Manipulation of NGS data with Bioconductor : Genomic Ranges library
Greg VOISIN
Wednesday, March 18, 2015
Manipulation of IRanges and GenomicRanges R objects:
load library
library(IRanges)
library(GenomicRanges)
library(GenomicFeatures)
library(rtracklayer)Illumina annotation
library(FDb.InfiniumMethylation.hg19)## Loading required package: Biostrings
## Loading required package: XVector
## Loading required package: BSgenome.Hsapiens.UCSC.hg19
## Loading required package: BSgenome
##
## Attaching package: 'BSgenome'
##
## The following object is masked from 'package:AnnotationDbi':
##
## species#acces to the data
infiniumMethylation <- features(FDb.InfiniumMethylation.hg19)
univers <- names(infiniumMethylation)
#object class
class(infiniumMethylation)## [1] "GRanges"
## attr(,"package")
## [1] "GenomicRanges"#acces a one element
infiniumMethylation["cg00000029"]## GRanges with 1 range and 14 metadata columns:
## seqnames ranges strand | addressA_450
## <Rle> <IRanges> <Rle> | <character>
## cg00000029 chr16 [53468112, 53468113] - | 14782418
## addressB_450 addressA_27 addressB_27 channel450 channel27
## <character> <character> <character> <character> <character>
## cg00000029 <NA> <NA> Both <NA>
## probeType percentGC platform
## <character> <character> <character>
## cg00000029 cg 0.46 HM450
## sourceSeq
## <character>
## cg00000029 GCTGTACTGACGAGAAAATGTCCAAAAGACACTGACGTGTGAAGGTTTCG
## probeStart probeEnd probeTarget probeExtension
## <character> <character> <character> <character>
## cg00000029 53468112 53468161 53468112 <NA>
## ---
## seqlengths:
## chr16 chr3 chr1 chr8 chr14 chr15 ... chr22 chrX chr13 chr5 chrY
## NA NA NA NA NA NA ... NA NA NA NA NA# acces au chr
as.vector(seqnames(infiniumMethylation["cg00000029"]))## [1] "chr16"# acces coord.
X= ranges(infiniumMethylation["cg00000029"])
start(X)## [1] 53468112end(X)## [1] 53468113Annotation hub:
library(AnnotationHub)
ah = AnnotationHub()
ensGene = ah$goldenpath.hg19.database.ensGene_0.0.1.RData
ensGene## UCSC track 'ensGene'
## UCSCData with 204940 ranges and 5 metadata columns:
## seqnames ranges strand |
## <Rle> <IRanges> <Rle> |
## [1] chr1 [66999066, 67210057] + |
## [2] chr1 [66999275, 67210768] + |
## [3] chr1 [66999298, 67145425] + |
## [4] chr1 [66999823, 67208882] + |
## [5] chr1 [66999839, 67142779] + |
## ... ... ... ... ...
## [204936] chr19_gl000209_random [ 57208, 68122] + |
## [204937] chr19_gl000209_random [ 70097, 84658] + |
## [204938] chr19_gl000209_random [ 86746, 96246] + |
## [204939] chr19_gl000209_random [147649, 156298] + |
## [204940] chr19_gl000209_random [147649, 156325] + |
## name score itemRgb thick
## <character> <numeric> <character> <IRanges>
## [1] ENST00000237247 0 <NA> [67000042, 67208778]
## [2] ENST00000371039 0 <NA> [67000042, 67208778]
## [3] ENST00000424320 0 <NA> [67000042, 67145425]
## [4] ENST00000371035 0 <NA> [67000042, 67208778]
## [5] ENST00000468286 0 <NA> [67142780, 67142779]
## ... ... ... ... ...
## [204936] ENST00000400854 0 <NA> [ 57249, 67717]
## [204937] ENST00000400848 0 <NA> [ 70108, 83979]
## [204938] ENST00000400846 0 <NA> [ 86746, 95742]
## [204939] ENST00000400827 0 <NA> [147649, 153110]
## [204940] ENST00000400829 0 <NA> [147649, 156325]
## blocks
## <IRangesList>
## [1] [ 1, 25] [ 864, 986] [92465, 92528] ...
## [2] [ 1, 81] [ 655, 777] [92256, 92319] ...
## [3] [ 1, 58] [ 632, 754] [92233, 92296] ...
## [4] [ 1, 229] [91708, 91771] [98931, 98955] ...
## [5] [ 1, 213] [91692, 91755] [98915, 98939] ...
## ... ...
## [204936] [ 1, 81] [ 281, 316] [1183, 1467] ...
## [204937] [ 1, 45] [1045, 1080] [1825, 2109] ...
## [204938] [ 1, 34] [ 768, 803] [1566, 1850] ...
## [204939] [ 1, 34] [ 764, 799] [3291, 3590] ...
## [204940] [ 1, 34] [ 764, 799] [1542, 1826] ...
## ---
## seqlengths:
## chr1 chr2 ... chr18_gl000207_random
## 249250621 243199373 ... 4262findOverlaps function
mask= seqnames(ensGene)== "chr1"
ensGene_chr1= ensGene[mask]
ov = findOverlaps(infiniumMethylation, ensGene_chr1)
head(ov)## Hits of length 6
## queryLength: 487173
## subjectLength: 17531
## queryHits subjectHits
## <integer> <integer>
## 1 9 2897
## 2 21 645
## 3 21 646
## 4 21 647
## 5 21 648
## 6 21 3929infiniumMethylation[head(queryHits(ov))]## GRanges with 6 ranges and 14 metadata columns:
## seqnames ranges strand | addressA_450
## <Rle> <IRanges> <Rle> | <character>
## cg00000363 chr1 [230560793, 230560794] - | 16661505
## cg00000957 chr1 [ 5937253, 5937254] - | 65648367
## cg00000957 chr1 [ 5937253, 5937254] - | 65648367
## cg00000957 chr1 [ 5937253, 5937254] - | 65648367
## cg00000957 chr1 [ 5937253, 5937254] - | 65648367
## cg00000957 chr1 [ 5937253, 5937254] - | 65648367
## addressB_450 addressA_27 addressB_27 channel450 channel27
## <character> <character> <character> <character> <character>
## cg00000363 <NA> <NA> Both <NA>
## cg00000957 36743439 <NA> <NA> Grn <NA>
## cg00000957 36743439 <NA> <NA> Grn <NA>
## cg00000957 36743439 <NA> <NA> Grn <NA>
## cg00000957 36743439 <NA> <NA> Grn <NA>
## cg00000957 36743439 <NA> <NA> Grn <NA>
## probeType percentGC platform
## <character> <character> <character>
## cg00000363 cg 0.42 HM450
## cg00000957 cg 0.7 HM450
## cg00000957 cg 0.7 HM450
## cg00000957 cg 0.7 HM450
## cg00000957 cg 0.7 HM450
## cg00000957 cg 0.7 HM450
## sourceSeq
## <character>
## cg00000363 TCTTGACTTGGCTTAGTTTTCTCCTTAATCTGAGAAACTTTCCCTGTCCG
## cg00000957 ATGCTACTGACCCATGCCCGGCAGGGCAAGGGGCCCCAGGACGTCAGCCG
## cg00000957 ATGCTACTGACCCATGCCCGGCAGGGCAAGGGGCCCCAGGACGTCAGCCG
## cg00000957 ATGCTACTGACCCATGCCCGGCAGGGCAAGGGGCCCCAGGACGTCAGCCG
## cg00000957 ATGCTACTGACCCATGCCCGGCAGGGCAAGGGGCCCCAGGACGTCAGCCG
## cg00000957 ATGCTACTGACCCATGCCCGGCAGGGCAAGGGGCCCCAGGACGTCAGCCG
## probeStart probeEnd probeTarget probeExtension
## <character> <character> <character> <character>
## cg00000363 230560793 230560842 230560793 <NA>
## cg00000957 5937253 5937302 5937253 <NA>
## cg00000957 5937253 5937302 5937253 <NA>
## cg00000957 5937253 5937302 5937253 <NA>
## cg00000957 5937253 5937302 5937253 <NA>
## cg00000957 5937253 5937302 5937253 <NA>
## ---
## seqlengths:
## chr16 chr3 chr1 chr8 chr14 chr15 ... chr22 chrX chr13 chr5 chrY
## NA NA NA NA NA NA ... NA NA NA NA NAensGene_chr1[head(subjectHits(ov))]## UCSC track 'ensGene'
## UCSCData with 6 ranges and 5 metadata columns:
## seqnames ranges strand | name score
## <Rle> <IRanges> <Rle> | <character> <numeric>
## [1] chr1 [230457392, 230561475] - | ENST00000391860 0
## [2] chr1 [ 5922871, 6052484] - | ENST00000478423 0
## [3] chr1 [ 5922873, 6052533] - | ENST00000489180 0
## [4] chr1 [ 5922878, 6052531] - | ENST00000378156 0
## [5] chr1 [ 5923325, 6052507] - | ENST00000378169 0
## [6] chr1 [ 5934965, 5937526] - | ENST00000506941 0
## itemRgb thick
## <character> <IRanges>
## [1] <NA> [230459171, 230493053]
## [2] <NA> [ 6052485, 6052484]
## [3] <NA> [ 5939565, 6046349]
## [4] <NA> [ 5923325, 6046349]
## [5] <NA> [ 6008196, 6046349]
## [6] <NA> [ 5937527, 5937526]
## blocks
## <IRangesList>
## [1] [ 1, 1975] [ 3665, 3770] [11199, 11396] ...
## [2] [ 1, 595] [1080, 1223] [1528, 1707] ...
## [3] [ 1, 593] [1078, 1221] [1526, 1705] ...
## [4] [ 1, 588] [1073, 1216] [1521, 1700] ...
## [5] [ 1, 141] [ 626, 769] [1074, 1253] ...
## [6] [ 1, 196] [2189, 2562]
## ---
## seqlengths:
## chr1 chr2 ... chr18_gl000207_random
## 249250621 243199373 ... 4262IRanges instance
Indicates the start and end positions of 7 genes.
ir <- IRanges(start=c(7, 9, 12, 14, 22:24),end=c(15, 11, 12, 18, 26, 27, 28))
ir## IRanges of length 7
## start end width
## [1] 7 15 9
## [2] 9 11 3
## [3] 12 12 1
## [4] 14 18 5
## [5] 22 26 5
## [6] 23 27 5
## [7] 24 28 5Some methods are available to manipulate the IRanges objects: - intra-range methods: flank, narrow, reflect, resize,restrict, and shift, among others
shift(ir, 5)## IRanges of length 7
## start end width
## [1] 12 20 9
## [2] 14 16 3
## [3] 17 17 1
## [4] 19 23 5
## [5] 27 31 5
## [6] 28 32 5
## [7] 29 33 5- inter-range methods : disjoin, reduce, gaps, and range.
reduce(ir)## IRanges of length 2
## start end width
## [1] 7 18 12
## [2] 22 28 7coverage(ir)## integer-Rle of length 28 with 12 runs
## Lengths: 6 2 4 1 2 3 3 1 1 3 1 1
## Values : 0 1 2 1 2 1 0 1 2 3 2 1- between range methods: intersect, setdiff, union, pintersect, psetdiff, and punion.
GenomicsRanges instance
genes <- GRanges( seqnames=Rle(c("Chr1", "X"), c(1,1)),
ranges=IRanges(start=c(19967117, 18962306), end=c(19973212, 18962925)),
strand=Rle(c("+", "-"),c(1,1)),
seqlengths=c("Chr1"=27905053L, "X"=22422827L)
)Remarks:
- GRanges object includes IRanges object.
- note the L in seqlengths args, which simply guarantees that a number which could be interpreted as 1 byte will always be interpreted as 4 bytes (signed as Long).
- the minimal information for GRanges object is seqnames, ranges and strand. - Rle object : Run Length Encoding is a common compression technique for storing long sequences with lengthy repeat)
Some methods are available to manipulate the GenomicRanges objects:
- inspection and accessor
genes## GRanges with 2 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] Chr1 [19967117, 19973212] +
## [2] X [18962306, 18962925] -
## ---
## seqlengths:
## Chr1 X
## 27905053 22422827 class(genes)## [1] "GRanges"
## attr(,"package")
## [1] "GenomicRanges" genes[2]## GRanges with 1 range and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] X [18962306, 18962925] -
## ---
## seqlengths:
## Chr1 X
## 27905053 22422827 strand(genes)## factor-Rle of length 2 with 2 runs
## Lengths: 1 1
## Values : + -
## Levels(3): + - * width(genes)## [1] 6096 620 length(genes)## [1] 2- add informations : names for each genes.
names(genes) <- c("FBgn0039155", "FBgn0085359")
genes## GRanges with 2 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## FBgn0039155 Chr1 [19967117, 19973212] +
## FBgn0085359 X [18962306, 18962925] -
## ---
## seqlengths:
## Chr1 X
## 27905053 22422827- optional informations for the genes: META columns.
genes## GRanges with 2 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## FBgn0039155 Chr1 [19967117, 19973212] +
## FBgn0085359 X [18962306, 18962925] -
## ---
## seqlengths:
## Chr1 X
## 27905053 22422827mcols(genes) <- DataFrame(EntrezId=c("42865", "2768869"), Symbol=c("kal-1", "CG34330"))
genes ## GRanges with 2 ranges and 2 metadata columns:
## seqnames ranges strand | EntrezId
## <Rle> <IRanges> <Rle> | <character>
## FBgn0039155 Chr1 [19967117, 19973212] + | 42865
## FBgn0085359 X [18962306, 18962925] - | 2768869
## Symbol
## <character>
## FBgn0039155 kal-1
## FBgn0085359 CG34330
## ---
## seqlengths:
## Chr1 X
## 27905053 22422827GRangesList instance
GRangesList represents a more complexe structure and used for sliced transcripts, all genes of the genome with the exon composition, …
gr1 <- GRanges(seqnames = "chr2", ranges = IRanges(3, 6), strand = "+", score = 5L, GC = 0.45)
gr2 <- GRanges(seqnames = c("chr1", "chr1"), ranges = IRanges(c(7,13), width = 3), strand = c("+", "-"), score = 3:4, GC = c(0.3, 0.5))
grlist <- GRangesList("txA" = gr1, "txB" = gr2)
grlist## GRangesList of length 2:
## $txA
## GRanges with 1 range and 2 metadata columns:
## seqnames ranges strand | score GC
## <Rle> <IRanges> <Rle> | <integer> <numeric>
## [1] chr2 [3, 6] + | 5 0.45
##
## $txB
## GRanges with 2 ranges and 2 metadata columns:
## seqnames ranges strand | score GC
## [1] chr1 [ 7, 9] + | 3 0.3
## [2] chr1 [13, 15] - | 4 0.5
##
## ---
## seqlengths:
## chr2 chr1
## NA NAWhy is interesting to work with a list ? In practice, the mclapply allows to parallize the job on a cluster, from a list object.
Manipulate a big GRange object
import a gff file
gff <- import.gff("DATA/gff3.gff", asRangedData=FALSE)
gff## GRanges with 449 ranges and 5 metadata columns:
## seqnames ranges strand | source type score
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
## [1] Chr1 [ 1, 30427671] + | TAIR10 chromosome <NA>
## [2] Chr1 [3631, 5899] + | TAIR10 gene <NA>
## [3] Chr1 [3631, 5899] + | TAIR10 mRNA <NA>
## [4] Chr1 [3760, 5630] + | TAIR10 protein <NA>
## [5] Chr1 [3631, 3913] + | TAIR10 exon <NA>
## ... ... ... ... ... ... ... ...
## [445] ChrM [11918, 12241] + | TAIR10 gene <NA>
## [446] ChrM [11918, 12241] + | TAIR10 mRNA <NA>
## [447] ChrM [11918, 12241] + | TAIR10 protein <NA>
## [448] ChrM [11918, 12241] + | TAIR10 exon <NA>
## [449] ChrM [11918, 12241] + | TAIR10 CDS <NA>
## phase
## <integer>
## [1] <NA>
## [2] <NA>
## [3] <NA>
## [4] <NA>
## [5] <NA>
## ... ...
## [445] <NA>
## [446] <NA>
## [447] <NA>
## [448] <NA>
## [449] 0
## group
## <factor>
## [1] ID=Chr1;Name=Chr1
## [2] ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
## [3] ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
## [4] ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
## [5] Parent=AT1G01010.1
## ... ...
## [445] ID=ATMG00030;Note=protein_coding_gene;Name=ATMG00030
## [446] ID=ATMG00030.1;Parent=ATMG00030;Name=ATMG00030.1;Index=1
## [447] ID=ATMG00030.1-Protein;Name=ATMG00030.1;Derives_from=ATMG00030.1
## [448] Parent=ATMG00030.1
## [449] Parent=ATMG00030.1,ATMG00030.1-Protein;
## ---
## seqlengths:
## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## NA NA NA NA NA NA NAAccessors the gff informations
seqlengths(gff) <- end(ranges(gff[which(values(gff)[,"type"]=="chromosome"),]))
names(gff) <- 1:length(gff)
gff[1:4,]## GRanges with 4 ranges and 5 metadata columns:
## seqnames ranges strand | source type score
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
## 1 Chr1 [ 1, 30427671] + | TAIR10 chromosome <NA>
## 2 Chr1 [3631, 5899] + | TAIR10 gene <NA>
## 3 Chr1 [3631, 5899] + | TAIR10 mRNA <NA>
## 4 Chr1 [3760, 5630] + | TAIR10 protein <NA>
## phase
## <integer>
## 1 <NA>
## 2 <NA>
## 3 <NA>
## 4 <NA>
## group
## <factor>
## 1 ID=Chr1;Name=Chr1
## 2 ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
## 3 ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
## 4 ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
## ---
## seqlengths:
## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## 30427671 19698289 23459830 18585056 26975502 154478 366924gff[1:4]## GRanges with 4 ranges and 5 metadata columns:
## seqnames ranges strand | source type score
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
## 1 Chr1 [ 1, 30427671] + | TAIR10 chromosome <NA>
## 2 Chr1 [3631, 5899] + | TAIR10 gene <NA>
## 3 Chr1 [3631, 5899] + | TAIR10 mRNA <NA>
## 4 Chr1 [3760, 5630] + | TAIR10 protein <NA>
## phase
## <integer>
## 1 <NA>
## 2 <NA>
## 3 <NA>
## 4 <NA>
## group
## <factor>
## 1 ID=Chr1;Name=Chr1
## 2 ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
## 3 ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
## 4 ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
## ---
## seqlengths:
## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## 30427671 19698289 23459830 18585056 26975502 154478 366924gff[1:4, c("type", "group")]## GRanges with 4 ranges and 2 metadata columns:
## seqnames ranges strand | type
## <Rle> <IRanges> <Rle> | <factor>
## 1 Chr1 [ 1, 30427671] + | chromosome
## 2 Chr1 [3631, 5899] + | gene
## 3 Chr1 [3631, 5899] + | mRNA
## 4 Chr1 [3760, 5630] + | protein
## group
## <factor>
## 1 ID=Chr1;Name=Chr1
## 2 ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
## 3 ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
## 4 ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
## ---
## seqlengths:
## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## 30427671 19698289 23459830 18585056 26975502 154478 366924c(gff[1:2], gff[401:402])## GRanges with 4 ranges and 5 metadata columns:
## seqnames ranges strand | source type score
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
## 1 Chr1 [ 1, 30427671] + | TAIR10 chromosome <NA>
## 2 Chr1 [3631, 5899] + | TAIR10 gene <NA>
## 401 Chr5 [5516, 5769] - | TAIR10 protein <NA>
## 402 Chr5 [5770, 5801] - | TAIR10 five_prime_UTR <NA>
## phase
## <integer>
## 1 <NA>
## 2 <NA>
## 401 <NA>
## 402 <NA>
## group
## <factor>
## 1 ID=Chr1;Name=Chr1
## 2 ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
## 401 ID=AT5G01015.2-Protein;Name=AT5G01015.2;Derives_from=AT5G01015.2
## 402 Parent=AT5G01015.2
## ---
## seqlengths:
## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## 30427671 19698289 23459830 18585056 26975502 154478 366924seqnames(gff)## factor-Rle of length 449 with 7 runs
## Lengths: 72 22 38 118 172 13 14
## Values : Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## Levels(7): Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrMranges(gff)## IRanges of length 449
## start end width names
## [1] 1 30427671 30427671 1
## [2] 3631 5899 2269 2
## [3] 3631 5899 2269 3
## [4] 3760 5630 1871 4
## [5] 3631 3913 283 5
## ... ... ... ... ...
## [445] 11918 12241 324 445
## [446] 11918 12241 324 446
## [447] 11918 12241 324 447
## [448] 11918 12241 324 448
## [449] 11918 12241 324 449strand(gff)## factor-Rle of length 449 with 13 runs
## Lengths: 18 54 28 21 12 117 1 171 1 12 1 8 5
## Values : + - + - + - + - + - + - +
## Levels(3): + - *seqlengths(gff) ## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## 30427671 19698289 23459830 18585056 26975502 154478 366924values(gff)## DataFrame with 449 rows and 5 columns
## source type score phase
## <factor> <factor> <numeric> <integer>
## 1 TAIR10 chromosome NA NA
## 2 TAIR10 gene NA NA
## 3 TAIR10 mRNA NA NA
## 4 TAIR10 protein NA NA
## 5 TAIR10 exon NA NA
## ... ... ... ... ...
## 445 TAIR10 gene NA NA
## 446 TAIR10 mRNA NA NA
## 447 TAIR10 protein NA NA
## 448 TAIR10 exon NA NA
## 449 TAIR10 CDS NA 0
## group
## <factor>
## 1 ID=Chr1;Name=Chr1
## 2 ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
## 3 ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
## 4 ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
## 5 Parent=AT1G01010.1
## ... ...
## 445 ID=ATMG00030;Note=protein_coding_gene;Name=ATMG00030
## 446 ID=ATMG00030.1;Parent=ATMG00030;Name=ATMG00030.1;Index=1
## 447 ID=ATMG00030.1-Protein;Name=ATMG00030.1;Derives_from=ATMG00030.1
## 448 Parent=ATMG00030.1
## 449 Parent=ATMG00030.1,ATMG00030.1-Protein;values(gff)[, "type"]## [1] chromosome gene mRNA protein
## [5] exon five_prime_UTR CDS exon
## [9] CDS exon CDS exon
## [13] CDS exon CDS exon
## [17] CDS three_prime_UTR gene mRNA
## [21] protein five_prime_UTR CDS exon
## [25] CDS exon CDS exon
## [29] CDS exon CDS exon
## [33] CDS exon CDS exon
## [37] CDS exon CDS three_prime_UTR
## [41] exon three_prime_UTR exon mRNA
## [45] protein five_prime_UTR CDS exon
## [49] CDS exon CDS exon
## [53] CDS exon CDS exon
## [57] CDS exon CDS three_prime_UTR
## [61] exon three_prime_UTR exon gene
## [65] mRNA protein five_prime_UTR exon
## [69] five_prime_UTR CDS three_prime_UTR exon
## [73] chromosome gene mRNA protein
## [77] exon CDS exon CDS
## [81] exon CDS three_prime_UTR gene
## [85] rRNA exon gene rRNA
## [89] exon gene mRNA protein
## [93] exon CDS chromosome gene
## [97] mRNA protein exon CDS
## [101] gene mRNA protein five_prime_UTR
## [105] CDS exon CDS exon
## [109] CDS exon CDS exon
## [113] CDS exon CDS exon
## [117] CDS exon CDS three_prime_UTR
## [121] exon gene mRNA protein
## [125] exon five_prime_UTR CDS exon
## [129] CDS exon CDS three_prime_UTR
## [133] chromosome gene mRNA protein
## [137] CDS exon gene mRNA
## [141] protein five_prime_UTR CDS exon
## [145] CDS exon CDS exon
## [149] CDS exon CDS exon
## [153] CDS exon CDS exon
## [157] CDS exon CDS exon
## [161] CDS exon CDS exon
## [165] CDS exon CDS exon
## [169] CDS exon CDS exon
## [173] CDS exon CDS exon
## [177] CDS exon CDS exon
## [181] CDS three_prime_UTR exon mRNA
## [185] protein CDS exon CDS
## [189] exon CDS exon CDS
## [193] exon CDS exon CDS
## [197] exon CDS exon CDS
## [201] exon CDS exon CDS
## [205] exon CDS exon CDS
## [209] exon CDS exon CDS
## [213] exon CDS exon CDS
## [217] exon CDS exon CDS
## [221] exon CDS exon CDS
## [225] exon CDS exon CDS
## [229] exon gene mRNA protein
## [233] five_prime_UTR CDS exon CDS
## [237] exon CDS exon CDS
## [241] exon CDS exon CDS
## [245] exon CDS exon CDS
## [249] three_prime_UTR exon chromosome gene
## [253] mRNA protein five_prime_UTR CDS
## [257] exon CDS exon CDS
## [261] exon CDS exon CDS
## [265] exon CDS exon CDS
## [269] exon CDS exon CDS
## [273] exon CDS exon CDS
## [277] exon CDS exon CDS
## [281] exon CDS exon CDS
## [285] three_prime_UTR exon mRNA protein
## [289] five_prime_UTR CDS exon CDS
## [293] exon CDS exon CDS
## [297] exon CDS exon CDS
## [301] exon CDS exon CDS
## [305] exon CDS exon CDS
## [309] exon CDS exon CDS
## [313] exon CDS exon CDS
## [317] exon CDS exon CDS
## [321] three_prime_UTR exon mRNA protein
## [325] five_prime_UTR CDS exon CDS
## [329] exon CDS exon CDS
## [333] exon CDS exon CDS
## [337] exon CDS exon CDS
## [341] exon CDS exon CDS
## [345] exon CDS exon CDS
## [349] exon CDS exon CDS
## [353] three_prime_UTR exon mRNA protein
## [357] five_prime_UTR CDS exon CDS
## [361] exon CDS exon CDS
## [365] exon CDS exon CDS
## [369] exon CDS exon CDS
## [373] exon CDS exon CDS
## [377] exon CDS exon CDS
## [381] exon CDS exon CDS
## [385] exon CDS exon CDS
## [389] three_prime_UTR exon gene mRNA
## [393] protein five_prime_UTR CDS exon
## [397] CDS three_prime_UTR exon mRNA
## [401] protein five_prime_UTR CDS exon
## [405] CDS three_prime_UTR exon gene
## [409] mRNA protein five_prime_UTR CDS
## [413] exon CDS exon CDS
## [417] exon CDS exon CDS
## [421] three_prime_UTR exon chromosome gene
## [425] tRNA exon gene mRNA
## [429] protein CDS exon gene
## [433] tRNA exon exon chromosome
## [437] gene mRNA protein CDS
## [441] exon gene rRNA exon
## [445] gene mRNA protein exon
## [449] CDS
## 10 Levels: CDS chromosome exon five_prime_UTR gene mRNA protein ... tRNAgff[elementMetadata(gff)[ ,"type"] == "gene"] ## GRanges with 22 ranges and 5 metadata columns:
## seqnames ranges strand | source type score
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
## 2 Chr1 [ 3631, 5899] + | TAIR10 gene <NA>
## 19 Chr1 [ 5928, 8737] - | TAIR10 gene <NA>
## 64 Chr1 [11649, 13714] - | TAIR10 gene <NA>
## 74 Chr2 [ 1025, 2810] + | TAIR10 gene <NA>
## 84 Chr2 [ 3706, 5513] + | TAIR10 gene <NA>
## ... ... ... ... ... ... ... ...
## 427 ChrC [ 383, 1444] - | TAIR10 gene <NA>
## 432 ChrC [ 1717, 4347] - | TAIR10 gene <NA>
## 437 ChrM [ 273, 734] - | TAIR10 gene <NA>
## 442 ChrM [ 8848, 11415] - | TAIR10 gene <NA>
## 445 ChrM [11918, 12241] + | TAIR10 gene <NA>
## phase group
## <integer> <factor>
## 2 <NA> ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
## 19 <NA> ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020
## 64 <NA> ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030
## 74 <NA> ID=AT2G01008;Note=protein_coding_gene;Name=AT2G01008
## 84 <NA> ID=AT2G01010;Note=rRNA;Name=AT2G01010
## ... ... ...
## 427 <NA> ID=ATCG00020;Note=protein_coding_gene;Name=ATCG00020
## 432 <NA> ID=ATCG00030;Note=tRNA;Name=ATCG00030
## 437 <NA> ID=ATMG00010;Note=protein_coding_gene;Name=ATMG00010
## 442 <NA> ID=ATMG00020;Note=rRNA;Name=ATMG00020
## 445 <NA> ID=ATMG00030;Note=protein_coding_gene;Name=ATMG00030
## ---
## seqlengths:
## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## 30427671 19698289 23459830 18585056 26975502 154478 366924Useful utilities for GRanges objects
Remove chromosome ranges
gff <- gff[values(gff)$type != "chromosome"] Erases the strand information
strand(gff) <- "*"Collapses overlapping ranges to continuous ranges.
reduce(gff)## GRanges with 22 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] Chr1 [ 3631, 5899] *
## [2] Chr1 [ 5928, 8737] *
## [3] Chr1 [11649, 13714] *
## [4] Chr2 [ 1025, 2810] *
## [5] Chr2 [ 3706, 5513] *
## ... ... ... ...
## [18] ChrC [ 383, 1444] *
## [19] ChrC [ 1717, 4347] *
## [20] ChrM [ 273, 734] *
## [21] ChrM [ 8848, 11415] *
## [22] ChrM [11918, 12241] *
## ---
## seqlengths:
## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## 30427671 19698289 23459830 18585056 26975502 154478 366924Returns uncovered regions.
gaps(gff)## GRanges with 43 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] Chr1 [ 1, 30427671] +
## [2] Chr1 [ 1, 30427671] -
## [3] Chr1 [ 1, 3630] *
## [4] Chr1 [5900, 5927] *
## [5] Chr1 [8738, 11648] *
## ... ... ... ...
## [39] ChrM [ 1, 366924] -
## [40] ChrM [ 1, 272] *
## [41] ChrM [ 735, 8847] *
## [42] ChrM [11416, 11917] *
## [43] ChrM [12242, 366924] *
## ---
## seqlengths:
## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## 30427671 19698289 23459830 18585056 26975502 154478 366924Returns disjoint ranges.
disjoin(gff) ## GRanges with 211 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] Chr1 [3631, 3759] *
## [2] Chr1 [3760, 3913] *
## [3] Chr1 [3914, 3995] *
## [4] Chr1 [3996, 4276] *
## [5] Chr1 [4277, 4485] *
## ... ... ... ...
## [207] ChrC [ 1752, 4310] *
## [208] ChrC [ 4311, 4347] *
## [209] ChrM [ 273, 734] *
## [210] ChrM [ 8848, 11415] *
## [211] ChrM [11918, 12241] *
## ---
## seqlengths:
## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## 30427671 19698289 23459830 18585056 26975502 154478 366924Returns coverage of ranges.
coverage(gff)## RleList of length 7
## $Chr1
## integer-Rle of length 30427671 with 45 runs
## Lengths: 3630 129 154 ... 161 380 30413957
## Values : 0 4 5 ... 2 4 0
##
## $Chr2
## integer-Rle of length 19698289 with 14 runs
## Lengths: 1024 248 185 ... 625 102 19691617
## Values : 0 5 3 ... 0 5 0
##
## $Chr3
## integer-Rle of length 23459830 with 29 runs
## Lengths: 1652 145 139 ... 148 156 23453781
## Values : 0 4 5 ... 5 4 0
##
## $Chr4
## integer-Rle of length 18585056 with 72 runs
## Lengths: 1179 357 1358 ... 114 74 18571697
## Values : 0 5 0 ... 5 4 0
##
## $Chr5
## integer-Rle of length 26975502 with 64 runs
## Lengths: 1222 28 28 ... 55 174 26967058
## Values : 0 4 7 ... 5 4 0
##
## ...
## <2 more elements>Returns the index pairings for the overlapping ranges.
findOverlaps(gff, gff[1:4])## Hits of length 55
## queryLength: 442
## subjectLength: 4
## queryHits subjectHits
## <integer> <integer>
## 1 1 1
## 2 1 2
## 3 1 3
## 4 1 4
## 5 2 1
## ... ... ...
## 51 16 1
## 52 16 2
## 53 16 3
## 54 17 1
## 55 17 2Counts overlapping ranges
countOverlaps(gff, gff[1:4]) ## 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
## 4 4 4 4 3 4 3 3 3 3 3 3 3 3 3 3 2 0
## 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 74
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 93 94 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 130 131 132 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 239 240 241 242 243 244 245 246 247 248 249 250 252 253 254 255 256 257
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 420 421 422 424 425 426 427 428 429 430 431 432 433 434 435 437 438 439
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 440 441 442 443 444 445 446 447 448 449
## 0 0 0 0 0 0 0 0 0 0Returns only overlapping ranges
subsetByOverlaps(gff, gff[1:4])## GRanges with 17 ranges and 5 metadata columns:
## seqnames ranges strand | source type score
## <Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
## 2 Chr1 [3631, 5899] * | TAIR10 gene <NA>
## 3 Chr1 [3631, 5899] * | TAIR10 mRNA <NA>
## 4 Chr1 [3760, 5630] * | TAIR10 protein <NA>
## 5 Chr1 [3631, 3913] * | TAIR10 exon <NA>
## 6 Chr1 [3631, 3759] * | TAIR10 five_prime_UTR <NA>
## ... ... ... ... ... ... ... ...
## 14 Chr1 [5174, 5326] * | TAIR10 exon <NA>
## 15 Chr1 [5174, 5326] * | TAIR10 CDS <NA>
## 16 Chr1 [5439, 5899] * | TAIR10 exon <NA>
## 17 Chr1 [5439, 5630] * | TAIR10 CDS <NA>
## 18 Chr1 [5631, 5899] * | TAIR10 three_prime_UTR <NA>
## phase
## <integer>
## 2 <NA>
## 3 <NA>
## 4 <NA>
## 5 <NA>
## 6 <NA>
## ... ...
## 14 <NA>
## 15 0
## 16 <NA>
## 17 0
## 18 <NA>
## group
## <factor>
## 2 ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
## 3 ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
## 4 ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
## 5 Parent=AT1G01010.1
## 6 Parent=AT1G01010.1
## ... ...
## 14 Parent=AT1G01010.1
## 15 Parent=AT1G01010.1,AT1G01010.1-Protein;
## 16 Parent=AT1G01010.1
## 17 Parent=AT1G01010.1,AT1G01010.1-Protein;
## 18 Parent=AT1G01010.1
## ---
## seqlengths:
## Chr1 Chr2 Chr3 Chr4 Chr5 ChrC ChrM
## 30427671 19698289 23459830 18585056 26975502 154478 366924Basic manipulations of genomic sequences
The output of NGS technology is essentially a collection of genomic sequences, so it’s interesting to have a R tools to manage this kind of objects.
Build a set of 3 DNA sequences:
myseq <- c("ATGCAGACATAGTG","ATGAACATAGATCC","GTACAGATCAC")
class(myseq)## [1] "character"length(myseq)## [1] 3Use the REGULAR EXPRESSION function to find a particular structure
WARNNING: it’S important to understand how to use correctly the regular expression functions: grep, strsplit, gsub …
grep("ATG", myseq)## [1] 1 2myseq[grep("ATG", myseq)]## [1] "ATGCAGACATAGTG" "ATGAACATAGATCC"Use the REGULAR EXPRESSION function to return the first structure found in each sequence
pos1 <- regexpr("AT", myseq)
pos1## [1] 1 1 7
## attr(,"match.length")
## [1] 2 2 2
## attr(,"useBytes")
## [1] TRUEUse the REGULAR EXPRESSION function to return all structure found in each sequence
pos2 <- gregexpr("AT", myseq)
pos2## [[1]]
## [1] 1 9
## attr(,"match.length")
## [1] 2 2
## attr(,"useBytes")
## [1] TRUE
##
## [[2]]
## [1] 1 7 11
## attr(,"match.length")
## [1] 2 2 2
## attr(,"useBytes")
## [1] TRUE
##
## [[3]]
## [1] 7
## attr(,"match.length")
## [1] 2
## attr(,"useBytes")
## [1] TRUEUse the REGULAR EXPRESSION function to substitute
gsub("^ATG", "atg", myseq)## [1] "atgCAGACATAGTG" "atgAACATAGATCC" "GTACAGATCAC"Parsing sequence
nchar(myseq)## [1] 14 14 11substring(myseq[1], c(1,3), c(2,5))## [1] "AT" "GCA"substring(myseq, c(1,4,7), c(2,6,10)) #hint: 2 arg is a start, 3 arg is a stop## [1] "AT" "AAC" "ATCA"Manipulation with a fasta file
Install Biostrings package:
source("http://bioconductor.org/biocLite.R")
biocLite(c("Biostrings")load library
library(Biostrings )Read FASTA, for arabidopsis collection sequences.
assembly = readDNAStringSet("DATA/tair10chr.fasta")inspect assembly object: assembly is a container allowing to store many sequences in one object.
class(assembly)## [1] "DNAStringSet"
## attr(,"package")
## [1] "Biostrings"assembly## A DNAStringSet instance of length 7
## width seq names
## [1] 30427671 CCCTAAACCCTAAACCCTA...TAGGGTTTAGGGTTTAGGG Chr1
## [2] 19698289 NNNNNNNNNNNNNNNNNNN...TAGGGTTTAGGGTTTAGGG Chr2
## [3] 23459830 NNNNNNNNNNNNNNNNNNN...AACCCTAAACCCTAAACCC Chr3
## [4] 18585056 NNNNNNNNNNNNNNNNNNN...TTAGGGTTTAGGGTTTAGG Chr4
## [5] 26975502 TATACCATGTACCCTCAAC...GATTTAGGGTTTTTAGATC Chr5
## [6] 154478 ATGGGCGAACGACGGGAAT...TAACTTGGTCCCGGGCATC ChrC
## [7] 366924 GGATCCGTTCGAAACAGGT...AATGGAAACAAACCGGATT ChrMlength(assembly)## [1] 7assembly[[1]]## 30427671-letter "DNAString" instance
## seq: CCCTAAACCCTAAACCCTAAACCCTAAACCTCTG...TAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGwidth(assembly) ## [1] 30427671 19698289 23459830 18585056 26975502 154478 366924summary(width(assembly))## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 154500 9476000 19700000 17100000 25220000 30430000sum(width(assembly))## [1] 119667750hist(log10( width(assembly)), 100)
unlist(assembly)## 119667750-letter "DNAString" instance
## seq: CCCTAAACCCTAAACCCTAAACCCTAAACCTCTG...CATTCTTATCGCAGAATGGAAACAAACCGGATTManipulate assembly object:
Subset [[ ]]
largest.contig = assembly[[ which(width(assembly)==max(width(assembly))) ]]
largest.contig## 30427671-letter "DNAString" instance
## seq: CCCTAAACCCTAAACCCTAAACCCTAAACCTCTG...TAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGSubset [ i ]
top.contigs = assembly[order(width(assembly),decreasing=TRUE)][1:5]
top.contigs## A DNAStringSet instance of length 5
## width seq names
## [1] 30427671 CCCTAAACCCTAAACCCTA...TAGGGTTTAGGGTTTAGGG Chr1
## [2] 26975502 TATACCATGTACCCTCAAC...GATTTAGGGTTTTTAGATC Chr5
## [3] 23459830 NNNNNNNNNNNNNNNNNNN...AACCCTAAACCCTAAACCC Chr3
## [4] 19698289 NNNNNNNNNNNNNNNNNNN...TAGGGTTTAGGGTTTAGGG Chr2
## [5] 18585056 NNNNNNNNNNNNNNNNNNN...TTAGGGTTTAGGGTTTAGG Chr4names
head( names(assembly) )## [1] "Chr1" "Chr2" "Chr3" "Chr4" "Chr5" "ChrC"Subset [boolean]
subsetChrC = assembly[grepl( "ChrC",names(assembly) )]
writeXStringSet(subsetChrC, file="DATA/subsetChrC.fasta", width=80)Subset names
assembly["Chr1"]## A DNAStringSet instance of length 1
## width seq names
## [1] 30427671 CCCTAAACCCTAAACCCTA...TAGGGTTTAGGGTTTAGGG Chr1subseq
subseq(assembly,start=1,end=10)## A DNAStringSet instance of length 7
## width seq names
## [1] 10 CCCTAAACCC Chr1
## [2] 10 NNNNNNNNNN Chr2
## [3] 10 NNNNNNNNNN Chr3
## [4] 10 NNNNNNNNNN Chr4
## [5] 10 TATACCATGT Chr5
## [6] 10 ATGGGCGAAC ChrC
## [7] 10 GGATCCGTTC ChrMnucleotide Content
head( alphabetFrequency(assembly) )## A C G T M R W S Y K V H D B N - +
## [1,] 9709674 5435374 5421151 9697113 76 36 124 30 82 53 0 0 0 0 163958 0 0
## [2,] 6315641 3542973 3520766 6316348 5 7 18 3 12 10 0 0 0 0 2506 0 0
## [3,] 7484757 4258333 4262704 7448059 2 4 2 1 2 0 0 0 0 0 5966 0 0
## [4,] 5940546 3371349 3356091 5914038 1 0 0 0 0 0 0 0 1 0 3030 0 0
## [5,] 8621974 4832253 4858759 8652238 0 0 0 0 0 0 0 0 0 0 10278 0 0
## [6,] 48546 28496 27570 49866 0 0 0 0 0 0 0 0 0 0 0 0 0
## .
## [1,] 0
## [2,] 0
## [3,] 0
## [4,] 0
## [5,] 0
## [6,] 0letterFrequency: e.g. GC content
head( alphabetFrequency(assembly) )## A C G T M R W S Y K V H D B N - +
## [1,] 9709674 5435374 5421151 9697113 76 36 124 30 82 53 0 0 0 0 163958 0 0
## [2,] 6315641 3542973 3520766 6316348 5 7 18 3 12 10 0 0 0 0 2506 0 0
## [3,] 7484757 4258333 4262704 7448059 2 4 2 1 2 0 0 0 0 0 5966 0 0
## [4,] 5940546 3371349 3356091 5914038 1 0 0 0 0 0 0 0 1 0 3030 0 0
## [5,] 8621974 4832253 4858759 8652238 0 0 0 0 0 0 0 0 0 0 10278 0 0
## [6,] 48546 28496 27570 49866 0 0 0 0 0 0 0 0 0 0 0 0 0
## .
## [1,] 0
## [2,] 0
## [3,] 0
## [4,] 0
## [5,] 0
## [6,] 0head(letterFrequency(assembly,letters=c("GC")) / width(assembly))## G|C
## [1,] 0.3567978
## [2,] 0.3585966
## [3,] 0.3632182
## [4,] 0.3619812
## [5,] 0.3592523
## [6,] 0.3629384sliding window frequency content (take some times)
plot(letterFrequencyInSlidingView(subseq(largest.contig,start=1,end=1000) , view.width=100, c("GC"))[,1] / 1000,ylab="GC content")
dinucl. freqs and oligonucleotide frequency (count k-mers!)
head(dinucleotideFrequency(assembly) )## AA AC AG AT CA CC CG CT
## [1,] 3519618 1588222 1794832 2806938 1923828 1016043 697370 1798103
## [2,] 2291425 1029112 1160656 1834436 1246761 672298 457572 1166332
## [3,] 2697321 1228425 1405657 2153326 1498572 804346 559031 1396363
## [4,] 2143949 980396 1109024 1707177 1184075 637230 439585 1110456
## [5,] 3123300 1402697 1598876 2497091 1702804 901933 630299 1597206
## [6,] 17908 6721 8406 15511 8159 6901 4639 8796
## GA GC GG GT TA TC TG TT
## [1,] 1930175 902333 1008853 1579773 2336000 1928742 1920078 3512237
## [2,] 1249470 584685 660361 1026240 1527965 1256872 1242169 2289325
## [3,] 1516523 714673 805350 1226145 1772312 1510873 1492648 2672201
## [4,] 1195081 560353 630133 970522 1417439 1193369 1177345 2125882
## [5,] 1731020 803651 909379 1414706 2064837 1723961 1720200 3143216
## [6,] 9819 4474 6351 6926 12659 10400 8174 18633head(oligonucleotideFrequency(assembly,width = 5) ) ## AAAAA AAAAC AAAAG AAAAT AAACA AAACC AAACG AAACT AAAGA AAAGC AAAGG
## [1,] 205544 91860 84424 134552 94382 56055 27954 69283 92900 41182 38159
## [2,] 136637 59561 55449 89124 60510 33690 17891 45225 60497 26195 25147
## [3,] 157744 69947 66624 100808 70753 39959 21826 52979 72604 31306 30688
## [4,] 123123 56124 51255 80489 57034 33390 17228 42802 56696 25540 23567
## [5,] 184244 81767 76044 119343 82386 46311 24922 61718 82901 37165 34569
## [6,] 1565 295 552 731 235 200 132 217 532 178 284
## AAAGT AAATA AAATC AAATG AAATT AACAA AACAC AACAG AACAT AACCA AACCC
## [1,] 59035 102963 70011 67405 108140 95971 39397 35820 63175 49630 26216
## [2,] 38686 69302 45418 42946 70864 62594 24182 21995 41171 32472 15438
## [3,] 45617 78209 53403 49987 81195 73647 28818 27444 48327 38163 18424
## [4,] 35832 62687 42355 40079 64850 58206 23509 21855 38366 30752 15445
## [5,] 52414 91595 61741 58700 96922 85065 32739 31125 55744 43879 20770
## [6,] 243 685 376 316 577 306 70 121 175 218 160
## AACCG AACCT AACGA AACGC AACGG AACGT AACTA AACTC AACTG AACTT AAGAA
## [1,] 18581 34164 25561 11425 13406 19585 44572 38648 28524 60003 111106
## [2,] 12287 21380 16992 6996 8680 12639 29731 24957 18417 39494 71655
## [3,] 14442 25261 20500 8678 10892 15309 33983 29503 22565 46632 86604
## [4,] 11982 20640 16264 7059 8645 11851 27777 23859 17570 37134 68480
## [5,] 17651 29131 23121 9760 12195 17417 40070 33235 25139 54232 100151
## [6,] 80 152 148 47 91 68 184 175 99 230 540
## AAGAC AAGAG AAGAT AAGCA AAGCC AAGCG AAGCT AAGGA AAGGC AAGGG AAGGT
## [1,] 35308 55549 67172 43091 21068 11869 45496 41881 17573 17676 30561
## [2,] 23611 35861 43551 27249 14122 7655 28111 28033 11499 11855 20007
## [3,] 28025 43505 52377 32754 16682 9308 34778 33812 14202 14470 24563
## [4,] 22596 33572 41218 26023 13270 7399 28798 26240 10849 11243 18781
## [5,] 32351 49170 60811 37899 19516 10413 40793 37566 15423 15656 27891
## [6,] 122 220 319 146 100 80 122 235 84 188 139
## AAGTA AAGTC AAGTG AAGTT AATAA AATAC AATAG AATAT AATCA AATCC AATCG
## [1,] 44179 29059 32958 60662 90772 35993 36478 88228 66830 35485 21921
## [2,] 28889 18916 21318 39539 60715 23737 24314 59237 43201 22467 14452
## [3,] 33894 23107 25543 46614 69724 27967 28293 66385 51344 26466 17696
## [4,] 26909 18447 19826 37244 55430 22208 22523 52953 40832 21634 13883
## [5,] 39262 25737 28342 54624 80780 31929 31912 78429 59310 29944 20298
## [6,] 225 113 140 244 615 239 393 471 289 295 190
## AATCT AATGA AATGC AATGG AATGT AATTA AATTC AATTG AATTT ACAAA ACAAC
## [1,] 61954 58757 27810 38493 53556 80197 48825 52566 107983 94211 39836
## [2,] 40257 38539 17655 24591 34770 52564 32221 33906 70349 60602 26300
## [3,] 47703 44893 21335 29630 40761 59543 38085 39986 81006 71313 31389
## [4,] 37661 35617 16615 23425 32183 47568 30086 31625 64844 57436 24600
## [5,] 55886 51843 24046 33813 47575 70507 44068 46444 96879 83761 35472
## [6,] 275 343 137 225 167 392 470 354 594 316 100
## ACAAG ACAAT ACACA ACACC ACACG ACACT ACAGA ACAGC ACAGG ACAGT ACATA
## [1,] 44069 53560 42546 18406 12302 29445 36740 15452 13891 23373 48846
## [2,] 28636 35583 26938 11977 7849 17794 22570 9496 8706 14647 32118
## [3,] 34276 41156 31700 14063 9975 20799 28639 12206 10797 17977 37492
## [4,] 27108 32504 25874 11700 7688 17382 22546 9614 8432 14273 29891
## [5,] 38709 47780 36042 16326 10868 24176 32161 13299 11933 20487 43809
## [6,] 141 203 91 65 39 48 108 73 83 64 190
## ACATC ACATG ACATT ACCAA ACCAC ACCAG ACCAT ACCCA ACCCC ACCCG ACCCT
## [1,] 31895 37206 53763 52012 23239 19349 36689 19977 7781 8226 19608
## [2,] 20489 23977 35006 33995 15721 12632 23846 13614 5263 5506 10905
## [3,] 24628 28703 41343 40100 18817 15980 27826 16054 6108 6513 13455
## [4,] 19472 22956 31890 32642 15124 12125 22225 12460 4828 5080 11939
## [5,] 28061 31930 47630 46117 21139 17442 32193 17723 6856 7490 14728
## [6,] 119 122 170 237 88 69 154 124 123 86 104
## ACCGA ACCGC ACCGG ACCGT ACCTA ACCTC ACCTG ACCTT ACGAA ACGAC ACGAG
## [1,] 14409 8217 11605 13095 21051 19807 16966 31710 25180 13527 15832
## [2,] 9651 5468 7517 8561 13423 13820 11205 20287 16272 8965 10234
## [3,] 11377 6590 9375 10058 15188 15906 13611 24506 19907 10691 13012
## [4,] 9419 5390 7224 7873 12617 12600 11058 19370 15461 8249 10362
## [5,] 13223 7912 10860 11508 17843 17909 15208 27538 22718 11884 14415
## [6,] 80 60 61 57 130 100 70 149 157 53 82
## ACGAT ACGCA ACGCC ACGCG ACGCT ACGGA ACGGC ACGGG ACGGT ACGTA ACGTC
## [1,] 19389 10643 6553 4318 9499 12746 7718 5899 12533 15268 10729
## [2,] 12650 6683 4178 2742 5792 8147 5045 4059 8307 9535 7148
## [3,] 15454 8345 5259 3534 7186 10373 6461 4885 10400 11533 8650
## [4,] 11951 6529 4115 2754 5670 8107 5069 3737 8146 8908 6705
## [5,] 17067 9304 5806 3895 8113 11896 6690 5541 11848 13117 9424
## [6,] 95 39 41 34 38 93 47 69 57 84 50
## ACGTG ACGTT ACTAA ACTAC ACTAG ACTAT ACTCA ACTCC ACTCG ACTCT ACTGA
## [1,] 13000 19463 43495 21984 20537 35167 31355 18669 14922 36009 26075
## [2,] 8351 12544 28375 13987 13644 23485 21097 11827 10033 23087 16818
## [3,] 10077 15099 32486 16531 15954 26630 24269 14591 12082 27665 20431
## [4,] 8059 11802 26776 13041 13088 21500 20422 11888 9875 21912 16339
## [5,] 11315 17472 37458 18764 18933 31313 28362 15928 13661 31145 23436
## [6,] 46 71 207 91 90 168 129 114 74 143 103
## ACTGC ACTGG ACTGT ACTTA ACTTC ACTTG ACTTT AGAAA AGAAC AGAAG AGAAT
## [1,] 14695 14352 23265 35683 33965 36786 59674 103107 37189 67429 54612
## [2,] 9303 9175 14743 23689 22075 24226 38791 65062 23917 43426 35497
## [3,] 11500 11501 17909 27189 26585 29269 45034 78564 29582 53645 42764
## [4,] 9055 8786 14040 22293 21336 22928 36151 61012 23883 42296 33667
## [5,] 12637 12871 20547 31962 30378 33505 53153 89917 33772 62967 48373
## [6,] 69 72 77 161 162 150 231 528 150 237 378
## AGACA AGACC AGACG AGACT AGAGA AGAGC AGAGG AGAGT AGATA AGATC AGATG
## [1,] 35956 16851 14733 27310 72060 23012 27294 35481 47212 34821 40760
## [2,] 23174 11226 9600 18144 46062 14624 17907 22629 30469 22567 26181
## [3,] 27729 13546 11900 22096 55923 18548 22005 27697 35846 27763 32176
## [4,] 22176 10725 9433 17779 43920 14004 16945 21540 28420 21521 25517
## [5,] 31756 15148 13383 25059 62888 20307 24693 31619 41722 30875 36630
## [6,] 113 82 60 89 206 97 116 132 260 212 139
## AGATT AGCAA AGCAC AGCAG AGCAT AGCCA AGCCC AGCCG AGCCT AGCGA AGCGC
## [1,] 62439 42793 14913 22908 29544 23060 9104 8639 16981 12063 4205
## [2,] 40350 26730 9508 14550 19338 15337 6134 5768 11009 7774 2773
## [3,] 47855 32668 11918 18196 22905 18273 7251 6898 13058 9289 3406
## [4,] 38482 25942 8866 14095 17989 14569 5695 5467 10350 7351 2666
## [5,] 56070 37298 12749 19911 26184 20195 8209 7716 15410 10805 3731
## [6,] 281 165 63 95 126 115 92 66 78 67 33
## AGCGG AGCGT AGCTA AGCTC AGCTG AGCTT AGGAA AGGAC AGGAG AGGAT AGGCA
## [1,] 7193 9067 27635 25302 24154 45320 43591 14472 28829 29000 16563
## [2,] 4623 5763 17668 16165 15234 28279 28196 9741 18912 19591 10922
## [3,] 5763 7230 21453 20349 19457 34833 35031 11771 22958 23333 13461
## [4,] 4639 5701 17235 15868 15251 28576 26842 9241 18025 18366 10442
## [5,] 6477 8052 24224 22121 21676 41050 38726 13136 25597 26067 14833
## [6,] 71 35 143 103 67 140 235 82 118 215 70
## AGGCC AGGCG AGGCT AGGGA AGGGC AGGGG AGGGT AGGTA AGGTC AGGTG AGGTT
## [1,] 8809 6975 17002 19591 6959 7753 16354 22862 14397 18144 32625
## [2,] 5930 4725 10821 12739 4722 5270 10848 14902 9606 11981 20908
## [3,] 7655 5805 13025 15974 5607 6256 13304 18131 11648 14758 25148
## [4,] 5666 4565 10400 12220 4329 4950 10397 13878 9079 11587 19899
## [5,] 8015 6306 14708 17400 6251 6849 14618 20949 12960 16456 29276
## [6,] 54 48 76 143 69 123 97 126 92 69 152
## AGTAA AGTAC AGTAG AGTAT AGTCA AGTCC AGTCG AGTCT AGTGA AGTGC AGTGG
## [1,] 42472 18369 23999 35352 28870 14166 10845 27436 32900 11532 20427
## [2,] 27703 11865 15993 22892 18066 9261 7395 17984 21562 7398 13381
## [3,] 32577 14585 19010 26904 21803 11014 8571 21876 25794 9343 16011
## [4,] 25793 11391 14933 21879 17976 8760 6855 17511 20496 7059 12736
## [5,] 37233 16366 21275 32089 24578 12351 10163 25011 29778 10069 18099
## [6,] 225 97 138 182 120 79 73 81 126 62 106
## AGTGT AGTTA AGTTC AGTTG AGTTT ATAAA ATAAC ATAAG ATAAT ATACA ATACC
## [1,] 28161 38077 29579 35477 70086 98388 39921 42050 76188 46891 21167
## [2,] 17902 24836 19325 23027 44756 64857 26543 27214 49901 29654 14085
## [3,] 21243 29568 22908 27158 52820 73760 30922 31962 57030 35631 16806
## [4,] 16882 23058 18668 21674 41886 58472 24320 26211 45494 28667 13067
## [5,] 25026 33658 26040 31708 62298 86463 35316 36554 66794 41409 18772
## [6,] 72 176 187 143 231 596 209 259 441 219 148
## ATACG ATACT ATAGA ATAGC ATAGG ATAGT ATATA ATATC ATATG ATATT ATCAA
## [1,] 13511 34794 44049 19644 17238 35319 104175 44613 52009 89561 73379
## [2,] 8648 23043 28826 12658 11547 23233 69163 29246 34540 58873 48142
## [3,] 10384 26854 33800 15228 13705 26692 77850 34839 39507 65950 57267
## [4,] 8363 22102 27024 11931 10519 21635 62228 27166 31850 53114 45443
## [5,] 12517 31034 38312 16990 15274 31031 92024 40082 46620 79433 66217
## [6,] 104 191 380 141 193 217 564 256 204 499 382
## ATCAC ATCAG ATCAT ATCCA ATCCC ATCCG ATCCT ATCGA ATCGC ATCGG ATCGT
## [1,] 32761 32331 63022 39506 16993 14003 29139 25920 10217 12428 19741
## [2,] 21333 20203 40664 25579 11260 9381 19332 17025 6751 8355 12600
## [3,] 26466 25155 49089 31141 13399 10970 23337 20609 8690 10099 15528
## [4,] 20470 19405 38611 24028 10940 8779 18642 16458 6661 7925 12034
## [5,] 29675 28267 56209 33973 15005 12524 26626 23572 9527 11643 17513
## [6,] 102 107 263 270 182 132 235 207 54 100 120
## ATCTA ATCTC ATCTG ATCTT ATGAA ATGAC ATGAG ATGAT ATGCA ATGCC ATGCG
## [1,] 41764 45107 31502 67469 66173 26971 35125 63277 36061 13904 9449
## [2,] 27550 28845 19812 43519 42853 17442 22776 41103 22876 9346 6032
## [3,] 31961 34714 24974 52168 51188 20967 26870 49066 27710 11278 7483
## [4,] 25499 27391 19038 40942 40077 16495 21707 38539 21619 8660 5678
## [5,] 36567 39701 28219 60249 58908 24565 31239 56125 31400 12375 8247
## [6,] 247 184 142 304 394 105 151 269 125 92 62
## ATGCT ATGGA ATGGC ATGGG ATGGT ATGTA ATGTC ATGTG ATGTT ATTAA ATTAC
## [1,] 29619 40596 18723 19986 36045 44553 28118 34892 62482 74118 36027
## [2,] 19058 26474 12117 12560 23364 29266 18598 22608 41298 49250 23347
## [3,] 22964 32039 14850 15588 27334 34229 22720 26789 47713 55657 28116
## [4,] 18072 25151 11826 12138 22209 26794 17827 21467 38252 44208 21758
## [5,] 26097 36711 16841 17872 31376 39054 25747 32136 56336 65892 32102
## [6,] 112 265 81 122 141 173 97 106 173 404 182
## ATTAG ATTAT ATTCA ATTCC ATTCG ATTCT ATTGA ATTGC ATTGG ATTGT ATTTA
## [1,] 40314 76051 56083 28395 19788 54787 56472 26672 35123 54213 79721
## [2,] 26238 49901 36814 18941 13329 36157 36628 17200 22279 35685 52720
## [3,] 30333 56540 43360 22799 15808 42457 43088 20796 27011 40976 59425
## [4,] 23930 45317 34135 17749 12560 33600 34727 16316 20801 32884 47546
## [5,] 35091 67341 49715 25396 18321 49170 50571 23501 30667 48660 71067
## [6,] 226 372 421 291 189 424 353 142 226 233 378
## ATTTC ATTTG ATTTT CAAAA CAAAC CAAAG CAAAT CAACA CAACC CAACG CAACT
## [1,] 61251 72384 134754 107943 49446 51700 71710 52715 23121 16080 34788
## [2,] 39928 46634 89219 69787 32586 32853 46382 33848 15663 10268 23272
## [3,] 46753 55108 99806 82029 38579 39855 55177 40773 18527 12951 27506
## [4,] 36972 43627 80103 65516 31244 32424 43943 32243 14694 10379 21797
## [5,] 54989 64979 120480 95045 44406 46464 63983 46138 21119 14501 30858
## [6,] 463 291 795 426 138 188 358 139 92 58 129
## CAAGA CAAGC CAAGG CAAGT CAATA CAATC CAATG CAATT CACAA CACAC CACAG
## [1,] 52391 24703 23283 37005 44718 35948 37768 52126 45824 21993 17577
## [2,] 33810 15877 15181 24251 29609 23896 24610 34194 29654 14250 11019
## [3,] 40925 19350 18505 29455 34124 28107 29750 39733 35172 16759 13949
## [4,] 32494 15719 14348 23037 27364 22601 23162 31439 27944 13653 10836
## [5,] 46788 21782 20294 32940 39746 32189 33842 46424 40053 18904 15221
## [6,] 195 80 113 145 288 172 148 375 126 47 49
## CACAT CACCA CACCC CACCG CACCT CACGA CACGC CACGG CACGT CACTA CACTC
## [1,] 35469 31131 8918 11920 18115 13837 6386 7614 12910 24778 20220
## [2,] 22794 20886 5942 7730 12601 8934 3993 5014 8330 15449 13173
## [3,] 27006 24924 7241 9461 14493 11382 5159 6585 10056 17792 15593
## [4,] 21515 20071 5758 7427 11554 8552 3872 4864 8048 14639 12584
## [5,] 31008 28178 7886 10596 16235 12136 5643 7157 11296 20556 17651
## [6,] 109 93 68 61 77 60 34 38 49 94 73
## CACTG CACTT CAGAA CAGAC CAGAG CAGAT CAGCA CAGCC CAGCG CAGCT CAGGA
## [1,] 16907 32272 41340 15773 29355 32000 21980 11502 7184 24295 17953
## [2,] 10732 21083 25410 10245 18024 19919 13648 7974 4506 15296 11555
## [3,] 13333 25005 32646 12690 23200 24755 17574 9432 5695 19410 14285
## [4,] 10342 19583 25482 9845 17930 19264 13485 7230 4470 15041 11343
## [5,] 14800 28784 36527 13915 25931 27716 18968 10153 6316 21244 16076
## [6,] 60 118 195 48 83 126 82 65 34 80 109
## CAGGC CAGGG CAGGT CAGTA CAGTC CAGTG CAGTT CATAA CATAC CATAG CATAT
## [1,] 8394 8837 17315 19014 13868 16939 29099 47328 23945 23264 52641
## [2,] 5481 5534 10793 12091 9306 10807 18165 30963 15500 15013 34219
## [3,] 6734 7151 13511 14727 10977 13240 22583 36143 18511 17774 39701
## [4,] 5205 5558 10545 11535 8852 10554 17283 28568 15339 14289 31833
## [5,] 7439 7659 15588 16515 12641 15035 25404 41244 21337 20328 46777
## [6,] 45 62 70 102 57 54 113 269 121 163 265
## CATCA CATCC CATCG CATCT CATGA CATGC CATGG CATGT CATTA CATTC CATTG
## [1,] 49224 20441 16374 42097 36590 18551 23011 36314 41422 31038 38670
## [2,] 31868 14131 10453 26378 23692 12006 14995 24136 27393 21081 24759
## [3,] 38866 17252 12889 32125 28300 14789 18191 28770 31975 25048 30011
## [4,] 30892 13262 10066 24885 22109 11270 14514 23140 24991 19212 23121
## [5,] 44750 18649 14613 36106 31739 15982 20571 33017 36741 28158 33728
## [6,] 124 128 83 145 156 90 108 115 187 184 141
## CATTT CCAAA CCAAC CCAAG CCAAT CCACA CCACC CCACG CCACT CCAGA CCAGC
## [1,] 66740 61402 25556 27645 34382 24804 18689 9561 20328 20807 11984
## [2,] 43742 39639 17223 18213 22814 16312 12876 6369 13659 13011 7955
## [3,] 50342 47191 20408 22419 26752 19734 15354 7811 16123 16550 10071
## [4,] 39315 38295 16019 17553 21037 15379 12287 6133 12552 12737 7568
## [5,] 59308 54201 22328 24123 30195 21945 17147 8448 17945 18432 10575
## [6,] 354 243 112 167 267 85 88 51 109 119 62
## CCAGG CCAGT CCATA CCATC CCATG CCATT CCCAA CCCAC CCCAG CCCAT CCCCA
## [1,] 8863 14541 28145 26777 23204 37990 26068 11721 8029 19687 11179
## [2,] 5821 9260 18268 17565 15237 25219 17222 7926 5246 13213 7609
## [3,] 7414 11443 21259 21289 18210 30031 20623 9676 6637 15837 8931
## [4,] 5762 8811 17022 16854 14401 22937 16675 7514 5055 12004 7090
## [5,] 8204 12751 23857 24031 20661 33864 23177 10382 7043 17417 9976
## [6,] 75 78 215 124 122 227 165 60 91 163 125
## CCCCC CCCCG CCCCT CCCGA CCCGC CCCGG CCCGT CCCTA CCCTC CCCTG CCCTT
## [1,] 4468 3145 7718 7668 4120 4712 6011 16047 11164 8744 17687
## [2,] 3243 2297 5524 5189 2937 3242 4141 8822 7901 5662 12202
## [3,] 3704 2741 6119 6386 3552 3768 4981 10345 9260 6936 14270
## [4,] 3068 2060 5041 5180 2592 2953 3605 9271 7494 5630 11574
## [5,] 4038 2867 6931 7172 3864 4373 5493 11682 10021 7783 15715
## [6,] 119 76 130 104 61 61 82 98 93 74 183
## CCGAA CCGAC CCGAG CCGAT CCGCA CCGCC CCGCG CCGCT CCGGA CCGGC CCGGG
## [1,] 14423 8226 10293 12650 7431 7715 3677 7178 11704 6374 4471
## [2,] 9549 5664 6873 8384 5178 5263 2533 4975 7622 4205 3225
## [3,] 11583 6605 8532 9958 6234 6306 3097 5773 9411 5078 3895
## [4,] 9379 5326 6775 8086 5152 4773 2329 4613 7396 3907 2943
## [5,] 12796 7406 9418 11560 7524 7015 3294 6530 10836 5812 4389
## [6,] 141 48 84 87 61 56 35 92 87 42 55
## CCGGT CCGTA CCGTC CCGTG CCGTT CCTAA CCTAC CCTAG CCTAT CCTCA CCTCC
## [1,] 11892 8843 9538 7751 13267 30466 11647 11334 17208 21105 18660
## [2,] 7629 5967 6367 5188 8789 16927 7575 7907 11725 14554 12922
## [3,] 9137 6919 7497 6484 10609 19691 8785 9132 13625 17418 15123
## [4,] 7283 5424 5757 4817 8228 17408 6881 7357 10619 13529 12077
## [5,] 10460 7840 8425 7147 12235 23310 9988 10412 15492 19243 17102
## [6,] 61 80 56 53 100 146 92 86 191 78 102
## CCTCG CCTCT CCTGA CCTGC CCTGG CCTGT CCTTA CCTTC CCTTG CCTTT CGAAA
## [1,] 10011 27718 18717 10602 8829 13334 21714 25806 22511 38090 27200
## [2,] 6684 18433 12206 7186 5801 8852 13959 17320 15144 25872 17723
## [3,] 8304 21769 14986 8634 7176 10954 16696 20501 18300 30295 21831
## [4,] 6572 17094 11972 6810 5795 8447 13570 16406 14530 23822 16635
## [5,] 8899 24612 16728 9627 7982 12157 18730 23046 21000 34262 24682
## [6,] 80 148 87 68 74 88 115 157 127 295 229
## CGAAC CGAAG CGAAT CGACA CGACC CGACG CGACT CGAGA CGAGC CGAGG CGAGT
## [1,] 12161 17640 20115 13679 8949 9607 10682 18907 9327 10097 15048
## [2,] 8226 11429 13138 9153 6217 6420 7447 12310 6042 6575 10092
## [3,] 10040 13897 15772 10753 7542 7875 8501 15333 7866 8456 12003
## [4,] 7987 11049 12469 8691 6071 5988 7122 12190 6102 6871 10147
## [5,] 11051 15783 18486 12254 8266 8707 10034 17303 8752 9202 13469
## [6,] 107 106 195 55 66 38 58 100 80 53 87
## CGATA CGATC CGATG CGATT CGCAA CGCAC CGCAG CGCAT CGCCA CGCCC CGCCG
## [1,] 15236 14726 16362 21997 11757 4684 7363 9394 9632 2631 7675
## [2,] 9964 10001 10323 14356 7772 3159 4641 6186 6290 2090 5001
## [3,] 11973 12230 12953 17506 9626 3877 5828 7666 7749 2569 6172
## [4,] 9482 9853 10004 13656 7989 2960 4794 5854 5917 1759 4955
## [5,] 13273 13393 14552 20091 11351 4339 6638 8365 8534 2579 6943
## [6,] 130 121 72 157 58 38 38 56 52 54 31
## CGCCT CGCGA CGCGC CGCGG CGCGT CGCTA CGCTC CGCTG CGCTT CGGAA CGGAC
## [1,] 6945 4415 2114 3567 4326 7433 6432 7092 12031 15358 5927
## [2,] 4703 2993 1432 2472 2760 4561 4507 4553 7759 9934 4076
## [3,] 5664 3692 1726 2911 3653 5303 5408 5646 9407 12280 5019
## [4,] 4353 2902 1406 2338 2631 4404 4339 4331 7196 9574 4082
## [5,] 6346 4027 1836 3312 3902 6249 5919 6342 10649 13505 5873
## [6,] 52 55 12 31 30 57 51 45 75 123 55
## CGGAG CGGAT CGGCA CGGCC CGGCG CGGCT CGGGA CGGGC CGGGG CGGGT CGGTA
## [1,] 13190 13795 6663 4741 7650 8518 8420 2850 3164 7777 9283
## [2,] 8302 9035 4325 3425 4835 5798 5434 2178 2322 5377 6163
## [3,] 10817 11171 5455 3701 6360 6776 6731 2525 2754 6371 7334
## [4,] 8101 8853 4061 3006 4987 5799 5256 1938 2035 4933 5672
## [5,] 11798 12825 5885 4214 6807 7829 7807 2763 2865 7449 8493
## [6,] 74 120 43 37 40 69 90 42 66 70 84
## CGGTC CGGTG CGGTT CGTAA CGTAC CGTAG CGTAT CGTCA CGTCC CGTCG CGTCT
## [1,] 7380 11753 18410 15665 8407 8901 13849 13274 7478 9745 14745
## [2,] 4931 7701 12047 10040 5473 5850 8752 8693 5178 6204 9704
## [3,] 6086 9726 14467 12306 6535 7069 10550 10538 6054 7981 11576
## [4,] 4641 7689 11805 9568 5262 5402 8110 8156 4656 6214 8959
## [5,] 6651 10730 17041 13622 7251 7894 12205 11758 6541 8939 13168
## [6,] 45 49 94 112 60 78 104 48 56 40 62
## CGTGA CGTGC CGTGG CGTGT CGTTA CGTTC CGTTG CGTTT CTAAA CTAAC CTAAG
## [1,] 13300 5483 9769 12328 14609 11195 16409 28108 56740 25216 22887
## [2,] 8447 3597 6302 8097 9347 7631 10306 17770 34551 15494 15174
## [3,] 10303 4545 8019 9785 11343 8990 12695 21736 38863 17859 17519
## [4,] 8117 3513 6135 7618 8998 7092 9983 16925 33542 15106 14238
## [5,] 11737 5054 8765 10904 13354 10178 14647 25112 45712 20468 20330
## [6,] 61 39 50 53 73 104 67 142 259 99 121
## CTAAT CTACA CTACC CTACG CTACT CTAGA CTAGC CTAGG CTAGT CTATA CTATC
## [1,] 40301 26981 12175 8957 24651 24216 13184 11263 21428 34479 21734
## [2,] 26062 17490 8295 5695 15921 16158 8841 7860 13343 22730 14444
## [3,] 30444 20950 9820 7099 18425 19167 10583 9226 15910 26238 17373
## [4,] 24741 16443 7737 5382 15161 15738 8264 7316 12882 20945 13513
## [5,] 35049 23975 11021 7872 21199 22586 11338 10109 18240 30200 18999
## [6,] 252 103 107 67 125 133 61 81 99 234 137
## CTATG CTATT CTCAA CTCAC CTCAG CTCAT CTCCA CTCCC CTCCG CTCCT CTCGA
## [1,] 22618 36780 42130 20065 20596 34829 32496 12761 12918 29184 18635
## [2,] 14997 24435 27595 13540 13532 22920 21210 8754 8531 18950 12301
## [3,] 17636 27844 32587 15999 16410 27136 25981 10497 10437 22997 15134
## [4,] 13785 22126 26988 12714 13005 21915 20546 8355 8263 17923 12253
## [5,] 20410 32402 37482 18224 18372 31781 28736 11489 11728 25509 17304
## [6,] 122 342 149 77 72 144 120 92 69 159 141
## CTCGC CTCGG CTCGT CTCTA CTCTC CTCTG CTCTT CTGAA CTGAC CTGAG CTGAT
## [1,] 8335 10378 16343 30877 40726 29247 56499 37277 13323 20198 31878
## [2,] 5860 6839 10495 20260 27465 18394 36395 23406 8711 13265 20106
## [3,] 7088 8449 12784 23861 33714 22717 43428 28975 10812 16540 24919
## [4,] 5495 6617 10061 18899 25368 17748 33825 23216 8552 12812 19379
## [5,] 7670 9150 14469 26934 37511 25731 49367 33138 12004 18393 28630
## [6,] 44 76 95 150 133 95 260 157 61 72 119
## CTGCA CTGCC CTGCG CTGCT CTGGA CTGGC CTGGG CTGGT CTGTA CTGTC CTGTG
## [1,] 25014 9659 7327 22843 19835 8350 7991 19724 20451 15111 17488
## [2,] 15345 6799 4772 14470 12646 5509 5451 12258 12704 9864 11151
## [3,] 19716 7898 6105 17835 16148 6788 6612 15516 16169 11750 13727
## [4,] 15340 6182 4570 14005 12408 5266 5130 12203 12553 9516 10639
## [5,] 21948 8753 6582 20238 18183 7591 7246 17466 18017 13363 15923
## [6,] 77 58 46 99 105 41 78 88 107 77 56
## CTGTT CTTAA CTTAC CTTAG CTTAT CTTCA CTTCC CTTCG CTTCT CTTGA CTTGC
## [1,] 35516 42456 24272 22247 42282 49775 31255 17574 69340 43121 22464
## [2,] 22553 27290 15635 15174 27062 32423 20557 11386 43274 27976 14495
## [3,] 27414 31991 18028 17628 31374 39420 25051 13780 52244 34402 17342
## [4,] 21134 25813 14657 14189 25555 30961 19372 11257 42854 27035 13844
## [5,] 31488 37638 21151 20346 36801 44665 27957 16044 60923 39614 19750
## [6,] 147 133 109 100 213 165 165 114 293 197 89
## CTTGG CTTGT CTTTA CTTTC CTTTG CTTTT GAAAA GAAAC GAAAG GAAAT GAACA
## [1,] 26971 43420 48353 46556 50599 85796 93178 49887 47558 61699 38184
## [2,] 17841 28516 31566 30936 33321 55330 60034 31800 30833 39634 24216
## [3,] 21768 34212 36329 36985 39792 64899 72656 38471 37190 46854 30273
## [4,] 17179 27165 29368 28782 31650 50975 55874 30600 28663 37458 23342
## [5,] 24849 39692 42475 42546 46346 76068 82863 44021 42256 55314 33919
## [6,] 153 160 227 280 191 601 527 180 267 459 145
## GAACC GAACG GAACT GAAGA GAAGC GAAGG GAAGT GAATA GAATC GAATG GAATT
## [1,] 22847 11243 28971 74645 32134 25805 34023 39354 39764 31981 48859
## [2,] 14976 7493 18914 48071 20020 17015 21942 25837 24906 21029 31862
## [3,] 17874 9117 22995 59480 24850 21080 26791 31168 30850 24850 38099
## [4,] 14542 7237 18699 45996 19875 16145 21042 24062 24401 19579 30075
## [5,] 20663 10102 26346 69177 29373 23360 30186 35095 35572 28036 44043
## [6,] 167 86 167 242 102 137 158 343 288 184 406
## GACAA GACAC GACAG GACAT GACCA GACCC GACCG GACCT GACGA GACGC GACGG
## [1,] 37392 16901 15397 28676 22780 9244 7396 14192 18647 6494 9242
## [2,] 24161 10840 9636 18972 14479 6460 5055 9522 12014 4204 6171
## [3,] 28802 12989 12196 22306 17814 7701 6014 11494 14741 5334 7561
## [4,] 23223 10361 9536 17860 14123 6026 4675 9203 11482 4110 6082
## [5,] 33492 14450 13320 25544 19842 8424 6849 12870 16722 5829 8384
## [6,] 118 55 59 101 96 99 52 81 71 25 50
## GACGT GACTA GACTC GACTG GACTT GAGAA GAGAC GAGAG GAGAT GAGCA GAGCC
## [1,] 10859 19715 17664 13828 28926 62143 24195 42178 44902 22015 12039
## [2,] 7168 13118 11730 9033 19138 39316 15543 27454 28805 13923 7855
## [3,] 8705 15123 14137 11084 23001 48500 19098 33513 35069 17348 9490
## [4,] 6718 12205 11779 8799 18503 37589 15265 26082 27861 13546 7564
## [5,] 9494 17391 16208 12815 26772 55361 21645 37235 39798 19351 10785
## [6,] 51 90 95 60 117 200 76 114 180 105 100
## GAGCG GAGCT GAGGA GAGGC GAGGG GAGGT GAGTA GAGTC GAGTG GAGTT GATAA
## [1,] 6606 24938 34293 12781 11330 20195 24801 17529 19899 37900 44581
## [2,] 4251 16107 22063 8238 7456 13083 16144 11618 12854 24976 29108
## [3,] 5258 20678 27395 10538 9170 16193 19676 14164 15762 29385 33694
## [4,] 4227 15932 21295 8065 7098 12766 15937 11669 12366 23368 27000
## [5,] 6204 22628 30516 11550 10272 18284 22420 16627 18138 33766 38706
## [6,] 50 109 119 49 78 86 129 89 71 159 261
## GATAC GATAG GATAT GATCA GATCC GATCG GATCT GATGA GATGC GATGG GATGT
## [1,] 21691 21863 45225 37515 21363 14932 35136 49160 20073 26743 31212
## [2,] 13874 14316 29352 24023 14162 9898 22577 31234 12733 16911 20699
## [3,] 17169 17077 34468 30251 17428 12471 27499 38843 16179 21025 24770
## [4,] 13618 13405 27374 23008 13659 9750 21782 30379 12496 16760 19347
## [5,] 19656 19320 40317 33229 19188 13586 31495 44234 18059 23931 29053
## [6,] 151 156 245 196 211 109 200 170 75 113 113
## GATTA GATTC GATTG GATTT GCAAA GCAAC GCAAG GCAAT GCACA GCACC GCACG
## [1,] 40481 39966 36416 68583 42097 21363 22381 26862 15464 9288 5693
## [2,] 26091 25538 23596 45383 27043 13655 14236 17384 9927 6515 3504
## [3,] 31052 30614 27896 53237 33012 16973 17679 21197 11843 7819 4561
## [4,] 24171 24826 22556 42045 25574 13663 13863 16905 9367 5900 3421
## [5,] 36068 35408 32713 62740 36629 19440 20369 24290 13606 8480 5059
## [6,] 189 307 185 346 148 54 77 134 33 45 41
## GCACT GCAGA GCAGC GCAGG GCAGT GCATA GCATC GCATG GCATT GCCAA GCCAC
## [1,] 11684 23741 16369 10569 14564 22333 20263 18053 28278 22931 12804
## [2,] 7550 14649 10445 6803 9327 14698 13035 12035 17649 15005 8693
## [3,] 9200 18810 13028 8491 11533 17316 16244 14857 21490 18405 10063
## [4,] 6931 14449 10106 6768 8822 13691 12356 11297 16672 14175 7853
## [5,] 10017 20902 14478 9715 12832 19647 18319 16192 24112 20101 11235
## [6,] 63 86 59 47 74 110 77 88 128 106 50
## GCCAG GCCAT GCCCA GCCCC GCCCG GCCCT GCCGA GCCGC GCCGG GCCGT GCCTA
## [1,] 8558 18580 10847 3489 2971 7003 7786 5681 6233 7718 10668
## [2,] 5511 12619 7254 2680 2128 4903 5219 3950 4192 5065 7180
## [3,] 6758 14966 8990 2985 2526 5625 6075 4680 5109 6498 8245
## [4,] 5296 11747 6764 2325 1944 4466 5075 3707 3868 4810 6581
## [5,] 7404 16838 9896 3226 2963 6153 6831 5163 5844 6910 10072
## [6,] 43 94 69 80 50 69 57 40 41 44 75
## GCCTC GCCTG GCCTT GCGAA GCGAC GCGAG GCGAT GCGCA GCGCC GCGCG GCGCT
## [1,] 13181 8124 17139 10929 6615 8474 10512 4365 3372 2096 4265
## [2,] 8449 5564 11720 7322 4459 5577 6782 2830 2380 1409 2833
## [3,] 10378 6702 13827 8888 5479 6888 8590 3471 2807 1736 3463
## [4,] 7858 5087 10875 6809 4332 5565 6674 2821 2133 1294 2655
## [5,] 11356 7560 15565 9789 6180 7586 9409 3904 3075 1827 3752
## [6,] 67 46 92 95 31 44 65 29 31 20 32
## GCGGA GCGGC GCGGG GCGGT GCGTA GCGTC GCGTG GCGTT GCTAA GCTAC GCTAG
## [1,] 8190 5773 3999 8169 6662 6618 6447 11050 24634 13100 12991
## [2,] 5253 3803 2830 5283 4332 4232 4001 6690 15701 8827 8510
## [3,] 6694 4617 3296 6801 5291 5214 5081 8693 18377 10457 10402
## [4,] 5112 3697 2550 5358 4200 4133 3932 6761 15324 8659 8253
## [5,] 7250 4969 3822 7601 5889 5854 5613 9857 20902 12199 11374
## [6,] 79 36 53 57 56 29 27 50 121 90 65
## GCTAT GCTCA GCTCC GCTCG GCTCT GCTGA GCTGC GCTGG GCTGT GCTTA GCTTC
## [1,] 19711 19602 14163 9746 22633 20939 16434 11832 15507 23249 32466
## [2,] 12497 12476 9215 6192 14779 13241 10218 7740 9702 15048 20079
## [3,] 15201 15230 11302 7813 18294 16665 12908 9966 11934 17959 24633
## [4,] 11787 12413 8881 6104 14044 13149 9936 7591 9393 14042 20062
## [5,] 16802 17032 12340 8500 20471 18760 14294 10794 13709 20740 28626
## [6,] 131 81 96 75 105 57 57 52 70 76 118
## GCTTG GCTTT GGAAA GGAAC GGAAG GGAAT GGACA GGACC GGACG GGACT GGAGA
## [1,] 24214 40854 45584 19758 31633 28672 16750 9953 7472 13998 36561
## [2,] 15794 26059 29873 12793 20226 18848 11014 6747 5002 9293 23385
## [3,] 19489 31132 36482 16007 24988 23127 13441 8137 6039 11089 29391
## [4,] 15634 24837 28240 12580 19332 17695 10571 6489 4690 8954 22654
## [5,] 22815 36704 41331 17744 28116 25804 14941 9107 6626 12892 32541
## [6,] 83 176 248 132 147 260 80 80 48 83 104
## GGAGC GGAGG GGAGT GGATA GGATC GGATG GGATT GGCAA GGCAC GGCAG GGCAT
## [1,] 14226 19399 18038 22499 21681 20358 34205 18344 7307 9902 13978
## [2,] 8972 12449 11912 15108 13975 13363 22023 11918 4977 6530 9347
## [3,] 11009 15592 14729 17760 17581 16873 26273 14808 6000 7996 11379
## [4,] 8998 11825 11361 14144 13379 13052 20841 11479 4507 5978 8820
## [5,] 12645 17213 16734 20274 19675 18792 30262 16290 6572 8916 12538
## [6,] 86 93 104 185 195 119 267 66 33 67 85
## GGCCA GGCCC GGCCG GGCCT GGCGA GGCGC GGCGG GGCGT GGCTA GGCTC GGCTG
## [1,] 11241 5171 4573 8941 9065 3430 7790 6674 12654 12118 11673
## [2,] 7683 3521 3288 5940 6193 2301 5016 4228 8345 7906 7721
## [3,] 9079 4338 3811 7388 7956 2876 6443 5295 9898 9655 9279
## [4,] 7113 3199 3015 5687 6097 2215 4844 4172 8221 7676 7371
## [5,] 10088 4763 4313 8005 8406 3229 6809 5781 11063 10809 10384
## [6,] 46 52 39 65 62 31 50 44 83 97 58
## GGCTT GGGAA GGGAC GGGAG GGGAT GGGCA GGGCC GGGCG GGGCT GGGGA GGGGC
## [1,] 21100 22972 9226 13506 16747 7455 5273 2629 8889 10778 3551
## [2,] 13708 14921 6049 8493 10632 5186 3566 2105 6029 7053 2595
## [3,] 16544 18409 7256 10543 13724 6145 4224 2564 7372 8814 2996
## [4,] 12993 14463 5837 8239 10272 4641 3316 1781 5736 6907 2312
## [5,] 19204 20947 8099 12010 15245 6692 4712 2508 8240 9801 3155
## [6,] 88 148 61 90 165 70 58 46 85 117 75
## GGGGG GGGGT GGGTA GGGTC GGGTG GGGTT GGTAA GGTAC GGTAG GGTAT GGTCA
## [1,] 4534 7491 11420 9040 8513 22859 26002 11962 12497 21638 17611
## [2,] 3183 5112 7221 6209 5735 15194 16751 7692 8255 13689 11441
## [3,] 3630 6201 8712 7833 7078 17955 20359 9374 9639 16706 13984
## [4,] 2970 4839 7037 6033 5409 13973 15802 7394 7647 12860 10420
## [5,] 4154 6917 9936 8793 7826 20544 23326 10571 11168 18998 15660
## [6,] 120 104 95 78 68 152 139 72 94 149 74
## GGTCC GGTCG GGTCT GGTGA GGTGC GGTGG GGTGT GGTTA GGTTC GGTTG GGTTT
## [1,] 9975 8921 16730 23881 9380 18829 17931 25728 23341 23348 51442
## [2,] 6920 6036 11031 15516 6130 12378 11788 16798 14881 15264 32899
## [3,] 8179 7299 13523 18904 7868 15977 14015 19733 17427 18342 39296
## [4,] 6346 6113 10682 14836 5885 12449 11333 15894 14339 14727 31447
## [5,] 9145 8333 15346 20988 8679 17526 16451 23879 20671 21077 46109
## [6,] 85 52 90 79 51 78 69 126 172 92 200
## GTAAA GTAAC GTAAG GTAAT GTACA GTACC GTACG GTACT GTAGA GTAGC GTAGG
## [1,] 47367 23521 24062 36292 21382 11731 8445 18359 26207 13569 10982
## [2,] 31160 15111 15710 23584 13657 7969 5380 11817 17119 8842 7590
## [3,] 36035 18026 18614 28176 16550 9448 6546 14473 20532 10486 9116
## [4,] 28843 14206 14476 22033 13167 7497 5119 11517 16219 8315 6998
## [5,] 41917 20812 20942 32139 18751 10440 7319 16366 23202 11899 9932
## [6,] 261 112 89 191 107 84 45 95 137 82 100
## GTAGT GTATA GTATC GTATG GTATT GTCAA GTCAC GTCAG GTCAT GTCCA GTCCC
## [1,] 21408 35668 21574 23745 36033 33511 17127 13637 26775 18705 9075
## [2,] 14027 22232 13911 15486 23797 21321 10923 8736 17697 12152 6211
## [3,] 16481 26149 17259 18591 27425 25536 13192 10768 21091 14413 7615
## [4,] 12983 21199 13208 14632 21777 20634 10353 8429 16606 11272 5883
## [5,] 19000 31366 19468 22062 32339 29203 14731 11793 24281 16118 8092
## [6,] 97 152 152 106 248 129 55 66 87 105 69
## GTCCG GTCCT GTCGA GTCGC GTCGG GTCGT GTCTA GTCTC GTCTG GTCTT GTGAA
## [1,] 6019 14427 14686 6669 8341 13325 20183 24276 15579 34767 37994
## [2,] 4252 9906 9980 4260 5518 8697 12917 15695 9998 23110 24495
## [3,] 4966 11689 11884 5291 6662 10732 15562 19181 12480 27941 28888
## [4,] 3945 9210 9913 4144 5382 8490 12290 14842 9773 22226 23168
## [5,] 5476 13227 13842 6206 7462 12125 17320 21807 14244 32233 33639
## [6,] 54 83 79 30 52 51 93 87 58 133 144
## GTGAC GTGAG GTGAT GTGCA GTGCC GTGCG GTGCT GTGGA GTGGC GTGGG GTGGT
## [1,] 17019 20389 33017 14936 7543 4725 14412 25207 12930 11721 23919
## [2,] 10591 13134 21548 9641 5045 3150 9337 16718 8488 7714 15405
## [3,] 13004 16140 25926 12192 5939 3858 11852 20564 10471 9567 18964
## [4,] 10513 12665 20189 9176 4527 2987 9070 16109 8013 7370 15098
## [5,] 14757 18540 29642 13428 6796 4370 13061 23019 11361 10930 21500
## [6,] 49 69 127 52 49 35 69 131 42 65 79
## GTGTA GTGTC GTGTG GTGTT GTTAA GTTAC GTTAG GTTAT GTTCA GTTCC GTTCG
## [1,] 23601 16227 21637 38184 39295 23542 23201 40004 31871 19646 12370
## [2,] 15389 10775 14157 24320 25934 14985 15026 26540 20711 13280 8325
## [3,] 17872 13104 16837 28885 30218 17984 17737 30919 24429 15796 9949
## [4,] 14721 10328 13368 22817 23863 14305 14365 24465 19529 12680 7778
## [5,] 21640 14722 19680 34256 35580 20692 22007 35922 28389 18058 11203
## [6,] 82 66 49 80 142 102 78 197 162 169 118
## GTTCT GTTGA GTTGC GTTGG GTTGT GTTTA GTTTC GTTTG GTTTT TAAAA TAAAC
## [1,] 38190 40603 21496 26248 40698 50238 49520 49132 92803 109715 56481
## [2,] 24182 26298 13677 16925 26282 32721 31341 32317 59016 74312 33369
## [3,] 29047 31252 16704 19978 31178 38190 38137 38534 69107 82693 38519
## [4,] 23556 24621 13470 15715 24387 30508 30033 30336 55209 66478 32485
## [5,] 33661 36070 19304 23296 35739 45207 44356 45023 82737 99247 45143
## [6,] 208 170 71 100 122 156 198 130 326 625 171
## TAAAG TAAAT TAACA TAACC TAACG TAACT TAAGA TAAGC TAAGG TAAGT TAATA
## [1,] 47595 80556 49083 26568 14700 38703 49199 23504 20444 36795 64436
## [2,] 31389 53388 31369 17247 9655 25186 32300 15045 14051 23783 43255
## [3,] 36546 59955 36438 19930 11485 29202 37503 18015 16774 27296 48867
## [4,] 29293 48082 29317 16193 8975 23042 30680 14356 13053 22515 39001
## [5,] 42284 70318 42231 23338 12968 33754 43617 20300 18313 32425 56614
## [6,] 230 406 153 151 78 175 232 88 112 176 402
## TAATC TAATG TAATT TACAA TACAC TACAG TACAT TACCA TACCC TACCG TACCT
## [1,] 40468 41462 80445 52489 24408 20662 44390 27749 11215 9429 23063
## [2,] 26157 26971 52120 34712 15286 12769 28653 18357 7448 6125 15231
## [3,] 30850 32032 59591 40513 17972 16030 34526 21822 8765 7483 17963
## [4,] 24653 25020 47759 32275 15122 12638 26468 17170 7078 5822 14248
## [5,] 35936 36699 70509 47112 21319 18214 39136 24992 9717 8407 20263
## [6,] 213 224 452 210 71 99 216 141 110 65 139
## TACGA TACGC TACGG TACGT TACTA TACTC TACTG TACTT TAGAA TAGAC TAGAG
## [1,] 15883 6708 8634 15106 32118 24423 19128 44907 47748 19574 30765
## [2,] 10180 4202 5693 9440 21193 16184 11857 29066 31521 12745 19883
## [3,] 12442 5153 7081 11289 24701 19374 14360 33440 36805 15458 23955
## [4,] 9725 4027 5468 8857 19783 15875 11509 27488 29307 12407 18825
## [5,] 14105 5886 8239 13121 28451 22002 16737 39210 42990 17435 27170
## [6,] 108 46 87 83 188 117 102 239 358 98 134
## TAGAT TAGCA TAGCC TAGCG TAGCT TAGGA TAGGC TAGGG TAGGT TAGTA TAGTC
## [1,] 41158 23073 13176 6869 27682 21765 10601 12815 19957 32200 20860
## [2,] 27291 15306 8297 4521 17832 14789 7180 8735 13514 21328 12866
## [3,] 31437 18015 9876 5427 21227 17600 8472 10350 15419 24779 15016
## [4,] 25597 13838 8017 4261 17159 13596 6954 7997 12351 19615 12134
## [5,] 36971 19924 11076 6131 24406 19368 9450 11531 17878 28765 17098
## [6,] 267 116 86 42 142 187 70 104 144 186 94
## TAGTG TAGTT TATAA TATAC TATAG TATAT TATCA TATCC TATCG TATCT TATGA
## [1,] 23225 45558 73867 34734 34644 104263 47924 22352 15079 46655 47039
## [2,] 15266 29264 47730 22319 22621 69015 31250 14792 9928 30514 30710
## [3,] 17847 33871 54114 26029 26281 77592 37516 17702 11871 36489 36055
## [4,] 14427 27391 43499 21034 20892 62198 29197 13834 9379 28542 28713
## [5,] 21457 39910 64398 30810 30047 92635 43079 20346 13758 41249 43020
## [6,] 101 221 360 151 219 542 245 185 99 257 250
## TATGC TATGG TATGT TATTA TATTC TATTG TATTT TCAAA TCAAC TCAAG TCAAT
## [1,] 22600 27103 48962 64410 39224 44829 104804 83088 39949 43288 55756
## [2,] 14918 18018 32165 42688 26401 29533 69027 54324 25873 28034 36528
## [3,] 17132 20965 37151 48076 30677 33979 76507 64124 30986 33861 42607
## [4,] 13649 16626 29670 38483 23921 27426 62044 51822 24831 27074 34120
## [5,] 20032 24485 43628 57110 34968 40514 92588 75308 35376 38603 49936
## [6,] 89 162 154 416 364 274 633 403 152 148 379
## TCACA TCACC TCACG TCACT TCAGA TCAGC TCAGG TCAGT TCATA TCATC TCATG
## [1,] 38049 23701 13191 32720 37180 21156 19176 26442 47854 49201 36003
## [2,] 24540 15791 8549 21434 23368 13529 12033 17136 30611 31742 23580
## [3,] 29609 18884 10835 25601 29292 16806 14978 20573 36062 38972 28282
## [4,] 23328 14923 8094 20283 22789 12938 11689 16318 29425 30423 22379
## [5,] 33593 20942 11856 29653 32594 18329 16910 23525 42374 43707 32526
## [6,] 122 101 50 125 139 67 81 110 303 161 137
## TCATT TCCAA TCCAC TCCAG TCCAT TCCCA TCCCC TCCCG TCCCT TCCGA TCCGC
## [1,] 57838 47974 25618 20259 41160 23502 10772 8168 19312 15729 7983
## [2,] 39101 31667 16876 12658 26611 15130 7487 5578 13255 10411 5594
## [3,] 44512 37641 20466 16104 32159 18799 8698 6907 15611 12840 6588
## [4,] 35140 29412 15860 12402 25237 14934 7038 5246 12523 9892 5178
## [5,] 52329 41451 22729 18073 35965 20424 9694 7582 17389 13954 7424
## [6,] 341 281 135 131 277 161 128 96 145 119 83
## TCCGG TCCGT TCCTA TCCTC TCCTG TCCTT TCGAA TCGAC TCGAG TCGAT TCGCA
## [1,] 11891 12575 22887 33342 17648 41585 26584 14549 18780 25770 10759
## [2,] 7730 8543 14709 22424 11614 28086 17372 10149 12335 16828 7067
## [3,] 9269 9971 17455 27071 14501 33188 21163 11896 15226 20660 8947
## [4,] 7484 7938 13796 21320 11249 26509 16491 9965 12608 16284 7095
## [5,] 10420 11736 19604 30570 15943 38220 24699 13789 17307 23273 9961
## [6,] 82 106 212 148 127 270 244 85 110 233 61
## TCGCC TCGCG TCGCT TCGGA TCGGC TCGGG TCGGT TCGTA TCGTC TCGTG TCGTT
## [1,] 9243 4331 12047 15630 7707 7842 14232 16049 18357 13682 26541
## [2,] 6263 2973 7780 10325 5331 5197 9623 10281 12032 8903 17031
## [3,] 7782 3615 9342 12809 6136 6305 11274 12717 14788 11010 20363
## [4,] 5963 2900 7332 9995 5180 4932 9020 9810 11390 8575 16207
## [5,] 8506 4061 10764 14019 7264 7132 13007 14126 16703 12385 23727
## [6,] 61 39 66 113 64 91 97 134 71 77 165
## TCTAA TCTAC TCTAG TCTAT TCTCA TCTCC TCTCG TCTCT TCTGA TCTGC TCTGG
## [1,] 46549 26033 25229 43525 45558 35867 19012 70989 36945 23112 20887
## [2,] 30278 17011 16141 28899 29461 23481 12587 46214 23223 14679 13148
## [3,] 34132 20521 19398 33635 35215 28895 15256 55994 29164 18512 16421
## [4,] 28119 16142 15502 26463 28258 22241 11875 42790 22499 14296 12835
## [5,] 39889 23116 21554 38404 41222 32092 17533 63315 33241 20962 18838
## [6,] 257 129 133 345 154 128 127 242 162 86 114
## TCTGT TCTTA TCTTC TCTTG TCTTT TGAAA TGAAC TGAAG TGAAT TGACA TGACC
## [1,] 36460 50611 75706 52466 92685 76431 32137 49905 56558 31980 17859
## [2,] 22975 32465 48166 33665 60431 49643 20663 31967 36151 20268 11326
## [3,] 28263 37176 58775 40667 71545 58294 24630 39671 43303 24370 13797
## [4,] 21962 30309 46640 32131 55965 46708 19370 30381 34284 19542 10742
## [5,] 32378 44504 67539 46585 83316 68525 28463 45230 50083 27855 15464
## [6,] 152 203 300 239 597 428 176 149 388 85 100
## TGACG TGACT TGAGA TGAGC TGAGG TGAGT TGATA TGATC TGATG TGATT TGCAA
## [1,] 13430 28143 45891 19033 21809 31562 48413 37718 49708 66806 39809
## [2,] 8535 18134 29360 12498 13909 20959 31109 24117 31710 43878 25898
## [3,] 10527 21659 35533 15352 17243 24557 36829 30075 38814 51165 31760
## [4,] 8281 17431 28033 12165 13583 20292 29351 23446 30409 40619 24595
## [5,] 11713 25201 41307 17264 19514 29129 42730 33556 45303 60506 35789
## [6,] 51 132 160 101 70 125 238 188 141 322 124
## TGCAC TGCAG TGCAT TGCCA TGCCC TGCCG TGCCT TGCGA TGCGC TGCGG TGCGT
## [1,] 15225 25070 36011 18940 7404 6531 16245 10987 4349 7581 10710
## [2,] 9852 15503 22546 12518 5220 4369 11261 7180 2946 5058 6505
## [3,] 11628 19842 27956 15092 5968 5481 13042 8908 3469 6291 8101
## [4,] 9286 15278 21353 11472 4846 4023 10011 7030 2616 4896 6522
## [5,] 13501 22462 31182 16761 6687 5776 14792 9725 3763 7043 9478
## [6,] 48 66 136 80 70 46 85 51 36 73 53
## TGCTA TGCTC TGCTG TGCTT TGGAA TGGAC TGGAG TGGAT TGGCA TGGCC TGGCG
## [1,] 22714 22292 21793 42333 43726 18548 32699 39201 18849 11103 9705
## [2,] 14961 14083 13393 27234 28689 12190 21012 25211 12339 7511 6073
## [3,] 17783 17227 17091 32429 34884 14659 26403 30258 15121 9037 7841
## [4,] 14163 13559 13116 25811 26968 11543 20473 23925 11640 7026 5995
## [5,] 19741 19494 19155 37984 39817 16458 29728 34867 16906 10229 8604
## [6,] 124 106 66 150 281 93 105 266 68 53 53
## TGGCT TGGGA TGGGC TGGGG TGGGT TGGTA TGGTC TGGTG TGGTT TGTAA TGTAC
## [1,] 23136 23663 10886 10903 20210 28534 22420 31611 49965 47103 21179
## [2,] 15032 14869 7391 7168 13022 18100 14682 20395 31693 31071 13793
## [3,] 18203 18413 9177 9001 15702 21902 17419 25202 37228 35608 16523
## [4,] 14326 14428 6895 7073 12283 17116 13808 19818 30730 28395 13253
## [5,] 20684 21293 9983 10159 18115 24685 20080 28632 44876 41629 18688
## [6,] 96 114 73 107 122 149 86 91 192 177 102
## TGTAG TGTAT TGTCA TGTCC TGTCG TGTCT TGTGA TGTGC TGTGG TGTGT TGTTA
## [1,] 26769 46181 31295 16606 13510 35894 38338 15221 24751 41229 47629
## [2,] 17480 30093 20477 11162 8820 23001 24243 10048 16264 26854 31504
## [3,] 20897 35265 24262 13437 10719 28189 28958 12085 19559 31654 36213
## [4,] 16533 27966 19470 10548 8747 21979 23086 9303 15270 25402 29048
## [5,] 23696 41943 28012 14876 12200 32079 34075 13854 22420 37918 43310
## [6,] 106 223 95 91 47 138 123 53 83 83 144
## TGTTC TGTTG TGTTT TTAAA TTAAC TTAAG TTAAT TTACA TTACC TTACG TTACT
## [1,] 37962 53811 92055 91854 40396 40943 74030 46695 26383 15418 42772
## [2,] 24662 34586 59970 61890 26309 27081 48956 30619 16812 9792 27519
## [3,] 29896 40917 70115 69055 30248 31491 55690 35911 19959 11936 32124
## [4,] 23444 31809 55828 55481 23895 25679 44165 28226 16017 9213 25875
## [5,] 34422 46977 83804 82900 35693 36829 65776 41646 23146 13643 37801
## [6,] 194 161 237 316 137 139 407 167 116 108 235
## TTAGA TTAGC TTAGG TTAGT TTATA TTATC TTATG TTATT TTCAA TTCAC TTCAG
## [1,] 44773 24403 25655 43688 73186 44089 47332 90893 73061 37708 37391
## [2,] 29337 15614 17220 28121 47560 28883 30788 60544 47701 24518 23595
## [3,] 34155 18249 19794 32428 53778 34107 35568 68020 56187 29271 29316
## [4,] 27154 14765 16066 26067 43251 27065 28391 54857 44782 23091 22895
## [5,] 40466 21309 22912 38959 64298 39883 42073 81005 66321 33414 32926
## [6,] 207 102 131 189 322 241 223 598 422 164 152
## TTCAT TTCCA TTCCC TTCCG TTCCT TTCGA TTCGC TTCGG TTCGT TTCTA TTCTC
## [1,] 66270 44304 22925 15238 42712 26442 11159 14264 25220 48512 61317
## [2,] 43753 28871 15225 10114 28646 17378 7212 9764 16455 31603 39738
## [3,] 50512 34835 18504 12295 34193 21318 8618 11314 19834 36302 47750
## [4,] 40235 27065 14563 9505 27099 16724 6990 9203 15397 29538 37563
## [5,] 58665 39391 20501 13806 38977 24351 9889 13167 22836 42142 55143
## [6,] 448 329 187 135 280 245 99 137 181 374 247
## TTCTG TTCTT TTGAA TTGAC TTGAG TTGAT TTGCA TTGCC TTGCG TTGCT TTGGA
## [1,] 41076 112732 73587 34099 42583 74473 40105 18014 12126 42258 48535
## [2,] 25821 71704 47671 21519 27550 48056 25937 12178 7735 26805 31264
## [3,] 32189 84626 56847 25570 33135 56972 31569 14468 9323 31880 37452
## [4,] 25033 68052 44282 20436 26889 45718 24377 10983 7829 25502 29241
## [5,] 37224 100096 66616 28907 39042 67698 36158 16092 10810 36979 42957
## [6,] 219 642 446 153 164 374 120 82 70 166 244
## TTGGC TTGGG TTGGT TTGTA TTGTC TTGTG TTGTT TTTAA TTTAC TTTAG TTTAT
## [1,] 22790 25964 52842 52627 37849 45522 95276 91355 47430 52757 97162
## [2,] 14841 16725 33843 35078 24223 29493 62551 61761 30775 33854 64271
## [3,] 18093 20526 39937 40022 29032 34903 73128 68617 35802 38928 72639
## [4,] 13882 16041 31962 32079 23073 27587 57926 55336 28611 31568 58227
## [5,] 20630 23501 47931 47245 33335 40528 86433 82088 42291 46202 87195
## [6,] 106 151 210 246 131 131 336 320 233 225 602
## TTTCA TTTCC TTTCG TTTCT TTTGA TTTGC TTTGG TTTGT TTTTA TTTTC TTTTG
## [1,] 76701 45883 27353 101320 84545 41871 61789 92943 110392 93930 109033
## [2,] 49620 30078 17769 65253 53894 27283 39627 60862 73654 60517 69394
## [3,] 58079 36181 21547 77119 63782 32397 47251 70720 82041 71053 80717
## [4,] 46378 28431 16719 60176 50942 25061 37431 56229 66320 55917 64050
## [5,] 68558 41265 24675 90851 76008 37484 56206 83450 99027 83458 96801
## [6,] 438 306 241 557 417 136 232 329 619 601 502
## TTTTT
## [1,] 206261
## [2,] 136085
## [3,] 152869
## [4,] 122775
## [5,] 185592
## [6,] 1846head(oligonucleotideFrequency(assembly,width = 6) ) ## AAAAAA AAAAAC AAAAAG AAAAAT AAAACA AAAACC AAAACG AAAACT AAAAGA AAAAGC
## [1,] 96046 31076 31283 47139 37141 18916 10700 25103 34585 13611
## [2,] 63657 20632 20332 32015 24409 11742 6838 16571 22777 8876
## [3,] 73794 23951 24642 35355 28503 14121 8278 19045 27077 10597
## [4,] 57177 19097 18612 28237 22653 11206 6668 15597 20859 8469
## [5,] 85858 28379 27846 42159 33301 16342 9472 22652 30683 12658
## [6,] 810 121 298 336 81 76 44 94 233 74
## AAAAGG AAAAGT AAAATA AAAATC AAAATG AAAATT AAACAA AAACAC AAACAG AAACAT
## [1,] 14646 21582 43376 25888 26253 39035 38365 16629 14537 24850
## [2,] 9516 14280 29417 17206 16695 25806 25634 9680 8808 16388
## [3,] 12051 16899 32827 19746 19030 29205 29634 11363 10901 18854
## [4,] 8913 13014 26280 15619 15442 23148 23597 9696 8616 15125
## [5,] 13201 19502 38661 23079 22657 34946 34585 13206 12644 21950
## [6,] 134 111 255 137 117 222 110 22 41 62
## AAACCA AAACCC AAACCG AAACCT AAACGA AAACGC AAACGG AAACGT AAACTA AAACTC
## [1,] 20042 13815 7704 14494 10426 5001 4821 7706 18548 15696
## [2,] 13112 7141 4940 8497 6914 2902 3121 4954 12155 9937
## [3,] 15197 8857 5869 10036 8304 3678 3768 6076 13918 11982
## [4,] 12158 7958 4691 8583 6539 3008 3019 4662 11310 9868
## [5,] 17455 10066 7064 11726 9314 4146 4398 7064 16513 13588
## [6,] 69 50 23 58 56 15 37 24 48 50
## AAACTG AAACTT AAAGAA AAAGAC AAAGAG AAAGAT AAAGCA AAAGCC AAAGCG AAAGCT
## [1,] 11604 23435 37544 12355 19678 23323 14407 7464 3826 15485
## [2,] 7684 15449 24467 8332 12779 14919 9321 4918 2484 9472
## [3,] 9105 17974 29302 9732 15680 17890 10950 5895 2951 11510
## [4,] 7214 14410 22835 8057 11858 13946 8683 4708 2294 9855
## [5,] 10403 21214 33063 11561 17506 20771 12640 7290 3398 13837
## [6,] 26 93 226 62 95 149 64 37 33 44
## AAAGGA AAAGGC AAAGGG AAAGGT AAAGTA AAAGTC AAAGTG AAAGTT AAATAA AAATAC
## [1,] 14546 6165 6632 10816 16076 10124 11332 21503 37921 13905
## [2,] 9648 3947 4452 7100 10528 6609 7426 14123 25719 9210
## [3,] 11720 4904 5352 8712 12158 8141 8821 16497 28963 10725
## [4,] 9046 3811 4153 6557 9563 6473 6695 13101 23071 8831
## [5,] 13285 5464 5857 9963 13903 9171 9786 19554 34092 12660
## [6,] 114 32 79 59 73 43 48 79 250 94
## AAATAG AAATAT AAATCA AAATCC AAATCG AAATCT AAATGA AAATGC AAATGG AAATGT
## [1,] 14644 36493 25573 13622 8148 22667 22199 10168 14636 20402
## [2,] 9546 24827 16528 8542 5314 15034 14564 6319 8969 13094
## [3,] 11013 27508 19632 10048 6527 17196 16597 7505 10816 15069
## [4,] 8826 21959 15284 8215 5106 13750 13315 5908 8705 12151
## [5,] 12593 32250 22494 11378 7441 20428 19625 8616 12402 18057
## [6,] 154 187 97 117 57 105 125 49 87 55
## AAATTA AAATTC AAATTG AAATTT AACAAA AACAAC AACAAG AACAAT AACACA AACACC
## [1,] 31030 18533 19906 38671 41082 16518 16791 21580 15594 6856
## [2,] 20609 12063 12641 25551 26289 10993 10691 14621 10245 4440
## [3,] 23026 14014 14971 29184 30885 12999 12845 16918 11996 5395
## [4,] 18282 11123 11865 23580 24594 10142 10368 13102 9681 4278
## [5,] 27634 16640 17512 35136 36035 14938 14794 19298 13431 6056
## [6,] 125 146 96 210 122 43 69 72 30 18
## AACACG AACACT AACAGA AACAGC AACAGG AACAGT AACATA AACATC AACATG AACATT
## [1,] 4167 12780 15863 5930 5149 8878 18083 12287 12805 20000
## [2,] 2657 6840 9644 3624 3279 5448 12027 7596 8507 13041
## [3,] 3588 7839 12103 4625 3962 6754 14094 9324 9911 14998
## [4,] 2544 7005 9759 3691 3063 5342 11225 7295 8037 11809
## [5,] 3722 9530 13644 5168 4444 7869 16241 10726 10904 17872
## [6,] 10 12 36 24 37 24 58 31 35 51
## AACCAA AACCAC AACCAG AACCAT AACCCA AACCCC AACCCG AACCCT AACCGA AACCGC
## [1,] 21214 7815 7154 13446 8602 3426 3432 10755 6079 3139
## [2,] 13770 5332 4523 8847 5840 2274 2267 5057 4124 2131
## [3,] 16021 6311 5622 10209 6814 2563 2658 6388 4903 2428
## [4,] 13342 5009 4327 8074 5291 2085 2087 5982 4090 2120
## [5,] 18603 7118 6368 11790 7622 2920 3112 7116 5764 3287
## [6,] 92 36 25 65 48 36 32 44 26 14
## AACCGG AACCGT AACCTA AACCTC AACCTG AACCTT AACGAA AACGAC AACGAG AACGAT
## [1,] 4643 4720 8976 7284 6014 11890 9303 4524 5058 6676
## [2,] 2969 3063 5187 4966 3967 7260 6058 3101 3336 4497
## [3,] 3711 3400 6059 5749 4677 8776 7308 3697 4234 5261
## [4,] 2926 2846 5044 4474 3838 7284 5788 2948 3374 4154
## [5,] 4621 3979 7004 6609 5425 10093 8297 4104 4754 5966
## [6,] 15 25 44 35 18 55 61 21 31 35
## AACGCA AACGCC AACGCG AACGCT AACGGA AACGGC AACGGG AACGGT AACGTA AACGTC
## [1,] 3964 2376 1484 3601 4401 2664 1905 4436 5178 3576
## [2,] 2483 1512 901 2100 2797 1749 1323 2811 3159 2362
## [3,] 3097 1873 1174 2534 3590 2206 1510 3586 3896 2934
## [4,] 2561 1501 903 2094 2840 1795 1214 2796 2953 2288
## [5,] 3471 2077 1291 2921 4100 2322 1736 4037 4366 3251
## [6,] 15 7 11 14 39 14 19 19 33 14
## AACGTG AACGTT AACTAA AACTAC AACTAG AACTAT AACTCA AACTCC AACTCG AACTCT
## [1,] 3817 7014 16734 7320 7379 13139 12370 7054 5168 14056
## [2,] 2509 4609 11197 4794 4893 8847 8492 4595 3421 8449
## [3,] 2967 5512 12743 5608 5667 9965 9559 5657 4143 10144
## [4,] 2345 4265 10336 4439 4923 8079 7974 4483 3266 8136
## [5,] 3347 6453 14863 6504 7164 11539 10981 6105 4631 11518
## [6,] 9 12 68 30 31 55 47 41 21 66
## AACTGA AACTGC AACTGG AACTGT AACTTA AACTTC AACTTG AACTTT AAGAAA AAGAAC
## [1,] 10074 4925 5240 8285 13195 12396 12747 21665 43983 15974
## [2,] 6536 3288 3365 5228 8888 7987 8378 14241 28536 10195
## [3,] 7942 4168 4120 6334 10255 9766 10170 16440 33824 12356
## [4,] 6331 3126 3189 4924 8358 7609 7916 13251 26549 10280
## [5,] 8926 4410 4673 7130 12174 10983 11734 19341 39210 14131
## [6,] 33 21 21 24 51 47 59 73 228 67
## AAGAAG AAGAAT AAGACA AAGACC AAGACG AAGACT AAGAGA AAGAGC AAGAGG AAGAGT
## [1,] 30287 20862 13579 5943 5633 10153 24513 8283 9817 12936
## [2,] 19508 13415 8903 4056 3627 7025 15986 5280 6320 8275
## [3,] 24102 16322 10424 4861 4459 8280 19180 6683 7707 9934
## [4,] 18913 12738 8420 3795 3467 6914 14951 5022 5985 7614
## [5,] 28428 18382 12213 5486 5105 9547 21703 7251 8767 11449
## [6,] 99 146 32 34 23 33 89 35 41 55
## AAGATA AAGATC AAGATG AAGATT AAGCAA AAGCAC AAGCAG AAGCAT AAGCCA AAGCCC
## [1,] 17454 12738 15265 21715 17710 5748 8324 11308 8229 3786
## [2,] 11380 8300 9929 13942 10867 3678 5330 7374 5468 2578
## [3,] 13340 10267 12103 16667 13062 4501 6513 8677 6553 3091
## [4,] 10514 7926 9469 13309 10583 3337 5194 6909 5301 2488
## [5,] 15962 11660 13611 19578 15461 4886 7455 10097 7319 3512
## [6,] 78 91 50 100 54 25 24 43 31 31
## AAGCCG AAGCCT AAGCGA AAGCGC AAGCGG AAGCGT AAGCTA AAGCTC AAGCTG AAGCTT
## [1,] 3008 6044 4292 1686 2632 3259 10175 9517 8841 16963
## [2,] 2012 4064 2749 1066 1695 2145 6260 5819 5557 10475
## [3,] 2293 4745 3237 1346 2039 2686 7742 7497 6968 12570
## [4,] 1777 3704 2588 1045 1665 2101 6514 5739 5488 11057
## [5,] 2625 6060 3740 1464 2290 2919 8639 8467 7911 15776
## [6,] 20 18 26 13 26 15 34 29 13 46
## AAGGAA AAGGAC AAGGAG AAGGAT AAGGCA AAGGCC AAGGCG AAGGCT AAGGGA AAGGGC
## [1,] 16887 5120 9950 9924 6081 3229 2420 5843 7097 2447
## [2,] 10876 3445 6743 6969 4005 2109 1672 3713 4609 1665
## [3,] 13429 4116 8121 8146 4891 2713 2022 4576 5829 2067
## [4,] 10322 3127 6468 6323 3742 2039 1590 3478 4481 1511
## [5,] 14905 4531 9077 9053 5302 2825 2225 5071 6185 2147
## [6,] 96 28 37 74 22 16 17 29 58 30
## AAGGGG AAGGGT AAGGTA AAGGTC AAGGTG AAGGTT AAGTAA AAGTAC AAGTAG AAGTAT
## [1,] 2713 5419 8465 4971 6096 11029 16369 6694 8332 12783
## [2,] 1860 3721 5537 3245 4152 7073 10675 4396 5623 8195
## [3,] 2163 4411 6841 3965 5029 8727 12386 5368 6543 9597
## [4,] 1732 3519 4998 3114 3935 6734 9881 4065 5198 7765
## [5,] 2351 4973 7698 4529 5569 10095 14318 5997 7499 11448
## [6,] 59 41 42 24 21 52 95 31 40 59
## AAGTCA AAGTCC AAGTCG AAGTCT AAGTGA AAGTGC AAGTGG AAGTGT AAGTTA AAGTTC
## [1,] 10431 5148 3758 9722 11236 4062 7129 10531 14036 10509
## [2,] 6724 3368 2458 6366 7597 2600 4655 6465 8931 6923
## [3,] 8042 4119 2947 7999 9114 3358 5601 7470 10601 8174
## [4,] 6460 3292 2459 6236 7044 2483 4377 5922 8276 6687
## [5,] 8983 4429 3379 8946 10059 3536 6191 8556 12233 9368
## [6,] 36 23 26 28 43 25 43 29 50 62
## AAGTTG AAGTTT AATAAA AATAAC AATAAG AATAAT AATACA AATACC AATACG AATACT
## [1,] 12811 23306 36537 13044 13334 27857 14558 6376 4006 11053
## [2,] 8416 15269 24463 8918 8944 18390 9269 4279 2631 7558
## [3,] 9828 18011 28002 10318 10409 20995 11081 5111 3126 8647
## [4,] 7854 14427 22029 8309 8517 16575 8706 3945 2470 7087
## [5,] 11635 21388 32522 11882 12053 24322 12626 5554 3771 9978
## [6,] 43 89 267 89 93 166 70 64 39 66
## AATAGA AATAGC AATAGG AATAGT AATATA AATATC AATATG AATATT AATCAA AATCAC
## [1,] 13734 6053 5294 11397 28348 14418 15358 30104 25252 10633
## [2,] 9090 3983 3544 7697 18911 9576 10322 20428 16702 6885
## [3,] 10812 4679 4101 8701 20951 11179 11513 22742 19494 8182
## [4,] 8423 3768 3308 7024 16643 8670 9526 18114 15531 6599
## [5,] 11943 5239 4630 10100 24460 12851 13979 27139 22676 9574
## [6,] 169 65 81 78 175 79 68 149 137 35
## AATCAG AATCAT AATCCA AATCCC AATCCG AATCCT AATCGA AATCGC AATCGG AATCGT
## [1,] 10547 20398 14197 6144 5281 9863 8536 3265 3852 6268
## [2,] 6574 13040 8899 3975 3210 6383 5650 2136 2636 4030
## [3,] 8096 15572 10688 4611 3706 7461 6740 2767 3060 5128
## [4,] 6307 12395 8353 3963 3165 6153 5323 2185 2497 3878
## [5,] 9203 17857 11766 5236 4370 8572 7876 3166 3637 5619
## [6,] 32 85 94 67 44 90 81 23 43 43
## AATCTA AATCTC AATCTG AATCTT AATGAA AATGAC AATGAG AATGAT AATGCA AATGCC
## [1,] 14631 15055 10888 21380 20971 8303 10662 18821 11467 4478
## [2,] 9721 9762 6983 13791 13967 5457 6920 12195 7077 3002
## [3,] 10925 11768 8576 16434 16071 6501 8088 14233 8335 3681
## [4,] 8794 9170 6661 13036 12846 5029 6460 11282 6741 2773
## [5,] 12875 13582 9927 19502 18870 7425 9216 16332 9641 3953
## [6,] 73 54 43 105 146 40 64 93 45 32
## AATGCG AATGCT AATGGA AATGGC AATGGG AATGGT AATGTA AATGTC AATGTG AATGTT
## [1,] 2848 9017 13024 6483 7218 11768 13951 9004 10622 19979
## [2,] 1755 5821 8459 4169 4243 7720 9278 5836 6842 12814
## [3,] 2328 6991 10410 5076 5186 8958 10629 7262 8010 14860
## [4,] 1609 5492 8043 3968 4175 7239 8334 5417 6311 12121
## [5,] 2357 8095 11858 5799 5980 10176 12302 8128 9420 17725
## [6,] 24 36 102 25 44 54 50 31 40 46
## AATTAA AATTAC AATTAG AATTAT AATTCA AATTCC AATTCG AATTCT AATTGA AATTGC
## [1,] 28316 11927 14269 25685 17874 8697 6219 16035 17720 7954
## [2,] 18689 7715 9046 17114 11616 5697 4245 10663 11342 4841
## [3,] 21047 9100 10111 19285 13779 6946 4920 12440 13387 6041
## [4,] 16622 7288 8356 15302 10848 5428 3950 9859 10721 4682
## [5,] 24897 10728 12077 22805 16134 7648 5743 14543 15738 6719
## [6,] 133 59 79 121 146 102 65 157 125 50
## AATTGG AATTGT AATTTA AATTTC AATTTG AATTTT ACAAAA ACAAAC ACAAAG ACAAAT
## [1,] 10599 16292 26865 19462 22622 39034 39266 15471 16779 22695
## [2,] 6828 10895 17316 12318 14889 25826 25200 10285 10534 14583
## [3,] 8101 12457 19711 14898 17510 28887 29367 12101 12603 17242
## [4,] 6218 10004 15986 11644 13777 23437 23423 9835 10473 13705
## [5,] 9463 14524 23838 17358 20778 34905 34544 14046 15048 20122
## [6,] 81 98 114 122 82 276 120 34 62 100
## ACAACA ACAACC ACAACG ACAACT ACAAGA ACAAGC ACAAGG ACAAGT ACAATA ACAATC
## [1,] 18299 6629 4464 10444 17024 7431 7822 11791 14859 10658
## [2,] 11620 4496 2907 7277 11267 4756 4919 7694 9776 7161
## [3,] 13997 5291 3644 8457 13158 5803 6099 9216 11161 8211
## [4,] 11021 4079 2831 6669 10421 4706 4762 7219 8950 6492
## [5,] 15833 5930 4174 9535 14905 6586 6598 10620 13056 9524
## [6,] 39 21 14 26 41 24 28 48 56 31
## ACAATG ACAATT ACACAA ACACAC ACACAG ACACAT ACACCA ACACCC ACACCG ACACCT
## [1,] 11639 16404 16283 8405 5500 12358 8407 2672 2726 4601
## [2,] 7816 10830 10453 5429 3366 7690 5433 1642 1799 3103
## [3,] 9540 12244 12133 6387 4318 8862 6366 1877 2162 3658
## [4,] 7294 9768 9999 5184 3408 7283 5440 1657 1625 2978
## [5,] 10704 14496 13839 7088 4727 10388 7679 2176 2372 4099
## [6,] 34 82 35 10 13 33 30 8 12 15
## ACACGA ACACGC ACACGG ACACGT ACACTA ACACTC ACACTG ACACTT ACAGAA ACAGAC
## [1,] 4305 1971 1972 4054 8514 6371 4639 9921 12955 4516
## [2,] 2694 1174 1303 2678 4974 3740 2863 6217 8095 2763
## [3,] 3575 1520 1689 3191 5420 4424 3538 7417 10177 3565
## [4,] 2534 1207 1296 2651 4979 3749 2855 5799 7916 2814
## [5,] 3844 1698 1734 3592 6636 5089 3891 8560 11371 3963
## [6,] 13 8 7 11 13 10 7 18 53 13
## ACAGAG ACAGAT ACAGCA ACAGCC ACAGCG ACAGCT ACAGGA ACAGGC ACAGGG ACAGGT
## [1,] 10329 8940 5270 2702 1679 5801 4719 2172 2414 4586
## [2,] 6133 5579 3095 1771 1043 3587 2983 1474 1491 2758
## [3,] 7970 6927 4100 2096 1399 4611 3713 1692 1975 3417
## [4,] 6321 5495 3211 1661 1055 3687 2855 1337 1464 2776
## [5,] 9081 7746 4475 2334 1535 4955 4024 1920 2039 3950
## [6,] 13 29 24 18 6 25 27 12 18 26
## ACAGTA ACAGTC ACAGTG ACAGTT ACATAA ACATAC ACATAG ACATAT ACATCA ACATCC
## [1,] 6065 3863 4901 8544 16240 8063 7009 17534 12663 5195
## [2,] 3854 2595 3048 5149 10762 5212 4727 11417 7995 3540
## [3,] 4746 3115 3775 6341 12319 6145 5586 13442 9689 4226
## [4,] 3716 2497 2994 5066 9928 4867 4419 10677 7697 3248
## [5,] 5236 3539 4387 7325 14358 7031 6580 15840 11193 4650
## [6,] 19 15 9 21 63 23 43 61 26 33
## ACATCG ACATCT ACATGA ACATGC ACATGG ACATGT ACATTA ACATTC ACATTG ACATTT
## [1,] 3932 10105 12253 6171 6880 11902 12892 9234 10807 20830
## [2,] 2496 6458 7756 3894 4439 7888 8517 6117 6992 13380
## [3,] 3050 7663 9112 5199 5223 9168 10102 7225 8520 15496
## [4,] 2470 6057 7390 3629 4382 7555 7856 5649 6432 11953
## [5,] 3539 8679 10156 5194 5987 10593 11537 8276 9465 18352
## [6,] 17 43 43 27 18 34 37 37 35 61
## ACCAAA ACCAAC ACCAAG ACCAAT ACCACA ACCACC ACCACG ACCACT ACCAGA ACCAGC
## [1,] 22433 8771 8983 11825 8015 6292 2691 6241 7458 4032
## [2,] 14448 5888 5653 8006 5209 4390 1764 4358 4744 2692
## [3,] 17064 6865 6867 9304 6325 5256 2163 5073 6026 3625
## [4,] 13888 5534 5842 7378 5100 4427 1670 3927 4627 2470
## [5,] 20238 7697 7647 10535 7165 5890 2406 5678 6648 3671
## [6,] 77 33 54 73 23 26 14 25 25 19
## ACCAGG ACCAGT ACCATA ACCATC ACCATG ACCATT ACCCAA ACCCAC ACCCAG ACCCAT
## [1,] 2940 4919 10117 8243 6616 11713 8172 3438 2329 6038
## [2,] 1939 3257 6038 5468 4405 7935 5690 2375 1476 4073
## [3,] 2451 3877 6892 6540 5277 9117 6391 2904 1905 4853
## [4,] 1921 3107 5531 5404 4070 7220 5253 2155 1438 3614
## [5,] 2681 4442 7839 7872 5922 10560 7485 2994 1938 5306
## [6,] 14 11 59 29 26 40 42 12 29 41
## ACCCCA ACCCCC ACCCCG ACCCCT ACCCGA ACCCGC ACCCGG ACCCGT ACCCTA ACCCTC
## [1,] 3296 1204 856 2425 3134 1341 1503 2248 8173 3235
## [2,] 2186 884 638 1555 2056 924 1034 1492 3436 2270
## [3,] 2608 947 738 1815 2476 1129 1195 1713 4515 2629
## [4,] 2072 817 549 1390 2041 801 922 1316 4391 2279
## [5,] 2965 1148 775 1968 2850 1255 1372 2013 4876 2794
## [6,] 34 33 24 32 20 23 14 29 25 16
## ACCCTG ACCCTT ACCGAA ACCGAC ACCGAG ACCGAT ACCGCA ACCGCC ACCGCG ACCGCT
## [1,] 2349 5851 4928 2452 3065 3964 2478 2224 1311 2204
## [2,] 1488 3711 3385 1656 2037 2573 1755 1416 805 1492
## [3,] 1852 4459 3947 1901 2491 3038 2038 1754 1019 1779
## [4,] 1527 3742 3277 1547 1941 2654 1838 1368 736 1448
## [5,] 2088 4970 4554 2255 2711 3703 2810 1963 1143 1996
## [6,] 18 45 28 9 21 22 12 12 9 27
## ACCGGA ACCGGC ACCGGG ACCGGT ACCGTA ACCGTC ACCGTG ACCGTT ACCTAA ACCTAC
## [1,] 4493 1860 1475 3777 3206 3102 2464 4323 9029 3256
## [2,] 2818 1192 1050 2457 2138 2016 1549 2858 5294 2222
## [3,] 3680 1463 1244 2988 2275 2327 2007 3449 5957 2536
## [4,] 2816 1162 939 2307 1911 1828 1492 2642 5220 2048
## [5,] 4376 1757 1389 3338 2695 2683 2221 3909 7191 2998
## [6,] 22 8 14 17 17 15 11 14 38 26
## ACCTAG ACCTAT ACCTCA ACCTCC ACCTCG ACCTCT ACCTGA ACCTGC ACCTGG ACCTGT
## [1,] 3356 5410 5797 4553 2601 6856 6464 3362 2753 4387
## [2,] 2256 3651 4043 3098 1776 4903 4216 2215 1826 2948
## [3,] 2537 4158 4719 3675 2155 5357 5086 2685 2295 3545
## [4,] 2111 3238 3735 2815 1778 4272 4209 2247 1838 2764
## [5,] 2925 4729 5341 4117 2310 6141 5710 2934 2542 4022
## [6,] 20 46 19 24 18 39 21 14 13 22
## ACCTTA ACCTTC ACCTTG ACCTTT ACGAAA ACGAAC ACGAAG ACGAAT ACGACA ACGACC
## [1,] 7015 7188 6430 11077 9182 3872 5954 6172 4396 2467
## [2,] 4111 4619 4201 7356 5985 2522 3696 4069 2821 1611
## [3,] 5058 5540 5206 8702 7439 3000 4561 4907 3421 1926
## [4,] 4192 4439 3960 6779 5671 2381 3563 3846 2607 1469
## [5,] 5706 6393 5603 9836 8489 3577 5265 5387 3828 2077
## [6,] 26 27 34 62 60 19 35 43 9 20
## ACGACG ACGACT ACGAGA ACGAGC ACGAGG ACGAGT ACGATA ACGATC ACGATG ACGATT
## [1,] 3347 3317 5793 2891 3132 4016 4723 3802 4867 5997
## [2,] 2269 2264 3788 1812 2009 2625 2940 2526 3047 4137
## [3,] 2766 2578 4672 2421 2728 3191 3645 3098 3857 4854
## [4,] 2120 2053 3794 1856 2103 2609 2752 2405 2981 3813
## [5,] 3075 2904 5343 2680 2807 3585 3925 3326 4299 5517
## [6,] 12 12 28 20 16 18 25 31 10 29
## ACGCAA ACGCAC ACGCAG ACGCAT ACGCCA ACGCCC ACGCCG ACGCCT ACGCGA ACGCGC
## [1,] 3841 1484 2204 3114 2414 774 1589 1776 1230 838
## [2,] 2337 1018 1345 1983 1503 556 966 1153 792 527
## [3,] 3012 1264 1636 2433 1960 664 1239 1396 994 643
## [4,] 2340 930 1365 1894 1523 526 1002 1064 837 514
## [5,] 3373 1327 1985 2619 2124 695 1383 1604 1114 693
## [6,] 15 7 5 12 9 17 2 13 14 3
## ACGCGG ACGCGT ACGCTA ACGCTC ACGCTG ACGCTT ACGGAA ACGGAC ACGGAG ACGGAT
## [1,] 918 1332 2304 1941 1876 3378 4106 1691 3197 3752
## [2,] 607 816 1222 1194 1188 2188 2530 1147 2124 2346
## [3,] 769 1128 1458 1542 1513 2673 3220 1464 2716 2973
## [4,] 582 821 1293 1279 1139 1959 2530 1303 1966 2308
## [5,] 867 1221 1750 1763 1601 2999 3699 1878 2848 3471
## [6,] 8 9 6 10 10 12 32 11 21 29
## ACGGCA ACGGCC ACGGCG ACGGCT ACGGGA ACGGGC ACGGGG ACGGGT ACGGTA ACGGTC
## [1,] 1956 1299 2133 2330 2137 880 803 2079 2701 2120
## [2,] 1259 858 1338 1590 1452 629 571 1407 1788 1397
## [3,] 1633 1065 1850 1913 1663 795 729 1698 2113 1943
## [4,] 1218 850 1404 1597 1338 591 476 1332 1607 1308
## [5,] 1590 1115 1913 2072 1963 846 718 2014 2536 2028
## [6,] 6 11 11 19 18 11 16 24 21 4
## ACGGTG ACGGTT ACGTAA ACGTAC ACGTAG ACGTAT ACGTCA ACGTCC ACGTCG ACGTCT
## [1,] 3366 4346 5199 3109 2579 4381 3590 1737 2125 3277
## [2,] 2181 2941 3091 2035 1650 2759 2358 1191 1402 2197
## [3,] 2753 3591 3743 2402 2033 3355 2801 1443 1761 2645
## [4,] 2339 2892 3009 1868 1497 2534 2102 1103 1456 2044
## [5,] 3168 4116 4412 2613 2269 3823 3129 1545 1941 2809
## [6,] 12 20 30 13 15 26 11 14 8 17
## ACGTGA ACGTGC ACGTGG ACGTGT ACGTTA ACGTTC ACGTTG ACGTTT ACTAAA ACTAAC
## [1,] 3924 1700 3181 4195 4411 3028 4178 7846 16905 7737
## [2,] 2591 1080 1997 2683 2837 2055 2639 5013 11102 4775
## [3,] 3083 1367 2496 3131 3401 2434 3187 6077 12538 5346
## [4,] 2429 1097 2016 2517 2753 1889 2528 4632 10600 4664
## [5,] 3443 1590 2750 3532 3953 2734 3907 6878 14551 6249
## [6,] 14 8 11 13 12 18 12 29 81 24
## ACTAAG ACTAAT ACTACA ACTACC ACTACG ACTACT ACTAGA ACTAGC ACTAGG ACTAGT
## [1,] 6086 12767 8346 3334 2523 7781 7371 3637 3149 6380
## [2,] 4212 8286 5291 2191 1587 4918 4966 2458 2170 4050
## [3,] 4776 9826 6413 2540 1867 5711 5631 2872 2623 4828
## [4,] 3757 7755 4698 2059 1491 4793 5053 2148 2009 3878
## [5,] 5498 11160 7154 2903 2092 6615 7452 2966 2826 5689
## [6,] 37 65 25 18 13 35 39 19 15 17
## ACTATA ACTATC ACTATG ACTATT ACTCAA ACTCAC ACTCAG ACTCAT ACTCCA ACTCCC
## [1,] 11367 6123 6384 11293 11378 5592 4946 9439 7212 2675
## [2,] 7459 4028 4220 7778 7789 3696 3423 6189 4761 1859
## [3,] 8386 4720 4926 8598 9004 4204 3925 7136 5811 2267
## [4,] 6895 3831 3927 6847 7587 3484 3204 6147 4944 1748
## [5,] 9862 5424 5921 10106 10198 4997 4425 8742 6425 2438
## [6,] 58 26 29 55 46 22 17 44 34 23
## ACTCCG ACTCCT ACTCGA ACTCGC ACTCGG ACTCGT ACTCTA ACTCTC ACTCTG ACTCTT
## [1,] 2514 6268 6014 2089 2632 4187 7782 8367 6311 13549
## [2,] 1609 3598 4076 1506 1736 2715 5097 5674 3893 8423
## [3,] 2022 4491 4942 1721 2107 3312 6052 6977 4860 9776
## [4,] 1555 3641 4202 1377 1733 2563 4911 5272 3865 7864
## [5,] 2211 4854 5815 1897 2373 3576 6789 7799 5309 11248
## [6,] 11 46 35 5 14 20 37 26 25 55
## ACTGAA ACTGAC ACTGAG ACTGAT ACTGCA ACTGCC ACTGCG ACTGCT ACTGGA ACTGGC
## [1,] 9821 3381 4750 8123 5667 2205 1633 5190 5149 2118
## [2,] 6293 2230 3125 5170 3404 1665 1092 3142 3240 1363
## [3,] 7572 2614 3947 6298 4338 1839 1472 3851 4173 1743
## [4,] 6093 2164 3076 5006 3390 1420 1065 3180 3096 1269
## [5,] 8852 3009 4347 7228 4909 1923 1539 4266 4712 1880
## [6,] 38 11 19 35 19 10 14 26 35 4
## ACTGGG ACTGGT ACTGTA ACTGTC ACTGTG ACTGTT ACTTAA ACTTAC ACTTAG ACTTAT
## [1,] 2091 4994 5952 3887 4511 8915 11462 6996 5855 11370
## [2,] 1369 3203 3551 2602 2908 5682 7517 4707 4112 7353
## [3,] 1687 3898 4609 3033 3548 6719 8730 5287 4677 8495
## [4,] 1377 3044 3672 2472 2810 5086 6976 4365 3986 6966
## [5,] 1841 4438 5144 3389 4106 7908 10403 6353 5354 9852
## [6,] 12 21 25 16 12 24 44 22 26 69
## ACTTCA ACTTCC ACTTCG ACTTCT ACTTGA ACTTGC ACTTGG ACTTGT ACTTTA ACTTTC
## [1,] 11361 6612 3479 12513 11254 6014 7570 11948 13825 11196
## [2,] 7424 4316 2340 7995 7648 3875 4978 7725 8547 7413
## [3,] 9064 5378 2687 9456 9302 4581 6154 9232 9986 8820
## [4,] 6979 4197 2467 7693 7284 3625 4693 7326 8213 7037
## [5,] 10304 5924 3422 10728 10883 5173 6858 10591 11692 10333
## [6,] 42 34 31 55 50 17 42 41 46 37
## ACTTTG ACTTTT AGAAAA AGAAAC AGAAAG AGAAAT AGAACA AGAACC AGAACG AGAACT
## [1,] 12588 22065 40550 20013 20074 22470 14806 7857 4132 10394
## [2,] 8519 14312 25259 12497 12899 14407 9397 5180 2626 6714
## [3,] 9944 16284 30749 15106 15617 17092 11792 6243 3295 8252
## [4,] 7954 12947 23551 11933 11918 13610 9239 5227 2633 6784
## [5,] 11479 19649 34902 17362 17662 19990 13069 7525 3640 9538
## [6,] 43 105 193 63 95 177 41 43 27 39
## AGAAGA AGAAGC AGAAGG AGAAGT AGAATA AGAATC AGAATG AGAATT AGACAA AGACAC
## [1,] 32531 12276 10339 12283 13630 13784 11240 15958 14229 5902
## [2,] 20992 7755 6679 8000 9083 8744 7247 10423 9006 3909
## [3,] 25792 9840 8274 9739 10757 10754 8683 12570 10791 4659
## [4,] 20147 8130 6377 7642 8408 8469 6878 9912 8666 3587
## [5,] 30526 12190 9232 11019 11923 12321 9692 14437 12679 5124
## [6,] 90 37 57 53 106 83 55 134 39 19
## AGACAG AGACAT AGACCA AGACCC AGACCG AGACCT AGACGA AGACGC AGACGG AGACGT
## [1,] 6010 9815 7062 2911 2344 4534 6430 2232 2845 3226
## [2,] 3602 6657 4602 1962 1598 3064 4172 1449 1828 2151
## [3,] 4608 7671 5730 2314 1938 3564 5078 1867 2342 2613
## [4,] 3648 6275 4552 1863 1461 2849 3904 1470 1942 2117
## [5,] 5163 8790 6463 2562 2107 4016 5791 2034 2632 2926
## [6,] 20 35 27 20 14 21 23 7 18 12
## AGACTA AGACTC AGACTG AGACTT AGAGAA AGAGAC AGAGAG AGAGAT AGAGCA AGAGCC
## [1,] 6481 6345 4711 9773 24878 9718 20214 17250 8021 4138
## [2,] 4515 4159 3002 6468 15611 6256 13206 10989 5067 2691
## [3,] 5197 5195 3808 7896 19340 7521 15784 13278 6344 3200
## [4,] 4182 4272 3012 6313 14922 6122 12353 10523 4818 2510
## [5,] 5912 5964 4277 8906 21479 8649 17731 15029 7084 3662
## [6,] 27 20 13 29 66 28 42 70 31 25
## AGAGCG AGAGCT AGAGGA AGAGGC AGAGGG AGAGGT AGAGTA AGAGTC AGAGTG AGAGTT
## [1,] 2490 8363 11932 4425 4037 6900 9003 6226 7181 13071
## [2,] 1571 5295 7790 2835 2672 4610 5783 3892 4453 8501
## [3,] 1953 7050 9504 3559 3414 5528 7115 5050 5619 9913
## [4,] 1487 5189 7457 2698 2464 4326 5481 3887 4362 7810
## [5,] 2310 7251 10759 3968 3778 6188 8050 5710 6308 11551
## [6,] 12 29 45 20 28 23 34 21 23 54
## AGATAA AGATAC AGATAG AGATAT AGATCA AGATCC AGATCG AGATCT AGATGA AGATGC
## [1,] 15818 7449 8010 15935 12037 6932 4719 11133 15361 6422
## [2,] 10388 4755 5187 10139 7772 4503 3016 7276 9919 4070
## [3,] 11784 5807 6335 11920 9759 5512 3799 8693 12043 5206
## [4,] 9498 4761 4811 9350 7366 4282 2957 6916 9670 3917
## [5,] 13610 7192 7002 13918 10806 6111 4259 9697 13689 5568
## [6,] 82 49 44 85 46 55 34 77 46 21
## AGATGG AGATGT AGATTA AGATTC AGATTG AGATTT AGCAAA AGCAAC AGCAAG AGCAAT
## [1,] 9107 9870 13675 13950 12262 22552 16278 8056 8370 10089
## [2,] 5779 6413 8830 8722 7949 14849 10146 5045 5335 6204
## [3,] 7256 7671 10528 10542 9429 17356 12518 6186 6508 7456
## [4,] 5701 6229 8193 8676 7696 13917 9588 5033 5059 6262
## [5,] 8240 9133 12414 12275 10938 20443 13917 6935 7789 8657
## [6,] 30 42 52 82 39 108 57 28 29 51
## AGCACA AGCACC AGCACG AGCACT AGCAGA AGCAGC AGCAGG AGCAGT AGCATA AGCATC
## [1,] 5358 3387 1917 4251 8495 6264 3140 5009 7331 7414
## [2,] 3489 2322 1173 2524 5261 4047 2093 3149 4941 4718
## [3,] 4272 2839 1627 3180 6837 4936 2496 3927 5800 5661
## [4,] 3269 2120 1157 2320 5182 3803 2076 3034 4559 4376
## [5,] 4637 3033 1711 3368 7333 5423 2894 4261 6515 6560
## [6,] 10 16 16 21 26 22 16 31 35 27
## AGCATG AGCATT AGCCAA AGCCAC AGCCAG AGCCAT AGCCCA AGCCCC AGCCCG AGCCCT
## [1,] 5646 9153 8494 4632 3101 6833 4258 1191 963 2692
## [2,] 3785 5894 5596 2990 2047 4704 2742 899 700 1793
## [3,] 4556 6888 6726 3607 2465 5475 3389 982 815 2065
## [4,] 3588 5466 5457 2743 1942 4427 2632 758 697 1608
## [5,] 5108 8001 7377 4011 2762 6045 3774 1091 1074 2270
## [6,] 27 37 44 17 17 37 26 31 11 24
## AGCCGA AGCCGC AGCCGG AGCCGT AGCCTA AGCCTC AGCCTG AGCCTT AGCGAA AGCGAC
## [1,] 2795 1825 1693 2326 3606 4872 2870 5633 3660 2245
## [2,] 1696 1268 1172 1632 2418 2832 1871 3888 2405 1462
## [3,] 2048 1523 1319 2008 2811 3450 2240 4557 2816 1725
## [4,] 1748 1185 1004 1530 2214 2749 1729 3658 2194 1346
## [5,] 2343 1714 1565 2094 3767 3867 2567 5209 3210 2090
## [6,] 19 13 18 16 17 22 13 26 28 10
## AGCGAG AGCGAT AGCGCA AGCGCC AGCGCG AGCGCT AGCGGA AGCGGC AGCGGG AGCGGT
## [1,] 2822 3336 1370 955 675 1205 2359 1611 1029 2194
## [2,] 1845 2062 856 680 428 809 1470 1060 717 1376
## [3,] 2199 2549 1105 808 549 944 1877 1277 814 1795
## [4,] 1740 2071 876 601 446 743 1513 1040 634 1452
## [5,] 2602 2903 1218 886 602 1025 2111 1394 973 1999
## [6,] 11 18 12 13 4 4 24 15 18 14
## AGCGTA AGCGTC AGCGTG AGCGTT AGCTAA AGCTAC AGCTAG AGCTAT AGCTCA AGCTCC
## [1,] 2011 1989 1846 3221 9481 4985 5488 7681 7743 5561
## [2,] 1311 1323 1163 1966 6191 3335 3472 4670 4845 3646
## [3,] 1616 1535 1552 2527 7202 4049 4374 5828 5942 4541
## [4,] 1294 1256 1140 2011 6171 3154 3486 4424 4947 3550
## [5,] 1776 1677 1630 2969 8371 4722 4718 6413 6610 4981
## [6,] 7 7 5 16 48 32 22 41 23 32
## AGCTCG AGCTCT AGCTGA AGCTGC AGCTGG AGCTGT AGCTTA AGCTTC AGCTTG AGCTTT
## [1,] 3706 8292 8053 5709 4522 5870 8410 12460 9018 15430
## [2,] 2414 5260 5116 3632 2838 3648 5452 7654 5704 9468
## [3,] 2911 6955 6424 4559 3763 4711 6497 9511 7301 11523
## [4,] 2400 4971 5135 3522 2956 3638 5123 8032 6068 9352
## [5,] 3201 7329 7309 5031 4088 5248 7539 10983 8728 13799
## [6,] 19 29 9 18 19 21 23 39 26 52
## AGGAAA AGGAAC AGGAAG AGGAAT AGGACA AGGACC AGGACG AGGACT AGGAGA AGGAGC
## [1,] 15878 6831 11920 8962 5156 2853 2319 4144 11672 4736
## [2,] 10385 4387 7520 5904 3481 1963 1589 2708 7826 2945
## [3,] 12698 5511 9378 7444 4047 2340 1948 3436 9491 3510
## [4,] 9919 4339 7106 5478 3332 1872 1456 2581 7395 3044
## [5,] 14159 6135 10419 8013 4730 2603 2081 3722 10657 4073
## [6,] 76 42 40 77 18 27 13 24 31 26
## AGGAGG AGGAGT AGGATA AGGATC AGGATG AGGATT AGGCAA AGGCAC AGGCAG AGGCAT
## [1,] 6778 5643 6784 6388 6331 9497 6317 2495 3139 4612
## [2,] 4426 3715 4536 4240 4275 6540 4141 1622 2101 3058
## [3,] 5436 4521 5410 5102 5343 7478 5083 2016 2650 3712
## [4,] 4160 3426 4383 3917 4211 5855 3928 1555 1963 2996
## [5,] 5990 4877 6093 5627 5850 8497 5600 2155 2930 4148
## [6,] 32 29 34 59 34 88 23 14 12 21
## AGGCCA AGGCCC AGGCCG AGGCCT AGGCGA AGGCGC AGGCGG AGGCGT AGGCTA AGGCTC
## [1,] 3293 1827 1170 2519 2243 993 1910 1829 3732 3482
## [2,] 2221 1249 824 1636 1611 707 1249 1158 2369 2233
## [3,] 2922 1642 1022 2069 2041 814 1581 1369 2806 2762
## [4,] 2079 1151 760 1676 1550 641 1235 1139 2305 2164
## [5,] 3024 1674 1081 2235 2086 918 1761 1541 2986 3086
## [6,] 11 13 5 25 13 9 12 14 18 21
## AGGCTG AGGCTT AGGGAA AGGGAC AGGGAG AGGGAT AGGGCA AGGGCC AGGGCG AGGGCT
## [1,] 3578 6210 7356 2950 4196 5089 2465 1197 762 2535
## [2,] 2302 3917 4721 1835 2793 3390 1623 823 558 1718
## [3,] 2832 4625 5898 2259 3360 4457 1983 950 666 2008
## [4,] 2101 3830 4672 1804 2542 3202 1496 763 455 1615
## [5,] 3118 5518 6559 2437 3749 4655 2199 1022 688 2342
## [6,] 19 18 51 19 24 49 22 15 11 21
## AGGGGA AGGGGC AGGGGG AGGGGT AGGGTA AGGGTC AGGGTG AGGGTT AGGTAA AGGTAC
## [1,] 3269 1050 1267 2167 3569 2440 2512 7833 8498 4082
## [2,] 2150 793 916 1411 2349 1701 1620 5178 5495 2578
## [3,] 2602 850 1055 1749 2971 2048 2069 6215 6735 3136
## [4,] 2049 715 853 1333 2306 1652 1547 4892 5115 2488
## [5,] 2790 911 1227 1921 3275 2322 2133 6888 7740 3636
## [6,] 31 27 33 32 20 15 16 46 42 20
## AGGTAG AGGTAT AGGTCA AGGTCC AGGTCG AGGTCT AGGTGA AGGTGC AGGTGG AGGTGT
## [1,] 3736 6546 4884 2726 2328 4459 6449 2451 4694 4550
## [2,] 2444 4385 3180 1888 1554 2984 4213 1591 3091 3086
## [3,] 2901 5359 3947 2200 1871 3629 5246 2050 3850 3612
## [4,] 2280 3995 2802 1701 1598 2978 4108 1490 3080 2909
## [5,] 3403 6170 4378 2374 2071 4137 5741 2311 4206 4198
## [6,] 21 43 22 28 10 32 17 17 19 16
## AGGTTA AGGTTC AGGTTG AGGTTT AGTAAA AGTAAC AGTAAG AGTAAT AGTACA AGTACC
## [1,] 7020 6275 6402 12928 15778 7725 7388 11581 6568 3725
## [2,] 4524 3806 4267 8311 10339 4920 4920 7524 4238 2450
## [3,] 5392 4590 5176 9990 12052 5993 5734 8798 5183 2929
## [4,] 4118 3709 4118 7954 9587 4733 4476 6997 4066 2270
## [5,] 6253 5453 5990 11580 13972 6663 6326 10272 5898 3177
## [6,] 27 46 19 60 83 38 35 69 26 29
## AGTACG AGTACT AGTAGA AGTAGC AGTAGG AGTAGT AGTATA AGTATC AGTATG AGTATT
## [1,] 2110 5966 8744 4479 3337 7439 10690 6884 6658 11120
## [2,] 1302 3875 5835 2988 2285 4885 6816 4343 4367 7366
## [3,] 1608 4865 7018 3598 2666 5728 7876 5247 5249 8532
## [4,] 1245 3810 5456 2773 2131 4573 6678 4043 4038 7120
## [5,] 1872 5419 7620 3953 2972 6730 9933 5824 6071 10261
## [6,] 19 23 43 28 28 39 44 44 24 70
## AGTCAA AGTCAC AGTCAG AGTCAT AGTCCA AGTCCC AGTCCG AGTCCT AGTCGA AGTCGC
## [1,] 11031 5223 4075 8541 5589 2756 1652 4169 3653 1844
## [2,] 6651 3286 2615 5514 3665 1770 1133 2693 2574 1238
## [3,] 7945 4008 3267 6583 4307 2228 1229 3250 2931 1443
## [4,] 6818 3210 2647 5301 3497 1674 1030 2559 2430 1152
## [5,] 9267 4387 3609 7315 4746 2464 1490 3651 3600 1744
## [6,] 46 14 23 37 25 20 14 20 26 12
## AGTCGG AGTCGT AGTCTA AGTCTC AGTCTG AGTCTT AGTGAA AGTGAC AGTGAG AGTGAT
## [1,] 2047 3301 5872 7191 4276 10097 11601 4997 6268 10034
## [2,] 1403 2180 3854 4641 2793 6696 7626 3245 4177 6514
## [3,] 1549 2648 4682 5706 3398 8090 8915 3923 4965 7991
## [4,] 1304 1969 3762 4488 2709 6552 7162 3125 3941 6268
## [5,] 1813 3006 5178 6510 3973 9350 10490 4471 6011 8806
## [6,] 16 19 17 20 12 32 42 16 23 45
## AGTGCA AGTGCC AGTGCG AGTGCT AGTGGA AGTGGC AGTGGG AGTGGT AGTGTA AGTGTC
## [1,] 4144 2129 1300 3959 6950 3618 3292 6567 6578 4642
## [2,] 2661 1434 863 2440 4611 2359 2162 4249 4258 3034
## [3,] 3413 1699 999 3232 5672 2844 2630 4865 5092 3778
## [4,] 2423 1344 797 2495 4435 2189 2036 4076 3977 2969
## [5,] 3665 1913 1142 3348 6319 3067 3047 5666 5813 4162
## [6,] 17 13 12 20 45 17 20 24 20 12
## AGTGTG AGTGTT AGTTAA AGTTAC AGTTAG AGTTAT AGTTCA AGTTCC AGTTCG AGTTCT
## [1,] 5311 11630 12216 6954 7028 11879 9753 5969 3229 10628
## [2,] 3529 7081 7860 4526 4425 8025 6273 4099 2212 6740
## [3,] 4310 8063 9406 5403 5376 9383 7362 4639 2643 8264
## [4,] 3214 6722 7268 4233 4162 7395 5916 3740 1989 7023
## [5,] 4893 10158 10613 6183 6075 10787 8505 5328 2930 9277
## [6,] 15 25 43 39 26 68 50 51 24 62
## AGTTGA AGTTGC AGTTGG AGTTGT AGTTTA AGTTTC AGTTTG AGTTTT ATAAAA ATAAAC
## [1,] 11668 5943 7084 10782 14793 15027 14005 26261 37439 17097
## [2,] 7447 3752 4698 7130 9580 9603 9071 16502 25036 10779
## [3,] 8682 4527 5542 8407 11118 11612 11128 18962 28070 12526
## [4,] 7006 3748 4409 6511 8934 9018 8712 15222 22316 9952
## [5,] 10359 5226 6580 9543 13199 13451 12818 22830 33336 14770
## [6,] 51 22 34 36 37 49 38 107 279 55
## ATAAAG ATAAAT ATAACA ATAACC ATAACG ATAACT ATAAGA ATAAGC ATAAGG ATAAGT
## [1,] 14939 28913 15994 7772 4231 11924 16218 7424 6251 12157
## [2,] 9786 19256 10495 5219 2781 8048 10661 4903 4267 7383
## [3,] 11643 21521 12170 6172 3370 9210 12525 5737 5154 8546
## [4,] 9123 17081 9666 4804 2599 7251 10409 4758 4083 6961
## [5,] 13217 25140 13987 7195 3628 10506 14399 6502 5539 10114
## [6,] 97 165 67 47 26 69 101 43 40 75
## ATAATA ATAATC ATAATG ATAATT ATACAA ATACAC ATACAG ATACAT ATACCA ATACCC
## [1,] 23783 12871 13219 26314 16895 8412 6104 15480 8241 3510
## [2,] 15891 8490 8564 16956 11051 5043 3602 9958 5564 2355
## [3,] 17883 10026 10014 19107 12940 5924 4653 12113 6521 2836
## [4,] 14204 7928 8025 15337 10571 5182 3717 9197 5154 2153
## [5,] 20614 11671 11728 22781 15387 7044 5470 13508 7407 3083
## [6,] 144 75 81 141 82 32 33 72 42 28
## ATACCG ATACCT ATACGA ATACGC ATACGG ATACGT ATACTA ATACTC ATACTG ATACTT
## [1,] 2666 6750 4841 2015 2397 4258 10025 7249 5209 12311
## [2,] 1797 4369 3094 1278 1515 2761 6589 4879 3300 8275
## [3,] 2145 5304 3748 1507 1849 3280 7608 5777 3988 9480
## [4,] 1666 4094 3045 1146 1645 2527 6103 5075 3197 7727
## [5,] 2427 5855 4478 1764 2538 3737 8502 6538 4695 11299
## [6,] 19 59 36 13 30 25 57 36 24 74
## ATAGAA ATAGAC ATAGAG ATAGAT ATAGCA ATAGCC ATAGCG ATAGCT ATAGGA ATAGGC
## [1,] 15521 5963 9535 13030 6641 3590 1934 7479 5814 3012
## [2,] 9994 3905 6213 8714 4470 2313 1257 4618 3879 2006
## [3,] 11803 4688 7425 9884 5282 2726 1548 5672 4737 2367
## [4,] 9281 3859 5918 7966 4069 2154 1167 4541 3546 1909
## [5,] 13145 5364 8252 11551 5854 3173 1654 6309 5274 2623
## [6,] 172 37 56 115 42 25 15 59 73 26
## ATAGGG ATAGGT ATAGTA ATAGTC ATAGTG ATAGTT ATATAA ATATAC ATATAG ATATAT
## [1,] 2949 5463 9969 5777 6355 13218 27595 13681 13165 49734
## [2,] 2107 3555 6668 3813 4174 8578 18366 8886 8450 33461
## [3,] 2531 4070 7542 4441 4848 9861 20655 10177 10053 36965
## [4,] 1784 3280 6022 3667 3991 7955 16394 8216 7785 29833
## [5,] 2687 4690 8852 4901 5568 11710 24458 12271 11332 43963
## [6,] 36 58 65 30 45 77 165 50 89 260
## ATATCA ATATCC ATATCG ATATCT ATATGA ATATGC ATATGG ATATGT ATATTA ATATTC
## [1,] 16601 7575 4825 15612 17118 8119 9279 17493 23019 14316
## [2,] 10843 5112 3238 10053 11485 5406 6234 11415 15218 9472
## [3,] 12911 5995 3776 12157 12915 6114 7083 13395 17122 10906
## [4,] 10059 4788 2994 9325 10722 4835 5674 10619 13653 8622
## [5,] 14912 6864 4606 13700 15857 7153 8085 15525 20544 12548
## [6,] 79 53 37 87 87 28 42 47 132 120
## ATATTG ATATTT ATCAAA ATCAAC ATCAAG ATCAAT ATCACA ATCACC ATCACG ATCACT
## [1,] 14404 37822 28625 13077 13098 18579 12216 7114 3828 9603
## [2,] 9742 24441 18907 8433 8367 12435 7784 4783 2339 6427
## [3,] 11107 26815 22234 10174 10270 14589 9877 5733 3126 7730
## [4,] 8853 21986 17879 8005 8180 11379 7467 4610 2243 6150
## [5,] 13434 32907 26159 11482 11638 16938 11015 6424 3339 8897
## [6,] 89 158 161 47 40 134 35 27 4 36
## ATCAGA ATCAGC ATCAGG ATCAGT ATCATA ATCATC ATCATG ATCATT ATCCAA ATCCAC
## [1,] 12481 6490 5239 8121 16171 17550 10857 18444 14699 7149
## [2,] 7712 3918 3281 5292 10315 10826 7129 12394 9750 4607
## [3,] 9634 4919 4192 6410 12612 13775 8594 14107 11594 5594
## [4,] 7406 3868 3157 4974 10000 10804 6678 11129 8976 4356
## [5,] 10806 5637 4563 7261 14167 15723 9690 16629 12745 6264
## [6,] 42 18 18 29 95 49 36 83 92 41
## ATCCAG ATCCAT ATCCCA ATCCCC ATCCCG ATCCCT ATCCGA ATCCGC ATCCGG ATCCGT
## [1,] 5567 12091 6910 2825 2053 5205 4986 2368 3091 3558
## [2,] 3479 7743 4221 1932 1357 3750 3322 1594 1935 2530
## [3,] 4469 9484 5301 2295 1674 4129 3833 1915 2368 2854
## [4,] 3444 7252 4306 1871 1215 3548 3154 1472 1829 2324
## [5,] 4807 10157 5859 2591 1865 4690 4420 2122 2621 3361
## [6,] 46 91 55 42 33 52 43 31 20 38
## ATCCTA ATCCTC ATCCTG ATCCTT ATCGAA ATCGAC ATCGAG ATCGAT ATCGCA ATCGCC
## [1,] 7001 7909 4290 9939 8722 4148 5124 7926 3237 2565
## [2,] 4455 5377 2886 6614 5590 2908 3341 5186 2053 1760
## [3,] 5442 6529 3450 7916 6734 3329 4207 6339 2863 2233
## [4,] 4316 5234 2808 6284 5324 2784 3568 4782 2119 1736
## [5,] 5866 7377 3902 9480 7940 3875 4684 7073 2980 2447
## [6,] 65 41 35 94 75 26 34 72 17 14
## ATCGCG ATCGCT ATCGGA ATCGGC ATCGGG ATCGGT ATCGTA ATCGTC ATCGTG ATCGTT
## [1,] 1201 3214 4875 1996 1834 3723 4495 4820 3407 7019
## [2,] 811 2127 3184 1345 1213 2613 2879 3109 2213 4399
## [3,] 1033 2561 4005 1575 1461 3058 3679 3902 2737 5210
## [4,] 810 1996 2953 1333 1165 2474 2793 2951 2061 4229
## [5,] 1171 2929 4496 1911 1713 3523 3996 4313 3058 6146
## [6,] 6 17 33 20 20 27 38 25 19 38
## ATCTAA ATCTAC ATCTAG ATCTAT ATCTCA ATCTCC ATCTCG ATCTCT ATCTGA ATCTGC
## [1,] 13851 7521 7129 13263 12793 9748 4994 17572 10907 6090
## [2,] 9451 4950 4477 8672 8165 6391 3227 11062 6904 3938
## [3,] 10474 5937 5378 10172 9826 7737 3861 13290 8736 4894
## [4,] 8440 4712 4417 7930 7940 6093 3084 10274 6587 3734
## [5,] 12422 6606 6036 11503 11427 8707 4462 15105 9886 5465
## [6,] 83 26 36 102 42 32 37 73 44 21
## ATCTGG ATCTGT ATCTTA ATCTTC ATCTTG ATCTTT ATGAAA ATGAAC ATGAAG ATGAAT
## [1,] 5552 8953 13306 17731 13114 23318 23970 10144 14610 17449
## [2,] 3369 5601 8843 11448 8273 14955 15717 6294 9318 11523
## [3,] 4291 7053 10115 14110 10052 17891 18453 7590 11724 13421
## [4,] 3386 5331 8027 11161 7926 13828 14433 6061 8851 10732
## [5,] 4988 7880 12405 15758 11424 20662 21399 8893 13117 15499
## [6,] 38 39 39 58 55 152 154 62 43 135
## ATGACA ATGACC ATGACG ATGACT ATGAGA ATGAGC ATGAGG ATGAGT ATGATA ATGATC
## [1,] 10018 4790 3975 8188 13928 5451 6055 9691 15875 11558
## [2,] 6316 3186 2523 5417 9081 3617 3854 6224 10167 7412
## [3,] 7642 3770 3072 6483 10573 4312 4741 7244 11854 9469
## [4,] 6042 2905 2358 5190 8503 3515 3716 5973 9576 7119
## [5,] 8802 4249 3549 7965 12147 4891 5384 8817 13647 10070
## [6,] 20 26 9 50 57 31 19 44 89 51
## ATGATG ATGATT ATGCAA ATGCAC ATGCAG ATGCAT ATGCCA ATGCCC ATGCCG ATGCCT
## [1,] 15857 19987 12189 4680 6429 12762 5502 2179 1711 4512
## [2,] 10193 13331 8210 2982 4064 7620 3621 1540 1093 3092
## [3,] 12522 15221 10098 3398 5084 9129 4463 1736 1368 3711
## [4,] 9542 12302 7580 2872 3919 7248 3401 1431 1018 2810
## [5,] 14430 17978 11007 3951 5881 10561 4836 1887 1539 4113
## [6,] 49 80 42 17 19 47 27 24 12 29
## ATGCGA ATGCGC ATGCGG ATGCGT ATGCTA ATGCTC ATGCTG ATGCTT ATGGAA ATGGAC
## [1,] 3292 1201 1890 3066 6900 6217 5353 11149 13323 5611
## [2,] 2061 820 1298 1853 4461 3820 3356 7421 8719 3782
## [3,] 2661 953 1582 2287 5225 4664 4257 8817 10615 4384
## [4,] 1935 676 1164 1903 4298 3777 3166 6831 8366 3608
## [5,] 2764 989 1757 2737 5785 5377 4713 10222 12249 4981
## [6,] 19 8 16 19 37 28 13 34 99 33
## ATGGAG ATGGAT ATGGCA ATGGCC ATGGCG ATGGCT ATGGGA ATGGGC ATGGGG ATGGGT
## [1,] 9824 11838 5732 3250 2912 6829 6845 3697 2900 6544
## [2,] 6412 7561 3664 2120 1830 4503 4463 2374 1899 3824
## [3,] 7828 9212 4450 2633 2378 5389 5629 2936 2440 4583
## [4,] 6005 7172 3582 2018 1883 4343 4256 2176 1955 3751
## [5,] 8804 10677 5172 2922 2603 6144 6384 3344 2760 5384
## [6,] 26 107 20 21 13 27 37 15 33 37
## ATGGTA ATGGTC ATGGTG ATGGTT ATGTAA ATGTAC ATGTAG ATGTAT ATGTCA ATGTCC
## [1,] 8229 6095 8701 13020 14839 6856 7401 15457 9832 4544
## [2,] 5250 3926 5550 8638 9734 4457 4851 10224 6459 3182
## [3,] 6319 4581 6714 9720 11213 5375 5881 11760 7631 4086
## [4,] 5093 3547 5534 8035 8830 4115 4611 9238 6228 2943
## [5,] 6946 5229 7572 11629 13044 5949 6594 13467 9125 4136
## [6,] 37 26 25 53 47 26 30 70 31 23
## ATGTCG ATGTCT ATGTGA ATGTGC ATGTGG ATGTGT ATGTTA ATGTTC ATGTTG ATGTTT
## [1,] 4031 9711 11524 4464 6964 11940 14269 10220 13539 24454
## [2,] 2512 6445 7390 2993 4593 7632 9458 6739 9023 16078
## [3,] 3076 7927 8861 3506 5462 8960 10524 8239 10568 18382
## [4,] 2479 6177 7149 2705 4386 7227 8713 6272 8287 14980
## [5,] 3502 8984 10412 4109 6453 11162 12637 9249 12193 22257
## [6,] 12 31 40 16 28 22 38 41 37 57
## ATTAAA ATTAAC ATTAAG ATTAAT ATTACA ATTACC ATTACG ATTACT ATTAGA ATTAGC
## [1,] 27618 11330 11498 23672 13543 6853 4166 11464 13097 6484
## [2,] 18296 7464 7637 15853 8764 4449 2661 7473 8564 4424
## [3,] 20755 8366 8870 17666 10513 5391 3361 8851 10073 4960
## [4,] 16458 6810 7055 13885 8273 4184 2525 6776 7956 4010
## [5,] 24654 10202 10160 20876 11907 6222 3606 10367 11605 5833
## [6,] 148 48 53 155 52 27 30 73 85 26
## ATTAGG ATTAGT ATTATA ATTATC ATTATG ATTATT ATTCAA ATTCAC ATTCAG ATTCAT
## [1,] 7242 13491 22236 12618 13327 27870 20253 9300 9172 17358
## [2,] 4903 8347 14679 8180 8601 18441 13121 6145 5820 11727
## [3,] 5564 9736 16218 9653 9937 20732 15516 7324 7088 13431
## [4,] 4277 7687 13053 7670 7839 16755 12214 5782 5555 10584
## [5,] 6516 11137 19785 11310 11811 24435 18127 8321 8042 15224
## [6,] 41 74 108 59 58 147 148 68 50 155
## ATTCCA ATTCCC ATTCCG ATTCCT ATTCGA ATTCGC ATTCGG ATTCGT ATTCTA ATTCTC
## [1,] 10903 5176 3512 8804 7358 2807 3540 6083 11366 13199
## [2,] 6995 3432 2419 6095 4888 1785 2445 4211 7778 8895
## [3,] 8761 4100 2915 7023 5923 2283 2709 4893 8771 10557
## [4,] 6601 3273 2260 5615 4761 1740 2299 3760 7096 8286
## [5,] 9449 4655 3342 7949 6789 2476 3470 5586 10404 12018
## [6,] 108 53 36 94 83 26 33 47 106 67
## ATTCTG ATTCTT ATTGAA ATTGAC ATTGAG ATTGAT ATTGCA ATTGCC ATTGCG ATTGCT
## [1,] 9200 21022 19022 8353 10055 19042 9890 4204 2776 9802
## [2,] 5881 13603 12196 5416 6585 12431 6467 2858 1760 6115
## [3,] 7098 16031 14633 6324 7698 14433 7841 3419 2168 7368
## [4,] 5582 12636 11354 5104 6534 11735 5982 2657 1852 5825
## [5,] 8186 18562 17137 7194 9145 17095 8642 3804 2479 8576
## [6,] 71 180 139 43 60 111 39 27 25 51
## ATTGGA ATTGGC ATTGGG ATTGGT ATTGTA ATTGTC ATTGTG ATTGTT ATTTAA ATTTAC
## [1,] 12035 5346 5868 11874 13016 8670 10955 21572 24557 13287
## [2,] 7290 3394 3864 7731 8849 5534 6723 14579 16638 8531
## [3,] 8912 4169 4738 9192 9691 6721 7680 16884 18091 10049
## [4,] 6803 3189 3667 7142 8081 5236 6367 13200 14714 7920
## [5,] 9939 4619 5285 10823 12044 7781 8984 19851 21998 11694
## [6,] 81 31 49 65 74 34 31 94 105 58
## ATTTAG ATTTAT ATTTCA ATTTCC ATTTCG ATTTCT ATTTGA ATTTGC ATTTGG ATTTGT
## [1,] 13612 28264 20928 10935 7212 22176 23656 11018 15504 22206
## [2,] 8772 18779 13538 7075 4768 14545 14749 7165 10092 14628
## [3,] 10096 21189 15519 8510 5647 17076 17592 8393 12153 16970
## [4,] 7996 16916 12585 6784 4393 13210 14169 6525 9426 13507
## [5,] 12041 25334 18629 9823 6548 19989 20910 9631 14245 20193
## [6,] 58 157 137 81 81 164 125 33 51 82
## ATTTTA ATTTTC ATTTTG ATTTTT CAAAAA CAAAAC CAAAAG CAAAAT CAAACA CAAACC
## [1,] 32212 25558 29440 47544 36548 23375 18891 29129 18424 11429
## [2,] 21936 16312 18824 32147 24019 14530 12309 18929 12096 7672
## [3,] 24081 19188 21562 34975 27827 17456 14546 22200 14229 8937
## [4,] 19486 15211 17372 28034 22121 14265 11861 17269 11438 7529
## [5,] 29575 22486 25812 42607 32732 20143 16737 25432 16592 10232
## [6,] 151 133 127 384 198 44 78 106 42 32
## CAAACG CAAACT CAAAGA CAAAGC CAAAGG CAAAGT CAAATA CAAATC CAAATG CAAATT
## [1,] 5453 14140 19453 10883 8567 12797 18626 16436 13975 22673
## [2,] 3567 9251 12505 6409 5584 8355 12487 10407 8717 14771
## [3,] 4352 11061 15579 7714 6649 9913 14695 12559 10655 17268
## [4,] 3475 8802 12236 6831 5378 7979 11805 9869 8356 13912
## [5,] 4920 12662 17814 9676 7617 11357 16962 14365 12203 20453
## [6,] 24 40 83 24 41 40 121 72 51 114
## CAACAA CAACAC CAACAG CAACAT CAACCA CAACCC CAACCG CAACCT CAACGA CAACGC
## [1,] 22106 8986 8004 13619 9652 3782 3223 6464 5941 2580
## [2,] 14390 5723 5013 8721 6478 2709 2131 4345 3815 1583
## [3,] 17134 6977 6293 10369 7683 3140 2518 5186 4851 2029
## [4,] 13405 5406 5080 8352 6053 2385 2203 4053 3801 1642
## [5,] 19369 7595 7135 12039 8577 3390 3097 6055 5385 2265
## [6,] 70 16 27 26 31 29 13 19 29 6
## CAACGG CAACGT CAACTA CAACTC CAACTG CAACTT CAAGAA CAAGAC CAAGAG CAAGAT
## [1,] 3348 4211 8548 7753 5793 12694 21126 7599 10772 12894
## [2,] 2124 2746 5687 5387 3827 8371 13443 5061 6963 8343
## [3,] 2761 3310 6704 6051 4701 10050 16376 5912 8321 10315
## [4,] 2279 2657 5411 4902 3601 7883 13029 4764 6563 8138
## [5,] 3174 3677 7795 6849 4991 11223 19228 6740 9421 11399
## [6,] 15 8 41 42 17 29 89 18 30 58
## CAAGCA CAAGCC CAAGCG CAAGCT CAAGGA CAAGGC CAAGGG CAAGGT CAAGTA CAAGTC
## [1,] 8319 4521 2578 9285 8934 4162 3736 6451 9275 7132
## [2,] 5384 3098 1636 5759 5907 2690 2504 4080 6040 4720
## [3,] 6785 3525 1941 7099 7067 3327 3090 5021 7408 5767
## [4,] 5239 2882 1664 5934 5581 2461 2252 4054 5890 4501
## [5,] 7539 3972 2156 8115 7859 3500 3184 5751 8386 6400
## [6,] 23 22 13 22 41 20 28 24 47 23
## CAAGTG CAAGTT CAATAA CAATAC CAATAG CAATAT CAATCA CAATCC CAATCG CAATCT
## [1,] 7524 13074 15640 7211 7099 14768 12997 6856 3969 12126
## [2,] 4847 8644 10347 4772 4837 9653 8456 4572 2894 7974
## [3,] 6014 10266 12045 5557 5602 10920 9956 5314 3400 9436
## [4,] 4662 7984 9893 4330 4420 8721 8215 4419 2553 7414
## [5,] 6505 11649 13820 6349 6382 13195 11668 5941 3788 10792
## [6,] 30 45 110 45 55 78 60 44 29 39
## CAATGA CAATGC CAATGG CAATGT CAATTA CAATTC CAATTG CAATTT CACAAA CACAAC
## [1,] 11932 6598 8523 10715 12675 9989 9378 20084 17859 8440
## [2,] 7929 4135 5507 7039 8471 6666 6254 12803 11401 5617
## [3,] 9150 5124 6884 8592 9501 8005 7328 14899 13364 6717
## [4,] 7322 3976 5369 6495 7540 6355 5678 11866 10943 5270
## [5,] 10690 5815 7806 9531 11392 9203 8393 17436 15469 7332
## [6,] 55 23 40 30 80 110 72 113 53 17
## CACAAG CACAAT CACACA CACACC CACACG CACACT CACAGA CACAGC CACAGG CACAGT
## [1,] 9202 10323 9783 4063 2578 5569 6505 3514 2914 4644
## [2,] 5973 6663 6260 2681 1689 3620 4130 2199 1753 2937
## [3,] 7275 7816 7196 3144 2122 4296 5254 2859 2291 3545
## [4,] 5607 6124 6019 2587 1660 3387 4134 2150 1703 2849
## [5,] 8122 9130 8322 3578 2353 4651 5721 2992 2432 4076
## [6,] 23 33 13 13 9 12 14 18 12 5
## CACATA CACATC CACATG CACATT CACCAA CACCAC CACCAG CACCAT CACCCA CACCCC
## [1,] 9547 7015 8053 10854 11089 6847 4635 8560 3521 1309
## [2,] 6222 4728 4940 6904 7445 4670 3029 5742 2430 949
## [3,] 7284 5492 6000 8230 8795 5513 3928 6688 3107 1049
## [4,] 5786 4342 4870 6517 6987 4620 2930 5534 2341 852
## [5,] 8617 6232 6844 9314 9791 6230 4296 7861 3227 1193
## [6,] 30 26 21 32 39 15 17 22 20 24
## CACCCG CACCCT CACCGA CACCGC CACCGG CACCGT CACCTA CACCTC CACCTG CACCTT
## [1,] 1348 2740 3245 2363 2848 3464 4140 4354 3558 6063
## [2,] 867 1696 2076 1525 1853 2276 2812 3204 2375 4210
## [3,] 1027 2058 2474 1909 2380 2698 3130 3459 2916 4988
## [4,] 849 1716 2013 1556 1803 2055 2497 2792 2435 3830
## [5,] 1240 2225 2860 2106 2526 3104 3606 3930 3280 5419
## [6,] 10 14 14 18 19 10 21 18 13 25
## CACGAA CACGAC CACGAG CACGAT CACGCA CACGCC CACGCG CACGCT CACGGA CACGGC
## [1,] 4530 2574 3314 3419 2156 1352 1037 1841 2358 1699
## [2,] 2912 1649 2127 2246 1409 812 670 1102 1491 1056
## [3,] 3747 2035 2885 2714 1653 1072 895 1539 1963 1470
## [4,] 2787 1535 2118 2112 1277 768 701 1126 1410 1066
## [5,] 3986 2228 2954 2968 1820 1187 951 1685 2159 1479
## [6,] 19 9 17 15 8 10 8 8 14 6
## CACGGG CACGGT CACGTA CACGTC CACGTG CACGTT CACTAA CACTAC CACTAG CACTAT
## [1,] 1284 2273 2998 2544 3642 3726 9309 4716 4397 6356
## [2,] 904 1563 1836 1699 2322 2473 5517 2931 2842 4159
## [3,] 1095 2057 2162 1973 2894 3027 6371 3286 3423 4712
## [4,] 856 1532 1691 1594 2354 2409 5480 2799 2594 3766
## [5,] 1277 2242 2494 2099 3296 3407 7349 3644 3893 5670
## [6,] 7 11 11 12 12 14 29 13 13 39
## CACTCA CACTCC CACTCG CACTCT CACTGA CACTGC CACTGG CACTGT CACTTA CACTTC
## [1,] 5833 4241 3099 7047 5448 3368 3185 4906 6606 7071
## [2,] 3884 2319 2189 4781 3463 2166 2031 3072 4285 4651
## [3,] 4594 2923 2638 5438 4351 2617 2598 3767 4927 5546
## [4,] 3684 2339 2151 4410 3372 2072 1984 2914 3927 4384
## [5,] 5298 3166 2929 6258 4841 2952 2772 4235 5753 6406
## [6,] 21 21 16 15 20 13 11 16 25 24
## CACTTG CACTTT CAGAAA CAGAAC CAGAAG CAGAAT CAGACA CAGACC CAGACG CAGACT
## [1,] 7501 11094 15619 6867 10019 8835 5981 3095 2228 4469
## [2,] 4851 7296 9397 4192 6178 5643 3883 1996 1486 2880
## [3,] 5919 8613 12051 5484 7932 7179 4834 2444 1894 3518
## [4,] 4549 6723 9285 4295 6329 5573 3744 1970 1414 2717
## [5,] 6653 9972 13545 6116 8935 7931 5225 2728 2045 3917
## [6,] 31 38 76 19 38 62 13 14 12 9
## CAGAGA CAGAGC CAGAGG CAGAGT CAGATA CAGATC CAGATG CAGATT CAGCAA CAGCAC
## [1,] 12571 4856 5536 6392 7434 6321 6895 11350 8188 3024
## [2,] 7895 2955 3386 3788 4720 3992 4226 6981 4995 1887
## [3,] 9974 3900 4477 4849 5688 5018 5409 8640 6415 2490
## [4,] 7750 3041 3378 3761 4418 3901 4244 6701 5075 1891
## [5,] 11099 4203 5072 5557 6365 5568 5902 9881 6876 2624
## [6,] 25 16 27 15 42 25 19 40 32 9
## CAGCAG CAGCAT CAGCCA CAGCCC CAGCCG CAGCCT CAGCGA CAGCGC CAGCGG CAGCGT
## [1,] 5385 5383 4696 1638 1795 3373 2780 891 1638 1875
## [2,] 3322 3444 3233 1163 1277 2301 1755 545 1011 1195
## [3,] 4339 4330 3863 1348 1470 2751 2243 666 1328 1458
## [4,] 3284 3235 2875 1044 1133 2178 1704 586 1028 1152
## [5,] 4592 4876 3995 1542 1565 3051 2425 811 1441 1639
## [6,] 23 18 25 14 11 15 9 7 13 5
## CAGCTA CAGCTC CAGCTG CAGCTT CAGGAA CAGGAC CAGGAG CAGGAT CAGGCA CAGGCC
## [1,] 5082 5492 4962 8759 6437 2644 4498 4374 2764 1594
## [2,] 3209 3495 3104 5488 3991 1796 2883 2885 1809 1066
## [3,] 4224 4297 4061 6827 5108 2175 3540 3462 2185 1336
## [4,] 3076 3302 3182 5481 4020 1719 2877 2727 1687 1006
## [5,] 4538 4491 4405 7810 5810 2462 3924 3880 2379 1454
## [6,] 25 20 13 22 33 17 25 34 14 6
## CAGGCG CAGGCT CAGGGA CAGGGC CAGGGG CAGGGT CAGGTA CAGGTC CAGGTG CAGGTT
## [1,] 1133 2903 3492 1345 1600 2400 4629 2872 3666 6148
## [2,] 755 1851 2203 862 998 1471 2874 1908 2236 3775
## [3,] 975 2238 2870 1103 1313 1865 3630 2286 2944 4651
## [4,] 710 1802 2198 830 1055 1475 2795 1855 2241 3654
## [5,] 1013 2593 3058 1173 1404 2024 4308 2555 3353 5372
## [6,] 12 13 19 11 18 14 23 17 12 18
## CAGTAA CAGTAC CAGTAG CAGTAT CAGTCA CAGTCC CAGTCG CAGTCT CAGTGA CAGTGC
## [1,] 6741 3109 4004 5160 4663 2596 1822 4787 6185 2217
## [2,] 4116 1949 2565 3461 3124 1734 1333 3115 3905 1412
## [3,] 5169 2397 3098 4063 3751 2053 1486 3687 4755 1773
## [4,] 3983 1936 2475 3141 3034 1641 1150 3027 3743 1414
## [5,] 5712 2824 3433 4546 4156 2379 1795 4311 5436 1966
## [6,] 27 17 30 28 29 9 10 9 19 12
## CAGTGG CAGTGT CAGTTA CAGTTC CAGTTG CAGTTT CATAAA CATAAC CATAAG CATAAT
## [1,] 3894 4642 5640 5345 5947 12167 17909 8358 8112 12949
## [2,] 2544 2946 3667 3447 3676 7375 11305 5624 5480 8554
## [3,] 3098 3614 4673 4187 4592 9131 13079 6628 6427 10009
## [4,] 2464 2933 3427 3176 3616 7064 10288 5180 5114 7986
## [5,] 3559 4074 5001 4674 5271 10458 15071 7471 7198 11504
## [6,] 17 6 20 39 19 35 103 32 57 77
## CATACA CATACC CATACG CATACT CATAGA CATAGC CATAGG CATAGT CATATA CATATC
## [1,] 9698 4921 2676 6650 8768 4518 3445 6533 16996 9365
## [2,] 6052 3341 1726 4381 5613 2829 2261 4310 11192 6177
## [3,] 7375 3989 2077 5070 6658 3440 2725 4951 12993 7535
## [4,] 6166 3128 1916 4129 5385 2713 2070 4121 10290 5840
## [5,] 8294 4501 2818 5724 7599 3873 2962 5894 15238 8503
## [6,] 43 24 25 29 54 23 44 42 86 56
## CATATG CATATT CATCAA CATCAC CATCAG CATCAT CATCCA CATCCC CATCCG CATCCT
## [1,] 10086 16194 17172 8685 7749 15618 7825 3772 2501 6343
## [2,] 6714 10136 11032 5708 4944 10184 5411 2567 1792 4360
## [3,] 7634 11539 13352 7015 6124 12375 6512 3089 2187 5464
## [4,] 6167 9536 10790 5414 4807 9881 4989 2410 1657 4206
## [5,] 8961 14075 15832 7832 6809 14277 7145 3356 2224 5924
## [6,] 32 91 50 14 20 40 39 31 20 38
## CATCGA CATCGC CATCGG CATCGT CATCTA CATCTC CATCTG CATCTT CATGAA CATGAC
## [1,] 5685 2781 2980 4928 8633 11009 6838 15617 12980 5956
## [2,] 3623 1817 1941 3072 5441 6770 4181 9986 8236 3774
## [3,] 4509 2148 2420 3812 6430 8096 5469 12130 9984 4433
## [4,] 3511 1741 1823 2991 5142 6324 4144 9275 7758 3550
## [5,] 4988 2501 2780 4344 7418 9120 6086 13482 11210 5155
## [6,] 42 12 11 18 31 40 25 49 67 20
## CATGAG CATGAT CATGCA CATGCC CATGCG CATGCT CATGGA CATGGC CATGGG CATGGT
## [1,] 6798 10856 7721 3211 1892 5727 8450 4310 3734 6517
## [2,] 4471 7210 4824 2142 1230 3810 5503 2772 2373 4347
## [3,] 5268 8615 6094 2699 1427 4569 6623 3458 2932 5178
## [4,] 4179 6622 4665 2012 1121 3472 5276 2758 2352 4128
## [5,] 5982 9392 6521 2815 1612 5034 7667 3811 3355 5738
## [6,] 30 39 24 21 17 28 47 19 21 21
## CATGTA CATGTC CATGTG CATGTT CATTAA CATTAC CATTAG CATTAT CATTCA CATTCC
## [1,] 9341 6775 7571 12627 13089 7526 7686 13121 10574 5926
## [2,] 6144 4439 4988 8565 8712 4886 5081 8714 7161 4151
## [3,] 7329 5488 6011 9941 9753 5967 6310 9945 8676 4979
## [4,] 5796 4513 5009 7822 7846 4568 4655 7922 6514 3773
## [5,] 8203 6023 7388 11403 11642 6834 6780 11485 9641 5464
## [6,] 38 25 18 34 67 31 35 54 50 45
## CATTCG CATTCT CATTGA CATTGC CATTGG CATTGT CATTTA CATTTC CATTTG CATTTT
## [1,] 3606 10932 11998 6759 8070 11843 13384 13148 13773 26435
## [2,] 2424 7345 7757 4464 4594 7944 9089 8734 8973 16946
## [3,] 2826 8567 9374 5412 5816 9409 10381 10096 10515 19350
## [4,] 2197 6728 7380 4092 4479 7170 8104 7817 8339 15055
## [5,] 3237 9816 10522 6011 6272 10923 12078 11852 12227 23151
## [6,] 27 62 45 31 32 33 73 102 46 133
## CCAAAA CCAAAC CCAAAG CCAAAT CCAACA CCAACC CCAACG CCAACT CCAAGA CCAAGC
## [1,] 24342 11545 10446 15069 9861 5329 3252 7114 10103 5247
## [2,] 15367 7499 6784 9989 6431 3663 2278 4851 6518 3379
## [3,] 18097 8917 8191 11986 7822 4270 2743 5573 7921 4218
## [4,] 14906 7181 6797 9411 6047 3365 2204 4403 6305 3423
## [5,] 20824 10367 9304 13706 8542 4732 2940 6114 8820 4532
## [6,] 83 38 50 72 24 32 16 40 54 31
## CCAAGG CCAAGT CCAATA CCAATC CCAATG CCAATT CCACAA CCACAC CCACAG CCACAT
## [1,] 4658 7637 8874 7591 7473 10444 9740 4381 3757 6926
## [2,] 3124 5192 5997 5059 4860 6898 6335 2867 2407 4703
## [3,] 3821 6459 6936 5995 5644 8177 7721 3382 3020 5611
## [4,] 3017 4808 5432 4916 4312 6377 5962 2765 2276 4376
## [5,] 4015 6756 7826 6784 6353 9232 8583 3917 3274 6171
## [6,] 41 41 76 55 38 98 32 12 13 28
## CCACCA CCACCC CCACCG CCACCT CCACGA CCACGC CCACGG CCACGT CCACTA CCACTC
## [1,] 8464 2059 3594 4572 3083 1456 1826 3196 4961 4348
## [2,] 5772 1408 2296 3400 2126 971 1249 2023 3345 3016
## [3,] 7128 1726 2806 3694 2637 1144 1573 2457 3878 3647
## [4,] 5706 1402 2257 2922 2050 979 1212 1892 2990 2816
## [5,] 7778 1945 3265 4159 2681 1311 1746 2710 4294 4049
## [6,] 20 24 18 26 17 10 12 12 30 25
## CCACTG CCACTT CCAGAA CCAGAC CCAGAG CCAGAT CCAGCA CCAGCC CCAGCG CCAGCT
## [1,] 3922 7097 7547 2998 4767 5495 3991 2080 1414 4499
## [2,] 2594 4704 4661 2052 3023 3275 2549 1482 940 2984
## [3,] 3118 5480 6045 2453 3807 4245 3251 1834 1144 3842
## [4,] 2388 4358 4644 1888 2983 3222 2481 1256 940 2891
## [5,] 3420 6182 6798 2595 4261 4778 3532 1845 1242 3956
## [6,] 24 30 48 13 27 31 15 15 11 21
## CCAGGA CCAGGC CCAGGG CCAGGT CCAGTA CCAGTC CCAGTG CCAGTT CCATAA CCATAC
## [1,] 3121 1458 1500 2784 3418 2734 3135 5254 9348 4167
## [2,] 2047 948 995 1831 2121 1773 2054 3312 6126 2955
## [3,] 2651 1167 1295 2301 2608 2137 2574 4124 7015 3390
## [4,] 2158 956 922 1726 2046 1714 2006 3045 5477 2671
## [5,] 2931 1311 1317 2645 2837 2475 2785 4654 7919 3741
## [6,] 35 12 14 14 25 12 12 29 72 39
## CCATAG CCATAT CCATCA CCATCC CCATCG CCATCT CCATGA CCATGC CCATGG CCATGT
## [1,] 5175 9455 9242 4434 3447 9654 7474 3639 5329 6762
## [2,] 2987 6200 6277 3101 2253 5934 4788 2343 3466 4640
## [3,] 3666 7188 7438 3970 2739 7141 5873 2745 4179 5413
## [4,] 3070 5804 6168 2979 2084 5623 4580 2197 3343 4281
## [5,] 4132 8065 8954 4143 2949 7985 6537 3036 4928 6160
## [6,] 45 59 27 39 26 32 46 25 29 22
## CCATTA CCATTC CCATTG CCATTT CCCAAA CCCAAC CCCAAG CCCAAT CCCACA CCCACC
## [1,] 8591 6678 8521 14200 11300 4397 4531 5840 4083 2821
## [2,] 5626 4587 5794 9212 7203 3053 3121 3845 2661 1956
## [3,] 6597 5462 7025 10947 8423 3586 3955 4659 3169 2631
## [4,] 5222 4190 5325 8200 7061 2812 3008 3794 2570 1834
## [5,] 7590 6151 7655 12468 9726 3943 4154 5354 3574 2637
## [6,] 44 53 32 98 54 25 44 42 13 19
## CCCACG CCCACT CCCAGA CCCAGC CCCAGG CCCAGT CCCATA CCCATC CCCATG CCCATT
## [1,] 1521 3296 3108 1643 1159 2119 4503 4571 3836 6777
## [2,] 1036 2273 1917 1187 781 1361 3152 3148 2506 4407
## [3,] 1270 2606 2480 1420 999 1738 3636 4004 2992 5205
## [4,] 975 2135 1873 1067 783 1332 2807 2879 2376 3942
## [5,] 1307 2864 2624 1454 1117 1848 3966 4344 3309 5798
## [6,] 14 14 37 13 24 17 47 29 31 56
## CCCCAA CCCCAC CCCCAG CCCCAT CCCCCA CCCCCC CCCCCG CCCCCT CCCCGA CCCCGC
## [1,] 4755 2058 1416 2950 1904 916 508 1140 1105 547
## [2,] 3039 1495 945 2130 1286 681 346 930 758 417
## [3,] 3780 1632 1148 2371 1486 828 417 973 933 481
## [4,] 3031 1361 863 1835 1210 674 292 892 736 372
## [5,] 4038 1929 1242 2767 1688 817 395 1137 1038 505
## [6,] 38 19 25 43 27 43 16 33 29 11
## CCCCGG CCCCGT CCCCTA CCCCTC CCCCTG CCCCTT CCCGAA CCCGAC CCCGAG CCCGAT
## [1,] 716 777 1917 1652 1601 2548 2603 1390 1919 1756
## [2,] 540 582 1279 1278 1077 1890 1677 929 1352 1231
## [3,] 570 757 1326 1355 1258 2180 2114 1154 1670 1448
## [4,] 471 481 1139 1120 1054 1728 1758 929 1298 1195
## [5,] 635 689 1559 1534 1450 2388 2403 1253 1860 1656
## [6,] 15 21 30 28 18 54 47 10 27 20
## CCCGCA CCCGCC CCCGCG CCCGCT CCCGGA CCCGGC CCCGGG CCCGGT CCCGTA CCCGTC
## [1,] 1205 1280 662 973 1570 813 718 1611 1358 1463
## [2,] 832 876 470 759 1114 573 505 1050 849 1000
## [3,] 1059 1051 549 893 1349 621 565 1233 1223 1139
## [4,] 758 722 421 691 988 518 459 988 788 810
## [5,] 1132 1157 589 986 1405 765 784 1419 1287 1277
## [6,] 22 8 9 22 19 14 11 17 26 19
## CCCGTG CCCGTT CCCTAA CCCTAC CCCTAG CCCTAT CCCTCA CCCTCC CCCTCG CCCTCT
## [1,] 1275 1915 8556 2051 2390 3050 3028 2600 1518 4018
## [2,] 953 1339 3691 1332 1702 2097 2337 1776 1034 2753
## [3,] 1111 1508 4449 1488 1893 2515 2488 2123 1264 3385
## [4,] 824 1183 4533 1133 1600 2005 2061 1753 1078 2602
## [5,] 1258 1671 5082 1712 2178 2710 2690 2359 1314 3658
## [6,] 10 27 24 17 25 32 10 26 21 36
## CCCTGA CCCTGC CCCTGG CCCTGT CCCTTA CCCTTC CCCTTG CCCTTT CCGAAA CCGAAC
## [1,] 3261 1782 1475 2226 3690 3854 3616 6527 5228 2453
## [2,] 2036 1219 989 1418 2320 2833 2524 4525 3250 1764
## [3,] 2513 1347 1164 1912 2778 3190 3018 5284 4124 2185
## [4,] 1980 1165 992 1493 2217 2682 2433 4242 3064 1787
## [5,] 2753 1669 1341 2020 3091 3592 3300 5732 4491 2295
## [6,] 19 17 19 19 32 46 27 78 56 19
## CCGAAG CCGAAT CCGACA CCGACC CCGACG CCGACT CCGAGA CCGAGC CCGAGG CCGAGT
## [1,] 3106 3636 2583 1854 1811 1978 3662 1861 2019 2751
## [2,] 2103 2432 1751 1263 1243 1407 2481 1209 1292 1891
## [3,] 2477 2797 2039 1483 1503 1580 3041 1607 1713 2171
## [4,] 2167 2361 1649 1159 1184 1334 2438 1239 1404 1694
## [5,] 2664 3346 2340 1624 1657 1785 3367 1807 1818 2426
## [6,] 22 44 13 13 5 17 23 25 12 24
## CCGATA CCGATC CCGATG CCGATT CCGCAA CCGCAC CCGCAG CCGCAT CCGCCA CCGCCC
## [1,] 2684 2967 2998 4001 2791 1101 1651 1888 2884 665
## [2,] 1798 2052 1958 2576 1966 779 1124 1309 1861 548
## [3,] 2081 2342 2418 3117 2351 937 1417 1529 2258 598
## [4,] 1685 2050 1869 2482 2042 740 1139 1231 1720 412
## [5,] 2402 2777 2714 3667 3108 1036 1569 1811 2577 607
## [6,] 15 28 15 29 15 13 14 19 14 13
## CCGCCG CCGCCT CCGCGA CCGCGC CCGCGG CCGCGT CCGCTA CCGCTC CCGCTG CCGCTT
## [1,] 2324 1842 1198 474 1066 939 1702 1347 1473 2656
## [2,] 1579 1275 858 317 738 620 1125 994 1063 1793
## [3,] 1935 1515 1066 381 838 812 1249 1195 1241 2088
## [4,] 1481 1160 802 313 668 546 1008 972 978 1655
## [5,] 2110 1721 1104 385 959 846 1464 1253 1443 2370
## [6,] 14 15 15 3 10 7 26 16 18 32
## CCGGAA CCGGAC CCGGAG CCGGAT CCGGCA CCGGCC CCGGCG CCGGCT CCGGGA CCGGGC
## [1,] 3809 1387 3591 2917 1522 1106 1992 1754 1872 549
## [2,] 2471 995 2218 1938 968 829 1290 1118 1206 455
## [3,] 3044 1071 2766 2530 1216 820 1660 1382 1614 477
## [4,] 2398 893 2228 1877 882 642 1299 1084 1191 364
## [5,] 3397 1334 3239 2866 1410 1017 1812 1573 1859 510
## [6,] 29 11 23 24 7 8 11 16 17 10
## CCGGGG CCGGGT CCGGTA CCGGTC CCGGTG CCGGTT CCGTAA CCGTAC CCGTAG CCGTAT
## [1,] 674 1376 2245 1855 2972 4820 3082 1583 1715 2463
## [2,] 555 1009 1478 1285 1895 2971 2008 1186 1137 1636
## [3,] 580 1224 1720 1439 2447 3531 2483 1260 1348 1828
## [4,] 465 923 1319 1136 1840 2988 1940 1017 1023 1444
## [5,] 635 1385 1987 1627 2564 4282 2637 1374 1561 2268
## [6,] 16 12 18 11 14 18 21 16 21 22
## CCGTCA CCGTCC CCGTCG CCGTCT CCGTGA CCGTGC CCGTGG CCGTGT CCGTTA CCGTTC
## [1,] 2683 1663 2284 2908 2886 998 1798 2069 2867 2289
## [2,] 1829 1141 1397 2000 1845 734 1249 1360 1819 1632
## [3,] 2085 1358 1831 2223 2275 824 1690 1695 2345 1843
## [4,] 1659 995 1390 1713 1768 661 1151 1237 1759 1435
## [5,] 2411 1397 1960 2657 2592 934 1771 1850 2620 2119
## [6,] 17 13 13 13 19 13 7 14 15 33
## CCGTTG CCGTTT CCTAAA CCTAAC CCTAAG CCTAAT CCTACA CCTACC CCTACG CCTACT
## [1,] 3352 4759 14126 4732 4091 7517 4427 2070 1458 3692
## [2,] 2204 3134 6440 3070 2739 4678 2862 1435 954 2324
## [3,] 2670 3751 7429 3494 3222 5546 3234 1737 1159 2655
## [4,] 2103 2931 7187 2967 2613 4641 2526 1312 866 2177
## [5,] 3014 4482 8862 3908 4094 6446 3721 1943 1342 2982
## [6,] 17 35 53 16 24 53 24 21 17 30
## CCTAGA CCTAGC CCTAGG CCTAGT CCTATA CCTATC CCTATG CCTATT CCTCAA CCTCAC
## [1,] 4199 2338 1754 3043 5198 3496 3323 5191 7670 3593
## [2,] 2855 1726 1189 2137 3457 2391 2283 3594 5298 2597
## [3,] 3229 1946 1362 2595 3958 2930 2650 4087 6155 3140
## [4,] 2647 1495 1146 2069 3238 2139 2079 3163 4911 2315
## [5,] 3799 2097 1595 2921 4649 3003 3053 4787 6865 3344
## [6,] 29 20 18 19 44 35 29 83 18 21
## CCTCAG CCTCAT CCTCCA CCTCCC CCTCCG CCTCCT CCTCGA CCTCGC CCTCGG CCTCGT
## [1,] 3909 5933 6774 2636 2786 6464 3197 1704 2028 3082
## [2,] 2640 4018 4615 1876 1901 4530 2186 1140 1277 2081
## [3,] 3233 4890 5466 2151 2195 5311 2641 1463 1658 2542
## [4,] 2582 3721 4258 1787 1789 4243 2085 1187 1276 2024
## [5,] 3531 5503 6095 2409 2565 6033 2841 1478 1766 2814
## [6,] 18 21 24 20 19 39 30 11 19 20
## CCTCTA CCTCTC CCTCTG CCTCTT CCTGAA CCTGAC CCTGAG CCTGAT CCTGCA CCTGCC
## [1,] 5060 6812 5541 10305 7385 2397 3914 5021 4634 1672
## [2,] 3618 4711 3567 6537 4710 1614 2638 3244 2967 1200
## [3,] 4074 5618 4339 7738 5787 2044 3176 3979 3721 1337
## [4,] 3166 4354 3423 6151 4698 1594 2482 3198 2925 1054
## [5,] 4545 6354 4918 8795 6453 2116 3613 4546 4100 1446
## [6,] 26 34 27 61 35 16 16 20 14 17
## CCTGCG CCTGCT CCTGGA CCTGGC CCTGGG CCTGGT CCTGTA CCTGTC CCTGTG CCTGTT
## [1,] 1272 3024 3299 1329 1210 2991 3232 2381 2974 4747
## [2,] 793 2226 2150 951 842 1858 2154 1610 1810 3278
## [3,] 996 2580 2707 1159 1008 2302 2655 1979 2328 3992
## [4,] 790 2041 2212 862 775 1946 2025 1554 1788 3080
## [5,] 1129 2952 3040 1207 1127 2608 2872 2183 2623 4479
## [6,] 13 24 23 13 22 16 22 12 15 39
## CCTTAA CCTTAC CCTTAG CCTTAT CCTTCA CCTTCC CCTTCG CCTTCT CCTTGA CCTTGC
## [1,] 7918 3659 3845 6292 8042 4894 2682 10188 6995 3728
## [2,] 4684 2384 2688 4203 5224 3431 1797 6868 4565 2463
## [3,] 5722 2864 3175 4935 6277 4123 2171 7930 5751 2961
## [4,] 4866 2259 2453 3992 5020 3045 1776 6565 4335 2415
## [5,] 6292 3091 3569 5778 6941 4306 2416 9383 6491 3334
## [6,] 27 27 20 41 32 43 22 60 34 20
## CCTTGG CCTTGT CCTTTA CCTTTC CCTTTG CCTTTT CGAAAA CGAAAC CGAAAG CGAAAT
## [1,] 4466 7321 7523 7422 8398 14747 9270 5696 5009 7225
## [2,] 3077 5039 5203 5223 5625 9821 6131 3690 3304 4598
## [3,] 3692 5895 5823 6074 6771 11627 8036 4430 3904 5461
## [4,] 3010 4770 4800 4738 5286 8998 5634 3535 3076 4390
## [5,] 4072 7103 6694 6749 7721 13098 8581 5098 4508 6495
## [6,] 37 36 47 61 43 144 85 38 44 62
## CGAACA CGAACC CGAACG CGAACT CGAAGA CGAAGC CGAAGG CGAAGT CGAATA CGAATC
## [1,] 4200 3362 1427 3172 7683 3665 2620 3672 4881 5226
## [2,] 2745 2229 1039 2213 4955 2228 1841 2405 3177 3390
## [3,] 3518 2735 1254 2533 6184 2784 2133 2796 3985 4170
## [4,] 2619 2283 916 2169 4740 2148 1761 2400 3018 3267
## [5,] 3731 3028 1339 2953 7002 3327 2403 3051 4711 4841
## [6,] 24 36 15 32 36 17 20 33 57 53
## CGAATG CGAATT CGACAA CGACAC CGACAG CGACAT CGACCA CGACCC CGACCG CGACCT
## [1,] 3734 6274 5189 2616 1864 4010 3734 1671 1198 2346
## [2,] 2325 4246 3392 1800 1265 2696 2542 1247 862 1566
## [3,] 2763 4854 4014 2093 1519 3127 3082 1480 1040 1940
## [4,] 2268 3916 3221 1725 1245 2500 2517 1167 833 1554
## [5,] 3156 5778 4673 2319 1643 3619 3368 1573 1201 2124
## [6,] 24 61 21 9 9 16 13 31 8 14
## CGACGA CGACGC CGACGG CGACGT CGACTA CGACTC CGACTG CGACTT CGAGAA CGAGAC
## [1,] 4014 1386 2134 2073 2689 2448 1726 3819 6722 2846
## [2,] 2599 867 1487 1467 2023 1629 1285 2510 4401 1819
## [3,] 3189 1053 1853 1780 2189 1875 1530 2907 5552 2345
## [4,] 2464 800 1361 1363 1743 1737 1247 2395 4332 1914
## [5,] 3626 1212 1974 1895 2553 2311 1845 3325 6396 2561
## [6,] 16 6 10 6 10 18 8 22 40 9
## CGAGAG CGAGAT CGAGCA CGAGCC CGAGCG CGAGCT CGAGGA CGAGGC CGAGGG CGAGGT
## [1,] 4419 4920 3014 1840 973 3500 4259 1724 1558 2556
## [2,] 2897 3193 1903 1184 682 2273 2715 1116 1013 1731
## [3,] 3577 3859 2475 1564 754 3073 3597 1497 1253 2109
## [4,] 2759 3185 1882 1148 683 2389 2796 1168 1067 1840
## [5,] 3804 4542 2657 1709 1016 3370 3884 1559 1336 2423
## [6,] 21 30 15 29 12 24 17 5 15 16
## CGAGTA CGAGTC CGAGTG CGAGTT CGATAA CGATAC CGATAG CGATAT CGATCA CGATCC
## [1,] 3899 2718 3246 5185 5178 2579 2522 4957 4726 2894
## [2,] 2645 1832 2170 3445 3409 1678 1578 3299 3143 2013
## [3,] 3183 2149 2666 4005 4062 2026 2059 3826 4041 2372
## [4,] 2738 1828 2251 3330 3249 1645 1573 3015 3094 1999
## [5,] 3548 2477 2906 4538 4484 2135 2226 4428 4228 2638
## [6,] 30 19 16 22 39 23 32 36 40 35
## CGATCG CGATCT CGATGA CGATGC CGATGG CGATGT CGATTA CGATTC CGATTG CGATTT
## [1,] 2440 4666 6493 2591 3386 3892 4709 4987 4095 8206
## [2,] 1686 3159 4041 1636 2044 2602 3021 3185 2721 5429
## [3,] 2083 3734 5076 2035 2728 3114 3751 4048 3336 6371
## [4,] 1771 2989 3914 1599 2126 2365 2844 3174 2525 5113
## [5,] 2266 4261 5799 2317 2988 3448 4179 4484 3802 7626
## [6,] 10 36 25 13 17 17 28 52 28 49
## CGCAAA CGCAAC CGCAAG CGCAAT CGCACA CGCACC CGCACG CGCACT CGCAGA CGCAGC
## [1,] 4294 2381 2376 2706 1647 1114 719 1204 2576 1937
## [2,] 2754 1694 1523 1801 1000 802 503 854 1543 1247
## [3,] 3417 2022 1960 2227 1281 977 601 1018 2000 1511
## [4,] 2806 1824 1557 1802 993 720 442 805 1661 1268
## [5,] 3870 2630 2246 2605 1459 1077 640 1163 2304 1754
## [6,] 15 8 15 20 8 8 8 14 7 10
## CGCAGG CGCAGT CGCATA CGCATC CGCATG CGCATT CGCCAA CGCCAC CGCCAG CGCCAT
## [1,] 1250 1600 2446 2248 1866 2834 3299 2141 1273 2919
## [2,] 785 1066 1583 1508 1293 1802 2150 1498 763 1879
## [3,] 1033 1284 1874 1973 1537 2282 2609 1731 971 2438
## [4,] 810 1055 1580 1441 1156 1677 2039 1301 745 1832
## [5,] 1107 1473 2125 2084 1714 2442 2908 1924 993 2709
## [6,] 10 11 10 10 16 20 20 9 9 14
## CGCCCA CGCCCC CGCCCG CGCCCT CGCCGA CGCCGC CGCCGG CGCCGT CGCCTA CGCCTC
## [1,] 1109 423 396 703 1690 1802 2070 2113 1321 2108
## [2,] 838 363 304 585 1108 1216 1330 1347 950 1375
## [3,] 1088 449 393 639 1317 1447 1669 1739 1030 1658
## [4,] 736 292 255 476 1096 1166 1329 1364 852 1309
## [5,] 1066 425 396 692 1521 1616 1882 1924 1199 1874
## [6,] 14 20 7 13 10 5 8 8 13 11
## CGCCTG CGCCTT CGCGAA CGCGAC CGCGAG CGCGAT CGCGCA CGCGCC CGCGCG CGCGCT
## [1,] 1116 2400 1310 870 985 1250 589 547 323 655
## [2,] 747 1631 931 526 697 839 349 421 225 437
## [3,] 1014 1962 1089 713 834 1056 412 487 272 555
## [4,] 713 1479 838 540 676 848 342 375 209 480
## [5,] 1058 2215 1234 725 900 1168 461 498 271 606
## [6,] 11 17 21 4 14 16 1 4 2 5
## CGCGGA CGCGGC CGCGGG CGCGGT CGCGTA CGCGTC CGCGTG CGCGTT CGCTAA CGCTAC
## [1,] 1043 745 621 1158 911 915 1098 1402 2864 1302
## [2,] 671 497 480 824 570 613 672 905 1562 907
## [3,] 781 600 524 1006 754 834 916 1149 1827 1041
## [4,] 754 478 347 759 564 557 656 854 1479 941
## [5,] 931 685 599 1097 835 822 954 1291 2089 1256
## [6,] 10 6 8 7 8 6 4 12 12 14
## CGCTAG CGCTAT CGCTCA CGCTCC CGCTCG CGCTCT CGCTGA CGCTGC CGCTGG CGCTGT
## [1,] 1414 1853 1657 1356 1039 2380 2158 1848 1360 1726
## [2,] 844 1248 1194 961 651 1701 1306 1189 928 1130
## [3,] 1032 1403 1410 1125 832 2041 1733 1499 1114 1300
## [4,] 789 1195 1160 947 618 1614 1270 1093 923 1045
## [5,] 1234 1670 1563 1245 878 2233 1935 1657 1240 1510
## [6,] 6 25 12 12 10 17 12 10 9 14
## CGCTTA CGCTTC CGCTTG CGCTTT CGGAAA CGGAAC CGGAAG CGGAAT CGGACA CGGACC
## [1,] 2369 3277 2579 3806 5718 2320 3488 3832 1952 1348
## [2,] 1440 2048 1703 2568 3760 1496 2292 2386 1300 976
## [3,] 1888 2623 2024 2872 4590 1952 2853 2885 1729 1122
## [4,] 1413 1962 1599 2222 3487 1497 2254 2336 1303 938
## [5,] 2133 2846 2283 3386 5158 2066 2997 3284 1802 1358
## [6,] 14 22 11 28 41 24 24 34 13 19
## CGGACG CGGACT CGGAGA CGGAGC CGGAGG CGGAGT CGGATA CGGATC CGGATG CGGATT
## [1,] 996 1631 5714 2168 2916 2392 3073 3350 2572 4800
## [2,] 686 1114 3501 1359 1825 1616 2090 2142 1695 3108
## [3,] 865 1303 4793 1654 2299 2071 2402 2865 2141 3763
## [4,] 614 1227 3382 1418 1801 1500 1946 2110 1734 3063
## [5,] 948 1765 5086 1821 2566 2325 2694 3502 2342 4287
## [6,] 7 16 19 21 17 17 32 39 18 31
## CGGCAA CGGCAC CGGCAG CGGCAT CGGCCA CGGCCC CGGCCG CGGCCT CGGCGA CGGCGC
## [1,] 2445 1038 1374 1806 1879 822 843 1197 2747 915
## [2,] 1560 750 824 1191 1295 611 652 867 1858 590
## [3,] 2146 866 1028 1415 1461 670 659 910 2371 727
## [4,] 1584 598 802 1077 1223 547 469 767 1932 602
## [5,] 2149 989 1113 1634 1600 783 763 1068 2570 839
## [6,] 10 5 15 13 9 13 9 6 16 4
## CGGCGG CGGCGT CGGCTA CGGCTC CGGCTG CGGCTT CGGGAA CGGGAC CGGGAG CGGGAT
## [1,] 2394 1594 1912 2011 1769 2826 3244 1252 1669 2255
## [2,] 1436 951 1272 1262 1312 1952 2141 836 1128 1329
## [3,] 1991 1271 1587 1504 1399 2286 2648 1018 1450 1615
## [4,] 1448 1005 1455 1292 1177 1875 2107 813 1014 1322
## [5,] 2020 1378 1880 1732 1597 2620 3103 1176 1601 1927
## [6,] 12 8 19 29 8 13 31 14 17 28
## CGGGCA CGGGCC CGGGCG CGGGCT CGGGGA CGGGGC CGGGGG CGGGGT CGGGTA CGGGTC
## [1,] 909 603 326 1012 1355 458 487 864 1566 1701
## [2,] 693 423 325 737 937 370 359 656 1136 1240
## [3,] 771 534 363 857 1102 473 389 790 1295 1531
## [4,] 566 411 270 691 825 310 316 584 1073 1152
## [5,] 824 589 395 955 1198 400 455 812 1499 1668
## [6,] 7 19 6 10 15 15 19 17 21 16
## CGGGTG CGGGTT CGGTAA CGGTAC CGGTAG CGGTAT CGGTCA CGGTCC CGGTCG CGGTCT
## [1,] 1267 3243 3386 1614 1732 2550 2252 1623 1152 2353
## [2,] 797 2204 2243 1109 1112 1699 1527 1084 837 1483
## [3,] 985 2560 2688 1370 1271 2005 1879 1206 957 2044
## [4,] 693 2015 2020 1078 985 1589 1411 939 848 1443
## [5,] 1201 3081 3010 1500 1464 2519 2059 1353 1165 2074
## [6,] 10 23 27 14 17 26 13 11 10 11
## CGGTGA CGGTGC CGGTGG CGGTGT CGGTTA CGGTTC CGGTTG CGGTTT CGTAAA CGTAAC
## [1,] 4081 1499 3419 2754 3877 3971 3320 7242 5649 2903
## [2,] 2738 1051 2252 1660 2610 2557 2100 4780 3490 1936
## [3,] 3267 1335 2980 2144 3091 2958 2545 5873 4286 2219
## [4,] 2555 1005 2391 1738 2625 2409 2055 4716 3365 1839
## [5,] 3590 1403 3314 2423 3735 3442 3004 6860 4772 2598
## [6,] 12 7 22 8 24 24 15 31 41 19
## CGTAAG CGTAAT CGTACA CGTACC CGTACG CGTACT CGTAGA CGTAGC CGTAGG CGTAGT
## [1,] 3002 4111 2894 1758 1657 2098 3346 1762 1354 2439
## [2,] 1952 2662 1859 1216 1019 1379 2102 1141 962 1645
## [3,] 2338 3463 2217 1442 1217 1659 2557 1399 1199 1914
## [4,] 1837 2527 1733 1162 1032 1335 1962 1076 859 1505
## [5,] 2491 3761 2523 1552 1354 1822 2911 1520 1193 2270
## [6,] 19 33 21 15 6 18 22 14 23 19
## CGTATA CGTATC CGTATG CGTATT CGTCAA CGTCAC CGTCAG CGTCAT CGTCCA CGTCCC
## [1,] 4155 2699 2803 4192 4487 2699 2132 3956 2688 1476
## [2,] 2546 1738 1791 2677 3039 1864 1332 2458 1738 1023
## [3,] 3091 2303 2060 3095 3660 2205 1568 3105 2099 1214
## [4,] 2349 1643 1789 2329 2826 1694 1270 2366 1585 909
## [5,] 3558 2479 2448 3720 4089 2452 1734 3483 2343 1223
## [6,] 16 23 19 46 20 10 8 10 18 15
## CGTCCG CGTCCT CGTCGA CGTCGC CGTCGG CGTCGT CGTCTA CGTCTC CGTCTG CGTCTT
## [1,] 1025 2289 2871 1649 1814 3411 2784 4154 2229 5578
## [2,] 766 1651 1858 1007 1207 2132 1888 2771 1402 3643
## [3,] 838 1903 2391 1295 1571 2723 2140 3264 1810 4362
## [4,] 662 1500 1751 983 1227 2253 1707 2419 1343 3490
## [5,] 904 2071 2570 1543 1741 3085 2457 3686 1963 5062
## [6,] 8 15 15 7 6 12 15 17 11 19
## CGTGAA CGTGAC CGTGAG CGTGAT CGTGCA CGTGCC CGTGCG CGTGCT CGTGGA CGTGGC
## [1,] 4612 2334 2630 3724 1846 1156 688 1793 3413 2081
## [2,] 2978 1464 1654 2351 1166 734 488 1209 2254 1307
## [3,] 3456 1786 2169 2892 1447 886 605 1607 2755 1672
## [4,] 2824 1440 1596 2257 1139 680 479 1215 2215 1219
## [5,] 3934 2045 2332 3426 1634 1001 671 1748 3142 1792
## [6,] 24 10 14 13 12 7 6 14 20 2
## CGTGGG CGTGGT CGTGTA CGTGTC CGTGTG CGTGTT CGTTAA CGTTAC CGTTAG CGTTAT
## [1,] 1527 2748 3004 2331 2712 4281 4604 3007 2655 4343
## [2,] 1019 1722 2008 1545 1742 2802 2947 1973 1683 2744
## [3,] 1382 2210 2330 2023 2113 3319 3603 2377 2124 3239
## [4,] 970 1731 1843 1516 1703 2556 2871 1917 1692 2518
## [5,] 1398 2433 2629 2234 2356 3685 4267 2708 2559 3820
## [6,] 16 12 19 13 10 11 17 23 9 24
## CGTTCA CGTTCC CGTTCG CGTTCT CGTTGA CGTTGC CGTTGG CGTTGT CGTTTA CGTTTC
## [1,] 3300 2297 1462 4136 5697 2776 3377 4559 5808 6082
## [2,] 2268 1574 1079 2710 3396 1758 2173 2979 3621 3697
## [3,] 2548 1883 1276 3283 4367 2176 2639 3513 4331 4704
## [4,] 2068 1504 997 2523 3382 1678 2079 2844 3425 3623
## [5,] 3023 2136 1349 3670 4780 2671 3053 4143 5102 5445
## [6,] 16 30 21 37 25 13 16 13 28 35
## CGTTTG CGTTTT CTAAAA CTAAAC CTAAAG CTAAAT CTAACA CTAACC CTAACG CTAACT
## [1,] 5511 10707 18790 14943 9197 13808 9134 5769 2714 7599
## [2,] 3605 6847 12575 6894 6179 8903 5458 3592 1842 4602
## [3,] 4393 8308 13802 7874 7023 10164 6303 4076 2088 5392
## [4,] 3410 6467 11389 7675 5907 8571 5496 3577 1681 4352
## [5,] 5038 9527 16333 9123 8318 11938 7277 4665 2311 6215
## [6,] 24 55 103 31 46 79 30 30 13 26
## CTAAGA CTAAGC CTAAGG CTAAGT CTAATA CTAATC CTAATG CTAATT CTACAA CTACAC
## [1,] 8189 4883 3715 6100 10224 8659 7602 13816 10693 4884
## [2,] 5474 2858 2596 4246 6945 5284 4999 8834 6832 3066
## [3,] 6402 3416 3090 4611 7981 6069 5999 10395 8100 3578
## [4,] 5026 2758 2530 3924 6487 5177 4643 8434 6428 3087
## [5,] 7166 3853 3407 5904 9069 7109 6770 12101 9202 4524
## [6,] 41 20 23 37 69 45 49 89 35 14
## CTACAG CTACAT CTACCA CTACCC CTACCG CTACCT CTACGA CTACGC CTACGG CTACGT
## [1,] 4030 7374 5154 1809 1602 3610 3172 1365 1685 2735
## [2,] 2672 4920 3455 1266 1086 2488 2036 918 1157 1584
## [3,] 3288 5984 4200 1361 1358 2901 2610 1108 1392 1989
## [4,] 2472 4456 3246 1188 1052 2251 1985 831 966 1600
## [5,] 3642 6607 4643 1609 1473 3296 2795 1223 1545 2309
## [6,] 25 29 33 29 18 27 18 12 22 15
## CTACTA CTACTC CTACTG CTACTT CTAGAA CTAGAC CTAGAG CTAGAT CTAGCA CTAGCC
## [1,] 6557 4990 3947 9157 8186 3553 5622 6855 4164 2179
## [2,] 4384 3455 2486 5596 5534 2360 3594 4670 2819 1550
## [3,] 4850 4197 2993 6385 6453 2930 4542 5242 3345 1761
## [4,] 4071 3277 2412 5401 5490 2357 3511 4380 2504 1377
## [5,] 5783 4588 3453 7375 7933 3296 4959 6398 3444 1896
## [6,] 38 21 28 38 63 12 24 34 18 15
## CTAGCG CTAGCT CTAGGA CTAGGC CTAGGG CTAGGT CTAGTA CTAGTC CTAGTG CTAGTT
## [1,] 1301 5540 3706 1868 2373 3316 5172 3928 4283 8044
## [2,] 857 3615 2647 1309 1621 2283 3372 2351 2857 4763
## [3,] 1044 4433 3102 1538 1977 2609 4208 2713 3374 5615
## [4,] 857 3526 2432 1282 1529 2073 3210 2242 2710 4720
## [5,] 1154 4844 3366 1671 2136 2936 4583 3168 3856 6633
## [6,] 8 20 30 13 21 17 28 18 11 42
## CTATAA CTATAC CTATAG CTATAT CTATCA CTATCC CTATCG CTATCT CTATGA CTATGC
## [1,] 10815 5225 5398 13041 7808 3481 2442 8003 7277 3730
## [2,] 7139 3426 3543 8622 5067 2417 1688 5272 4557 2443
## [3,] 8084 4123 4078 9953 6111 2833 2028 6401 5524 2845
## [4,] 6430 3181 3388 7946 4997 2176 1518 4822 4501 2283
## [5,] 9256 4682 4597 11665 6912 3049 2138 6900 6426 3349
## [6,] 57 35 44 98 40 30 19 48 52 13
## CTATGG CTATGT CTATTA CTATTC CTATTG CTATTT CTCAAA CTCAAC CTCAAG CTCAAT
## [1,] 4571 7040 8791 6044 7358 14587 15209 8048 8902 9971
## [2,] 3134 4863 5789 4093 4809 9744 9839 5232 6052 6472
## [3,] 3645 5622 6738 4887 5516 10703 11543 6250 7143 7651
## [4,] 2740 4261 5354 3661 4474 8637 9781 5198 5757 6252
## [5,] 4223 6412 7775 5489 6372 12766 13555 7111 8021 8795
## [6,] 34 23 81 82 43 136 55 17 21 56
## CTCACA CTCACC CTCACG CTCACT CTCAGA CTCAGC CTCAGG CTCAGT CTCATA CTCATC
## [1,] 6625 4605 2562 6273 6799 4748 3990 5058 8141 9468
## [2,] 4366 3168 1810 4196 4360 3384 2583 3205 5318 6178
## [3,] 5146 3717 2293 4843 5367 3972 3158 3913 6297 7446
## [4,] 4220 2993 1572 3929 4292 3019 2519 3175 5404 5827
## [5,] 5869 4118 2412 5825 6152 4219 3506 4495 7914 8322
## [6,] 19 18 12 28 16 17 13 26 44 25
## CTCATG CTCATT CTCCAA CTCCAC CTCCAG CTCCAT CTCCCA CTCCCC CTCCCG CTCCCT
## [1,] 6797 10423 11215 6538 5023 9720 4920 2148 1611 4082
## [2,] 4477 6947 7379 4341 3006 6484 3173 1663 1157 2761
## [3,] 5333 8060 8909 5467 3859 7746 3978 1812 1411 3296
## [4,] 4243 6441 7146 4280 3101 6019 3095 1526 1080 2654
## [5,] 6118 9427 9689 5908 4373 8766 4331 1918 1524 3716
## [6,] 25 50 36 26 26 32 24 23 17 28
## CTCCGA CTCCGC CTCCGG CTCCGT CTCCTA CTCCTC CTCCTG CTCCTT CTCGAA CTCGAC
## [1,] 3982 2276 3433 3227 5523 9226 4397 10038 5267 3889
## [2,] 2573 1596 2325 2037 3201 6105 2887 6757 3433 2773
## [3,] 3130 1887 2753 2667 3719 7429 3606 8243 4215 3241
## [4,] 2495 1495 2290 1983 3011 5757 2796 6359 3277 2772
## [5,] 3469 2165 3130 2964 4226 8309 3903 9070 4822 3734
## [6,] 20 15 15 19 47 34 32 46 55 18
## CTCGAG CTCGAT CTCGCA CTCGCC CTCGCG CTCGCT CTCGGA CTCGGC CTCGGG CTCGGT
## [1,] 4383 5096 2412 2097 994 2832 3332 2048 1907 3091
## [2,] 2824 3271 1700 1485 709 1966 2134 1420 1269 2016
## [3,] 3467 4211 1987 1985 863 2253 2734 1633 1676 2406
## [4,] 2760 3444 1707 1359 675 1754 2092 1347 1233 1945
## [5,] 3937 4810 2109 2030 930 2601 2786 1810 1810 2744
## [6,] 21 47 8 12 15 9 18 9 30 19
## CTCGTA CTCGTC CTCGTG CTCGTT CTCTAA CTCTAC CTCTAG CTCTAT CTCTCA CTCTCC
## [1,] 3451 4139 3306 5447 10045 6037 5497 9298 9404 7670
## [2,] 2175 2685 2082 3553 6316 3927 3699 6317 6151 5207
## [3,] 2660 3328 2682 4114 7185 4710 4459 7507 7497 6512
## [4,] 2006 2581 2161 3313 5945 3724 3500 5730 5861 4862
## [5,] 3037 3604 3038 4790 8426 5261 4843 8404 8588 7104
## [6,] 36 9 17 33 34 36 21 59 30 32
## CTCTCG CTCTCT CTCTGA CTCTGC CTCTGG CTCTGT CTCTTA CTCTTC CTCTTG CTCTTT
## [1,] 4251 19401 7989 6161 4730 10367 10560 15675 10345 19919
## [2,] 2897 13210 4962 3951 3104 6377 6441 10207 6950 12796
## [3,] 3703 16002 6094 4992 3805 7826 7323 12199 8569 15337
## [4,] 2714 11931 4852 3790 2929 6177 6000 9399 6545 11881
## [5,] 4063 17756 6969 5640 4288 8834 8388 13837 9507 17635
## [6,] 28 43 30 21 21 23 39 67 43 111
## CTGAAA CTGAAC CTGAAG CTGAAT CTGACA CTGACC CTGACG CTGACT CTGAGA CTGAGC
## [1,] 13742 5542 8562 9431 4350 2993 2015 3965 7851 3624
## [2,] 8676 3563 5546 5621 2769 2045 1271 2626 5043 2353
## [3,] 10684 4296 6898 7097 3513 2354 1617 3328 6383 2900
## [4,] 8799 3324 5456 5637 2775 1905 1282 2590 4826 2255
## [5,] 12271 5005 7926 7936 3903 2761 1704 3636 7011 3274
## [6,] 54 25 19 59 16 19 9 17 25 21
## CTGAGG CTGAGT CTGATA CTGATC CTGATG CTGATT CTGCAA CTGCAC CTGCAG CTGCAT
## [1,] 3980 4743 7315 6303 7723 10537 9630 3285 5589 6510
## [2,] 2531 3338 4622 3962 4845 6677 5893 2179 3350 3923
## [3,] 3264 3993 5760 4913 6179 8067 7539 2602 4433 5142
## [4,] 2392 3339 4472 3912 4641 6354 5972 2059 3443 3866
## [5,] 3622 4486 6597 5594 7092 9347 8388 2902 4983 5675
## [6,] 17 9 25 24 23 47 31 9 9 28
## CTGCCA CTGCCC CTGCCG CTGCCT CTGCGA CTGCGC CTGCGG CTGCGT CTGCTA CTGCTC
## [1,] 3952 1358 1275 3074 2497 995 1589 2246 4310 4641
## [2,] 2628 1019 882 2270 1622 632 1144 1374 2859 3087
## [3,] 3128 1161 1074 2535 2026 806 1493 1780 3353 3888
## [4,] 2356 974 833 2019 1527 631 1058 1354 2652 2953
## [5,] 3519 1316 1087 2831 2229 885 1537 1931 3761 4247
## [6,] 15 14 13 16 7 12 21 6 26 22
## CTGCTG CTGCTT CTGGAA CTGGAC CTGGAG CTGGAT CTGGCA CTGGCC CTGGCG CTGGCT
## [1,] 5390 8502 6813 2744 4936 5342 2485 1622 1116 3127
## [2,] 3215 5309 4340 1830 3103 3373 1631 1117 765 1996
## [3,] 4121 6473 5598 2246 4072 4232 2017 1303 952 2516
## [4,] 3243 5157 4176 1785 3115 3332 1513 1097 743 1913
## [5,] 4653 7576 6294 2545 4385 4959 2138 1570 1027 2856
## [6,] 20 31 38 11 18 38 10 7 9 15
## CTGGGA CTGGGC CTGGGG CTGGGT CTGGTA CTGGTC CTGGTG CTGGTT CTGTAA CTGTAC
## [1,] 3129 1254 1345 2263 4120 3514 4687 7403 7328 3015
## [2,] 2013 977 937 1524 2566 2364 2926 4402 4600 1813
## [3,] 2480 1115 1122 1895 3478 2824 3807 5407 5653 2441
## [4,] 1972 852 912 1394 2504 2305 2950 4444 4493 1964
## [5,] 2713 1154 1275 2104 3537 3241 4325 6363 6374 2643
## [6,] 20 17 22 19 23 16 13 36 40 20
## CTGTAG CTGTAT CTGTCA CTGTCC CTGTCG CTGTCT CTGTGA CTGTGC CTGTGG CTGTGT
## [1,] 4222 5886 4683 2779 1912 5737 6015 2268 3780 5425
## [2,] 2576 3715 3105 1832 1299 3628 3725 1485 2434 3507
## [3,] 3371 4704 3621 2133 1473 4523 4509 1903 3059 4256
## [4,] 2516 3580 2904 1798 1252 3562 3575 1403 2270 3391
## [5,] 3570 5430 4106 2374 1697 5186 5472 2073 3316 5062
## [6,] 22 25 14 20 11 32 16 9 14 17
## CTGTTA CTGTTC CTGTTG CTGTTT CTTAAA CTTAAC CTTAAG CTTAAT CTTACA CTTACC
## [1,] 6787 6217 8148 14364 15752 7725 7419 11559 8614 5279
## [2,] 4480 3982 5142 8949 9946 4847 4948 7549 5380 3468
## [3,] 5396 4671 6322 11025 11268 5963 5916 8844 6254 3948
## [4,] 4107 3761 4940 8326 9376 4650 4805 6982 5061 3209
## [5,] 6169 5442 7229 12648 14110 6668 6637 10223 7309 4592
## [6,] 33 41 28 45 43 25 13 52 23 25
## CTTACG CTTACT CTTAGA CTTAGC CTTAGG CTTAGT CTTATA CTTATC CTTATG CTTATT
## [1,] 2918 7460 7367 4739 4029 6112 12025 8353 8632 13272
## [2,] 1937 4850 5008 3184 2801 4181 7349 5539 5374 8800
## [3,] 2230 5596 5720 3776 3211 4921 8398 6610 6293 10073
## [4,] 1736 4651 4609 2878 2844 3858 7098 5289 5092 8076
## [5,] 2697 6553 6644 4271 3832 5599 9969 7776 7168 11888
## [6,] 17 44 26 23 24 27 57 33 35 88
## CTTCAA CTTCAC CTTCAG CTTCAT CTTCCA CTTCCC CTTCCG CTTCCT CTTCGA CTTCGC
## [1,] 16569 9681 8864 14661 10511 5715 3624 11405 5792 2781
## [2,] 10831 6365 5574 9653 6714 3938 2273 7632 3836 1766
## [3,] 13095 7782 7004 11539 8370 4654 2829 9198 4590 2147
## [4,] 10426 6163 5371 9001 6388 3597 2187 7200 3651 1763
## [5,] 15359 8738 7656 12912 9476 5148 3080 10253 5375 2472
## [6,] 55 23 31 56 57 46 25 37 31 14
## CTTCGG CTTCGT CTTCTA CTTCTC CTTCTG CTTCTT CTTGAA CTTGAC CTTGAG CTTGAT
## [1,] 3150 5851 10779 16940 10079 31542 14376 6456 9161 13128
## [2,] 2047 3737 6877 10880 6256 19261 9521 4298 5738 8419
## [3,] 2415 4628 7880 13201 7791 23371 11344 5343 7260 10455
## [4,] 2080 3763 6823 10584 6209 19238 8895 4095 5797 8248
## [5,] 2904 5292 9186 15396 8871 27470 13066 5745 8575 12228
## [6,] 33 36 61 57 45 130 77 36 28 56
## CTTGCA CTTGCC CTTGCG CTTGCT CTTGGA CTTGGC CTTGGG CTTGGT CTTGTA CTTGTC
## [1,] 7913 3848 2387 8316 9340 4595 4537 8499 10066 7904
## [2,] 4896 2640 1577 5382 6159 3087 3010 5585 6760 5095
## [3,] 6019 2975 1897 6451 7349 3804 3756 6859 7883 6382
## [4,] 4703 2276 1582 5283 5673 2982 2863 5661 6303 4960
## [5,] 6867 3379 2197 7307 8124 4200 4100 8425 9013 7163
## [6,] 25 13 15 36 46 26 37 44 48 18
## CTTGTG CTTGTT CTTTAA CTTTAC CTTTAG CTTTAT CTTTCA CTTTCC CTTTCG CTTTCT
## [1,] 9103 16347 15247 8646 9601 14859 13622 8581 4844 19509
## [2,] 5891 10770 9953 5471 6073 10069 8872 5886 3271 12907
## [3,] 7077 12870 11396 6377 7073 11483 10576 7279 3848 15282
## [4,] 5493 10409 9192 5118 5943 9115 8462 5416 3061 11843
## [5,] 8257 15259 13353 7623 8184 13315 12268 7926 4517 17835
## [6,] 25 69 55 40 42 90 80 56 47 97
## CTTTGA CTTTGC CTTTGG CTTTGT CTTTTA CTTTTC CTTTTG CTTTTT GAAAAA GAAAAC
## [1,] 15987 8230 10412 15970 17840 17043 19485 31428 33552 17136
## [2,] 10106 5546 6819 10850 12020 10802 12178 20330 22097 11217
## [3,] 12343 6635 8303 12511 13599 13012 14394 23894 26425 13762
## [4,] 9728 5089 6557 10276 10867 10131 11184 18793 19850 10604
## [5,] 14717 7627 9625 14377 15867 15074 16977 28150 29958 15499
## [6,] 67 19 54 51 80 117 87 317 234 59
## GAAAAG GAAAAT GAAACA GAAACC GAAACG GAAACT GAAAGA GAAAGC GAAAGG GAAAGT
## [1,] 16783 25707 19045 10066 6047 14729 20088 8362 7569 11539
## [2,] 10783 15937 11963 6499 3781 9557 12989 5390 4999 7455
## [3,] 13583 18884 14094 7861 4784 11732 15571 6551 6139 8928
## [4,] 10125 15295 11500 6207 3589 9304 12137 5024 4795 6707
## [5,] 14958 22448 16325 9038 5331 13327 17854 7584 6711 10107
## [6,] 104 130 62 45 27 46 120 40 61 46
## GAAATA GAAATC GAAATG GAAATT GAACAA GAACAC GAACAG GAACAT GAACCA GAACCC
## [1,] 15861 12849 13345 19644 15367 6248 6144 10425 9073 3961
## [2,] 10376 8413 8382 12463 9796 3966 3711 6743 5953 2596
## [3,] 11986 10109 9911 14848 12222 4814 4877 8360 7195 3022
## [4,] 9675 8012 7970 11801 9330 3858 3793 6361 5841 2359
## [5,] 13993 11835 11871 17615 13826 5369 5542 9182 8315 3361
## [6,] 163 90 89 117 63 14 30 38 61 42
## GAACCG GAACCT GAACGA GAACGC GAACGG GAACGT GAACTA GAACTC GAACTG GAACTT
## [1,] 3785 6028 4102 1684 2309 3148 6788 6693 5310 10180
## [2,] 2500 3927 2776 1108 1530 2079 4564 4395 3343 6612
## [3,] 2968 4689 3301 1341 1948 2527 5215 5423 4154 8203
## [4,] 2618 3724 2724 1129 1497 1887 4550 4280 3387 6482
## [5,] 3726 5261 3836 1497 2037 2732 6085 5899 4705 9657
## [6,] 22 42 31 15 21 19 47 39 27 54
## GAAGAA GAAGAC GAAGAG GAAGAT GAAGCA GAAGCC GAAGCG GAAGCT GAAGGA GAAGGC
## [1,] 32505 9118 15289 17733 11453 5097 3279 12305 10640 3988
## [2,] 20681 6024 9835 11531 7182 3345 2074 7419 7082 2631
## [3,] 25781 7568 11931 14200 8749 3987 2586 9528 8730 3271
## [4,] 19882 5740 9438 10936 7044 3071 2006 7754 6705 2456
## [5,] 29938 8541 13901 16797 10574 4557 2902 11340 9545 3537
## [6,] 114 21 57 50 35 17 15 35 47 16
## GAAGGG GAAGGT GAAGTA GAAGTC GAAGTG GAAGTT GAATAA GAATAC GAATAG GAATAT
## [1,] 4026 7151 8650 5857 7060 12456 13218 5960 6103 14073
## [2,] 2631 4671 5470 3789 4606 8077 8604 3979 3961 9293
## [3,] 3324 5755 6641 4717 5602 9831 10388 4916 4900 10964
## [4,] 2624 4360 5114 3899 4339 7690 8264 3630 3754 8414
## [5,] 3713 6565 7463 5224 6266 11233 11771 5243 5357 12724
## [6,] 50 24 57 19 30 52 109 51 100 83
## GAATCA GAATCC GAATCG GAATCT GAATGA GAATGC GAATGG GAATGT GAATTA GAATTC
## [1,] 13499 7366 5187 13712 10794 5029 6822 9336 11070 9200
## [2,] 8599 4675 3189 8443 7089 3217 4570 6153 7293 6105
## [3,] 10577 5676 3953 10644 8384 3904 5378 7184 8629 7517
## [4,] 8371 4574 3217 8239 6644 3075 4192 5668 6922 5658
## [5,] 12125 6324 4712 12411 9343 4261 6073 8359 9916 8332
## [6,] 84 71 57 76 68 30 42 44 91 104
## GAATTG GAATTT GACAAA GACAAC GACAAG GACAAT GACACA GACACC GACACG GACACT
## [1,] 10360 18229 14425 6357 7940 8670 6621 3120 2509 4651
## [2,] 6690 11774 9221 4044 5247 5649 4141 2077 1573 3049
## [3,] 8034 13919 11215 4920 6192 6475 4892 2500 1944 3653
## [4,] 6488 11007 9044 3826 5061 5292 3832 2005 1613 2911
## [5,] 9198 16597 13299 5730 6909 7554 5455 2756 2155 4084
## [6,] 92 119 54 16 16 32 25 13 8 9
## GACAGA GACAGC GACAGG GACAGT GACATA GACATC GACATG GACATT GACCAA GACCAC
## [1,] 6223 2691 2555 3928 7142 5494 6996 9044 8765 3916
## [2,] 3915 1644 1597 2480 4785 3601 4508 6078 5536 2664
## [3,] 4886 2227 1974 3109 5413 4375 5295 7223 6829 3268
## [4,] 3826 1710 1560 2440 4494 3554 4397 5415 5443 2601
## [5,] 5459 2382 2163 3316 6420 4930 6018 8176 7878 3613
## [6,] 23 14 10 12 30 23 24 24 49 11
## GACCAG GACCAT GACCCA GACCCC GACCCG GACCCT GACCGA GACCGC GACCGG GACCGT
## [1,] 3555 6544 3662 1345 1824 2413 2291 1183 1838 2084
## [2,] 2461 3818 2574 930 1224 1732 1592 767 1276 1420
## [3,] 3004 4713 2995 1135 1543 2028 1799 976 1456 1783
## [4,] 2353 3726 2353 842 1113 1718 1520 712 1145 1298
## [5,] 3170 5181 3333 1257 1653 2181 2099 1066 1714 1970
## [6,] 6 30 27 28 24 20 25 11 10 6
## GACCTA GACCTC GACCTG GACCTT GACGAA GACGAC GACGAG GACGAT GACGCA GACGCC
## [1,] 3196 3178 2810 5008 6058 3624 4082 4883 2149 1453
## [2,] 2146 2237 1900 3239 3817 2400 2710 3087 1313 1029
## [3,] 2445 2763 2226 4060 4815 2771 3345 3810 1735 1260
## [4,] 2131 2186 1854 3032 3667 2149 2714 2952 1315 987
## [5,] 2806 2999 2567 4498 5482 3227 3707 4306 1954 1336
## [6,] 27 17 11 26 32 5 16 18 6 6
## GACGCG GACGCT GACGGA GACGGC GACGGG GACGGT GACGTA GACGTC GACGTG GACGTT
## [1,] 916 1976 3082 1894 1363 2903 2280 2328 2599 3652
## [2,] 580 1282 2013 1268 915 1975 1530 1582 1640 2416
## [3,] 745 1594 2504 1589 1114 2354 1895 1952 2034 2824
## [4,] 586 1222 1929 1247 872 2034 1531 1409 1613 2165
## [5,] 829 1710 2696 1632 1323 2733 2142 1973 2179 3200
## [6,] 4 9 16 6 18 10 14 7 13 17
## GACTAA GACTAC GACTAG GACTAT GACTCA GACTCC GACTCG GACTCT GACTGA GACTGC
## [1,] 6788 3721 3557 5649 5644 3301 2756 5963 4508 2680
## [2,] 4518 2315 2473 3812 3718 2140 1851 4021 3041 1667
## [3,] 5220 2744 2797 4362 4403 2570 2191 4973 3615 2123
## [4,] 4069 2188 2388 3560 3655 2377 1817 3930 2955 1719
## [5,] 5896 3233 3107 5155 5381 2961 2469 5397 4251 2300
## [6,] 32 15 16 27 28 22 20 25 17 14
## GACTGG GACTGT GACTTA GACTTC GACTTG GACTTT GAGAAA GAGAAC GAGAAG GAGAAT
## [1,] 2696 3944 5823 5890 7165 10048 24380 7668 16736 13359
## [2,] 1702 2623 3806 3829 4794 6709 14921 5007 10830 8558
## [3,] 2184 3162 4411 4660 5778 8152 18221 6258 13555 10465
## [4,] 1670 2455 3546 4020 4559 6378 13956 4805 10524 8304
## [5,] 2552 3712 5001 5634 6793 9344 20683 7003 15826 11849
## [6,] 22 7 29 25 24 39 72 15 55 58
## GAGACA GAGACC GAGACG GAGACT GAGAGA GAGAGC GAGAGG GAGAGT GAGATA GAGATC
## [1,] 9011 3987 4144 7053 21297 5503 6870 8508 10818 8512
## [2,] 5690 2620 2690 4543 13689 3577 4626 5562 6909 5370
## [3,] 6961 3222 3334 5581 16534 4549 5704 6726 8172 6785
## [4,] 5541 2515 2719 4490 13112 3310 4341 5319 6583 5244
## [5,] 7881 3611 3681 6472 18390 4943 6259 7643 9331 7442
## [6,] 30 11 15 20 49 19 22 24 48 42
## GAGATG GAGATT GAGCAA GAGCAC GAGCAG GAGCAT GAGCCA GAGCCC GAGCCG GAGCCT
## [1,] 10359 15213 8182 2941 4829 6063 5140 1594 1912 3393
## [2,] 6704 9822 5123 1905 2994 3901 3301 1138 1230 2186
## [3,] 8336 11776 6411 2458 3825 4654 3914 1364 1561 2651
## [4,] 6535 9499 4989 1794 2982 3781 3100 1047 1211 2206
## [5,] 9260 13765 7347 2480 4159 5365 4417 1470 1774 3124
## [6,] 31 59 36 17 21 31 31 20 23 26
## GAGCGA GAGCGC GAGCGG GAGCGT GAGCTA GAGCTC GAGCTG GAGCTT GAGGAA GAGGAC
## [1,] 2470 795 1433 1908 5201 5031 5337 9369 12691 3878
## [2,] 1565 562 910 1214 3437 3346 3360 5964 8141 2515
## [3,] 1898 694 1158 1508 4189 4418 4328 7743 10172 3123
## [4,] 1481 565 975 1206 3370 3351 3393 5818 7966 2531
## [5,] 2298 749 1343 1814 4605 4531 4797 8695 11286 3435
## [6,] 16 8 16 10 41 18 20 30 45 15
## GAGGAG GAGGAT GAGGCA GAGGCC GAGGCG GAGGCT GAGGGA GAGGGC GAGGGG GAGGGT
## [1,] 9387 8337 4287 1935 2111 4448 4897 1514 1691 3228
## [2,] 6073 5334 2764 1264 1364 2846 3157 1059 1177 2063
## [3,] 7527 6573 3564 1742 1788 3444 3959 1205 1382 2624
## [4,] 5741 5057 2727 1217 1383 2738 2926 1039 1050 2083
## [5,] 8475 7320 4015 1812 1880 3843 4336 1497 1526 2913
## [6,] 22 37 14 12 8 15 26 13 21 18
## GAGGTA GAGGTC GAGGTG GAGGTT GAGTAA GAGTAC GAGTAG GAGTAT GAGTCA GAGTCC
## [1,] 4892 3254 4354 7695 8351 3890 5066 7493 5929 2925
## [2,] 3206 2239 2886 4752 5483 2549 3408 4704 3864 1926
## [3,] 3984 2856 3507 5846 6492 2972 4350 5862 4959 2203
## [4,] 3104 2116 2865 4681 5348 2486 3321 4782 4051 1788
## [5,] 4569 3046 3927 6742 7274 3366 4549 7231 5593 2538
## [6,] 19 19 16 32 42 24 30 33 28 23
## GAGTCG GAGTCT GAGTGA GAGTGC GAGTGG GAGTGT GAGTTA GAGTTC GAGTTG GAGTTT
## [1,] 2490 6185 7202 2489 4446 5762 7615 6741 7908 15636
## [2,] 1687 4141 4691 1564 2901 3698 5239 4481 5283 9973
## [3,] 1991 5011 5795 1885 3521 4561 6039 5353 6166 11827
## [4,] 1558 4272 4602 1442 2885 3437 4856 4343 4836 9333
## [5,] 2600 5896 6913 2119 4014 5092 6823 5983 7091 13869
## [6,] 19 19 21 14 23 13 35 38 36 50
## GATAAA GATAAC GATAAG GATAAT GATACA GATACC GATACG GATACT GATAGA GATAGC
## [1,] 16341 7212 8390 12638 8507 3857 2728 6599 8830 3574
## [2,] 10589 4637 5559 8323 5398 2540 1721 4215 5750 2378
## [3,] 12088 5588 6520 9498 6676 3173 2184 5136 6669 2738
## [4,] 9620 4308 5514 7558 5381 2368 1612 4257 5418 2177
## [5,] 14191 6143 7336 11036 7869 3353 2399 6035 7671 3163
## [6,] 105 31 51 74 54 27 18 52 66 21
## GATAGG GATAGT GATATA GATATC GATATG GATATT GATCAA GATCAC GATCAG GATCAT
## [1,] 3389 6070 12823 8066 9664 14672 13615 5951 6477 11472
## [2,] 2212 3976 8435 5074 6301 9542 8937 3748 4069 7269
## [3,] 2973 4697 9771 6249 7488 10960 10990 5144 5051 9066
## [4,] 2060 3750 7759 4859 5872 8884 8525 3760 3814 6909
## [5,] 3066 5420 11418 7183 8515 13201 12150 5423 5589 10067
## [6,] 28 41 70 47 36 92 88 26 28 54
## GATCCA GATCCC GATCCG GATCCT GATCGA GATCGC GATCGG GATCGT GATCTA GATCTC
## [1,] 8509 3314 3305 6235 6055 1983 2926 3968 7067 8451
## [2,] 5445 2278 2312 4127 4124 1308 1996 2470 4764 5445
## [3,] 6897 2802 2740 4988 5015 1903 2464 3089 5734 6601
## [4,] 5247 2207 2061 4144 4132 1278 1982 2358 4578 5278
## [5,] 7371 3006 3145 5666 5580 1740 2787 3479 6370 7582
## [6,] 68 45 37 61 42 13 24 30 58 36
## GATCTG GATCTT GATGAA GATGAC GATGAG GATGAT GATGCA GATGCC GATGCG GATGCT
## [1,] 6360 13258 15995 6376 9380 17409 7608 2964 2289 7211
## [2,] 4069 8299 9995 4134 6044 11061 4850 1848 1487 4548
## [3,] 5007 10157 12752 5092 7372 13627 6266 2308 1896 5709
## [4,] 3829 8097 9867 3864 5892 10756 4660 1795 1491 4549
## [5,] 5702 11841 14199 5748 8459 15828 6944 2630 2082 6403
## [6,] 32 74 68 20 23 59 26 17 8 24
## GATGGA GATGGC GATGGG GATGGT GATGTA GATGTC GATGTG GATGTT GATTAA GATTAC
## [1,] 9578 3909 4553 8703 6980 5383 7079 11770 12359 6677
## [2,] 6066 2503 2981 5361 4593 3590 4618 7898 7911 4343
## [3,] 7552 3125 3957 6391 5500 4414 5565 9291 9476 5500
## [4,] 5943 2508 2909 5400 4230 3585 4289 7243 7321 4075
## [5,] 8371 3558 4390 7612 6308 5267 6687 10791 11026 5938
## [6,] 43 17 22 31 33 18 27 35 61 32
## GATTAG GATTAT GATTCA GATTCC GATTCG GATTCT GATTGA GATTGC GATTGG GATTGT
## [1,] 8167 13278 13119 7033 5282 14532 12171 5321 7507 11417
## [2,] 5389 8448 8545 4492 3559 8942 8068 3532 5010 6984
## [3,] 6133 9943 10085 5509 4235 10785 9525 4264 6003 8104
## [4,] 4852 7923 8287 4417 3336 8786 7865 3407 4638 6646
## [5,] 7269 11835 11646 6285 4922 12555 11293 4857 6982 9581
## [6,] 34 62 106 66 57 78 71 22 50 42
## GATTTA GATTTC GATTTG GATTTT GCAAAA GCAAAC GCAAAG GCAAAT GCAACA GCAACC
## [1,] 13921 12814 16307 25541 15298 7397 8567 10835 8758 3910
## [2,] 9400 8449 10313 17221 9969 4791 5462 6821 5549 2571
## [3,] 10956 9994 12730 19557 12064 5812 6856 8280 6887 3204
## [4,] 8430 7966 9933 15716 9301 4639 5112 6522 5491 2590
## [5,] 12856 11743 14950 23191 13374 6461 7453 9341 7841 3773
## [6,] 67 90 61 128 66 14 21 47 20 8
## GCAACG GCAACT GCAAGA GCAAGC GCAAGG GCAAGT GCAATA GCAATC GCAATG GCAATT
## [1,] 2822 5873 8475 4008 3731 6167 6833 5304 6800 7925
## [2,] 1732 3803 5392 2570 2453 3821 4402 3577 4381 5024
## [3,] 2200 4682 6769 3237 3057 4616 5109 4481 5555 6052
## [4,] 1800 3782 5320 2589 2269 3685 4371 3409 4311 4814
## [5,] 2576 5250 8170 3578 3369 5252 6041 4997 6247 7005
## [6,] 8 18 27 11 24 15 40 24 27 43
## GCACAA GCACAC GCACAG GCACAT GCACCA GCACCC GCACCG GCACCT GCACGA GCACGC
## [1,] 5786 2733 2322 4623 4169 1199 1498 2422 1996 922
## [2,] 3874 1744 1449 2860 2873 832 1067 1743 1296 532
## [3,] 4578 2037 1826 3402 3435 1056 1311 2016 1542 815
## [4,] 3490 1611 1467 2799 2668 748 960 1524 1222 541
## [5,] 5370 2252 1960 4024 3814 1085 1382 2199 1729 856
## [6,] 11 4 6 12 13 11 8 13 15 7
## GCACGG GCACGT GCACTA GCACTC GCACTG GCACTT GCAGAA GCAGAC GCAGAG GCAGAT
## [1,] 1051 1724 3086 2282 2239 4077 7999 3070 6288 6384
## [2,] 627 1049 1829 1564 1438 2719 4836 2000 3862 3951
## [3,] 842 1362 2286 1945 1792 3177 6444 2368 5118 4880
## [4,] 622 1036 1676 1480 1349 2426 4993 1856 3821 3779
## [5,] 1003 1471 2342 2059 1999 3617 7163 2682 5692 5365
## [6,] 7 12 15 16 7 25 33 6 18 29
## GCAGCA GCAGCC GCAGCG GCAGCT GCAGGA GCAGGC GCAGGG GCAGGT GCAGTA GCAGTC
## [1,] 5818 2847 1872 5832 3796 1723 1710 3340 3477 2604
## [2,] 3716 1939 1157 3633 2483 1067 1103 2150 2157 1752
## [3,] 4701 2300 1471 4556 3054 1445 1346 2646 2664 2049
## [4,] 3515 1861 1163 3567 2415 1110 1162 2081 2064 1611
## [5,] 5066 2540 1620 5252 3565 1572 1551 3027 2965 2382
## [6,] 23 7 7 22 16 9 8 14 21 14
## GCAGTG GCAGTT GCATAA GCATAC GCATAG GCATAT GCATCA GCATCC GCATCG GCATCT
## [1,] 3327 5156 6995 3787 3719 7832 7604 3436 2568 6655
## [2,] 2227 3191 4427 2423 2540 5308 4885 2306 1688 4155
## [3,] 2675 4145 5438 2918 2909 6051 6126 2915 2096 5107
## [4,] 2110 3037 4228 2417 2269 4777 4659 2264 1652 3781
## [5,] 2913 4572 6023 3281 3257 7086 6903 3171 2464 5781
## [6,] 13 26 33 22 18 37 17 17 12 30
## GCATGA GCATGC GCATGG GCATGT GCATTA GCATTC GCATTG GCATTT GCCAAA GCCAAC
## [1,] 5443 3249 3468 5893 6166 4784 7311 10017 9181 3653
## [2,] 3656 2175 2316 3888 4035 3159 4159 6296 5861 2522
## [3,] 4344 2621 2814 5077 4897 4024 5150 7419 7197 2980
## [4,] 3266 2109 2229 3693 3818 2960 3986 5908 5828 2241
## [5,] 4915 2885 3041 5351 5438 4288 5668 8718 8155 3225
## [6,] 27 12 24 25 22 22 24 60 37 13
## GCCAAG GCCAAT GCCACA GCCACC GCCACG GCCACT GCCAGA GCCAGC GCCAGG GCCAGT
## [1,] 4712 5385 4130 3057 1923 3694 3193 1822 1412 2131
## [2,] 3121 3501 2829 2184 1348 2332 2046 1186 929 1350
## [3,] 4156 4072 3251 2432 1629 2751 2504 1432 1115 1707
## [4,] 2999 3107 2456 1976 1259 2162 1919 1186 880 1311
## [5,] 4195 4526 3623 2747 1750 3115 2819 1525 1228 1832
## [6,] 22 34 13 13 4 20 20 6 10 7
## GCCATA GCCATC GCCATG GCCATT GCCCAA GCCCAC GCCCAG GCCCAT GCCCCA GCCCCC
## [1,] 3967 3872 4344 6397 4062 1780 1272 3733 1433 580
## [2,] 2791 2621 2897 4310 2657 1237 882 2478 1077 466
## [3,] 3276 3287 3355 5048 3640 1436 1065 2849 1197 496
## [4,] 2611 2491 2669 3976 2534 1182 830 2218 900 419
## [5,] 3654 3477 4004 5703 3788 1568 1160 3380 1287 526
## [6,] 29 17 20 28 28 12 11 18 21 15
## GCCCCG GCCCCT GCCCGA GCCCGC GCCCGG GCCCGT GCCCTA GCCCTC GCCCTG GCCCTT
## [1,] 468 1008 946 520 618 887 1733 1490 1350 2430
## [2,] 343 794 691 408 433 596 1278 1043 866 1716
## [3,] 450 842 911 454 451 710 1257 1284 1078 2006
## [4,] 315 691 714 336 371 523 1042 1023 842 1559
## [5,] 469 944 991 526 599 847 1457 1390 1134 2172
## [6,] 17 27 17 9 12 12 12 14 16 27
## GCCGAA GCCGAC GCCGAG GCCGAT GCCGCA GCCGCC GCCGCG GCCGCT GCCGGA GCCGGC
## [1,] 2349 1412 1984 2041 1492 1844 765 1580 2466 1124
## [2,] 1485 1001 1364 1369 1049 1207 569 1125 1668 763
## [3,] 1706 1198 1600 1571 1266 1511 632 1271 2005 957
## [4,] 1613 884 1336 1242 1067 1137 503 1000 1603 617
## [5,] 1912 1303 1873 1743 1410 1610 683 1460 2384 978
## [6,] 25 10 15 7 9 9 8 14 16 7
## GCCGGG GCCGGT GCCGTA GCCGTC GCCGTG GCCGTT GCCTAA GCCTAC GCCTAG GCCTAT
## [1,] 791 1852 1464 1895 1711 2648 3858 1844 1954 3012
## [2,] 575 1186 997 1283 1120 1665 2564 1265 1327 2024
## [3,] 718 1429 1254 1583 1503 2158 2990 1399 1514 2342
## [4,] 505 1143 954 1170 1048 1638 2375 1188 1235 1783
## [5,] 775 1707 1231 1613 1550 2516 3845 1691 1766 2770
## [6,] 10 8 15 4 10 15 23 12 14 26
## GCCTCA GCCTCC GCCTCG GCCTCT GCCTGA GCCTGC GCCTGG GCCTGT GCCTTA GCCTTC
## [1,] 3504 2906 1801 4970 2877 1670 1500 2077 3222 3975
## [2,] 2375 2038 1101 2935 1955 1183 997 1429 2302 2634
## [3,] 3109 2356 1479 3433 2375 1445 1138 1744 2646 2994
## [4,] 2133 1916 1063 2746 1792 1100 902 1293 2060 2560
## [5,] 3326 2582 1561 3887 2718 1520 1342 1980 2929 3473
## [6,] 24 19 6 18 10 9 12 15 11 19
## GCCTTG GCCTTT GCGAAA GCGAAC GCGAAG GCGAAT GCGACA GCGACC GCGACG GCGACT
## [1,] 3998 5944 3832 1493 2805 2799 2013 1126 1673 1803
## [2,] 2707 4077 2568 982 1932 1840 1381 775 1064 1239
## [3,] 3223 4964 3120 1269 2256 2242 1616 957 1404 1502
## [4,] 2502 3753 2461 948 1706 1694 1332 815 968 1217
## [5,] 3714 5449 3525 1301 2499 2464 1825 1032 1418 1905
## [6,] 22 40 32 18 17 28 8 10 5 8
## GCGAGA GCGAGC GCGAGG GCGAGT GCGATA GCGATC GCGATG GCGATT GCGCAA GCGCAC
## [1,] 3158 1373 1733 2210 2287 1983 2762 3480 1502 610
## [2,] 2119 890 1128 1440 1482 1302 1820 2178 1003 408
## [3,] 2676 1101 1381 1730 1833 1799 2288 2670 1251 484
## [4,] 2047 874 1264 1380 1505 1364 1689 2116 1042 376
## [5,] 2887 1266 1540 1893 2016 1761 2529 3103 1369 537
## [6,] 17 10 9 8 17 16 14 18 8 4
## GCGCAG GCGCAT GCGCCA GCGCCC GCGCCG GCGCCT GCGCGA GCGCGC GCGCGG GCGCGT
## [1,] 1014 1239 1194 295 927 956 564 250 434 848
## [2,] 616 803 811 264 612 693 415 178 312 504
## [3,] 790 946 975 271 762 799 493 238 377 628
## [4,] 661 742 747 230 566 590 388 172 256 478
## [5,] 897 1101 1095 280 825 875 540 229 364 694
## [6,] 10 7 9 9 3 10 8 4 3 5
## GCGCTA GCGCTC GCGCTG GCGCTT GCGGAA GCGGAC GCGGAG GCGGAT GCGGCA GCGGCC
## [1,] 870 777 937 1680 2659 836 2434 2261 1302 784
## [2,] 569 561 614 1089 1699 571 1462 1521 858 561
## [3,] 705 681 733 1344 2033 743 2078 1840 1097 579
## [4,] 537 527 602 989 1591 569 1442 1510 838 475
## [5,] 722 733 805 1492 2276 800 2088 2086 1190 673
## [6,] 9 8 6 9 22 17 12 28 12 6
## GCGGCG GCGGCT GCGGGA GCGGGC GCGGGG GCGGGT GCGGTA GCGGTC GCGGTG GCGGTT
## [1,] 1876 1811 1740 444 517 1298 1475 1108 2266 3320
## [2,] 1116 1267 1127 371 414 918 1050 702 1461 2070
## [3,] 1513 1428 1390 410 483 1013 1334 900 2045 2522
## [4,] 1172 1212 1081 331 354 784 1034 720 1448 2156
## [5,] 1544 1562 1610 480 478 1254 1452 942 2141 3066
## [6,] 6 12 19 8 10 16 21 7 14 15
## GCGTAA GCGTAC GCGTAG GCGTAT GCGTCA GCGTCC GCGTCG GCGTCT GCGTGA GCGTGC
## [1,] 2169 1059 1411 2023 1892 1028 1418 2280 2081 889
## [2,] 1464 652 946 1270 1174 725 898 1435 1228 562
## [3,] 1785 886 1115 1505 1490 852 1114 1758 1540 818
## [4,] 1454 667 895 1184 1135 713 843 1442 1218 525
## [5,] 1965 936 1210 1778 1663 957 1203 2031 1840 762
## [6,] 19 5 14 18 5 10 4 10 9 5
## GCGTGG GCGTGT GCGTTA GCGTTC GCGTTG GCGTTT GCTAAA GCTAAC GCTAAG GCTAAT
## [1,] 1565 1912 2140 1668 2563 4679 8724 4477 4679 6754
## [2,] 989 1222 1273 1059 1583 2775 5699 2544 3159 4299
## [3,] 1172 1551 1600 1380 2093 3620 6406 3141 3722 5108
## [4,] 928 1261 1261 1062 1594 2844 5442 2471 3239 4172
## [5,] 1336 1675 1882 1552 2292 4131 7641 3380 4258 5623
## [6,] 9 4 11 18 7 14 41 20 24 36
## GCTACA GCTACC GCTACG GCTACT GCTAGA GCTAGC GCTAGG GCTAGT GCTATA GCTATC
## [1,] 4866 2102 1728 4404 4509 2582 2365 3535 5424 3485
## [2,] 3184 1523 1151 2969 2995 1627 1670 2218 3464 2282
## [3,] 3877 1805 1358 3417 3735 1965 1889 2813 4299 2813
## [4,] 3431 1420 1059 2749 2856 1693 1535 2169 3214 2146
## [5,] 4839 1974 1495 3891 4039 2207 2066 3062 4642 3042
## [6,] 33 17 12 28 21 5 19 20 40 21
## GCTATG GCTATT GCTCAA GCTCAC GCTCAG GCTCAT GCTCCA GCTCCC GCTCCG GCTCCT
## [1,] 4387 6415 7071 3195 3750 5586 5418 1967 2044 4734
## [2,] 2863 3888 4377 2042 2360 3697 3423 1386 1439 2967
## [3,] 3587 4502 5373 2536 2962 4359 4296 1612 1706 3688
## [4,] 2642 3785 4415 2069 2384 3545 3395 1285 1356 2845
## [5,] 3901 5217 6033 2787 3251 4961 4636 1706 1882 4116
## [6,] 18 52 34 14 15 18 28 20 15 33
## GCTCGA GCTCGC GCTCGG GCTCGT GCTCTA GCTCTC GCTCTG GCTCTT GCTGAA GCTGAC
## [1,] 3356 1332 1891 3167 4174 5321 4879 8259 7137 2662
## [2,] 2083 1044 1230 1835 2922 3421 2998 5438 4297 1719
## [3,] 2717 1165 1622 2309 3402 4656 3785 6449 5493 2283
## [4,] 2127 928 1230 1819 2751 3448 2849 4996 4410 1790
## [5,] 2879 1272 1698 2651 4001 4933 4111 7426 6282 2436
## [6,] 25 11 19 20 38 20 12 35 21 8
## GCTGAG GCTGAT GCTGCA GCTGCC GCTGCG GCTGCT GCTGGA GCTGGC GCTGGG GCTGGT
## [1,] 4711 6429 5928 2290 1886 6330 4405 1680 1646 4101
## [2,] 3190 4035 3574 1543 1289 3812 2904 1093 1195 2548
## [3,] 3926 4963 4687 1825 1558 4838 3683 1413 1439 3431
## [4,] 3083 3866 3606 1436 1193 3701 2775 1180 1028 2608
## [5,] 4340 5702 5092 2078 1677 5447 4026 1589 1545 3634
## [6,] 13 15 13 8 9 27 18 7 13 14
## GCTGTA GCTGTC GCTGTG GCTGTT GCTTAA GCTTAC GCTTAG GCTTAT GCTTCA GCTTCC
## [1,] 3344 2589 3504 6070 6978 4443 4431 7397 9581 6068
## [2,] 2059 1671 2210 3762 4521 2838 2856 4833 6163 3901
## [3,] 2550 2058 2767 4559 5501 3309 3426 5723 7583 4636
## [4,] 2068 1696 2070 3559 4252 2650 2621 4519 5922 3768
## [5,] 2914 2348 3182 5265 6410 3827 3879 6624 8698 5331
## [6,] 15 15 9 31 12 18 17 29 31 21
## GCTTCG GCTTCT GCTTGA GCTTGC GCTTGG GCTTGT GCTTTA GCTTTC GCTTTG GCTTTT
## [1,] 3480 13337 7889 3990 4812 7523 8196 8399 10480 13779
## [2,] 2214 7801 5061 2668 3251 4814 5394 5373 6593 8699
## [3,] 2883 9531 6408 3239 3975 5867 6250 6690 7878 10314
## [4,] 2178 8194 5037 2488 3406 4703 5093 5065 6319 8360
## [5,] 3299 11298 7357 3602 5039 6817 7447 7582 9481 12194
## [6,] 17 49 31 14 15 23 34 44 28 70
## GGAAAA GGAAAC GGAAAG GGAAAT GGAACA GGAACC GGAACG GGAACT GGAAGA GGAAGC
## [1,] 16753 9000 8731 11100 7478 4110 2206 5964 13624 6458
## [2,] 11174 5929 5661 7109 4754 2770 1545 3724 8708 3911
## [3,] 13536 7141 7181 8624 6112 3271 1924 4700 10923 4678
## [4,] 10403 5704 5320 6813 4618 2620 1510 3832 8424 3667
## [5,] 15299 8155 7909 9968 6681 3672 2127 5264 12491 5268
## [6,] 97 31 44 76 35 33 20 44 62 19
## GGAAGG GGAAGT GGAATA GGAATC GGAATG GGAATT GGACAA GGACAC GGACAG GGACAT
## [1,] 4857 6694 6708 7158 6073 8733 6510 2794 2723 4723
## [2,] 3280 4327 4384 4557 4148 5759 4269 1807 1786 3152
## [3,] 4142 5245 5530 5668 4826 7102 5120 2156 2266 3899
## [4,] 3157 4084 4095 4452 3740 5408 4173 1703 1765 2930
## [5,] 4471 5886 5975 6476 5353 8000 5775 2481 2382 4303
## [6,] 33 33 72 58 41 89 31 10 15 24
## GGACCA GGACCC GGACCG GGACCT GGACGA GGACGC GGACGG GGACGT GGACTA GGACTC
## [1,] 4232 1528 1614 2579 2987 1013 1576 1896 3375 2901
## [2,] 2790 1073 1084 1800 1996 699 1075 1232 2214 1915
## [3,] 3402 1356 1237 2142 2397 903 1267 1472 2506 2321
## [4,] 2681 1019 1000 1789 1824 667 1081 1118 2086 1894
## [5,] 3775 1436 1424 2472 2696 923 1422 1585 2966 2631
## [6,] 22 20 12 26 19 7 10 12 20 26
## GGACTG GGACTT GGAGAA GGAGAC GGAGAG GGAGAT GGAGCA GGAGCC GGAGCG GGAGCT
## [1,] 2654 5068 13766 5193 7792 9809 4691 2430 1449 5656
## [2,] 1780 3384 8490 3348 5201 6346 2966 1576 886 3544
## [3,] 2045 4217 10629 4094 6569 8098 3527 1835 1145 4502
## [4,] 1670 3304 8152 3231 5038 6233 2934 1600 942 3522
## [5,] 2349 4946 11941 4650 7073 8877 4114 2113 1336 5082
## [6,] 13 24 35 14 26 29 27 25 10 24
## GGAGGA GGAGGC GGAGGG GGAGGT GGAGTA GGAGTC GGAGTG GGAGTT GGATAA GGATAC
## [1,] 9205 3064 2630 4500 4166 3150 3664 7058 7457 3848
## [2,] 5795 1946 1730 2978 2825 2126 2388 4573 4987 2685
## [3,] 7109 2440 2084 3959 3392 2645 2900 5792 5754 3218
## [4,] 5454 1852 1597 2922 2646 2230 2128 4357 4697 2480
## [5,] 7895 2744 2300 4274 3629 3353 3288 6464 6492 3663
## [6,] 33 16 22 22 31 16 22 35 56 35
## GGATAG GGATAT GGATCA GGATCC GGATCG GGATCT GGATGA GGATGC GGATGG GGATGT
## [1,] 3474 7720 7430 4163 2988 7100 7466 3355 4420 5117
## [2,] 2446 4990 4665 2892 2004 4414 4711 2225 2933 3494
## [3,] 2771 6017 6003 3609 2469 5499 5951 3007 3698 4217
## [4,] 2208 4759 4469 2654 1946 4310 4492 2333 2911 3316
## [5,] 3227 6892 6494 3897 2654 6630 6715 3268 4139 4670
## [6,] 39 55 53 63 33 46 42 24 34 19
## GGATTA GGATTC GGATTG GGATTT GGCAAA GGCAAC GGCAAG GGCAAT GGCACA GGCACC
## [1,] 7181 7139 7312 12572 6808 3356 3870 4310 2682 1385
## [2,] 4538 4660 4329 8496 4490 2099 2479 2850 1804 1056
## [3,] 5528 5519 5210 10016 5476 2629 3169 3534 2149 1222
## [4,] 4228 4589 4201 7823 4268 2059 2407 2745 1655 921
## [5,] 6125 6418 6180 11539 5994 2884 3378 4034 2419 1315
## [6,] 48 79 42 98 24 5 11 26 6 11
## GGCACG GGCACT GGCAGA GGCAGC GGCAGG GGCAGT GGCATA GGCATC GGCATG GGCATT
## [1,] 1108 2132 3639 2398 1605 2260 3346 2937 3105 4590
## [2,] 684 1433 2359 1496 1122 1553 2304 1951 2111 2981
## [3,] 844 1785 2904 1896 1288 1908 2584 2363 2693 3739
## [4,] 672 1259 2178 1452 1018 1330 2098 1905 2010 2807
## [5,] 977 1861 3349 2053 1485 2029 2880 2754 2900 4004
## [6,] 7 9 24 15 12 16 23 14 22 26
## GGCCAA GGCCAC GGCCAG GGCCAT GGCCCA GGCCCC GGCCCG GGCCCT GGCCGA GGCCGC
## [1,] 4201 2124 1740 3176 2752 528 664 1227 1496 735
## [2,] 2867 1476 1117 2223 1840 430 440 811 1139 521
## [3,] 3465 1650 1391 2573 2324 454 585 975 1226 626
## [4,] 2629 1331 1125 2028 1683 364 386 766 1075 492
## [5,] 3754 1887 1472 2975 2564 546 596 1057 1361 684
## [6,] 17 9 7 13 11 9 15 17 15 5
## GGCCGG GGCCGT GGCCTA GGCCTC GGCCTG GGCCTT GGCGAA GGCGAC GGCGAG GGCGAT
## [1,] 1001 1341 2157 1919 1583 3282 2752 1616 2106 2591
## [2,] 760 868 1487 1320 1086 2047 1840 1161 1408 1784
## [3,] 893 1066 1707 1824 1288 2569 2350 1441 1947 2218
## [4,] 671 777 1386 1215 995 2091 1769 1213 1431 1684
## [5,] 1078 1190 1899 1794 1523 2789 2494 1547 1953 2412
## [6,] 7 12 21 12 10 22 27 9 11 15
## GGCGCA GGCGCC GGCGCG GGCGCT GGCGGA GGCGGC GGCGGG GGCGGT GGCGTA GGCGTC
## [1,] 1014 842 583 991 2536 1952 1197 2105 1378 1466
## [2,] 687 538 421 655 1580 1224 842 1370 941 962
## [3,] 832 694 509 841 2058 1504 1005 1876 1102 1203
## [4,] 701 541 354 619 1448 1202 807 1387 869 957
## [5,] 976 803 538 911 2131 1563 1122 1993 1189 1358
## [6,] 9 4 8 10 20 9 5 16 23 5
## GGCGTG GGCGTT GGCTAA GGCTAC GGCTAG GGCTAT GGCTCA GGCTCC GGCTCG GGCTCT
## [1,] 1429 2401 4428 2443 2065 3718 3744 2444 1845 4085
## [2,] 883 1441 2887 1676 1532 2250 2376 1639 1233 2658
## [3,] 1074 1916 3384 1977 1787 2750 2946 1942 1587 3180
## [4,] 821 1525 2835 1782 1416 2188 2378 1583 1164 2551
## [5,] 1141 2093 3804 2337 1911 3011 3302 2065 1682 3760
## [6,] 9 7 24 15 16 28 20 27 25 25
## GGCTGA GGCTGC GGCTGG GGCTGT GGCTTA GGCTTC GGCTTG GGCTTT GGGAAA GGGAAC
## [1,] 3865 3036 2058 2714 4083 5077 4430 7510 8785 3318
## [2,] 2573 1947 1420 1781 2755 3195 2923 4835 5590 2181
## [3,] 3142 2365 1735 2037 3210 3931 3518 5885 6948 2729
## [4,] 2520 1843 1314 1694 2483 3073 2819 4618 5442 2220
## [5,] 3438 2656 1894 2396 3700 4622 4070 6812 7993 3074
## [6,] 19 13 10 16 17 18 17 36 43 23
## GGGAAG GGGAAT GGGACA GGGACC GGGACG GGGACT GGGAGA GGGAGC GGGAGG GGGAGT
## [1,] 5767 5102 3439 1667 1499 2621 5943 1965 2789 2809
## [2,] 3764 3386 2194 1091 1029 1735 3521 1291 1793 1888
## [3,] 4596 4136 2654 1410 1155 2037 4488 1623 2225 2207
## [4,] 3513 3288 2199 1066 919 1653 3475 1306 1692 1766
## [5,] 5197 4683 2998 1475 1288 2338 5047 1903 2632 2428
## [6,] 42 40 16 15 9 21 24 18 21 27
## GGGATA GGGATC GGGATG GGGATT GGGCAA GGGCAC GGGCAG GGGCAT GGGCCA GGGCCC
## [1,] 3772 3535 3669 5771 2757 1032 1479 2187 1944 656
## [2,] 2491 2044 2287 3810 1885 762 1009 1530 1262 450
## [3,] 2926 2837 3167 4794 2292 877 1185 1791 1474 564
## [4,] 2209 2116 2214 3733 1774 667 853 1347 1211 399
## [5,] 3426 3063 3462 5293 2522 956 1289 1925 1694 615
## [6,] 49 42 27 47 16 6 23 25 13 12
## GGGCCG GGGCCT GGGCGA GGGCGC GGGCGG GGGCGT GGGCTA GGGCTC GGGCTG GGGCTT
## [1,] 806 1867 880 311 641 797 1842 1569 1591 3887
## [2,] 598 1256 730 252 530 593 1294 1140 1104 2491
## [3,] 676 1510 990 281 644 649 1485 1330 1317 3240
## [4,] 549 1157 640 214 414 513 1176 1094 1111 2355
## [5,] 778 1625 849 320 600 739 1710 1534 1465 3530
## [6,] 16 17 14 7 11 14 19 21 13 32
## GGGGAA GGGGAC GGGGAG GGGGAT GGGGCA GGGGCC GGGGCG GGGGCT GGGGGA GGGGGC
## [1,] 4181 1557 2235 2805 1341 589 418 1203 1808 609
## [2,] 2716 999 1519 1819 957 414 367 857 1126 510
## [3,] 3374 1237 1914 2289 1110 483 415 988 1441 505
## [4,] 2647 937 1566 1757 866 366 283 797 1208 402
## [5,] 3827 1359 2107 2508 1157 510 409 1079 1631 555
## [6,] 39 11 24 43 22 11 14 28 38 17
## GGGGGG GGGGGT GGGGTA GGGGTC GGGGTG GGGGTT GGGTAA GGGTAC GGGTAG GGGTAT
## [1,] 875 1242 1627 1326 1277 3261 3918 1704 1746 4052
## [2,] 690 857 1095 872 957 2188 2592 1166 1248 2215
## [3,] 657 1027 1338 1140 1151 2572 3111 1363 1455 2782
## [4,] 517 843 1073 892 963 1911 2585 1110 1156 2186
## [5,] 753 1215 1564 1345 1180 2828 3662 1521 1680 3073
## [6,] 47 18 27 25 19 33 29 15 23 28
## GGGTCA GGGTCC GGGTCG GGGTCT GGGTGA GGGTGC GGGTGG GGGTGT GGGTTA GGGTTC
## [1,] 3124 1461 1695 2760 2968 1156 2103 2286 4179 3813
## [2,] 2038 1123 1164 1884 1943 791 1439 1562 2885 2579
## [3,] 2572 1495 1436 2330 2459 956 1759 1904 3339 2920
## [4,] 1919 1000 1248 1866 1793 769 1369 1478 2552 2425
## [5,] 2918 1516 1663 2696 2629 1101 1902 2194 3751 3438
## [6,] 17 19 19 23 22 14 15 17 31 48
## GGGTTG GGGTTT GGTAAA GGTAAC GGTAAG GGTAAT GGTACA GGTACC GGTACG GGTACT
## [1,] 3852 11015 9413 4491 5202 6896 4382 2103 1785 3692
## [2,] 2524 7206 6177 2842 3282 4450 2721 1448 1204 2319
## [3,] 3048 8648 7316 3527 4088 5428 3410 1660 1478 2826
## [4,] 2405 6591 5812 2602 3178 4210 2676 1308 1155 2255
## [5,] 3473 9881 8490 4031 4629 6176 3864 1846 1543 3318
## [6,] 26 47 63 22 22 32 25 11 10 26
## GGTAGA GGTAGC GGTAGG GGTAGT GGTATA GGTATC GGTATG GGTATT GGTCAA GGTCAC
## [1,] 4776 2244 2106 3371 6594 3847 4880 6317 6676 3036
## [2,] 3097 1470 1509 2179 3759 2432 3240 4258 4236 2014
## [3,] 3674 1689 1683 2593 4447 3146 4102 5011 5219 2478
## [4,] 2879 1348 1387 2033 3634 2375 3082 3769 3952 1880
## [5,] 4261 1941 1941 3025 5378 3463 4538 5619 5895 2787
## [6,] 40 17 19 18 35 37 22 55 25 12
## GGTCAG GGTCAT GGTCCA GGTCCC GGTCCG GGTCCT GGTCGA GGTCGC GGTCGG GGTCGT
## [1,] 3092 4807 4126 1653 1397 2799 3567 1120 1877 2357
## [2,] 2028 3163 2759 1092 1018 2051 2485 726 1258 1567
## [3,] 2417 3870 3179 1507 1170 2322 2922 951 1497 1929
## [4,] 1761 2827 2472 1113 950 1811 2643 725 1237 1508
## [5,] 2641 4337 3646 1483 1325 2691 3368 1100 1741 2124
## [6,] 18 19 28 15 16 26 18 7 12 15
## GGTCTA GGTCTC GGTCTG GGTCTT GGTGAA GGTGAC GGTGAG GGTGAT GGTGCA GGTGCC
## [1,] 3716 3958 3109 5947 8506 3514 4792 7069 3391 1441
## [2,] 2575 2568 1872 4016 5598 2199 2974 4744 2244 987
## [3,] 3153 3172 2404 4794 6530 2889 3719 5765 2958 1229
## [4,] 2416 2438 1953 3875 5211 2216 2940 4469 2166 920
## [5,] 3283 3587 2814 5662 7311 3033 4243 6401 3074 1363
## [6,] 23 17 16 34 32 10 13 24 11 13
## GGTGCG GGTGCT GGTGGA GGTGGC GGTGGG GGTGGT GGTGTA GGTGTC GGTGTG GGTGTT
## [1,] 1221 3327 6373 3104 2908 6444 4103 3023 3982 6823
## [2,] 783 2116 4210 2052 1885 4231 2703 2145 2679 4261
## [3,] 967 2714 5301 2642 2451 5583 3093 2499 3096 5327
## [4,] 759 2040 4201 2026 1921 4301 2615 2043 2608 4067
## [5,] 1119 3123 5886 2845 2715 6080 3725 2853 3680 6192
## [6,] 8 19 38 8 14 18 21 13 12 23
## GGTTAA GGTTAC GGTTAG GGTTAT GGTTCA GGTTCC GGTTCG GGTTCT GGTTGA GGTTGC
## [1,] 8028 4697 5210 7792 7202 4074 3423 8642 7408 4019
## [2,] 5404 2869 3472 5053 4718 2763 2286 5114 4836 2563
## [3,] 6211 3500 3991 6031 5497 3278 2614 6038 5921 3118
## [4,] 4905 2698 3429 4862 4562 2653 2192 4932 4634 2698
## [5,] 7412 4113 5386 6968 6517 3786 3167 7201 6644 3676
## [6,] 42 19 18 47 54 31 36 51 34 9
## GGTTGG GGTTGT GGTTTA GGTTTC GGTTTG GGTTTT GTAAAA GTAAAC GTAAAG GTAAAT
## [1,] 5111 6810 11546 9850 11255 18791 16835 8877 8436 13219
## [2,] 3474 4391 7672 6337 7430 11460 11192 5826 5503 8639
## [3,] 4070 5233 8843 7726 8836 13891 13024 6713 6540 9758
## [4,] 3171 4224 7282 6132 7065 10968 10267 5471 5261 7844
## [5,] 4876 5881 10556 8843 10357 16353 15377 7697 7427 11416
## [6,] 27 22 56 39 32 73 104 42 52 63
## GTAACA GTAACC GTAACG GTAACT GTAAGA GTAAGC GTAAGG GTAAGT GTAATA GTAATC
## [1,] 8922 4499 3198 6902 9124 4300 3541 7097 9790 6785
## [2,] 5610 2993 1964 4544 5813 2815 2460 4622 6478 4423
## [3,] 6710 3513 2490 5313 6755 3484 2931 5444 7697 5481
## [4,] 5444 2787 1835 4140 5348 2598 2177 4353 5943 4168
## [5,] 7801 4005 2738 6268 7766 3788 3109 6279 8731 6092
## [6,] 22 26 26 38 36 13 20 20 61 28
## GTAATG GTAATT GTACAA GTACAC GTACAG GTACAT GTACCA GTACCC GTACCG GTACCT
## [1,] 7678 12039 7534 3991 3048 6809 4268 1776 1695 3992
## [2,] 4932 7751 4972 2469 1856 4360 2937 1187 1072 2773
## [3,] 5953 9045 5786 2953 2377 5434 3527 1424 1276 3221
## [4,] 4693 7229 4710 2483 1852 4122 2751 1140 1061 2545
## [5,] 6656 10660 6596 3421 2653 6081 3850 1564 1482 3544
## [6,] 41 61 34 10 21 42 32 20 13 19
## GTACGA GTACGC GTACGG GTACGT GTACTA GTACTC GTACTG GTACTT GTAGAA GTAGAC
## [1,] 2585 1122 1579 3159 4687 3736 3073 6863 8846 3783
## [2,] 1687 674 1063 1956 2983 2454 1955 4425 5789 2399
## [3,] 2011 871 1327 2337 3801 3027 2376 5269 7006 3009
## [4,] 1621 679 1024 1795 2822 2387 1925 4383 5511 2376
## [5,] 2227 953 1481 2658 4174 3435 2788 5968 7781 3332
## [6,] 20 3 11 11 22 22 18 33 41 28
## GTAGAG GTAGAT GTAGCA GTAGCC GTAGCG GTAGCT GTAGGA GTAGGC GTAGGG GTAGGT
## [1,] 6132 7446 4564 2445 1324 5236 4015 1797 1858 3312
## [2,] 3915 5016 2893 1661 900 3388 2795 1289 1238 2268
## [3,] 4668 5849 3430 1943 1132 3980 3486 1469 1524 2637
## [4,] 3631 4701 2616 1592 907 3200 2512 1175 1254 2057
## [5,] 5432 6657 3863 2166 1207 4663 3564 1648 1715 3005
## [6,] 30 38 27 19 10 26 39 9 22 30
## GTAGTA GTAGTC GTAGTG GTAGTT GTATAA GTATAC GTATAG GTATAT GTATCA GTATCC
## [1,] 6136 3569 4286 7417 11316 5172 5239 13941 7625 3979
## [2,] 4000 2303 2816 4908 6661 3272 3496 8803 4844 2551
## [3,] 4808 2657 3218 5798 7812 3982 3981 10374 6127 3214
## [4,] 3718 2077 2646 4542 6647 3117 3258 8177 4567 2439
## [5,] 5463 3087 3897 6553 9976 4647 4593 12150 6851 3770
## [6,] 36 13 14 34 48 24 32 48 37 44
## GTATCG GTATCT GTATGA GTATGC GTATGG GTATGT GTATTA GTATTC GTATTG GTATTT
## [1,] 2551 7419 7565 3711 4286 8183 8798 5794 7303 14138
## [2,] 1635 4881 4999 2473 2802 5212 5706 3980 4689 9422
## [3,] 1957 5961 6177 2941 3389 6084 6518 4735 5427 10745
## [4,] 1516 4686 4726 2405 2649 4852 5231 3622 4392 8532
## [5,] 2180 6667 7583 3353 3977 7149 7791 5183 6744 12621
## [6,] 23 48 31 12 31 32 49 48 44 107
## GTCAAA GTCAAC GTCAAG GTCAAT GTCACA GTCACC GTCACG GTCACT GTCAGA GTCAGC
## [1,] 12873 5918 6704 8016 5953 3636 2255 5283 4915 2891
## [2,] 7797 3872 4314 5338 3755 2361 1553 3254 3164 1772
## [3,] 9514 4569 5239 6214 4435 2933 1838 3986 3915 2254
## [4,] 7819 3609 4133 5073 3511 2199 1436 3207 3165 1710
## [5,] 10939 5296 5726 7242 5149 3086 2047 4449 4323 2394
## [6,] 44 24 22 39 13 21 4 17 27 9
## GTCAGG GTCAGT GTCATA GTCATC GTCATG GTCATT GTCCAA GTCCAC GTCCAG GTCCAT
## [1,] 2461 3370 6761 6216 5601 8197 6689 3527 2810 5679
## [2,] 1587 2213 4187 4152 3689 5669 4314 2336 1799 3703
## [3,] 1923 2676 4932 5105 4585 6469 5145 2790 2229 4249
## [4,] 1510 2044 4137 3925 3623 4921 3862 2104 1674 3632
## [5,] 2065 3011 5781 5528 5530 7442 5709 3019 2548 4842
## [6,] 17 13 24 16 10 37 36 18 16 35
## GTCCCA GTCCCC GTCCCG GTCCCT GTCCGA GTCCGC GTCCGG GTCCGT GTCCTA GTCCTC
## [1,] 3492 1625 1279 2679 2083 823 1360 1753 2949 3686
## [2,] 2376 1059 885 1891 1349 646 997 1260 2043 2511
## [3,] 3036 1179 1092 2308 1884 706 1065 1311 2339 3138
## [4,] 2205 1023 828 1827 1273 582 915 1175 1861 2428
## [5,] 3047 1367 1151 2527 1723 844 1243 1666 2625 3456
## [6,] 29 11 13 16 21 15 9 9 24 14
## GTCCTG GTCCTT GTCGAA GTCGAC GTCGAG GTCGAT GTCGCA GTCGCC GTCGCG GTCGCT
## [1,] 2633 5159 4306 2370 3910 4100 1930 1671 814 2254
## [2,] 1793 3559 2867 1615 2695 2803 1219 1169 499 1373
## [3,] 2180 4031 3356 1922 3245 3361 1583 1356 664 1688
## [4,] 1679 3242 2723 1562 2901 2727 1178 1053 550 1363
## [5,] 2516 4630 4138 2239 3733 3732 1971 1499 762 1974
## [6,] 21 24 24 11 16 28 12 8 3 7
## GTCGGA GTCGGC GTCGGG GTCGGT GTCGTA GTCGTC GTCGTG GTCGTT GTCTAA GTCTAC
## [1,] 3070 1405 1390 2476 2710 3462 2585 4568 6662 3814
## [2,] 1983 1058 944 1533 1698 2345 1644 3010 4142 2401
## [3,] 2411 1227 1120 1904 2161 2824 2015 3732 5034 2962
## [4,] 2037 933 883 1529 1697 2280 1590 2923 3894 2256
## [5,] 2717 1271 1264 2210 2381 3320 2244 4180 5424 3396
## [6,] 19 15 6 12 14 6 11 20 27 15
## GTCTAG GTCTAT GTCTCA GTCTCC GTCTCG GTCTCT GTCTGA GTCTGC GTCTGG GTCTGT
## [1,] 3687 6020 6467 5094 2859 9856 5310 2927 3029 4313
## [2,] 2399 3975 4257 3356 1906 6176 3420 1846 1929 2803
## [3,] 2991 4575 5086 4161 2342 7592 4175 2421 2367 3517
## [4,] 2351 3789 4061 3181 1792 5808 3223 1928 1845 2777
## [5,] 3235 5265 5938 4537 2582 8750 4817 2714 2688 4025
## [6,] 17 34 24 10 22 31 18 10 10 20
## GTCTTA GTCTTC GTCTTG GTCTTT GTGAAA GTGAAC GTGAAG GTGAAT GTGACA GTGACC
## [1,] 6134 9074 7336 12223 13274 5425 9931 9364 6260 2892
## [2,] 4069 5885 5028 8128 8544 3606 6265 6080 3757 1886
## [3,] 4864 7317 5987 9773 9916 4154 7563 7255 4488 2520
## [4,] 3848 5775 4616 7987 8025 3375 6061 5707 3603 1973
## [5,] 5656 8438 6759 11380 11977 4614 8586 8462 5215 2750
## [6,] 20 30 22 61 56 24 23 41 13 13
## GTGACG GTGACT GTGAGA GTGAGC GTGAGG GTGAGT GTGATA GTGATC GTGATG GTGATT
## [1,] 2758 5109 7903 3153 3771 5562 7867 5895 8593 10662
## [2,] 1707 3241 5016 2065 2523 3530 4865 3877 5692 7114
## [3,] 2102 3894 6242 2509 3119 4270 5763 4885 6937 8341
## [4,] 1811 3126 4813 1958 2481 3413 4537 3829 5418 6405
## [5,] 2450 4342 6980 2772 3557 5231 6745 5183 8017 9697
## [6,] 9 14 18 16 18 17 33 26 22 46
## GTGCAA GTGCAC GTGCAG GTGCAT GTGCCA GTGCCC GTGCCG GTGCCT GTGCGA GTGCGC
## [1,] 5020 2164 3274 4478 2782 1170 1091 2500 1512 582
## [2,] 3291 1335 2102 2913 1886 710 737 1712 1033 415
## [3,] 3942 1658 2733 3859 2209 879 892 1959 1226 489
## [4,] 3005 1315 2025 2831 1659 713 662 1493 1023 348
## [5,] 4572 1933 2951 3972 2540 1015 941 2300 1407 516
## [6,] 16 5 12 19 12 6 10 21 6 2
## GTGCGG GTGCGT GTGCTA GTGCTC GTGCTG GTGCTT GTGGAA GTGGAC GTGGAG GTGGAT
## [1,] 1093 1538 3016 2837 2902 5657 8226 3496 6644 6841
## [2,] 728 974 2076 1911 1848 3502 5458 2284 4219 4757
## [3,] 932 1211 2496 2398 2565 4392 6705 2823 5528 5508
## [4,] 672 944 1970 1807 1912 3381 5120 2203 4378 4408
## [5,] 1064 1383 2710 2616 2715 5020 7582 3124 6089 6224
## [6,] 15 12 16 18 9 26 48 18 25 40
## GTGGCA GTGGCC GTGGCG GTGGCT GTGGGA GTGGGC GTGGGG GTGGGT GTGGTA GTGGTC
## [1,] 4004 2096 2215 4615 4418 1810 2123 3370 4914 4009
## [2,] 2634 1392 1438 3024 2843 1252 1332 2287 3060 2607
## [3,] 3283 1663 1797 3728 3452 1500 1777 2838 3681 3244
## [4,] 2407 1338 1346 2922 2772 1158 1391 2049 2952 2548
## [5,] 3539 1892 1952 3978 4036 1654 2002 3238 4281 3662
## [6,] 11 5 7 19 21 10 17 17 28 10
## GTGGTG GTGGTT GTGTAA GTGTAC GTGTAG GTGTAT GTGTCA GTGTCC GTGTCG GTGTCT
## [1,] 6953 8043 7123 3833 4698 7947 5276 2671 2429 5851
## [2,] 4561 5177 4767 2504 3089 5029 3427 1787 1727 3834
## [3,] 5929 6110 5385 2943 3503 6041 4116 2085 2135 4768
## [4,] 4580 5018 4396 2383 3007 4935 3258 1615 1827 3628
## [5,] 6442 7115 6310 3511 4207 7612 4648 2401 2367 5306
## [6,] 15 26 21 14 15 32 26 13 10 17
## GTGTGA GTGTGC GTGTGG GTGTGT GTGTTA GTGTTC GTGTTG GTGTTT GTTAAA GTTAAC
## [1,] 6418 2667 4254 8298 7521 6135 9346 15182 14317 6391
## [2,] 4195 1769 2889 5304 4809 3960 5942 9609 9436 4368
## [3,] 5049 2122 3346 6320 5731 4926 6976 11252 10790 5066
## [4,] 3975 1624 2684 5085 4524 3799 5330 9164 8507 3994
## [5,] 5767 2470 3987 7456 6618 5589 7766 14283 12818 5990
## [6,] 23 5 13 8 12 24 19 25 38 20
## GTTAAG GTTAAT GTTACA GTTACC GTTACG GTTACT GTTAGA GTTAGC GTTAGG GTTAGT
## [1,] 7252 11335 8434 4641 2882 7585 7734 3830 4478 7159
## [2,] 4768 7362 5425 2922 1768 4870 4923 2503 3011 4589
## [3,] 5720 8641 6472 3352 2216 5944 5826 3044 3469 5398
## [4,] 4509 6853 5082 2727 1748 4748 4749 2362 2783 4471
## [5,] 6583 10189 7559 3860 2526 6747 7432 3473 3916 7186
## [6,] 30 54 29 15 21 37 30 19 13 16
## GTTATA GTTATC GTTATG GTTATT GTTCAA GTTCAC GTTCAG GTTCAT GTTCCA GTTCCC
## [1,] 11077 7282 8372 13273 10883 5359 5427 10202 7221 3227
## [2,] 7188 4785 5624 8943 7137 3540 3558 6476 4974 2240
## [3,] 8538 5697 6438 10246 8370 4131 4363 7564 5795 2653
## [4,] 6635 4408 5264 8158 6702 3250 3437 6140 4726 2235
## [5,] 9756 6382 7519 12265 9828 4727 4865 8969 6716 2989
## [6,] 43 35 36 83 64 20 19 59 53 26
## GTTCCG GTTCCT GTTCGA GTTCGC GTTCGG GTTCGT GTTCTA GTTCTC GTTCTG GTTCTT
## [1,] 2327 6871 4371 1563 2473 3963 7425 7750 6704 16311
## [2,] 1619 4447 2875 1122 1767 2561 4609 4962 4285 10326
## [3,] 1898 5450 3636 1170 2089 3054 5211 6078 5563 12195
## [4,] 1451 4268 2779 970 1648 2381 4443 4968 4210 9935
## [5,] 2158 6195 3998 1325 2362 3518 5963 7091 6307 14300
## [6,] 32 58 54 17 26 21 62 32 28 86
## GTTGAA GTTGAC GTTGAG GTTGAT GTTGCA GTTGCC GTTGCG GTTGCT GTTGGA GTTGGC
## [1,] 13077 5996 8315 13215 7656 3217 2677 7946 8707 3688
## [2,] 8426 3892 5439 8541 4970 2129 1647 4931 5755 2480
## [3,] 10236 4640 6309 10067 6186 2642 1907 5969 6715 2969
## [4,] 7915 3598 5023 8085 4848 2075 1716 4831 5249 2242
## [5,] 11841 5171 7094 11964 7174 2860 2266 7004 7764 3362
## [6,] 76 25 25 44 16 12 13 30 31 9
## GTTGGG GTTGGT GTTGTA GTTGTC GTTGTG GTTGTT GTTTAA GTTTAC GTTTAG GTTTAT
## [1,] 4376 9477 8660 6935 8449 16654 14741 8660 10408 16429
## [2,] 2930 5760 5729 4054 5629 10870 9638 5657 6932 10494
## [3,] 3493 6801 6658 4926 6673 12921 11151 6666 8022 12351
## [4,] 2779 5445 5253 3992 5171 9971 8958 5157 6505 9888
## [5,] 4195 7975 7587 5555 7500 15097 13409 7784 9424 14590
## [6,] 24 36 27 17 27 51 30 39 28 59
## GTTTCA GTTTCC GTTTCG GTTTCT GTTTGA GTTTGC GTTTGG GTTTGT GTTTTA GTTTTC
## [1,] 15144 9073 5674 19629 14933 7132 11540 15527 20703 17527
## [2,] 9659 5895 3609 12178 9959 4613 7572 10173 12930 11224
## [3,] 11569 7190 4443 14935 11746 5602 9116 12070 14877 13231
## [4,] 9146 5821 3479 11587 9444 4371 7141 9380 12001 10573
## [5,] 13467 8289 4978 17622 13884 6538 10622 13979 17847 15768
## [6,] 54 40 30 74 41 20 34 35 64 54
## GTTTTG GTTTTT TAAAAA TAAAAC TAAAAG TAAAAT TAAACA TAAACC TAAACG TAAACT
## [1,] 23015 31558 39398 20273 17467 32577 19772 15644 5754 15311
## [2,] 14537 20325 26863 13182 12025 22242 12042 7776 3705 9846
## [3,] 17355 23644 29694 14778 13853 24368 13927 9039 4412 11141
## [4,] 13749 18886 23975 12158 10657 19688 11442 8448 3496 9099
## [5,] 20796 28326 35694 17746 16503 29304 16168 10699 5199 13077
## [6,] 70 138 323 71 72 159 50 47 37 37
## TAAAGA TAAAGC TAAAGG TAAAGT TAAATA TAAATC TAAATG TAAATT TAACAA TAACAC
## [1,] 18774 8326 7377 13117 25100 14837 13831 26788 20132 7534
## [2,] 12226 5520 5048 8595 17022 9391 9152 17823 12774 4813
## [3,] 14377 6444 5849 9876 18701 10989 10391 19874 14657 5664
## [4,] 11464 5216 4481 8132 14927 8855 8311 15989 11874 4549
## [5,] 16550 7246 7040 11448 21979 12462 11969 23908 17285 6569
## [6,] 96 40 48 46 146 77 59 124 63 18
## TAACAG TAACAT TAACCA TAACCC TAACCG TAACCT TAACGA TAACGC TAACGG TAACGT
## [1,] 7135 14281 10862 4658 3869 7178 5092 2160 2928 4520
## [2,] 4463 9319 6928 2992 2716 4611 3487 1403 1905 2860
## [3,] 5373 10744 8088 3405 3087 5350 4044 1630 2415 3396
## [4,] 4366 8528 6700 2743 2470 4280 3200 1280 1850 2645
## [5,] 5804 12573 9532 3953 3764 6089 4586 1852 2586 3944
## [6,] 23 49 57 39 22 33 32 11 18 17
## TAACTA TAACTC TAACTG TAACTT TAAGAA TAAGAC TAAGAG TAAGAT TAAGCA TAAGCC
## [1,] 10687 8506 5817 13693 19931 6236 9810 13222 8911 3986
## [2,] 7325 5238 3563 9060 13064 4194 6284 8758 5362 2761
## [3,] 8146 6047 4605 10404 15145 4813 7573 9972 6270 3275
## [4,] 6506 4809 3368 8359 12734 4035 5713 8198 5057 2609
## [5,] 9677 6899 5040 12138 17922 5509 8342 11844 7146 3697
## [6,] 48 44 29 54 111 21 38 62 24 24
## TAAGCG TAAGCT TAAGGA TAAGGC TAAGGG TAAGGT TAAGTA TAAGTC TAAGTG TAAGTT
## [1,] 2186 8421 7761 3258 3282 6143 10178 5946 7042 13629
## [2,] 1461 5461 5396 2231 2268 4156 6851 3798 4439 8695
## [3,] 1830 6639 6295 2700 2704 5075 7687 4482 5106 10020
## [4,] 1435 5255 4908 2121 2214 3810 6342 3574 4130 8469
## [5,] 1957 7500 6877 2922 2902 5612 9510 4942 5785 12188
## [6,] 19 21 33 16 31 32 48 28 32 68
## TAATAA TAATAC TAATAG TAATAT TAATCA TAATCC TAATCG TAATCT TAATGA TAATGC
## [1,] 23993 8917 8632 22894 14761 7641 4617 13449 13832 6015
## [2,] 16045 5776 5970 15464 9618 4678 3055 8806 8957 3984
## [3,] 18328 6769 6778 16992 11179 5428 3816 10427 10762 4802
## [4,] 14202 5417 5523 13859 8962 4426 3007 8258 8336 3656
## [5,] 21097 7677 7580 20260 13023 6301 4357 12255 12185 5354
## [6,] 146 49 84 123 48 63 47 55 95 35
## TAATGG TAATGT TAATTA TAATTC TAATTG TAATTT TACAAA TACAAC TACAAG TACAAT
## [1,] 8512 13103 25421 11103 12922 30999 20845 8521 10136 12987
## [2,] 5545 8484 16191 7387 8321 20221 13691 5646 6725 8650
## [3,] 6552 9916 18387 8549 9653 23002 15849 6753 7964 9947
## [4,] 5159 7869 14824 6950 7594 18391 12855 5362 6072 7986
## [5,] 7532 11628 21565 9893 11341 27710 18958 7472 8884 11798
## [6,] 56 38 96 110 94 152 87 24 33 66
## TACACA TACACC TACACG TACACT TACAGA TACAGC TACAGG TACAGT TACATA TACATC
## [1,] 10548 4367 3048 6445 8149 3317 3273 5923 14074 7099
## [2,] 6292 2779 1930 4285 4881 2029 2077 3782 9084 4564
## [3,] 7616 3024 2321 5011 6396 2495 2570 4569 10701 5437
## [4,] 6342 2830 1871 4079 4827 2063 2106 3642 8386 4281
## [5,] 8834 3936 2638 5911 7337 2757 2894 5226 12531 6173
## [6,] 23 21 12 15 35 17 24 23 72 39
## TACATG TACATT TACCAA TACCAC TACCAG TACCAT TACCCA TACCCC TACCCG TACCCT
## [1,] 9352 13865 10944 4661 4005 8139 4192 1701 1622 3700
## [2,] 6022 8983 7244 3055 2619 5439 2770 1110 1148 2420
## [3,] 7496 10892 8455 3725 3426 6216 3138 1361 1285 2981
## [4,] 5652 8149 6870 2894 2515 4891 2475 1049 1031 2523
## [5,] 8164 12268 9845 4178 3608 7361 3541 1486 1485 3205
## [6,] 42 63 57 26 21 37 29 35 20 26
## TACCGA TACCGC TACCGG TACCGT TACCTA TACCTC TACCTG TACCTT TACGAA TACGAC
## [1,] 2794 1532 2276 2827 4739 4991 4584 8749 5289 2805
## [2,] 1859 1045 1419 1802 3278 3412 2963 5578 3484 1815
## [3,] 2201 1277 1828 2177 3554 3935 3792 6682 4037 2188
## [4,] 1796 1002 1350 1674 2945 3148 2931 5224 3219 1617
## [5,] 2500 1453 1999 2455 4427 4371 3936 7528 4953 2325
## [6,] 15 17 17 16 38 30 28 43 45 18
## TACGAG TACGAT TACGCA TACGCC TACGCG TACGCT TACGGA TACGGC TACGGG TACGGT
## [1,] 3378 4411 2374 1372 881 2081 2905 1461 1347 2921
## [2,] 2061 2820 1478 825 591 1308 1846 972 917 1958
## [3,] 2548 3669 1860 1054 720 1519 2316 1196 1166 2403
## [4,] 2156 2733 1376 859 564 1228 1928 961 795 1784
## [5,] 3000 3827 2059 1206 824 1797 2941 1257 1205 2836
## [6,] 18 27 10 18 11 7 24 21 25 17
## TACGTA TACGTC TACGTG TACGTT TACTAA TACTAC TACTAG TACTAT TACTCA TACTCC
## [1,] 4812 2281 2942 5071 10664 6227 5204 10023 7508 4073
## [2,] 3010 1505 1880 3045 7143 3947 3436 6667 5003 2773
## [3,] 3580 1791 2182 3736 8151 4893 4067 7590 5713 3441
## [4,] 2733 1414 1747 2963 6890 3615 3183 6095 5109 2689
## [5,] 4115 2101 2493 4412 9350 5383 4769 8949 6702 3696
## [6,] 26 17 12 28 78 33 30 47 33 30
## TACTCG TACTCT TACTGA TACTGC TACTGG TACTGT TACTTA TACTTC TACTTG TACTTT
## [1,] 3899 8943 6045 3722 3231 6130 10059 8608 9373 16867
## [2,] 2572 5836 3778 2182 2077 3820 6710 5608 6203 10545
## [3,] 3110 7110 4523 2592 2599 4646 7596 6613 7402 11829
## [4,] 2641 5436 3681 2138 1943 3747 6462 5323 5904 9799
## [5,] 3632 7972 5418 2975 2874 5470 9034 7355 8325 14496
## [6,] 17 37 33 21 18 30 56 66 36 81
## TAGAAA TAGAAC TAGAAG TAGAAT TAGACA TAGACC TAGACG TAGACT TAGAGA TAGAGC
## [1,] 19125 6680 10387 11556 7385 3826 2728 5635 13679 4370
## [2,] 12208 4523 6909 7881 4698 2554 1797 3696 8492 2812
## [3,] 14468 5484 8056 8797 5510 3018 2213 4717 10235 3416
## [4,] 11222 4503 6530 7052 4471 2445 1833 3658 8107 2631
## [5,] 16479 6522 9778 10211 6437 3323 2552 5123 11695 3910
## [6,] 152 49 45 112 38 23 10 27 43 27
## TAGAGG TAGAGT TAGATA TAGATC TAGATG TAGATT TAGCAA TAGCAC TAGCAG TAGCAT
## [1,] 5071 7645 11506 7250 8241 14161 8713 3200 4370 6790
## [2,] 3575 5004 7460 4905 5322 9604 5745 2038 2904 4619
## [3,] 4117 6187 8646 5691 6328 10772 6780 2469 3519 5244
## [4,] 3241 4846 6905 4450 5269 8973 5295 1844 2635 4064
## [5,] 4595 6970 10064 6204 7857 12846 7614 2759 3705 5846
## [6,] 26 38 92 54 39 82 43 12 27 34
## TAGCCA TAGCCC TAGCCG TAGCCT TAGCGA TAGCGC TAGCGG TAGCGT TAGCTA TAGCTC
## [1,] 4995 2086 1924 4171 2521 833 1490 2025 7177 5262
## [2,] 3335 1255 1249 2458 1705 600 1007 1209 4762 3505
## [3,] 3943 1448 1574 2911 1911 700 1238 1578 5298 4136
## [4,] 3293 1116 1346 2262 1578 470 971 1242 4275 3476
## [5,] 4464 1685 1752 3175 2342 707 1402 1680 6442 4632
## [6,] 28 27 12 19 16 5 16 5 43 36
## TAGCTG TAGCTT TAGGAA TAGGAC TAGGAG TAGGAT TAGGCA TAGGCC TAGGCG TAGGCT
## [1,] 5014 10229 7576 2830 4994 6365 3431 2051 1311 3808
## [2,] 3213 6352 5188 1985 3213 4403 2344 1491 934 2411
## [3,] 4100 7693 6321 2357 3770 5152 2821 1864 1020 2767
## [4,] 3188 6220 4534 1864 2939 4259 2286 1404 882 2382
## [5,] 4563 8769 6725 2708 4121 5814 3137 1924 1188 3201
## [6,] 21 42 61 22 34 70 20 20 11 19
## TAGGGA TAGGGC TAGGGG TAGGGT TAGGTA TAGGTC TAGGTG TAGGTT TAGTAA TAGTAC
## [1,] 4105 1653 1749 5307 4876 3300 4028 7753 11011 4676
## [2,] 2770 1136 1235 3593 3285 2214 2707 5308 7428 2971
## [3,] 3316 1232 1398 4404 3676 2541 3278 5924 8530 3847
## [4,] 2615 949 1113 3320 2981 1994 2546 4830 6581 2904
## [5,] 3821 1434 1568 4708 4374 2830 3607 7067 9929 4178
## [6,] 40 15 25 24 42 32 20 50 61 25
## TAGTAG TAGTAT TAGTCA TAGTCC TAGTCG TAGTCT TAGTGA TAGTGC TAGTGG TAGTGT
## [1,] 6597 9916 7847 3497 2775 6741 8277 2764 4958 7226
## [2,] 4397 6532 4354 2233 1917 4362 5369 1822 3281 4793
## [3,] 5019 7382 5051 2639 2147 5179 6130 2327 3791 5598
## [4,] 3939 6191 4431 2039 1688 3976 5107 1720 3010 4590
## [5,] 5794 8864 5846 3005 2389 5858 7370 2448 4335 7304
## [6,] 38 62 27 24 18 25 43 11 23 24
## TAGTTA TAGTTC TAGTTG TAGTTT TATAAA TATAAC TATAAG TATAAT TATACA TATACC
## [1,] 10786 6984 8811 18977 27601 11307 12214 22744 14128 6013
## [2,] 6999 4474 5652 12139 18500 7364 7231 14634 8935 3925
## [3,] 8254 5194 6572 13851 20591 8388 8606 16528 10499 4532
## [4,] 6499 4462 5368 11062 16535 6523 7066 13375 8414 3626
## [5,] 9601 6015 7711 16583 24679 9820 9967 19932 12620 5364
## [6,] 71 48 45 57 121 57 58 124 52 33
## TATACG TATACT TATAGA TATAGC TATAGG TATAGT TATATA TATATC TATATG TATATT
## [1,] 4101 10492 12717 5499 5109 11319 46008 12764 16901 28590
## [2,] 2570 6889 8373 3468 3530 7250 30624 8419 11203 18767
## [3,] 2997 8001 9661 4371 3906 8343 34134 9876 12872 20709
## [4,] 2365 6629 7798 3273 3081 6740 27536 7797 10285 16580
## [5,] 3529 9297 11099 4715 4616 9617 40907 11545 15165 25018
## [6,] 22 44 91 32 40 56 233 74 68 167
## TATCAA TATCAC TATCAG TATCAT TATCCA TATCCC TATCCG TATCCT TATCGA TATCGC
## [1,] 17340 7492 7558 15534 8975 3763 2916 6698 5644 2188
## [2,] 11471 4992 4616 10171 5824 2440 2067 4461 3628 1490
## [3,] 13431 6125 5884 12076 7044 2897 2337 5424 4345 1872
## [4,] 10597 4697 4477 9426 5439 2360 1896 4139 3492 1457
## [5,] 15559 6846 6666 14008 7691 3406 2785 6464 5128 2120
## [6,] 107 27 27 84 69 39 31 46 42 6
## TATCGG TATCGT TATCTA TATCTC TATCTG TATCTT TATGAA TATGAC TATGAG TATGAT
## [1,] 2670 4577 11433 10592 7416 17214 16227 6336 8285 16191
## [2,] 1782 3028 7624 6868 4579 11443 10655 4077 5341 10637
## [3,] 2155 3499 8871 8249 5922 13447 12381 4941 6142 12591
## [4,] 1623 2807 6985 6619 4404 10534 9606 4052 5176 9879
## [5,] 2439 4071 9904 9417 6504 15424 14628 6237 7582 14573
## [6,] 22 29 85 54 42 76 113 25 34 78
## TATGCA TATGCC TATGCG TATGCT TATGGA TATGGC TATGGG TATGGT TATGTA TATGTC
## [1,] 9265 3251 2420 7664 9544 4021 4481 9057 14281 6956
## [2,] 6125 2354 1560 4879 6446 2673 2963 5936 9251 4733
## [3,] 7015 2590 1832 5695 7454 3191 3513 6807 10771 5556
## [4,] 5553 2080 1457 4559 5889 2592 2702 5442 8434 4312
## [5,] 8294 2977 2196 6565 8815 3673 4147 7850 12241 6329
## [6,] 30 22 13 24 73 20 34 35 52 23
## TATGTG TATGTT TATTAA TATTAC TATTAG TATTAT TATTCA TATTCC TATTCG TATTCT
## [1,] 9620 18105 20354 9897 10192 23967 14516 6739 4681 13288
## [2,] 6160 12021 13938 6403 6722 15625 9492 4601 3101 9207
## [3,] 7203 13621 15381 7549 7779 17367 10820 5365 3827 10665
## [4,] 5858 11066 12419 5827 6067 14170 8486 4131 3077 8227
## [5,] 8641 16417 18327 8602 8965 21216 12294 5999 4419 12256
## [6,] 21 58 143 60 78 135 119 78 40 127
## TATTGA TATTGC TATTGG TATTGT TATTTA TATTTC TATTTG TATTTT TCAAAA TCAAAC
## [1,] 14583 6638 8947 14661 25551 15827 19682 43744 29036 15033
## [2,] 9461 4363 5847 9862 16915 10427 12459 29226 19251 10011
## [3,] 10802 5079 7091 11006 18377 11765 14353 32012 22501 11749
## [4,] 8761 4135 5466 9064 15026 9545 11578 25895 17886 9589
## [5,] 13018 5914 7950 13632 22295 14036 17024 39233 26303 13532
## [6,] 112 39 63 60 124 149 102 258 157 52
## TCAAAG TCAAAT TCAACA TCAACC TCAACG TCAACT TCAAGA TCAAGC TCAAGG TCAAGT
## [1,] 15908 23111 15797 7253 5542 11357 16789 8017 7072 11410
## [2,] 10073 14989 10248 4933 3351 7341 10633 5172 4685 7544
## [3,] 12205 17669 12066 5762 4364 8794 13077 6092 5528 9164
## [4,] 10042 14305 9684 4660 3544 6943 10448 5001 4300 7325
## [5,] 14659 20814 13922 6684 4811 9959 14893 7086 6312 10312
## [6,] 55 139 56 31 20 45 73 14 20 41
## TCAATA TCAATC TCAATG TCAATT TCACAA TCACAC TCACAG TCACAT TCACCA TCACCC
## [1,] 14152 12395 11856 17353 14015 6474 5998 11562 10091 2988
## [2,] 9434 8099 7553 11442 8992 4210 3797 7541 6808 2060
## [3,] 10917 9420 9011 13259 10740 4953 4785 9131 7995 2582
## [4,] 8611 7784 7245 10480 8493 4093 3685 7057 6257 1951
## [5,] 12823 10884 10538 15691 12261 5647 5260 10425 8907 2680
## [6,] 116 62 49 152 48 21 17 36 30 25
## TCACCG TCACCT TCACGA TCACGC TCACGG TCACGT TCACTA TCACTC TCACTG TCACTT
## [1,] 4102 6520 4453 2037 2765 3936 8217 7219 6107 11177
## [2,] 2568 4355 2818 1316 1835 2580 5301 4853 3837 7443
## [3,] 3182 5125 3628 1680 2481 3046 6208 5577 4885 8931
## [4,] 2585 4130 2746 1145 1734 2469 4994 4539 3750 7000
## [5,] 3577 5778 3882 1778 2674 3522 7284 6454 5490 10425
## [6,] 23 23 15 9 12 14 36 22 22 45
## TCAGAA TCAGAC TCAGAG TCAGAT TCAGCA TCAGCC TCAGCG TCAGCT TCAGGA TCAGGC
## [1,] 12839 5189 7971 11181 6901 3873 2219 8163 6317 3041
## [2,] 7818 3430 5006 7114 4288 2782 1366 5092 4042 1992
## [3,] 9980 4304 6305 8703 5522 3202 1681 6401 4867 2429
## [4,] 7929 3287 4805 6768 4278 2452 1312 4896 3915 1802
## [5,] 11195 4675 6897 9827 5895 3434 1919 7081 5556 2636
## [6,] 61 16 25 37 20 25 10 12 31 12
## TCAGGG TCAGGT TCAGTA TCAGTC TCAGTG TCAGTT TCATAA TCATAC TCATAG TCATAT
## [1,] 3213 6605 6054 4667 5576 10145 14745 7928 7361 17820
## [2,] 1945 4054 3959 3186 3478 6513 9648 4910 4759 11294
## [3,] 2535 5147 4709 3676 4215 7973 11371 6058 5613 13020
## [4,] 2010 3962 3709 3030 3444 6135 8935 5384 4531 10575
## [5,] 2752 5966 5477 4245 4950 8853 12944 7284 6359 15786
## [6,] 22 16 37 16 20 37 101 37 57 108
## TCATCA TCATCC TCATCG TCATCT TCATGA TCATGC TCATGG TCATGT TCATTA TCATTC
## [1,] 19715 7376 6427 15683 11420 5492 7334 11757 13772 10342
## [2,] 12711 5184 4016 9831 7492 3594 4774 7720 9215 7218
## [3,] 15613 6141 5004 12214 8971 4224 5975 9112 10379 8337
## [4,] 12368 4771 3860 9424 6873 3335 4560 7611 8095 6413
## [5,] 17700 6685 5661 13661 10131 4867 6615 10913 12176 9443
## [6,] 54 39 28 40 40 26 37 34 84 72
## TCATTG TCATTT TCCAAA TCCAAC TCCAAG TCCAAT TCCACA TCCACC TCCACG TCCACT
## [1,] 12031 21693 18488 8735 9419 11332 8576 6519 3426 7097
## [2,] 7814 14854 12127 5760 6318 7462 5613 4346 2221 4696
## [3,] 9316 16480 14506 6977 7441 8717 6989 5035 2749 5693
## [4,] 7378 13254 11518 5432 5704 6758 5253 4050 2229 4328
## [5,] 10940 19770 16081 7463 8127 9780 7583 5873 2985 6288
## [6,] 50 135 75 41 47 118 36 30 19 50
## TCCAGA TCCAGC TCCAGG TCCAGT TCCATA TCCATC TCCATG TCCATT TCCCAA TCCCAC
## [1,] 7048 4487 3352 5372 9558 10091 8408 13103 9079 4445
## [2,] 4304 2890 2172 3292 6287 6328 5429 8567 5836 2819
## [3,] 5540 3594 2849 4121 7455 7458 6585 10661 6812 3704
## [4,] 4318 2845 2178 3061 6072 6080 5286 7799 5857 2816
## [5,] 6341 3925 3178 4629 8398 8338 7426 11803 7866 3891
## [6,] 37 24 27 43 80 49 45 103 57 17
## TCCCAG TCCCAT TCCCCA TCCCCC TCCCCG TCCCCT TCCCGA TCCCGC TCCCGG TCCCGT
## [1,] 3012 6966 4546 1768 1313 3145 2483 1712 1875 2098
## [2,] 1943 4532 3060 1212 970 2245 1684 1188 1235 1471
## [3,] 2519 5764 3640 1433 1136 2489 2066 1488 1552 1801
## [4,] 1924 4337 2908 1158 904 2068 1689 1083 1189 1285
## [5,] 2703 5964 4036 1547 1228 2882 2293 1578 1767 1944
## [6,] 26 61 43 28 19 38 38 18 20 20
## TCCCTA TCCCTC TCCCTG TCCCTT TCCGAA TCCGAC TCCGAG TCCGAT TCCGCA TCCGCC
## [1,] 4223 4787 3444 6858 4543 2972 3325 4889 2256 2367
## [2,] 2829 3310 2231 4885 3002 2078 2120 3211 1542 1764
## [3,] 3246 3991 2748 5625 3816 2352 2771 3901 1871 1990
## [4,] 2699 3072 2207 4545 2731 1966 2200 2995 1489 1546
## [5,] 3790 4303 3111 6185 3927 2595 2974 4458 2172 2285
## [6,] 31 35 22 57 41 19 21 38 18 27
## TCCGCG TCCGCT TCCGGA TCCGGC TCCGGG TCCGGT TCCGTA TCCGTC TCCGTG TCCGTT
## [1,] 939 2421 3175 2577 1487 4652 2815 3078 2301 4381
## [2,] 689 1599 2022 1677 1095 2936 1983 2068 1566 2926
## [3,] 897 1830 2377 2037 1368 3487 2166 2448 1863 3494
## [4,] 669 1474 1989 1610 1040 2845 1771 1949 1453 2765
## [5,] 879 2088 2671 2312 1441 3996 2627 2852 2118 4139
## [6,] 9 29 30 13 20 19 22 18 22 44
## TCCTAA TCCTAC TCCTAG TCCTAT TCCTCA TCCTCC TCCTCG TCCTCT TCCTGA TCCTGC
## [1,] 9021 4496 3634 5736 8776 8601 4091 11874 6115 3788
## [2,] 5378 2756 2622 3953 5799 6010 2773 7842 3999 2569
## [3,] 6295 3362 3188 4610 7102 6969 3406 9594 5012 3157
## [4,] 5280 2512 2411 3593 5600 5593 2653 7474 3991 2298
## [5,] 7191 3587 3543 5283 7886 8044 3714 10926 5547 3504
## [6,] 61 37 27 87 25 33 35 55 37 28
## TCCTGG TCCTGT TCCTTA TCCTTC TCCTTG TCCTTT TCGAAA TCGAAC TCGAAG TCGAAT
## [1,] 3101 4644 7787 10789 8467 14542 8958 4343 5775 7508
## [2,] 1989 3057 5226 7234 5712 9914 5920 2958 3698 4796
## [3,] 2579 3753 6214 8776 6853 11345 7148 3586 4603 5826
## [4,] 2063 2897 5101 6725 5635 9048 5439 2871 3613 4568
## [5,] 2757 4135 7004 9587 8383 13245 8177 3878 5355 7289
## [6,] 30 32 46 65 44 115 81 51 32 80
## TCGACA TCGACC TCGACG TCGACT TCGAGA TCGAGC TCGAGG TCGAGT TCGATA TCGATC
## [1,] 4687 3502 2776 3584 6294 3202 3213 6071 5542 5974
## [2,] 3200 2568 1844 2537 3922 2131 2146 4136 3744 4121
## [3,] 3677 3176 2202 2841 4944 2737 2634 4911 4414 4991
## [4,] 3103 2628 1716 2518 3911 2133 2100 4464 3540 4034
## [5,] 4260 3533 2557 3439 5706 2999 3037 5565 4930 5529
## [6,] 25 23 16 21 32 25 16 37 73 46
## TCGATG TCGATT TCGCAA TCGCAC TCGCAG TCGCAT TCGCCA TCGCCC TCGCCG TCGCCT
## [1,] 5735 8519 3623 1489 2494 3153 3140 897 2835 2371
## [2,] 3498 5465 2466 954 1556 2091 2115 722 1844 1582
## [3,] 4390 6865 3012 1192 1985 2758 2556 1036 2236 1954
## [4,] 3465 5245 2565 914 1629 1987 1927 591 1906 1539
## [5,] 5010 7804 3501 1439 2187 2834 2738 997 2625 2146
## [6,] 33 81 20 14 9 18 20 15 12 14
## TCGCGA TCGCGC TCGCGG TCGCGT TCGCTA TCGCTC TCGCTG TCGCTT TCGGAA TCGGAC
## [1,] 1423 552 1149 1207 2557 2367 2806 4317 4784 2013
## [2,] 928 410 815 820 1645 1758 1688 2689 3234 1363
## [3,] 1139 464 927 1085 1891 1990 2159 3302 3983 1741
## [4,] 875 407 832 786 1566 1561 1612 2593 3055 1317
## [5,] 1269 529 1122 1141 2313 2170 2493 3788 4133 1861
## [6,] 18 2 10 9 16 17 11 22 40 16
## TCGGAG TCGGAT TCGGCA TCGGCC TCGGCG TCGGCT TCGGGA TCGGGC TCGGGG TCGGGT
## [1,] 3968 4865 1883 1552 1649 2623 2671 977 1170 3024
## [2,] 2498 3230 1240 1177 1091 1823 1649 723 782 2043
## [3,] 3257 3828 1509 1237 1337 2053 2064 843 962 2436
## [4,] 2465 3158 1123 1039 1112 1906 1646 652 740 1894
## [5,] 3623 4402 1695 1409 1538 2622 2375 927 1034 2796
## [6,] 18 39 18 12 12 22 36 13 24 18
## TCGGTA TCGGTC TCGGTG TCGGTT TCGTAA TCGTAC TCGTAG TCGTAT TCGTCA TCGTCC
## [1,] 2862 2297 3149 5924 5215 2656 3196 4982 5109 3050
## [2,] 1847 1547 2164 4065 3477 1600 2117 3087 3332 2121
## [3,] 2167 1803 2481 4823 4295 1987 2573 3862 4162 2401
## [4,] 1712 1477 2062 3769 3165 1710 1987 2948 3260 1845
## [5,] 2518 2054 2857 5577 4608 2328 2854 4336 4555 2642
## [6,] 24 23 9 41 42 26 28 38 15 19
## TCGTCG TCGTCT TCGTGA TCGTGC TCGTGG TCGTGT TCGTTA TCGTTC TCGTTG TCGTTT
## [1,] 3918 6280 4409 1896 3225 4152 5191 4210 6316 10824
## [2,] 2507 4072 2783 1221 2067 2832 3418 2885 3880 6848
## [3,] 3275 4950 3405 1536 2661 3408 3997 3333 4745 8288
## [4,] 2525 3760 2702 1230 2040 2603 3225 2706 3758 6518
## [5,] 3835 5671 3862 1768 2908 3847 4899 3773 5434 9621
## [6,] 15 22 19 13 23 22 35 35 31 64
## TCTAAA TCTAAC TCTAAG TCTAAT TCTACA TCTACC TCTACG TCTACT TCTAGA TCTAGC
## [1,] 16985 8270 8031 13263 9342 4669 3248 8774 8137 4627
## [2,] 11310 5105 5064 8799 6153 3145 2003 5710 5342 3030
## [3,] 12490 5878 5799 9964 7426 3738 2715 6642 6572 3800
## [4,] 10313 5004 4629 8173 5788 2946 1966 5442 5182 2928
## [5,] 14658 6931 6480 11820 8261 4201 2943 7711 7296 4068
## [6,] 84 39 36 98 21 51 25 32 44 17
## TCTAGG TCTAGT TCTATA TCTATC TCTATG TCTATT TCTCAA TCTCAC TCTCAG TCTCAT
## [1,] 3995 8470 12490 8630 8524 13881 16011 7685 7991 13871
## [2,] 2831 4938 8350 5743 5631 9175 10131 5205 5109 9016
## [3,] 3352 5674 9595 6910 6473 10657 12055 6119 6290 10751
## [4,] 2626 4766 7598 5397 5137 8331 10075 4846 4835 8502
## [5,] 3622 6568 11047 7530 7535 12292 14386 7096 7165 12575
## [6,] 29 43 92 55 46 152 51 20 22 61
## TCTCCA TCTCCC TCTCCG TCTCCT TCTCGA TCTCGC TCTCGG TCTCGT TCTCTA TCTCTC
## [1,] 13092 5483 5574 11718 6068 3210 3827 5907 13861 20226
## [2,] 8411 3633 3582 7855 3956 2170 2596 3864 8623 13659
## [3,] 10408 4467 4514 9506 4834 2739 3062 4621 10333 16463
## [4,] 7949 3535 3563 7194 3839 2003 2378 3655 8071 12294
## [5,] 11580 4936 5070 10506 5769 3023 3313 5428 11599 18425
## [6,] 34 29 24 41 51 17 24 35 49 53
## TCTCTG TCTCTT TCTGAA TCTGAC TCTGAG TCTGAT TCTGCA TCTGCC TCTGCG TCTGCT
## [1,] 12516 24386 12934 4883 6823 12305 8785 3492 2536 8299
## [2,] 7936 15996 8106 3148 4312 7657 5400 2391 1598 5290
## [3,] 9733 19465 10123 3871 5491 9679 6970 2897 2079 6566
## [4,] 7611 14814 8015 3004 4171 7309 5419 2272 1522 5083
## [5,] 11393 21898 11551 4443 6093 11154 7847 3306 2237 7572
## [6,] 31 109 63 26 24 49 31 23 10 22
## TCTGGA TCTGGC TCTGGG TCTGGT TCTGTA TCTGTC TCTGTG TCTGTT TCTTAA TCTTAC
## [1,] 6982 3223 3044 7638 7923 6254 6499 15784 16098 9174
## [2,] 4352 2102 2045 4649 4940 3981 4223 9831 10568 5706
## [3,] 5585 2473 2478 5885 6355 4680 5084 12144 12037 6568
## [4,] 4325 1955 1950 4605 4788 3794 3971 9409 9719 5383
## [5,] 6404 2915 2733 6786 7087 5443 6012 13836 14533 7880
## [6,] 29 17 31 37 45 34 20 53 50 42
## TCTTAG TCTTAT TCTTCA TCTTCC TCTTCG TCTTCT TCTTGA TCTTGC TCTTGG TCTTGT
## [1,] 8116 17223 20791 13681 7933 33301 16983 8732 10123 16628
## [2,] 5518 10673 13612 8909 5035 20610 10702 5489 6535 10938
## [3,] 6350 12221 16496 10914 6039 25326 12941 6561 7947 13218
## [4,] 5129 10078 13040 8362 4836 20402 10379 5316 6070 10366
## [5,] 7544 14547 18722 12396 6907 29514 14883 7641 8880 15181
## [6,] 37 74 60 67 44 129 82 38 59 60
## TCTTTA TCTTTC TCTTTG TCTTTT TGAAAA TGAAAC TGAAAG TGAAAT TGAACA TGAACC
## [1,] 18808 19539 19133 35205 26605 15178 13744 20904 11700 7518
## [2,] 12422 12927 12584 22498 17470 9684 8969 13520 7320 4797
## [3,] 14270 15401 15199 26674 20335 11794 10488 15677 8851 5625
## [4,] 11262 11942 12091 20670 16286 9428 8349 12645 6866 4412
## [5,] 16642 17882 17665 31127 24081 13406 12177 18861 10438 6438
## [6,] 100 138 77 282 152 48 84 144 45 55
## TGAACG TGAACT TGAAGA TGAAGC TGAAGG TGAAGT TGAATA TGAATC TGAATG TGAATT
## [1,] 3478 9441 20807 9735 7989 11374 14135 13596 10934 17893
## [2,] 2283 6263 13416 6126 5215 7210 9193 8215 7309 11433
## [3,] 2644 7510 16581 7548 6531 9011 10896 10257 8578 13571
## [4,] 2178 5914 12685 5930 4850 6916 8541 8213 6693 10837
## [5,] 2996 8591 19158 8588 7254 10230 12486 11934 9835 15828
## [6,] 24 52 54 29 27 39 108 94 64 122
## TGACAA TGACAC TGACAG TGACAT TGACCA TGACCC TGACCG TGACCT TGACGA TGACGC
## [1,] 11464 5588 4800 10128 7752 3134 2240 4733 5216 1863
## [2,] 7494 3324 2983 6467 4545 2178 1511 3092 3247 1189
## [3,] 8877 4081 3803 7609 5600 2550 1799 3848 4077 1511
## [4,] 7163 3346 2878 6155 4373 1977 1381 3011 3290 1173
## [5,] 10365 4526 4132 8832 6236 2853 2117 4258 4609 1660
## [6,] 27 17 15 26 34 28 18 20 13 5
## TGACGG TGACGT TGACTA TGACTC TGACTG TGACTT TGAGAA TGAGAC TGAGAG TGAGAT
## [1,] 2687 3664 7170 5970 4737 10266 16777 6438 9753 12923
## [2,] 1781 2318 4365 4027 2966 6776 10814 4119 6150 8277
## [3,] 2099 2840 5231 4746 3701 7981 12978 5138 7583 9834
## [4,] 1698 2120 4194 3876 2870 6491 10183 3998 5932 7920
## [5,] 2356 3088 5960 5302 4344 9595 15545 5785 8627 11350
## [6,] 12 21 33 31 26 42 59 25 25 51
## TGAGCA TGAGCC TGAGCG TGAGCT TGAGGA TGAGGC TGAGGG TGAGGT TGAGTA TGAGTC
## [1,] 6289 3631 1694 7419 8897 3568 3105 6239 7733 5435
## [2,] 3987 2404 1112 4995 5763 2341 2041 3764 4891 3768
## [3,] 5002 2891 1406 6053 7185 3042 2419 4597 5986 4319
## [4,] 3912 2306 1115 4832 5588 2347 1970 3678 5072 3724
## [5,] 5496 3301 1542 6925 7978 3279 2858 5399 7193 5087
## [6,] 32 21 16 32 24 8 13 25 34 33
## TGAGTG TGAGTT TGATAA TGATAC TGATAG TGATAT TGATCA TGATCC TGATCG TGATCT
## [1,] 5808 12586 16128 7815 7857 16613 13322 7374 4785 12237
## [2,] 3843 8457 10324 4756 5105 10924 8443 4754 3192 7728
## [3,] 4577 9675 12094 6118 5912 12705 10448 5934 4120 9573
## [4,] 3625 7871 9556 4732 4813 10250 8079 4724 3076 7567
## [5,] 5636 11213 14120 6666 6865 15079 11701 6542 4406 10907
## [6,] 10 48 84 44 41 69 57 58 32 41
## TGATGA TGATGC TGATGG TGATGT TGATTA TGATTC TGATTG TGATTT TGCAAA TGCAAC
## [1,] 19840 7705 9830 12333 14916 13890 12747 25253 14717 7570
## [2,] 12563 4802 6155 8190 9702 8971 8597 16608 9653 4817
## [3,] 15773 5930 7343 9768 11245 10505 9921 19494 11601 6136
## [4,] 12303 4647 6022 7437 8906 8387 8134 15192 8912 4747
## [5,] 18031 6906 8564 11802 13350 12231 11793 23132 12848 6991
## [6,] 57 17 32 35 61 94 76 91 52 13
## TGCAAG TGCAAT TGCACA TGCACC TGCACG TGCACT TGCAGA TGCAGC TGCAGG TGCAGT
## [1,] 7765 9757 5777 3402 1949 4097 9031 5770 4574 5695
## [2,] 4899 6529 3634 2335 1144 2739 5486 3655 2803 3559
## [3,] 6042 7980 4141 2781 1489 3217 7069 4685 3674 4414
## [4,] 4840 6096 3450 2139 1150 2547 5428 3583 2864 3403
## [5,] 6956 8994 5090 3055 1731 3625 7916 5248 4229 5069
## [6,] 22 37 9 10 10 19 29 12 9 16
## TGCATA TGCATC TGCATG TGCATT TGCCAA TGCCAC TGCCAG TGCCAT TGCCCA TGCCCC
## [1,] 9210 7664 7436 11701 6937 3907 2444 5652 2728 1347
## [2,] 5870 4858 4846 6972 4392 2729 1584 3813 1834 988
## [3,] 7058 6246 6071 8581 5605 3075 1931 4480 2189 1100
## [4,] 5454 4634 4543 6722 4050 2478 1484 3460 1713 911
## [5,] 8126 6921 6470 9665 6062 3413 2177 5109 2492 1164
## [6,] 42 26 23 45 25 15 10 30 18 20
## TGCCCG TGCCCT TGCCGA TGCCGC TGCCGG TGCCGT TGCCTA TGCCTC TGCCTG TGCCTT
## [1,] 948 2381 1805 1319 1469 1938 3584 4282 2555 5824
## [2,] 684 1714 1276 945 930 1218 2325 2922 1860 4154
## [3,] 733 1946 1484 1084 1228 1685 2697 3446 2160 4739
## [4,] 606 1616 1156 864 864 1139 2129 2585 1650 3647
## [5,] 897 2134 1606 1149 1319 1702 3207 3821 2412 5352
## [6,] 17 15 13 17 8 8 24 22 12 27
## TGCGAA TGCGAC TGCGAG TGCGAT TGCGCA TGCGCC TGCGCG TGCGCT TGCGGA TGCGGC
## [1,] 3207 1884 2561 3335 1392 1028 515 1414 2252 1465
## [2,] 2146 1310 1627 2097 938 741 335 932 1532 1022
## [3,] 2633 1600 1908 2767 1122 818 406 1123 1978 1236
## [4,] 2008 1233 1718 2071 902 616 285 813 1397 977
## [5,] 2850 1818 2131 2926 1249 888 416 1210 2077 1327
## [6,] 19 8 8 16 7 10 6 13 25 6
## TGCGGG TGCGGT TGCGTA TGCGTC TGCGTG TGCGTT TGCTAA TGCTAC TGCTAG TGCTAT
## [1,] 1152 2712 2362 2248 2074 4026 7861 4370 4024 6459
## [2,] 791 1713 1510 1334 1283 2378 5061 2909 2662 4329
## [3,] 953 2124 1819 1642 1539 3101 5964 3390 3209 5220
## [4,] 762 1760 1473 1363 1315 2371 4839 2782 2562 3980
## [5,] 1128 2511 2089 1997 1888 3504 6638 3884 3511 5708
## [6,] 22 20 18 11 9 15 37 29 21 37
## TGCTCA TGCTCC TGCTCG TGCTCT TGCTGA TGCTGC TGCTGG TGCTGT TGCTTA TGCTTC
## [1,] 6458 4802 3156 7876 6863 5841 3892 5197 8386 11652
## [2,] 4061 2969 1894 5159 4246 3450 2554 3143 5401 7182
## [3,] 4932 3694 2483 6118 5366 4485 3354 3886 6364 8568
## [4,] 3928 2801 1922 4908 4224 3478 2398 3016 5023 6995
## [5,] 5557 4049 2739 7149 6078 4950 3572 4555 7368 10175
## [6,] 26 25 21 34 17 16 14 19 22 39
## TGCTTG TGCTTT TGGAAA TGGAAC TGGAAG TGGAAT TGGACA TGGACC TGGACG TGGACT
## [1,] 8187 14108 15203 7289 10458 10776 6203 4085 2658 5602
## [2,] 5464 9187 10138 4729 6650 7172 4039 2717 1698 3736
## [3,] 6645 10852 12246 5815 8161 8662 5010 3265 2071 4313
## [4,] 5148 8645 9392 4524 6459 6593 3736 2613 1701 3493
## [5,] 7734 12707 14021 6469 9503 9824 5411 3671 2309 5067
## [6,] 29 60 88 43 41 109 33 19 19 22
## TGGAGA TGGAGC TGGAGG TGGAGT TGGATA TGGATC TGGATG TGGATT TGGCAA TGGCAC
## [1,] 13232 5357 6916 7194 8870 8408 7786 14137 6824 2742
## [2,] 8537 3377 4405 4693 5991 5549 5106 8565 4332 1843
## [3,] 10619 4222 5632 5930 7022 6776 6222 10238 5286 2241
## [4,] 8402 3230 4172 4669 5606 5236 4893 8190 4193 1687
## [5,] 11751 4848 6025 7104 8061 7483 7138 12185 6019 2472
## [6,] 30 21 23 31 70 55 40 101 17 8
## TGGCAG TGGCAT TGGCCA TGGCCC TGGCCG TGGCCT TGGCGA TGGCGC TGGCGG TGGCGT
## [1,] 3910 5373 4125 1866 1754 3358 3195 1211 2845 2454
## [2,] 2596 3568 2905 1211 1214 2181 1994 752 1801 1526
## [3,] 3133 4461 3222 1462 1454 2899 2554 1054 2227 2006
## [4,] 2360 3400 2600 1102 1237 2087 1975 758 1747 1515
## [5,] 3584 4831 3770 1691 1691 3077 2901 1152 2428 2123
## [6,] 17 26 13 14 9 17 19 11 15 8
## TGGCTA TGGCTC TGGCTG TGGCTT TGGGAA TGGGAC TGGGAG TGGGAT TGGGCA TGGGCC
## [1,] 5168 5056 4735 8177 8191 3467 5406 6598 2740 2884
## [2,] 3410 3271 3003 5348 5343 2379 3053 4094 1913 1906
## [3,] 4020 4059 3731 6393 6489 2742 3819 5363 2281 2257
## [4,] 3285 3126 2982 4933 5037 2283 3117 3991 1713 1776
## [5,] 4487 4457 4204 7536 7458 3127 4553 6155 2512 2591
## [6,] 27 26 18 25 27 17 25 45 19 13
## TGGGCG TGGGCT TGGGGA TGGGGC TGGGGG TGGGGT TGGGTA TGGGTC TGGGTG TGGGTT
## [1,] 1123 4139 4346 1434 1905 3218 4658 3573 3457 8522
## [2,] 855 2717 2840 922 1218 2188 2641 2396 2361 5624
## [3,] 1120 3519 3669 1168 1529 2635 3108 3113 2873 6608
## [4,] 773 2633 2825 885 1284 2079 2585 2337 2206 5155
## [5,] 1016 3864 4182 1289 1719 2969 3598 3458 3312 7747
## [6,] 15 26 33 16 21 37 27 22 23 50
## TGGTAA TGGTAC TGGTAG TGGTAT TGGTCA TGGTCC TGGTCG TGGTCT TGGTGA TGGTGC
## [1,] 10200 4562 5283 8489 7351 4165 3746 7158 10383 4274
## [2,] 6420 2839 3451 5390 4696 2825 2481 4680 6622 2697
## [3,] 7825 3505 4012 6560 5586 3278 3035 5520 7932 3527
## [4,] 6082 2718 3226 5090 4288 2706 2419 4395 6380 2621
## [5,] 8914 3914 4621 7236 6305 3902 3434 6439 9028 3864
## [6,] 41 23 33 52 22 27 13 24 28 13
## TGGTGG TGGTGT TGGTTA TGGTTC TGGTTG TGGTTT TGTAAA TGTAAC TGTAAG TGTAAT
## [1,] 8613 8341 10652 9282 9774 20257 16527 8402 8470 13704
## [2,] 5596 5480 6779 5939 6373 12602 11154 5413 5556 8948
## [3,] 7388 6355 7911 6959 7573 14785 12381 6287 6454 10486
## [4,] 5609 5208 6599 5796 6149 12186 10079 5032 4985 8299
## [5,] 8104 7636 10140 8338 8610 17788 14683 7520 7496 11930
## [6,] 22 28 44 54 32 62 74 33 13 57
## TGTACA TGTACC TGTACG TGTACT TGTAGA TGTAGC TGTAGG TGTAGT TGTATA TGTATC
## [1,] 7538 4145 2893 6603 9341 5084 4185 8159 14229 8144
## [2,] 4839 2855 1855 4244 6085 3243 2834 5318 9111 5398
## [3,] 5740 3417 2243 5123 7283 3800 3568 6246 10735 6563
## [4,] 4692 2757 1687 4117 5922 3118 2621 4872 8538 5146
## [5,] 6466 3865 2550 5807 8410 4485 3826 6975 12497 7702
## [6,] 35 29 10 28 32 23 30 21 57 48
## TGTATG TGTATT TGTCAA TGTCAC TGTCAG TGTCAT TGTCCA TGTCCC TGTCCG TGTCCT
## [1,] 9404 14404 11317 6169 4338 9471 6302 3189 1945 5170
## [2,] 6088 9496 7395 3759 2761 6562 3990 2326 1335 3511
## [3,] 7180 10787 8712 4501 3516 7533 4828 2666 1729 4214
## [4,] 5723 8559 7038 3569 2751 6112 3718 2187 1303 3340
## [5,] 9005 12739 9952 5105 3809 9146 5383 2922 1757 4814
## [6,] 41 77 38 19 17 21 34 19 16 22
## TGTCGA TGTCGC TGTCGG TGTCGT TGTCTA TGTCTC TGTCTG TGTCTT TGTGAA TGTGAC
## [1,] 4595 2056 2603 4256 7811 8973 5965 13145 13275 6174
## [2,] 3063 1289 1650 2818 4600 5715 3931 8755 8292 3683
## [3,] 3640 1602 2045 3432 5587 7039 4868 10695 9987 4406
## [4,] 3089 1284 1614 2760 4405 5497 3768 8309 7971 3732
## [5,] 4304 1819 2167 3910 6402 8024 5494 12159 11904 5208
## [6,] 20 4 18 5 38 33 19 48 46 13
## TGTGAG TGTGAT TGTGCA TGTGCC TGTGCG TGTGCT TGTGGA TGTGGC TGTGGG TGTGGT
## [1,] 6699 12190 5555 2817 1516 5333 8471 4127 3994 8159
## [2,] 4329 7939 3570 1890 1016 3572 5643 2770 2648 5203
## [3,] 5287 9278 4374 2125 1287 4299 6836 3313 3104 6306
## [4,] 4188 7195 3448 1583 952 3320 5258 2579 2443 4990
## [5,] 5954 11009 5055 2519 1438 4842 7672 3657 3770 7321
## [6,] 19 45 12 16 9 16 28 15 15 25
## TGTGTA TGTGTC TGTGTG TGTGTT TGTTAA TGTTAC TGTTAG TGTTAT TGTTCA TGTTCC
## [1,] 9916 6231 9632 15450 14447 8884 8308 15990 11616 7306
## [2,] 6420 4051 6207 10176 9723 5617 5446 10718 7452 4844
## [3,] 7357 4804 7318 12175 10997 6704 6246 12266 9022 5996
## [4,] 6286 3800 5843 9472 8819 5457 5082 9690 6983 4783
## [5,] 9473 5473 8751 14221 13288 7688 7987 14347 10344 6808
## [6,] 22 28 12 21 40 21 25 58 42 57
## TGTTCG TGTTCT TGTTGA TGTTGC TGTTGG TGTTGT TGTTTA TGTTTC TGTTTG TGTTTT
## [1,] 4256 14784 15830 8758 10676 18547 18091 18561 18360 37043
## [2,] 2748 9618 10619 5604 6580 11782 11848 11704 12211 24207
## [3,] 3416 11462 12282 6883 7727 14025 13898 14095 14177 27945
## [4,] 2600 9078 9599 5346 6056 10808 10867 11260 11149 22552
## [5,] 3757 13513 14287 7731 8787 16172 16350 16617 16810 34027
## [6,] 37 58 60 27 23 51 35 75 36 91
## TTAAAA TTAAAC TTAAAG TTAAAT TTAACA TTAACC TTAACG TTAACT TTAAGA TTAAGC
## [1,] 36651 15564 15023 24616 15033 8528 4557 12278 15668 6897
## [2,] 25509 9870 9921 16590 9806 5443 3068 7992 10352 4469
## [3,] 27797 11406 11340 18512 11255 6169 3537 9287 11819 5378
## [4,] 22506 9387 9002 14586 8711 5025 2860 7299 9897 4242
## [5,] 34201 13553 13322 21824 13165 7473 4290 10765 14286 6157
## [6,] 139 43 35 99 34 48 13 42 54 12
## TTAAGG TTAAGT TTAATA TTAATC TTAATG TTAATT TTACAA TTACAC TTACAG TTACAT
## [1,] 6937 11441 20639 12153 12963 28275 17367 7121 7480 14727
## [2,] 4728 7532 13941 7960 8476 18579 11857 4708 4639 9415
## [3,] 5599 8695 15306 9274 10066 21044 13687 5517 5712 10995
## [4,] 4263 7277 12367 7380 7659 16759 10566 4370 4597 8693
## [5,] 6258 10128 18200 11064 11545 24967 15927 6330 6449 12940
## [6,] 29 44 128 65 53 161 59 15 20 73
## TTACCA TTACCC TTACCG TTACCT TTACGA TTACGC TTACGG TTACGT TTACTA TTACTC
## [1,] 10086 4120 3466 8711 5285 2206 2973 4954 10849 8448
## [2,] 6401 2640 2170 5601 3363 1332 1958 3139 7237 5396
## [3,] 7574 3144 2704 6537 4073 1667 2513 3683 8442 6373
## [4,] 6019 2597 2043 5358 3074 1371 1833 2935 6787 5136
## [5,] 9092 3461 3025 7568 4605 1946 2675 4417 9992 7441
## [6,] 34 33 15 34 34 18 24 32 71 38
## TTACTG TTACTT TTAGAA TTAGAC TTAGAG TTAGAT TTAGCA TTAGCC TTAGCG TTAGCT
## [1,] 6899 16576 15195 6275 9476 13827 7704 4962 2310 9427
## [2,] 4116 10770 10204 4081 6161 8891 5124 2772 1507 6211
## [3,] 5003 12306 11543 4830 7320 10462 5958 3446 1703 7142
## [4,] 3975 9977 9025 3815 5764 8550 4649 2894 1330 5892
## [5,] 5801 14567 14131 5443 8527 12365 6762 3841 2116 8590
## [6,] 32 94 82 21 24 80 29 27 9 37
## TTAGGA TTAGGC TTAGGG TTAGGT TTAGTA TTAGTC TTAGTG TTAGTT TTATAA TTATAC
## [1,] 8230 3924 5635 7866 10923 7586 8301 16878 24140 10656
## [2,] 5468 2576 3769 5407 7288 4399 5419 11015 15564 6735
## [3,] 6275 3098 4318 6103 8220 5205 6406 12597 17562 7747
## [4,] 5106 2588 3430 4941 6665 4148 5080 10174 14028 6520
## [5,] 7164 3508 4993 7247 9867 5942 8136 15014 20708 9209
## [6,] 45 22 25 39 57 33 31 68 90 42
## TTATAG TTATAT TTATCA TTATCC TTATCG TTATCT TTATGA TTATGC TTATGG TTATGT
## [1,] 10842 27547 15890 7317 5261 15621 15079 7040 8967 16246
## [2,] 7132 18129 10496 4712 3367 10308 9669 4596 5848 10675
## [3,] 8169 20300 12367 5660 4110 11970 11438 5232 6848 12050
## [4,] 6461 16242 9574 4431 3351 9709 8764 4126 5563 9938
## [5,] 9525 24856 14404 6663 4834 13982 13154 6177 8200 14542
## [6,] 54 136 89 58 20 74 80 36 55 52
## TTATTA TTATTC TTATTG TTATTT TTCAAA TTCAAC TTCAAG TTCAAT TTCACA TTCACC
## [1,] 23802 13070 15764 38257 26381 12906 14584 19190 13255 8346
## [2,] 15975 8856 10293 25419 17781 8336 9301 12283 8635 5479
## [3,] 17698 10149 11929 28244 20833 9993 11208 14153 10151 6501
## [4,] 14245 8016 9707 22889 16343 8019 9004 11416 8130 5121
## [5,] 20999 11748 13964 34294 24655 11487 13218 16961 11560 7314
## [6,] 154 114 98 232 143 64 65 150 55 35
## TTCACG TTCACT TTCAGA TTCAGC TTCAGG TTCAGT TTCATA TTCATC TTCATG TTCATT
## [1,] 4546 11561 12985 7027 7486 9893 16781 15967 12748 20774
## [2,] 2847 7557 8132 4455 4582 6426 10791 10586 8285 14091
## [3,] 3577 9042 10376 5661 5705 7574 12220 12646 9770 15876
## [4,] 2843 6997 7926 4341 4503 6125 9884 9867 7835 12649
## [5,] 4058 10482 11313 6079 6776 8758 14512 14134 11188 18831
## [6,] 30 44 54 23 33 42 140 71 66 171
## TTCCAA TTCCAC TTCCAG TTCCAT TTCCCA TTCCCC TTCCCG TTCCCT TTCCGA TTCCGC
## [1,] 15371 8404 6859 13670 8180 4174 3225 7346 4678 2516
## [2,] 10224 5592 4374 8681 5360 2833 2179 4853 3167 1758
## [3,] 11993 6615 5547 10680 6484 3412 2730 5878 3993 2080
## [4,] 9428 5120 4183 8334 5328 2618 2123 4494 2970 1629
## [5,] 13308 7538 6345 12200 7187 3817 3042 6455 4342 2293
## [6,] 117 50 43 119 53 52 33 49 35 22
## TTCCGG TTCCGT TTCCTA TTCCTC TTCCTG TTCCTT TTCGAA TTCGAC TTCGAG TTCGAT
## [1,] 4007 4037 7414 12521 6328 16449 8289 4142 5363 8648
## [2,] 2473 2716 5010 8431 4048 11156 5482 2853 3475 5568
## [3,] 3083 3139 5955 9975 5265 12998 6858 3404 4307 6749
## [4,] 2450 2456 4608 7901 3966 10624 5167 2847 3379 5331
## [5,] 3426 3745 6887 11428 5622 15040 7799 3941 4953 7658
## [6,] 38 40 76 59 39 106 90 30 39 86
## TTCGCA TTCGCC TTCGCG TTCGCT TTCGGA TTCGGC TTCGGG TTCGGT TTCGTA TTCGTC
## [1,] 3180 2910 1322 3747 4353 2258 2711 4942 5393 5936
## [2,] 2095 1849 954 2314 3024 1508 1771 3461 3529 3893
## [3,] 2514 2208 1055 2840 3659 1701 2048 3906 4217 4734
## [4,] 2091 1815 865 2219 2913 1567 1651 3072 3314 3578
## [5,] 2901 2530 1198 3260 4020 2272 2345 4530 4712 5466
## [6,] 24 27 15 33 43 20 35 39 46 31
## TTCGTG TTCGTT TTCTAA TTCTAC TTCTAG TTCTAT TTCTCA TTCTCC TTCTCG TTCTCT
## [1,] 4384 9507 15991 8661 8916 14944 16894 13355 6908 24160
## [2,] 2964 6069 10369 5733 5566 9935 10888 8527 4557 15766
## [3,] 3576 7307 11439 6912 6570 11381 12805 10485 5350 19110
## [4,] 2763 5742 9840 5450 5234 9014 10396 8105 4285 14777
## [5,] 4045 8611 13617 7853 7440 13232 15269 11744 6426 21704
## [6,] 30 74 113 52 59 150 58 54 40 95
## TTCTGA TTCTGC TTCTGG TTCTGT TTCTTA TTCTTC TTCTTG TTCTTT TTGAAA TTGAAC
## [1,] 12739 7934 7576 12827 20610 33226 21671 37225 25445 11026
## [2,] 7937 4944 4746 8194 13112 20626 13414 24552 16706 7200
## [3,] 10159 6205 5958 9867 14874 25149 16059 28544 19241 8590
## [4,] 7837 4844 4675 7677 12434 20305 13044 22269 15451 6610
## [5,] 11568 7143 6874 11639 18055 29506 18895 33639 22878 9951
## [6,] 70 34 45 70 105 145 119 273 164 65
## TTGAAG TTGAAT TTGACA TTGACC TTGACG TTGACT TTGAGA TTGAGC TTGAGG TTGAGT
## [1,] 16802 20314 11352 7184 4682 10881 16209 6805 8003 11566
## [2,] 10838 12927 7426 4209 3034 6850 10220 4463 5001 7866
## [3,] 13486 15530 8727 5153 3736 7954 12335 5631 6119 9050
## [4,] 10013 12208 7122 3959 2830 6525 9891 4437 4994 7567
## [5,] 15601 18186 9935 5704 4010 9258 15169 6327 6951 10595
## [6,] 64 153 36 42 24 51 60 33 16 55
## TTGATA TTGATC TTGATG TTGATT TTGCAA TTGCAC TTGCAG TTGCAT TTGCCA TTGCCC
## [1,] 17356 13962 17535 25620 12970 5096 9778 12261 6704 2697
## [2,] 11455 8866 10980 16755 8504 3356 5987 8090 4383 1951
## [3,] 13452 10808 13176 19536 10181 3970 7592 9826 5292 2192
## [4,] 10766 8586 10808 15558 8038 3040 5891 7408 4056 1728
## [5,] 15741 12709 15764 23484 11822 4715 8647 10974 5866 2469
## [6,] 91 87 47 149 35 17 26 42 26 26
## TTGCCG TTGCCT TTGCGA TTGCGC TTGCGG TTGCGT TTGCTA TTGCTC TTGCTG TTGCTT
## [1,] 2454 6159 3686 1571 3009 3860 8488 8597 8148 17025
## [2,] 1657 4187 2464 1079 1888 2304 5565 5265 4973 11002
## [3,] 2147 4837 2995 1221 2284 2823 6709 6277 6147 12747
## [4,] 1510 3689 2545 961 2002 2321 5243 5022 4795 10442
## [5,] 2209 5548 3325 1373 2685 3427 7485 7254 7074 15166
## [6,] 11 19 19 14 21 16 45 38 24 59
## TTGGAA TTGGAC TTGGAG TTGGAT TTGGCA TTGGCC TTGGCG TTGGCT TTGGGA TTGGGC
## [1,] 15363 6697 11295 15180 6628 4135 3462 8565 9271 4125
## [2,] 10172 4294 7278 9520 4410 2882 2040 5509 5550 2788
## [3,] 11965 5206 8975 11306 5371 3438 2714 6570 6852 3626
## [4,] 9306 3947 6975 9013 4138 2573 2023 5148 5428 2709
## [5,] 13692 5808 10450 13007 6057 3845 3022 7706 8160 3831
## [6,] 96 31 36 81 27 20 24 35 36 31
## TTGGGG TTGGGT TTGGTA TTGGTC TTGGTG TTGGTT TTGTAA TTGTAC TTGTAG TTGTAT
## [1,] 4535 8033 11271 8802 11270 21499 17813 7475 10448 16891
## [2,] 3000 5387 7224 5785 7358 13476 11970 5019 6964 11125
## [3,] 3662 6386 8424 6770 8752 15991 13357 5764 8142 12759
## [4,] 2815 5089 6567 5408 6754 13233 10676 4791 6399 10213
## [5,] 4121 7389 9921 7948 10293 19769 15901 6585 9325 15434
## [6,] 35 49 61 34 38 77 69 42 39 96
## TTGTCA TTGTCC TTGTCG TTGTCT TTGTGA TTGTGC TTGTGG TTGTGT TTGTTA TTGTTC
## [1,] 11504 6612 5138 14595 14381 5822 9753 15566 19052 15390
## [2,] 7486 4361 3282 9094 8933 3801 6348 10411 12757 9981
## [3,] 8894 5133 4035 10970 10539 4554 7692 12118 14562 12060
## [4,] 7080 4192 3189 8612 8387 3571 5930 9699 11704 9612
## [5,] 10133 5965 4634 12603 12424 5202 8664 14238 17886 14142
## [6,] 24 35 14 58 44 23 28 36 61 88
## TTGTTG TTGTTT TTTAAA TTTAAC TTTAAG TTTAAT TTTACA TTTACC TTTACG TTTACT
## [1,] 22778 38055 34167 14950 14774 27464 16104 9610 5452 16263
## [2,] 14479 25334 24212 9630 9727 18192 11050 5973 3426 10326
## [3,] 17051 29455 26241 10852 10985 20539 12672 7268 4129 11733
## [4,] 13252 23358 21140 8441 9310 16445 9810 5897 3204 9700
## [5,] 19789 34616 31318 12833 13449 24488 14871 8472 4814 14134
## [6,] 77 110 87 44 43 146 63 49 40 81
## TTTAGA TTTAGC TTTAGG TTTAGT TTTATA TTTATC TTTATG TTTATT TTTCAA TTTCAC
## [1,] 16575 9350 9906 16926 27848 15836 17001 36477 25356 13368
## [2,] 10842 5503 6505 11004 18344 10379 11189 24359 16612 8468
## [3,] 12536 6469 7550 12373 20624 12147 12899 26969 19206 10034
## [4,] 9840 5515 6162 10051 16465 9698 10196 21868 15440 7896
## [5,] 14785 7732 8648 15037 24788 14415 15575 32417 23007 11628
## [6,] 66 34 53 72 114 114 94 280 155 53
## TTTCAG TTTCAT TTTCCA TTTCCC TTTCCG TTTCCT TTTCGA TTTCGC TTTCGG TTTCGT
## [1,] 13928 24049 15669 8807 5775 15632 8921 4008 5101 9323
## [2,] 8643 15897 10188 5615 3803 10472 5779 2539 3505 5946
## [3,] 10861 17978 11909 7097 4653 12522 7169 3018 4101 7259
## [4,] 8532 14510 9350 5458 3607 10016 5533 2517 3176 5493
## [5,] 12363 21560 13750 7709 5226 14580 8189 3616 4431 8439
## [6,] 52 178 111 62 42 91 77 42 45 77
## TTTCTA TTTCTC TTTCTG TTTCTT TTTGAA TTTGAC TTTGAG TTTGAT TTTGCA TTTGCC
## [1,] 18942 23428 15093 43857 27112 13294 15052 29087 14646 6745
## [2,] 12339 15001 9399 28514 17528 7913 9788 18665 9604 4551
## [3,] 14439 17914 11737 33029 20634 9263 11868 22017 11522 5432
## [4,] 11176 13725 9032 26243 16118 7639 9535 17650 8844 3975
## [5,] 16589 20638 13860 39764 24572 10797 14228 26411 13475 6049
## [6,] 145 91 75 246 154 49 51 163 40 30
## TTTGCG TTTGCT TTTGGA TTTGGC TTTGGG TTTGGT TTTGTA TTTGTC TTTGTG TTTGTT
## [1,] 4286 16194 18453 9161 11183 22992 20885 14340 17015 40703
## [2,] 2751 10377 12059 5880 6921 14767 13740 9540 11250 26332
## [3,] 3351 12092 14476 7151 8539 17085 15790 11003 13473 30453
## [4,] 2679 9563 11516 5469 6732 13714 12442 8885 10556 24346
## [5,] 3868 14092 17130 8449 9920 20707 18601 12836 15787 36226
## [6,] 17 49 86 40 41 65 97 62 48 122
## TTTTAA TTTTAC TTTTAG TTTTAT TTTTCA TTTTCC TTTTCG TTTTCT TTTTGA TTTTGC
## [1,] 36810 16837 19135 37610 27007 17294 9623 40006 29969 15491
## [2,] 25532 11116 12077 24929 17551 11222 6121 25623 19080 9959
## [3,] 27979 12710 13737 27615 20415 13202 7609 29826 22100 11767
## [4,] 22472 10416 11124 22308 16185 10410 5786 23536 17601 9076
## [5,] 33328 15190 16553 33956 24194 15227 8632 35405 26497 13688
## [6,] 130 96 97 296 167 129 83 222 184 64
## TTTTGG TTTTGT TTTTTA TTTTTC TTTTTG TTTTTT
## [1,] 24333 39240 39636 33802 37093 95730
## [2,] 15144 25211 26768 22179 23854 63283
## [3,] 17679 29169 29484 25622 27406 70355
## [4,] 14307 23066 23966 20002 21745 57062
## [5,] 21714 34901 35738 30129 33215 86509
## [6,] 93 161 324 297 218 1007reverse-complement
assembly.rc = reverseComplement(assembly)
assembly.rc## A DNAStringSet instance of length 7
## width seq names
## [1] 30427671 CCCTAAACCCTAAACCCTA...TAGGGTTTAGGGTTTAGGG Chr1
## [2] 19698289 CCCTAAACCCTAAACCCTA...NNNNNNNNNNNNNNNNNNN Chr2
## [3] 23459830 GGGTTTAGGGTTTAGGGTT...NNNNNNNNNNNNNNNNNNN Chr3
## [4] 18585056 CCTAAACCCTAAACCCTAA...NNNNNNNNNNNNNNNNNNN Chr4
## [5] 26975502 GATCTAAAAACCCTAAATC...GTTGAGGGTACATGGTATA Chr5
## [6] 154478 GATGCCCGGGACCAAGTTA...ATTCCCGTCGTTCGCCCAT ChrC
## [7] 366924 AATCCGGTTTGTTTCCATT...ACCTGTTTCGAACGGATCC ChrMduplicated
duplicated(assembly[c(1,3)])## [1] FALSE FALSEunique to remove duplicates
unique(assembly[c(1,3)])## A DNAStringSet instance of length 2
## width seq names
## [1] 30427671 CCCTAAACCCTAAACCCTA...TAGGGTTTAGGGTTTAGGG Chr1
## [2] 23459830 NNNNNNNNNNNNNNNNNNN...AACCCTAAACCCTAAACCC Chr3Manipulate fastQ file
Install ShortRead package:
source("http://bioconductor.org/biocLite.R")
biocLite("ShortRead")Load library
library(ShortRead )Read the FastQ file and create a ShortReadQ file
fq <- readFastq("DATA/SRR031724_1_subset.fastq")
fq## class: ShortReadQ
## length: 1000000 reads; width: 37 cyclesCountLines in a fastQ file;
countLines("DATA/SRR031724_1_subset.fastq")## SRR031724_1_subset.fastq
## 4000000Inspect the first three reads : sequence, quality, id
head(sread(fq), 3)## A DNAStringSet instance of length 3
## width seq
## [1] 37 GTTTTGTCCAAGTTCTGGTAGCTGAATCCTGGGGCGC
## [2] 37 GTTGTCGCATTCCTTACTCTCATTCGGGAATTCTGTT
## [3] 37 GAATTTTTTGAGAGCGAAATGATAGCCGATGCCCTGAhead(quality(fq), 3)## class: FastqQuality
## quality:
## A BStringSet instance of length 3
## width seq
## [1] 37 IIIIIIIIIIIIIIIIIIIIIIIIIIII+HIIII<IE
## [2] 37 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
## [3] 37 IIIIIIIIIIIIIIIIIIIIII'IIIIIGBIIII2I+head(id(fq), 3)## A BStringSet instance of length 3
## width seq
## [1] 58 SRR031724.1 HWI-EAS299_4_30M2BAAXX:5:1:1513:1024 length=37
## [2] 57 SRR031724.2 HWI-EAS299_4_30M2BAAXX:5:1:937:1157 length=37
## [3] 58 SRR031724.4 HWI-EAS299_4_30M2BAAXX:5:1:1443:1122 length=37Example of report generated with Bioconductor: the code is not provided (more advanced) this report gives interesting information about the QC of fastQ file
browseURL("DATA/GSM461176_81_qa_report/index.html")GC content:
alf0 <- alphabetFrequency(sread(fq), as.prob=TRUE, collapse=TRUE)
sum(alf0[c("G", "C")])## [1] 0.5457237Alphabet by cycle:
abc <- alphabetByCycle(sread(fq))
matplot(t(abc[c("A", "C", "G", "T"),]), type="l")
Adaptor trimming
head(sread(fq), 3)## A DNAStringSet instance of length 3
## width seq
## [1] 37 GTTTTGTCCAAGTTCTGGTAGCTGAATCCTGGGGCGC
## [2] 37 GTTGTCGCATTCCTTACTCTCATTCGGGAATTCTGTT
## [3] 37 GAATTTTTTGAGAGCGAAATGATAGCCGATGCCCTGAfqtrim <- trimLRPatterns(Lpattern="GTT", subject=fq)
sread(fqtrim)[1:2]## A DNAStringSet instance of length 2
## width seq
## [1] 34 TTGTCCAAGTTCTGGTAGCTGAATCCTGGGGCGC
## [2] 34 GTCGCATTCCTTACTCTCATTCGGGAATTCTGTT