# enhancerHomologSearch Guide

## Introduction

There is an increasing requirement for the tools to identify of putative mammalian orthologs to enhancers in species other than human and mouse, such as zebrafish, which is lacking whole genome comparison analysis data. Take zebrafish as an example, there are two major methods to identify the orthologs to enhancers in human and mouse,

1. use the whole genome comparison analysis data and conservation data1,

2. use spotted gar genome as bridge genome to search the orthologs2.

Both methods will work well in the coding region. However, there is lacking comparative data in distal regulation region such as enhancers and silencers.

In 2020, Emily S. Wong et. al. provides a new method for identification of putative human orthologs to enhancers of zebrafish3. They used the method to interrogate conserved syntenic regions and human and mouse using candidate sponge enhancer sequences. First, they looked for overlap with available functional genomics information. For example, they used mouse ENCODE data to infer enhancer activity based on histone marks in specific tissues. Second, they select the best-aligned region by whole genome alignment from the candidates regions for human and mouse as orthologs. This method provides the possibility to search orthologs for enhancers or silencers even there is not genome comparative data available.

This package is modified from Wong’s methods and provide the easy-to-use script for researchers to quick search putative mammalian orthologs to enhancers. The modified algorithm is: The candidate regions were determined by ENCODE histone marks (default is H3K4me1) in specific tissue for human and mouse. The mapping score were calculated by pairwise Transcription Factors Binding Pattern Similarity (TFBPS) between enhancer sequences and candidates by fast motif match4. The Z-score were calculated from mapping score and then converted to P-value based on two-side test from a normal distribution. The candidates were filtered by p-value and distance from the TSS of target homologs. And then the top candidates from human and mouse were aligned to each other and exported as multiple alignments with given enhancer.

## Installation

First install `enhancerHomologSearch` and other packages required to run the examples. Please note the example dataset used here is from zebrafish. To run analysis with dataset from a different species or different assembly, please install the corresponding Bsgenome and TxDb. For example, to analyze cattle data aligned to bosTau9, please install BSgenome.Btaurus.UCSC.bosTau9, and TxDb.Btaurus.UCSC.bosTau9.refGene. You can also generate a TxDb object by functions makeTxDbFromGFF from a local gff file, or makeTxDbFromUCSC, makeTxDbFromBiomart, and makeTxDbFromEnsembl, from online resources in GenomicFeatures package.

    if (!"BiocManager" %in% rownames(installed.packages()))
         install.packages("BiocManager")
    library(BiocManager)
    BiocManager::install(c("enhancerHomologSearch",
                           "BiocParallel",
                           "BSgenome.Drerio.UCSC.danRer10",
                           "BSgenome.Hsapiens.UCSC.hg38",
                           "BSgenome.Mmusculus.UCSC.mm10",
                           "TxDb.Hsapiens.UCSC.hg38.knownGene",
                           "TxDb.Mmusculus.UCSC.mm10.knownGene",
                           "org.Hs.eg.db",
                           "org.Mm.eg.db",
                           "MotifDb",
                           "motifmatchr"))

If you have trouble in install enhancerHomologSearch, please check your R version first. The `enhancerHomologSearch` package require R >= 4.1.0.

    R.version

    ##                _
    ## platform       x86_64-pc-linux-gnu
    ## arch           x86_64
    ## os             linux-gnu
    ## system         x86_64, linux-gnu
    ## status
    ## major          4
    ## minor          6.0
    ## year           2026
    ## month          04
    ## day            24
    ## svn rev        89956
    ## language       R
    ## version.string R version 4.6.0 (2026-04-24)
    ## nickname       Because it was There

## Step 1, prepare target enhancer sequences.

In this example, we will use an enhancer of `lepb` gene in zebrafish.

    # load genome sequences
    library(BSgenome.Drerio.UCSC.danRer10)
    # define the enhancer genomic coordinates
    LEN <- GRanges("chr4", IRanges(19050041, 19051709))
    # extract the sequences as Biostrings::DNAStringSet object
    (seqEN <- getSeq(BSgenome.Drerio.UCSC.danRer10, LEN))

    ## DNAStringSet object of length 1:
    ##     width seq
    ## [1]  1669 TGGCATACACAGCAAACATCATGAATTTAATTTA...TAGATAAATAGAAACAGAAGCAAATTGGCGAGT

## Step 2, download candidate regions of enhancers from ENCODE by H3K4me1 marks

By default, the hisone marker is H3K4me1. Users can also define the markers by `markers` parameter in the function `getENCODEdata`. To make sure the markers are tissue specific, we can filter the data by `biosample_name` and `biosample_type` parameters. For additional filters, please refer `?getENCODEdata`.

    # load library
    library(enhancerHomologSearch)
    library(BSgenome.Hsapiens.UCSC.hg38)
    library(BSgenome.Mmusculus.UCSC.mm10)
    # download enhancer candidates for human heart tissue
    hs <- getENCODEdata(genome=Hsapiens,
                        partialMatch=c(biosample_summary = "heart"))

    # download enhancer candidates for mouse heart tissue
    mm <- getENCODEdata(genome=Mmusculus,
                        partialMatch=c(biosample_summary = "heart"))

## Step 3, get alignment score for target enhancer and candidate enhancers.

Previous methods were get alignment score from the alignment of enhancer and candidate enhancers via the function `alignmentOne`. However, most of the enhancer evolution are rapid. This package is modified from Wong’s methods and calculate the alignment score by pairwise Transcription Factors Binding Pattern Similarity (TFBPS) between enhancer sequences and candidates. This step is time consuming step. For quick run, users can subset the data by given genomic coordinates.

    # subset the data for test run
    # in human, the homolog LEP gene is located at chromosome 7
    # In this test run, we will only use upstream 1M and downstream 1M of homolog
    # gene
    library(TxDb.Hsapiens.UCSC.hg38.knownGene)
    library(org.Hs.eg.db)
    eid <- mget("LEP", org.Hs.egALIAS2EG)[[1]]
    g_hs <- select(TxDb.Hsapiens.UCSC.hg38.knownGene,
                   keys=eid,
                   columns=c("GENEID", "TXCHROM", "TXSTART", "TXEND", "TXSTRAND"),
                   keytype="GENEID")
    g_hs <- range(with(g_hs, GRanges(TXCHROM, IRanges(TXSTART, TXEND))))
    expandGR <- function(x, ext){
      stopifnot(length(x)==1)
      start(x) <- max(1, start(x)-ext)
      end(x) <- end(x)+ext
      GenomicRanges::trim(x)
    }
    hs <- subsetByOverlaps(hs, expandGR(g_hs, ext=1000000))
    # in mouse, the homolog Lep gene is located at chromosome 6
    # Here we use the subset of 1M upstream and downstream of homolog gene.
    library(TxDb.Mmusculus.UCSC.mm10.knownGene)
    library(org.Mm.eg.db)
    eid <- mget("Lep", org.Mm.egALIAS2EG)[[1]]
    g_mm <- select(TxDb.Mmusculus.UCSC.mm10.knownGene,
                   keys=eid,
                   columns=c("GENEID", "TXCHROM", "TXSTART", "TXEND", "TXSTRAND"),
                   keytype="GENEID")
    g_mm <- range(with(g_mm,
                       GRanges(TXCHROM,
                               IRanges(TXSTART, TXEND),
                               strand=TXSTRAND)))
    g_mm <- g_mm[seqnames(g_mm) %in% "chr6" & strand(g_mm) %in% "+"]
    mm <- subsetByOverlaps(mm, expandGR(g_mm, ext=1000000))

    # search the binding pattern
    data(motifs)
    ## In the package, there are 10 sets of motif cluster sets.
    ## In this example, we use motif clusters merged by distance 60, which
    ## is calculated by matalgin (motifStack implementation)
    PWMs <- motifs[["dist60"]]
    ## Here we set maximalShuffleEnhancers = 100 to decrease the computation time.
    ## The defaults of maximalShuffleEnhancers is 1000. Increase the shuffle number
    ## may help to get accurate P-value.
    aln_hs <- searchTFBPS(seqEN, hs, PWMs = PWMs,
                          queryGenome = Drerio,
                          maximalShuffleEnhancers = 100)
    aln_mm <- searchTFBPS(seqEN, mm, PWMs = PWMs,
                          queryGenome = Drerio,
                          maximalShuffleEnhancers = 100)
    ## if you want to stick to sequence similarity search, try to use ?alignmentOne

## Step 4, filter the candidate regions.

Here we will filter the candidate regions more than 5K from TSS of homolog but within 100K from the gene body. The candidates will be also filtered by p-value.

    # Step4
    ext <- 100000
    aln_hs <- subsetByOverlaps(aln_hs, ranges = expandGR(g_hs, ext=ext))
    ## filter by distance
    distance(aln_hs) <- distance(peaks(aln_hs), g_hs, ignore.strand=TRUE)
    aln_hs <- subset(aln_hs, pval<0.1 & distance >5000)
    aln_hs

    ## This is an object with  1  Enhancers for  Homo sapiens

    aln_mm <- subsetByOverlaps(aln_mm, ranges = expandGR(g_mm, ext=ext))
    ## filter by distance
    distance(aln_mm) <- distance(peaks(aln_mm), g_mm, ignore.strand=TRUE)
    aln_mm <- subset(aln_mm, pval<0.1 & distance >5000)
    aln_mm

    ## This is an object with  3  Enhancers for  Mus musculus

## Step 5, alignment for the enhancer and the orthologs

This step will create alignments for all combination of the enhancer and the orthologs.

    aln_list <- list(human=aln_hs, mouse=aln_mm)
    al <- alignment(seqEN, aln_list,
                    method="ClustalW", order="input")
    al

    ## [[1]]
    ## DNAMultipleAlignment with 3 rows and 1676 columns
    ##      aln                                                    names
    ## [1] TGGCATACACAGCAAACATCATGAAT...TAGAAACAGAAGCAAATTGGCGAGT Enhancer
    ## [2] --------------------------...------------------------- human_chr7:128264...
    ## [3] --------------------------...------------------------- mouse_chr6:290320...
    ##
    ## [[2]]
    ## DNAMultipleAlignment with 3 rows and 1707 columns
    ##      aln                                                    names
    ## [1] TGGCATACACAGCAAACATCATGAAT...TAGAAACAGAAGCAAATTGGCGAGT Enhancer
    ## [2] --------------------------...------------------------- human_chr7:128264...
    ## [3] --------------------------...------------------------- mouse_chr6:291474...
    ##
    ## [[3]]
    ## DNAMultipleAlignment with 3 rows and 1683 columns
    ##      aln                                                    names
    ## [1] TGGCATACACAGCAAACATCATGAAT...TAGAAACAGAAGCAAATTGGCGAGT Enhancer
    ## [2] --------------------------...------------------------- human_chr7:128264...
    ## [3] --------------------------...------------------------- mouse_chr6:290312...

## Step 6a, for quick evolution enhancers, check the conserved motifs in the orthologs

Different form finding motif hits from the consensus of multiple alignment results, the `conservedMotifs` function will search the user defined motifs form available homologs.

    cm <- conservedMotifs(al[[1]], aln_list, PWMs, Drerio)

## Step 6b, for slow evolution enhancers, export the multiple alignments in order.

The selected candidates will be aligned cross human and mouse and then output as phylip multiple alignment file in `text` or `html` format.

    library(MotifDb)
    motifs <- query(MotifDb, "JASPAR_CORE")
    consensus <- sapply(motifs, consensusString)
    consensus <- DNAStringSet(gsub("\\?", "N", consensus))
    tmpfolder <- tempdir()
    saveAlignments(al, output_folder = tmpfolder, motifConsensus=consensus)
    readLines(file.path(tmpfolder, "aln1.phylip.txt"))

    ##   [1] " 5 1676"
    ##   [2] "TGGCATACAC AGCAAACATC ATGAATTTAA TTTAATTTAA TTTAATTTAA TTTAATTTTT TTAATTTAAT TTTAATATTT TAAAATAAAA TAAAATAAAA TAAAATAAAA TAAAAGATAA AGATAAAGAT AAAATAAAAT TCAACTCAAT TAAATTAAAA CTAAGCTAAA ATAAAAATAC AATAAAATAA ATTTCAATTT AATGTAATTT AATTTAAAAA GGGACTACGC CGAAAAGAAA ATGAATGAAT GGATGAATAA ATAATTTAAT TTAATTTAAT TTAATTTAAT TTAATTTAAT TTAATTTAAT TTAATTTAAT TTAATTTAAT TTAATTTAAT TTAATTTAAT TTAATTTAAT TTGTTCGGCA CAGTATAATA TGCTAGCATC TCAGTTATTT CACGTGTGTT GTTACTATAA AATAAGCAAA ACAGTGATAA AATAAGTTTG TGTTGCTTAT CTTATGACTG GTGGAATGTA ACAGGGAAAA AAAGCACATA CTGTGACTTT GACAAAACTG AGTGACTGAT GATAATAAAC TTCTCTTCTC GTAAGCTGAC AGTTCATAAA ACCTCTGCTT GTTTTTTTGT ACTTTTAATC TTAAGGTGAC GCATGTAGCT TCCTGTCCTT CT-CAGTTTA CTGACAGAGG TTAGGGTTTA -ATCCCAGAT ATCCAGTCTG ACTGTACAGT AGTTCAGGAG ACCGACGCAG ATTTATAGCA TCATTCGTCA AACCCTGAGG ATAATCATTT GTCACAGCTT CCTTTGGTCA TCATTACTGT GCAAATAAAC TGTTAGAGCA TGAGCCAGCA AAAACAGTGG GAAACGCAGC AATTTCCTGT ATTTAATAGT CTGTGAGATA TACTTTAATG AGATGAAATT GAAGAAAACT GAGTCATTAG AAAGGCATTC ACATAAACTT TCCTGGTGTA TATTTCCTAA CTCTCTTCCA GTGTTTTCTA CACCAGAAGA GTTCATTACA TCATTGAAGG ACAATGCTGA AAAATAAGAA CGCGTTTGGT TTTTCATAAA CCACATGGTC TTGTGGGTCA TGTTGTTTTG TTTCTTTAGA TTTGAGAGAC GGGGAATGAT GTGATTTTGC CCAGTCAGCA TGGATATGAT TTGGACTTCC ATCTGTTTAA GATTAAATGG TAGACAGAGA GAAATATTTC TGTTTTTTTT ATCCATGATT GCAAATCTGT GGGTTCAAAG TCTGCTTTTG TTCCAAATAA TCATTCAAAC CTGCCGTACT GTGTGGGGTG GGAAGTGAAG GAGGATCTTA TCTGGAA--A TCATGTGCTG TATGATGAAG GCAGGATATG GAAAACTCC- AAATATGGAC ACC-TTTATG TGTGCAAGGG AGAAAGTCTG AAGGATGCAA CCTGTTCATA ACATTTTCAT TCAAATTTAA ACTAGTTTGA TTAATTCCAA ATGCACATTT GATTTGTTGT GTTTTTATGA TGTATTTCAC AATACTGTTG CATAAAATAT CTAAAAAAAA CATTTAGTTA TATGGAAGAC ACTTGGACAA CTGGTTGTTA TTTGTTTGTC TATTTTTATG AATGCCTCAA AGATCAAATA GTTACACAC- TTAATGCAAT CGAGCTTAGA GAGAGAAATT AAAAGTCTTA AATAAATTGT GATTAGATAA ATAGAAACAG AAGCAAATTG GCGAGT   TGGCATACAC AGCAAACATC ATGAATTTAA TTTAATTTAA TTTAATTTAA"
    ##   [3] "---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ------GAAC AGAGAGGATT GCCTGGAG-- -GTTCCTAGG ACCACAGCAA GAGGTGTT-- GTGGGGGGCT T---CCCGGC T-TCCCGGAG GCCCTTCTTC CCATGACAGG AGG---GACA GTGGAGATAG CACCTACTCT GGTGACCTTG C--TCTCTGC TTTT---GTC TTGTGACC-T GCTTGTGG-- --GTGAGCCC TACCCCTTGG -TTTCCACGT GACCCAT-AA AGTCTACTCA TTTTCTGTCC AG-GGTTCA- -GGCACAGAG AGAAAAGGCA AGGATGTGGA GGGAGAGGAG AGTC-CCTGG AAGGAATGTC CCC-AGCATA T-CAGCCTGG AGTTTCCATT CAGGAAATTT CCCCAGCTCC CCAGACCCTC CCA--GACTT GCCTCCTCCC TCCTGACAAA GCCCCAGCCC -TACC-CATA GCCCCAGCCA CCACCCCCTT T-GAGGAGAG AAGGTGCTGG GTTGGGTGAG GAGCTCTGCG GGAGGACTGA AC-CA-AGCT --GTGGGCTC CTGGGC---A CCTGCCCA-- --TG--AGCC AGGCCTGCAT CTCCCAGACC TGCTTGTGGG TGAGCCTGCA TGCTGACATG CTTGGCTGGG CTCTAGCC-- TTGGCTATTG GTGGC--CCA GGGTGTGTGT GTGTGTGCGT GCATGTGTGT GTGTGTCC-C TTTGGAGCTA TGTAGTTTGT GTACCAAAAT AAGAAGGGAG CTGGGGAGTT GAGCCCTGAT GAACTTTGTA ACAATAA--A GCCTTATCTT GTTAAATAAA TCAAGCCTTG AATAAATGC- CTGCTTATTC CTTGCCAATA TTTTCCTGCT ACCTAAGGCA ACATAGCTCT GTGACCTGTA ACCAGTCACT TAACCTCTCT GG------GT CTATTTCCAT ATCTATAGAA AGTGGATATA ATACT-ATT- TGTTCTCCTC AATGCTGCTT ATTGTAGAGA TCAAATGTAA TAACG---TG TGTGAAAG-- ---TGCTTTA TAGATGGCAA GGTGCTGTTC TGCTGTAAGG AATCCTTCTG ATCATTACGC TTTTTGTAAA GCAATCAGAA CAGCCATC-- ---------- ---------- ---------- ---------- ---------- ---------- ------   ---------- ---------- ---------- ---------- ----------"
    ##   [4] "---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---TCTGAAC TGCCTTGTTT ACCAGCTG-- -TCTTGCTAA ACCTCAGCCT ATGCCGGTA- GCAGGCTGTT TAGGCCGGGT TATTCTAGAG CTTGGATCTT TAGTGGTTTA ATGTTTAAGG ATGCATCAGG GGCTTCCGAT GGCCAGCCTG CGGCTGCTTC CGAT---GAC AGATATCCAT GCGTATGGC- TCGTGACACT CTTCCCGTGG -CATCCAGCA GAATTG--GA GCTCCAAGCA GACCTGGTCT GCCAGTTGC- -AAAACGTCT TCCATACAAA GAGGCATGTC AGAATGCAAG CAAC-CGTCT GGGCATCATT ACG-GGGTTA T-GTGGAATC TGTTCTAATT GATTAAAACC AGGAAGATCA TCAATCATTC GAA--AGCCT CGACAGTTTG TTATTAGGTA GCCACTTGCC -TATGACACA CCTCAAAACT GCTCCAGGCA T-GCAGCATG TTAGGACACC GCTGTGGGAA AAACCGCTGG TCACGATGAT GC-CAGAGCC --GCCAGTTG TGAAAT---G AAAACCAA-- --TGCCAGCT AACTAATTGT TTCAACTACC C-TGTGCCAA AGAATCGATT GGGGAGAACA TTTTGTCCAC ACTCACCCGA TTGGC--TTG GTGGT--CTT GGTCCTGTAG AGATGCAGCC GGAGTATCAG GAATGTGG-G CCTAGTGTCA GGTA--TCAG AATTCGAGGC TGGAAGGAGC CTCCAGAGAG AGAGTTTCAT GCATTCCCTT CATGTCACCA ACAAGGATCA GAGGGAGCAG CCAGGCTGCT GAAGGGCGCG CCACACAATT GTGGACTATT GTTTTCAGAA A--GAGGTCA ATGAGGGCAC ATCTTTGCCC ACAGCATTTT TAACATTTTC GC------AG CTATTTCAGA ATC---ACGG TGCCCACTGA ATGGC-ATTG CGTACTTTCT AAAAGTAGAC A----AGAAT TTGAGAAACA CCCCG---TG -GTGCAAC-- ---TG-TTCA TTGCTTA-AA CCTACTGCTG ACTCATTTG- ---CCCTTCG ATACTT---C TTTACCAACA TCGGTGGTGG CATCT----- ---------- ---------- ---------- ---------- ---------- ---------- ------   ---------- ---------- ---------- ---------- ----------"
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    ##   [9] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
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    ##  [14] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TAAAATAAAA TAAAAGATAA AGATAAAGAT AAAATAAAAT TCAACTCAAT"
    ##  [15] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
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    ##  [21] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
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    ##  [26] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      AATGTAATTT AATTTAAAAA GGGACTACGC CGAAAAGAAA ATGAATGAAT"
    ##  [27] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [28] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [29] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [30] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [31] ""
    ##  [32] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GGATGAATAA ATAATTTAAT TTAATTTAAT TTAATTTAAT TTAATTTAAT"
    ##  [33] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [34] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [35] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [36] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [37] ""
    ##  [38] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TTAATTTAAT TTAATTTAAT TTAATTTAAT TTAATTTAAT TTAATTTAAT"
    ##  [39] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [40] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [41] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [42] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [43] ""
    ##  [44] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TTAATTTAAT TTGTTCGGCA CAGTATAATA TGCTAGCATC TCAGTTATTT"
    ##  [45] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [46] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [47] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [48] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [49] ""
    ##  [50] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CACGTGTGTT GTTACTATAA AATAAGCAAA ACAGTGATAA AATAAGTTTG"
    ##  [51] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [52] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [53] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [54] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [55] ""
    ##  [56] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TGTTGCTTAT CTTATGACTG GTGGAATGTA ACAGGGAAAA AAAGCACATA"
    ##  [57] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [58] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [59] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [60] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [61] ""
    ##  [62] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CTGTGACTTT GACAAAACTG AGTGACTGAT GATAATAAAC TTCTCTTCTC"
    ##  [63] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ------GAAC AGAGAGGATT"
    ##  [64] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---TCTGAAC TGCCTTGTTT"
    ##  [65] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- -----T-AAC T-C--T--T-"
    ##  [66] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [67] ""
    ##  [68] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GTAAGCTGAC AGTTCATAAA ACCTCTGCTT GTTTTTTTGT ACTTTTAATC"
    ##  [69] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GCCTGGAG-- -GTTCCTAGG ACCACAGCAA GAGGTGTT-- GTGGGGGGCT"
    ##  [70] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ACCAGCTG-- -TCTTGCTAA ACCTCAGCCT ATGCCGGTA- GCAGGCTGTT"
    ##  [71] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      G--AGCTG-- -GTTC-TAAA ACCTC-GC-T GT--T-TT-- -C------T-"
    ##  [72] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [73] ""
    ##  [74] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TTAAGGTGAC GCATGTAGCT TCCTGTCCTT CT-CAGTTTA CTGACAGAGG"
    ##  [75] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      T---CCCGGC T-TCCCGGAG GCCCTTCTTC CCATGACAGG AGG---GACA"
    ##  [76] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TAGGCCGGGT TATTCTAGAG CTTGGATCTT TAGTGGTTTA ATGTTTAAGG"
    ##  [77] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      T------G-C ---T-TAG-- -CC-GTCCTT C----GTTTA -TG---GAGG"
    ##  [78] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [79] ""
    ##  [80] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TTAGGGTTTA -ATCCCAGAT ATCCAGTCTG ACTGTACAGT AGTTCAGGAG"
    ##  [81] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GTGGAGATAG CACCTACTCT GGTGACCTTG C--TCTCTGC TTTT---GTC"
    ##  [82] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ATGCATCAGG GGCTTCCGAT GGCCAGCCTG CGGCTGCTTC CGAT---GAC"
    ##  [83] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      -T-G-G-T-- -A-C-C-GAT --CCAG-CTG ----T-C-G- -GTT---GA-"
    ##  [84] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ------NGAT N--------- ---------- ----------"
    ##  [85] ""
    ##  [86] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ACCGACGCAG ATTTATAGCA TCATTCGTCA AACCCTGAGG ATAATCATTT"
    ##  [87] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TTGTGACC-T GCTTGTGG-- --GTGAGCCC TACCCCTTGG -TTTCCACGT"
    ##  [88] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      AGATATCCAT GCGTATGGC- TCGTGACACT CTTCCCGTGG -CATCCAGCA"
    ##  [89] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      A---A--CA- --TTAT-GC- TC-T--G-C- -ACCC-G-GG -TA--CA--T"
    ##  [90] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [91] ""
    ##  [92] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GTCACAGCTT CCTTTGGTCA TCATTACTGT GCAAATAAAC TGTTAGAGCA"
    ##  [93] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GACCCAT-AA AGTCTACTCA TTTTCTGTCC AG-GGTTCA- -GGCACAGAG"
    ##  [94] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GAATTG--GA GCTCCAAGCA GACCTGGTCT GCCAGTTGC- -AAAACGTCT"
    ##  [95] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      G-C-CA---- -CT-T--TCA T--TT--T-T GC-A-T--A- -G--A-AGC-"
    ##  [96] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ##  [97] ""
    ##  [98] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TGAGCCAGCA AAAACAGTGG GAAACGCAGC AATTTCCTGT ATTTAATAGT"
    ##  [99] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      AGAAAAGGCA AGGATGTGGA GGGAGAGGAG AGTC-CCTGG AAGGAATGTC"
    ## [100] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TCCATACAAA GAGGCATGTC AGAATGCAAG CAAC-CGTCT GGGCATCATT"
    ## [101] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TGA----GCA AA-ACA--G- G-AA-GCA-- AAT--CCTGT A---AATA-T"
    ## [102] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [103] ""
    ## [104] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CTGTGAGATA TACTTTAATG AGATGAAATT GAAGAAAACT GAGTCATTAG"
    ## [105] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CCC-AGCATA T-CAGCCTGG AGTTTCCATT CAGGAAATTT CCCCAGCTCC"
    ## [106] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ACG-GGGTTA T-GTGGAATC TGTTCTAATT GATTAAAACC AGGAAGATCA"
    ## [107] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      C-G-G-GATA T-CT--AATG AG-T--AATT GA-GAAAACT --G----T--"
    ## [108] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [109] ""
    ## [110] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      AAAGGCATTC ACATAAACTT TCCTGGTGTA TATTTCCTAA CTCTCTTCCA"
    ## [111] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CCAGACCCTC CCA--GACTT GCCTCCTCCC TCCTGACAAA GCCCCAGCCC"
    ## [112] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TCAATCATTC GAA--AGCCT CGACAGTTTG TTATTAGGTA GCCACTTGCC"
    ## [113] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      --AG-CATTC -CA--AACTT -CCT-GT-T- T--TT-C-AA --C-CTTCC-"
    ## [114] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [115] ""
    ## [116] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GTGTTTTCTA CACCAGAAGA GTTCATTACA TCATTGAAGG ACAATGCTGA"
    ## [117] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      -TACC-CATA GCCCCAGCCA CCACCCCCTT T-GAGGAGAG AAGGTGCTGG"
    ## [118] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      -TATGACACA CCTCAAAACT GCTCCAGGCA T-GCAGCATG TTAGGACACC"
    ## [119] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      -T-T----TA C-CCA-AA-A G-TC----CA T----GAA-G A-A-TGCTG-"
    ## [120] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [121] ""
    ## [122] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      AAAATAAGAA CGCGTTTGGT TTTTCATAAA CCACATGGTC TTGTGGGTCA"
    ## [123] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GTTGGGTGAG GAGCTCTGCG GGAGGACTGA AC-CA-AGCT --GTGGGCTC"
    ## [124] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GCTGTGGGAA AAACCGCTGG TCACGATGAT GC-CAGAGCC --GCCAGTTG"
    ## [125] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ----T--GAA ----T-TGG- T----AT-AA -C-CA--G-C --GTGGGT--"
    ## [126] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [127] ""
    ## [128] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TGTTGTTTTG TTTCTTTAGA TTTGAGAGAC GGGGAATGAT GTGATTTTGC"
    ## [129] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CTGGGC---A CCTGCCCA-- --TG--AGCC AGGCCTGCAT CTCCCAGACC"
    ## [130] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TGAAAT---G AAAACCAA-- --TGCCAGCT AACTAATTGT TTCAACTACC"
    ## [131] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TG--GT---G --T----A-- --TG--AG-C -GG-AAT-AT -T-A--T--C"
    ## [132] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [133] ""
    ## [134] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CCAGTCAGCA TGGATATGAT TTGGACTTCC ATCTGTTTAA GATTAAATGG"
    ## [135] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TGCTTGTGGG TGAGCCTGCA TGCTGACATG CTTGGCTGGG CTCTAGCC--"
    ## [136] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      C-TGTGCCAA AGAATCGATT GGGGAGAACA TTTTGTCCAC ACTCACCCGA"
    ## [137] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      C--GT--G-A TG-AT-TG-T T-GGA---C- -T-TGTT-A- --TTA---G-"
    ## [138] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [139] ""
    ## [140] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TAGACAGAGA GAAATATTTC TGTTTTTTTT ATCCATGATT GCAAATCTGT"
    ## [141] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TTGGCTATTG GTGGC--CCA GGGTGTGTGT GTGTGTGCGT GCATGTGTGT"
    ## [142] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TTGGC--TTG GTGGT--CTT GGTCCTGTAG AGATGCAGCC GGAGTATCAG"
    ## [143] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      T-G-C----- G---T---T- -GTT-T-T-T AT---TG--T GCA--T-TGT"
    ## [144] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [145] ""
    ## [146] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GGGTTCAAAG TCTGCTTTTG TTCCAAATAA TCATTCAAAC CTGCCGTACT"
    ## [147] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GTGTGTCC-C TTTGGAGCTA TGTAGTTTGT GTACCAAAAT AAGAAGGGAG"
    ## [148] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GAATGTGG-G CCTAGTGTCA GGTA--TCAG AATTCGAGGC TGGAAGGAGC"
    ## [149] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      G-GT-----G TCTG-T-TT- T------TA- --AT--AAAC --G--G-A--"
    ## [150] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [151] ""
    ## [152] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GTGTGGGGTG GGAAGTGAAG GAGGATCTTA TCTGGAA--A TCATGTGCTG"
    ## [153] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CTGGGGAGTT GAGCCCTGAT GAACTTTGTA ACAATAA--A GCCTTATCTT"
    ## [154] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CTCCAGAGAG AGAGTTTCAT GCATTCCCTT CATGTCACCA ACAAGGATCA"
    ## [155] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      -TG-GG-GTG GGA--T--A- GA---TC-TA -CTG-AA--A -CATG--CT-"
    ## [156] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [157] ""
    ## [158] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TATGATGAAG GCAGGATATG GAAAACTCC- AAATATGGAC ACC-TTTATG"
    ## [159] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GTTAAATAAA TCAAGCCTTG AATAAATGC- CTGCTTATTC CTTGCCAATA"
    ## [160] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GAGGGAGCAG CCAGGCTGCT GAAGGGCGCG CCACACAATT GTGGACTATT"
    ## [161] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      -ATGA-GAAG -CAGG-T-TG GAAAA-T-C- --A-AT---C ------TAT-"
    ## [162] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [163] ""
    ## [164] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TGTGCAAGGG AGAAAGTCTG AAGGATGCAA CCTGTTCATA ACATTTTCAT"
    ## [165] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TTTTCCTGCT ACCTAAGGCA ACATAGCTCT GTGACCTGTA ACCAGTCACT"
    ## [166] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GTTTTCAGAA A--GAGGTCA ATGAGGGCAC ATCTTTGCCC ACAGCATTTT"
    ## [167] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      T-T-C-AG-- A---AG---- A-G-A-GCA- ----TT--TA ACA--TT--T"
    ## [168] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- --------TA ACA-------"
    ## [169] ""
    ## [170] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TCAAATTTAA ACTAGTTTGA TTAATTCCAA ATGCACATTT GATTTGTTGT"
    ## [171] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TAACCTCTCT GG------GT CTATTTCCAT ATCTATAGAA AGTGGATATA"
    ## [172] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TAACATTTTC GC------AG CTATTTCAGA ATC---ACGG TGCCCACTGA"
    ## [173] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      T-A-ATTT-- -C------G- -TA-TTCCAA AT--A-A--- --T---TTG-"
    ## [174] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [175] ""
    ## [176] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GTTTTTATGA TGTATTTCAC AATACTGTTG CATAAAATAT CTAAAAAAAA"
    ## [177] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ATACT-ATT- TGTTCTCCTC AATGCTGCTT ATTGTAGAGA TCAAATGTAA"
    ## [178] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ATGGC-ATTG CGTACTTTCT AAAAGTAGAC A----AGAAT TTGAGAAACA"
    ## [179] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      -T--T-AT-- TGTA-TTC-C AATACTG-T- --T--A--AT -TAAAAAAAA"
    ## [180] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [181] ""
    ## [182] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CATTTAGTTA TATGGAAGAC ACTTGGACAA CTGGTTGTTA TTTGTTTGTC"
    ## [183] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TAACG---TG TGTGAAAG-- ---TGCTTTA TAGATGGCAA GGTGCTGTTC"
    ## [184] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CCCCG---TG -GTGCAAC-- ---TG-TTCA TTGCTTA-AA CCTACTGCTG"
    ## [185] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CA------T- T-TG-AAG-- ---TG----A -TG-TTG--A --TG-T--TC"
    ## [186] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [187] ""
    ## [188] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TATTTTTATG AATGCCTCAA AGATCAAATA GTTACACAC- TTAATGCAAT"
    ## [189] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      TGCTGTAAGG AATCCTTCTG ATCATTACGC TTTTTGTAAA GCAATCAGAA"
    ## [190] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ACTCATTTG- ---CCCTTCG ATACTT---C TTTACCAACA TCGGTGGTGG"
    ## [191] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      T-TT-TTA-G AAT-CCTC-- A-A---A--- -TTAC--AC- T-AATG--A-"
    ## [192] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [193] ""
    ## [194] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CGAGCTTAGA GAGAGAAATT AAAAGTCTTA AATAAATTGT GATTAGATAA"
    ## [195] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CAGCCATC-- ---------- ---------- ---------- ----------"
    ## [196] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CATCT----- ---------- ---------- ---------- ----------"
    ## [197] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      C---C-T--- ---------- ---------- ---------- ----------"
    ## [198] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ---------- ---------- ----------"
    ## [199] ""
    ## [200] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ATAGAAACAG AAGCAAATTG GCGAGT"
    ## [201] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ------"
    ## [202] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ------"
    ## [203] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ------"
    ## [204] "                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ---------- ---------- ------"

## Session info

    sessionInfo()

    ## R version 4.6.0 (2026-04-24)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
    ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
    ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
    ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
    ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    ##
    ## time zone: Etc/UTC
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats4    stats     graphics  grDevices utils     datasets  methods
    ## [8] base
    ##
    ## other attached packages:
    ##  [1] motifmatchr_1.35.0
    ##  [2] MotifDb_1.55.0
    ##  [3] org.Mm.eg.db_3.23.0
    ##  [4] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0
    ##  [5] org.Hs.eg.db_3.23.1
    ##  [6] TxDb.Hsapiens.UCSC.hg38.knownGene_3.22.0
    ##  [7] GenomicFeatures_1.65.0
    ##  [8] AnnotationDbi_1.75.0
    ##  [9] Biobase_2.73.1
    ## [10] BSgenome.Mmusculus.UCSC.mm10_1.4.3
    ## [11] BSgenome.Hsapiens.UCSC.hg38_1.4.5
    ## [12] GenomeInfoDb_1.49.1
    ## [13] BSgenome.Drerio.UCSC.danRer10_1.4.2
    ## [14] BSgenome_1.81.0
    ## [15] rtracklayer_1.73.0
    ## [16] BiocIO_1.23.3
    ## [17] Biostrings_2.81.3
    ## [18] XVector_0.53.0
    ## [19] GenomicRanges_1.65.0
    ## [20] Seqinfo_1.3.0
    ## [21] IRanges_2.47.2
    ## [22] S4Vectors_0.51.3
    ## [23] BiocGenerics_0.59.7
    ## [24] generics_0.1.4
    ## [25] enhancerHomologSearch_1.19.2
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] DBI_1.3.0                   bitops_1.0-9
    ##  [3] httr2_1.2.2                 rlang_1.2.0
    ##  [5] magrittr_2.0.5              otel_0.2.0
    ##  [7] matrixStats_1.5.0           compiler_4.6.0
    ##  [9] RSQLite_3.53.1              png_0.1-9
    ## [11] vctrs_0.7.3                 pwalign_1.9.1
    ## [13] pkgconfig_2.0.3             crayon_1.5.3
    ## [15] fastmap_1.2.0               dbplyr_2.5.2
    ## [17] caTools_1.18.3              splitstackshape_1.4.8.1
    ## [19] Rsamtools_2.29.0            rmarkdown_2.31
    ## [21] UCSC.utils_1.9.0            DirichletMultinomial_1.55.0
    ## [23] purrr_1.2.2                 bit_4.6.0
    ## [25] xfun_0.58                   cachem_1.1.0
    ## [27] cigarillo_1.3.0             jsonlite_2.0.0
    ## [29] blob_1.3.0                  DelayedArray_0.39.3
    ## [31] BiocParallel_1.47.0         parallel_4.6.0
    ## [33] R6_2.6.1                    bslib_0.11.0
    ## [35] jquerylib_0.1.4             Rcpp_1.1.1-1.1
    ## [37] SummarizedExperiment_1.43.0 knitr_1.51
    ## [39] BiocBaseUtils_1.15.1        Matrix_1.7-5
    ## [41] tidyselect_1.2.1            abind_1.4-8
    ## [43] yaml_2.3.12                 codetools_0.2-20
    ## [45] curl_7.1.0                  lattice_0.22-9
    ## [47] tibble_3.3.1                withr_3.0.2
    ## [49] KEGGREST_1.53.0             evaluate_1.0.5
    ## [51] BiocFileCache_3.3.0         pillar_1.11.1
    ## [53] filelock_1.0.3              MatrixGenerics_1.25.0
    ## [55] RCurl_1.98-1.19             gtools_3.9.5
    ## [57] glue_1.8.1                  MultipleAlignment_0.99.4
    ## [59] maketools_1.3.2             seqLogo_1.79.0
    ## [61] tools_4.6.0                 TFMPvalue_1.0.0
    ## [63] sys_3.4.3                   data.table_1.18.4
    ## [65] GenomicAlignments_1.49.0    buildtools_1.0.0
    ## [67] XML_3.99-0.23               TFBSTools_1.51.0
    ## [69] grid_4.6.0                  restfulr_0.0.16
    ## [71] cli_3.6.6                   rappdirs_0.3.4
    ## [73] S4Arrays_1.13.0             dplyr_1.2.1
    ## [75] sass_0.4.10                 digest_0.6.39
    ## [77] SparseArray_1.13.2          rjson_0.2.23
    ## [79] memoise_2.0.1               htmltools_0.5.9
    ## [81] lifecycle_1.0.5             httr_1.4.8
    ## [83] bit64_4.8.2

1.
Howe, K. et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498–503 (2013).
2.
Braasch, I. et al. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature genetics 48, 427–437 (2016).
3.
Wong, E. S. et al. Deep conservation of the enhancer regulatory code in animals. Science 370, (2020).
4.
A, S. Motifmatchr: Fast motif matching in r. R package version