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] 53468112
end(X)
## [1] 53468113

Annotation 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 ...                  4262

findOverlaps 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        3929
infiniumMethylation[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    NA
ensGene_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 ...                  4262

IRanges 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     5

Some 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     7
coverage(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 22422827
mcols(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 22422827

GRangesList 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   NA

Why 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   NA

Accessors 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   366924
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   366924
gff[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   366924
c(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   366924
seqnames(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 ChrM
ranges(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   449
strand(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   366924
values(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 ... tRNA
gff[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   366924

Useful 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   366924

Returns 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   366924

Returns 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   366924

Returns 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           2

Counts 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   0

Returns 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   366924

Basic 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] 3

Use 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 2
myseq[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] TRUE

Use 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] TRUE

Use the REGULAR EXPRESSION function to substitute

 gsub("^ATG", "atg", myseq)
## [1] "atgCAGACATAGTG" "atgAACATAGATCC" "GTACAGATCAC"

Parsing sequence

nchar(myseq)
## [1] 14 14 11
substring(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 ChrM
length(assembly)
## [1] 7
assembly[[1]]
##   30427671-letter "DNAString" instance
## seq: CCCTAAACCCTAAACCCTAAACCCTAAACCTCTG...TAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG
width(assembly)             
## [1] 30427671 19698289 23459830 18585056 26975502   154478   366924
summary(width(assembly))
##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
##   154500  9476000 19700000 17100000 25220000 30430000
sum(width(assembly))
## [1] 119667750
hist(log10( width(assembly)), 100)

unlist(assembly)
##   119667750-letter "DNAString" instance
## seq: CCCTAAACCCTAAACCCTAAACCCTAAACCTCTG...CATTCTTATCGCAGAATGGAAACAAACCGGATT

Manipulate assembly object:

Subset [[ ]]

largest.contig = assembly[[ which(width(assembly)==max(width(assembly))) ]]
largest.contig
##   30427671-letter "DNAString" instance
## seq: CCCTAAACCCTAAACCCTAAACCCTAAACCTCTG...TAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG

Subset [ 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 Chr4

names

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 Chr1

subseq

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                                   ChrM

nucleotide 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,] 0

letterFrequency: 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,] 0
head(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,] 0.3629384

sliding 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   18633
head(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,]   1846
head(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   1007

reverse-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 ChrM

duplicated

duplicated(assembly[c(1,3)])
## [1] FALSE FALSE

unique 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 Chr3

Manipulate 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 cycles

CountLines in a fastQ file;

countLines("DATA/SRR031724_1_subset.fastq")
## SRR031724_1_subset.fastq 
##                  4000000

Inspect 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 GAATTTTTTGAGAGCGAAATGATAGCCGATGCCCTGA
head(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=37

Example 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] 0.5457237

Alphabet 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 GAATTTTTTGAGAGCGAAATGATAGCCGATGCCCTGA
fqtrim <- trimLRPatterns(Lpattern="GTT", subject=fq)
sread(fqtrim)[1:2]
##   A DNAStringSet instance of length 2
##     width seq
## [1]    34 TTGTCCAAGTTCTGGTAGCTGAATCCTGGGGCGC
## [2]    34 GTCGCATTCCTTACTCTCATTCGGGAATTCTGTT