Last data update: 2014.03.03

 R: MultipleAlignment objects
MultipleAlignment-classR Documentation

MultipleAlignment objects

Description

The MultipleAlignment class is a container for storing multiple sequence alignments.

Usage

## Constructors:
DNAMultipleAlignment(x=character(), start=NA, end=NA, width=NA,
    use.names=TRUE, rowmask=NULL, colmask=NULL)
RNAMultipleAlignment(x=character(), start=NA, end=NA, width=NA,
    use.names=TRUE, rowmask=NULL, colmask=NULL)
AAMultipleAlignment(x=character(), start=NA, end=NA, width=NA,
    use.names=TRUE, rowmask=NULL, colmask=NULL)

## Read functions:
readDNAMultipleAlignment(filepath, format)
readRNAMultipleAlignment(filepath, format)
readAAMultipleAlignment(filepath, format)

## Write funtions:
write.phylip(x, filepath)

## ... and more (see below)

Arguments

x

Either a character vector (with no NAs), or an XString, XStringSet or XStringViews object containing strings with the same number of characters. If writing out a Phylip file, then x would be a MultipleAlignment object

start,end,width

Either NA, a single integer, or an integer vector of the same length as x specifying how x should be "narrowed" (see ?narrow in the IRanges package for the details).

use.names

TRUE or FALSE. Should names be preserved?

filepath

A character vector (of arbitrary length when reading, of length 1 when writing) containing the paths to the files to read or write. Note that special values like "" or "|cmd" (typically supported by other I/O functions in R) are not supported here. Also filepath cannot be a connection.

format

Either "fasta" (the default), stockholm, or "clustal".

rowmask

a NormalIRanges object that will set masking for rows

colmask

a NormalIRanges object that will set masking for columns

Details

The MultipleAlignment class is designed to hold and represent multiple sequence alignments. The rows and columns within an alignment can be masked for ad hoc analyses.

Accessor methods

In the code snippets below, x is a MultipleAlignment object.

unmasked(x): The underlying XStringSet object containing the multiple sequence alignment.

rownames(x): NULL or a character vector of the same length as x containing a short user-provided description or comment for each sequence in x.

rowmask(x), rowmask(x, append, invert) <- value: Gets and sets the NormalIRanges object representing the masked rows in x. The append argument takes union, replace or intersect to indicate how to combine the new value with rowmask(x). The invert argument takes a logical argument to indicate whether or not to invert the new mask. The value argument can be of any class that is coercible to a NormalIRanges via the as function.

colmask(x), colmask(x, append, invert) <- value: Gets and sets the NormalIRanges object representing the masked columns in x. The append argument takes union, replace or intersect to indicate how to combine the new value with colmask(x). The invert argument takes a logical argument to indicate whether or not to invert the new mask. The value argument can be of any class that is coercible to a NormalIRanges via the as function.

maskMotif(x, motif, min.block.width=1, ...): Returns a MultipleAlignment object with a modified column mask based upon motifs found in the consensus string where the consensus string keeps all the columns but drops the masked rows.

motif

The motif to mask.

min.block.width

The minimum width of the blocks to mask.

...

Additional arguments for matchPattern.

maskGaps(x, min.fraction, min.block.width): Returns a MultipleAlignment object with a modified column mask based upon gaps in the columns. In particular, this mask is defined by min.block.width or more consecutive columns that have min.fraction or more of their non-masked rows containing gap codes.

min.fraction

A value in [0, 1] that indicates the minimum fraction needed to call a gap in the consensus string (default is 0.5).

min.block.width

A positive integer that indicates the minimum number of consecutive gaps to mask, as defined by min.fraction (default is 4).

nrow(x): Returns the number of sequences aligned in x.

ncol(x): Returns the number of characters for each alignment in x.

dim(x): Equivalent to c(nrow(x), ncol(x)).

maskednrow(x): Returns the number of masked aligned sequences in x.

maskedncol(x): Returns the number of masked aligned characters in x.

maskeddim(x): Equivalent to c(maskednrow(x), maskedncol(x)).

maskedratio(x): Equivalent to maskeddim(x) / dim(x).

nchar(x): Returns the number of unmasked aligned characters in x, i.e. ncol(x) - maskedncol(x).

alphabet(x): Equivalent to alphabet(unmasked(x)).

Coercion

In the code snippets below, x is a MultipleAlignment object.

as(from, "DNAStringSet"), as(from, "RNAStringSet"), as(from, "AAStringSet"), as(from, "BStringSet"): Creates an instance of the specified XStringSet object subtype that contains the unmasked regions of the multiple sequence alignment in x.

as.character(x, use.names): Convert x to a character vector containing the unmasked regions of the multiple sequence alignment. use.names controls whether or not rownames(x) should be used to set the names of the returned vector (default is TRUE).

as.matrix(x, use.names): Returns a character matrix containing the "exploded" representation of the unmasked regions of the multiple sequence alignment. use.names controls whether or not rownames(x) should be used to set the row names of the returned matrix (default is TRUE).

Utilities

In the code snippets below, x is a MultipleAlignment object.

consensusMatrix(x, as.prob, baseOnly): Creates an integer matrix containing the column frequencies of the underlying alphabet with masked columns being represented with NA values. If as.prob is TRUE, then probabilities are reported, otherwise counts are reported (the default). If baseOnly is TRUE, then the non-base letters are collapsed into an "other" category.

consensusString(x, ...): Creates a consensus string for x with the symbol "#" representing a masked column. See consensusString for details on the arguments.

consensusViews(x, ...): Similar to the consensusString method. It returns a XStringViews on the consensus string containing subsequence contigs of non-masked columns. Unlike the consensusString method, the masked columns in the underlying string contain a consensus value rather than the "#" symbol.

alphabetFrequency(x, as.prob, collapse): Creates an integer matrix containing the row frequencies of the underlying alphabet. If as.prob is TRUE, then probabilities are reported, otherwise counts are reported (the default). If collapse is TRUE, then returns the overall frequency instead of the frequency by row.

detail(x, invertColMask, hideMaskedCols): Allows for a full pager driven display of the object so that masked cols and rows can be removed and the entire sequence can be visually inspected. If hideMaskedCols is set to it's default value of TRUE then the output will hide all the the masked columns in the output. Otherwise, all columns will be displayed along with a row to indicate the masking status. If invertColMask is TRUE then any displayed mask will be flipped so as to represent things in a way consistent with Phylip style files instead of the mask that is actually stored in the MultipleAlignment object. Please notice that invertColMask will be ignored if hideMaskedCols is set to its default value of TRUE since in that case it will not make sense to show any masking information in the output. Masked rows are always hidden in the output.

Author(s)

P. Aboyoun and M. Carlson

See Also

XStringSet-class, MaskedXString-class

Examples

## create an object from file
origMAlign <-
  readDNAMultipleAlignment(filepath =
                           system.file("extdata",
                                       "msx2_mRNA.aln",
                                       package="Biostrings"),
                           format="clustal")

## list the names of the sequences in the alignment
rownames(origMAlign)

## rename the sequences to be the underlying species for MSX2
rownames(origMAlign) <- c("Human","Chimp","Cow","Mouse","Rat",
                          "Dog","Chicken","Salmon")
origMAlign

## See a detailed pager view
if (interactive()) {
detail(origMAlign)
}

## operations to mask rows
## For columns, just use colmask() and do the same kinds of operations
rowMasked <- origMAlign
rowmask(rowMasked) <- IRanges(start=1,end=3)
rowMasked

## remove rowumn masks
rowmask(rowMasked) <- NULL
rowMasked

## "select" rows of interest
rowmask(rowMasked, invert=TRUE) <- IRanges(start=4,end=7)
rowMasked

## or mask the rows that intersect with masked rows
rowmask(rowMasked, append="intersect") <- IRanges(start=1,end=5)
rowMasked

## TATA-masked
tataMasked <- maskMotif(origMAlign, "TATA")
colmask(tataMasked)

## automatically mask rows based on consecutive gaps
autoMasked <- maskGaps(origMAlign, min.fraction=0.5, min.block.width=4)
colmask(autoMasked)
autoMasked

## calculate frequencies
alphabetFrequency(autoMasked)
consensusMatrix(autoMasked, baseOnly=TRUE)[, 84:90]

## get consensus values
consensusString(autoMasked)
consensusViews(autoMasked)

## cluster the masked alignments
sdist <- stringDist(as(autoMasked,"DNAStringSet"), method="hamming")
clust <- hclust(sdist, method = "single")
plot(clust)
fourgroups <- cutree(clust, 4)
fourgroups

## write out the alignement object (with current masks) to Phylip format
write.phylip(x = autoMasked, filepath = tempfile("foo.txt",tempdir()))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(Biostrings)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Biostrings/MultipleAlignment-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MultipleAlignment-class
> ### Title: MultipleAlignment objects
> ### Aliases: class:MultipleAlignment MultipleAlignment-class
> ###   MultipleAlignment class:DNAMultipleAlignment
> ###   DNAMultipleAlignment-class DNAMultipleAlignment
> ###   class:RNAMultipleAlignment RNAMultipleAlignment-class
> ###   RNAMultipleAlignment class:AAMultipleAlignment
> ###   AAMultipleAlignment-class AAMultipleAlignment
> ###   unmasked,MultipleAlignment-method rownames,MultipleAlignment-method
> ###   rownames<-,MultipleAlignment-method rowmask
> ###   rowmask,MultipleAlignment-method rowmask<-
> ###   rowmask<-,MultipleAlignment,NULL-method
> ###   rowmask<-,MultipleAlignment,NormalIRanges-method
> ###   rowmask<-,MultipleAlignment,ANY-method colmask
> ###   colmask,MultipleAlignment-method colmask<-
> ###   colmask<-,MultipleAlignment,NULL-method
> ###   colmask<-,MultipleAlignment,NormalIRanges-method
> ###   colmask<-,MultipleAlignment,ANY-method
> ###   maskMotif,MultipleAlignment,ANY-method maskGaps
> ###   maskGaps,MultipleAlignment-method nrow,MultipleAlignment-method
> ###   ncol,MultipleAlignment-method dim,MultipleAlignment-method maskednrow
> ###   maskednrow,MultipleAlignment-method maskedncol
> ###   maskedncol,MultipleAlignment-method maskeddim
> ###   maskeddim,MultipleAlignment-method
> ###   maskedratio,MultipleAlignment-method nchar,MultipleAlignment-method
> ###   seqtype,MultipleAlignment-method readDNAMultipleAlignment
> ###   readRNAMultipleAlignment readAAMultipleAlignment write.phylip
> ###   coerce,MultipleAlignment,DNAStringSet-method
> ###   coerce,MultipleAlignment,RNAStringSet-method
> ###   coerce,MultipleAlignment,AAStringSet-method
> ###   coerce,MultipleAlignment,BStringSet-method
> ###   coerce,character,DNAMultipleAlignment-method
> ###   coerce,character,RNAMultipleAlignment-method
> ###   coerce,character,AAMultipleAlignment-method
> ###   as.character,MultipleAlignment-method
> ###   as.matrix,MultipleAlignment-method
> ###   consensusMatrix,MultipleAlignment-method
> ###   consensusString,MultipleAlignment-method
> ###   consensusString,DNAMultipleAlignment-method
> ###   consensusString,RNAMultipleAlignment-method
> ###   consensusString,AAMultipleAlignment-method consensusViews
> ###   consensusViews,MultipleAlignment-method
> ###   consensusViews,DNAMultipleAlignment-method
> ###   consensusViews,RNAMultipleAlignment-method
> ###   consensusViews,AAMultipleAlignment-method
> ###   alphabetFrequency,MultipleAlignment-method
> ###   show,MultipleAlignment-method detail,MultipleAlignment-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> ## create an object from file
> origMAlign <-
+   readDNAMultipleAlignment(filepath =
+                            system.file("extdata",
+                                        "msx2_mRNA.aln",
+                                        package="Biostrings"),
+                            format="clustal")
> 
> ## list the names of the sequences in the alignment
> rownames(origMAlign)
[1] "gi|84452153|ref|NM_002449.4|"   "gi|208431713|ref|NM_001135625."
[3] "gi|118601823|ref|NM_001079614." "gi|114326503|ref|NM_013601.2|" 
[5] "gi|119220589|ref|NM_012982.3|"  "gi|148540149|ref|NM_001003098."
[7] "gi|45383056|ref|NM_204559.1|"   "gi|213515133|ref|NM_001141603."
> 
> ## rename the sequences to be the underlying species for MSX2
> rownames(origMAlign) <- c("Human","Chimp","Cow","Mouse","Rat",
+                           "Dog","Chicken","Salmon")
> origMAlign
DNAMultipleAlignment with 8 rows and 2343 columns
     aln                                                    names               
[1] -----TCCCGTCTCCGCAGCAAAAAA...TCACAATTAAAAAAAAAAAAAAAAA Human
[2] --------------------------...------------------------- Chimp
[3] --------------------------...------------------------- Cow
[4] ----------------------AAAA...------------------------- Mouse
[5] --------------------------...------------------------- Rat
[6] --------------------------...------------------------- Dog
[7] --------------CGGCTCCGCAGC...------------------------- Chicken
[8] GGGGGAGACTTCAGAAGTTGTTGTCC...------------------------- Salmon
> 
> ## See a detailed pager view
> #if (interactive()) {
> detail(origMAlign)
 8 2343
Human     -----TCCCG TCTCCGCAGC AAAAAAGTTT GAGTCGCCGC TGCCGGGTTG
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     ---------- ---------- --AAAAGTTG GAGTCTTCGC TTGAGAGTTG
Rat       ---------- ---------- ---------- ---------- ----------
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ----CGGCTC CGCAGCGCCT CACTCGCGCA GTCCCCGCGC
Salmon    GGGGGAGACT TCAGAAGTTG TTGTCCTCTC CGCTGATAAC AGTTGAGATG

Human     CCAGCGGAGT CGCGCGTCGG GAGCTACGTA GGGCAGAGAA GTCA-TGGCT
Chimp     ---------- ---------- ---------- ---------- ---A-TGGCT
Cow       ---------- ---------- ---------- ---GAGAGAA GTCA-TGGCT
Mouse     CCAGCGGAGT CGCGCGCCGA CAGCTACGCG GCGCAGA-AA GTCA-TGGCT
Rat       ---------- ---------- ---------- ---------- ---A-TGGCT
Dog       ---------- ---------- ---------- ---------- ---A-TGGCT
Chicken   AGGGCCGGGC AGAGGCGCAC GCAGCTCCCC GGGCGGCCCC GCTC-CAGCC
Salmon    CGCATATTAT TATTACCTTT AGGACAAGTT GAATGTGTTC GTCAACATCT

Human     TCTCCGTCCA AAGGCAATGA CTTGTTTTCG CCCGACGAGG AGGGCCCAGC
Chimp     TCTCCGTCCA AAGGCAATGA CTTGTTTTCG CCCGACGAGG AGGGCCCAGC
Cow       TCTCCGTCCA AAGGCAATGA CCTGTTTTCG TCCGATGAGG AGGGCCCGGC
Mouse     TCTCCGACTA AAGGCGGTGA CTTGTTTTCG TCGGATGAGG AGGGCCCCGC
Rat       TCTCCGTCCA AAGGCGGTGA CTTGTTTTCG TCTGATGAGG AGGGCCCCGC
Dog       TCTCCGTCCA AAGGCAGTGA CCTGTTCTCG TCCGATGAGG AGGGCCCGGC
Chicken   ACGCTCCGCA TTCGCGATGG CTTCTCCTTC CAAAGCGAAG GAGGTT----
Salmon    GATTTTGGCA TAATAAGAAG CATGGATTC- TCCAGTAGAT TCGACAGATG

Human     AGTGGTGGCC GGACCAGGCC CGGGGCCTGG GGGCGCCGAG GGGGCCGCGG
Chimp     AGTGGTGGCC GGACCAGGCC CGGGGCCTGG GGGCGCCGAG GGGGCCGCGG
Cow       GATGGTGGCC GGACCGGGCC CGGGGCCTGG GGGCGCCGAA GGAGCAGCGG
Mouse     GGTACTGGCC GGCCCGGGTC CCGGGCCTGG AGGAGCCGAG GGCAGCGCAG
Rat       GGTGCTGGCC GGCCCGGGCC CCGGGCCTGG AGGAGCCGAG GGCGGCGCGG
Dog       GGCGCTGGCC GGGCCGGGCC CGGGGCCTGG GGGCGCGGAG GGGGCGGCCG
Chicken   --TTCTCCTC CGACGAGG-- -AGGGCCCGG CGGCC----- GGCGCCGAGG
Salmon    ACTTTTCAAC CTATGAGG-- -ACACTCCTC GACCACCGAC GCAGCTCAAG

Human     AGGAGCGCCG CGTCAAGGTC TCCAGCCTGC CCTTCAGCGT GGAGGCGCTC
Chimp     AGGAGCGCCG CGTCAAGGTC TCCAGCCTGC CCTTCAGCGT GGAGGCGCTC
Cow       AGGAGCGCCG CGTCAAGGTC TCCAGCCTGC CCTTCAGTGT GGAGGCGCTC
Mouse     AGGAACGCAG GGTCAAGGTC TCCAGCCTGC CCTTCAGCGT GGAGGCGCTC
Rat       AGGAGCGCAG GGTCAAGGTC TCCAGCCTGC CCTTCAGCGT GGAGGCGCTC
Dog       AGGAGCGCCG CGTCAAGGTC TCCAGCCTGC CCTTCAGCGT CGAGGCGCTC
Chicken   AGCACCACAA AGTCAAGGTG TCCAGCTTGC CGTTCAGCGT GGAAGCCCTC
Salmon    GAGCGAAAAA CACCTGAATC ACC--TTTAC CTTTCAGTGT GGATGCGATC

Human     ATGTCCGACA AGAAGCCGCC CAAGGAGGCG TCCCCGCTGC CGGCCGAAAG
Chimp     ATGTCCGACA AGAAGCCGCC CAAGGAGGCG TCCCCGCTGC CGGCCGAAAG
Cow       ATGTCGGACA AGAAGCCGCC CAAGGAGACG TCCCCGCGGC CAGCCGAAAG
Mouse     ATGTCCGACA AGAAGCCGCC CAAGGAATCG CCCGCGGTGC CACCCGACTG
Rat       ATGTCCGACA AGAAGCCGCC CAAGGAATCG CCCGCGGTGC CACCCGACTG
Dog       ATGTCGGACA AGAAGCCGCC CAAGGGGGCG TCCCCGCGGC CGGCAGACAG
Chicken   ATGTCCGACA AGAAACCCCC TAAAGAGCTG CCGCTGGCCG CGGCGGGGGG
Salmon    ATGTTGGATA GAAGAACTCC TGGCGA---- CGGAGGGAGA CGCC--ACAG

Human     CGCCTCGGCC GGGGCCACCC TGCGG----C CA-----CTG CTGCTGTCGG
Chimp     CGCCTCGGCC GGGGCCACCC TGCGG----C CA-----CTG CTGCTGTCGG
Cow       CGCCTCCGCC GGGGCCACCC TGCGG----C CG-----CTT CTGCTGCCTG
Mouse     CGCCTCGGCT GGCGCTGTCC TGCGG----C CG-----CTG CTGCTGCCGG
Rat       CGCCTCGGCT GGCGCTGTCC TGCGG----C CG-----CTG TTGCTGCCGG
Dog       CGCCTCTGCC GGGGCCGCCC TGCGG----C CG-----CTG CTGCTGCCGG
Chicken   CAGCGCCGAC GGGGCGACCG TGGGCACCTC CAGGAACCTG CTGCTGCCGG
Salmon    CGGTACGATA ATCTCTCCCC TGGGG----- ---------- -AATTACTCT

Human     GGCACGGCGC TCGG-GAAGC GCACAGCCCC ---GGGCCGC TGGTGAAGCC
Chimp     GGCACGGCGC TCGG-GAAGC GCACAGCCCC ---GGGCCGC TGGTGAAGCC
Cow       GCCACGGCGT CCGG-GAAGC TCACAGCCCC ---GGGCCGC TGGTCAAACC
Mouse     GACACGGCGT CCGG-GACGC TCACAGTCCC ---GGGCCTC TCGTCAAGCC
Rat       GACACGGCGT CCGG-GACGC TCACAGTCCC ---GGGCCTC TCGTCAAGCC
Dog       GACACGGCGC CCGG-GAAGC CCCCAGCCCC ---GGGCCGC CGGGGAAGCC
Chicken   GCCACGGCTC CCGG-GACGC GCACAGCCCC CCCGGGGCTC TTACAAAAAC
Salmon    ATATCGGTGT CCAGAGAGGC GTCTAGTACA G--AAGACTT TCCTCACAAC

Human     CTTCGAGACC GCCTCGGTCA AGTCGGAAAA TTCAGAAGAT GGAGCGGCGT
Chimp     CTTCGAGACC GCCTCGGTCA AGTCGGAAAA CTCAGAAGAT GGAGCGGCGT
Cow       CTTCGAGACC GCCTCGGTCA AGTCGGAAAA TTCAGAAGAC GGAGCGGCGT
Mouse     CTTCGAGACC GCCTCGGTCA AGTCGGAAAA TTCCGAAGAC GGAGCACCGT
Rat       CTTCGAGACC GCCTCGGTCA AGTCGGAAAA TTCCGAAGAC GGAGCGCCGT
Dog       CTTCGAGGCC GCCTCGGTCA AGTCGGAGAG CGCCGAGGAC GGAGCCGCGT
Chicken   CTTCGACACC GCTTCGGTCA AATCGGAGAA CTCGGAGGAC GGCACGTCCT
Salmon    TTT--GGCCC GTCTTCTTCG A--CAGTTAA ATCAGAG--- ---ACGTC--

Human     GGATGCAGGA ACCCGGCCGA TATTCGCCGC CGCCAAGACA TATGAGCCCT
Chimp     GGATGCAGGA ACCCGGCCGA TATTCGCCGC CGCCAAGACA TATGAGCCCT
Cow       GGATGCAGGA ACCGGGCAGA TACTCGCCGC CGCCAAGACA CATGAGCCCC
Mouse     GGATACAGGA GCCCGGCAGA TACTCCCCGC CGCCCAGACA TATGAGCCCC
Rat       GGATACAGGA GCCCGGCAGA TACTCCCCGC CGCCCAGACA CATGAGCCCC
Dog       GGATGCAGGA GCCCGGCAGA TACTCGCCGC CGCCAAGACA TATGAGCCCC
Chicken   GGATCCAAGA GGCCGGGAGA TATTCGCCTC CTCCAAGACA CCTGAGCCCT
Salmon    GGAACCAGGG GACT---TTG CGTCCAATTT CGCTCCAGCG CTCCACCAGC

Human     ACCACCTGCA CCCTGAGGAA ACACAAGACC AATCGGAAGC CGCGCACGCC
Chimp     ACCACCTGCA CCCTGAGGAA ACACAAGACC AATCGGAAGC CGCGCANNNC
Cow       ACCACCTGCA CCCTGCGGAA ACACAAGACC AATCGGAAGC CCCGCACACC
Mouse     ACCACCTGCA CCCTGAGGAA ACACAAGACC AACCGGAAGC CACGCACACC
Rat       ACCACCTGCA CCCTGAGGAA ACACAAGACC AACCGGAAGC CACGCACACC
Dog       ACCACCTGCA CCCTGCGGAA GCACAAGACC AATCGGAAGC CGAGAACGCC
Chicken   ACAGCCTGCA CTCTGAGGAA GCACAAGACG AATCGGAAGC CCCGCACCCC
Salmon    TCAGTCC-CT CCTTGAGGAA ACACAAGACC AACAGGAAGC CCCGGACCCC

Human     CTTTACCACA TCCCAGCTCC TCGCCCTGGA GCGCAAGTTC CGTCAGAAAC
Chimp     CTTTACCACA TCCCAGCTCC TCGCCCTGGA GCGCAAGTTC CGTCAGAAAC
Cow       CTTTACCACG TCCCAGCTCC TCGCTCTGGA GCGCAAGTTC CGCCAGAAAC
Mouse     CTTCACCACA TCCCAGCTTC TAGCCTTGGA GCGCAAGTTC CGCCAGAAAC
Rat       GTTCACCACG TCCCAGCTTC TAGCCTTGGA GCGCAAGTTC CGCCAGAAAC
Dog       CTTCACCACG TCGCAGCTCC TCGCCCTGGA GCGCAAGTTC CGCCAGAAAC
Chicken   ATTCACTACT TCCCAGCTGC TGGCCCTGGA GCGCAAGTTC CGCCAGAAGC
Salmon    CTTCACCTCC TCCCAGCTCC TGTCCCTGGA GAGGAAGTTC CATCAGAAAC

Human     AGTACCTCTC CATTGCAGAG CGTGCAGAGT TCTCCAGCTC TCTGAACCTC
Chimp     AGTACCTCTC CATTGCAGAG CGTGCAGAGT TCTCCAGCTC TCTGAACCTC
Cow       AGTACCTCTC CATCGCAGAG CGGGCAGAGT TCTCCAGCTC TCTGAACCTC
Mouse     AGTACCTGTC CATAGCAGAG CGGGCCGAGT TCTCCAGCTC TCTGAACCTT
Rat       AGTACCTCTC CATCGCAGAG CGGGCCGAGT TCTCCAGCTC TCTGAACCTT
Dog       AATACCTCTC CATTGCAGAG CGCGCGGAGT TCTCCAGCTC TCTGAACCTC
Chicken   AGTACCTGTC CATCGCCGAG CGAGCCGAAT TCTCCAGCTC CCTCAACCTC
Salmon    AGTACCTGTC CATTGCAGAG CGGGCCGAGT TCTCCTCCTC CCTGTCCCTC

Human     ACAGAGACCC AGGTCAAAAT CTGGTTCCAG AACCGAAGGG CCAAGGCGAA
Chimp     ACAGAGACCC AGGTCAAAAT CTGGTTCCAG AACCGAAGGG CCAAGGCGAA
Cow       ACAGAGACCC AGGTCAAAAT CTGGTTCCAG AACCGAAGAG CCAAGGCGAA
Mouse     ACAGAGACCC AGGTCAAAAT CTGGTTCCAG AACCGAAGGG CTAAGGCGAA
Rat       ACAGAAACCC AGGTCAAAAT CTGGTTCCAG AACCGAAGGG CTAAGGCAAA
Dog       ACAGAGACCC AGGTTAAAAT CTGGTTCCAA AACCGAAGGG CCAAGGCGAA
Chicken   ACAGAGACCC AGGTCAAAAT CTGGTTCCAA AATCGGAGGG CCAAGGCCAA
Salmon    TCAGAGACCC AGGTAAAGAT CTGGTTCCAG AATCGACGGG CTAAAGCCAA

Human     AAGACTGCAG GAGGCAGAAC TGGAAAAGCT GAAAATGGCT GCAAAACCTA
Chimp     AAGACTGCAG GAGGCAGAAC TGGAAAAGCT GAAAATGGCT GCAAAACCTA
Cow       AAGACTGCAG GAGGCAGAAC TGGAAAAGCT GAAAATGGCT GCAAAACCTA
Mouse     AAGACTGCAA GAGGCGGAAC TGGAAAAGCT GAAAATGGCT GCCAAGCCTA
Rat       AAGACTGCAG GAGGCGGAAC TGGAAAAGCT GAAAATGGCT GCCAAACCTA
Dog       AAGACTGCAG GAGGCAGAAC TAGAAAAGCT GAAGATGGCT GCAAAACCTA
Chicken   GAGACTGCAG GAGGCTGAGC TAGAGAAGCT CAAAATGGCA GCGAAGCCAA
Salmon    GAGAGTACAG GAGGCAGAGG CGGAGAAACT CAAGATGGCC GCCA--CAGG

Human     TGCTGCCCTC CAGCTTCAGT CTCCCTTTCC CCATCAGCTC GCCCCTGCAG
Chimp     TGCTGCCCTC CAGCTTCAGT CTCCCTTTCC CCATCAGCTC GCCCCTGCAG
Cow       TGCTGCCCTC CGGCTTCAGC CTCCCTTTCC CCATCAACTC TCCCCTGCAA
Mouse     TGCTGCCCTC AGGCTTCAGT CTGCCCTTCC CTATCAACTC ACCCCTGCAA
Rat       TGCTGCCCTC GGGCTTCAGT CTGCCCTTCC CTATCAACTC CCCCTTGCAA
Dog       TGCTGCCCTC TGGCTTCAGC CTTCCTTTCC CCATCAACTC GCCTCTGCAA
Chicken   TGTTGCCGTC GGGGTTCAGC CTCCCTTTCC CCATCAACTC CCCCATCCAG
Salmon    TGTTGGATCC AAGC--CGGG GTTCTATCAC CCG--GGGTT CTCCTCACTG

Human     GCAGCGTCCA TATATGGAGC ATCCTACCCG TTCCATAGAC CTGTGC---T
Chimp     GCAGCGTCCA TATATGGAGC ATCCTACCCG TTCCATAGAC CTGTGC---T
Cow       GCAGCATCTC TATATGGTGC ATCTTACCCT TTCCATAGAC CTGTGC---T
Mouse     GCAGCATCCA TATACGGCGC ATCCTACCCC TTCCATAGAC CTGTGC---T
Rat       GCGGCATCCA TATACAGCGC CTCCTACCCC TTCCATAGAC CTGTGC---T
Dog       GCAGCATCCA TATACGGAGC GTCCTACCCT TTCCATAGAC CTGTGC---T
Chicken   GCCGCCTCAC TGTACGGAAC ATCCTACCCT TTTCACAGAC CTGTGC---T
Salmon    CCGTTTCCCC TCTGTGTCA- GTTTGGGTGG TCTAGGGGGT CTGGGTGGGT

Human     TCCCATCCCG CCTGT-GGGA CTCTATGCCA CGCCAGTGGG ATATGGCATG
Chimp     TCCCATCCCG CCTGT-GGGA CTCTATGCCA CGCCAGTGGG ATATGGCATG
Cow       CCCCATCCCG CCCGT-CGGA CTCTATGCGA CTCCAGTGGG ATATGGCATG
Mouse     CCCCATCCCG CCTGT-TGGA CTCTATGCCA CGCCGGTTGG ATATGGCATG
Rat       TCCCATCCCG CCTGT-GGGA CTCTATGCCA CGCCGGTGGG ATATGGCATG
Dog       CCCCATCCCG CCCGT-CGGA CTCTATGCGA CCCCAGTCGG ATATGGCATG
Chicken   TCCTATCCCG CCCGT-TGGA CTCTATGCTA CTCCTGTCGG ATATAGCATG
Salmon    GGGTCTCAGG TATGTACGGA GAACAGGGGT TCCCCTTAAG ACACACCCCT

Human     TACCACCTGT CCTAAGGAAG ACCAGATCAA T-AGACTCCA TGATGGATGC
Chimp     TACCACCTGT CCTAA----- ---------- ---------- ----------
Cow       TACCACCTAT CCTAAGGAAG ACCAGCTCAA T-AGACTCCG GGATGGATGT
Mouse     TACCATCTAT CCTAAGGAAG ACCAGATGGA CCAGACTCCA GGATGGATGT
Rat       TACCATCTAT CCTAAAGAAG ACCAGATGGA C-ACACTCTA GGATGGATGT
Dog       TACCATCTAT CCTAA----- ---------- ---------- ----------
Chicken   TACCACTTAT CTTAAGGA-G ATCAGAAAGG CACGGTGACA GCGAGAGAGA
Salmon    CTGTTAAAAA CAGAACCAAA TCTGGGGGTG TACACCTCAC CTATGGGGTA

Human     TTGTTTCAAA GGGTTTCCTC TCCCTCTCCA CGAAGGCAGT ACCAGCCAGT
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       TTGTTTAAAA GCCTCCCCCG TCCCTCTCCA AGAAGACAGT CCCGCTCTAC
Mouse     TTGCATAAAA GCATCCCCC- TCCCTCTCCG AGAAGGTGGT GCCAACTC-T
Rat       TTGTG-GAAA GCATTCCCC- TCCCTCTCCA GGAAGGCGGT GCCAATTT-T
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   CTTCCTGGTG GA---TCTCA TCCAGCCTCA AGAATGCAGT ACCCAACC--
Salmon    CGGACTGTTC CACCTGTCCT GAAAGGTTTG TGTGTGC-GT GCGAATGTGA

Human     ACTCCTGCTC TGCTAACCCT GCGTGCACCA CCCTAAGCGG CTAGGCTG--
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       AAACCT---- TGCATGCACC AC---CCTCA GCCTCAGCGG CTAGGTCG--
Mouse     GCTCCTGAA- TGCGAGCCTT GCAT-TGTCA CCCTAAGCGA CAGG------
Rat       GCTCCTGAA- CGCAAACCCT GCGT-TGTCG CCCTAAGCAA CAGGCCTGTG
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   GGTACTGGC- CGTTCTTTCT GCACGCTTCT ATCT-GCCAT CCCGAGTGT-
Salmon    TGAACCTCAC AACAAGATTT GAAA-TGATA CCCTAACTCT CAGGGATGC-

Human     ACAGGGCCAC ACGACATAGC TGAAATTTGT TCTGTAGGC- GGAGGCACC-
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ACAGGGCCAC A-GACATAGT TCAAATTGCT TCTTTTGACT GGAGACACCC
Mouse     -----GCCAC TTGATACAGA GTGAATTTGT TATTTAGGTG AGAGGCACT-
Rat       GGGGGGCCAC TTGATACAGA GTGAATTTGT TATTTACGTG AGAGGCACT-
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ACAGGAGTTC GCGTTAGCAA AGCAAGGCAT CCTGTATGCA ACAGGC----
Salmon    -CTTGAATAT CTTGTGCTGG ACCAACTT-T GATATAGTCA ACAGATGTGG

Human     AAGCCCTGTT TTCTTGGTGT AATCTTCCAG ATGC--CCCC TTTTCCTTTC
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       AAGCCCTGTT TTCTTGGT-T AATCTGCCAG ATGCGCCCCC TACCCCTTTC
Mouse     AAGACCTGTT TTGTTTTCAT AATTTTCCAA ATGC--CCCC TTT-CCTCTC
Rat       AAGACCGATT TTGTTTTCAT AATTTCCCAA ATGT--CCCC TTTTCCTCTC
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   -----TGGGT GTCTTCTGAG AGCGCTCTGA GTGCTCACAG TCTGATCCTC
Salmon    AAG--TGTGC ATGGTTATAC GGTACCTTGT GTTCCCTGGT TTGTTACGGA

Human     ACAAA-GATT GGCTCTGATG GTTTTTATGT ATAAATATAT ATATATAATA
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ATAAAAGATT GGCTCTGACA GTTTTTATAT ATAAATATAT ATAT--AATA
Mouse     ACAAA-TATT GGCTCTGCTA GTTTTTATGT ATAAATATAT A------ATA
Rat       ACAGT-TATT GGCTCTGCTA GTTTTTATGT ATAAATATAT A------ATA
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   AGAGTGTTT- ---------- ---------- ---------- ----------
Salmon    AGAGCCTAGT GCATCAGAAC ACCCCATAGT TCCAGCACCC ATAGTACAAG

Human     AAATATAATA CA-TTTTTAT ACAGCAGACG TAAAAATTCA AATTATTTTA
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       AAATATAATA CA-TTTTTAT ACAGCAAAAA AAAAAAAAAA A---------
Mouse     AAATATAAGA C--TTTTTAT ATGCCAGATG TAAAAATTCA AGTTATTTTA
Rat       AAATATAAGA C--TTTTTAT ATGCCAGATG TAAAAATTCA AGTTATTTTG
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    CTCCATGGCA GGGTAATTGT TCATTTATTC TATAGCCCTG ACCTGTGCTG

Human     AAA--GGCAA AATTTATATA CATATGTGCT TTTTTTC--- -----TATAT
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     AAA--GGCAA AATTTATATA TACATTTATC CATTTTCTTT TTTTTTCTAG
Rat       GAA--GGCAA AATTTATATA TACGCTTATC CATTTT---- -----TCTAG
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    TATTTGCCAA AGTTTGTTGG ATCGTTTCGT AGGATACTGA TCCACCGTGT

Human     CTCACCTTCC CAAAAGACAC TGTGT-AAGT CCATTTGTTG TATTTTCTTA
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     ATAGCATCTT CCTAAGATAT TGTGTTAAGT CCATTTGCTA CATTTTCTTA
Rat       ATAGCATTTT CTTAAGATAT TGTGTTTAGT CCATTTGCTA CCTTTTCTTA
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    GTCTGATCAC TCCCTAAATA CCAGATTAGC TC-------- ----------

Human     AAGAGGGAGA CAAATTATTT GCAAAATGTG CTAAAGTCAA TGATTTTTAC
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     AAGGGAAAGA -GATTAATT- GCAGAATTTG CAAGGATGGT GGACT-----
Rat       AAGGGAAAGA -GATTTGTTT GCAGAACTTT CAAGGAGGAT GGACT-----
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     GGGATTATTG ACTTCTGCTT ATGGAAAACA AAGAAACAGA CACAATGCAC
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     ---------- --TGCTTATG GAAAACATAG CAGAAGTAGA CACATTCCAT
Rat       ---------- --TGCTTATG GAGGACATGC CAGGAGTAGA CATAGTGCAT
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     ACAGAAAATA TTAGATATGG AGAGATTATT CAAAGTGAAG GGGACACATC
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     ACAGGATGTC ACTTCAGACA GATTCTTGCA AGTGAAGGGG GAGGTGTAAC
Rat       ACAAGATACA GTTTCAGATA TATTCTTGCA AGGGAAGGGG GATGTGTAAC
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     ATATT--TCT GCATTTTACT TGCATTAAAA GAA--ACCTC TTTATATACT
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     GTGTTTATTT GCATTTCTG- TGCACAAGAA AAAGAAATCT CTTGA--TGC
Rat       ATGTTCTTAT GCATTTTAGG TGCGTAAGAA ACA-AAACCT CTTGAGATGC
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     ACAGTTGTTC CTATCTCTCC CCCGCCCCCC ACCGCCCCAC CACACACATA
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     ACATTTGATC CTATTTTTTT TCTCTTTTTC TCCATTCCA- --------TA
Rat       ACATTTGATC TTATTTTTCT ----CTCTTC TCCATTCCA- --------TG
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     TTTTTAAAGT TTTTCCTTTT TTAAGAATAT TTTTGTAAGA CCAATACCTG
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     TTATTAAATC TTTGTTGTTG TTTTAAGATC GATGAAAAGA ----------
Rat       TTGTCAAATC T--------- ---------- ---------- ----------
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     GGATGAGAAG AATCCTGAGA CTGCCTGGAG GTGAGGTAGA AAATTAGAAA
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     GGATGAGAAT AACTCTGAGA GTTACTCAGG GTAAAGTAGA AAATAGGAAA
Rat       ----GAGGAT AACTCTGAGA ATTACTCAGG GTAA------ AAGTGGG--A
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     TACTTCCTAA TTCTTCTCAA GGCTGTTGGT AACTTTATTT CAGATAATTG
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     CTCCATGTCA GGTCCCTGGA G--------- ---------- ----TGAGAG
Rat       TTCCATTTCA GGGCCCTGGC G--------- ---------- ----TGCGAG
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     GAGAGTAAAA TGTTAAAACC TGTTGAGAGG AATTGATGGT TTCTGAGAAA
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     GGGGTTAGAA GGTGAAATAT TGTTTGTAAG AATTGAT--- TTCTATGAAA
Rat       GGT-TTAGAA GATAAAAC-T TG--TGTAGG AATTGGT--- TTCTGTGAAA
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     TACTAGGTAC ATTCATCCTC ACAGATTGCA AAGGTGATTT GGGTGGGGGT
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     TGCTATCTAC ATCAGTCCTC ACACGGTACA GAGGTGATTG GAAGAGGACA
Rat       TGCTAACTAC ATCAGTCCTC ACAGGGCACA GAGGAGATTG CAAGAGGGCG
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     TTAGTAATTT TCTGCTTAAA AAATGAGTAT CTTGTAACCA TTACCTATAT
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     TGGT-AAATC TCTTCTTAAA AA-TGAGTGT CTTATAACTG TGGCCTATAT
Rat       TAGTTAAATA TCTGCTTAGA AA-TGAGTGT CTTGTAACTG TTGCCTATAT
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     GCTAAATATT CTTGAACAAT TAGTAGATCC AGAAAGAAAA AAAAATAT--
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     TTTAAATATT CTTCAACAGT CCATAGAATG AGGAAGGAAA ACATGCCTTC
Rat       TTGAAAGATT CTTCAACAGT CCATAGAATC AGGAAGGGGA AAAAAT----
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     ---------- ---------- ---------- ---------- ------GCTT
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     TCTCTCTCTC TCTCTCTCTC TCTCTCTCTC TCTCTCTCTC TCTCTAGCTC
Rat       ---------- ---------- ---------- ---------- ------GCTT
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     TCTCTGTGTG TGTACCTGTT GTATGTCCTA AACTTATTAG -----AAAAT
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     TCTCTGTGTG TGTGTGTGTG TGTGTGTGTG TGTGTGTGTG TGTGTGTGTG
Rat       TCTCTCTGTG TGTGTGTACT TAC------- TGTATGTGC- ------TAAA
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     TTTATATACT TTTTTACATG TTGGGGGGCA GAAGGTAAAG CC--ATGTTT
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     TGTACTTTGT GTGCTAAACT TCTTAGGGAA ATTTATATAC TCTAACGTGT
Rat       TGTATTAGGG ACTCGAACGT GTTTGGGGTA GACAATGAAG CC--ATGTGT
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     TGACTTGGTG AAAATGGGA- ---------T TGTC--AAAC AGCCCATTAA
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     TGGGCAGATG GAGAAGCCAT GTGCTTGAGT TGCTGGAGAT GGCGTTGTCA
Rat       TGGGCT--TG GTGGAAACAA ACG---GTGT TGTC--AGAC AACACAGTCA
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     GTTCCCTGGT ATTTCACCTT CCTGTCCATC TGTCCCCTCC CTCCGGTATA
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     GTCAGCACCT GGGTGTCTCA CCTTCCTGTC CATCTCTTCC CCC-AGTATA
Rat       GCTAGCCCCT TGGTCTTTCA CCTGCCTGTC CACCTCTTCC C---AATATA
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     CCTTTATCCC TTTGAAAGGG TG-CTTGTAC AATTTGATAT ATTTTATTGA
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     TTTTTATCCC GTTGAATGGG TATCTTGTAT AATTTTATAT ATTTTATTGA
Rat       TTTTTATCCC GTTGAAAGGG TATCTTGTAT AATTTTATAT ATTTTATTGA
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- ---------- ---------- ---------- ----------
Salmon    ---------- ---------- ---------- ---------- ----------

Human     AGAGTTATCT CTTATTCTGA ATT--AAATT AAGC--ATTT GTTTTATTGC
Chimp     ---------- ---------- ---------- ---------- ----------
Cow       ---------- ---------- ---------- ---------- ----------
Mouse     AGAGTTATTT CTTATCTCTT ACTCTGAATT AAATTAAAAT ATTTTATTGC
Rat       AGAGTTATTT CTTATCTCAT ACTCTGAATT AAATTAAAAT GTTTTATTGC
Dog       ---------- ---------- ---------- ---------- ----------
Chicken   ---------- -------


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO