 0 0 1
## AGCCCSub11 0 0 1 NA NA NA NA NA NA
## CGATGTSub6 NA NA 1 NA NA NA NA NA NA
## CTAGCSub3 NA NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 0 1 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 1 0 0 0 0 1
## GCCAATSub4 NA NA 1 NA NA NA NA NA NA
## GGACCTASub10 0 0 1 1 0 0 0 0 1
## GTATTSub12 NA NA 0 0 0 0 0 0 1
## TGACCASub2 0 0 1 0 0 0 0 0 0
## ACAGTGCau2 1 1 0 0 0 0 0 0 0
## ACAGTGCau3 1 1 0 0 0 0 0 0 0
## ACTATCau11 1 1 0 0 0 0 1 1 0
## ACTATCau9 1 1 0 0 0 0 0 0 0
## AGCCCCau7 1 1 0 NA NA NA NA NA NA
## ATGAAACCau12 1 1 0 NA NA NA NA 1 0
## CTAGCCau5 1 1 0 1 0 0 1 0 0
## [,713] [,714] [,715] [,716] [,717] [,718] [,719] [,720] [,721]
## ACAAANel3 1 0 0 0 0 0 0 0 0
## ACAGTGNel5 1 0 0 0 0 0 0 0 0
## AGCATNel8 1 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 1 0 0 0 0 0 0 0 0
## CGATGTNel4 1 0 0 0 0 0 0 0 0
## CTAGCNel7 1 0 0 0 0 0 0 0 0
## CTGTANel12 1 0 0 0 0 0 0 0 0
## CTGTANel9 1 0 0 0 0 0 0 0 0
## CTTGANel2 1 0 0 0 0 0 0 0 0
## GGACCTANel11 1 0 0 0 0 0 0 0 0
## GGACCTANel13 1 0 0 0 0 0 0 0 0
## GTATTNel14 1 0 0 0 0 0 0 0 0
## TCACCNel6 1 0 0 1 0 0 0 0 0
## TGACCANel1 1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 1 0 0 0 0 0 0 0 0
## ACAAAAlt11 1 0 0 0 0 0 0 0 1
## ACAGTGAlt3 1 0 0 0 0 0 0 0 0
## AGCCCAlt13 1 0 0 0 0 0 0 0 0
## ATCACGAlt5 1 0 0 0 0 0 0 0 0
## ATCACGAlt7 1 0 0 0 0 0 0 0 1
## CGATGTAlt1 1 0 0 0 0 0 0 0 0
## CTGTAAlt14 1 0 0 0 0 0 0 0 0
## CTTGAAlt10 1 0 0 0 0 0 0 0 0
## GAATTCAAlt15 1 0 0 0 0 0 0 0 0
## GCCAATAlt4 1 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 1 0 0 0 0 0 0 0 0
## TTAGGCAlt6 1 0 0 0 0 0 0 0 0
## TTAGGCAlt8 1 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 NA NA NA NA 0 0 NA
## ACAAASub1 NA 0 0 0 0 0 0 0 NA
## ACTATSub7 1 0 0 0 0 0 0 0 0
## AGCATSub13 1 0 0 0 0 0 0 0 0
## AGCCCSub11 NA 0 0 0 0 0 0 0 0
## CGATGTSub6 NA 0 0 0 0 NA 0 0 NA
## CTAGCSub3 NA 0 0 0 0 NA 0 NA NA
## CTTGCTTSub14 0 0 0 0 0 NA 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 0 0 0 0 0 0 1
## GCCAATSub4 NA 0 NA NA NA NA 0 NA NA
## GGACCTASub10 1 0 0 0 0 0 0 0 0
## GTATTSub12 1 0 0 0 0 NA 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 NA 0
## ACAGTGCau2 0 0 0 0 0 0 0 1 0
## ACAGTGCau3 0 0 0 0 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 0 1 0
## AGCCCCau7 NA 0 0 0 0 0 0 1 0
## ATGAAACCau12 0 0 0 0 0 0 0 1 NA
## CTAGCCau5 0 0 0 0 0 0 0 1 0
## [,722] [,723] [,724] [,725] [,726] [,727] [,728] [,729] [,730]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 NA NA NA 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 NA NA NA 0 0 0
## GGACCTANel11 0 0 0 1 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 NA NA NA 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 1 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 1 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 NA NA NA 0 0 0
## ACAAASub1 NA 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 1
## CGATGTSub6 NA 0 0 NA NA NA 0 0 0
## CTAGCSub3 NA NA 0 NA NA NA 0 0 0
## CTTGCTTSub14 0 0 0 NA NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 NA NA NA 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 NA NA NA NA 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 NA NA NA 0 0 1
## ACAGTGCau3 1 0 0 0 0 0 0 0 1
## ACTATCau11 1 0 0 0 0 0 0 0 1
## ACTATCau9 1 0 0 0 0 0 0 0 1
## AGCCCCau7 0 0 0 0 0 0 0 0 1
## ATGAAACCau12 NA 0 0 NA NA NA 0 0 1
## CTAGCCau5 1 0 0 NA NA NA 0 0 1
## [,731] [,732] [,733] [,734] [,735] [,736] [,737] [,738] [,739]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 NA 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 1 1 1 1 0
## ACTATSub7 0 NA 0 0 0 0 0 0 0
## AGCATSub13 0 NA 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA 0 NA NA 0 0 0 0 0
## CTTGCTTSub14 NA 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA 0 1 0 0 0 0 0 0
## ACAGTGCau3 NA NA 1 0 0 0 0 0 0
## ACTATCau11 0 0 1 0 0 0 0 0 0
## ACTATCau9 1 0 1 0 0 0 0 0 0
## AGCCCCau7 0 0 1 0 0 0 0 0 0
## ATGAAACCau12 NA 0 1 0 0 0 0 0 0
## CTAGCCau5 1 0 1 0 0 0 0 0 0
## [,740] [,741] [,742] [,743] [,744] [,745] [,746] [,747] [,748]
## ACAAANel3 0 0 1 0 NA 0 0 0 1
## ACAGTGNel5 0 0 1 0 1 0 0 0 0
## AGCATNel8 0 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 0 0 0 1 0 0 0 0
## ATGAAACNel15 0 0 0 0 1 0 0 0 0
## CGATGTNel4 0 0 0 0 NA 0 0 0 1
## CTAGCNel7 0 0 0 0 NA 0 0 0 0
## CTGTANel12 0 0 0 0 1 0 0 0 1
## CTGTANel9 0 0 0 0 1 0 0 0 0
## CTTGANel2 0 0 0 0 NA 0 0 0 0
## GGACCTANel11 0 0 0 0 1 0 0 0 0
## GGACCTANel13 0 0 0 0 1 0 0 0 1
## GTATTNel14 0 0 0 0 1 0 1 0 0
## TCACCNel6 0 0 0 0 1 0 0 0 0
## TGACCANel1 0 0 0 0 1 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 0 1 0 0 0 0
## ACAGTGAlt3 0 0 0 0 1 0 0 0 0
## AGCCCAlt13 0 0 0 0 NA 0 0 0 0
## ATCACGAlt5 0 0 0 0 NA NA 0 0 0
## ATCACGAlt7 0 0 0 0 1 0 0 0 0
## CGATGTAlt1 0 0 1 0 1 0 0 0 0
## CTGTAAlt14 0 0 0 0 1 0 0 0 0
## CTTGAAlt10 0 0 0 0 1 0 0 0 0
## GAATTCAAlt15 0 0 0 0 1 0 0 0 0
## GCCAATAlt4 0 0 1 0 1 0 0 0 0
## GCCAATAlt9 0 0 0 0 1 0 0 0 0
## TTAGGCAlt2 0 0 0 0 1 0 0 0 0
## TTAGGCAlt6 0 0 0 0 1 0 0 0 0
## TTAGGCAlt8 0 0 0 0 1 0 0 0 0
## AAAAGTTSub15 0 0 NA NA 1 NA NA NA NA
## ACAAASub1 0 1 0 NA 1 0 NA NA 0
## ACTATSub7 0 0 0 0 NA 0 0 0 0
## AGCATSub13 0 0 0 0 1 0 0 0 0
## AGCCCSub11 0 0 0 NA 1 NA 0 0 1
## CGATGTSub6 0 0 NA 0 1 0 0 0 NA
## CTAGCSub3 0 0 NA NA 1 NA NA NA NA
## CTTGCTTSub14 0 0 NA NA 1 0 NA NA NA
## CTTGCTTSub8 NA NA NA NA 1 NA NA NA NA
## GAATTCASub9 0 0 0 0 1 0 0 0 0
## GCCAATSub4 NA NA NA NA 1 NA NA NA NA
## GGACCTASub10 0 0 0 0 1 0 0 0 0
## GTATTSub12 0 0 NA 0 1 0 NA NA 0
## TGACCASub2 0 0 0 0 1 1 0 0 NA
## ACAGTGCau2 0 0 0 1 0 NA 0 0 NA
## ACAGTGCau3 0 0 0 1 0 0 NA NA 0
## ACTATCau11 0 0 0 1 NA 0 0 0 0
## ACTATCau9 0 0 0 1 NA 0 0 0 0
## AGCCCCau7 0 0 0 1 1 0 0 0 0
## ATGAAACCau12 0 0 0 1 1 0 NA NA NA
## CTAGCCau5 0 0 0 1 0 0 0 0 0
## [,749] [,750] [,751] [,752] [,753] [,754] [,755] [,756] [,757]
## ACAAANel3 0 1 0 0 0 0 0 0 0
## ACAGTGNel5 1 0 0 0 0 0 0 0 0
## AGCATNel8 1 0 0 0 0 0 0 1 0
## ATGAAACNel10 1 1 0 0 0 0 0 0 0
## ATGAAACNel15 1 0 0 0 0 0 0 0 0
## CGATGTNel4 1 0 0 0 0 0 0 0 0
## CTAGCNel7 1 1 0 0 0 0 0 0 0
## CTGTANel12 1 0 0 0 0 0 0 0 0
## CTGTANel9 1 1 0 0 0 0 0 0 0
## CTTGANel2 1 0 0 0 0 0 0 1 0
## GGACCTANel11 1 1 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 1 0 0 0 0 0 0 0 0
## TCACCNel6 1 1 0 0 0 0 0 0 0
## TGACCANel1 1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 1 1 0 0 0 0 0 0 0
## ACAAAAlt11 1 1 0 0 0 0 0 0 0
## ACAGTGAlt3 1 0 0 0 0 0 0 0 0
## AGCCCAlt13 1 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 1 0 0 0 0 0 0 0 0
## CGATGTAlt1 1 0 0 0 0 0 0 0 0
## CTGTAAlt14 1 0 0 0 0 0 0 0 0
## CTTGAAlt10 1 0 0 0 0 0 0 0 0
## GAATTCAAlt15 1 0 0 0 0 0 1 0 0
## GCCAATAlt4 1 0 0 0 0 0 0 0 0
## GCCAATAlt9 1 0 0 0 0 0 0 0 0
## TTAGGCAlt2 1 0 0 0 0 0 0 0 0
## TTAGGCAlt6 1 1 0 0 0 0 0 0 0
## TTAGGCAlt8 1 0 1 1 1 1 0 0 0
## AAAAGTTSub15 NA 0 0 0 0 0 0 0 NA
## ACAAASub1 NA 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 1 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 0 0 0 0 0 0
## CTTGCTTSub14 NA 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 0 0 0 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 1 0 0 0 0 0 0 NA
## ACAGTGCau3 NA 1 0 0 0 0 0 0 0
## ACTATCau11 0 1 0 0 0 0 0 0 0
## ACTATCau9 0 1 0 0 0 0 0 0 0
## AGCCCCau7 0 1 0 0 0 0 0 0 0
## ATGAAACCau12 NA 1 0 0 0 0 0 0 0
## CTAGCCau5 0 1 0 0 0 0 0 0 0
## [,758] [,759] [,760] [,761] [,762] [,763] [,764] [,765] [,766]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 NA NA 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 NA NA 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 NA NA 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 NA NA 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 NA NA NA NA
## ACAAASub1 0 0 0 0 0 NA NA NA NA
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 NA 0 0 0 0 0
## AGCCCSub11 NA NA 0 0 1 0 1 0 1
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 0 0 NA NA NA NA
## CTTGCTTSub14 0 0 0 0 0 0 1 0 1
## CTTGCTTSub8 NA NA 0 0 NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 0 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 1 0 1
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 1 0 0 1 NA NA NA NA
## ACAGTGCau3 0 0 0 0 1 0 0 0 0
## ACTATCau11 0 1 0 0 1 0 0 0 0
## ACTATCau9 0 1 0 0 1 0 0 0 0
## AGCCCCau7 0 0 0 0 1 0 0 0 0
## ATGAAACCau12 0 1 0 0 0 0 0 0 0
## CTAGCCau5 0 1 NA NA 1 0 0 0 0
## [,767] [,768] [,769] [,770] [,771] [,772] [,773] [,774] [,775]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 1 0 0
## GTATTNel14 0 0 0 0 0 0 NA NA 0
## TCACCNel6 0 0 0 0 0 0 1 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 1 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA NA NA
## ACAAASub1 NA 0 0 0 0 NA 0 0 0
## ACTATSub7 0 0 0 0 0 0 1 0 0
## AGCATSub13 0 0 0 0 0 0 1 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 NA
## CGATGTSub6 0 0 0 0 0 NA NA NA 0
## CTAGCSub3 NA NA NA NA NA 0 NA NA 0
## CTTGCTTSub14 0 NA NA NA NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 1 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 NA NA 1
## GTATTSub12 0 0 0 0 0 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 1 0 NA
## ACAGTGCau2 NA 0 0 0 0 0 NA NA 0
## ACAGTGCau3 0 0 0 0 1 0 1 0 0
## ACTATCau11 0 0 0 0 0 0 1 0 0
## ACTATCau9 0 0 0 0 0 0 1 0 0
## AGCCCCau7 0 0 0 0 0 0 1 0 0
## ATGAAACCau12 0 NA NA NA NA NA 1 0 0
## CTAGCCau5 0 0 0 0 0 0 1 0 0
## [,776] [,777] [,778] [,779] [,780] [,781] [,782] [,783] [,784]
## ACAAANel3 0 1 0 0 0 0 0 0 1
## ACAGTGNel5 1 1 1 0 0 0 0 0 0
## AGCATNel8 1 1 1 0 0 0 0 0 1
## ATGAAACNel10 0 1 0 0 0 0 0 0 1
## ATGAAACNel15 1 0 1 0 0 0 0 0 1
## CGATGTNel4 1 0 1 0 0 0 0 0 1
## CTAGCNel7 1 1 0 0 0 0 0 0 1
## CTGTANel12 1 1 1 0 0 0 0 0 0
## CTGTANel9 1 1 1 0 0 0 0 0 1
## CTTGANel2 0 1 0 0 0 0 0 0 1
## GGACCTANel11 0 1 0 0 0 0 0 0 1
## GGACCTANel13 1 1 0 0 0 0 0 0 1
## GTATTNel14 1 0 1 0 0 0 0 0 1
## TCACCNel6 1 0 1 0 0 0 1 0 1
## TGACCANel1 1 1 1 0 0 0 0 0 1
## AAAAGTTAlt12 0 1 0 0 0 0 0 0 0
## ACAAAAlt11 1 0 1 0 1 0 0 0 0
## ACAGTGAlt3 0 1 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 1 0 0 0 0 0
## ATCACGAlt5 0 1 0 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 0 0 0 0 0
## CGATGTAlt1 1 1 0 0 0 0 0 0 0
## CTGTAAlt14 1 0 1 1 0 0 0 0 1
## CTTGAAlt10 1 1 1 0 0 0 0 0 1
## GAATTCAAlt15 1 1 0 1 0 0 0 0 1
## GCCAATAlt4 1 0 0 0 0 0 0 0 0
## GCCAATAlt9 1 1 0 1 0 0 0 0 1
## TTAGGCAlt2 1 1 0 0 0 0 0 0 1
## TTAGGCAlt6 1 0 1 0 0 0 0 0 0
## TTAGGCAlt8 1 1 1 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA 1 0 NA NA NA NA
## ACAAASub1 NA NA NA 1 0 NA 0 NA 1
## ACTATSub7 1 0 1 0 0 0 0 0 1
## AGCATSub13 0 1 0 1 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 NA NA 0 0 0 NA
## CTAGCSub3 NA NA NA NA NA NA 0 NA 1
## CTTGCTTSub14 NA NA NA NA NA NA NA NA 1
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 1 0 0 0 0 0 1
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 1 0 1 1 0 0 0 0 1
## GTATTSub12 0 0 0 NA NA NA 0 NA NA
## TGACCASub2 0 0 0 1 0 0 0 0 1
## ACAGTGCau2 0 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 NA NA NA 0 0 NA 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,785] [,786] [,787] [,788] [,789] [,790] [,791] [,792] [,793]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 1 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 NA NA NA 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 NA 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA 0 NA
## ACAAASub1 NA NA NA NA NA 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 NA
## CGATGTSub6 NA NA 0 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 0 0 NA NA 0 NA
## CTTGCTTSub14 NA 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 0 0 NA NA 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA 0 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 1 0 0 0 0 0 0 NA
## ACAGTGCau3 0 1 0 0 0 1 1 0 1
## ACTATCau11 0 1 1 0 0 1 1 0 1
## ACTATCau9 0 1 1 0 0 1 1 0 1
## AGCCCCau7 0 NA 0 0 0 1 1 0 NA
## ATGAAACCau12 0 1 1 0 0 1 1 NA 1
## CTAGCCau5 0 1 0 0 0 1 1 0 1
## [,794] [,795] [,796] [,797] [,798] [,799] [,800] [,801] [,802]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 1 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 1 0 0 0 0 0 0 0 0
## CTAGCNel7 1 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 1 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 1 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA NA NA
## ACAAASub1 NA NA 1 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 NA NA 0 0 1 0 0 0 0
## CGATGTSub6 0 0 0 0 0 NA NA 0 0
## CTAGCSub3 NA NA 0 NA NA NA NA 0 0
## CTTGCTTSub14 0 0 0 0 0 NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 NA NA NA NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 0 0 NA NA 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 1
## ACAGTGCau2 NA NA 0 0 1 NA NA 0 0
## ACAGTGCau3 0 0 0 NA NA 0 1 0 0
## ACTATCau11 0 0 0 1 1 0 1 0 0
## ACTATCau9 0 0 0 0 1 NA NA 0 0
## AGCCCCau7 NA NA 0 0 1 0 1 0 0
## ATGAAACCau12 0 0 0 NA NA NA NA 0 0
## CTAGCCau5 0 0 0 0 1 0 1 0 0
## [,803] [,804] [,805] [,806] [,807] [,808] [,809] [,810] [,811]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 1 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 1 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 1 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 NA NA 0 0 0 0
## ACAAASub1 NA 0 0 NA 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 NA 0 1 0 0 0
## CTAGCSub3 NA 0 0 0 NA 0 0 0 0
## CTTGCTTSub14 0 0 0 NA NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 NA NA 0 0 NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 NA 0 0 0 0
## TGACCASub2 1 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 1
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 NA 0 0 0 NA NA
## CTAGCCau5 0 0 0 0 1 0 0 0 0
## [,812] [,813] [,814] [,815] [,816] [,817] [,818] [,819] [,820]
## ACAAANel3 0 0 0 0 1 1 0 0 0
## ACAGTGNel5 1 0 0 0 1 1 0 0 0
## AGCATNel8 0 0 0 0 1 1 0 0 0
## ATGAAACNel10 0 0 0 0 1 NA 0 0 0
## ATGAAACNel15 0 0 0 0 1 NA 0 0 0
## CGATGTNel4 1 0 0 0 0 1 0 0 0
## CTAGCNel7 1 0 0 0 1 1 0 0 0
## CTGTANel12 0 0 0 0 0 1 0 0 1
## CTGTANel9 0 0 0 0 0 1 0 0 0
## CTTGANel2 0 1 0 0 1 NA 0 0 1
## GGACCTANel11 1 0 0 1 0 1 1 0 0
## GGACCTANel13 0 0 0 0 0 NA 0 0 0
## GTATTNel14 0 0 0 0 1 0 0 0 1
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 1 0 0 0
## AAAAGTTAlt12 0 0 0 0 1 1 1 0 0
## ACAAAAlt11 0 0 0 1 0 1 0 0 1
## ACAGTGAlt3 0 0 0 0 1 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 1 1 0 0
## ATCACGAlt5 0 0 0 0 1 0 0 0 0
## ATCACGAlt7 0 0 0 0 1 1 1 0 0
## CGATGTAlt1 0 0 0 1 0 1 0 0 1
## CTGTAAlt14 0 0 0 0 1 1 0 0 0
## CTTGAAlt10 0 0 0 0 0 1 1 0 0
## GAATTCAAlt15 1 0 0 1 0 0 0 0 1
## GCCAATAlt4 0 0 0 1 0 1 0 0 1
## GCCAATAlt9 0 0 0 0 1 1 0 0 0
## TTAGGCAlt2 0 0 0 0 0 1 0 0 0
## TTAGGCAlt6 0 0 0 0 1 1 0 0 0
## TTAGGCAlt8 0 0 0 0 0 1 1 0 0
## AAAAGTTSub15 NA 0 NA NA NA NA 0 0 NA
## ACAAASub1 0 0 0 0 1 1 0 0 1
## ACTATSub7 0 0 0 0 1 1 0 0 0
## AGCATSub13 0 0 0 0 1 1 0 0 1
## AGCCCSub11 0 0 0 0 1 NA 0 0 0
## CGATGTSub6 0 0 0 0 1 0 NA NA 0
## CTAGCSub3 NA NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 NA NA NA NA NA 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 1 1 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA 0
## GGACCTASub10 0 0 0 0 1 0 1 0 1
## GTATTSub12 0 NA 0 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 1 0 0 0 NA
## ACAGTGCau2 0 NA 0 0 0 0 0 1 0
## ACAGTGCau3 0 0 0 0 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 0 1 0
## AGCCCCau7 0 0 0 0 0 0 0 1 0
## ATGAAACCau12 0 0 0 0 0 0 0 1 0
## CTAGCCau5 0 0 0 0 0 0 0 1 0
## [,821] [,822] [,823] [,824] [,825] [,826] [,827] [,828] [,829]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 1 0 1 0 0 0 0 0 0
## CTGTANel9 1 0 1 0 0 0 0 0 0
## CTTGANel2 1 0 1 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 1 0 1 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 1 0 1 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 1 0 1 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 1 0 1 0 0 0 0 0 0
## GCCAATAlt4 1 0 1 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA 0 NA NA NA NA
## ACAAASub1 1 0 1 0 0 0 0 NA NA
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 1 1 1 1 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 NA NA
## CTAGCSub3 NA NA NA NA 0 NA NA 0 0
## CTTGCTTSub14 NA NA NA NA 0 NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 0 0 NA NA NA NA
## GGACCTASub10 1 1 1 1 0 0 0 0 0
## GTATTSub12 NA NA NA NA 0 NA NA NA NA
## TGACCASub2 NA NA NA NA 0 NA NA 1 0
## ACAGTGCau2 0 0 0 0 0 NA NA 1 0
## ACAGTGCau3 0 0 0 0 0 NA NA 1 0
## ACTATCau11 0 0 0 0 0 1 1 1 0
## ACTATCau9 0 0 0 0 0 0 1 1 0
## AGCCCCau7 0 0 0 0 0 NA NA NA NA
## ATGAAACCau12 0 0 0 0 1 0 1 NA NA
## CTAGCCau5 0 0 0 0 0 0 1 1 0
## [,830] [,831] [,832] [,833] [,834] [,835] [,836] [,837] [,838]
## ACAAANel3 0 0 0 0 1 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 1 0 0 0 0 0 0 0
## ATGAAACNel10 0 1 0 0 0 0 0 0 0
## ATGAAACNel15 0 1 0 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 0 0
## CTAGCNel7 0 1 0 0 0 0 0 0 1
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 1 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 1 0 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 1 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 1 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 NA NA 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 1 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 1 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA NA NA NA NA NA 0
## ACAAASub1 0 0 0 NA NA NA 0 0 1
## ACTATSub7 0 1 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 1 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 NA NA 0 0 0
## CTAGCSub3 NA NA NA 0 0 0 0 NA 0
## CTTGCTTSub14 NA NA NA NA 0 0 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 NA NA NA NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0 1
## GTATTSub12 NA NA NA NA NA NA 0 NA 0
## TGACCASub2 0 0 0 0 NA NA 0 NA 0
## ACAGTGCau2 0 NA NA 0 0 0 0 NA 0
## ACAGTGCau3 0 0 1 0 0 0 0 NA 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 NA 0
## AGCCCCau7 0 0 NA NA 0 0 0 0 0
## ATGAAACCau12 0 NA NA 0 0 0 0 NA NA
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,839] [,840] [,841] [,842] [,843] [,844] [,845] [,846] [,847]
## ACAAANel3 0 0 0 0 1 0 0 0 0
## ACAGTGNel5 0 1 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 1 0 0 1 0 0 1 0
## ATGAAACNel15 0 1 0 0 1 1 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 1 0
## CTAGCNel7 0 1 1 0 1 0 0 0 0
## CTGTANel12 1 1 0 0 0 0 0 0 0
## CTGTANel9 0 1 0 0 1 0 0 0 0
## CTTGANel2 0 1 0 0 1 0 0 0 0
## GGACCTANel11 0 0 1 0 1 0 0 0 0
## GGACCTANel13 0 0 0 0 1 0 0 0 0
## GTATTNel14 0 0 0 0 1 0 0 0 0
## TCACCNel6 0 1 0 0 1 0 0 0 0
## TGACCANel1 1 1 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 1 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 1 0 0 0 0 0 0
## ACAGTGAlt3 0 1 0 0 1 0 0 0 0
## AGCCCAlt13 0 1 0 0 1 0 0 0 0
## ATCACGAlt5 0 0 1 0 1 0 0 0 0
## ATCACGAlt7 0 1 0 0 1 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 1 0 0 0 0 1 0 0
## CTTGAAlt10 0 1 0 0 1 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0 0
## GCCAATAlt4 0 1 0 0 1 0 0 0 0
## GCCAATAlt9 0 1 0 0 1 0 0 0 0
## TTAGGCAlt2 NA 1 0 0 1 0 0 0 0
## TTAGGCAlt6 0 1 0 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 1 0 0 1 0
## AAAAGTTSub15 NA NA NA NA NA NA 0 0 NA
## ACAAASub1 1 NA NA NA NA NA 0 0 0
## ACTATSub7 NA 0 0 0 1 0 0 0 0
## AGCATSub13 0 1 0 0 1 0 0 1 0
## AGCCCSub11 0 0 0 0 1 0 0 0 0
## CGATGTSub6 0 NA NA NA NA NA 0 0 0
## CTAGCSub3 NA NA NA NA NA NA 0 NA NA
## CTTGCTTSub14 0 NA NA NA 1 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 1 0 0 1 0
## GCCAATSub4 NA NA NA NA NA NA 0 0 NA
## GGACCTASub10 0 1 0 0 1 0 0 1 0
## GTATTSub12 0 1 0 0 NA NA 0 0 NA
## TGACCASub2 0 0 0 0 1 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 NA NA NA 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,848] [,849] [,850] [,851] [,852] [,853] [,854] [,855] [,856]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 1 0 0 0
## ATGAAACNel10 0 0 0 0 0 1 0 0 0
## ATGAAACNel15 0 0 0 0 0 1 0 0 0
## CGATGTNel4 0 0 0 0 0 1 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 1 1 0 0
## CTGTANel9 0 0 0 0 0 1 0 0 0
## CTTGANel2 0 0 0 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 0 1 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 1 0 0 0
## TCACCNel6 0 0 0 0 0 1 0 0 0
## TGACCANel1 0 0 0 0 0 1 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 1 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 1 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 1 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 1 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 1 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 1 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA 1 NA 0 0
## ACAAASub1 0 0 0 0 0 0 NA 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 1 0 0 NA 0 0 0
## CGATGTSub6 NA NA NA NA NA NA 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA 0 0
## CTTGCTTSub14 0 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 1 0 0 0
## GTATTSub12 0 0 0 0 0 1 0 0 0
## TGACCASub2 0 0 0 0 0 1 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 1 0
## [,857] [,858] [,859] [,860] [,861] [,862] [,863] [,864] [,865]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 1 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 NA 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 1 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 NA 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 NA NA NA 0 NA
## ACAAASub1 0 0 0 0 NA NA NA 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 NA NA 0 0 0
## CGATGTSub6 NA 0 0 1 0 0 0 0 0
## CTAGCSub3 NA NA NA 0 0 0 NA 0 0
## CTTGCTTSub14 NA NA NA NA NA NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA NA 0 NA NA NA 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA 0 0 NA 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 NA NA 0 0 0 0 0 0
## ACAGTGCau3 0 0 1 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 NA NA 0 0 0 0 0 0
## AGCCCCau7 0 0 1 0 0 0 0 0 NA
## ATGAAACCau12 0 0 0 NA 0 0 0 0 NA
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,866] [,867] [,868] [,869] [,870] [,871] [,872] [,873] [,874]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 NA 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 1 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 1 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 1 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA 0 0 0 NA 0 0 0
## ACAAASub1 NA 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 NA 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 0 NA 0 NA NA NA NA NA NA
## CTTGCTTSub14 0 NA 0 0 0 NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA 0 0 0 NA 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA 0 0 0 NA NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 NA NA NA NA
## ACAGTGCau3 NA 0 0 0 1 0 1 0 0
## ACTATCau11 0 0 0 0 0 0 1 0 0
## ACTATCau9 0 0 0 0 0 0 1 0 0
## AGCCCCau7 0 0 0 0 0 0 1 0 0
## ATGAAACCau12 0 NA 0 0 0 0 1 0 0
## CTAGCCau5 0 0 0 0 0 0 1 0 0
## [,875] [,876] [,877] [,878] [,879] [,880] [,881] [,882] [,883]
## ACAAANel3 0 0 0 0 0 0 0 0 1
## ACAGTGNel5 0 0 1 0 0 1 0 0 1
## AGCATNel8 0 0 0 0 0 0 0 0 1
## ATGAAACNel10 0 0 0 0 0 0 0 0 1
## ATGAAACNel15 0 1 0 0 0 0 0 0 1
## CGATGTNel4 0 1 0 0 0 0 0 0 NA
## CTAGCNel7 0 0 0 0 0 0 0 0 1
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 1
## CTTGANel2 0 0 0 0 0 0 0 0 1
## GGACCTANel11 0 0 0 0 0 0 0 0 NA
## GGACCTANel13 0 0 0 0 0 0 0 0 1
## GTATTNel14 0 0 0 0 0 0 0 0 1
## TCACCNel6 0 0 0 0 0 0 0 0 1
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 1 0 0 0 0 0 NA
## AGCCCAlt13 0 0 1 0 0 0 0 0 1
## ATCACGAlt5 0 0 1 0 0 0 0 0 1
## ATCACGAlt7 0 0 1 0 0 0 0 0 1
## CGATGTAlt1 0 0 1 0 0 0 0 0 1
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 1
## GAATTCAAlt15 0 0 1 0 0 0 0 0 NA
## GCCAATAlt4 0 0 1 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 1 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0 1
## TTAGGCAlt8 0 0 0 0 0 0 0 0 1
## AAAAGTTSub15 0 0 0 NA 0 NA NA 0 1
## ACAAASub1 0 NA NA 0 0 NA 0 0 1
## ACTATSub7 0 0 1 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 0 NA
## CGATGTSub6 0 0 1 0 0 0 0 0 1
## CTAGCSub3 NA 0 0 0 0 NA 0 NA NA
## CTTGCTTSub14 0 0 0 0 0 NA 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 1
## GCCAATSub4 0 NA NA 0 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 1
## GTATTSub12 NA 0 0 0 0 NA 0 0 1
## TGACCASub2 0 0 0 0 0 0 0 0 NA
## ACAGTGCau2 NA 0 0 0 0 0 0 0 NA
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,884] [,885] [,886] [,887] [,888] [,889] [,890] [,891] [,892]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 1 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 1 0 0 0 0 0
## ATGAAACNel15 0 0 0 1 0 0 0 0 0
## CGATGTNel4 NA 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 1 0 0 0 0 0
## GGACCTANel11 NA 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 1 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 1 0 0 0 0 0
## ACAGTGAlt3 NA 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 1 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 NA 0 0 1 0 0 0 0 0
## GCCAATAlt4 0 0 0 1 0 0 0 0 0
## GCCAATAlt9 0 0 0 1 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 1 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA NA NA 0 0 0 0
## ACAAASub1 0 0 0 NA 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 NA 0 0 1 0 NA NA NA NA
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA NA
## CTTGCTTSub14 NA 0 0 NA NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0 0
## GCCAATSub4 NA 0 0 NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 NA NA NA NA NA
## TGACCASub2 NA 0 0 1 0 0 0 0 0
## ACAGTGCau2 NA NA NA 0 0 0 1 0 0
## ACAGTGCau3 1 0 0 0 0 0 0 0 0
## ACTATCau11 1 0 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 NA 0 0 0 0 0
## AGCCCCau7 1 0 0 0 0 0 0 0 0
## ATGAAACCau12 1 0 0 0 NA 0 0 0 0
## CTAGCCau5 1 0 0 0 0 0 0 0 0
## [,893] [,894] [,895] [,896] [,897] [,898] [,899] [,900] [,901]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 1 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 1 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 1 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 NA NA NA NA NA NA
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 NA NA NA 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 NA NA NA
## CTAGCSub3 NA NA NA 0 0 0 NA NA NA
## CTTGCTTSub14 0 0 0 NA NA NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA NA NA 0 0 0
## TGACCASub2 0 0 0 NA NA NA NA NA NA
## ACAGTGCau2 1 1 0 0 0 0 0 0 1
## ACAGTGCau3 0 0 0 0 0 0 0 0 1
## ACTATCau11 0 0 0 0 0 0 0 0 1
## ACTATCau9 0 0 0 0 0 0 0 0 1
## AGCCCCau7 0 0 0 NA NA NA 0 0 1
## ATGAAACCau12 0 0 0 NA NA NA 0 0 1
## CTAGCCau5 0 0 0 0 0 0 0 0 1
## [,902] [,903] [,904] [,905] [,906] [,907] [,908] [,909] [,910]
## ACAAANel3 1 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 1 0 0 0 0 0 0 0 0
## ATGAAACNel10 1 0 0 0 0 0 0 0 0
## ATGAAACNel15 1 0 0 0 0 1 0 0 0
## CGATGTNel4 1 0 0 0 0 0 0 0 0
## CTAGCNel7 1 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 1 0 0 0 0 1 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 1 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 1 0 0 0 0 1 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 1 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 1 0 0 0 0 1 0 0 0
## AGCCCAlt13 1 1 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 1 0 0 0 0 0 0 0 0
## CTGTAAlt14 1 0 0 0 0 0 0 0 0
## CTTGAAlt10 1 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 1 0 0 0 0 0
## TTAGGCAlt2 0 1 0 0 0 1 0 0 0
## TTAGGCAlt6 1 0 0 0 0 0 0 0 0
## TTAGGCAlt8 1 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA 0 0 NA 0 0 0
## ACAAASub1 1 0 NA 0 0 0 0 0 0
## ACTATSub7 1 0 0 0 0 0 0 0 0
## AGCATSub13 1 0 0 0 0 1 0 0 0
## AGCCCSub11 1 0 0 0 0 1 0 0 0
## CGATGTSub6 NA NA 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA 0 0 NA 0 NA NA
## CTTGCTTSub14 NA NA NA 0 0 NA 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 0 0 0 1 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 1 0 0 0 0 1 0 0 0
## GTATTSub12 1 0 NA NA NA NA 0 0 NA
## TGACCASub2 NA NA 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 NA 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 1 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 NA 0 0 NA 0 NA 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,911] [,912] [,913] [,914] [,915] [,916] [,917] [,918] [,919]
## ACAAANel3 0 1 0 0 0 0 0 1 0
## ACAGTGNel5 0 0 0 0 0 0 0 1 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 1 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 1 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 1 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 1 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 1 1
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0 1
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 NA NA NA NA NA 0 0
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 0 0 0 0 0 1 0
## AGCCCSub11 0 0 NA NA NA NA NA NA 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA 0 NA NA NA NA NA 0 0
## CTTGCTTSub14 NA 0 NA NA NA NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 1 0
## GCCAATSub4 NA 0 0 0 0 0 0 NA 0
## GGACCTASub10 0 0 0 0 0 0 0 1 0
## GTATTSub12 NA 0 0 0 0 0 0 1 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,920] [,921] [,922] [,923] [,924] [,925] [,926] [,927] [,928]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 1 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 1 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA 0 NA NA NA NA NA 0
## ACAAASub1 0 0 0 NA NA 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 NA 0 0 0
## CTAGCSub3 0 NA 0 0 0 NA NA NA 0
## CTTGCTTSub14 0 0 0 NA NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0 0
## GCCAATSub4 0 NA 0 NA NA NA NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 NA NA 0 0 NA 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 1 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 1 0 0 0
## ACTATCau9 0 0 0 0 0 1 0 0 0
## AGCCCCau7 0 0 0 0 0 NA 0 0 0
## ATGAAACCau12 0 0 0 0 0 1 0 NA 0
## CTAGCCau5 0 0 0 0 0 1 0 0 0
## [,929] [,930] [,931] [,932] [,933] [,934] [,935] [,936] [,937]
## ACAAANel3 1 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 1 0 0 0 0 0 0 0 0
## ATGAAACNel10 1 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 1 0 1 0 0 0 0 0 0
## CTAGCNel7 1 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 1 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 1 0 0 0 0 0 0 0 0
## GTATTNel14 1 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 1 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 1 0 0 0 0 0 0 0 0
## CGATGTAlt1 1 0 0 0 0 0 0 0 0
## CTGTAAlt14 1 0 0 0 0 0 0 0 0
## CTTGAAlt10 1 0 0 0 0 0 0 0 0
## GAATTCAAlt15 1 0 0 0 0 0 0 0 0
## GCCAATAlt4 1 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 1 0 0 0 0 0 1 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA 0 NA NA NA
## ACAAASub1 0 0 NA NA NA 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 NA NA 0 0 NA NA 0
## CGATGTSub6 0 0 NA NA 0 0 NA NA 0
## CTAGCSub3 NA NA NA NA NA 0 0 0 0
## CTTGCTTSub14 0 0 0 0 NA 0 NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 0 NA 0 NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 0 0 0 NA NA 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA NA NA NA 0 0 0 0 0
## ACAGTGCau3 0 1 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 1 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 NA 0 NA NA 0
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,938] [,939] [,940] [,941] [,942] [,943] [,944] [,945] [,946]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 1 0
## CTGTANel12 0 0 0 1 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 1 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 NA
## TCACCNel6 0 0 0 0 0 0 0 0 NA
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA NA NA NA NA NA 1
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 NA
## CGATGTSub6 0 0 0 0 0 0 0 NA NA
## CTAGCSub3 NA NA 0 NA NA NA NA NA NA
## CTTGCTTSub14 0 0 NA 0 0 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA NA 0 NA 0 NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 NA 0 0 NA
## ACAGTGCau2 0 0 NA 0 0 NA NA 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 NA
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 NA 0 0 0
## CTAGCCau5 0 0 0 0 0 NA 0 0 0
## [,947] [,948] [,949] [,950] [,951] [,952] [,953] [,954] [,955]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 1 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 NA NA NA NA NA NA 0 0 0
## TCACCNel6 NA NA NA NA NA NA 0 0 0
## TGACCANel1 0 1 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 1 0 0 1 0 0 0 NA NA
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 NA NA NA NA NA NA 0 0 0
## CGATGTSub6 NA NA NA NA NA NA 0 0 0
## CTAGCSub3 NA NA NA NA NA NA 0 NA NA
## CTTGCTTSub14 NA NA NA NA NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 0 0 0 0 NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA NA NA 0 NA NA
## TGACCASub2 NA NA NA NA NA NA 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 1 0
## ACTATCau11 NA NA NA NA NA NA 0 0 0
## ACTATCau9 0 0 1 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 NA NA
## CTAGCCau5 0 0 0 0 0 0 0 0 0
## [,956] [,957] [,958] [,959] [,960] [,961] [,962] [,963] [,964]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 1 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 1 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA NA NA
## ACAAASub1 0 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA 0
## CTTGCTTSub14 0 0 0 0 0 0 NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA NA NA NA NA 0
## TGACCASub2 0 0 0 0 0 0 0 0 NA
## ACAGTGCau2 0 0 0 0 0 0 0 0 NA
## ACAGTGCau3 0 0 1 1 1 0 0 0 1
## ACTATCau11 0 0 0 0 0 0 0 0 1
## ACTATCau9 0 0 0 0 0 0 0 0 1
## AGCCCCau7 0 0 0 0 0 0 0 0 1
## ATGAAACCau12 NA NA NA NA NA NA 0 0 NA
## CTAGCCau5 0 0 0 0 0 0 0 0 1
## [,965] [,966] [,967] [,968] [,969] [,970] [,971] [,972] [,973]
## ACAAANel3 0 0 0 0 0 0 0 0 1
## ACAGTGNel5 1 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 1 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 NA 0 0 0
## CTGTANel9 0 0 1 0 0 NA 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 NA 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 1 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 1 0 0 0 0 NA 0 0 0
## ACAGTGAlt3 0 0 0 0 0 NA 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 1 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 NA 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 NA 0 0 0
## GCCAATAlt4 0 0 0 0 0 NA 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 NA 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 NA NA NA 0 NA NA NA
## ACAAASub1 0 0 0 0 0 0 0 NA 0
## ACTATSub7 0 0 0 0 0 NA 0 0 0
## AGCATSub13 0 0 0 0 0 NA 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 0
## CTAGCSub3 0 0 NA NA NA 0 NA NA NA
## CTTGCTTSub14 NA 0 0 0 NA 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA 0 NA NA NA
## GAATTCASub9 0 0 0 0 0 NA 0 0 0
## GCCAATSub4 NA 0 0 0 NA 0 0 NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 NA 0 0 NA NA
## TGACCASub2 NA 0 0 0 NA 0 0 0 0
## ACAGTGCau2 NA NA 0 0 NA 0 NA 0 0
## ACAGTGCau3 0 1 0 0 0 NA 1 0 0
## ACTATCau11 0 0 0 0 0 NA 1 0 0
## ACTATCau9 0 1 0 0 0 0 1 0 0
## AGCCCCau7 0 0 0 0 0 0 1 0 NA
## ATGAAACCau12 NA 0 0 0 NA 0 1 NA 0
## CTAGCCau5 0 0 0 0 0 0 1 0 0
## [,974] [,975] [,976] [,977] [,978] [,979] [,980] [,981] [,982]
## ACAAANel3 0 1 0 0 1 0 0 0 1
## ACAGTGNel5 0 0 0 0 1 0 0 0 1
## AGCATNel8 0 0 0 0 0 0 0 0 1
## ATGAAACNel10 0 0 0 0 1 0 0 0 1
## ATGAAACNel15 0 NA NA NA 1 0 0 0 1
## CGATGTNel4 0 1 0 0 1 0 1 0 1
## CTAGCNel7 0 1 0 0 1 0 0 0 1
## CTGTANel12 0 0 0 0 1 0 0 0 1
## CTGTANel9 0 0 0 0 1 0 0 0 1
## CTTGANel2 0 0 0 0 1 0 0 0 1
## GGACCTANel11 0 0 0 0 0 0 0 0 1
## GGACCTANel13 0 0 0 0 1 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 1
## TCACCNel6 0 0 0 0 1 0 0 0 1
## TGACCANel1 1 0 0 0 1 0 0 0 1
## AAAAGTTAlt12 0 0 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 0 1 0 0 0 1
## ACAGTGAlt3 0 0 0 0 1 0 0 0 1
## AGCCCAlt13 0 0 0 0 1 0 0 0 1
## ATCACGAlt5 0 1 0 0 0 0 0 NA 1
## ATCACGAlt7 0 0 0 0 0 0 0 0 1
## CGATGTAlt1 0 0 0 0 0 0 0 0 1
## CTGTAAlt14 0 0 0 0 1 0 0 0 1
## CTTGAAlt10 0 0 0 0 1 0 0 0 1
## GAATTCAAlt15 0 0 0 0 1 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 1 0 0 0 1
## TTAGGCAlt6 0 0 0 0 1 0 0 0 1
## TTAGGCAlt8 0 0 0 0 1 0 0 0 1
## AAAAGTTSub15 0 0 0 0 NA NA NA NA NA
## ACAAASub1 0 0 0 0 1 NA 0 NA 1
## ACTATSub7 0 0 0 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 1 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 0 NA
## CGATGTSub6 0 0 0 0 1 NA NA NA NA
## CTAGCSub3 0 0 0 0 0 NA 0 NA NA
## CTTGCTTSub14 0 0 0 0 0 0 1 NA NA
## CTTGCTTSub8 NA 0 0 0 NA NA NA NA NA
## GAATTCASub9 0 0 0 0 1 0 0 0 1
## GCCAATSub4 0 0 0 0 NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 1 0 1
## GTATTSub12 0 0 0 0 0 NA 0 0 1
## TGACCASub2 0 0 0 0 1 0 1 0 1
## ACAGTGCau2 0 0 0 0 0 NA 0 0 0
## ACAGTGCau3 0 0 0 0 0 NA 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0 1
## ACTATCau9 0 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 NA 0 0 NA
## ATGAAACCau12 0 0 0 0 0 NA 0 NA 0
## CTAGCCau5 0 NA NA NA 0 0 0 0 0
## [,983] [,984] [,985] [,986] [,987] [,988] [,989] [,990] [,991]
## ACAAANel3 NA NA NA NA NA NA NA NA 0
## ACAGTGNel5 0 0 0 0 0 0 0 0 0
## AGCATNel8 NA NA NA NA NA NA NA NA 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 0
## CTTGANel2 NA NA NA NA NA NA NA NA 0
## GGACCTANel11 NA NA NA NA NA NA NA NA 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0 0
## ACAAASub1 NA NA NA NA NA NA NA NA 0
## ACTATSub7 NA NA NA NA NA NA NA NA 0
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0 NA
## CTAGCSub3 NA NA NA NA NA NA NA NA 0
## CTTGCTTSub14 0 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA NA
## GGACCTASub10 NA NA NA NA NA NA NA NA 0
## GTATTSub12 0 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0 1
## ACAGTGCau3 0 0 0 0 0 0 0 0 1
## ACTATCau11 NA NA NA NA NA NA NA NA 1
## ACTATCau9 NA NA NA NA NA NA NA NA 1
## AGCCCCau7 0 0 0 0 0 0 0 0 1
## ATGAAACCau12 0 0 0 0 0 0 0 0 1
## CTAGCCau5 1 0 0 0 1 0 0 1 1
## [,992] [,993] [,994] [,995] [,996] [,997] [,998] [,999] [,1000]
## ACAAANel3 0 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 1 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0 1
## CTGTANel12 0 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0 1
## CTTGANel2 0 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 1 0 0 0 0
## TGACCANel1 0 0 0 0 1 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 1 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 1 0 NA NA 0
## AAAAGTTSub15 0 0 0 NA NA 0 0 0 1
## ACAAASub1 0 0 0 0 NA 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 0 0 0 0 0
## AGCCCSub11 0 NA NA 0 0 0 0 0 0
## CGATGTSub6 NA 0 0 0 0 0 0 0 1
## CTAGCSub3 0 0 0 NA NA 0 0 0 NA
## CTTGCTTSub14 0 0 0 NA 0 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 NA NA NA 0 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA NA NA NA NA 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0 0
## ACAGTGCau2 1 0 1 NA 0 1 0 0 0
## ACAGTGCau3 1 0 0 0 0 1 0 0 0
## ACTATCau11 1 0 0 0 0 1 0 0 0
## ACTATCau9 1 0 0 0 0 1 0 0 0
## AGCCCCau7 1 0 1 0 0 1 0 0 0
## ATGAAACCau12 1 0 0 NA 0 1 0 0 0
## CTAGCCau5 1 0 1 0 0 1 0 0 0
## [,1001] [,1002] [,1003] [,1004] [,1005] [,1006] [,1007] [,1008]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 1 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 NA NA
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 NA NA
## TCACCNel6 0 1 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 NA NA
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 NA NA
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 NA NA
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 NA NA
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA 0 0
## ACAAASub1 0 0 0 1 1 0 NA NA
## ACTATSub7 0 1 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 1 0 0 1 0 0 0
## CGATGTSub6 0 0 NA NA NA NA NA NA
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 NA NA 0 0 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 0 0 0 0 0
## TGACCASub2 1 0 0 0 0 0 NA NA
## ACAGTGCau2 1 0 NA NA NA NA NA NA
## ACAGTGCau3 1 0 0 0 1 0 0 1
## ACTATCau11 1 0 1 0 1 0 0 1
## ACTATCau9 1 0 0 1 1 0 0 1
## AGCCCCau7 1 0 1 0 1 0 0 0
## ATGAAACCau12 1 0 NA NA NA NA NA NA
## CTAGCCau5 1 0 1 0 1 0 0 1
## [,1009] [,1010] [,1011] [,1012] [,1013] [,1014] [,1015] [,1016]
## ACAAANel3 0 0 1 0 0 0 0 0
## ACAGTGNel5 0 0 1 0 0 0 0 0
## AGCATNel8 0 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 1 0 0 0 0 0
## ATGAAACNel15 0 0 1 0 0 0 0 0
## CGATGTNel4 NA NA NA NA NA 0 0 0
## CTAGCNel7 0 0 1 0 0 0 0 0
## CTGTANel12 0 0 1 0 0 0 0 0
## CTGTANel9 0 0 1 0 0 0 0 0
## CTTGANel2 0 0 1 0 0 0 0 0
## GGACCTANel11 0 0 1 0 0 0 0 0
## GGACCTANel13 0 0 1 0 0 0 0 0
## GTATTNel14 NA NA NA NA NA 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 0 1 0 0 0 0 0
## ACAAAAlt11 NA NA NA NA NA 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 1 0 0 0 0 0
## ATCACGAlt5 0 0 1 0 0 0 0 0
## ATCACGAlt7 0 0 1 0 0 0 0 0
## CGATGTAlt1 NA NA NA NA NA 1 0 0
## CTGTAAlt14 0 0 1 0 0 0 0 0
## CTTGAAlt10 0 0 1 0 0 0 0 0
## GAATTCAAlt15 NA NA NA NA NA 0 0 0
## GCCAATAlt4 0 0 1 0 0 NA NA 0
## GCCAATAlt9 0 0 1 0 0 0 0 0
## TTAGGCAlt2 0 0 1 0 0 1 0 0
## TTAGGCAlt6 NA NA NA NA NA 0 0 0
## TTAGGCAlt8 0 0 1 0 0 0 0 0
## AAAAGTTSub15 0 0 1 0 0 NA NA NA
## ACAAASub1 NA NA NA NA NA 1 0 0
## ACTATSub7 0 0 1 0 0 0 0 0
## AGCATSub13 0 0 1 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 NA NA NA NA NA 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 NA NA NA NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 0 0 1 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 1 0 0 0 0 0
## GTATTSub12 0 0 1 0 0 1 0 0
## TGACCASub2 NA NA NA NA NA 0 0 0
## ACAGTGCau2 NA NA NA NA NA 0 0 0
## ACAGTGCau3 0 0 1 1 1 0 0 0
## ACTATCau11 0 0 1 1 1 0 0 0
## ACTATCau9 0 0 1 1 1 0 0 0
## AGCCCCau7 0 0 0 0 0 NA NA NA
## ATGAAACCau12 NA NA NA NA NA 1 0 0
## CTAGCCau5 0 0 1 1 1 0 0 1
## [,1017] [,1018] [,1019] [,1020] [,1021] [,1022] [,1023] [,1024]
## ACAAANel3 0 0 0 1 0 0 0 0
## ACAGTGNel5 0 0 0 1 0 0 0 0
## AGCATNel8 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 0 0 1 0 0 0 0
## ATGAAACNel15 0 0 0 1 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 1 0 0 0 0
## CTGTANel12 0 0 0 1 0 0 0 0
## CTGTANel9 0 0 0 1 0 0 0 0
## CTTGANel2 0 0 0 1 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 1 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 NA NA NA NA NA
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 1 1 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 1 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 1 0 0 0 0
## CTGTAAlt14 0 0 1 1 0 0 0 0
## CTTGAAlt10 0 0 0 1 0 0 0 0
## GAATTCAAlt15 0 0 0 1 0 0 0 0
## GCCAATAlt4 0 0 0 NA 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 1 0 0 0 0
## AAAAGTTSub15 0 0 0 NA NA NA NA NA
## ACAAASub1 NA NA NA NA NA NA NA NA
## ACTATSub7 0 0 0 1 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 NA NA NA NA NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0
## GCCAATSub4 0 0 0 NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA NA NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 NA NA NA NA NA
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1025] [,1026] [,1027] [,1028] [,1029] [,1030] [,1031] [,1032]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 NA NA NA 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 1
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 1
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 1
## AAAAGTTSub15 NA NA NA NA 0 0 0 0
## ACAAASub1 NA NA NA 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA 0 0 0 0 0
## CTTGCTTSub14 NA NA NA 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA 0 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA NA NA 0 NA NA NA NA
## ACAGTGCau3 0 0 0 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1033] [,1034] [,1035] [,1036] [,1037] [,1038] [,1039] [,1040]
## ACAAANel3 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 1 1 1 0 0
## ATGAAACNel10 0 0 0 0 1 0 0 0
## ATGAAACNel15 0 0 0 0 0 1 0 0
## CGATGTNel4 0 0 0 1 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 1 0 0 0
## CTGTANel9 0 0 0 0 0 1 0 0
## CTTGANel2 0 0 0 0 0 1 0 0
## GGACCTANel11 0 1 0 0 0 1 0 0
## GGACCTANel13 0 0 0 0 0 1 0 0
## GTATTNel14 0 0 0 0 0 1 0 0
## TCACCNel6 0 0 0 0 0 1 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 1 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 1 0 0 0
## ATCACGAlt5 1 0 0 0 0 1 0 0
## ATCACGAlt7 0 0 0 0 1 1 0 0
## CGATGTAlt1 0 0 0 0 1 0 0 0
## CTGTAAlt14 0 0 0 1 0 1 0 0
## CTTGAAlt10 0 0 0 1 1 1 0 0
## GAATTCAAlt15 0 0 0 0 0 1 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 1 0 1 0 0
## TTAGGCAlt2 0 0 0 0 0 1 0 0
## TTAGGCAlt6 0 0 0 0 1 1 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA 0 NA 0 0
## ACAAASub1 0 0 0 0 NA 0 0 0
## ACTATSub7 0 0 0 0 0 1 0 0
## AGCATSub13 0 0 0 0 0 1 0 0
## AGCCCSub11 0 0 0 0 0 NA 0 0
## CGATGTSub6 0 0 0 0 0 1 0 0
## CTAGCSub3 0 0 0 0 NA NA 0 0
## CTTGCTTSub14 0 0 0 0 NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0
## GCCAATSub4 0 0 0 0 NA NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 1
## ACAGTGCau3 0 0 0 0 0 0 0 1
## ACTATCau11 0 0 0 0 0 0 0 1
## ACTATCau9 0 0 0 0 0 0 0 1
## AGCCCCau7 0 0 0 0 0 0 0 1
## ATGAAACCau12 0 0 0 0 0 0 0 1
## CTAGCCau5 0 0 0 0 0 0 0 1
## [,1041] [,1042] [,1043] [,1044] [,1045] [,1046] [,1047] [,1048]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 0 0 1 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 1 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 1 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 1 0 0 0 0
## TGACCANel1 0 0 0 0 0 1 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 1 0 0 0 0
## ATCACGAlt5 0 0 0 1 0 0 0 0
## ATCACGAlt7 0 0 0 1 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 1 0 0 0 0
## CTTGAAlt10 0 0 0 1 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 1 0 1
## GCCAATAlt9 0 0 0 1 0 0 0 1
## TTAGGCAlt2 0 0 0 1 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 1 0 0
## TTAGGCAlt8 0 0 0 1 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 0 NA NA NA
## ACAAASub1 NA 0 0 0 0 0 NA 0
## ACTATSub7 0 0 0 1 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 NA
## CGATGTSub6 NA 0 0 NA NA 0 NA 0
## CTAGCSub3 0 NA NA 1 0 0 NA NA
## CTTGCTTSub14 NA 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 NA NA NA NA NA
## GGACCTASub10 0 0 0 1 0 0 0 0
## GTATTSub12 NA NA NA NA NA 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 NA NA 0 1 0 0 0
## ACAGTGCau3 NA NA NA 0 1 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 1 0 1 0 0 0
## AGCCCCau7 0 NA NA 0 1 0 0 0
## ATGAAACCau12 NA 0 0 0 0 0 0 0
## CTAGCCau5 0 NA NA 0 1 0 0 0
## [,1049] [,1050] [,1051] [,1052] [,1053] [,1054] [,1055] [,1056]
## ACAAANel3 0 1 0 0 1 0 0 0
## ACAGTGNel5 0 0 0 0 0 1 0 0
## AGCATNel8 0 1 0 0 1 0 0 0
## ATGAAACNel10 0 0 0 0 1 0 0 0
## ATGAAACNel15 0 0 0 0 0 1 0 0
## CGATGTNel4 0 1 0 NA NA NA NA NA
## CTAGCNel7 0 1 0 NA NA NA NA NA
## CTGTANel12 0 0 0 0 1 0 0 0
## CTGTANel9 0 1 0 0 0 1 0 0
## CTTGANel2 0 0 0 0 1 0 0 0
## GGACCTANel11 0 1 0 NA NA NA NA NA
## GGACCTANel13 0 1 0 0 1 0 0 0
## GTATTNel14 0 0 0 0 0 1 0 0
## TCACCNel6 0 0 0 NA NA NA NA NA
## TGACCANel1 0 0 0 NA NA NA NA NA
## AAAAGTTAlt12 0 1 0 1 1 1 0 0
## ACAAAAlt11 0 1 0 0 0 1 0 0
## ACAGTGAlt3 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 1 0 0
## ATCACGAlt5 0 1 0 0 1 1 0 0
## ATCACGAlt7 0 1 0 NA NA NA NA NA
## CGATGTAlt1 0 0 0 0 1 0 0 0
## CTGTAAlt14 0 1 0 0 0 1 0 1
## CTTGAAlt10 0 1 0 NA NA NA NA NA
## GAATTCAAlt15 0 0 0 NA NA NA NA NA
## GCCAATAlt4 0 0 0 NA NA NA NA NA
## GCCAATAlt9 0 0 0 NA NA NA NA NA
## TTAGGCAlt2 0 0 0 0 1 0 0 0
## TTAGGCAlt6 0 1 0 1 0 1 0 0
## TTAGGCAlt8 0 1 0 NA NA NA NA NA
## AAAAGTTSub15 0 NA 0 0 0 1 0 0
## ACAAASub1 0 0 0 NA NA NA NA NA
## ACTATSub7 0 1 0 0 1 0 0 0
## AGCATSub13 0 1 0 0 0 1 0 0
## AGCCCSub11 0 0 0 0 0 1 0 0
## CGATGTSub6 0 1 0 NA NA NA NA NA
## CTAGCSub3 NA NA 0 0 0 1 0 0
## CTTGCTTSub14 0 0 0 0 0 1 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 1 0 0 0
## GCCAATSub4 NA 0 0 NA NA NA NA NA
## GGACCTASub10 0 1 0 0 0 1 0 0
## GTATTSub12 0 0 0 NA NA NA NA NA
## TGACCASub2 0 0 0 NA NA NA NA NA
## ACAGTGCau2 0 0 1 0 1 0 0 0
## ACAGTGCau3 0 0 1 0 0 1 0 0
## ACTATCau11 0 0 1 NA NA NA NA NA
## ACTATCau9 0 0 1 NA NA NA NA NA
## AGCCCCau7 0 0 1 0 0 1 0 0
## ATGAAACCau12 0 0 1 NA NA NA NA NA
## CTAGCCau5 0 0 1 NA NA NA NA NA
## [,1057] [,1058] [,1059] [,1060] [,1061] [,1062] [,1063] [,1064]
## ACAAANel3 0 0 0 0 0 0 0 1
## ACAGTGNel5 1 0 0 0 0 0 1 0
## AGCATNel8 0 0 1 0 1 0 0 1
## ATGAAACNel10 0 0 0 0 0 0 0 1
## ATGAAACNel15 0 0 0 0 0 0 1 0
## CGATGTNel4 NA NA NA NA NA NA NA NA
## CTAGCNel7 NA NA NA NA NA NA NA NA
## CTGTANel12 0 0 0 0 0 0 0 1
## CTGTANel9 0 0 0 0 0 0 1 0
## CTTGANel2 0 0 1 0 1 0 0 1
## GGACCTANel11 NA NA NA NA NA NA NA NA
## GGACCTANel13 0 0 0 0 0 0 0 1
## GTATTNel14 0 0 0 0 0 0 1 0
## TCACCNel6 NA NA NA NA NA NA NA NA
## TGACCANel1 NA NA NA NA NA NA NA NA
## AAAAGTTAlt12 0 0 0 0 1 0 0 1
## ACAAAAlt11 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 1 0 1 0 0 1
## AGCCCAlt13 1 0 0 0 0 0 1 0
## ATCACGAlt5 0 0 0 0 0 0 1 0
## ATCACGAlt7 NA NA NA NA NA NA NA NA
## CGATGTAlt1 0 0 0 0 0 0 0 1
## CTGTAAlt14 1 0 0 0 0 0 0 0
## CTTGAAlt10 NA NA NA NA NA NA NA NA
## GAATTCAAlt15 NA NA NA NA NA NA NA NA
## GCCAATAlt4 NA NA NA NA NA NA NA NA
## GCCAATAlt9 NA NA NA NA NA NA NA NA
## TTAGGCAlt2 0 0 1 0 1 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 1 0
## TTAGGCAlt8 NA NA NA NA NA NA NA NA
## AAAAGTTSub15 0 0 0 0 0 1 1 0
## ACAAASub1 NA NA NA NA NA NA NA NA
## ACTATSub7 0 0 1 0 1 0 0 1
## AGCATSub13 0 0 0 0 0 0 1 0
## AGCCCSub11 0 0 0 0 0 1 1 0
## CGATGTSub6 NA NA NA NA NA NA NA NA
## CTAGCSub3 0 0 0 0 0 1 1 0
## CTTGCTTSub14 0 0 0 0 0 1 1 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 0 1 0 0 1
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 1 1 0
## GTATTSub12 NA NA NA NA NA NA NA NA
## TGACCASub2 NA NA NA NA NA NA NA NA
## ACAGTGCau2 0 0 1 0 1 1 1 1
## ACAGTGCau3 0 0 0 0 0 0 1 0
## ACTATCau11 NA NA NA NA NA NA NA NA
## ACTATCau9 NA NA NA NA NA NA NA NA
## AGCCCCau7 1 0 0 0 0 0 1 0
## ATGAAACCau12 NA NA NA NA NA NA NA NA
## CTAGCCau5 NA NA NA NA NA NA NA NA
## [,1065] [,1066] [,1067] [,1068] [,1069] [,1070] [,1071] [,1072]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 1 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 NA NA 0 0 0 0 0 0
## CTAGCNel7 NA NA 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 1 0 0 0 0 0 0 0
## GGACCTANel11 NA NA 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 NA NA 0 0 0 0 0 0
## TGACCANel1 NA NA 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 1 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 NA NA 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 NA NA 0 0 0 0 0 0
## GAATTCAAlt15 NA NA 0 0 0 0 0 0
## GCCAATAlt4 NA NA 0 0 0 0 0 0
## GCCAATAlt9 NA NA 0 1 0 0 0 0
## TTAGGCAlt2 1 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 NA NA NA NA
## TTAGGCAlt8 NA NA 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 1 0 0 1
## ACAAASub1 NA NA 0 0 0 0 0 0
## ACTATSub7 1 0 1 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 NA NA 0 0 0 0 0 0
## CTAGCSub3 0 0 0 0 1 0 0 1
## CTTGCTTSub14 0 0 0 0 1 0 0 1
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 NA 1 0 0 1
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 0 1 0 0 1
## TGACCASub2 NA NA 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 1 0 0 1
## ACAGTGCau3 0 0 1 0 0 0 0 0
## ACTATCau11 NA NA 1 0 NA NA NA NA
## ACTATCau9 NA NA 1 0 0 0 0 0
## AGCCCCau7 0 0 1 0 0 0 0 0
## ATGAAACCau12 NA NA 1 0 NA NA NA NA
## CTAGCCau5 NA NA 1 0 1 0 0 1
## [,1073] [,1074] [,1075] [,1076] [,1077] [,1078] [,1079] [,1080]
## ACAAANel3 0 0 0 0 0 0 1 1
## ACAGTGNel5 0 1 0 0 0 0 1 1
## AGCATNel8 0 0 0 0 0 0 1 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 1 0 0 0 0 1 0
## CGATGTNel4 0 1 0 0 0 0 1 0
## CTAGCNel7 0 1 0 0 0 0 0 1
## CTGTANel12 0 1 0 0 0 0 1 0
## CTGTANel9 0 0 0 0 0 0 0 1
## CTTGANel2 0 1 0 0 0 0 1 1
## GGACCTANel11 0 1 0 0 0 0 1 1
## GGACCTANel13 0 1 0 0 0 0 0 0
## GTATTNel14 0 1 0 0 0 0 0 1
## TCACCNel6 0 0 0 0 0 0 1 1
## TGACCANel1 0 1 0 0 0 0 0 1
## AAAAGTTAlt12 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 1 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0
## AGCCCAlt13 0 1 0 0 0 0 1 0
## ATCACGAlt5 0 0 0 0 0 0 1 0
## ATCACGAlt7 0 0 0 0 0 0 1 0
## CGATGTAlt1 0 0 0 0 0 0 0 1
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 1 0 0 0 0 1 0
## GAATTCAAlt15 0 1 0 0 0 0 1 0
## GCCAATAlt4 0 1 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 1 1
## TTAGGCAlt2 0 1 0 0 0 0 0 0
## TTAGGCAlt6 NA NA NA NA NA 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 1 1 NA NA NA
## ACAAASub1 0 1 0 0 0 0 1 0
## ACTATSub7 0 1 0 0 0 0 1 0
## AGCATSub13 0 1 0 0 0 0 1 0
## AGCCCSub11 0 1 0 0 0 NA NA NA
## CGATGTSub6 0 1 1 0 0 NA NA NA
## CTAGCSub3 0 1 0 0 0 NA NA NA
## CTTGCTTSub14 0 1 0 0 0 0 1 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 1 0
## GCCAATSub4 0 0 0 1 0 NA NA NA
## GGACCTASub10 0 1 0 0 0 0 0 1
## GTATTSub12 0 0 0 1 1 0 0 0
## TGACCASub2 0 1 0 0 0 0 1 0
## ACAGTGCau2 0 1 0 1 0 0 0 0
## ACAGTGCau3 0 1 0 0 0 0 0 0
## ACTATCau11 NA NA NA NA NA 0 0 0
## ACTATCau9 0 1 1 0 0 0 0 0
## AGCCCCau7 0 1 0 0 0 0 0 0
## ATGAAACCau12 NA NA NA NA NA 0 0 0
## CTAGCCau5 0 1 0 1 1 0 0 0
## [,1081] [,1082] [,1083] [,1084] [,1085] [,1086] [,1087] [,1088]
## ACAAANel3 0 0 0 0 0 0 0 1
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 1
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 1
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 1
## GGACCTANel11 0 0 0 0 0 0 0 1
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 NA NA NA
## TGACCANel1 0 0 0 0 0 NA NA NA
## AAAAGTTAlt12 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 0 NA NA NA
## ACAGTGAlt3 0 0 0 0 0 0 0 1
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 1 0 0 0 NA NA NA
## ATCACGAlt7 0 0 0 0 0 0 0 1
## CGATGTAlt1 0 1 0 0 0 0 0 1
## CTGTAAlt14 0 1 0 0 0 0 0 1
## CTTGAAlt10 0 0 0 0 0 0 0 1
## GAATTCAAlt15 0 0 0 0 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 NA NA NA
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 1
## AAAAGTTSub15 NA NA NA 0 0 NA NA NA
## ACAAASub1 0 0 0 0 0 NA NA NA
## ACTATSub7 0 0 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 0 0 0 NA
## AGCCCSub11 NA NA 0 NA NA NA NA NA
## CGATGTSub6 NA NA 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 NA NA 0 0 1
## CTTGCTTSub14 0 0 0 NA NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 1 0
## GCCAATSub4 0 0 0 NA NA 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 NA NA NA
## TGACCASub2 0 0 0 NA NA 0 0 0
## ACAGTGCau2 NA NA 0 0 0 NA NA NA
## ACAGTGCau3 1 0 0 0 0 0 0 0
## ACTATCau11 1 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 0 0 0 0 1
## AGCCCCau7 1 0 0 0 0 NA NA NA
## ATGAAACCau12 1 0 0 0 0 0 0 0
## CTAGCCau5 1 0 0 0 0 0 0 0
## [,1089] [,1090] [,1091] [,1092] [,1093] [,1094] [,1095] [,1096]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 NA 0 0 0 1
## ACAGTGAlt3 0 0 0 0 0 0 0 1
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 0 0 0 1
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 1
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 1 0 NA NA 0 0 1
## ACAAASub1 0 0 0 0 NA 0 0 1
## ACTATSub7 0 0 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 0 0 0 1
## AGCCCSub11 NA NA NA NA 0 0 0 1
## CGATGTSub6 0 0 0 0 0 0 NA NA
## CTAGCSub3 NA NA NA NA NA 0 NA NA
## CTTGCTTSub14 0 0 0 0 NA 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 1
## GCCAATSub4 NA NA NA NA NA 0 NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA 0 0 0 0 0 1
## TGACCASub2 0 0 0 0 NA 0 0 0
## ACAGTGCau2 NA 0 NA 0 0 0 1 0
## ACAGTGCau3 0 0 0 0 0 0 NA NA
## ACTATCau11 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 NA 0 0 0 1 0
## AGCCCCau7 0 0 0 0 0 0 1 0
## ATGAAACCau12 0 0 0 0 NA 0 1 0
## CTAGCCau5 0 0 0 0 0 0 1 0
## [,1097] [,1098] [,1099] [,1100] [,1101] [,1102] [,1103] [,1104]
## ACAAANel3 0 1 0 0 0 0 0 0
## ACAGTGNel5 0 1 0 0 0 0 0 0
## AGCATNel8 0 1 0 0 0 0 0 0
## ATGAAACNel10 0 1 0 0 0 0 0 0
## ATGAAACNel15 0 1 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 0
## CTAGCNel7 0 1 0 0 0 0 0 0
## CTGTANel12 0 1 0 0 0 0 0 0
## CTGTANel9 0 1 0 0 0 0 0 0
## CTTGANel2 0 1 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 0 0 0 0
## GGACCTANel13 0 1 0 0 0 0 0 0
## GTATTNel14 0 1 0 0 0 0 0 0
## TCACCNel6 0 1 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 1 0 0
## AAAAGTTAlt12 0 1 0 0 0 0 0 0
## ACAAAAlt11 0 1 0 0 0 0 0 0
## ACAGTGAlt3 0 1 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 1 0 0 0 0 0 0
## GCCAATAlt9 0 1 0 0 0 0 0 0
## TTAGGCAlt2 0 1 0 0 0 0 0 0
## TTAGGCAlt6 0 1 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 0 0 0 NA NA
## ACAAASub1 0 1 0 0 0 0 NA 0
## ACTATSub7 0 1 0 0 0 0 0 0
## AGCATSub13 0 1 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 0 0 0 0 NA
## CTTGCTTSub14 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 0 0 0 NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA 1 0 0 0 0 NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 1 0 0 0 0 0 0 0
## ACTATCau11 1 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1105] [,1106] [,1107] [,1108] [,1109] [,1110] [,1111] [,1112]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 1 0 0 0
## CGATGTNel4 0 0 0 0 1 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 1 0 0 0
## CTGTANel9 0 0 0 1 1 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 1 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 1 0 0 0
## AAAAGTTAlt12 0 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 1 0 0 0 0
## ACAGTGAlt3 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 1 0 0 0
## ATCACGAlt5 0 0 0 0 1 0 0 0
## ATCACGAlt7 0 0 0 0 1 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 1 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 0 0 NA 0 0
## ACAAASub1 NA NA 0 0 1 NA 0 0
## ACTATSub7 0 0 0 1 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 1 0 0 0 NA
## CGATGTSub6 NA NA 0 0 1 NA 0 0
## CTAGCSub3 NA NA NA NA NA 0 NA NA
## CTTGCTTSub14 0 0 0 0 NA NA 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 0 1 NA 0 NA
## GGACCTASub10 0 0 0 0 1 0 0 0
## GTATTSub12 NA NA 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 NA 0 0 NA
## ACAGTGCau2 1 1 0 0 0 1 0 NA
## ACAGTGCau3 NA NA 0 0 0 NA 0 0
## ACTATCau11 0 0 0 0 0 1 0 0
## ACTATCau9 1 1 0 0 0 1 0 0
## AGCCCCau7 1 1 0 0 0 NA 0 NA
## ATGAAACCau12 NA NA 1 0 0 NA 0 NA
## CTAGCCau5 1 1 0 0 0 1 0 0
## [,1113] [,1114] [,1115] [,1116] [,1117] [,1118] [,1119] [,1120]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 1 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 1 0
## ATCACGAlt7 0 0 0 0 0 NA NA NA
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 0 0 NA NA NA
## ACAAASub1 NA NA 0 0 0 NA NA NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 NA 0 0 0
## CGATGTSub6 NA NA 0 0 0 NA NA NA
## CTAGCSub3 NA NA NA NA NA 0 0 0
## CTTGCTTSub14 0 0 0 0 NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA 0 NA 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA NA NA 0 NA 0 0 0
## ACAGTGCau3 1 0 NA 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 NA NA 0 0 NA 0 0 0
## ATGAAACCau12 0 0 0 0 NA 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1121] [,1122] [,1123] [,1124] [,1125] [,1126] [,1127] [,1128]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 NA NA NA NA 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA 0 0 0 0
## ACAAASub1 NA NA NA NA 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 NA NA NA 0
## CGATGTSub6 NA NA NA NA NA NA NA 0
## CTAGCSub3 0 0 0 0 NA NA NA NA
## CTTGCTTSub14 NA NA NA NA NA NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 NA NA NA 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 1 0 1 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1129] [,1130] [,1131] [,1132] [,1133] [,1134] [,1135] [,1136]
## ACAAANel3 1 0 0 0 1 1 1 1
## ACAGTGNel5 1 0 0 1 0 0 0 0
## AGCATNel8 1 0 0 0 0 0 0 0
## ATGAAACNel10 1 0 0 0 1 0 0 0
## ATGAAACNel15 1 0 0 0 1 1 1 1
## CGATGTNel4 1 0 0 0 1 1 1 1
## CTAGCNel7 0 0 0 0 1 0 0 0
## CTGTANel12 1 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 1 1 1 1
## CTTGANel2 1 0 0 0 0 0 0 0
## GGACCTANel11 1 0 0 0 1 0 0 0
## GGACCTANel13 1 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 1 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 1 0 0 0
## ACAAAAlt11 1 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 1 0 0 0
## ATCACGAlt7 0 0 NA 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 1 0 0 0 NA NA NA NA
## CTTGAAlt10 1 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 NA NA NA NA
## GCCAATAlt4 1 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 1 1 1 1
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 1 0 0 0 1 1 1 1
## TTAGGCAlt8 1 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA 0 0 1 0 0 0
## ACAAASub1 NA 0 0 0 NA NA NA NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 1 0 0 0
## AGCCCSub11 0 0 0 0 NA NA NA NA
## CGATGTSub6 0 0 0 0 NA NA NA NA
## CTAGCSub3 NA NA 0 0 0 0 0 0
## CTTGCTTSub14 0 NA 1 0 NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 NA NA NA NA
## GCCAATSub4 NA NA 0 0 1 1 1 1
## GGACCTASub10 1 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 1 1 1 1
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 1 0 0 0 0 0
## ACTATCau11 0 0 1 0 0 0 0 0
## ACTATCau9 0 0 1 0 0 0 0 0
## AGCCCCau7 0 0 1 0 0 0 0 0
## ATGAAACCau12 0 0 1 0 NA NA NA NA
## CTAGCCau5 0 0 1 0 0 0 0 0
## [,1137] [,1138] [,1139] [,1140] [,1141] [,1142] [,1143] [,1144]
## ACAAANel3 1 0 0 0 0 0 1 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 1 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 1 0
## ATGAAACNel15 1 0 0 0 0 0 0 0
## CGATGTNel4 1 0 0 0 0 0 0 0
## CTAGCNel7 1 0 0 0 0 0 1 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 1 0 0 0 0 0 1 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 1 0 0 0 0 0 0 0
## GGACCTANel13 1 0 0 0 0 0 1 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 1 0 0 0 0 0 0 0
## TGACCANel1 1 0 0 0 0 0 0 0
## AAAAGTTAlt12 1 0 0 0 1 0 1 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 1 0 0 0 0 0 1 0
## AGCCCAlt13 1 0 0 0 0 0 1 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 NA 0 0 0 0 0 1 0
## CTTGAAlt10 1 0 0 0 0 0 0 0
## GAATTCAAlt15 NA 0 0 0 0 0 1 1
## GCCAATAlt4 1 0 0 0 0 0 0 0
## GCCAATAlt9 1 0 0 0 0 0 0 0
## TTAGGCAlt2 1 0 0 0 0 0 1 0
## TTAGGCAlt6 1 0 0 0 0 0 0 0
## TTAGGCAlt8 1 0 0 0 0 0 1 0
## AAAAGTTSub15 1 0 NA NA NA 0 NA NA
## ACAAASub1 NA 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 NA NA 0 0 0 0 0 0
## CGATGTSub6 NA 0 0 0 0 0 1 NA
## CTAGCSub3 1 NA 0 0 0 NA NA 0
## CTTGCTTSub14 NA 0 0 0 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 NA 0 0 0 0 0 0 0
## GCCAATSub4 1 0 NA NA NA 0 NA NA
## GGACCTASub10 1 0 0 0 0 0 0 0
## GTATTSub12 0 NA 0 0 0 0 NA 0
## TGACCASub2 1 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 NA 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 NA 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1145] [,1146] [,1147] [,1148] [,1149] [,1150] [,1151] [,1152]
## ACAAANel3 0 0 0 1 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 1
## AGCATNel8 0 0 0 1 1 0 0 1
## ATGAAACNel10 0 1 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 1
## CGATGTNel4 0 1 0 0 0 0 0 0
## CTAGCNel7 0 1 0 0 0 0 0 0
## CTGTANel12 0 0 0 1 0 0 0 1
## CTGTANel9 0 0 0 0 0 0 0 1
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 1 0 1 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 1
## TGACCANel1 0 0 0 1 0 0 0 1
## AAAAGTTAlt12 0 1 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 1 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 1 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 1 0 0 0 0
## CGATGTAlt1 0 0 0 1 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 1 0 0 0 0 0 1
## GAATTCAAlt15 0 0 0 1 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 1 0 1 0 0 0 1
## TTAGGCAlt2 0 0 0 1 0 0 0 0
## TTAGGCAlt6 0 1 0 1 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA 0 0 0
## ACAAASub1 0 1 0 0 0 NA NA 0
## ACTATSub7 0 0 0 0 0 0 0 1
## AGCATSub13 0 1 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 1
## CGATGTSub6 0 0 0 0 0 0 0 1
## CTAGCSub3 NA NA NA 0 0 0 0 NA
## CTTGCTTSub14 NA 0 0 0 0 0 0 1
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 1
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 1 0 0 0 0 0 1
## GTATTSub12 NA NA NA 0 0 0 0 1
## TGACCASub2 0 NA NA 0 0 0 0 1
## ACAGTGCau2 NA NA NA 0 0 NA NA NA
## ACAGTGCau3 NA 0 0 0 0 1 0 0
## ACTATCau11 1 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 0 0 0 1 0
## AGCCCCau7 1 0 0 0 0 NA NA 0
## ATGAAACCau12 NA 0 0 0 0 1 0 NA
## CTAGCCau5 1 0 0 0 0 1 0 0
## [,1153] [,1154] [,1155] [,1156] [,1157] [,1158] [,1159] [,1160]
## ACAAANel3 0 0 0 0 0 NA NA 0
## ACAGTGNel5 0 1 0 0 0 NA NA 1
## AGCATNel8 0 1 0 0 0 0 1 0
## ATGAAACNel10 0 0 0 0 0 0 1 0
## ATGAAACNel15 0 0 0 0 0 0 1 0
## CGATGTNel4 0 0 0 0 0 0 1 1
## CTAGCNel7 0 0 0 0 0 NA NA 1
## CTGTANel12 0 0 0 0 0 0 1 0
## CTGTANel9 0 0 0 0 0 0 1 0
## CTTGANel2 0 0 0 0 0 0 1 0
## GGACCTANel11 0 0 0 0 0 0 1 1
## GGACCTANel13 0 0 0 0 0 NA NA 0
## GTATTNel14 0 0 0 0 0 0 1 0
## TCACCNel6 0 0 0 0 0 NA NA 0
## TGACCANel1 0 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 1 0
## ACAAAAlt11 0 0 0 0 0 NA NA 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 1 0
## ATCACGAlt7 0 0 0 0 0 0 1 0
## CGATGTAlt1 0 0 0 0 0 0 1 0
## CTGTAAlt14 0 0 0 0 0 0 1 0
## CTTGAAlt10 0 0 0 0 0 NA NA 0
## GAATTCAAlt15 0 0 0 0 0 0 1 1
## GCCAATAlt4 0 0 0 0 0 0 1 0
## GCCAATAlt9 0 0 0 0 0 0 1 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0
## TTAGGCAlt8 0 0 0 0 0 NA NA 0
## AAAAGTTSub15 0 0 0 0 0 0 1 0
## ACAAASub1 0 0 0 0 0 0 1 0
## ACTATSub7 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 0 0 0 0 1 0
## AGCCCSub11 0 0 0 0 0 0 1 0
## CGATGTSub6 0 0 0 0 0 0 1 0
## CTAGCSub3 NA NA 0 0 0 NA NA NA
## CTTGCTTSub14 0 0 0 0 0 NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 1 NA
## GCCAATSub4 NA NA 0 0 0 NA NA NA
## GGACCTASub10 0 0 0 0 0 0 1 0
## GTATTSub12 0 0 0 0 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 1 NA
## ACAGTGCau2 NA NA 0 0 0 0 1 0
## ACAGTGCau3 1 0 0 0 0 0 1 0
## ACTATCau11 1 0 0 0 0 0 1 0
## ACTATCau9 1 0 0 0 0 0 1 0
## AGCCCCau7 1 0 0 0 0 0 1 0
## ATGAAACCau12 NA NA 0 0 0 NA NA 0
## CTAGCCau5 1 0 0 0 0 0 1 0
## [,1161] [,1162] [,1163] [,1164] [,1165] [,1166] [,1167] [,1168]
## ACAAANel3 0 0 0 0 0 0 0 1
## ACAGTGNel5 0 0 0 0 0 0 0 1
## AGCATNel8 0 0 0 0 0 0 0 1
## ATGAAACNel10 0 0 0 0 0 0 1 0
## ATGAAACNel15 0 0 0 0 0 0 0 1
## CGATGTNel4 0 0 0 0 0 0 1 1
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 1
## CTGTANel9 0 0 0 0 0 0 1 1
## CTTGANel2 0 0 0 0 0 0 1 1
## GGACCTANel11 0 0 0 0 0 0 0 1
## GGACCTANel13 0 0 0 0 0 0 1 0
## GTATTNel14 0 0 0 0 0 0 0 1
## TCACCNel6 0 0 0 0 0 0 1 1
## TGACCANel1 0 0 0 0 0 0 1 1
## AAAAGTTAlt12 0 0 0 0 0 0 1 1
## ACAAAAlt11 0 0 0 0 0 0 0 1
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 1
## ATCACGAlt5 0 0 0 0 0 0 1 0
## ATCACGAlt7 0 0 0 0 0 0 0 1
## CGATGTAlt1 0 0 0 0 0 0 0 1
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 1
## GCCAATAlt4 1 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 1
## AAAAGTTSub15 NA NA NA NA 0 NA NA NA
## ACAAASub1 NA NA NA 0 0 NA NA NA
## ACTATSub7 0 0 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 0 1 0 1
## AGCCCSub11 0 0 0 0 0 0 NA NA
## CGATGTSub6 0 0 0 0 0 NA 0 0
## CTAGCSub3 NA NA NA NA NA 0 NA NA
## CTTGCTTSub14 NA NA NA NA 0 NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 1 0 0
## GTATTSub12 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 1 0 1
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 NA 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 NA
## ACTATCau9 0 0 0 0 1 0 0 0
## AGCCCCau7 0 0 0 0 1 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 NA
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1169] [,1170] [,1171] [,1172] [,1173] [,1174] [,1175] [,1176]
## ACAAANel3 1 0 0 0 1 0 1 1
## ACAGTGNel5 1 0 0 0 1 0 1 NA
## AGCATNel8 0 0 0 0 1 0 0 0
## ATGAAACNel10 0 0 0 0 1 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 1 0
## CGATGTNel4 0 0 0 0 1 0 0 1
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 1 0 0 0
## CTGTANel9 0 0 0 0 1 0 0 1
## CTTGANel2 0 0 0 0 1 0 0 0
## GGACCTANel11 0 1 0 0 0 0 0 1
## GGACCTANel13 0 0 0 0 1 0 1 1
## GTATTNel14 1 0 0 0 1 0 0 NA
## TCACCNel6 0 0 0 0 1 0 1 1
## TGACCANel1 0 0 0 0 1 0 0 1
## AAAAGTTAlt12 0 0 0 0 1 0 0 0
## ACAAAAlt11 0 0 0 0 1 0 0 1
## ACAGTGAlt3 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 1 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 1 NA
## ATCACGAlt7 0 0 0 0 1 0 0 NA
## CGATGTAlt1 0 0 0 0 1 0 1 NA
## CTGTAAlt14 0 0 0 0 0 0 1 NA
## CTTGAAlt10 0 0 0 0 1 0 0 1
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 1 NA
## GCCAATAlt9 0 0 0 0 1 0 1 NA
## TTAGGCAlt2 0 0 0 0 1 0 1 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0
## TTAGGCAlt8 0 0 0 0 1 0 0 0
## AAAAGTTSub15 NA NA 0 0 NA 0 0 NA
## ACAAASub1 NA NA 0 0 0 NA NA NA
## ACTATSub7 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 0 0 0 0 1 0
## AGCCCSub11 NA NA 0 0 0 0 0 0
## CGATGTSub6 0 0 NA NA 0 NA NA 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 0 NA NA 0 NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 1 0
## GCCAATSub4 NA NA 0 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 NA NA NA NA
## TGACCASub2 1 0 NA NA 0 0 0 0
## ACAGTGCau2 0 0 NA NA NA NA NA NA
## ACAGTGCau3 0 0 0 1 0 0 0 0
## ACTATCau11 NA NA 0 1 0 0 0 0
## ACTATCau9 0 0 0 1 0 0 0 0
## AGCCCCau7 0 0 0 1 0 0 0 0
## ATGAAACCau12 NA NA 0 1 0 0 0 0
## CTAGCCau5 0 0 0 1 0 0 0 0
## [,1177] [,1178] [,1179] [,1180] [,1181] [,1182] [,1183] [,1184]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 NA 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 NA 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 NA 0 0 0 0 0 0 0
## ATCACGAlt7 NA 0 0 0 0 0 0 0
## CGATGTAlt1 NA 0 0 0 0 0 0 0
## CTGTAAlt14 NA 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 NA 0 0 0 0 0 0 0
## GCCAATAlt9 NA 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 NA NA NA NA NA NA
## ACAAASub1 NA 0 0 NA 0 NA NA NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 NA 0 0 0
## CTAGCSub3 NA 0 NA 0 0 NA NA NA
## CTTGCTTSub14 0 0 0 0 0 NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 NA NA NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA 0 0 0 NA 0 1 NA
## ACAGTGCau3 0 0 0 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 1 1
## AGCCCCau7 0 0 0 0 0 0 1 0
## ATGAAACCau12 0 0 0 0 0 0 1 0
## CTAGCCau5 0 0 0 0 0 0 1 0
## [,1185] [,1186] [,1187] [,1188] [,1189] [,1190] [,1191] [,1192]
## ACAAANel3 0 0 1 0 0 1 0 0
## ACAGTGNel5 0 1 1 0 0 1 0 1
## AGCATNel8 0 0 1 0 1 1 0 0
## ATGAAACNel10 0 0 1 0 0 1 0 0
## ATGAAACNel15 0 0 1 0 0 1 0 0
## CGATGTNel4 0 1 1 0 0 1 0 0
## CTAGCNel7 0 0 1 0 0 1 0 0
## CTGTANel12 0 0 1 0 0 1 0 0
## CTGTANel9 0 0 1 0 0 0 0 0
## CTTGANel2 0 0 1 0 0 1 0 0
## GGACCTANel11 0 0 1 0 0 1 0 0
## GGACCTANel13 0 0 1 0 0 1 0 0
## GTATTNel14 0 1 1 0 0 1 0 0
## TCACCNel6 0 0 1 0 0 1 0 0
## TGACCANel1 0 0 1 0 0 1 0 0
## AAAAGTTAlt12 0 1 1 0 0 1 0 0
## ACAAAAlt11 0 0 1 0 0 1 0 0
## ACAGTGAlt3 0 1 1 0 0 0 0 0
## AGCCCAlt13 0 0 1 0 0 1 0 0
## ATCACGAlt5 0 0 1 0 0 0 0 0
## ATCACGAlt7 0 0 1 0 0 1 0 0
## CGATGTAlt1 0 0 1 0 0 1 0 0
## CTGTAAlt14 0 0 1 0 0 1 0 0
## CTTGAAlt10 0 0 1 0 0 1 1 0
## GAATTCAAlt15 0 1 1 0 0 1 0 0
## GCCAATAlt4 0 0 1 0 0 1 0 0
## GCCAATAlt9 0 0 1 0 0 1 0 0
## TTAGGCAlt2 0 0 1 0 0 1 0 0
## TTAGGCAlt6 0 0 1 0 0 1 0 0
## TTAGGCAlt8 0 1 1 0 0 1 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA NA
## ACAAASub1 0 NA NA NA NA NA 0 0
## ACTATSub7 0 1 1 0 0 1 0 0
## AGCATSub13 0 0 1 0 0 0 0 0
## AGCCCSub11 0 1 1 0 0 1 0 0
## CGATGTSub6 0 0 NA NA NA NA 0 0
## CTAGCSub3 NA NA NA 0 0 0 0 NA
## CTTGCTTSub14 0 1 NA NA NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 0 0 1 0 0
## GCCAATSub4 NA NA NA NA NA NA 0 NA
## GGACCTASub10 0 1 1 0 0 0 0 0
## GTATTSub12 0 NA 1 0 0 1 0 NA
## TGACCASub2 0 1 1 0 0 1 0 0
## ACAGTGCau2 NA 0 0 1 0 0 0 0
## ACAGTGCau3 0 0 0 1 0 0 0 0
## ACTATCau11 0 0 0 1 0 0 0 0
## ACTATCau9 0 0 0 1 0 0 0 0
## AGCCCCau7 NA 0 0 1 0 0 0 0
## ATGAAACCau12 NA 0 0 1 0 0 0 0
## CTAGCCau5 1 0 0 1 0 0 0 0
## [,1193] [,1194] [,1195] [,1196] [,1197] [,1198] [,1199] [,1200]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 1 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 1 0
## CGATGTNel4 0 0 0 0 0 1 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 1 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 1 0 0
## GGACCTANel13 1 1 0 0 0 1 1 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 1 1 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 1 0 0
## GAATTCAAlt15 0 0 0 0 0 1 0 0
## GCCAATAlt4 1 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 1 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 1
## TTAGGCAlt8 0 0 0 0 0 0 1 0
## AAAAGTTSub15 NA NA NA 0 0 0 1 0
## ACAAASub1 NA 0 0 NA NA NA NA NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 1 0
## AGCCCSub11 0 0 0 NA NA NA 0 0
## CGATGTSub6 0 NA NA 0 0 0 0 0
## CTAGCSub3 NA NA NA 0 0 0 NA NA
## CTTGCTTSub14 NA 0 0 NA NA NA 1 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 1 0
## GCCAATSub4 NA 0 0 0 0 0 1 0
## GGACCTASub10 0 0 0 0 0 0 1 0
## GTATTSub12 NA 0 0 NA NA NA 1 0
## TGACCASub2 0 0 0 NA NA NA 1 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 1 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 NA NA 0 0 0 0 0
## ATGAAACCau12 0 NA NA 0 0 0 0 0
## CTAGCCau5 0 NA NA 0 0 0 0 0
## [,1201] [,1202] [,1203] [,1204] [,1205] [,1206] [,1207] [,1208]
## ACAAANel3 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 1 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 1 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA 0 0
## CTTGCTTSub14 NA NA 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA NA NA 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 0 0 0 0 0
## AGCCCCau7 NA NA 0 0 0 0 0 0
## ATGAAACCau12 NA NA 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1209] [,1210] [,1211] [,1212] [,1213] [,1214] [,1215] [,1216]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 1 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 1 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 1 0
## AAAAGTTSub15 0 0 NA NA NA NA 0 0
## ACAAASub1 0 0 0 0 NA NA 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 NA NA 0 0
## CTAGCSub3 0 0 NA NA NA NA 0 0
## CTTGCTTSub14 0 0 NA 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 NA NA NA NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 NA NA NA 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 NA 0 NA NA 0 0
## ACAGTGCau3 0 0 0 0 1 1 0 1
## ACTATCau11 0 0 0 1 1 1 0 0
## ACTATCau9 0 0 0 0 1 1 0 0
## AGCCCCau7 0 0 0 0 1 1 0 0
## ATGAAACCau12 0 0 NA 0 1 1 0 0
## CTAGCCau5 0 0 1 0 1 1 0 0
## [,1217] [,1218] [,1219] [,1220] [,1221] [,1222] [,1223] [,1224]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 1 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 1 1 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 1 0 0
## CTAGCNel7 0 1 0 0 0 0 0 0
## CTGTANel12 0 1 0 0 0 NA NA 0
## CTGTANel9 0 1 0 0 0 0 0 0
## CTTGANel2 0 1 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 0 0 0 0
## GGACCTANel13 0 1 0 0 0 0 0 0
## GTATTNel14 0 1 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 1 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 1 0 0
## CTGTAAlt14 0 1 0 0 0 0 0 0
## CTTGAAlt10 0 1 0 0 0 1 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0
## GCCAATAlt4 0 1 0 0 0 0 0 0
## GCCAATAlt9 0 1 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 1 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 1 0 0
## AAAAGTTSub15 0 0 NA 0 0 0 0 0
## ACAAASub1 0 0 NA 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 NA 0 0 0 0 NA
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 0 0 0 0 0 NA NA 0
## CTTGCTTSub14 0 0 NA 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 0
## GCCAATSub4 0 0 NA 0 0 NA NA 0
## GGACCTASub10 0 1 0 0 0 0 0 1
## GTATTSub12 NA NA 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 1 0 0
## ACAGTGCau2 0 0 0 0 0 NA NA 1
## ACAGTGCau3 1 0 0 0 0 0 0 1
## ACTATCau11 0 0 0 0 0 0 0 1
## ACTATCau9 0 0 0 0 0 0 0 1
## AGCCCCau7 0 0 0 0 0 0 0 NA
## ATGAAACCau12 0 0 0 0 0 0 0 1
## CTAGCCau5 0 0 0 0 0 0 0 1
## [,1225] [,1226] [,1227] [,1228] [,1229] [,1230] [,1231] [,1232]
## ACAAANel3 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 1 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 1 0
## CGATGTNel4 0 0 0 0 0 1 1 0
## CTAGCNel7 0 0 0 0 0 1 0 0
## CTGTANel12 0 0 0 0 0 1 0 0
## CTGTANel9 0 0 0 0 0 1 1 0
## CTTGANel2 0 0 0 0 0 1 0 0
## GGACCTANel11 0 0 0 0 0 1 1 0
## GGACCTANel13 0 0 0 0 0 0 1 0
## GTATTNel14 0 1 0 0 0 0 1 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 1 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 1 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 1 0 1 0 0
## CTGTAAlt14 0 0 0 0 0 1 0 0
## CTTGAAlt10 0 0 0 0 0 1 0 0
## GAATTCAAlt15 0 0 0 1 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 1 0
## AAAAGTTSub15 0 NA NA 0 NA NA NA 0
## ACAAASub1 0 0 0 0 NA NA NA 0
## ACTATSub7 0 0 0 0 0 1 0 0
## AGCATSub13 0 0 0 0 0 1 0 0
## AGCCCSub11 NA 0 0 0 0 0 NA 0
## CGATGTSub6 0 0 0 0 NA NA NA 0
## CTAGCSub3 0 0 0 0 0 1 NA 0
## CTTGCTTSub14 0 0 0 NA NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0
## GCCAATSub4 0 0 0 0 NA NA 0 0
## GGACCTASub10 1 0 0 0 0 1 0 0
## GTATTSub12 0 NA NA 0 0 1 NA NA
## TGACCASub2 0 0 0 0 0 1 0 0
## ACAGTGCau2 1 0 0 0 0 0 0 0
## ACAGTGCau3 1 0 0 0 0 0 0 0
## ACTATCau11 1 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 0 0 0 0 0
## AGCCCCau7 NA 0 0 0 0 0 0 0
## ATGAAACCau12 1 0 0 0 0 0 0 0
## CTAGCCau5 1 0 1 0 0 0 0 0
## [,1233] [,1234] [,1235] [,1236] [,1237] [,1238] [,1239] [,1240]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 1 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 NA NA NA NA NA NA NA
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 1 0 0 1
## TCACCNel6 0 NA NA NA NA NA NA NA
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 NA NA NA NA NA NA NA
## CTGTAAlt14 0 NA NA NA NA NA NA NA
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 NA NA NA NA NA NA NA
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 1 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 NA NA NA NA NA NA NA
## AAAAGTTSub15 0 0 0 1 1 0 0 1
## ACAAASub1 0 NA NA NA NA NA NA NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 NA 0 0 1 1 0 0 0
## CGATGTSub6 0 0 0 1 1 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 NA 0 0 1 1 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 1 1 0 0 0
## GTATTSub12 NA 0 0 1 1 0 0 0
## TGACCASub2 0 0 0 1 1 0 0 0
## ACAGTGCau2 NA 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 1 0 0 1
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 NA NA NA NA NA NA NA
## ATGAAACCau12 0 0 0 1 1 0 0 0
## CTAGCCau5 0 NA NA 0 1 0 0 NA
## [,1241] [,1242] [,1243] [,1244] [,1245] [,1246] [,1247] [,1248]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 1 0 0
## AGCATNel8 0 0 0 0 0 0 1 0
## ATGAAACNel10 0 0 0 0 0 0 1 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 1 0
## CTGTANel12 0 0 NA 0 0 0 0 0
## CTGTANel9 NA NA 0 0 0 0 1 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 NA NA 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 NA NA 0 0 0 0 0 0
## CTGTAAlt14 NA NA 0 0 1 0 1 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 NA NA 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 NA NA 0 0 0 0 0 0
## AAAAGTTSub15 0 0 NA 0 0 0 NA 0
## ACAAASub1 NA NA 0 NA NA NA NA 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 NA 0
## CGATGTSub6 0 0 0 NA NA NA 1 0
## CTAGCSub3 NA NA 0 NA NA NA NA 0
## CTTGCTTSub14 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 NA NA NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 1 0
## ACAGTGCau2 0 0 1 1 0 0 0 1
## ACAGTGCau3 0 0 1 1 0 0 0 1
## ACTATCau11 0 0 1 1 0 0 0 1
## ACTATCau9 0 0 1 1 0 0 0 1
## AGCCCCau7 NA NA 1 1 0 0 0 1
## ATGAAACCau12 0 0 1 1 0 0 0 1
## CTAGCCau5 0 0 1 1 0 0 0 1
## [,1249] [,1250] [,1251] [,1252] [,1253] [,1254] [,1255] [,1256]
## ACAAANel3 0 1 0 0 0 0 1 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 1 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 1 0 0
## CTGTANel9 0 0 0 1 0 0 1 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 1 0
## GGACCTANel13 0 0 1 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 1 0
## ATCACGAlt5 0 0 0 0 0 0 1 0
## ATCACGAlt7 0 0 0 0 0 0 1 0
## CGATGTAlt1 0 0 0 0 0 0 1 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0
## TTAGGCAlt8 0 0 0 0 0 0 1 0
## AAAAGTTSub15 0 0 NA NA NA 0 0 0
## ACAAASub1 0 0 0 0 0 NA 0 0
## ACTATSub7 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 NA NA NA 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 0 0 NA NA NA 0 0 0
## CTTGCTTSub14 0 0 NA NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA NA NA NA 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 NA NA NA 0 0 0
## ACAGTGCau3 0 0 0 1 0 0 0 0
## ACTATCau11 0 0 0 1 0 0 0 0
## ACTATCau9 0 0 0 1 0 0 0 0
## AGCCCCau7 0 0 0 1 0 0 0 0
## ATGAAACCau12 0 0 NA NA NA 0 NA NA
## CTAGCCau5 1 0 0 1 0 0 0 0
## [,1257] [,1258] [,1259] [,1260] [,1261] [,1262] [,1263] [,1264]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 1 1 1 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 1 1 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 1 1 1 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 1 1 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 0 0 0 0 0 0 0 0
## CTTGCTTSub14 0 0 0 0 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 0 0 0 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 1
## ACAGTGCau2 NA NA 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 0 0 0 0 0
## AGCCCCau7 1 0 0 0 0 0 0 0
## ATGAAACCau12 NA NA 0 0 0 0 0 0
## CTAGCCau5 1 0 0 1 0 0 0 0
## [,1265] [,1266] [,1267] [,1268] [,1269] [,1270] [,1271] [,1272]
## ACAAANel3 0 1 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 1 1 0 0 0 0 1
## ATGAAACNel15 0 0 1 0 0 0 0 1
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 1 0 0 0 0 1
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 1 0 0 0 0 1
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 1 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 1
## AGCCCAlt13 0 0 0 1 0 0 0 0
## ATCACGAlt5 0 1 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 1 0 0 0 0 1
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 1 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 0 0 0 0
## ACAAASub1 NA 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA 0 0 0 0 0 0 0
## CTTGCTTSub14 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 0 0 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 0 0 0 0
## TGACCASub2 0 0 1 0 0 0 0 1
## ACAGTGCau2 NA 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 NA 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1273] [,1274] [,1275] [,1276] [,1277] [,1278] [,1279] [,1280]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 1 0 0 0 1 0 0
## ATGAAACNel10 1 0 0 0 0 0 0 0
## ATGAAACNel15 1 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 1 0 0 0 0 0 0 NA
## CTGTANel12 0 0 0 0 0 0 0 NA
## CTGTANel9 1 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 1 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 1 0 0 0 0 0 NA
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 1 0 0 0 0 0 0 NA
## AGCCCAlt13 0 0 0 0 0 0 0 NA
## ATCACGAlt5 0 1 0 0 0 1 0 NA
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 1 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 1 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 1 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 NA
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 NA 0
## ACAAASub1 0 0 0 0 0 0 NA 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 1 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 NA 0
## CTAGCSub3 0 NA NA NA NA NA NA NA
## CTTGCTTSub14 0 0 0 0 0 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA NA NA NA NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA NA NA NA NA 0 0
## TGACCASub2 1 NA NA NA NA NA 0 0
## ACAGTGCau2 0 NA NA NA NA NA 0 0
## ACAGTGCau3 0 1 1 0 0 0 0 0
## ACTATCau11 0 1 1 0 0 0 0 NA
## ACTATCau9 0 1 1 0 0 0 0 0
## AGCCCCau7 0 NA NA NA NA NA NA 0
## ATGAAACCau12 0 1 1 0 0 0 0 0
## CTAGCCau5 0 1 1 0 0 0 0 0
## [,1281] [,1282] [,1283] [,1284] [,1285] [,1286] [,1287] [,1288]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 NA NA NA NA NA NA NA NA
## CTGTANel12 NA NA NA NA NA NA NA NA
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 NA NA NA NA NA NA NA NA
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 NA NA NA NA NA NA NA NA
## AGCCCAlt13 NA NA NA NA NA NA NA NA
## ATCACGAlt5 NA NA NA NA NA NA NA NA
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 NA NA NA NA NA NA NA NA
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 0 0 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 NA NA NA NA NA NA NA NA
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 1 0 1 0 0
## [,1289] [,1290] [,1291] [,1292] [,1293] [,1294] [,1295] [,1296]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 1 0
## ATGAAACNel15 0 0 0 0 0 0 1 0
## CGATGTNel4 0 0 0 0 0 0 1 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 1 1 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 1 0
## GGACCTANel11 0 0 0 0 0 1 0 1
## GGACCTANel13 0 0 0 0 0 0 1 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 1 0 0
## TGACCANel1 0 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 1 0 0 1 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 1 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 NA 0 0 0
## AAAAGTTSub15 0 NA NA NA NA 0 0 0
## ACAAASub1 0 NA NA 0 0 0 0 0
## ACTATSub7 0 1 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 NA 0 NA 0 0 0 0 0
## CGATGTSub6 0 0 NA NA 0 0 0 0
## CTAGCSub3 NA NA 0 NA NA 0 NA NA
## CTTGCTTSub14 NA NA 0 0 0 1 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA 0 NA NA
## GGACCTASub10 0 1 0 0 0 0 0 0
## GTATTSub12 0 NA NA NA 0 0 NA NA
## TGACCASub2 0 1 0 0 0 1 0 0
## ACAGTGCau2 0 0 0 1 NA 0 0 0
## ACAGTGCau3 0 0 0 1 0 0 0 0
## ACTATCau11 0 0 0 1 0 0 0 0
## ACTATCau9 0 0 0 1 0 0 0 0
## AGCCCCau7 0 0 NA 1 1 0 0 0
## ATGAAACCau12 0 0 NA NA 1 0 NA NA
## CTAGCCau5 0 0 0 1 0 0 0 0
## [,1297] [,1298] [,1299] [,1300] [,1301] [,1302] [,1303] [,1304]
## ACAAANel3 0 1 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 1 0 0 0
## AGCATNel8 0 1 0 0 0 0 1 0
## ATGAAACNel10 1 1 0 0 0 0 0 0
## ATGAAACNel15 1 0 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 1 0 0 0 0 0 0
## CTGTANel9 0 1 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 1 1 0 0 0 0 0 0
## GTATTNel14 0 1 0 0 1 0 0 0
## TCACCNel6 0 1 0 0 1 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 1 0 0 1 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 1 0 0 0 1 0 0 0
## AGCCCAlt13 1 0 0 0 1 0 0 0
## ATCACGAlt5 0 0 0 0 1 0 0 0
## ATCACGAlt7 0 0 0 0 1 0 0 0
## CGATGTAlt1 1 0 0 0 1 0 0 0
## CTGTAAlt14 1 0 0 0 1 0 0 0
## CTTGAAlt10 0 1 0 0 1 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 1 0 0 0
## GCCAATAlt9 0 1 0 0 1 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 1 1 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA 0 NA 0
## ACAAASub1 NA 0 0 0 0 0 NA 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 1 0 0 0 0 0 0
## CGATGTSub6 0 NA NA NA 0 0 NA 0
## CTAGCSub3 0 NA NA NA 0 0 NA 0
## CTTGCTTSub14 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA 0 NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 NA
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 NA NA NA NA 0 0 0 NA
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1305] [,1306] [,1307] [,1308] [,1309] [,1310] [,1311] [,1312]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 1 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 1 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 1 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 NA NA 0 NA NA
## ACAAASub1 0 0 0 NA NA 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 NA 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 0 0 NA NA 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 NA
## GTATTSub12 NA 0 0 NA NA NA NA 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA 0 0 0 0 NA NA 0
## ACAGTGCau3 0 0 0 NA NA 1 1 0
## ACTATCau11 0 0 0 1 0 1 0 0
## ACTATCau9 0 0 0 0 0 1 0 0
## AGCCCCau7 0 0 0 NA NA 1 1 0
## ATGAAACCau12 0 0 0 0 0 1 0 0
## CTAGCCau5 0 0 0 0 0 1 1 0
## [,1313] [,1314] [,1315] [,1316] [,1317] [,1318] [,1319] [,1320]
## ACAAANel3 0 0 0 1 0 0 0 0
## ACAGTGNel5 0 0 0 1 0 0 0 0
## AGCATNel8 0 0 0 0 0 1 0 0
## ATGAAACNel10 0 0 0 1 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 1
## CGATGTNel4 0 0 0 0 0 1 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 1 0 1 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 1 0 0 0 0
## GGACCTANel11 0 0 0 1 0 0 0 0
## GGACCTANel13 0 0 0 1 0 0 0 0
## GTATTNel14 0 0 0 1 0 0 0 0
## TCACCNel6 0 0 0 1 0 0 0 0
## TGACCANel1 0 0 0 1 0 0 0 0
## AAAAGTTAlt12 0 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 1 0 1 0 0
## ACAGTGAlt3 0 0 0 1 0 1 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 1 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 1 NA NA 0 0
## CTGTAAlt14 0 0 0 0 0 1 0 0
## CTTGAAlt10 0 0 0 1 0 0 0 0
## GAATTCAAlt15 0 0 0 1 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 1 0 0 0 0
## TTAGGCAlt2 0 0 0 1 0 0 0 0
## TTAGGCAlt6 0 0 0 1 0 1 0 0
## TTAGGCAlt8 0 0 0 1 0 0 0 0
## AAAAGTTSub15 0 NA NA NA 0 0 0 NA
## ACAAASub1 0 NA 0 1 0 0 0 NA
## ACTATSub7 0 0 0 1 0 1 0 0
## AGCATSub13 0 0 0 1 0 0 0 0
## AGCCCSub11 NA 0 1 0 0 0 0 0
## CGATGTSub6 0 0 0 NA 0 0 0 NA
## CTAGCSub3 NA NA 0 0 0 0 0 NA
## CTTGCTTSub14 NA NA 0 NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0
## GCCAATSub4 NA NA NA NA 0 0 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA 0 NA 0 0 0 0 0
## ACAGTGCau3 0 0 1 0 1 0 0 0
## ACTATCau11 0 0 1 0 1 0 0 0
## ACTATCau9 1 0 1 0 1 0 0 0
## AGCCCCau7 0 0 1 0 1 0 0 0
## ATGAAACCau12 1 0 1 0 1 0 0 0
## CTAGCCau5 1 0 1 0 1 0 0 0
## [,1321] [,1322] [,1323] [,1324] [,1325] [,1326] [,1327] [,1328]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 1
## CGATGTNel4 0 0 0 0 1 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 1 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 1 1
## TTAGGCAlt2 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA 0
## ACAAASub1 NA 0 0 0 NA NA NA 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 NA
## CGATGTSub6 NA 0 NA NA NA NA 0 0
## CTAGCSub3 NA 0 0 0 NA NA NA NA
## CTTGCTTSub14 0 0 NA NA 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 0 0 NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 NA 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 1 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 NA
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1329] [,1330] [,1331] [,1332] [,1333] [,1334] [,1335] [,1336]
## ACAAANel3 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 0 0 NA 1 0 0
## AGCATNel8 0 0 0 0 0 1 0 0
## ATGAAACNel10 0 0 0 0 NA 0 0 0
## ATGAAACNel15 0 0 0 0 0 1 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 NA NA NA
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 NA 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 1 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 1 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 1 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 NA 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 NA 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA 0 0 NA NA NA NA NA
## CTTGCTTSub14 NA 0 0 0 0 NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 NA NA NA
## ACAGTGCau3 0 0 0 0 0 NA NA NA
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 NA 0 0 0 0 NA NA NA
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1337] [,1338] [,1339] [,1340] [,1341] [,1342] [,1343] [,1344]
## ACAAANel3 1 0 0 0 0 0 0 0
## ACAGTGNel5 1 0 0 0 0 0 0 0
## AGCATNel8 1 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 1 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 1 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 NA 1 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 1 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 1 0 0 0 0 0 0
## ACAGTGAlt3 0 0 NA 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 1 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 1 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 1 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 1 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 1 0
## AGCCCSub11 0 0 0 0 0 0 1 0
## CGATGTSub6 0 0 0 NA 0 0 0 0
## CTAGCSub3 NA NA 0 0 0 0 0 0
## CTTGCTTSub14 NA 0 0 0 0 0 1 0
## CTTGCTTSub8 NA NA 0 NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 NA 0 0 0 0
## GGACCTASub10 0 0 0 0 0 0 1 0
## GTATTSub12 NA 0 NA 0 0 0 0 0
## TGACCASub2 0 0 NA 0 0 0 1 0
## ACAGTGCau2 NA 0 NA 0 0 0 1 0
## ACAGTGCau3 NA 0 0 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 1 0
## AGCCCCau7 0 0 0 NA 0 0 1 0
## ATGAAACCau12 NA 0 0 0 NA NA 1 0
## CTAGCCau5 0 0 0 0 0 0 1 0
## [,1345] [,1346] [,1347] [,1348] [,1349] [,1350] [,1351] [,1352]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 1 0 0 0 0
## ATGAAACNel15 0 0 0 1 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 1 1 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 1 0 0 1 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 1 1 0 0 0 0 0
## ACAGTGAlt3 0 0 0 1 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 1 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 1 1 0 0 0 0 0
## CTGTAAlt14 0 1 1 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 1 0 0 0
## TTAGGCAlt6 0 0 0 0 1 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 NA 0 0 NA NA
## ACAAASub1 NA NA NA NA 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 1 0 0 0 0
## AGCCCSub11 0 0 0 1 0 0 0 0
## CGATGTSub6 NA NA NA 0 0 0 0 0
## CTAGCSub3 NA NA NA NA 0 0 NA NA
## CTTGCTTSub14 0 0 0 NA 0 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA 0 0 NA NA
## GGACCTASub10 0 0 0 1 0 0 0 0
## GTATTSub12 0 0 0 NA NA 0 NA 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 NA 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 1 0 0
## AGCCCCau7 0 0 0 0 0 1 0 NA
## ATGAAACCau12 NA NA NA NA 0 1 NA 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1353] [,1354] [,1355] [,1356] [,1357] [,1358] [,1359] [,1360]
## ACAAANel3 0 0 1 0 0 0 1 0
## ACAGTGNel5 0 0 1 0 0 0 1 0
## AGCATNel8 0 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 1 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 1 0 0 0 1 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 1 0 0
## GGACCTANel11 0 0 1 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 1 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 1 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 1 0
## ATCACGAlt5 1 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 1 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 1 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 1 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 NA NA NA NA NA NA
## ACAAASub1 0 0 NA NA NA NA 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 0 NA NA NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 0 0 NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 1 1 0 0 0
## ACTATCau9 0 0 0 1 1 0 0 0
## AGCCCCau7 0 0 NA NA NA NA 0 0
## ATGAAACCau12 0 NA 0 1 1 0 0 0
## CTAGCCau5 0 0 0 1 1 0 0 0
## [,1361] [,1362] [,1363] [,1364] [,1365] [,1366] [,1367] [,1368]
## ACAAANel3 0 0 0 0 0 0 1 0
## ACAGTGNel5 0 0 0 0 0 0 1 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 1 0
## ATGAAACNel15 0 0 0 0 0 0 1 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 1 0 0
## CTGTANel9 0 0 0 0 0 0 1 0
## CTTGANel2 0 0 0 0 0 0 1 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 1 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 1 0 0 0 0 0 1 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 1 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 NA NA 0 NA NA NA
## ACAAASub1 0 0 0 NA 0 NA NA NA
## ACTATSub7 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 0 0 0 0 1 0
## AGCCCSub11 0 0 0 NA NA NA NA NA
## CGATGTSub6 0 NA NA 0 0 0 1 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 0 0 NA NA 0 1 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 1 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 1 0
## GTATTSub12 NA NA NA 0 NA NA NA NA
## TGACCASub2 0 0 0 0 0 0 1 0
## ACAGTGCau2 0 0 0 1 NA NA NA NA
## ACAGTGCau3 0 0 0 1 NA 0 1 0
## ACTATCau11 0 0 0 1 0 0 0 1
## ACTATCau9 0 0 0 1 0 0 1 0
## AGCCCCau7 0 0 0 NA 0 NA NA NA
## ATGAAACCau12 0 0 NA NA NA 0 0 0
## CTAGCCau5 0 0 0 1 0 0 0 0
## [,1369] [,1370] [,1371] [,1372] [,1373] [,1374] [,1375] [,1376]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 1 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 1 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 1 1 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 1 0 0
## ACAGTGAlt3 0 0 0 0 0 1 0 0
## AGCCCAlt13 1 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 1 0 0 0 0 0
## AAAAGTTSub15 NA NA NA 0 NA 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 NA 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA 0
## CTTGCTTSub14 NA NA NA NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA 0 0 0 0 0
## TGACCASub2 0 0 0 NA 0 0 0 0
## ACAGTGCau2 NA NA NA 0 0 0 0 0
## ACAGTGCau3 NA NA NA 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 NA NA NA NA 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1377] [,1378] [,1379] [,1380] [,1381] [,1382] [,1383] [,1384]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 1 1 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 1 1 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 1 1 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 1 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 1 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 NA NA NA NA NA NA
## ACAAASub1 0 0 NA 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 NA 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 0 0 NA 0 NA NA NA NA
## CTTGCTTSub14 0 0 0 0 NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA 0 0 0 0 0
## TGACCASub2 1 1 0 0 0 0 0 0
## ACAGTGCau2 1 1 0 0 NA NA NA NA
## ACAGTGCau3 1 1 0 0 0 1 1 0
## ACTATCau11 1 1 0 0 0 1 1 0
## ACTATCau9 1 1 0 0 0 1 1 0
## AGCCCCau7 1 1 NA 0 0 1 1 0
## ATGAAACCau12 1 1 NA 0 0 1 1 0
## CTAGCCau5 1 1 0 1 0 1 0 0
## [,1385] [,1386] [,1387] [,1388] [,1389] [,1390] [,1391] [,1392]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 NA 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 1 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 NA NA NA NA 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 NA 0 0 0 0 0 0
## CGATGTSub6 0 NA 0 NA NA NA 0 0
## CTAGCSub3 0 0 NA NA NA NA 0 NA
## CTTGCTTSub14 0 NA 0 0 0 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA 0 NA NA NA NA 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 1 0 0 0 0 1
## ACAGTGCau3 0 0 1 NA NA NA 0 1
## ACTATCau11 0 0 1 0 0 0 0 1
## ACTATCau9 0 0 1 0 0 0 0 1
## AGCCCCau7 0 0 1 NA NA NA 0 1
## ATGAAACCau12 0 0 NA NA NA NA 0 1
## CTAGCCau5 0 0 1 0 0 0 0 1
## [,1393] [,1394] [,1395] [,1396] [,1397] [,1398] [,1399] [,1400]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 1 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 1 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 1 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 1 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 1 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 1 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 1 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 1 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 1 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 1 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 1 0 0 0 0 1 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA NA 0 0 0 0
## ACAAASub1 0 NA NA NA 0 0 0 0
## ACTATSub7 0 1 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 1 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 NA NA NA 0 0 NA 0
## CTAGCSub3 NA NA NA NA NA NA NA 0
## CTTGCTTSub14 NA NA NA NA 0 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA 0
## GGACCTASub10 0 1 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 NA NA NA 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 NA NA NA NA NA NA 1
## ACAGTGCau3 0 0 1 0 0 0 0 1
## ACTATCau11 0 0 1 0 0 0 0 1
## ACTATCau9 0 0 1 0 0 0 0 1
## AGCCCCau7 0 0 1 0 0 0 0 1
## ATGAAACCau12 0 0 1 0 0 0 NA 1
## CTAGCCau5 0 0 1 0 0 0 0 1
## [,1401] [,1402] [,1403] [,1404] [,1405] [,1406] [,1407] [,1408]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 1 0 0 0 0 0
## AGCATNel8 0 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 1 0 0 0 0 1
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 1
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 1 0 0 1
## GGACCTANel11 0 0 1 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 1
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 1 1 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 1 0 0 0
## ACAGTGAlt3 0 0 0 0 1 0 0 1
## AGCCCAlt13 0 0 0 0 1 0 0 1
## ATCACGAlt5 0 1 0 0 1 0 0 1
## ATCACGAlt7 0 0 0 0 1 0 0 1
## CGATGTAlt1 0 0 0 0 0 0 0 1
## CTGTAAlt14 1 0 0 0 0 0 0 1
## CTTGAAlt10 0 0 0 0 1 0 0 1
## GAATTCAAlt15 0 0 0 0 1 0 0 0
## GCCAATAlt4 0 1 0 0 1 0 0 1
## GCCAATAlt9 0 0 1 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 1 0 0 0
## TTAGGCAlt8 0 1 0 0 1 0 0 0
## AAAAGTTSub15 0 NA NA NA 0 NA NA NA
## ACAAASub1 0 NA 0 NA 1 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 NA NA NA 0 0
## CTAGCSub3 0 NA NA NA NA NA 0 NA
## CTTGCTTSub14 0 NA NA 0 0 NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 1 0 0 0
## GTATTSub12 0 NA NA NA NA NA 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 NA 0 0 0 0 0
## ACAGTGCau3 0 0 NA 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 NA 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1409] [,1410] [,1411] [,1412] [,1413] [,1414] [,1415] [,1416]
## ACAAANel3 0 0 0 1 0 0 1 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 1 0 1 0
## ATGAAACNel10 0 0 0 0 0 0 1 0
## ATGAAACNel15 0 0 0 0 1 0 1 0
## CGATGTNel4 0 0 0 0 0 0 1 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 1 0 0 0 0
## CTGTANel9 0 0 0 0 1 0 0 0
## CTTGANel2 0 0 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 1 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 1 0 0 0
## ACAGTGAlt3 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 1 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 1 0 0 0
## CTGTAAlt14 0 0 0 0 1 0 1 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 1 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0
## TTAGGCAlt6 0 0 0 0 1 0 1 0
## TTAGGCAlt8 0 0 0 0 1 0 0 0
## AAAAGTTSub15 0 0 NA 0 NA NA NA NA
## ACAAASub1 0 0 0 0 NA 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 NA 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 0 0 NA NA NA NA NA NA
## CTTGCTTSub14 0 0 NA 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0
## GCCAATSub4 0 0 NA NA NA 0 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 1 NA NA NA 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 1 0 0 0 0 0
## ACAGTGCau3 0 0 1 0 0 0 0 0
## ACTATCau11 0 0 1 0 0 0 0 0
## ACTATCau9 0 0 1 0 0 0 0 0
## AGCCCCau7 1 0 1 0 0 0 0 0
## ATGAAACCau12 0 0 1 0 0 0 0 NA
## CTAGCCau5 0 0 1 0 0 0 0 0
## [,1417] [,1418] [,1419] [,1420] [,1421] [,1422] [,1423] [,1424]
## ACAAANel3 1 0 0 0 0 1 0 1
## ACAGTGNel5 0 0 0 0 0 1 0 1
## AGCATNel8 0 0 0 0 0 1 0 1
## ATGAAACNel10 0 0 0 0 0 1 0 1
## ATGAAACNel15 0 0 0 0 0 0 0 1
## CGATGTNel4 0 0 0 0 0 1 0 1
## CTAGCNel7 0 0 1 0 0 0 0 1
## CTGTANel12 0 0 1 1 0 1 0 0
## CTGTANel9 1 0 0 0 0 0 0 1
## CTTGANel2 0 0 0 0 0 1 0 1
## GGACCTANel11 0 0 0 0 0 0 0 1
## GGACCTANel13 1 0 0 0 0 1 0 1
## GTATTNel14 1 0 0 0 0 1 0 0
## TCACCNel6 1 0 0 0 0 0 0 1
## TGACCANel1 0 0 0 0 0 1 0 1
## AAAAGTTAlt12 1 0 0 0 0 0 0 1
## ACAAAAlt11 1 0 0 0 0 1 0 0
## ACAGTGAlt3 1 0 0 0 0 1 0 1
## AGCCCAlt13 1 0 0 0 0 0 0 1
## ATCACGAlt5 1 0 0 0 0 0 1 1
## ATCACGAlt7 1 0 0 0 0 1 0 1
## CGATGTAlt1 1 0 0 0 0 1 0 1
## CTGTAAlt14 1 0 0 0 0 0 0 1
## CTTGAAlt10 1 0 0 0 0 0 0 1
## GAATTCAAlt15 1 0 0 0 0 0 0 0
## GCCAATAlt4 1 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 1 0 1
## TTAGGCAlt2 1 0 0 0 0 1 0 1
## TTAGGCAlt6 1 0 0 0 0 1 0 1
## TTAGGCAlt8 1 0 0 0 0 0 0 1
## AAAAGTTSub15 0 0 0 0 NA NA NA NA
## ACAAASub1 0 0 0 0 0 1 0 0
## ACTATSub7 0 0 0 0 0 1 0 1
## AGCATSub13 1 0 0 0 0 1 0 0
## AGCCCSub11 1 0 0 0 NA 0 0 1
## CGATGTSub6 1 0 0 0 0 1 0 1
## CTAGCSub3 1 0 0 0 NA 1 0 NA
## CTTGCTTSub14 1 0 0 0 NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 0 0 0 1 0 1
## GCCAATSub4 NA 0 0 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 1
## GTATTSub12 0 0 0 0 0 NA NA 1
## TGACCASub2 1 0 0 0 NA 1 0 NA
## ACAGTGCau2 0 0 0 0 1 0 0 NA
## ACAGTGCau3 0 0 0 0 1 0 0 0
## ACTATCau11 0 0 0 0 1 0 0 0
## ACTATCau9 0 0 0 0 1 0 0 0
## AGCCCCau7 0 0 0 0 1 0 0 0
## ATGAAACCau12 0 0 0 0 1 0 0 NA
## CTAGCCau5 0 0 0 0 1 0 0 0
## [,1425] [,1426] [,1427] [,1428] [,1429] [,1430] [,1431] [,1432]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 1 0 1 0 0 0
## AGCATNel8 0 0 0 0 1 1 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 1 1 0 1
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 1 1 0 0
## CTGTANel12 0 1 0 0 1 0 0 0
## CTGTANel9 0 0 0 0 1 0 0 1
## CTTGANel2 0 0 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 1 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 1 0 0 0
## TCACCNel6 0 0 0 0 1 1 0 0
## TGACCANel1 0 0 0 0 1 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 0 1 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 1 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 1 1 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 1 0 0 0
## GCCAATAlt9 0 0 0 0 1 0 0 0
## TTAGGCAlt2 0 0 1 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 1 0 0 0
## TTAGGCAlt8 0 0 0 0 0 1 0 0
## AAAAGTTSub15 NA 0 NA NA NA 0 NA 0
## ACAAASub1 0 0 0 0 0 NA 0 0
## ACTATSub7 0 0 0 0 1 0 0 0
## AGCATSub13 0 0 0 0 1 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 NA 0 0 0 0 0 1 0
## CTAGCSub3 NA 0 NA NA NA NA NA NA
## CTTGCTTSub14 0 0 0 NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 1 0 0 0
## GCCAATSub4 NA 0 NA NA NA NA 0 0
## GGACCTASub10 0 0 0 0 1 0 0 0
## GTATTSub12 NA 0 NA 0 0 0 0 0
## TGACCASub2 0 0 0 NA NA 1 0 0
## ACAGTGCau2 0 NA 0 NA NA 0 1 0
## ACAGTGCau3 0 0 0 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 1 0
## AGCCCCau7 0 0 0 0 0 0 1 0
## ATGAAACCau12 0 0 0 0 0 0 1 0
## CTAGCCau5 0 0 0 0 0 0 1 0
## [,1433] [,1434] [,1435] [,1436] [,1437] [,1438] [,1439] [,1440]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 1
## AGCATNel8 0 0 0 0 0 0 0 1
## ATGAAACNel10 0 0 0 0 0 0 0 1
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 1
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 1
## CTGTANel9 0 0 0 0 0 0 0 1
## CTTGANel2 0 0 0 0 0 0 0 1
## GGACCTANel11 0 0 0 0 0 0 0 1
## GGACCTANel13 0 0 0 0 0 0 0 1
## GTATTNel14 0 0 0 0 0 0 0 1
## TCACCNel6 0 0 0 0 0 0 0 1
## TGACCANel1 0 0 0 0 0 0 0 1
## AAAAGTTAlt12 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 0 0 0 1
## ACAGTGAlt3 0 0 0 0 0 0 0 1
## AGCCCAlt13 0 0 0 0 0 0 0 1
## ATCACGAlt5 0 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 0 0 0 0 0 1
## CGATGTAlt1 0 0 0 0 0 0 0 1
## CTGTAAlt14 0 0 0 0 0 0 0 1
## CTTGAAlt10 0 0 0 0 0 0 0 1
## GAATTCAAlt15 0 0 0 0 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 1
## TTAGGCAlt8 0 0 0 0 0 0 0 1
## AAAAGTTSub15 0 NA 0 NA NA NA NA NA
## ACAAASub1 0 0 0 0 0 0 NA 1
## ACTATSub7 0 0 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 NA 0 0 0 0 1
## CGATGTSub6 0 NA 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 NA NA NA NA NA
## CTTGCTTSub14 0 NA 0 0 0 0 0 1
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 1
## GCCAATSub4 NA NA 0 NA NA NA 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 1
## GTATTSub12 NA NA 0 0 NA NA 0 NA
## TGACCASub2 NA 0 0 0 0 0 0 NA
## ACAGTGCau2 0 NA 0 1 0 0 NA NA
## ACAGTGCau3 0 1 0 1 0 1 1 0
## ACTATCau11 0 1 0 1 1 0 1 0
## ACTATCau9 0 1 0 1 0 0 1 1
## AGCCCCau7 0 1 0 1 0 0 1 0
## ATGAAACCau12 0 NA 0 1 0 0 NA 1
## CTAGCCau5 0 1 0 1 NA NA 1 1
## [,1441] [,1442] [,1443] [,1444] [,1445] [,1446] [,1447] [,1448]
## ACAAANel3 0 0 1 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 NA NA 0
## ATGAAACNel15 0 1 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 NA NA 0
## CTAGCNel7 0 0 0 0 0 1 1 0
## CTGTANel12 0 0 1 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 NA NA 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 NA NA 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 1 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 1 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 1 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 NA NA 0
## TTAGGCAlt8 0 0 1 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA 0 NA NA NA
## ACAAASub1 NA NA NA NA 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 1 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 NA 0 NA NA 0
## CTAGCSub3 0 0 0 NA NA NA NA NA
## CTTGCTTSub14 0 0 0 0 0 NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 NA NA NA 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 1 0 0 0 0 0
## ACAGTGCau3 0 0 1 0 0 0 0 NA
## ACTATCau11 0 0 1 0 0 0 0 0
## ACTATCau9 0 0 1 0 0 0 0 0
## AGCCCCau7 0 0 1 0 0 0 0 0
## ATGAAACCau12 0 0 1 0 NA 0 0 NA
## CTAGCCau5 0 0 1 0 0 0 0 1
## [,1449] [,1450] [,1451] [,1452] [,1453] [,1454] [,1455] [,1456]
## ACAAANel3 0 0 0 1 0 0 0 0
## ACAGTGNel5 0 0 1 1 0 0 0 0
## AGCATNel8 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 0 0 1 0 0 0 0
## ATGAAACNel15 0 0 1 0 0 0 0 0
## CGATGTNel4 0 0 0 1 0 0 0 0
## CTAGCNel7 0 0 1 1 0 0 0 0
## CTGTANel12 0 0 0 1 0 0 0 0
## CTGTANel9 0 0 0 1 0 0 0 0
## CTTGANel2 0 1 0 1 0 0 0 0
## GGACCTANel11 0 0 0 1 0 0 0 0
## GGACCTANel13 0 0 0 1 0 0 0 0
## GTATTNel14 0 0 0 1 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 1 0 0 0 0
## AAAAGTTAlt12 0 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 1 0 1 0 0
## ACAGTGAlt3 0 0 0 1 0 0 0 0
## AGCCCAlt13 0 0 0 1 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 1 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 1 0 0
## CTGTAAlt14 0 0 0 1 0 0 0 0
## CTTGAAlt10 0 0 0 1 0 0 0 0
## GAATTCAAlt15 0 0 0 1 0 1 0 0
## GCCAATAlt4 0 0 1 1 0 0 0 0
## GCCAATAlt9 0 0 1 1 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 1 0 0 0 0
## TTAGGCAlt8 0 0 0 1 0 0 0 0
## AAAAGTTSub15 NA 0 1 NA 0 0 0 0
## ACAAASub1 0 0 1 NA 0 0 0 0
## ACTATSub7 0 0 1 1 0 0 0 0
## AGCATSub13 0 0 1 1 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 1 1 0 0 0 0
## CTAGCSub3 NA 0 1 1 NA NA 0 0
## CTTGCTTSub14 NA 0 0 1 NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0
## GCCAATSub4 NA 0 1 NA NA NA 0 0
## GGACCTASub10 0 0 1 1 0 0 0 0
## GTATTSub12 0 0 1 1 NA NA 0 0
## TGACCASub2 0 0 1 1 0 0 0 0
## ACAGTGCau2 0 0 0 0 NA NA 0 0
## ACAGTGCau3 NA 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 NA 0 0 0 0 0 NA NA
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1457] [,1458] [,1459] [,1460] [,1461] [,1462] [,1463] [,1464]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 1 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 1 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 NA 0 0 0 0 0
## TCACCNel6 0 1 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 NA 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 NA 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 1 NA NA NA 1 NA 0
## ACAAASub1 NA NA 1 NA NA 0 NA 0
## ACTATSub7 0 1 0 0 0 0 0 0
## AGCATSub13 0 1 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 1
## CGATGTSub6 NA NA NA NA NA 0 0 0
## CTAGCSub3 NA NA NA 0 0 NA NA 0
## CTTGCTTSub14 0 0 NA NA NA 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA NA 0 0 0
## TGACCASub2 NA NA 1 0 0 0 0 NA
## ACAGTGCau2 NA NA NA 0 0 0 0 1
## ACAGTGCau3 0 0 0 0 0 0 0 1
## ACTATCau11 0 0 0 0 0 0 0 1
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 1
## ATGAAACCau12 0 0 NA 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 1
## [,1465] [,1466] [,1467] [,1468] [,1469] [,1470] [,1471] [,1472]
## ACAAANel3 0 0 0 0 0 NA NA 0
## ACAGTGNel5 0 0 0 0 0 1 0 0
## AGCATNel8 1 0 0 0 0 1 0 0
## ATGAAACNel10 0 0 0 0 0 1 0 0
## ATGAAACNel15 0 0 0 0 0 NA NA 0
## CGATGTNel4 0 0 0 0 0 1 0 0
## CTAGCNel7 0 0 0 0 0 NA NA 0
## CTGTANel12 0 0 0 0 0 1 0 0
## CTGTANel9 0 0 0 0 0 1 0 0
## CTTGANel2 0 1 0 0 0 1 0 0
## GGACCTANel11 0 1 0 0 0 1 0 0
## GGACCTANel13 0 0 0 0 0 1 0 0
## GTATTNel14 0 0 0 0 0 1 0 0
## TCACCNel6 0 0 0 0 0 1 0 0
## TGACCANel1 0 0 0 0 0 1 0 0
## AAAAGTTAlt12 0 0 0 0 0 1 0 0
## ACAAAAlt11 0 0 0 0 0 1 0 0
## ACAGTGAlt3 0 0 0 0 0 1 0 0
## AGCCCAlt13 0 0 0 0 0 1 0 0
## ATCACGAlt5 0 0 0 0 0 1 0 1
## ATCACGAlt7 0 0 0 0 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 1 0 0
## CTGTAAlt14 0 0 0 0 0 1 0 0
## CTTGAAlt10 0 0 0 0 0 1 0 0
## GAATTCAAlt15 0 0 0 0 0 1 0 0
## GCCAATAlt4 0 0 0 0 0 1 0 0
## GCCAATAlt9 0 0 0 0 0 1 0 0
## TTAGGCAlt2 0 0 0 0 0 NA NA 0
## TTAGGCAlt6 0 0 0 0 0 1 0 0
## TTAGGCAlt8 0 0 0 0 0 1 0 0
## AAAAGTTSub15 NA NA 0 0 0 1 0 0
## ACAAASub1 0 0 0 0 0 1 0 0
## ACTATSub7 0 0 0 0 0 1 0 0
## AGCATSub13 0 0 0 0 0 1 0 0
## AGCCCSub11 0 0 0 0 0 1 0 0
## CGATGTSub6 0 0 0 0 0 1 0 0
## CTAGCSub3 0 0 0 NA NA NA NA 0
## CTTGCTTSub14 0 0 0 0 0 NA NA 0
## CTTGCTTSub8 NA NA 0 NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0
## GCCAATSub4 NA NA 0 0 0 NA NA 0
## GGACCTASub10 0 0 0 0 0 1 0 0
## GTATTSub12 NA NA 0 0 0 1 0 0
## TGACCASub2 0 0 0 0 0 1 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 NA NA 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1473] [,1474] [,1475] [,1476] [,1477] [,1478] [,1479] [,1480]
## ACAAANel3 0 0 0 0 0 1 1 0
## ACAGTGNel5 0 0 0 0 0 1 1 0
## AGCATNel8 0 0 0 0 0 0 1 0
## ATGAAACNel10 0 0 0 0 0 0 1 0
## ATGAAACNel15 0 0 0 0 0 1 1 0
## CGATGTNel4 0 0 0 0 0 0 1 0
## CTAGCNel7 0 0 0 0 0 0 1 0
## CTGTANel12 0 0 0 0 0 1 1 0
## CTGTANel9 0 0 0 0 0 0 1 0
## CTTGANel2 0 0 0 0 0 1 1 0
## GGACCTANel11 0 0 0 0 0 0 1 0
## GGACCTANel13 0 0 0 0 0 0 1 0
## GTATTNel14 0 0 0 0 0 0 1 0
## TCACCNel6 0 0 0 0 0 1 1 0
## TGACCANel1 0 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 1 0
## ACAAAAlt11 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0
## AGCCCAlt13 0 0 0 0 0 0 1 0
## ATCACGAlt5 0 0 0 0 0 0 1 0
## ATCACGAlt7 0 0 0 0 0 0 1 0
## CGATGTAlt1 0 0 0 0 0 0 1 0
## CTGTAAlt14 0 0 1 0 0 1 1 0
## CTTGAAlt10 0 0 0 0 0 1 1 0
## GAATTCAAlt15 0 0 0 0 0 0 1 0
## GCCAATAlt4 0 0 0 0 0 1 1 0
## GCCAATAlt9 0 0 0 0 0 1 1 0
## TTAGGCAlt2 0 0 1 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 1 0
## TTAGGCAlt8 0 0 0 0 1 1 1 0
## AAAAGTTSub15 NA 0 0 0 NA 1 1 NA
## ACAAASub1 NA 0 0 0 NA 1 NA NA
## ACTATSub7 0 0 0 0 0 1 1 0
## AGCATSub13 0 0 0 0 0 1 1 0
## AGCCCSub11 0 0 0 0 0 0 1 NA
## CGATGTSub6 NA 0 0 0 0 1 1 0
## CTAGCSub3 NA 0 0 0 NA 1 NA NA
## CTTGCTTSub14 NA 0 0 0 NA 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 1 0
## GCCAATSub4 NA 0 0 0 NA 1 NA NA
## GGACCTASub10 0 0 0 0 0 0 1 0
## GTATTSub12 0 0 0 0 0 0 NA NA
## TGACCASub2 0 0 0 0 0 0 NA 0
## ACAGTGCau2 1 0 0 0 0 0 NA 0
## ACAGTGCau3 NA 0 0 0 0 0 0 0
## ACTATCau11 1 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 0 0 0 0 0
## AGCCCCau7 NA 0 0 0 0 0 0 0
## ATGAAACCau12 1 0 0 0 NA 0 NA NA
## CTAGCCau5 1 0 0 0 0 0 0 0
## [,1481] [,1482] [,1483] [,1484] [,1485] [,1486] [,1487] [,1488]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 1 0 0 0 0
## AGCATNel8 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 1 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 1 0 0 0 0
## GGACCTANel11 0 0 0 1 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 1 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 1 0 0 NA 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 1 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 1 0 0 0 0
## GCCAATAlt9 0 0 0 1 0 0 0 0
## TTAGGCAlt2 0 0 0 1 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 1 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 1 0 0 NA 0
## ACAAASub1 NA NA 0 1 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 NA NA 0 1 0 0 0 0
## CGATGTSub6 0 0 NA NA 0 1 0 0
## CTAGCSub3 NA NA NA NA 0 NA 0 NA
## CTTGCTTSub14 0 0 NA NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA 0 NA
## GGACCTASub10 0 0 0 1 0 0 1 0
## GTATTSub12 NA NA 0 1 0 0 0 NA
## TGACCASub2 0 0 0 1 0 0 0 0
## ACAGTGCau2 0 0 0 0 1 1 0 0
## ACAGTGCau3 0 0 0 0 0 1 0 0
## ACTATCau11 0 0 0 0 0 1 0 0
## ACTATCau9 0 0 0 0 0 1 0 0
## AGCCCCau7 0 0 NA NA NA 1 0 0
## ATGAAACCau12 NA NA NA NA 1 1 0 0
## CTAGCCau5 0 0 0 0 0 1 0 0
## [,1489] [,1490] [,1491] [,1492] [,1493] [,1494] [,1495] [,1496]
## ACAAANel3 0 0 0 0 0 0 1 0
## ACAGTGNel5 0 0 0 0 0 0 1 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 1 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 1 0
## TCACCNel6 0 0 0 0 0 0 1 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 1 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 0 0 0 0 0
## CTTGCTTSub14 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 0 0 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 0 NA NA 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 NA NA 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1497] [,1498] [,1499] [,1500] [,1501] [,1502] [,1503] [,1504]
## ACAAANel3 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 1 0 0 0 0 0
## AGCATNel8 0 0 0 1 1 1 0 0
## ATGAAACNel10 0 0 1 0 1 1 0 0
## ATGAAACNel15 0 0 0 0 1 0 0 0
## CGATGTNel4 0 0 0 0 1 1 0 0
## CTAGCNel7 0 0 0 0 1 1 0 0
## CTGTANel12 0 0 0 0 1 1 0 0
## CTGTANel9 0 0 0 0 1 0 0 0
## CTTGANel2 0 0 0 0 1 1 0 0
## GGACCTANel11 0 0 0 0 1 0 0 0
## GGACCTANel13 0 1 0 0 1 1 0 0
## GTATTNel14 1 0 1 0 1 1 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 1 0 1 0 1 0 0
## AAAAGTTAlt12 0 0 1 0 1 0 0 0
## ACAAAAlt11 0 0 1 0 0 1 0 0
## ACAGTGAlt3 0 0 0 0 0 1 0 0
## AGCCCAlt13 0 0 0 0 1 1 0 0
## ATCACGAlt5 0 0 0 0 1 1 0 0
## ATCACGAlt7 0 0 0 1 0 1 0 0
## CGATGTAlt1 0 0 0 0 1 0 0 0
## CTGTAAlt14 0 0 0 0 1 1 0 0
## CTTGAAlt10 0 0 0 0 1 0 0 0
## GAATTCAAlt15 0 0 0 0 1 1 0 0
## GCCAATAlt4 0 0 0 0 1 1 0 0
## GCCAATAlt9 0 0 0 0 1 1 0 0
## TTAGGCAlt2 0 0 0 0 1 1 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 1 1 0 0
## AAAAGTTSub15 0 NA NA NA 0 0 NA NA
## ACAAASub1 NA 0 0 0 NA 0 0 0
## ACTATSub7 0 0 0 0 0 1 0 0
## AGCATSub13 0 0 1 0 0 0 0 0
## AGCCCSub11 NA NA NA NA NA 0 1 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA 0 NA NA
## CTTGCTTSub14 0 0 0 0 NA 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 1 0 1 0
## GCCAATSub4 NA NA NA NA NA 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA NA NA 0 0
## TGACCASub2 0 NA NA NA 0 1 1 0
## ACAGTGCau2 0 0 0 0 NA 0 1 0
## ACAGTGCau3 0 0 0 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 1 0
## AGCCCCau7 0 0 0 0 0 0 NA 0
## ATGAAACCau12 0 NA NA NA 0 0 1 0
## CTAGCCau5 0 0 0 0 0 0 1 0
## [,1505] [,1506] [,1507] [,1508] [,1509] [,1510] [,1511] [,1512]
## ACAAANel3 0 0 0 0 0 1 1 1
## ACAGTGNel5 0 0 0 0 0 1 1 1
## AGCATNel8 0 0 0 0 0 1 1 1
## ATGAAACNel10 0 0 NA NA NA NA NA NA
## ATGAAACNel15 0 0 0 0 0 1 1 1
## CGATGTNel4 0 0 0 0 0 1 1 1
## CTAGCNel7 0 0 0 0 0 1 1 1
## CTGTANel12 0 0 0 0 0 1 1 1
## CTGTANel9 0 0 1 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 1 1 1
## GGACCTANel11 0 0 NA NA NA NA NA NA
## GGACCTANel13 0 0 0 0 0 1 1 1
## GTATTNel14 0 0 0 0 0 1 1 1
## TCACCNel6 0 0 0 0 0 1 1 1
## TGACCANel1 0 0 0 0 0 1 1 1
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 NA NA NA NA NA NA
## ACAGTGAlt3 0 0 0 0 0 1 1 1
## AGCCCAlt13 0 0 NA NA NA NA NA NA
## ATCACGAlt5 0 0 0 0 0 1 1 1
## ATCACGAlt7 0 0 NA NA NA NA NA NA
## CGATGTAlt1 0 1 NA NA NA NA NA NA
## CTGTAAlt14 0 0 0 0 0 1 1 1
## CTTGAAlt10 0 0 0 0 0 1 1 1
## GAATTCAAlt15 0 0 0 0 0 1 1 1
## GCCAATAlt4 0 0 0 0 0 1 1 1
## GCCAATAlt9 0 1 NA NA NA NA NA NA
## TTAGGCAlt2 0 0 0 0 0 1 1 1
## TTAGGCAlt6 0 0 NA NA NA NA NA NA
## TTAGGCAlt8 0 1 1 1 0 0 0 0
## AAAAGTTSub15 NA NA 0 0 0 1 1 1
## ACAAASub1 0 0 0 0 0 1 1 1
## ACTATSub7 0 0 NA NA NA NA NA NA
## AGCATSub13 0 0 1 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 1 1 1
## CGATGTSub6 0 0 0 0 0 1 1 1
## CTAGCSub3 0 0 0 0 0 1 1 1
## CTTGCTTSub14 0 0 0 0 0 1 1 1
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 1 0 0 0 0
## GCCAATSub4 0 0 0 0 0 1 1 1
## GGACCTASub10 0 0 1 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 1 1 1
## TGACCASub2 0 0 0 0 0 1 1 1
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 1 1 1
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 1 1 1
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1513] [,1514] [,1515] [,1516] [,1517] [,1518] [,1519] [,1520]
## ACAAANel3 1 0 0 0 0 0 0 0
## ACAGTGNel5 1 0 0 0 0 0 1 0
## AGCATNel8 1 0 0 0 0 0 1 0
## ATGAAACNel10 NA NA 1 0 0 0 1 0
## ATGAAACNel15 1 0 0 0 0 0 0 0
## CGATGTNel4 1 0 0 0 0 0 1 1
## CTAGCNel7 1 0 0 0 0 0 1 0
## CTGTANel12 1 0 0 0 1 0 1 0
## CTGTANel9 0 0 0 0 0 0 1 0
## CTTGANel2 1 0 0 0 0 0 0 0
## GGACCTANel11 NA NA 0 0 0 0 1 0
## GGACCTANel13 1 0 1 0 0 0 1 0
## GTATTNel14 1 0 0 0 0 0 1 1
## TCACCNel6 1 0 0 0 0 0 1 0
## TGACCANel1 1 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 1 0 0 0 0 0 0
## ACAAAAlt11 NA NA 0 0 0 0 1 0
## ACAGTGAlt3 1 0 0 0 0 0 1 0
## AGCCCAlt13 NA NA 0 0 0 0 1 0
## ATCACGAlt5 1 0 0 0 0 0 1 0
## ATCACGAlt7 NA NA 0 0 0 0 1 0
## CGATGTAlt1 NA NA 0 0 0 0 0 0
## CTGTAAlt14 1 0 0 0 0 0 0 0
## CTTGAAlt10 1 0 0 0 0 0 0 0
## GAATTCAAlt15 1 0 0 0 0 0 1 0
## GCCAATAlt4 1 0 0 0 0 0 1 0
## GCCAATAlt9 NA NA 0 0 0 0 1 0
## TTAGGCAlt2 1 0 0 0 0 0 0 0
## TTAGGCAlt6 NA NA 0 0 0 0 1 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 1 0 0 0 0 NA NA NA
## ACAAASub1 1 0 0 0 0 NA NA NA
## ACTATSub7 NA NA 0 0 0 0 1 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 1 0 0 0 0 0 1 0
## CGATGTSub6 1 0 0 0 0 NA NA NA
## CTAGCSub3 1 0 0 0 0 NA NA NA
## CTTGCTTSub14 1 0 0 0 0 0 1 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 1 0 NA 0 0 NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 1 0 0 0 0 NA NA NA
## TGACCASub2 1 0 0 0 0 0 1 0
## ACAGTGCau2 0 0 NA 0 0 NA NA NA
## ACAGTGCau3 1 0 0 0 0 NA NA NA
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 1 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1521] [,1522] [,1523] [,1524] [,1525] [,1526] [,1527] [,1528]
## ACAAANel3 0 0 0 0 0 0 1 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 1 0 NA 0 0 0 0
## ATGAAACNel10 0 0 0 0 NA 0 0 0
## ATGAAACNel15 0 0 0 0 NA 0 0 0
## CGATGTNel4 0 0 0 0 0 0 1 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 1 1
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 1
## GGACCTANel11 0 0 0 0 NA 0 1 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 1 0
## TCACCNel6 0 0 0 0 NA 0 0 0
## TGACCANel1 0 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 1 1
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 1 0
## CGATGTAlt1 0 0 0 0 NA 0 0 0
## CTGTAAlt14 0 0 0 0 NA 0 0 1
## CTTGAAlt10 0 0 0 NA 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 NA 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 1 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 NA NA 0 0 NA
## ACAAASub1 NA 0 0 NA NA 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 0 NA NA 0 0 NA
## CGATGTSub6 NA 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA 0 0 NA
## CTTGCTTSub14 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 NA NA 0 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 NA 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA 0 NA 1 0 0 0 0
## ACAGTGCau3 NA 0 1 1 0 0 0 0
## ACTATCau11 0 0 1 1 0 0 0 0
## ACTATCau9 0 0 1 0 0 0 0 0
## AGCCCCau7 0 0 1 NA 0 0 0 0
## ATGAAACCau12 0 0 0 1 0 NA 0 NA
## CTAGCCau5 0 0 1 1 0 0 0 0
## [,1529] [,1530] [,1531] [,1532] [,1533] [,1534] [,1535] [,1536]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 1
## GGACCTANel11 0 0 0 0 0 0 0 1
## GGACCTANel13 0 0 0 0 0 0 0 1
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 0 0 0 0 0 1
## CGATGTAlt1 0 0 0 0 0 0 0 1
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 0 0 0 NA
## ACAAASub1 NA 0 0 0 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 1
## AGCCCSub11 NA 0 1 1 0 0 0 0
## CGATGTSub6 0 0 0 1 0 0 0 NA
## CTAGCSub3 NA 0 0 0 0 0 NA NA
## CTTGCTTSub14 0 0 1 0 0 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 0 0 NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA 1 0 1 0 0 NA NA
## TGACCASub2 0 0 1 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 NA 0
## ACAGTGCau3 0 0 0 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 1 0
## ACTATCau9 0 NA NA NA NA NA 1 0
## AGCCCCau7 0 NA NA NA NA NA NA 0
## ATGAAACCau12 NA 0 0 0 0 0 NA NA
## CTAGCCau5 0 0 0 0 0 0 NA 0
## [,1537] [,1538] [,1539] [,1540] [,1541] [,1542] [,1543] [,1544]
## ACAAANel3 NA 0 0 0 0 0 0 0
## ACAGTGNel5 NA NA NA NA NA NA NA NA
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 1 1 1 0 1 1 1
## CGATGTNel4 NA NA NA NA NA NA NA NA
## CTAGCNel7 NA NA NA NA NA NA NA NA
## CTGTANel12 NA NA NA NA NA NA NA NA
## CTGTANel9 NA NA NA NA NA NA NA NA
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 NA NA NA NA NA NA NA NA
## GTATTNel14 0 1 1 1 0 1 1 1
## TCACCNel6 NA NA NA NA NA NA NA NA
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 1 1 1 0 1 1 1
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 NA NA NA NA NA NA NA NA
## ATCACGAlt5 NA NA NA NA NA NA NA NA
## ATCACGAlt7 NA NA NA NA NA NA NA NA
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 NA NA NA NA NA NA NA NA
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 1 1 1 0 1 1 1
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 NA NA NA NA NA NA NA NA
## AAAAGTTSub15 NA NA NA NA NA NA NA NA
## ACAAASub1 0 1 1 1 0 1 1 1
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 NA NA NA NA NA NA NA NA
## CGATGTSub6 0 1 1 1 0 1 1 1
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 NA NA NA NA NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 1 1 1 0 1 1 1
## GTATTSub12 0 1 1 1 0 1 1 1
## TGACCASub2 NA NA NA NA NA NA NA NA
## ACAGTGCau2 NA NA NA NA NA NA NA NA
## ACAGTGCau3 0 1 1 1 0 1 1 1
## ACTATCau11 0 1 1 1 0 1 1 1
## ACTATCau9 0 1 1 1 0 1 1 1
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 NA NA NA NA NA NA NA NA
## CTAGCCau5 NA NA NA NA NA NA NA NA
## [,1545] [,1546] [,1547] [,1548] [,1549] [,1550] [,1551] [,1552]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 1 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 NA NA 1 0 0 0 0 0
## CTGTANel9 0 0 1 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 1 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 1
## GTATTNel14 0 1 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 1 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 1 0 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 0 0 0 1 0
## CTGTAAlt14 0 1 0 0 0 0 1 0
## CTTGAAlt10 0 0 1 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 1 NA 0 0 0 0 0
## TTAGGCAlt2 0 0 1 0 0 0 0 0
## TTAGGCAlt6 0 0 1 0 0 0 0 0
## TTAGGCAlt8 0 0 1 0 0 0 1 0
## AAAAGTTSub15 0 0 0 NA NA 0 0 0
## ACAAASub1 0 1 0 NA NA 1 1 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 NA NA NA
## CTAGCSub3 NA NA 0 NA NA NA NA NA
## CTTGCTTSub14 NA NA 0 NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 NA NA 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA 0 NA NA 0 0 0
## TGACCASub2 0 0 1 0 0 0 0 0
## ACAGTGCau2 NA NA 0 0 0 0 1 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 NA NA 0 0 0
## ATGAAACCau12 NA NA 0 NA NA 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1553] [,1554] [,1555] [,1556] [,1557] [,1558] [,1559] [,1560]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 1 0 0 0 1 0 0 1
## ATGAAACNel10 0 0 0 0 1 0 0 0
## ATGAAACNel15 0 0 0 0 1 0 0 0
## CGATGTNel4 0 0 0 0 1 0 0 0
## CTAGCNel7 0 0 0 0 1 0 0 0
## CTGTANel12 0 0 0 0 1 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 1
## GTATTNel14 0 1 0 0 1 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 1 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 1
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA 0 0 0 NA NA
## ACAAASub1 0 0 0 0 0 0 NA NA
## ACTATSub7 0 0 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 1
## CGATGTSub6 0 0 0 0 0 0 0 1
## CTAGCSub3 NA NA NA NA 0 0 NA NA
## CTTGCTTSub14 0 0 0 0 NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 0 0 NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 NA 0 0 0 1
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA 0 1 0 1 0 0 0
## ACAGTGCau3 0 0 1 0 1 0 0 0
## ACTATCau11 0 0 1 0 1 0 0 0
## ACTATCau9 0 0 1 0 1 0 0 0
## AGCCCCau7 0 0 1 0 1 0 0 0
## ATGAAACCau12 0 0 1 0 1 0 0 0
## CTAGCCau5 0 0 1 0 1 0 0 0
## [,1561] [,1562] [,1563] [,1564] [,1565] [,1566] [,1567] [,1568]
## ACAAANel3 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 1 0 0 0 1 0
## AGCATNel8 0 1 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 1 0 0
## ATGAAACNel15 0 0 0 0 0 1 0 0
## CGATGTNel4 0 0 0 0 0 1 0 1
## CTAGCNel7 0 1 0 0 0 0 1 0
## CTGTANel12 0 0 1 1 0 1 0 1
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 1 0 0 1 0 0
## GGACCTANel13 0 0 0 0 0 0 0 1
## GTATTNel14 0 0 0 0 0 0 0 1
## TCACCNel6 0 0 0 1 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 1 0 0
## AGCCCAlt13 0 0 0 0 0 1 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 1
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 1 0 0 0 1 1 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 1 0 0 0 0 0
## GCCAATAlt4 0 0 1 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 NA NA NA 0 0
## ACAAASub1 NA 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 1 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 1 0 0 0 NA 0 0
## CGATGTSub6 0 0 0 0 0 0 0 NA
## CTAGCSub3 NA NA NA 0 NA NA 0 NA
## CTTGCTTSub14 0 NA NA 0 NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 1
## GCCAATSub4 NA NA NA 0 NA NA 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 1
## GTATTSub12 0 NA NA 0 NA NA 0 NA
## TGACCASub2 0 0 0 0 0 0 0 NA
## ACAGTGCau2 0 NA NA 0 0 0 0 NA
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 NA 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1569] [,1570] [,1571] [,1572] [,1573] [,1574] [,1575] [,1576]
## ACAAANel3 0 0 1 0 0 0 0 0
## ACAGTGNel5 0 0 1 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 0 NA
## CTAGCNel7 0 1 0 0 1 1 0 1
## CTGTANel12 0 1 0 0 0 0 0 0
## CTGTANel9 0 1 0 0 0 0 0 0
## CTTGANel2 0 1 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 1 1 0 0
## GTATTNel14 0 0 1 0 0 0 0 0
## TCACCNel6 0 1 0 0 0 0 0 1
## TGACCANel1 0 1 0 0 0 0 0 0
## AAAAGTTAlt12 0 1 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 1
## AGCCCAlt13 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 1 0 0 0 0 1
## CGATGTAlt1 0 1 0 0 0 0 0 1
## CTGTAAlt14 0 1 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0
## GCCAATAlt4 0 1 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 1 0 0 0 0 0 0
## TTAGGCAlt6 0 1 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA 0 0 0 NA 0
## ACAAASub1 0 0 1 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 1 0 0 0 0 0 0
## AGCCCSub11 0 0 1 0 0 0 0 0
## CGATGTSub6 0 0 1 0 0 0 NA 0
## CTAGCSub3 NA NA NA 0 0 0 0 1
## CTTGCTTSub14 NA NA NA 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA 0 0 0 0 0
## TGACCASub2 0 0 NA 0 0 0 0 0
## ACAGTGCau2 NA NA NA 0 0 0 1 0
## ACAGTGCau3 1 1 0 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 1 0
## AGCCCCau7 NA NA 0 1 0 0 NA 0
## ATGAAACCau12 0 0 NA 0 0 0 NA 0
## CTAGCCau5 0 0 0 1 0 0 1 0
## [,1577] [,1578] [,1579] [,1580] [,1581] [,1582] [,1583] [,1584]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 1 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 NA NA NA NA NA 0 0 NA
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 1 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 1 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 1 0
## AAAAGTTSub15 0 0 0 0 0 NA 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 0 0 0 1 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 NA 0 0
## CTAGCSub3 0 0 0 0 0 0 0 0
## CTTGCTTSub14 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 1 0
## GCCAATSub4 0 0 0 0 0 1 0 0
## GGACCTASub10 0 0 0 0 0 0 1 0
## GTATTSub12 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 1 0 0
## ACAGTGCau2 0 0 0 1 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1585] [,1586] [,1587] [,1588] [,1589] [,1590] [,1591] [,1592]
## ACAAANel3 0 0 0 0 0 0 0 1
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 1
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 1
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 1
## AAAAGTTAlt12 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 0 0 0 1
## ACAGTGAlt3 0 0 0 0 0 1 1 1
## AGCCCAlt13 0 0 0 0 0 1 1 0
## ATCACGAlt5 0 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 1
## CTGTAAlt14 0 1 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 1
## GAATTCAAlt15 0 0 0 0 0 0 0 1
## GCCAATAlt4 1 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 1
## TTAGGCAlt2 1 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 1
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA NA 0 0 0 NA
## ACAAASub1 0 0 0 NA 0 0 0 1
## ACTATSub7 0 0 0 0 0 0 0 1
## AGCATSub13 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 NA NA NA 1
## CGATGTSub6 0 NA NA 0 0 0 0 0
## CTAGCSub3 0 NA NA NA NA NA NA 1
## CTTGCTTSub14 0 NA NA NA NA NA NA 1
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 1
## GCCAATSub4 0 NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 1
## GTATTSub12 0 NA NA NA NA NA NA 1
## TGACCASub2 0 0 0 0 0 0 0 1
## ACAGTGCau2 0 NA NA NA NA NA NA 0
## ACAGTGCau3 0 NA NA 0 1 0 0 0
## ACTATCau11 0 0 0 0 1 0 0 0
## ACTATCau9 0 0 0 0 1 0 0 0
## AGCCCCau7 0 0 0 0 1 0 0 1
## ATGAAACCau12 0 NA NA NA 1 0 0 0
## CTAGCCau5 0 0 0 0 1 0 0 0
## [,1593] [,1594] [,1595] [,1596] [,1597] [,1598] [,1599] [,1600]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 NA 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 1 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 1 0 0 0
## CTTGANel2 0 0 0 NA 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 1
## GGACCTANel13 0 0 0 0 1 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 NA 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 1 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 1
## AGCCCAlt13 0 0 0 0 1 0 0 0
## ATCACGAlt5 0 0 0 0 1 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 1
## CGATGTAlt1 0 0 0 0 1 0 0 1
## CTGTAAlt14 0 0 0 0 1 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 1
## GAATTCAAlt15 0 0 0 0 1 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 1 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 NA 1 0 0 NA
## ACAAASub1 0 0 0 NA 1 0 0 NA
## ACTATSub7 0 0 0 NA 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 NA NA NA 0
## CTAGCSub3 NA NA 0 0 1 0 0 NA
## CTTGCTTSub14 0 0 0 0 NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 1
## GCCAATSub4 0 0 0 NA 1 0 0 NA
## GGACCTASub10 0 0 0 0 1 0 0 0
## GTATTSub12 0 0 0 NA 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 1 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1601] [,1602] [,1603] [,1604] [,1605] [,1606] [,1607] [,1608]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 1 0 0 0 0 0
## ATGAAACNel15 0 0 1 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 1 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 1 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA NA NA NA
## ACAAASub1 NA NA 0 0 NA 0 NA NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 NA NA 0 0 0 0
## CGATGTSub6 0 0 NA NA 0 NA 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 NA NA 0 0 NA 0 NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA 0 NA 0 0
## TGACCASub2 0 0 0 0 NA 0 0 0
## ACAGTGCau2 0 0 0 0 NA 1 0 0
## ACAGTGCau3 0 0 0 0 1 1 0 0
## ACTATCau11 0 0 0 0 1 1 0 1
## ACTATCau9 0 0 0 0 1 1 0 1
## AGCCCCau7 0 0 0 0 1 1 0 0
## ATGAAACCau12 0 0 NA NA 1 1 NA NA
## CTAGCCau5 0 0 0 0 1 1 0 1
## [,1609] [,1610] [,1611] [,1612] [,1613] [,1614] [,1615] [,1616]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 1 1 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 1 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 0 0 0
## AAAAGTTAlt12 1 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0
## ATCACGAlt5 1 0 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 0 0 1 0
## CGATGTAlt1 1 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 1 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 1 0
## GCCAATAlt4 0 1 0 0 0 0 0 0
## GCCAATAlt9 0 1 0 0 0 0 1 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 1 0
## AAAAGTTSub15 0 0 0 NA NA NA 0 NA
## ACAAASub1 1 0 0 0 0 NA 0 0
## ACTATSub7 0 1 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 NA 0 NA
## CGATGTSub6 0 0 0 0 0 NA 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 NA 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 1 0 NA NA NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA 1 0 NA NA 0 0 0
## TGACCASub2 NA 0 0 0 0 0 0 1
## ACAGTGCau2 0 0 0 1 0 0 0 1
## ACAGTGCau3 0 0 0 1 1 0 0 1
## ACTATCau11 0 0 0 1 1 0 0 1
## ACTATCau9 0 0 0 1 1 0 0 1
## AGCCCCau7 0 0 0 1 1 NA 0 NA
## ATGAAACCau12 0 0 0 1 1 0 0 1
## CTAGCCau5 0 0 0 1 1 0 0 1
## [,1617] [,1618] [,1619] [,1620] [,1621] [,1622] [,1623] [,1624]
## ACAAANel3 1 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 1 0 0 0 0 0
## AGCATNel8 1 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 1 0 0 0 0 0
## ATGAAACNel15 0 0 1 0 0 0 0 0
## CGATGTNel4 0 0 1 1 0 0 0 0
## CTAGCNel7 1 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 1 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 1 0 0 0 0 0
## GTATTNel14 0 0 1 0 0 0 0 0
## TCACCNel6 0 0 1 0 0 0 0 0
## TGACCANel1 0 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 1 0 1 0 0 0 0 0
## AGCCCAlt13 1 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 1 0 0 0 0 0
## ATCACGAlt7 1 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 1 0 0 0 0 0
## CTGTAAlt14 0 0 1 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 1 1 0 0 0 0 0 0
## GCCAATAlt9 1 0 1 0 0 0 0 0
## TTAGGCAlt2 0 0 1 0 0 0 0 0
## TTAGGCAlt6 0 0 1 0 0 0 0 0
## TTAGGCAlt8 0 0 1 0 0 0 0 0
## AAAAGTTSub15 NA NA NA 0 0 NA NA 0
## ACAAASub1 0 0 1 0 0 0 0 0
## ACTATSub7 0 0 1 0 0 0 0 0
## AGCATSub13 0 0 1 0 0 0 0 0
## AGCCCSub11 NA 0 NA 0 0 0 0 0
## CGATGTSub6 0 0 NA 0 0 NA NA 0
## CTAGCSub3 NA NA NA NA NA NA NA 0
## CTTGCTTSub14 0 NA 1 0 0 NA NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 0 0 0 1 0
## GCCAATSub4 0 NA NA 0 0 NA NA 0
## GGACCTASub10 1 0 1 0 0 0 0 0
## GTATTSub12 0 0 NA 0 0 NA NA 0
## TGACCASub2 1 0 1 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 1 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 1
## AGCCCCau7 NA 0 0 0 0 0 0 1
## ATGAAACCau12 1 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1625] [,1626] [,1627] [,1628] [,1629] [,1630] [,1631] [,1632]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 1 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 1 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 1 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 1 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 NA NA 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 NA 0 0
## CGATGTSub6 NA 0 0 0 0 0 0 0
## CTAGCSub3 NA 0 NA NA NA NA 0 0
## CTTGCTTSub14 NA 0 0 0 0 NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA 0 NA NA NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 NA 0 NA 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 NA 0 1
## ACAGTGCau3 NA 0 0 0 0 0 0 1
## ACTATCau11 0 0 0 0 0 0 0 1
## ACTATCau9 0 0 0 0 1 0 0 1
## AGCCCCau7 0 0 0 0 NA 0 0 1
## ATGAAACCau12 NA 0 0 0 0 0 0 1
## CTAGCCau5 0 0 0 0 0 0 0 1
## [,1633] [,1634] [,1635] [,1636] [,1637] [,1638] [,1639] [,1640]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 1 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 1 0 0
## GGACCTANel13 0 0 0 1 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 1 0 0 0 0 0
## TGACCANel1 0 0 0 1 0 1 0 0
## AAAAGTTAlt12 0 0 0 1 0 1 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 1 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 0 1 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 1 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA 0 NA NA NA NA 0
## ACAAASub1 0 0 0 0 0 0 NA 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 NA NA 0 NA 0
## CTAGCSub3 0 NA 0 NA NA NA NA 0
## CTTGCTTSub14 0 NA 0 NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA 0 NA NA NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA 0 NA NA NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 NA 0 NA NA 0 0 0
## ACAGTGCau3 0 0 0 0 0 NA 0 0
## ACTATCau11 1 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 NA 0 NA NA 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1641] [,1642] [,1643] [,1644] [,1645] [,1646] [,1647] [,1648]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 1
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 1 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA 0 NA NA 0
## ACAAASub1 0 NA NA NA 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 NA NA NA 0 0 0 0
## CGATGTSub6 NA 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA 0 0 0
## CTTGCTTSub14 0 0 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 NA 1 0 0
## GGACCTASub10 0 1 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 NA 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 NA NA 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1649] [,1650] [,1651] [,1652] [,1653] [,1654] [,1655] [,1656]
## ACAAANel3 0 0 0 1 0 0 1 0
## ACAGTGNel5 0 0 0 0 0 0 1 0
## AGCATNel8 0 0 0 1 0 0 1 0
## ATGAAACNel10 0 0 0 0 0 0 1 0
## ATGAAACNel15 0 0 0 1 0 0 1 0
## CGATGTNel4 0 1 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 1 0
## CTGTANel12 0 0 0 0 0 0 1 0
## CTGTANel9 0 0 0 0 0 0 1 0
## CTTGANel2 0 0 0 1 0 0 1 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 1 0 1 0 0 0 0
## GTATTNel14 1 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 1 0
## TGACCANel1 0 0 0 1 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 1 0
## ACAAAAlt11 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 1 0
## AGCCCAlt13 0 0 0 0 0 1 1 0
## ATCACGAlt5 0 0 0 0 0 0 1 0
## ATCACGAlt7 0 0 0 0 0 1 1 0
## CGATGTAlt1 0 0 0 0 0 1 1 0
## CTGTAAlt14 0 0 0 1 0 0 1 0
## CTTGAAlt10 0 0 0 0 0 0 1 0
## GAATTCAAlt15 0 0 0 NA NA 0 1 0
## GCCAATAlt4 0 0 0 1 1 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 1 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0
## TTAGGCAlt6 0 0 0 1 1 0 0 0
## TTAGGCAlt8 0 0 0 NA 0 0 1 0
## AAAAGTTSub15 0 NA 0 0 0 NA NA 0
## ACAAASub1 0 0 0 0 0 0 1 0
## ACTATSub7 0 0 0 NA NA 0 1 0
## AGCATSub13 0 0 0 0 0 0 1 0
## AGCCCSub11 0 0 0 0 0 0 1 0
## CGATGTSub6 0 NA 0 0 0 NA NA 0
## CTAGCSub3 0 NA NA 0 0 NA NA NA
## CTTGCTTSub14 0 0 0 1 0 0 1 0
## CTTGCTTSub8 NA NA NA 0 0 NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA NA NA NA 0 0 NA
## GGACCTASub10 0 0 0 0 0 0 1 0
## GTATTSub12 0 NA 0 0 0 NA NA NA
## TGACCASub2 0 0 0 1 0 0 1 0
## ACAGTGCau2 0 0 0 1 1 0 0 0
## ACAGTGCau3 0 0 0 1 1 0 0 NA
## ACTATCau11 0 0 0 1 1 0 0 0
## ACTATCau9 0 0 0 1 1 0 0 0
## AGCCCCau7 0 0 0 0 1 0 0 0
## ATGAAACCau12 0 0 0 1 1 0 0 0
## CTAGCCau5 0 0 0 1 1 0 0 0
## [,1657] [,1658] [,1659] [,1660] [,1661] [,1662] [,1663] [,1664]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 1
## AGCATNel8 0 0 0 0 0 0 0 1
## ATGAAACNel10 0 0 0 0 0 0 0 1
## ATGAAACNel15 0 0 0 0 0 0 0 1
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 1
## CTGTANel12 0 0 0 0 0 0 0 1
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 1
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 1
## GTATTNel14 0 0 0 0 0 0 0 1
## TCACCNel6 0 0 0 0 0 0 0 1
## TGACCANel1 0 0 0 0 0 0 0 1
## AAAAGTTAlt12 0 0 0 0 0 0 0 1
## ACAAAAlt11 0 0 0 0 0 0 0 1
## ACAGTGAlt3 0 0 0 0 0 0 0 1
## AGCCCAlt13 0 0 0 0 0 0 0 1
## ATCACGAlt5 0 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 0 0 0 0 0 1
## CGATGTAlt1 0 0 0 0 0 0 0 1
## CTGTAAlt14 0 0 0 0 0 0 0 1
## CTTGAAlt10 0 0 0 0 0 0 0 1
## GAATTCAAlt15 0 0 0 0 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 1
## TTAGGCAlt8 0 0 0 0 0 0 0 1
## AAAAGTTSub15 0 0 0 0 0 0 0 NA
## ACAAASub1 0 0 0 0 0 NA 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 NA
## CGATGTSub6 0 0 0 0 0 NA 0 NA
## CTAGCSub3 0 0 0 0 0 0 NA 0
## CTTGCTTSub14 0 0 0 0 0 NA 0 1
## CTTGCTTSub8 NA NA NA NA NA NA 0 NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 0 0 NA 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 1
## GTATTSub12 0 0 0 0 0 NA NA NA
## TGACCASub2 0 0 0 0 0 NA 0 1
## ACAGTGCau2 NA NA NA NA NA 1 0 0
## ACAGTGCau3 0 0 0 1 0 1 0 0
## ACTATCau11 0 1 0 1 0 1 0 0
## ACTATCau9 0 1 0 1 0 1 0 0
## AGCCCCau7 0 1 0 1 0 1 0 0
## ATGAAACCau12 0 1 0 0 0 1 0 0
## CTAGCCau5 0 1 0 1 0 1 0 0
## [,1665] [,1666] [,1667] [,1668] [,1669] [,1670] [,1671] [,1672]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 1 0 0 0 0 0 0 0
## CTAGCNel7 1 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 1 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 1 0 0 0 0 0 0 0
## GTATTNel14 1 0 0 0 0 0 0 0
## TCACCNel6 1 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 1 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 1 0 0 0 0
## AGCCCAlt13 1 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 1 0 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 1 1 0 0 0 0 0 0
## TTAGGCAlt2 0 1 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA 0 0 0 0 NA
## ACAAASub1 0 0 0 0 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 NA 0 0 0 0
## CGATGTSub6 0 0 0 0 0 NA NA 0
## CTAGCSub3 0 0 0 NA 0 NA NA NA
## CTTGCTTSub14 0 0 0 NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0
## GCCAATSub4 NA NA NA NA 0 NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 NA 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1673] [,1674] [,1675] [,1676] [,1677] [,1678] [,1679] [,1680]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 NA 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 1 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 1 0 0 0 0 0
## CTTGANel2 0 0 1 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 NA 0 0 0 0 0
## TCACCNel6 0 0 NA 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 1 0 0 0 0 0
## ACAAAAlt11 0 0 NA 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 1 0 0 0 0 0
## ATCACGAlt5 0 NA 1 0 0 0 0 0
## ATCACGAlt7 0 0 1 0 0 0 0 0
## CGATGTAlt1 0 0 1 0 0 0 0 0
## CTGTAAlt14 0 NA 1 0 0 0 0 0
## CTTGAAlt10 0 0 1 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 1 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 NA 0 0 0 0 0
## TTAGGCAlt2 0 0 1 0 0 0 0 0
## TTAGGCAlt6 0 0 1 0 0 0 0 0
## TTAGGCAlt8 1 0 1 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA 0 0 0 0
## ACAAASub1 NA 0 0 0 0 0 0 0
## ACTATSub7 1 0 0 0 0 0 0 0
## AGCATSub13 1 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 NA 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA 0 0
## CTTGCTTSub14 0 NA NA NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 NA NA 0 0 0 0
## GGACCTASub10 1 0 0 0 0 0 0 0
## GTATTSub12 NA 0 NA NA 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 NA 0 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 NA NA 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1681] [,1682] [,1683] [,1684] [,1685] [,1686] [,1687] [,1688]
## ACAAANel3 1 0 0 0 0 0 1 0
## ACAGTGNel5 0 0 0 0 1 0 1 0
## AGCATNel8 0 0 0 0 1 0 1 0
## ATGAAACNel10 1 0 0 0 0 0 1 0
## ATGAAACNel15 1 0 0 0 1 0 1 0
## CGATGTNel4 1 0 0 0 0 0 1 0
## CTAGCNel7 0 0 0 0 1 0 1 0
## CTGTANel12 NA 0 0 0 1 0 0 0
## CTGTANel9 0 0 0 0 0 0 1 0
## CTTGANel2 0 0 0 0 1 0 1 0
## GGACCTANel11 0 0 0 0 1 0 1 0
## GGACCTANel13 0 0 0 0 1 0 1 0
## GTATTNel14 0 0 0 0 1 0 1 0
## TCACCNel6 0 0 0 0 1 0 1 0
## TGACCANel1 1 0 0 0 1 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 1 0
## ACAAAAlt11 0 0 0 0 0 0 1 0
## ACAGTGAlt3 1 0 0 0 1 0 1 0
## AGCCCAlt13 0 0 0 0 1 0 1 0
## ATCACGAlt5 1 0 0 0 1 0 1 0
## ATCACGAlt7 0 0 0 0 1 0 1 0
## CGATGTAlt1 1 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 1 0 1 0
## CTTGAAlt10 0 0 0 0 0 0 1 0
## GAATTCAAlt15 0 0 0 0 1 0 1 0
## GCCAATAlt4 0 0 0 0 1 0 0 0
## GCCAATAlt9 0 0 0 0 1 0 1 0
## TTAGGCAlt2 1 0 0 0 1 0 1 0
## TTAGGCAlt6 0 0 0 0 1 0 1 0
## TTAGGCAlt8 1 0 0 0 NA NA 1 1
## AAAAGTTSub15 NA 0 0 0 0 0 0 NA
## ACAAASub1 0 0 0 0 NA NA 1 NA
## ACTATSub7 1 0 0 0 0 0 1 0
## AGCATSub13 1 0 0 0 1 0 1 0
## AGCCCSub11 1 0 0 0 0 0 1 0
## CGATGTSub6 0 0 0 0 0 0 NA NA
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 1 NA 0 0 0 0 1 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 0 0 0 0 1 0
## GCCAATSub4 1 NA 0 0 NA NA 1 NA
## GGACCTASub10 1 0 0 0 1 0 1 0
## GTATTSub12 1 0 0 0 NA NA NA NA
## TGACCASub2 1 1 0 0 NA NA 1 0
## ACAGTGCau2 0 1 0 0 0 0 0 NA
## ACAGTGCau3 0 1 0 0 0 0 0 0
## ACTATCau11 0 1 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 1 0 0 0 0 0 0
## ATGAAACCau12 0 NA 0 0 NA NA 0 0
## CTAGCCau5 0 1 0 0 0 1 0 0
## [,1689] [,1690] [,1691] [,1692] [,1693] [,1694] [,1695] [,1696]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 1
## ATGAAACNel10 0 0 0 0 0 0 0 1
## ATGAAACNel15 0 0 0 0 0 0 0 1
## CGATGTNel4 0 0 0 0 0 0 0 1
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 1
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 1
## GGACCTANel13 0 0 0 0 0 0 0 1
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 1
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 1
## ACAAAAlt11 1 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 0 0 0 0 0 1
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 1
## CTTGAAlt10 0 0 0 0 0 1 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 1
## GCCAATAlt4 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 1
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA 0 NA NA NA 0
## ACAAASub1 0 0 0 0 0 0 NA 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 NA NA NA 0 NA NA 0 0
## CTAGCSub3 NA NA NA 0 NA NA NA NA
## CTTGCTTSub14 0 0 0 0 NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA 0 NA NA NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA 0 NA NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 1
## ACAGTGCau2 NA NA NA 0 NA NA 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1697] [,1698] [,1699] [,1700] [,1701] [,1702] [,1703] [,1704]
## ACAAANel3 0 0 0 1 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 NA 0 0 0 0
## CTGTANel12 0 1 0 NA 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 1 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 NA 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 NA 0 NA 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 NA 0 NA 0 1
## CGATGTSub6 0 0 0 NA 0 0 0 0
## CTAGCSub3 NA NA NA NA 0 NA 0 0
## CTTGCTTSub14 NA 0 0 NA 0 NA 0 1
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA NA NA NA NA 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 NA 0 0 0
## ACAGTGCau2 1 0 0 0 0 NA 0 0
## ACAGTGCau3 1 0 0 0 0 0 0 0
## ACTATCau11 1 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 0 0 0 1 0
## AGCCCCau7 0 0 0 0 NA 0 0 0
## ATGAAACCau12 1 0 0 0 0 0 0 0
## CTAGCCau5 1 0 0 0 0 0 0 0
## [,1705] [,1706] [,1707] [,1708] [,1709] [,1710] [,1711] [,1712]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 1 0 0 1 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 1 0 0 0 0 0
## ATGAAACNel15 0 0 1 0 0 0 0 1
## CGATGTNel4 0 0 1 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 1
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 1 0 1
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 1 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 1 0 0 0 0 0
## ATCACGAlt5 0 0 1 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 1
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 1 0 0 1 0 1
## CTTGAAlt10 0 0 1 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 1 0 0 0 0 0
## TTAGGCAlt2 0 0 1 0 0 1 0 0
## TTAGGCAlt6 0 0 1 0 0 0 0 0
## TTAGGCAlt8 0 0 1 0 0 0 0 0
## AAAAGTTSub15 0 0 NA NA NA 0 0 0
## ACAAASub1 NA NA 1 0 0 0 0 0
## ACTATSub7 0 0 1 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 NA 0 0 0
## CTAGCSub3 NA NA 1 0 0 0 0 0
## CTTGCTTSub14 0 0 0 NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 1
## GCCAATSub4 NA NA NA NA 0 0 0 0
## GGACCTASub10 0 0 1 0 0 0 0 1
## GTATTSub12 NA NA NA NA NA 0 0 0
## TGACCASub2 0 0 1 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 NA 0 0 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 NA 0 1 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 NA NA 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1713] [,1714] [,1715] [,1716] [,1717] [,1718] [,1719] [,1720]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 1 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 1 0 0 0 0
## GGACCTANel13 0 0 1 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 1 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 NA NA 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 1 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 NA NA 0 0 0
## ACAAASub1 0 0 0 NA NA 0 0 0
## ACTATSub7 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 1 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 NA NA 0 0 0 NA NA 0
## CTAGCSub3 0 0 0 NA NA 0 0 0
## CTTGCTTSub14 NA NA 0 NA NA 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 NA NA 0
## GCCAATSub4 NA NA 0 NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 NA NA NA NA 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 1 NA NA NA NA 0
## ACAGTGCau3 0 0 0 NA NA 0 0 0
## ACTATCau11 0 0 0 0 1 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 1 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1721] [,1722] [,1723] [,1724] [,1725] [,1726] [,1727] [,1728]
## ACAAANel3 0 0 0 0 0 1 1 0
## ACAGTGNel5 0 0 0 1 0 0 1 0
## AGCATNel8 0 0 0 0 0 1 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 1 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 1 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 1 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 1 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 1 0 0
## GAATTCAAlt15 0 0 0 0 0 1 0 0
## GCCAATAlt4 0 0 0 1 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0
## TTAGGCAlt6 0 0 0 1 0 0 0 0
## TTAGGCAlt8 0 0 0 1 0 0 0 0
## AAAAGTTSub15 0 0 NA NA 0 NA NA NA
## ACAAASub1 0 0 0 1 NA 1 0 NA
## ACTATSub7 0 0 0 0 0 1 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 NA NA 0 1 0 NA
## CGATGTSub6 0 0 0 0 0 1 0 0
## CTAGCSub3 0 0 NA 0 NA NA NA NA
## CTTGCTTSub14 0 0 NA NA 0 1 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0
## GCCAATSub4 NA 0 NA 0 NA NA NA NA
## GGACCTASub10 0 0 0 0 0 1 0 0
## GTATTSub12 0 0 NA 1 0 1 0 0
## TGACCASub2 0 0 0 NA 0 1 0 0
## ACAGTGCau2 0 0 0 0 1 0 0 1
## ACAGTGCau3 0 0 NA 0 1 0 0 1
## ACTATCau11 0 0 0 0 1 0 0 1
## ACTATCau9 0 0 0 0 1 0 0 1
## AGCCCCau7 0 0 NA 0 1 0 0 1
## ATGAAACCau12 0 0 NA 0 1 0 0 1
## CTAGCCau5 0 0 0 0 1 0 0 1
## [,1729] [,1730] [,1731] [,1732] [,1733] [,1734] [,1735] [,1736]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 1 0 0 0 0 0
## AGCATNel8 0 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 1 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 1 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 0 0 NA 0
## ACAAASub1 0 NA NA NA 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 NA NA NA 0 0 0 0
## CTAGCSub3 0 NA NA NA NA NA NA NA
## CTTGCTTSub14 0 0 0 0 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 NA NA NA NA
## GGACCTASub10 0 NA NA NA 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 NA
## ACAGTGCau3 0 0 0 0 0 0 0 NA
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 1 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1737] [,1738] [,1739] [,1740] [,1741] [,1742] [,1743] [,1744]
## ACAAANel3 0 0 0 1 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 1 0 0 0 0
## ATGAAACNel10 0 0 0 1 0 0 0 0
## ATGAAACNel15 0 0 0 1 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 1 0
## CTAGCNel7 0 0 0 1 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 1 0
## CTGTANel9 0 0 0 1 0 0 1 0
## CTTGANel2 0 0 0 1 0 0 0 0
## GGACCTANel11 0 0 0 1 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 1 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 1 0 0 0 0
## AAAAGTTAlt12 0 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 1 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 1 0 0 1 0
## ATCACGAlt5 0 0 0 1 0 0 1 0
## ATCACGAlt7 0 0 0 1 0 0 1 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 1 0 0 0 0
## CTTGAAlt10 0 0 0 1 0 0 1 0
## GAATTCAAlt15 0 0 0 1 0 0 0 0
## GCCAATAlt4 0 0 0 1 0 0 0 0
## GCCAATAlt9 0 0 0 1 0 0 1 0
## TTAGGCAlt2 0 0 0 1 0 0 0 0
## TTAGGCAlt6 0 0 0 1 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 1 0
## AAAAGTTSub15 0 0 0 0 0 0 0 NA
## ACAAASub1 0 0 NA NA NA NA 0 NA
## ACTATSub7 0 0 0 1 0 0 0 0
## AGCATSub13 0 0 0 1 0 0 0 0
## AGCCCSub11 0 0 NA NA 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 0 0 NA NA 0 0 NA NA
## CTTGCTTSub14 0 0 0 0 NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0
## GCCAATSub4 0 0 NA NA NA NA 0 0
## GGACCTASub10 0 0 0 1 0 0 0 0
## GTATTSub12 0 0 NA NA 0 0 NA 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 NA NA 0 0
## ACAGTGCau3 0 0 0 0 0 1 0 0
## ACTATCau11 0 0 1 0 0 1 0 0
## ACTATCau9 0 0 NA NA 0 1 0 0
## AGCCCCau7 0 0 0 0 0 1 0 NA
## ATGAAACCau12 0 0 0 0 0 1 0 NA
## CTAGCCau5 0 0 0 0 0 1 0 0
## [,1745] [,1746] [,1747] [,1748] [,1749] [,1750] [,1751] [,1752]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 NA NA 0 0 0 0
## CGATGTSub6 NA NA 0 0 0 0 0 0
## CTAGCSub3 0 0 NA NA NA NA NA 0
## CTTGCTTSub14 0 0 NA NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA 0 NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 NA NA 0 0 NA 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 1 NA NA 0 0 0 1
## ACAGTGCau3 0 1 0 0 1 1 NA 1
## ACTATCau11 0 0 0 0 1 0 0 1
## ACTATCau9 0 1 0 0 0 1 0 1
## AGCCCCau7 0 1 0 0 1 0 0 0
## ATGAAACCau12 0 1 NA NA NA 0 NA 1
## CTAGCCau5 0 1 0 0 0 0 0 1
## [,1753] [,1754] [,1755] [,1756] [,1757] [,1758] [,1759] [,1760]
## ACAAANel3 0 0 0 0 0 0 0 1
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 NA NA NA 0 0
## ATGAAACNel15 0 0 0 NA NA NA 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 1 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 1 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 1 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 1 NA NA NA NA NA NA NA
## ACAAASub1 1 NA NA 0 0 0 0 NA
## ACTATSub7 1 0 0 0 0 0 0 0
## AGCATSub13 1 0 0 0 0 0 0 0
## AGCCCSub11 1 0 0 0 0 0 0 0
## CGATGTSub6 NA 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA 0 NA
## CTTGCTTSub14 NA 0 0 0 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 1 0 0 0 0 0 0 0
## GTATTSub12 1 0 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 1 NA
## ACAGTGCau3 0 NA NA 0 0 0 1 0
## ACTATCau11 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 1 0
## AGCCCCau7 0 1 1 0 0 0 1 0
## ATGAAACCau12 0 NA NA 0 0 0 1 NA
## CTAGCCau5 0 0 0 0 0 0 1 0
## [,1761] [,1762] [,1763] [,1764] [,1765] [,1766] [,1767] [,1768]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 1 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 NA NA
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 NA NA
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 1 0 NA NA
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 NA NA
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 1 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 1 0 0 1 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 NA NA
## GCCAATAlt4 0 1 0 0 0 0 0 0
## GCCAATAlt9 0 1 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 1 0 0 0
## AAAAGTTSub15 NA 1 0 NA NA NA 0 0
## ACAAASub1 NA NA 0 NA NA NA 0 0
## ACTATSub7 0 1 0 0 1 0 0 0
## AGCATSub13 0 0 0 0 0 0 NA NA
## AGCCCSub11 NA NA 0 NA NA NA 0 0
## CGATGTSub6 0 NA 0 0 0 0 NA NA
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 0 0 NA NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0
## GCCAATSub4 NA NA 0 1 0 0 NA NA
## GGACCTASub10 0 1 0 0 0 0 0 0
## GTATTSub12 0 1 0 NA NA NA 0 0
## TGACCASub2 0 1 0 0 0 0 0 0
## ACAGTGCau2 NA 0 0 1 0 0 NA NA
## ACAGTGCau3 1 0 0 1 0 0 1 0
## ACTATCau11 0 0 0 1 0 0 1 0
## ACTATCau9 0 0 0 1 0 0 1 0
## AGCCCCau7 0 0 0 1 0 0 1 0
## ATGAAACCau12 NA 0 0 1 0 0 1 0
## CTAGCCau5 1 0 0 1 0 0 1 0
## [,1769] [,1770] [,1771] [,1772] [,1773] [,1774] [,1775] [,1776]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 NA 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 NA 0 0 0
## CTAGCNel7 0 0 0 0 NA 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 NA 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 NA 0 0 0
## ATCACGAlt7 0 0 0 0 NA 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 NA 0 NA NA 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 1 0 0 NA 0 0 0
## AGCCCSub11 0 0 0 0 NA 0 0 0
## CGATGTSub6 0 0 0 0 0 NA NA 0
## CTAGCSub3 NA NA 0 0 NA NA NA NA
## CTTGCTTSub14 0 0 0 0 NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 NA 0 0 0
## GCCAATSub4 NA NA 0 0 0 NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 1 0 0 0 0 1 0 NA
## ACAGTGCau3 NA NA 0 0 NA 1 0 0
## ACTATCau11 1 0 0 0 0 1 0 0
## ACTATCau9 1 0 0 0 0 1 0 0
## AGCCCCau7 NA NA 0 0 0 NA NA 0
## ATGAAACCau12 1 0 0 0 0 NA NA 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1777] [,1778] [,1779] [,1780] [,1781] [,1782] [,1783] [,1784]
## ACAAANel3 0 0 1 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 1 0 0 0 0 0
## ATGAAACNel10 0 0 1 0 0 0 0 0
## ATGAAACNel15 0 0 1 0 0 0 0 0
## CGATGTNel4 0 0 1 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 1 0 1 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 1 0 0 0 0 0
## GGACCTANel11 0 0 1 0 0 0 0 0
## GGACCTANel13 0 0 1 0 1 0 0 0
## GTATTNel14 0 0 1 0 0 0 0 0
## TCACCNel6 0 0 0 1 0 0 0 0
## TGACCANel1 0 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 1 0 0 0 0 0
## ACAGTGAlt3 0 0 1 0 0 0 0 0
## AGCCCAlt13 0 0 1 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 1 0 1 0 0 0
## CTGTAAlt14 0 0 1 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 1 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 1 0 0 0 0 0
## TTAGGCAlt8 0 0 1 0 0 0 0 0
## AAAAGTTSub15 0 0 1 0 0 NA NA NA
## ACAAASub1 0 0 1 0 0 0 0 0
## ACTATSub7 0 0 1 0 0 0 0 0
## AGCATSub13 0 0 1 0 0 0 0 0
## AGCCCSub11 0 0 1 0 0 NA NA NA
## CGATGTSub6 0 0 NA NA NA 0 0 0
## CTAGCSub3 0 0 NA NA NA NA NA NA
## CTTGCTTSub14 0 0 NA NA NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 1 0 0 0 0 0
## GCCAATSub4 0 0 NA NA NA NA NA NA
## GGACCTASub10 0 0 1 0 0 0 0 0
## GTATTSub12 0 0 NA NA NA 0 0 0
## TGACCASub2 0 0 NA NA NA 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 0 1 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 1 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 NA NA NA
## CTAGCCau5 0 1 0 0 0 0 0 0
## [,1785] [,1786] [,1787] [,1788] [,1789] [,1790] [,1791] [,1792]
## ACAAANel3 0 0 0 0 0 1 0 0
## ACAGTGNel5 0 0 0 0 0 1 0 0
## AGCATNel8 0 0 0 0 0 1 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 1 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 1 0 0
## CTGTANel12 0 0 0 0 1 0 0 0
## CTGTANel9 0 0 0 0 0 1 0 0
## CTTGANel2 0 0 0 0 0 0 1 0
## GGACCTANel11 0 0 0 0 0 1 0 0
## GGACCTANel13 0 0 0 0 0 1 0 0
## GTATTNel14 0 0 0 0 0 1 0 0
## TCACCNel6 0 0 0 0 1 0 0 0
## TGACCANel1 0 0 0 0 0 1 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 1 0 0 0
## AGCCCAlt13 0 0 0 0 0 1 0 0
## ATCACGAlt5 1 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 1 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 1 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 1 0 1 0 0 1 0 0
## TTAGGCAlt8 0 0 0 0 0 1 0 0
## AAAAGTTSub15 0 NA NA NA NA NA NA NA
## ACAAASub1 1 NA NA 0 1 1 NA 0
## ACTATSub7 0 0 1 0 1 1 0 0
## AGCATSub13 0 0 0 0 1 0 0 0
## AGCCCSub11 0 NA NA 0 NA 0 0 0
## CGATGTSub6 0 NA NA 0 1 NA 0 0
## CTAGCSub3 1 0 1 0 1 NA NA NA
## CTTGCTTSub14 1 0 1 0 NA 1 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 1 0 0 0 0 1 0 0
## GCCAATSub4 1 0 0 NA NA NA NA NA
## GGACCTASub10 0 0 1 0 0 0 0 0
## GTATTSub12 0 NA NA 0 0 1 NA NA
## TGACCASub2 0 0 1 0 0 NA 0 0
## ACAGTGCau2 0 0 1 0 0 0 NA NA
## ACAGTGCau3 1 0 1 0 0 0 0 NA
## ACTATCau11 1 0 1 0 0 0 0 0
## ACTATCau9 1 0 1 0 0 0 0 0
## AGCCCCau7 1 0 1 0 0 0 0 0
## ATGAAACCau12 0 0 1 0 0 0 0 NA
## CTAGCCau5 0 0 1 0 0 0 0 0
## [,1793] [,1794] [,1795] [,1796] [,1797] [,1798] [,1799] [,1800]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 1 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 1 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 1 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 1 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 NA NA NA NA NA NA NA 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 1 0 0 0
## TTAGGCAlt8 0 0 0 0 1 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 NA
## ACAAASub1 0 0 0 0 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 1 0
## CGATGTSub6 0 0 0 0 0 1 0 0
## CTAGCSub3 0 0 0 0 0 0 0 NA
## CTTGCTTSub14 0 0 0 0 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 0 0 0 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 0 1 NA
## ACAGTGCau3 0 0 0 0 0 0 1 1
## ACTATCau11 0 0 0 0 0 0 1 0
## ACTATCau9 0 0 0 0 0 0 1 0
## AGCCCCau7 0 0 0 0 0 0 1 1
## ATGAAACCau12 0 0 0 0 0 0 1 NA
## CTAGCCau5 0 0 0 0 0 0 1 0
## [,1801] [,1802] [,1803] [,1804] [,1805] [,1806] [,1807] [,1808]
## ACAAANel3 0 1 0 0 0 0 0 0
## ACAGTGNel5 0 1 0 0 0 0 0 0
## AGCATNel8 0 1 0 0 0 0 0 0
## ATGAAACNel10 0 1 0 0 0 0 0 0
## ATGAAACNel15 0 1 0 0 0 0 0 0
## CGATGTNel4 0 1 1 0 0 0 0 0
## CTAGCNel7 0 1 0 0 0 0 0 0
## CTGTANel12 0 1 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 1 0 0 0 0 0 0
## GGACCTANel11 0 1 0 0 0 0 0 0
## GGACCTANel13 0 1 0 0 0 0 0 0
## GTATTNel14 0 1 0 0 0 0 0 0
## TCACCNel6 0 1 0 0 0 0 0 0
## TGACCANel1 0 1 0 0 0 0 0 0
## AAAAGTTAlt12 0 1 0 0 0 0 0 0
## ACAAAAlt11 0 1 0 0 0 0 0 0
## ACAGTGAlt3 0 1 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 1 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 1 0 0
## CGATGTAlt1 0 1 0 0 0 0 0 0
## CTGTAAlt14 0 1 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 1 0 0
## GCCAATAlt4 0 1 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 1 0 0 0 0 0 0
## TTAGGCAlt6 0 1 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA NA 0 0 0
## ACAAASub1 NA 1 0 0 0 0 0 0
## ACTATSub7 0 1 0 0 0 0 0 0
## AGCATSub13 0 1 0 0 0 0 0 0
## AGCCCSub11 1 1 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA 0 0
## CTTGCTTSub14 NA 1 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA 0 0
## GGACCTASub10 0 1 0 0 0 0 0 0
## GTATTSub12 NA NA NA NA NA 0 0 0
## TGACCASub2 0 NA NA NA NA 0 0 0
## ACAGTGCau2 NA NA NA NA NA NA 0 0
## ACAGTGCau3 0 0 0 0 1 0 0 0
## ACTATCau11 1 0 0 0 1 0 0 0
## ACTATCau9 1 0 0 0 1 0 0 0
## AGCCCCau7 0 0 0 0 1 0 0 0
## ATGAAACCau12 NA NA NA NA NA 0 0 0
## CTAGCCau5 1 0 0 0 1 0 0 0
## [,1809] [,1810] [,1811] [,1812] [,1813] [,1814] [,1815] [,1816]
## ACAAANel3 0 0 0 0 0 0 1 0
## ACAGTGNel5 0 0 0 0 0 0 1 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 1 0 0 0 1 0
## ATGAAACNel15 0 0 0 0 0 0 1 0
## CGATGTNel4 0 0 0 0 0 0 1 0
## CTAGCNel7 0 0 0 0 0 0 1 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 1 0 0 0 1 0
## CTTGANel2 0 0 0 0 0 0 1 0
## GGACCTANel11 0 0 0 0 0 0 1 0
## GGACCTANel13 0 0 0 0 0 0 1 0
## GTATTNel14 0 0 1 0 0 0 1 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 1 0
## ACAAAAlt11 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 1 0 0 0 1 0
## CTGTAAlt14 0 0 0 0 0 0 1 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 1 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 1 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 NA NA NA 0 0 NA
## ACAAASub1 0 0 0 0 0 0 1 0
## ACTATSub7 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 NA NA 0
## CGATGTSub6 0 0 0 0 0 0 1 0
## CTAGCSub3 0 NA 0 0 0 NA NA 0
## CTTGCTTSub14 0 0 0 0 0 0 1 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 NA NA NA 0 1 NA
## GGACCTASub10 0 0 0 0 0 0 1 0
## GTATTSub12 0 0 0 0 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 1 0
## ACAGTGCau2 0 1 0 0 0 0 0 0
## ACAGTGCau3 0 1 0 0 0 0 0 0
## ACTATCau11 0 1 0 0 0 1 0 0
## ACTATCau9 0 1 0 0 0 0 0 0
## AGCCCCau7 0 1 0 0 0 0 0 0
## ATGAAACCau12 0 1 0 0 0 0 0 0
## CTAGCCau5 0 1 0 0 0 0 0 0
## [,1817] [,1818] [,1819] [,1820] [,1821] [,1822] [,1823] [,1824]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 1 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 NA NA NA NA
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 NA NA NA NA
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 NA NA NA NA
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 NA NA NA NA
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA NA NA 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 1 0 0 0 NA NA NA NA
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 NA NA NA NA
## CGATGTSub6 NA NA 0 0 0 0 0 0
## CTAGCSub3 0 0 NA NA NA NA NA NA
## CTTGCTTSub14 NA NA NA NA NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA 0 0 0 1
## GGACCTASub10 0 0 0 0 0 0 0 1
## GTATTSub12 0 0 NA NA NA NA NA NA
## TGACCASub2 0 0 0 0 0 1 0 1
## ACAGTGCau2 0 0 NA NA 0 0 0 0
## ACAGTGCau3 0 0 0 1 NA NA NA NA
## ACTATCau11 0 0 0 0 1 0 0 1
## ACTATCau9 0 0 0 0 0 1 0 0
## AGCCCCau7 0 0 NA NA 0 0 0 0
## ATGAAACCau12 0 0 NA NA 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1825] [,1826] [,1827] [,1828] [,1829] [,1830] [,1831] [,1832]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 1 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 NA NA NA NA NA NA NA NA
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 NA NA NA NA NA NA NA NA
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 NA NA NA NA NA NA NA NA
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 NA NA NA NA NA NA NA NA
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 1 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 1 1 1
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 NA NA NA NA NA NA NA NA
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 NA NA NA NA NA NA NA NA
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 NA NA NA NA NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 1 1 0 0 1 1 1
## GGACCTASub10 0 0 0 0 0 1 1 1
## GTATTSub12 NA NA NA NA NA NA NA NA
## TGACCASub2 0 1 1 0 0 1 1 1
## ACAGTGCau2 0 0 0 0 0 0 0 0
## ACAGTGCau3 NA NA NA NA NA NA NA NA
## ACTATCau11 0 1 0 0 0 1 1 NA
## ACTATCau9 0 0 0 0 0 1 1 1
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 0 0 0 0 0 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1833] [,1834] [,1835] [,1836] [,1837] [,1838] [,1839] [,1840]
## ACAAANel3 0 0 0 0 0 0 0 1
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 1 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 1
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 1
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 0 0 0 NA
## ACAAASub1 0 0 0 0 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 NA
## CTAGCSub3 NA NA NA NA NA 0 0 NA
## CTTGCTTSub14 0 NA 0 0 0 0 0 NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 0 0 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 1 0 0 0
## ACAGTGCau3 0 0 0 0 1 0 0 0
## ACTATCau11 0 0 0 0 1 0 0 0
## ACTATCau9 0 0 0 0 1 0 0 0
## AGCCCCau7 0 0 0 0 1 0 0 0
## ATGAAACCau12 0 0 0 0 1 0 0 NA
## CTAGCCau5 0 0 0 0 1 0 0 0
## [,1841] [,1842] [,1843] [,1844] [,1845] [,1846] [,1847] [,1848]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 1 0 0 0 0
## ATGAAACNel15 0 0 0 1 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 1 0 0 0 1
## CTGTANel9 0 0 0 1 0 0 0 0
## CTTGANel2 0 0 0 0 1 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 1 0 0 0 0
## TGACCANel1 0 0 0 1 0 0 0 0
## AAAAGTTAlt12 0 0 0 1 0 0 0 0
## ACAAAAlt11 0 0 0 0 NA NA NA 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 1 0 0 0 0
## ATCACGAlt5 0 0 0 1 0 0 0 0
## ATCACGAlt7 0 0 0 1 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 1 0 0 0 0
## GCCAATAlt4 0 0 0 1 0 0 0 0
## GCCAATAlt9 0 0 0 1 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 1 0 0 0 0
## AAAAGTTSub15 NA NA NA NA 0 1 1 0
## ACAAASub1 NA 0 NA NA 0 0 0 0
## ACTATSub7 0 0 0 1 0 0 0 0
## AGCATSub13 0 0 0 1 0 0 0 0
## AGCCCSub11 0 0 0 1 0 1 1 0
## CGATGTSub6 NA NA 0 0 0 0 0 0
## CTAGCSub3 NA NA 0 0 0 0 0 0
## CTTGCTTSub14 NA 0 0 0 0 1 1 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 1 0 0 0 0
## GCCAATSub4 NA NA 0 1 0 0 0 0
## GGACCTASub10 0 0 0 1 0 1 1 0
## GTATTSub12 0 NA 0 0 0 0 0 0
## TGACCASub2 0 NA 0 0 0 0 0 0
## ACAGTGCau2 0 1 NA NA 0 0 0 0
## ACAGTGCau3 0 1 0 0 0 1 1 0
## ACTATCau11 0 1 0 0 0 0 0 0
## ACTATCau9 0 1 0 0 0 0 0 0
## AGCCCCau7 0 1 0 0 0 1 1 0
## ATGAAACCau12 NA NA 0 0 0 0 0 0
## CTAGCCau5 0 1 0 0 0 0 0 0
## [,1849] [,1850] [,1851] [,1852] [,1853] [,1854] [,1855] [,1856]
## ACAAANel3 0 0 1 0 0 1 1 0
## ACAGTGNel5 0 0 0 0 0 1 1 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 1 1 0
## ATGAAACNel15 0 0 1 0 0 0 1 0
## CGATGTNel4 0 0 0 0 0 1 1 0
## CTAGCNel7 0 0 0 0 1 1 0 0
## CTGTANel12 0 1 1 0 0 1 0 0
## CTGTANel9 0 0 0 0 0 1 1 1
## CTTGANel2 0 1 1 0 0 1 0 0
## GGACCTANel11 0 0 1 0 0 1 1 0
## GGACCTANel13 0 0 1 0 0 1 1 0
## GTATTNel14 0 0 1 0 0 1 0 0
## TCACCNel6 0 0 0 0 0 0 1 0
## TGACCANel1 0 0 1 1 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 1 1 0
## ACAAAAlt11 0 0 1 0 1 1 0 0
## ACAGTGAlt3 0 0 1 0 0 1 1 0
## AGCCCAlt13 1 0 0 0 0 1 0 0
## ATCACGAlt5 0 0 1 0 0 1 0 0
## ATCACGAlt7 0 0 0 0 0 1 0 0
## CGATGTAlt1 0 0 1 0 1 1 1 0
## CTGTAAlt14 0 0 0 0 0 1 1 0
## CTTGAAlt10 0 0 0 0 0 1 1 0
## GAATTCAAlt15 0 0 1 0 0 1 0 0
## GCCAATAlt4 0 0 1 0 1 1 1 0
## GCCAATAlt9 0 0 0 0 0 1 1 0
## TTAGGCAlt2 0 0 0 0 0 1 0 0
## TTAGGCAlt6 0 0 1 0 1 1 0 0
## TTAGGCAlt8 0 0 1 0 0 1 0 NA
## AAAAGTTSub15 0 0 NA NA 0 NA 0 0
## ACAAASub1 0 0 NA 0 0 1 0 0
## ACTATSub7 0 0 1 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 1 0 0
## AGCCCSub11 0 0 1 NA 0 1 0 NA
## CGATGTSub6 0 0 0 0 0 1 0 0
## CTAGCSub3 0 NA NA NA 0 0 NA NA
## CTTGCTTSub14 0 NA 0 NA 0 1 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 1 0 0
## GCCAATSub4 0 NA NA NA 0 0 NA 0
## GGACCTASub10 0 0 1 0 0 1 0 0
## GTATTSub12 0 NA NA NA 0 NA NA 0
## TGACCASub2 0 0 0 0 0 1 0 0
## ACAGTGCau2 0 0 0 NA 0 0 NA 0
## ACAGTGCau3 0 0 0 0 0 0 NA 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 0 0 0 0
## ATGAAACCau12 0 0 NA NA 0 0 NA 0
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1857] [,1858] [,1859] [,1860] [,1861] [,1862] [,1863] [,1864]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 1 0 0 1
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 1 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 1 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 1 0 0 0 0 0 0 0
## TTAGGCAlt2 1 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 NA 0 0 0 0 0 0 0
## AAAAGTTSub15 0 NA NA NA NA NA NA NA
## ACAAASub1 0 NA NA NA NA NA NA NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 NA 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA NA NA NA
## CTTGCTTSub14 0 NA NA NA NA NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA NA NA NA NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 1 0 0 0 0 0 0
## ACAGTGCau3 0 1 0 0 0 0 0 0
## ACTATCau11 0 1 0 0 0 0 0 0
## ACTATCau9 0 1 0 0 0 0 0 0
## AGCCCCau7 0 NA NA NA NA NA NA NA
## ATGAAACCau12 0 NA NA NA NA NA NA NA
## CTAGCCau5 0 1 0 0 0 0 0 0
## [,1865] [,1866] [,1867] [,1868] [,1869] [,1870] [,1871] [,1872]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 1 0 1 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 NA 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 0 0 0 0
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA 0 0 0 0 NA NA NA
## CTTGCTTSub14 NA 0 0 0 0 NA NA NA
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA 0 0 0 0 NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA NA 0 0 0 NA NA NA
## ACAGTGCau3 0 1 0 0 0 0 0 0
## ACTATCau11 0 1 0 0 0 0 0 0
## ACTATCau9 1 1 0 0 0 0 0 0
## AGCCCCau7 0 1 0 0 0 0 0 0
## ATGAAACCau12 0 1 0 0 0 NA NA NA
## CTAGCCau5 1 1 0 0 0 0 0 0
## [,1873] [,1874] [,1875] [,1876] [,1877] [,1878] [,1879] [,1880]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 NA NA 0 0 0 0 0
## TCACCNel6 0 NA NA 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 NA NA 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 1 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 0 0 0 0 NA 0 NA NA
## ACAAASub1 0 0 0 0 NA 0 NA NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 0 0 0 0 0 0 NA 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA 0 NA 0 NA NA
## CTTGCTTSub14 NA NA NA 0 0 0 NA 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA 0 NA 0 NA 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA NA 0 0 0 0 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 NA 0 0 0 0 0 0 0
## ACAGTGCau3 1 0 0 0 0 0 0 0
## ACTATCau11 1 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 0 0 0 0 0
## AGCCCCau7 NA 0 0 0 0 0 0 0
## ATGAAACCau12 NA 0 0 0 NA 0 NA NA
## CTAGCCau5 1 0 0 0 0 0 0 0
## [,1881] [,1882] [,1883] [,1884] [,1885] [,1886] [,1887] [,1888]
## ACAAANel3 0 0 0 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 1 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 1
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 0 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 1 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 0 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 1 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 1
## CTTGAAlt10 0 1 0 0 0 0 0 0
## GAATTCAAlt15 0 1 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 1 0 0 0 0 0 0
## AAAAGTTSub15 NA 0 0 NA 0 0 1 NA
## ACAAASub1 NA 0 0 NA 0 0 0 NA
## ACTATSub7 0 0 0 0 0 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 1
## AGCCCSub11 0 0 0 0 0 0 0 NA
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA 0 0 NA NA NA NA NA
## CTTGCTTSub14 0 0 0 NA 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 0 0 0 NA 0 0 0 NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 0 0 NA NA NA NA 0
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 NA NA NA NA 0
## ACAGTGCau3 0 0 0 0 0 0 0 0
## ACTATCau11 0 0 0 0 0 1 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 NA NA NA NA 0
## ATGAAACCau12 NA 0 0 NA 1 0 0 NA
## CTAGCCau5 0 0 0 0 0 0 0 0
## [,1889] [,1890] [,1891] [,1892] [,1893] [,1894] [,1895] [,1896]
## ACAAANel3 0 0 0 0 1 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 0 0
## AGCATNel8 0 0 0 0 0 0 0 0
## ATGAAACNel10 0 0 0 0 0 0 0 0
## ATGAAACNel15 0 0 0 0 0 0 0 0
## CGATGTNel4 0 0 0 0 0 0 0 0
## CTAGCNel7 0 0 0 0 0 0 0 0
## CTGTANel12 0 0 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 0 0
## CTTGANel2 0 0 0 0 0 0 0 0
## GGACCTANel11 0 0 0 0 0 0 0 0
## GGACCTANel13 0 0 0 0 0 0 0 0
## GTATTNel14 0 0 0 0 0 0 0 0
## TCACCNel6 0 0 0 0 1 0 0 0
## TGACCANel1 0 0 0 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 0 0 0 0
## ACAAAAlt11 0 0 0 0 0 0 0 0
## ACAGTGAlt3 0 0 0 0 0 0 0 0
## AGCCCAlt13 0 0 0 0 0 0 0 0
## ATCACGAlt5 0 0 0 0 1 0 0 0
## ATCACGAlt7 0 0 0 0 0 0 0 0
## CGATGTAlt1 0 0 0 0 0 0 0 0
## CTGTAAlt14 0 0 0 0 0 0 0 0
## CTTGAAlt10 0 0 0 0 0 0 0 0
## GAATTCAAlt15 0 0 0 0 0 0 0 0
## GCCAATAlt4 0 0 0 0 0 0 0 0
## GCCAATAlt9 0 0 0 0 0 0 0 0
## TTAGGCAlt2 0 0 0 0 0 0 0 0
## TTAGGCAlt6 0 0 0 0 0 0 0 0
## TTAGGCAlt8 0 0 0 0 0 0 0 0
## AAAAGTTSub15 NA NA 0 NA NA NA NA NA
## ACAAASub1 NA 0 0 0 1 0 0 0
## ACTATSub7 0 0 0 0 1 0 0 0
## AGCATSub13 0 0 0 0 0 0 0 0
## AGCCCSub11 NA 0 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA NA NA NA NA 0 0 0
## CTTGCTTSub14 0 NA 0 0 0 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA 0 0 0
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 0 NA NA 0 0 NA NA NA
## TGACCASub2 0 0 0 0 0 0 0 0
## ACAGTGCau2 0 0 0 0 0 NA NA NA
## ACAGTGCau3 0 0 NA 0 0 1 0 0
## ACTATCau11 0 0 0 0 0 1 0 0
## ACTATCau9 1 NA 0 0 0 1 0 0
## AGCCCCau7 0 0 NA 0 0 1 0 0
## ATGAAACCau12 NA 0 0 NA NA 1 0 0
## CTAGCCau5 0 0 0 1 0 1 0 0
## [,1897] [,1898] [,1899] [,1900] [,1901] [,1902] [,1903] [,1904]
## ACAAANel3 0 0 0 0 NA NA 1 0
## ACAGTGNel5 0 0 0 0 0 0 1 0
## AGCATNel8 0 1 0 0 0 0 1 0
## ATGAAACNel10 1 0 0 0 NA NA 1 0
## ATGAAACNel15 1 0 0 0 0 0 0 0
## CGATGTNel4 0 1 0 0 0 0 1 0
## CTAGCNel7 0 0 0 0 0 0 1 0
## CTGTANel12 0 1 0 0 0 0 0 0
## CTGTANel9 0 0 0 0 0 0 1 0
## CTTGANel2 0 0 0 0 0 0 1 0
## GGACCTANel11 0 0 0 0 0 0 1 0
## GGACCTANel13 0 NA NA NA 0 0 1 0
## GTATTNel14 0 0 0 0 NA NA 1 0
## TCACCNel6 0 1 0 0 0 0 1 0
## TGACCANel1 0 0 0 0 0 0 1 0
## AAAAGTTAlt12 0 0 0 0 0 0 1 0
## ACAAAAlt11 0 0 0 0 0 0 1 0
## ACAGTGAlt3 1 0 0 0 0 0 1 0
## AGCCCAlt13 0 0 0 0 0 0 1 0
## ATCACGAlt5 0 0 0 0 NA NA 0 0
## ATCACGAlt7 0 0 0 0 0 0 1 0
## CGATGTAlt1 1 0 0 0 0 0 1 0
## CTGTAAlt14 1 1 0 0 0 0 1 0
## CTTGAAlt10 1 0 0 0 0 0 1 0
## GAATTCAAlt15 1 0 0 0 0 0 1 0
## GCCAATAlt4 0 0 0 0 0 0 1 0
## GCCAATAlt9 1 0 0 0 0 0 1 0
## TTAGGCAlt2 0 0 0 0 0 0 1 0
## TTAGGCAlt6 1 0 0 0 NA NA 1 0
## TTAGGCAlt8 0 0 0 0 NA NA 1 0
## AAAAGTTSub15 0 0 0 0 0 0 0 0
## ACAAASub1 0 0 0 0 NA NA 0 0
## ACTATSub7 0 NA NA NA 0 0 0 0
## AGCATSub13 0 1 0 0 0 0 0 0
## AGCCCSub11 NA 1 0 0 0 0 0 0
## CGATGTSub6 0 0 0 0 0 0 0 0
## CTAGCSub3 NA 0 1 0 NA NA 0 0
## CTTGCTTSub14 NA 1 0 0 NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 NA 0 0 0 0 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 0 0 0 0 0 0 0 0
## GTATTSub12 NA 0 0 0 NA NA NA 0
## TGACCASub2 0 0 0 0 0 0 0 1
## ACAGTGCau2 NA 1 0 0 NA NA 0 0
## ACAGTGCau3 0 0 0 0 1 0 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 0 0 0 0 0 0 0 0
## AGCCCCau7 0 0 0 0 NA NA 0 0
## ATGAAACCau12 NA 0 0 0 1 0 NA 0
## CTAGCCau5 0 0 0 0 1 0 0 0
## [,1905] [,1906] [,1907] [,1908] [,1909] [,1910] [,1911] [,1912]
## ACAAANel3 0 0 1 0 0 0 0 0
## ACAGTGNel5 0 0 0 0 0 0 1 0
## AGCATNel8 0 0 1 0 NA NA NA NA
## ATGAAACNel10 0 0 1 0 0 0 1 0
## ATGAAACNel15 0 0 1 0 0 NA NA NA
## CGATGTNel4 0 0 1 0 0 0 1 0
## CTAGCNel7 0 0 1 0 0 NA NA NA
## CTGTANel12 0 0 1 0 0 0 1 0
## CTGTANel9 0 0 1 0 NA 0 1 0
## CTTGANel2 0 0 1 0 0 0 0 0
## GGACCTANel11 0 0 1 0 0 0 0 0
## GGACCTANel13 0 0 1 0 NA 0 1 0
## GTATTNel14 0 0 1 0 NA 0 1 0
## TCACCNel6 0 0 1 0 NA 0 0 0
## TGACCANel1 0 0 1 0 0 0 0 0
## AAAAGTTAlt12 0 0 0 0 NA NA NA NA
## ACAAAAlt11 0 0 0 0 0 0 1 0
## ACAGTGAlt3 0 0 1 0 NA 0 1 0
## AGCCCAlt13 0 NA 0 0 NA 0 1 0
## ATCACGAlt5 0 0 1 0 NA 0 0 0
## ATCACGAlt7 0 NA 0 0 NA 0 1 0
## CGATGTAlt1 0 0 1 0 0 0 1 0
## CTGTAAlt14 0 0 1 0 0 0 1 0
## CTTGAAlt10 0 0 1 0 0 0 1 0
## GAATTCAAlt15 0 0 0 0 0 0 1 0
## GCCAATAlt4 0 0 1 0 0 NA NA NA
## GCCAATAlt9 0 0 1 0 0 0 1 0
## TTAGGCAlt2 0 0 1 0 0 NA NA NA
## TTAGGCAlt6 0 0 0 0 0 NA NA NA
## TTAGGCAlt8 0 0 1 0 NA 1 1 0
## AAAAGTTSub15 NA 0 NA NA NA 0 1 0
## ACAAASub1 0 0 1 NA 0 0 1 0
## ACTATSub7 0 0 0 0 0 0 1 0
## AGCATSub13 0 0 1 0 0 0 1 0
## AGCCCSub11 0 NA NA 0 NA 0 1 0
## CGATGTSub6 0 0 1 NA NA 0 1 0
## CTAGCSub3 NA NA NA NA NA 0 1 0
## CTTGCTTSub14 0 NA 0 NA 0 0 1 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 0 0 0 0 0 1 0
## GCCAATSub4 NA NA 1 NA 0 NA NA NA
## GGACCTASub10 0 0 1 0 0 0 1 0
## GTATTSub12 NA NA NA 0 0 0 1 0
## TGACCASub2 0 NA 0 0 NA 0 1 0
## ACAGTGCau2 0 NA 0 0 NA 0 1 0
## ACAGTGCau3 0 0 0 NA 0 0 1 0
## ACTATCau11 0 0 1 0 0 0 1 0
## ACTATCau9 0 0 0 1 0 0 1 0
## AGCCCCau7 0 0 1 0 0 0 1 0
## ATGAAACCau12 0 NA 1 NA 0 0 1 0
## CTAGCCau5 0 0 0 1 0 0 1 0
## [,1913] [,1914] [,1915] [,1916] [,1917] [,1918] [,1919] [,1920]
## ACAAANel3 1 1 0 0 0 1 1 0
## ACAGTGNel5 0 1 0 0 0 1 NA NA
## AGCATNel8 NA 0 0 0 0 1 0 0
## ATGAAACNel10 0 1 0 0 0 1 0 0
## ATGAAACNel15 NA 0 0 0 0 1 0 0
## CGATGTNel4 0 1 0 0 0 1 0 0
## CTAGCNel7 NA 1 0 0 0 1 0 0
## CTGTANel12 0 NA 0 0 0 1 0 0
## CTGTANel9 0 NA 0 0 0 1 0 1
## CTTGANel2 1 1 0 0 0 1 0 0
## GGACCTANel11 1 1 0 0 0 1 NA NA
## GGACCTANel13 0 0 0 0 0 1 0 0
## GTATTNel14 1 1 0 0 0 1 0 0
## TCACCNel6 0 1 0 0 0 1 NA NA
## TGACCANel1 0 NA 0 0 0 1 0 0
## AAAAGTTAlt12 NA NA NA NA NA NA NA NA
## ACAAAAlt11 0 1 0 0 0 1 0 0
## ACAGTGAlt3 0 1 0 0 0 1 0 0
## AGCCCAlt13 0 1 0 0 0 1 NA NA
## ATCACGAlt5 0 NA 0 0 0 1 0 0
## ATCACGAlt7 0 1 0 0 0 1 0 0
## CGATGTAlt1 0 0 0 0 0 1 0 0
## CTGTAAlt14 0 1 0 0 0 1 0 0
## CTTGAAlt10 1 1 0 0 0 1 0 0
## GAATTCAAlt15 0 1 0 0 0 1 0 0
## GCCAATAlt4 NA 1 0 0 0 1 NA NA
## GCCAATAlt9 0 1 0 0 0 1 0 0
## TTAGGCAlt2 NA NA 0 0 0 1 0 0
## TTAGGCAlt6 NA 1 NA NA NA NA 0 0
## TTAGGCAlt8 0 NA 0 0 0 0 0 0
## AAAAGTTSub15 0 1 NA NA NA NA 0 0
## ACAAASub1 0 1 0 0 0 1 0 0
## ACTATSub7 0 1 0 0 0 1 0 0
## AGCATSub13 0 1 0 0 0 1 0 0
## AGCCCSub11 1 NA NA NA NA NA 0 0
## CGATGTSub6 0 NA 0 0 0 1 0 0
## CTAGCSub3 0 1 0 0 0 1 NA NA
## CTTGCTTSub14 0 NA NA NA NA NA 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 0 1 0 0 0 1 0 0
## GCCAATSub4 NA NA NA NA NA NA NA NA
## GGACCTASub10 1 0 0 0 0 1 0 0
## GTATTSub12 1 NA NA NA NA NA 0 0
## TGACCASub2 1 NA NA NA NA NA 0 0
## ACAGTGCau2 1 0 0 0 0 1 0 0
## ACAGTGCau3 0 0 1 1 1 1 0 0
## ACTATCau11 0 0 0 0 0 0 0 0
## ACTATCau9 1 0 0 0 0 0 0 0
## AGCCCCau7 1 0 0 0 0 1 0 0
## ATGAAACCau12 1 0 0 0 0 0 0 0
## CTAGCCau5 1 0 0 0 0 0 0 0
## [,1921] [,1922] [,1923] [,1924] [,1925] [,1926] [,1927] [,1928]
## ACAAANel3 1 0 1 0 NA NA NA NA
## ACAGTGNel5 NA 0 1 NA 0 0 0 0
## AGCATNel8 1 NA NA NA NA NA NA NA
## ATGAAACNel10 1 0 1 NA 0 0 0 0
## ATGAAACNel15 1 NA NA 0 0 0 0 0
## CGATGTNel4 1 NA NA 0 NA NA NA NA
## CTAGCNel7 1 0 0 0 0 0 0 0
## CTGTANel12 1 NA NA 0 1 0 0 0
## CTGTANel9 0 NA NA 0 NA NA NA NA
## CTTGANel2 1 NA NA NA 0 0 0 0
## GGACCTANel11 NA 0 1 0 0 0 0 0
## GGACCTANel13 1 0 1 0 0 0 0 0
## GTATTNel14 1 0 1 0 0 0 0 0
## TCACCNel6 NA 0 1 NA 1 0 0 0
## TGACCANel1 1 0 1 0 NA NA NA NA
## AAAAGTTAlt12 NA NA NA NA NA NA NA NA
## ACAAAAlt11 1 0 1 0 0 0 0 0
## ACAGTGAlt3 1 0 1 0 NA NA NA NA
## AGCCCAlt13 NA NA NA 0 0 0 0 0
## ATCACGAlt5 1 NA NA 0 0 0 0 0
## ATCACGAlt7 1 0 1 0 0 0 0 0
## CGATGTAlt1 1 NA NA 0 NA NA NA NA
## CTGTAAlt14 1 0 1 0 NA NA NA NA
## CTTGAAlt10 1 0 1 0 0 0 0 0
## GAATTCAAlt15 1 NA NA NA NA NA NA NA
## GCCAATAlt4 NA 0 1 NA NA NA NA NA
## GCCAATAlt9 1 0 1 0 0 0 0 0
## TTAGGCAlt2 1 0 1 0 NA NA NA NA
## TTAGGCAlt6 1 NA NA 0 0 0 0 0
## TTAGGCAlt8 1 0 1 0 1 0 0 0
## AAAAGTTSub15 1 NA NA NA 0 0 0 0
## ACAAASub1 1 0 0 NA NA NA NA NA
## ACTATSub7 1 0 0 0 NA NA NA NA
## AGCATSub13 1 NA NA 0 0 0 0 0
## AGCCCSub11 1 0 0 0 0 0 0 0
## CGATGTSub6 1 0 0 NA 0 0 0 0
## CTAGCSub3 NA 0 1 NA NA NA NA NA
## CTTGCTTSub14 1 NA NA 0 1 0 0 0
## CTTGCTTSub8 NA NA NA NA NA NA NA NA
## GAATTCASub9 1 NA NA 0 NA NA NA NA
## GCCAATSub4 NA NA NA NA 0 0 0 0
## GGACCTASub10 1 0 0 0 NA NA NA NA
## GTATTSub12 1 NA NA NA 0 0 0 0
## TGACCASub2 1 0 1 0 0 0 0 0
## ACAGTGCau2 1 0 1 NA 0 0 0 0
## ACAGTGCau3 1 0 NA 0 0 0 0 0
## ACTATCau11 1 NA NA 0 0 0 0 0
## ACTATCau9 1 0 1 0 0 0 0 0
## AGCCCCau7 1 0 1 0 NA NA NA NA
## ATGAAACCau12 1 0 1 0 0 0 0 0
## CTAGCCau5 1 NA NA 0 0 0 0 0
## [,1929]
## ACAAANel3 NA
## ACAGTGNel5 0
## AGCATNel8 NA
## ATGAAACNel10 0
## ATGAAACNel15 0
## CGATGTNel4 NA
## CTAGCNel7 0
## CTGTANel12 0
## CTGTANel9 NA
## CTTGANel2 0
## GGACCTANel11 0
## GGACCTANel13 0
## GTATTNel14 0
## TCACCNel6 0
## TGACCANel1 NA
## AAAAGTTAlt12 NA
## ACAAAAlt11 0
## ACAGTGAlt3 NA
## AGCCCAlt13 0
## ATCACGAlt5 0
## ATCACGAlt7 0
## CGATGTAlt1 NA
## CTGTAAlt14 NA
## CTTGAAlt10 0
## GAATTCAAlt15 NA
## GCCAATAlt4 NA
## GCCAATAlt9 0
## TTAGGCAlt2 NA
## TTAGGCAlt6 1
## TTAGGCAlt8 0
## AAAAGTTSub15 0
## ACAAASub1 NA
## ACTATSub7 NA
## AGCATSub13 0
## AGCCCSub11 0
## CGATGTSub6 0
## CTAGCSub3 NA
## CTTGCTTSub14 0
## CTTGCTTSub8 NA
## GAATTCASub9 NA
## GCCAATSub4 0
## GGACCTASub10 NA
## GTATTSub12 0
## TGACCASub2 0
## ACAGTGCau2 0
## ACAGTGCau3 0
## ACTATCau11 0
## ACTATCau9 0
## AGCCCCau7 NA
## ATGAAACCau12 0
## CTAGCCau5 0
## [ reached getOption("max.print") -- omitted 21 rows ]