Abstract:
This invention relates to the determination of expression patterns, DNA methylation patterns and chromatin properties of families of transposable elements in order to determine, classify and characterize the potential of stem cells to differentiate into germ layers including various types of somatic cell lineages.

Description:
[0001]     This application claims priority to U.S. provisional application Ser. No. 60/466,801, filed Apr. 29, 2003, which is herein incorporated by this reference in its entirety. 
     
    
     FIELD OF THE INVENTION  
       [0002]     This invention relates to the determination of expression patterns, DNA methylation patterns and chromatin properties of families of transposable elements in order to determine, classify and characterize the potential of stem cells to differentiate into germ layers including various types of somatic cell lineages.  
       BACKGROUND  
       [0003]     The fertilized eggs (oocytes) of human and other multi-cellular animals have the potential to divide and give rise to progeny cells of the great variety of specialized cell types that comprise the fully developed organism. Cells that possess this full developmental potential are referred to as pluripotent (totipotent) stem cells. In addition to fertilized oocytes, cells isolated from primordial germ cells (PGCs) (e.g See Matsui et al. 1992 Derivation of pluripotential embryonic stem cells from murine primordial germ cells in culture.  Cell  70: 841-847; Shamblott et al 1998 Derivation of pluripotent stem cells from cultured human-primordial germ cells  Proc Natl Acad Sci., USA  95: 13726-13731), from early staged embryos (e.g. blastocists) (e.g, Evans and Kaufman 1981 Establishment in culture of pluripotential cells from mouse embryos  Nature  292: 154-156.; Amit et al. 2000 Clonally derived human embryonic stem cell lines maintain pluripotency and proliferative potential for prolonged periods of culture.  Dev Biol  227: 271-278) and from embryonic carcinomas (EC) (e.g Pierce 1967 Teratocarcinoma: a model for a developmental concept of cancer.  Curr Topiccs Dev Biol  2: 223-246.), have also been shown to be pluripotent, i.e., to have the potential to divide and give rise to progeny cells of a great variety of specialized cell types. As embryos develop and their cells become determined to give rise to specialized cell types (e.g., neural cells, liver cells, etc.), they typically lose their pluripotency. The molecular genetic basis of pluripotency and the progressive loss of pluripotency as cells become determined to develop into specialized cell lineages, is a complex process associated with progressive changes in the chromatin status of chromosomes. The chromosomes of pluripotent stem cells are in a generally open configuration (euchromatin) due in part to the fact that most of the DNA comprising these chromosomes is hypomethylated (i.e., not methylated or displaying substantially reduced levels of methylation relative to differentiated cells) (Tada and Tada 2001 Toti-/pluripotential stem cells and epigenetic modifications  Cell Struc and Func  26: 149-160). In contrast, the chromosomes of differentiated cells that have lost their pluripotency are typically condensed (heterochromatic) at numerous chromosomal locations due, in part, to the fact that the DNA comprising the condensed chromosomal regions are hypermethylated (Razin and Kafri 1994 DNA methylation from embryo to adult.  Prog Nucleic Acid Res Mol Biol  48: 53-81). Gene sequences contained within heterochromatic, hypermethylated DNA are typically transcriptionally silent while genes contained within euchromatic, hypomethylated DNA may be transcriptionally active.  
         [0004]     Recent studies have shown that when the nuclei (cellular organelle that contains chromosomes) isolated from even fully differentiated cells are transplanted into an unfertilized oocyte, the nuclei can become reprogrammed from the fully differentiated state to a fully pluripotent state. The molecular basis of this reprogramming is associated with hypomethylation of the DNA of the differentiated nuclei, a general opening of the chromatin structure and a general increase in gene transcription. Thus, the loss of pluripotency can be reacquired by factors contained in unfertilized oocytes.  
         [0005]     The human genome comprises numerous families of transposable elements, such as retroelements, i.e., LIs (long interspersed nuclear elements), SINES (short interspersed nuclear elements) and LTR (long terminal repeat) elements, e.g. HERVs (human endogenous retroviruses) and DNA elements, i.e. Charlie- and Tigger groups (see Smit (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes.  Current Opinion in Genetics  &amp;  Development,  9: 657-663) that are widely distributed throughout the genome. To date, over 50 families of retroviral elements have been identified and the members of these families make up greater than 43% of the genome (See Li et al. (2001) Evolutionary analysis of the human genome.  Nature,  409 (6822): 847-9). Each family can include hundreds to thousands of retroelements and the expression of these retroelement genes is known to be suppressed in differentiated cells due to hypermethylation (Yoder et al 1997 Cytosine methylation and the ecology of intragenomic parasites.  Trends Genet  13: 335-340). In pluripotent stem cells retroelements are hypomethylated and the expression of retroelement genes is activated (Tada and Tada 2001). The present invention provides methods of determining patterns of transposable element expression and transposable element DNA methylation as well as methods for determining the chromatin status of transposable elements within the genome such that these patterns can be used as molecular markers of the developmental status of cells.  
         [0006]     The present invention provides methods of determining patterns of transposable element expression, transposable element methylation and chromatin status of transposable elements within the genome such that these patterns can be used to classify and assess the developmental potential of a cell. All of the methods of the present invention can be utilized to analyze full-length transposable element sequences or fragments thereof. These transposable elements include retrolements and fragments thereof as well as DNA elements and fragments thereof from mammalian species. Thus, the present invention provides methods of determining patterns of retroelement expression, retroelement methylation and chromatin status of retroelements within the genome such that these patterns can be used to characterize the developmental potential of a cell. Also provided are methods of determining DNA element expression, DNA element methylation and chromatin state of DNA elements within the genome such that these patterns can be used to characterize the developmental potential of a cell.  
       SUMMARY OF THE INVENTION  
       [0007]     The present invention provides a method of determining an expression pattern of one or more families of transposable elements in a stem cell comprising determining expression of one or more families of transposable elements.  
         [0008]     The present invention provides a method of assigning an expression pattern of transposable elements to the level of developmental potential of a cell comprising: a) determining expression of one or more families of transposable elements; and b) assigning the expression pattern obtained from step a) to the level of developmental potential of a cell.  
         [0009]     Also provided by the present invention is a method of determining the developmental potential of a stem cell comprising: a) determining expression of one or more families of transposable elements in a stem cell to obtain an expression pattern;b) matching the expression pattern of step a) with a known expression pattern for a cell at different stages of developmental potential ranging from a fully pluripotent stem cell to a fully differentiated cell and; c) determining the developmental potential of the stem cell based on matching the expression pattern of a) with a known expression pattern for a cell at a specific developmental stage.  
         [0010]     Further provided is a method of identifying a cellular differentiation induction factor comprising: a) determining expression of one or more families of transposable elements in a stem cell to obtain a first expression pattern; b) administering a putative induction factor to the cell; c) determining expression of one or more families of transposable elements in the cell after administration of the putative induction factor to obtain a second expression pattern; and d) comparing the second expression pattern with the first expression pattern such that if transposable elements are differentially expressed in the second expression pattern as compared to the first expression pattern, the induction factor is a cellular differentiation induction factor.  
         [0011]     Also provided by the present invention is a method of identifying a factor that increases the developmental potential of a cell comprising: a) determining expression of one or more families of transposable elements in a cell to obtain a first expression pattern; b) administering a putative factor that increases developmental potential to the cell; c) determining expression of one or more families of transposable elements in the cell after administration of the putative factor to obtain a second expression pattern; and d) comparing the second expression pattern with the first expression pattern such that if transposable elements are differentially expressed in the second expression pattern as compared to the first expression pattern, the factor is effective in increasing the developmental potential of the cell.  
         [0012]     Also provided by the present invention is a method of assigning a methylation pattern of transposable elements to the level of developmental potential of a cell comprising: a) determining methylation of one or more families of transposable elements; and b) assigning the methylation pattern obtained from step a) to the level of developmental potential of a cell.  
         [0013]     Also provided by the present invention is a method of determining the developmental potential of a stem cell comprising: a) determining methylation of one or more families of transposable elements in a stem cell to obtain a methylation pattern; b) matching the methyation pattern of step a) with a known methylation pattern for a cell at different stages of developmental potential ranging from a fully pluripotent stem cell to a fully differentiated cell and; c) determining the developmental potential of the stem cell based on matching the methylation pattern of a) with a known methylation pattern for a cell at a specific developmental stage.  
         [0014]     Further provided by the present invention is a method of identifying a cellular differentiation induction factor comprising: a) determining methylation of one or more families of transposable elements in a stem cell to obtain a first methylation pattern; b) administering a putative induction factor to the cell; c) determining methylation of one or more families of transposable elements in the cell after administration of the putative induction factor to obtain a second methylation pattern; and d) comparing the second methylation pattern with the first methylation pattern such that if there is a change in the second methylation pattern as compared to the first methylation pattern, the induction factor is a cellular differentiation induction factor.  
         [0015]     Also provided is a method of identifying a factor that increases the developmental potential of a cell comprising: a) determining methylation of one or more families of transposable elements in a differentiated cell to obtain a first expression pattern; b) administering a putative factor that increases developmental potential to the cell; c) determining expression of one or more families of transposable elements in the cell after administration of the putative factor to obtain a second methylation pattern; and d) comparing the second methylation pattern with the first methylation pattern such that if there is a change in the second methylation pattern as compared to the first methylation pattern, the factor is effective in increasing the developmental potential of the cell.  
         [0016]     Further provided is a method of assigning a chromatin status pattern of transposable elements to the level of developmental potential of a cell comprising: a) determining chromatin status of one or more families of transposable elements; and b) assigning the chromatin status pattern obtained from step a) to the level of developmental potential of a cell.  
         [0017]     The present invention also provides a method of determining the developmental potential of a stem cell comprising: a) determining chromatin status of one or more families of transposable elements in a stem cell to obtain a chromatin status pattern; b) matching the chromatin status pattern of step a) with a known chromatin status pattern for a cell at different stages of developmental potential ranging from a fully pluripotent stem cell to a fully differentiated cell and; c) determining the developmental potential of the stem cell based on matching the chromatin status pattern of a) with a known chromatin status pattern for a cell at a specific developmental stage.  
         [0018]     Also provided is a method of identifying a cellular differentiation induction factor comprising: a) determining chromatins status of one or more families of transposable elements in a stem cell to obtain a first chromatin status pattern; b) administering a putative induction factor to the cell; c) determining the chromatin status of one or more families of transposable elements in the cell after administration of the putative induction factor to obtain a second chromatin status pattern; and d) comparing the second chromatin status pattern with the first chromatin status pattern such that if there is a change in the second chromatin status pattern as compared to the first chromatin status pattern, the induction factor is a cellular differentiation induction factor.  
         [0019]     Further provided is a method of identifying a factor that increases the developmental potential of a cell comprising: a) determining chromatin status of one or more families of transposable elements in a differentiated cell to obtain a first chromatin status pattern; b) administering a putative factor that increases developmental potential to the cell; c) determining expression of one or more families of transposable elements in the cell after administration of the putative factor to obtain a second chromatin status pattern; and d) comparing the second chromatin status pattern with the first chromatin status pattern such that if there is a change in the second chromatin status pattern as compared to the first chromatin status pattern, the factor is effective in increasing the developmental potential of the cell. 
     
    
     DETAILED DESCRIPTION OF THE INVENTION  
       [0020]     The present invention may be understood more readily by reference to the following detailed description of the preferred embodiments of the invention and the Examples included therein.  
         [0021]     Before methods are disclosed and described, it is to be understood that this invention is not limited to specific methods, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.  
         [0022]     It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a nucleic acid” includes multiple copies of the nucleic acid and can also include more than one particular species of nucleic acid molecule. Similarly, reference to “a cell” includes one or more cells, including populations of cells.  
         [0000]     Analysis of Expression Patterns  
         [0023]     The present invention provides a method of determining an expression pattern of one or more families of transposable elements in a stem cell comprising determining expression of one or more families of transposable elements.  
         [0024]     As used herein a “sample” can be of any type of stem cell from any organism and can be, but is not limited to, pluripotent stem cells derived from fertilized oocytes, from primordial germ cells (PGCs), from early staged embryos (e.g. blastocysts) and from embryonic carcinomas (EC). It is further contemplated that the biological sample of this invention can also be whole cells or cell organelles (e.g., nuclei). The cells may be part of a living tissue or growing in cell culture according to standard protocols widely available in the art.  
         [0025]     As used here a “sample” can also be any determined and/or differentiated cell of a specialized type from any organism and can be, but is not limited to, differentiated brain or other neural cells, hepatic or liver cells, muscle cells, skin cells, connective tissue cells, etc. It is further contemplated that the biological sample of this invention can also be whole cells or cell organelles (e.g., nuclei). The cells may be part of a living tissue or growing in cell culture according to standard protocols widely available in the art.  
         [0026]     The sample can be derived from a tissue or from an established cultured cell line. As utilized herein, the “cells” of the methods described herein can be derived from any animal. In a preferred embodiment, the organism of the present invention is a human. In addition, determination of expression patterns, methylation patterns and chromatin status is also contemplated for non-human animals which can include, but are not limited to, cats, dogs, birds, horses, cows, goats, sheep, pigs, guinea pigs, hamsters, gerbils, mice and rabbits.  
         [0027]     The present invention also provides for the analysis of a sample comprising pluripotent stem cells or differentiated cells from a particular tissue or cell culture. The patterns obtained from differentiated cells can be compared to the expression patterns, methylation patterns and/or chromatin status patterns for pluripotent stem cells in order to access the differences between pluripotent cells and those that have lost their pluripotency, e.g. those that are differentiated.  
         [0028]     The term “fully pluripotent” or “totipotent” when used herein refers to or describes the molecular or physiological status of a cell that is typically characterized by the potential to grow and differentiate into any specialized cell type. The term “pluripotency,” when used herein refers to or describes the molecular or physiological status of a cell that is typically characterized by the potential to grow and differentiate into specific cell subtypes, such as neural cells, muscle cells, hepatic cells, skin cells etc. Examples of fully pluripotent cells include but are not limited to fertilized oocytes, pluripotent stem cells isolated from primordial germ cells (PGCs), from early staged embryos (e.g. blastocists) and from embryonic carcinomas (EC).  
         [0029]     There are numerous transposable element families that can be analyzed by the methods of the present invention, including, but not limited to, retroelement families and DNA element families. The retroelement families that can be analyzed utilizing the methods of this invention include but are not limited to, endogenous retroviruses (ERVs), short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), the vertebrate long terminal repeat (LTR)-containing elements, and the poly(A) retrotransposons. The DNA element families that can be analyzed by the methods of the present invention include, but are not limited to the Mariner/Tci superfamily (e.g. human Mariner, Tigger, Marna, Golem, Zombi), hAT (hobo/Activator/Tam3) superfamily, TTAA superfamily (e.g. Looper), MITEs (e.g. MER85), MuDR superfamily (e.g. Ricksha), T2-family (e.g. Kanga 2) and others. Any combination of retroelement families and the members of these retroelement families can be analyzed by the methods of the present invention to determine a pattern of expression, a retroelement methylation pattern and/or a retroelement chromatin status pattern. For example, one of skill in the art could analyze the expression of ERVs as well as the expression of SIMEs or one of skill in the art could analyze the expression of SINEs, LINEs and ERVs. As stated above, any combination of families and members of transposable element families may be analyzed to provide an expression pattern, chromatin status pattern and/or a methylation pattern. Therefore, combinations of retroelement families and DNA element families can also be also analyzed by the methods of the present invention. A publicly available database, RepBase Update, contains consensus sequences of genomic repeats from different organisms that can be utilized to design the oligonucleotides utilized in the methods of the present invention. This database can be accessed at www.girinst.org. This database was utilized to identify consensus sequences for numerous retroelements which were then used to design oligonucleotide probes for the microarrays of the present invention.  
         [0030]     Files were obtained from RepBase Update containing human-specific repeats (consensus sequences for transposon families). Selected RepBase files were then input into the OligoArray program, a publicly available software tool for microarray oligo-design at http://berry.engin.umich.edu/oligoarray and the design algorithm was run. The BLAST algorithm at http://www.ncbi.nlm.nih.gov/BLAST/(Altschul S F, Gish W, Miller W, Myers E W, Lipman D J  Basic local alignment search tool.  in J Mol Biol 1990 Oct 5;215(3):403-10)) was then utilized to verify compatibility of oligonucleotides in the OligoArray output file with transposon sequences in the human genome sequence (http://www.ncbi.nlh.nih.gov/genome/guide/human/). Selection of appropriate oligonucleotides was based on several criteria such as, the quality of match/specificity, technical parameters and the broad representation of transposable element families. Utilizing this approach, numerous oligonucleotides were designed based on these consensus sequences. The identifiers of retroelement consensus sequences and their corresponding oligonucleotide sequences which can utilized in the methods described herein, are listed in Table 1. Similar analyses can be performed to obtain consensus sequences for non-retroelement transposable element sequences.  
                           TABLE 1                           FLA   GAGTTCGAGACCAGCCTGGGCAACATAGCGAGACCCCGTCTCTAAAAAAA   SEQ ID NO: 1                   FLAM_A   GGAGTTCGAGACCAGCCTGGGCAACATAGCGAGACCCCGTCTCTAAAAAA   SEQ ID NO: 2               FLAM_C   GGAGTTCGAGACCAGCCTGGGCAACATAGCGAGACCCCGTCTCTAAAAAA   SEQ ID NO: 3               AluJo   GAGGCAGGAGGATCGCTTGAGCCCAGGAGTTCGAGGCTGCAGTGAGCTAT   SEQ ID NO: 4               AluJb   GGAGTTCGAGACCAGCCTGGGCAACATGGTGAAACCCCGTCTCTACAAAA   SEQ ID NO: 5               AluSc   TCACGAGGTCAAGAGATCGAGACCATCCTGGCCAACATGGTGAAACCCCG   SEQ ID NO: 6               AluSg   CCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGC   SEQ ID NO: 7               AluSp   CCAGCCTGACCAACATGGAGAAACCCCGTCTCTACTAAAAATACAAAAAT   SEQ ID NO: 8               AluSq   CAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCG   SEQ ID NO: 9               AluSx   CCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGC   SEQ ID NO: 10               AluSz   CCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGC   SEQ ID NO: 11               AluY   GAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAA   SEQ ID NO: 12               AluYa5   CGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTG   SEQ ID NO: 13               AluYa8   GAAACCCCGTCTCTACTAAAACTACAAAAAATAGCCGGGCGTAGTGGCGG   SEQ ID NO: 14               AluYb8   AGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAATACAAA   SEQ ID NO: 15               AluYb9   AGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAAATACAAA   SEQ ID NO: 16               AluYc1   GAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAA   SEQ ID NO: 17               AluYc2   GAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCGTCTCTACTAAAA   SEQ ID NO: 18               AluYd3a1   CGCCTGTAGTCCCAGCTACTCGGAGAGGCTGAGGCAGGAGAATGGCGTGA   SEQ ID NO: 19               AluYe   ACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAA   SEQ ID NO: 20               LTR26B   ATGGATTTGAGGTTTCCTCCCATCTCCTCATTCGGCGGCCCTACGATTAA   SEQ ID NO: 21               LTR26C   ACGGATTTGAGGTTTCCTCCCATCTCCTCATTCGGCAGCCCTACGATTAA   SEQ ID NO: 22               LTR26D   GGCGTATTGACTTGCTGTGTGCATCGGGCAATGAACCTATTACGGTTACA   SEQ ID NO: 23               AluYa1   GAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAA   SEQ ID NO: 24               AIuYa4   CGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAAAACGGTG   SEQ ID NO: 25               AluYb3a1   GAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAA   SEQ ID NO: 26               AluYb3a2   GAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAA   SEQ ID NO: 27               AluYe5   ACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAA   SEQ ID NO: 28               AluYf1   GAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAA   SEQ ID NO: 29               AluYg6   GAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAA   SEQ ID NO: 30               AluYh9   GAGATCGAGACCATCCTGGCTAACGCGGTGAAACCCCGCCTCTACTAAAA   SEQ ID NO: 31               AluYl6   AGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAA   SEQ ID NO: 32               AluYbc3a   AGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAA   SEQ ID NO: 33               AluYe2   GACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAA   SEQ ID NO: 34               AluYf2   GATCGAGACCATCCTGGCTAACACAGTGAAACCCCGTCTCTACTAAAAAA   SEQ ID NO: 35               ALU   GAGGCAGGAGGATCGCTTGAGCCCAGGAGTTCGAGGCTGCAGTGAGCTAT   SEQ ID NO: 36               MIR   GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCT   SEQ ID NO: 37               L1PA2   ATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGG   SEQ ID NO: 38               L1PA7   CCTGTCGGGGGGTGGGGGGCTAGGGGAGGGATAGCATTAGGAGAAATACC   SEQ ID NO: 39               L1PA11   TGGGCTTAATACCTAGGTGATGGGATGATCTGTGCAGCAAACCACCATGG   SEQ ID NO: 40               L1PA15   TCGGGTACTATGCTTATTACCTGGGTGACGAAATAATCTGTACACCAAAC   SEQ ID NO: 41               L1PB1   ATCTCAGAAATCACCACTAAAGAACTTATTCATGTAACCAAACACCACCT   SEQ ID NO: 42               L1PB3   AAGTGGGAGCTAAGCTATGGGTACGCAAAGGCATACAGAGTGGTATAATG   SEQ ID NO: 43               L1MA2   GGGAAGGGTAGTGGGGGGTTGGTGGGGAGGTGGGGATGGTTAATGGGTAC   SEQ ID NO: 44               L1MA5   ATAGGGAGAGGTTGGTTAATGGATACAAAATTACAGCTAGATAGGAGGAA   SEQ ID NO: 45               L1MA9   AGATCTTAAGTGTTCTCACCACACAAAAAAAAATGGTAACTATGTGAGGT   SEQ ID NO: 46               THE1B   CTGCACAWGCTCTCTTGCCTGCCGCCATGTAAGACGTGMCTTTGCTCCTC   SEQ ID NO: 47               MSTA   TCCCCTTGGTGCTGTCCTCGTGATAGTGAGTGAGTTCTCGTGAGATCTGG   SEQ ID NO: 48               MSTC   GATTAATGGATTAATGGGTTATCATGGGAGTGGGACTGGTGGCTTTATAA   SEQ ID NO: 49               MLT1A   TGAGGACACAGTGAGAAGGCGCCGTCTACGAACCAGGGAATGAGCCCTCA   SEQ ID NO: 50               MLT1B   GGAGAAGACGGCCATCTACAAGCCAAGGAGAGAGGCCTCAGAAGAAACCA   SEQ ID NO: 51               MLT1C   CCAGCAAACCACCAGAAGCTAGGGGAGAGGCATGGAACAGATTCTCCCTC   SEQ ID NO: 52               MLT1D   GGTCAGAGTCAGAGAAGGAGATGTGACGACGGAAGCAGAGGTCGGAGTGA   SEQ ID NO: 53               MLT1E   GATTCCGTCTTGNCGNCANTCTTGCTGAGAGNCTCTCTTGCTGGCTTTGA   SEQ ID NO: 54               MLT1F   TGTAGTCCCCTCCCACATTGAATAGGGCTGACCTGTGTGACCAATAGAAT   SEQ ID NO: 55               THE1BR   CAAGAGGTGACTTGGGTGCTGTTAAAGGCATTCAGTTTTAAAAGGGAAGC   SEQ ID NO: 56               MSTAR   TCTTTTTGATTTTACAGGCTCATAGGTGGAAGGAACTTGCCTTGTCTCAG   SEQ ID NO: 57               MLT1R   AGCCTGATCATGTAACAGAAANNNCAATAGCGTTCTCTGGAAAGAANACC   SEQ ID NO: 58               MLT2A1   GGGTGTTGCCAAAGGAGGTTAACATTGGACTCAGTGGGCTGGGGAGAGGC   SEQ ID NO: 59               MLT2B2   TTCCAGATGAGATTAGCATTTGAATCAGCGGACTGAGTAAAGAAGATTGC   SEQ ID NO: 60               MLT2C2   CTCAAGACTGCAACGTGGAAATCCTGCTGNTTTWCCAGCCTCCAAGCCTT   SEQ ID NO: 61               MLT2D   GGCTAGGCTATGGTGTCCAGACGTTTGGTCAAACATTAGTCTGGGTGTTT   SEQ ID NO: 62               LTR2   CAATGCTCCCAGCTGATTAAAGCCTCTTCCTTCATAGAACCGGTGTCTAA   SEQ ID NO: 63               LTR3   GCAAGGAGCCCCCTGACCCCTTCTTCCAAACATACTCTTTTGTCTTTGTC   SEQ ID NO: 64               LTR4   ATCCTCCTGTCCCACCCATTGGTCTCTCCTGTCCCTTGATTCCTGCAACA   SEQ ID NO: 65               LTR5   ACTCAGAGGCTGGTGGGATCCTCCATATGCTGAACGTTGGTTCCCCGGGC   SEQ ID NO: 66               LTR11   AACTCCGTCACTGTAATCCCAATGTAAAGCAAGAATTCCAAACCAGGAAA   SEQ ID NO: 67               LTR12   GCTTCATTCTTGAAGTCAGCGAGACCAAGAACCCACCGGAAGGAACCAAT   SEQ ID NO: 68               LTR13   CTTGTGTCTTTATTTCTACACTCTCTCGTCTCCGCACACGGGGAGAAAAA   SEQ ID NO: 69               MER1A   AAGCTTCATCTGTAKTTACAGCCGCTCCCCATCACTCGCATTACCGCCTG   SEQ ID NO: 70               MER1B   TGATCTGAGGTGGAACAGTTTCATCCCGAAACCATCCCCGCCCCCCGGTC   SEQ ID NO: 71               MER2   AAAATCCACGGATGCTCAAGTCCCTGATATAAAATGGCGTAGTATTTGCA   SEQ ID NO: 72               MER3   ATGTGGCTAYTGAGCACTTGAAATGTGGYTAGTGCGACTGAGGAACTGAA   SEQ ID NO: 73               MER4A   GGACCTCAAGATCTTTACCCTAAAACAGTTCTGYTGAVYTTCACCTTGGC   SEQ ID NO: 74               MER4B   TTGGTCTCCGCAACCCCTTATNTCATAACCCGGACATTCCTTTCCATTGA   SEQ ID NO: 75               MER4C   CCTCCCTCTTTCCCCTCCAGCCCGCTTTTCCCCTTTAAATATTGAAGCCC   SEQ ID NO: 76               MER5A   GTCCCCGGACCAGCAGCATCAGCATCACCTGGGAACTTGTTAGAAATGCA   SEQ ID NO: 77               MER5B   TCAGTATTTTTTAAARCTCYYCAGGTGATTCCAATGTGCAGCCAAGGTTG   SEQ ID NO: 78               MER6   AAGTCGCAGTTTCCAAGAACCTATCGACGACGTTAAGTGAGGACTTACTG   SEQ ID NO: 79               MER8   AAAAATCCGCGTATAAGTGGACCCACGCAGTTCAAACCCGTGTTGTTCAA   SEQ ID NO: 80               MER9   GCTGTGAGACCCCTGATTTCCCACTTCACACCTCTATATTTCTGTGTGTG   SEQ ID NO: 81               MER11A   TGATTTTGCCCTTGTCCTGTTTCCTCAGAAGCATGTGATCTTTGTTCTCC   SEQ ID NO: 82               MER11B   ACTTGCTGGTTTTTGCGGCTTGTGGGGCATCACGGAACCTACCGACATGT   SEQ ID NO: 83               MER20   CCCCACAACAAAGAATTATCCGGCCCAAAATGTCGATAGTGCCAAGGTTG   SEQ ID NO: 84               MER21   SAGCAGAGGTAAAACATGGTTTGAGAGAGGTTTTYCTGMAAYAGRAGGGC   SEQ ID NO: 85               MER21B   CGGTCAGAAGCACAGGTNACAACCTGGNGCTTGCGACTGGCATCTGAAGT   SEQ ID NO: 86               MER22   TGAGTCTCCCCAAAAGTGGAGCCCTTGTGATGACGAGCACAGGTCCGCCT   SEQ ID NO: 87               MER28   AAGACGANGAGGATGAAGACCTTTATGATGATCCACTTCCACTTAATGAA   SEQ ID NO: 88               MER30   TTTTAAGAAAGTTTACGAATTTGTGTTGGGCCGCATTCAAAGCCATCCTG   SEQ ID NO: 89               MER35   GATGAAAAGGGGATCCTGTGCAGAAACCACACTACCCATCAGAGAAGCAA   SEQ ID NO: 90               MER39   GGCAGGTCATAGAAACTAGAACTCCTCTCCCCCAAAGCAAGCCATAAAAC   SEQ ID NO: 91               MER44A   AGGGTTCGGTACTATCCGCGGTTTCAGGCATCCACTGGGGGTCTTGGAAC   SEQ ID NO: 92               MER44C   CGCACCTCAAACTGCAAAAGTTACGGCCACAGTGCGTGATAAGTGCTTAG   SEQ ID NO: 93               MER45   GAAATTCTTAATAATTTTTGAACAAGGGGCCCCGCATTTTCATTTTGCAC   SEQ ID NO: 94               MER48   TGTTGTTGTGGACGCGCTCTCGGGGTTSGAACCGAYACAAGARCCTTACA   SEQ ID NO: 95               LOR1   TCTTCCTTGGCAATAMTYRTTGTCTCAGTGATTGGCTTTCTGTGCAGTGA   SEQ ID NO: 96               SVA   GGGGAAAGGTGGGGAAAAGATTGAGAAATCGGATGGTTGCCGTGTCTGTG   SEQ ID NO: 97               ALR   GTGGAGATTTCAGCCGCTTTGAGGTCAATGGTAGAATAGGAAATATCTTC   SEQ ID NO: 98               MSR1   GGAGTCAAGACCCCCCAGCCCCTCCTCCCTCAGACTCATGAGTCCAGACC   SEQ ID NO: 99               TAR1   ACTCATGGAGGGTTAGGGTTCAGGTTCGGGTTCGGGTTCGGGTTCGGGTT   SEQ ID NO: 100               CER   GGTTCTGAGTGTTTGTCCCTCACATAGGATTCCAGAACACTGCTGCTGGG   SEQ ID NO: 101               BSR   TCACAATGCCCCTGTAGGCAGAGCCTAGACAAGAGTTACATCACCTGGGT   SEQ ID NO: 102               HSATII   GGGTCCATTCGATGATGATCACACTGGATTTCATTCCATAATTCTATTCG   SEQ ID NO: 103               HSATI   CCACTGTCTGTGCTGTGTCTTTCAAAGGTCAGAAGAGATTGNACCTTTGT   SEQ ID NO: 104               R66   TGCRTTTACAAACCTTTAGCTAGACACAGAGCGCTGATTGGTGCGTTTTT   SEQ ID NO: 105               SN5   CCTGACTCCTGAGTCACGTTACTGTCCCACTATACGTTAAGAGGAGGGAA   SEQ ID NO: 106               HIR   AATATCAGGAACACCGGCATGTGCACTTAGGACCATGTTTTAATTTTTCA   SEQ ID NO: 107               GGAAT   GGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAAT   SEQ ID NO: 108               KER   GGATGAGGCAGGAAAGACAGCTGAGGGTCAGAACCCAGGCAGGTCCAATG   SEQ ID NO: 109               TIGGER1   ACTCGCTGAAGGCTCAGATGATCGTTAGCATTTTTTAGCAATAAAGTATT   SEQ ID NO: 110               TIGGER2   TAAAGTTACACCGAGTGTGCCTGCCTCTCCTGCCTCCCCTTCCACCTCCT   SEQ ID NO: 111               GSAT   GGGACTCAGGAGGATGTTGAGGGAGACAGAGGGGTGAAGCGTTGAGACGA   SEQ ID NO: 112               GSATX   CAGGCGGCCAGNCTTTCAGGGGGAGGATGAAGTAGGCCTGGGACAAAAGC   SEQ ID NO: 113               HERVL   AGGACTCTACTTCTAATAGTATGGAGAACACTGATAGTCCTTGGCATGAA   SEQ ID NO: 114               HERVK   CCCTGTCACTTGGGTTAAGACCATTGGAAGTACATCGATTATAAATCTCA   SEQ ID NO: 115               HERVR   AACCCAACAGTATCAGGTGCTCAGAACCGATGAAGAAGCTCAAGATTGAG   SEQ ID NO: 116               HRES1   TGGTTAATGTGTAACAAGGAGGCAGTAGGCCCCAGGTGTCCAGCCAGAGG   SEQ ID NO: 117               HERVE   AAAAGTGAGGACGAGAGTAAGAACTCCCACTAAAAGTGAAAATTCTCAAA   SEQ ID NO: 118               HERVH   CATACCACCCCCCAAAAATTTTCACTGCCCCAACACTTCAACACTATTTT   SEQ ID NO: 119               HERVI   TTGTAGGATGCTGTGTCATACCCTGTGCCCTAGGATTAATACAAAAGCTC   SEQ ID NO: 120               LTR14   GCCTCCACTCTTTATGAACTCTTAACCTGTCTCTTCTCATTCCTTTGTCA   SEQ ID NO: 121               HERVKC4   CCGGATCATTCACAGAGTTCAATTCAATTAACAGTTTAAGCCCCCAAAAA   SEQ ID NO: 122               MER4I   AGAGATCAGACGAAACCTGAGACCAGAGACTCATTTTCTTCTAAAATGCT   SEQ ID NO: 123               MER49   ACATGCATGTTTGTTCAATACGCATGCGTCAGGACCACCTTCATGAATAT   SEQ ID NO: 124               MER4D   CAACCCCCCTTATCTTAACTCAAGCTGACTTCAACTCTTCAGGCAGAGCT   SEQ ID NO: 125               MER39B   GCCCTCCTGTCTCTCAGTCCCATTCTCCCCCGAGGCTAGCCATAGAAACT   SEQ ID NO: 126               IN25   TCTTGGAGAAGGGATCCTTGTTCCCCNCTGGCNCTGGTANNCCACTGCAG   SEQ ID NO: 127               MER61   AAGCCTAAWTTTTCGTGGCCGTGTGACAAGGACCCCGTCTTTAGCTGAAC   SEQ ID NO: 128               HERV3   CAACCCTTGCCAAATGAAGAGAACTGCCTTCNCATGAAGAATTAANTAGT   SEQ ID NO: 129               HERV9   GCACAGAGCCATACAACTAATACCCCTACTTATAGGGTTAGGAATGGCTA   SEQ ID NO: 130               HERVS71   AAACTGGACTAATGTCCTTGTCCCAACAGGTAGATGCTGATTTAAATAAC   SEQ ID NO: 131               HSMAR1   CACTTCTTCAAGCATCTCGACAACTTTTTGCAGGGAAAACGCTTCCACAA   SEQ ID NO: 132               HSMAR2   TGGTATCATCGCTTACAAAAGTGTCTTGAACTTGATGGAGCTTATGTTGA   SEQ ID NO: 133               L1   AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAA   SEQ ID NO: 134               L1MA10   GTGATGGTTTCACGGGTGTATGCATATGTCCAAACTCATCAAATTGTATA   SEQ ID NO: 135               L1MB3   TCAGTTTGGGAAGATGAAAAAGTTCTGGAGATGGATGGTGGTGATGGTTG   SEQ ID NO: 136               L1MB7   AGATAGTGGTGATGGTTGCACAACTCTGTGAATATACTAAAAACCACTGA   SEQ ID NO: 137               L1MC2   ATGTTAATAATAGGGGAAACTGTGTGNGGGNGGGGTGAGGGGGTATATGG   SEQ ID NO: 138               L1MC3   CTGTTGGAGTGGGAGGTTACAGATAAGCAAGGGGAGGAGGCTAGAATGAT   SEQ ID NO: 139               L1MC4   TATTTAGGGGTAANGGGGCATCATGTCTGCAACTTACTCTCAAATGGTTC   SEQ ID NO: 140               L1MD1   GCAGGAGGGAAGTGGGTGTGGCTATAAAAGGGCAACATGAGGGATCCTTG   SEQ ID NO: 141               L1MD2   GNGNGGGGGAAGGGAGGTGGGTGTGGCTATAAAAGGGCAGCACGAGGGAT   SEQ ID NO: 142               L1ME2   AGTGGTTGCCTCTGGGGAGGGTGANTGACTGGAAAGGGGCATGAGGGAAC   SEQ ID NO: 143               L1ME3A   GGCAAAACTAATCTATGSTGTTAGAAGTCAGGATAGTGGTTACCCTTGGG   SEQ ID NO: 144               LSAU   GGTGTTGGGAGAGCCTCAGCCGGAATTTCGTGGACGGACAAGGGCACAGA   SEQ ID NO: 145               LTR1   CTAGAGGTTTGAGCAGCGGGGCACTGAAGAAGCGAGCCACACCCCCATCG   SEQ ID NO: 146               LTR15   ATCCTCCTCAACCCCATCGGTCTCTCTGATTCCTAAATCATCCCCAAACA   SEQ ID NO: 147               LTR8   TTTCTCTATTGCAATTCCCCTGTCTTGATGAATCGGCTCTGTCTAGGCAG   SEQ ID NO: 148               LTR9   TAAACTCCTCGTGTGTGTCCGTGTCCTAAATTTTCCTGGCGCGNGACGAC   SEQ ID NO: 149               MER31   CCTGTACCTATCGCAATGGTCCTGAATAAAGTCTGCCTTACCGTGCTTTA   SEQ ID NO: 150               MER34   GCCCAAACCCCTTTGTCTTGTCACGTTTTCACAATTTACTACTCTTTGTC   SEQ ID NO: 151               MER41A   GCAACGTCAGGAAGTTACCCTATATGGTCTAAAAAGGGGAGGCATGAATA   SEQ ID NO: 152               MER41B   TGCCATGGCAACGTCAGGAAGTTACCCTATATGGTCTAAAAAGGGGAGGA   SEQ ID NO: 153               MER41C   TAGCAGAGCACATCTCCCCCGTAATGTTCTTTGGCTTTGTTATCCTATAT   SEQ ID NO: 154               MER50   TGGCCCTCTTCCAAGTGTACTTCGCTTCCTTTCGTTCCTGCTCTAAAACT   SEQ ID NO: 155               MER63A   TTCAAGCTACCAACGTGATGTCACTGAATGSGGAGTTGGGAAAAGATATA   SEQ ID NO: 156               MER63B   ATGTCACTGAATGSGGAGTTGGGAAGAGATGCACAGTAGCACACYATTAT   SEQ ID NO: 157               MER63C   ACAATGTAACGGCTACAGACACGACACACTTTTAAGTTTAATCTGCATTA   SEQ ID NO: 158               MER65A   GAATATGCACATAGTTTACTATGGCACGCGTATTCCCATTGCAATGCTCT   SEQ ID NO: 159               MER65B   ACATTTGCCTGACAACTGTCTCACRAACCTAGCTACTGCAAGAGCCTACT   SEQ ID NO: 160               MER66A   AGACTAGCTGAAACAGGGCCAGGGCAAAAGCACCTCTCCATAAGACACAC   SEQ ID NO: 161               MER66B   CTTGAACACCAGACCAAATTGAAGACTAGCTGAAACAGGGCCAGGGCAAA   SEQ ID NO: 162               MER67A   GCCTCAACCTCGGCCTATAAAGACTTGAACAAACACTAACATAGTTTCTA   SEQ ID NO: 163               MER67B   CACAGAACAACTCCATCCAAACCCCTGCACTAAGAGACTTGACCAAACTC   SEQ ID NO: 164               MER67C   TCTTGAGAACATGTATGTAATGGGCTGTATCTGCTCGGCTATATAAAAGG   SEQ ID NO: 165               MER68A   AACCCTGGGCACTGAGTCTCTAATGAGCTTCCCTGGTAGACAACATTTCA   SEQ ID NO: 166               MER68B   TTCCCTTTGCTGATCTTGCCGTGTATCCTTACNRTGTCGCTGTAATAAAT   SEQ ID NO: 167               MER69A   CCCCCAAATTGTATAAGCTTCAGGCCCCACAAAACCTGGATCTGCCCCTG   SEQ ID NO: 168               MER69B   TTACAAAATCATTGTCATATGAAGAGGCGATCAAAGAGTATGCAGCCAAA   SEQ ID NO: 169               MER70A   TGTTCTGTCTCACCGGACTCAGACAAGTTGGTAACCAGTGCACAGTGAAC   SEQ ID NO: 170               MER70B   TCNGACCCCTATTCCTGGTGGTTGGCATAGTGATGATCTTTGCTATTCTC   SEQ ID NO: 171               MER72   GGCATGAAGCTCAATTGCACATGTGCATGTTTCTCCTTTCATAAATATTC   SEQ ID NO: 172               MER73   GGTGACGGGGTACGACTGGGTTTCAAACAACTTATGTCAGGCCTAAAAAT   SEQ ID NO: 173               MER74   GGGGGTATGGGCTCTGGATTGGTTGGTTTGCATATGAAAGGCGCGCTCCC   SEQ ID NO: 174               MER75   TGGCCGAAGATTCATTTGATGAATCCGATTTTTCCGAAATAGACGATTCT   SEQ ID NO: 175               MER76   TGTTGCCTTAATCGGCTNCTCTGACACCCGGCAGCTCAGCTCTCTCTCCA   SEQ ID NO: 176               MER77   GGTGAGCTTCCCTGGTTGGCAATACTCTNTGCATGTTGTCACACATCGTT   SEQ ID NO: 177               MER80   CCATAGGCTTCACCAGACTGCCAAAGGGGCCCATGGCACAAAAAAGGTTA   SEQ ID NO: 178               MER82   NTGCAAATGACCGNGAAAGTGCTNCAAGTATTGATTTTGGGGTTACAAAT   SEQ ID NO: 179               MLT1G   CACAAATTCTTTGACACTCTTCCCATCGAGGAGTGGGGTCCGTNTCCTCT   SEQ ID NO: 180               PABL_A   AATAAAAACTCTCTTCCTCCCCAGTTCATCTGCATCTCGTTATTGGGCCA   SEQ ID NO: 181               PABL_B   CCAGTTCATCTGCATCTCGTTATTGGGCCACGAGAATAAGCAGCCCGACC   SEQ ID NO: 182               MER57I   GCAGTTATGGGGGATACTCGGCTCTTTGCACATTTGGATNAGAGAAGCAT   SEQ ID NO: 183               MER65I   CCTGGATAAATTCCCCTGGGGAACTTGAGGCCCCATATACACGAAATTAC   SEQ ID NO: 184               MER41I   TTTGTTGGGAACTCAGTTACAAATAACCCTCACCATACCAGTACTTTCTG   SEQ ID NO: 185               PTR5   CATGCTTAAGGAGCCCTTCAGCCTGCCACTGCACTGTGGGAACACTGGCC   SEQ ID NO: 188               LIM2_5   CGCCTCCTCCACAAAGAAGAACCAAAATAGCGAGTAGATAATCACACTTT   SEQ ID NO: 187               LTR10A   TGCTCCATCTGCGAGACGCACCCTTCTATAGAAGTAAAATTGCCTTGCTG   SEQ ID NO: 188               LTR10B   GCTGAGAGACCCTTTGTCCTTTGGCTCAGTGTTGGTTCTTCTTTGCAGCA   SEQ ID NO: 189               LTR10C   CAGTGTACTCTCATGGCAAAACTGCTGGTGAGTGTACCCTTTCTGCAGAA   SEQ ID NO: 190               LTR16A   CTGCATTGCAGCCCAACTTCTCCCTCTGCCCAATCCTGCTTCCTTCCCTT   SEQ ID NO: 191               LTR17   CCAAGAACCCCAGGTCAGAGAACACGAGGCTTGCCACCATCTTGGAAGTG   SEQ ID NO: 192               MER41D   GCACGTAGGCACAGCTTAGTTTAGTCTTTACATAGACAAGACTCCTATAT   SEQ ID NO: 193               MER51A   TCCGCAACCAATCAGACGTTTGCATAGGAGTGTAACTTTGTAACTTCACT   SEQ ID NO: 194               MER51B   CTTTACTTCGTCCTCTTCATTTACATAGGGCGTACCCCAAGTAACCAATG   SEQ ID NO: 195               MER57A   ATCTTCTACCACATGGCTGCACTGGAGTCTCTGAACCTACTCTGGTTCTG   SEQ ID NO: 198               MER57B   TATAAATTTGTTCCGACCACGAGGCATCCCTGGAGTCTCTCTGAATCTGC   SEQ ID NO: 197               MER65C   CAACCCTGGCTGCTGAAACTGCCTGTTGTAACCTGAAACCAGTTTTATCT   SEQ ID NO: 198               MER83   TCTGCAGCCCAAGAACCATCCTATAAAATCTCCAGCAAGCCTTTGTCTCC   SEQ ID NO: 199               MER84   CATAAATGCTCCTAAGGAAAAATCCACCGCGGCGCGCTCAGTCCTCTCTT   SEQ ID NO: 200               HERV16   TTGACTATGATGTGTAGGAGGGGTAGGGCTGCTTTAGTAAAATGAGTAAG   SEQ ID NO: 201               HERV17   GAAGGCACCCCTCCCGAGGAAATCTCAACTGCACGACCCCTACTACGCCC   SEQ ID NO: 202               PMER1   GTTCTCAACCTTCCTAATGCCGCGGCCCTTTAATACAGTTCCTGTGGGTC   SEQ ID NO: 203               MER54   TGAAAGATACACTGTAAACACCCACAACCAMCTTCCCTGGAGCCCCATCA   SEQ ID NO: 204               LTR18A   TGTACATACGGCTTGCGCCCAGGCTCACTCGCGCCCAGAGAGAGAGTAAA   SEQ ID NO: 205               LTR18B   ATGAGAGAGCTGCTGAATAAAACCATATTTCACCTGCCTACGGCCCCCCG   SEQ ID NO: 206               LTR19A   AGAGAGTGCTCCTGACTGAAATCGGCCAGAAGCCCCTCTCAGGTTTATTC   SEQ ID NO: 207               LTR19B   GACTGKWGAGCCGCTTTTCGTGTTTCTTTCCTCTTTCTTTAATTCTTACA   SEQ ID NO: 208               LTR20   AATAAATTCTGCTCYACCTCACCCTTCAATGTGTCTGCATGCCTAATTCT   SEQ ID NO: 209               LTR16C   GTAACTNGCTTGATAACGCACCCTTTATTGGCTTCCTTCCCTTCCCTGTC   SEQ ID NO: 210               LTR21A   CTGCTTYCCTTGACTGTKAWGGGGGCAGCCGRCAGGTTAATAAARGCTTG   SEQ ID NO: 211               LTR21B   CAATAAAGCTTGCTTGCCTGACTTTGGGTCTCYTCATCCTTTCTCTCGGC   SEQ ID NO: 212               MER85   TTGAGCAGTAGGATATAAATAACTCCCACATGCTTAGCGTTCCAATAATG   SEQ ID NO: 213               LTR22   GTGCYAGCTGNTTAGGGCCAGCWGCWGTKACAAACCTYYCTTGGWGTSTG   SEQ ID NO: 214               LTR23   CCTTTAAAAACCACTTGTAACTGCTGCTAATTGGAGTGTATATTCAGGGC   SEQ ID NO: 215               LTR24   AAACCTTAACTTCTCCACTTTGGAACGCTGACCCCATTCCTTTGGAGTCT   SEQ ID NO: 216               HERV23   GTCCTGTCCCCCCAACCATGTGAGATAGAGCCATCTGGGAATGAGCTTTA   SEQ ID NO: 217               HERV18   AGCGGGAATATTAGTGGTGAGTTGTTGCTCCCTGTATTGTTGCTGTGGCC   SEQ ID NO: 218               MER87   ACTTACTGGCTGTCGWGCGGTGAGCAGTACCAGCTTTGGATTCAGTTACA   SEQ ID NO: 219               MER74A   AATGGCAGTCGTCTCCTGATCTGTTGGCCTTACCATACCTGAATAATAAT   SEQ ID NO: 220               MER74B   CTTTTCAATGGCAGTCGTCTCCTGATCTGTTGGCCTTACCATACCTSAAT   SEQ ID NO: 221               MER88   AGGGGAACTTGTGGCAGGGACCAGCCTTATCACACTGGTGCACCTGGTCA   SEQ ID NO: 222               MER54B   GAGCCCAGTCTGCTAGGCGGGAGAGATGCCTCTAAGTTCTTATCTCTGGC   SEQ ID NO: 223               MER31A   GGCTCCTGAACCTTCTCCTAGGCCCATCTGTGCACTTCCTTGTAAAATCC   SEQ ID NO: 224               MER31B   GCCCTGTCCTTGGCCTGCWTAGCCCAGTTTTAGCAAGAATCCTGCTAAGT   SEQ ID NO: 225               MER67D   ATCCACCTGCCTTTTGTTTCAGNGGAGTTGAGTTCAANCTCTAACCCCTA   SEQ ID NO: 226               MER31I   GATGATTCAGCTGGTCCTTAATGAACAAAAGGCMACCCAACAAGAAAATG   SEQ ID NO: 227               CHARLIE1   TTCCACATTGCAACTAACCTTTAAGAAACTACCACTTGTCGAGTTTTGGT   SEQ ID NO: 228               CHARLIE1A   CACCGCAACTAACCTTTAAGAAACTACCACTTGTTGAGTTTTGGTGTAGT   SEQ ID NO: 229               CHARLIE1B   CAGTGGAGTTTTCCAGAGGCTACATGACGTGTGATGTCGCAACAGATTGA   SEQ ID NO: 230               CHARLIE2   TAAAATTCTGTGGGGGAAGTGGAATGGAAATACGAGTTCAAGGAGAAAAA   SEQ ID NO: 231               MER30B   CAATCTTTTGGCTTCCCTGGGCCACATTGGAAGAAGAATTGTCTTGGGCC   SEQ ID NO: 232               MER45B   CCGCATACGAGTTAAATGCTCTTATATTTGCATTTAAAACTGGCATTGCA   SEQ ID NO: 233               MER45C   GCGAGTATCCCCGTGCCCGAGGGAGCGTGACATTAAATAGCAAATAAAAA   SEQ ID NO: 234               LTR25   CTCTCCGCTGRCAGAGAGCTTTCTTCTTTCACTTATTAAACTTTCACTCC   SEQ ID NO: 235               LTR26   TCTCAGTGTAATTGGTCTGTTACTGCGCAGTGGGCATATGAACCTGTTGG   SEQ ID NO: 236               HERVK9I   ATCCCGACTCCTGCGAGAAGTAGCTCACCGTGACAAAGCTGCCTTTGCTT   SEQ ID NO: 237               HERVH48I   TCTCTCAAGAATACCCCAAAAATTAAGTTTTTCTTTTTCCAAGGTGCCCA   SEQ ID NO: 238               MER11C   CCTGTGATCTCGCCCTGCCTCCACTTGCCTTGTGATATTCTATTACCYTG   SEQ ID NO: 239               MER11D   TTCATCCCCATGTGACCATCTCACCTCATAATCAAATGACCCTAAATCCC   SEQ ID NO: 240               LTR10D   GGCGACTGGCCAAGGAGAAGCACCCCTCTGCGCAGAAGTAAAATTGCTTT   SEQ ID NO: 241               LTR14A   CCACACTCGCGATGGCCCCCTGGTCCCACTTTCTCTCTCAAACTGTCTTT   SEQ ID NO: 242               LTR14B   TTTGCAGCCTCCATACTTAGCGTTGGCCCCCTGGACCCACTTTCTCTCTC   SEQ ID NO: 243               LTR27   GTGGGACAAGAACTTGGGAATCAGTGCACAAGCCAGACTTGGCCTGGGAA   SEQ ID NO: 244               LTR28   ATTGATCCCCACCCTTCACCTATTTTACATATACCCACCCTTTCCTAATT   SEQ ID NO: 245               LTR29   TTAATCAATCTGCCTTNTGTCAGTGATTTTTCAGCGAACCTTCAGGGGGC   SEQ ID NO: 246               LTR30   CTTTTTTTCTCTCTTGGTCCGATCCGTGTCTCTCWCTCGCCGCGGGCWGC   SEQ ID NO: 247               LTR31   TTTCTCTTTTGCAAAACCCATCGTCACAGTGATTGRCTTACTGCGCGCGG   SEQ ID NO: 248               MER61B   ACCCTTTCCTGACTGATTCTCTCTGAATAATGCCCACCTGCGCACTGGGA   SEQ ID NO: 249               MER61C   CCGACCCGCCCCACAAGTGTTTACATCAGATGCTTTTGTGCAGATGAGGG   SEQ ID NO: 250               MER92A   CGCTTGCCCACTGTCYCCTTTCTACTGGTTCTGCTTAYCYCTCCCTATAA   SEQ ID NO: 251               MER92B   TTCTGCCTGAACTTTGAGATGCTTGCAGATCTTATGGTCAGAGCGTTCTC   SEQ ID NO: 252               MER92C   TATCTACCCCTTCCTATAAAAGTCCAAGGCAAAACCACCCTGCCGAGACA   SEQ ID NO: 253               MER93   GCCCTGGGTTCCTACGTAAGCAAACCGAAACCTAACTCAGNCGTTTCTTA   SEQ ID NO: 254               MLT1H   CACAGATGCATGAGGGAGCCCAGCCGAGACCAGAAGAACCACCCAGCTGA   SEQ ID NO: 255               LIP_MA2   GAACCCAGAAACAAATCCATACATYTACAGCGAACTCATTTTCGACAAAG   SEQ ID NO: 256               LTR32   ATGTAAGTCCCCAATAAACCCTATGTCTCATTTGCTGGCTCTGGGTCTCT   SEQ ID NO: 257               GOLEM   GCACAACGACGAAATCGCCTAACGACGCATTTCTCAGAACGTATCCCCGT   SEQ ID NO: 258               ZOMBI   TAGTGACACCTTTGCTTTCTGATGGTTCAATGTACACAAACTTTGTTTCA   SEQ ID NO: 259               ZOMBI_A   CGGATTTTCAGATTTGGGATGCTCAACCGGTAAGTATAATGCAAATATTC   SEQ ID NO: 260               ZOMBI_B   NCTGCCAGNCAACNACAGNTTGTGCACCTNGNTGGCARAGANACTGACAC   SEQ ID NO: 261               LTR33   CGCTGTTGCTAGCCCCGGGGTGCTTCACCATCCCTTGTTGGTTTCCCTTA   SEQ ID NO: 262               L1PA12_5   AAGTCAGCTTCAAATAAAGACCCTGCACAAAGCCTCGGCCCGGTGAAAAC   SEQ ID NO: 263               L1PA16_5   GACAGCCANACAATAGACAGCCTGTCAATAGANATAGCCACACAATAATA   SEQ ID NO: 264               L1PBA_5   AAGAATCTGAACAGCAGCCCTTGAGTCCCAGATCTTCCCTCTGACATAGT   SEQ ID NO: 265               L1PBB_5   AATCTACCCACCTGCTTTAGCCACARCTGGTKYYTACCCAKGGAYACCTC   SEQ ID NO: 266               L1M3A_5   AAGAAACATAWTCACATTCAARGGAGTCCCAATATGGCTATCAGCAGATT   SEQ ID NO: 267               L1M3B_5   AGTGGMAATCTCATCAGCCCAGGGATCTRACAGGAGAAGGTCTTCCTCCC   SEQ ID NO: 268               L1M3C_5   YACATCMATAGAAAAGGTCTGAGAGAGYCCCAGAATCCCTAGCCAGGCTG   SEQ ID NO: 269               L1M3D_5   GTCGCGCTACGCTGATANGATTNANCATACCCTANATGCTCGGCGACTGC   SEQ ID NO: 270               L1MB6_5   CACTCAGTGCGAAMAGCATTATACCTGGGGGCATTTGTTGAAAACAWTTA   SEQ ID NO: 271               L1MCA_5   TGAAAGTGGACTTGGATTAGTTGTAAATGTATATTGCAAACTCTAGGGCA   SEQ ID NO: 272               L1MCB_5   CTGACACCTACAGCTACAGCAAACAGTAAACACAGTCTAACTCTTAGCCA   SEQ ID NO: 273               L1MEA_5   ACCACAGCCACTGGAAAGAGTGGGGAAAATCCCGGAAAGGAGAGAGCCAG   SEQ ID NO: 274               L1MEC_5   ACAAAAATATCCAGCACCCAACAAGGTAAAATTCACAATGTCTGGCATCC   SEQ ID NO: 275               L1ME_ORF2   TCGTGACCTTGGGYTAGGCAAWGATTTCTTAGATATGACACMAAAAGCAC   SEQ ID NO: 276               MER89   AAGCTCTGAATAAATAGCCTTTGCTTGTTCTCATTTGGKTGGTCTTCATT   SEQ ID NO: 277               MER90   CCTCGCTGCARCGAGCAATAAACCCAACTTGTTCAACCACAGGTGTGTTC   SEQ ID NO: 278               CHARLIE3   ACAGCAACCAAAACGAGATTACGGAGTAGACTGGACATAAGCAACACACT   SEQ ID NO: 279               MER91_B   ATAATGACAATTTTCCAACAGATGGCAGTAAAGTGTCTTGAGGAAGGGGC   SEQ ID NO: 280               HARLEQUIN   CCTGTACTTCTTCAAATGATAAAAAGCTTCATCGCTACCTTAGTTCACCA   SEQ ID NO: 281               CHESHIRE   TGCCTTCCAAGCAATGAATATGCTCAATTNAAATCATATGCTCGTGATTG   SEQ ID NO: 282               GOLEM_A   GAAATTGCCTAATGACGCATTTCTCAGAACGTATCCCCGTCGTTAAGCGA   SEQ ID NO: 283               GOLEM_B   TCCTGCAAGCTCCATTCATGGTAAGTGCYCTATACAGGTGTACCATTTTT   SEQ ID NO: 264               LTR34   TGTGTCTGTGGCTCGCGTTTTTCCCGGACATGCCCTAAAGCTGGCTTAAT   SEQ ID NO: 285               LTR35   CGTGTTATTTCYATTACATGGRGAGCCCAGGAACCTGTGGTCNNTAAACA   SEQ ID NO: 286               LTR36   CCTGTACTTCTTCCCCCTAAGCTAGCTTTGGAATAAAAAGTCACTTTCTT   SEQ ID NO: 287               MLT2A2   CAGACTGAAGGCTGCACTGTYGGCTTCCCTACTTTTGAGGTTTTGGGACT   SEQ ID NO: 286               HAL1   GNAGGGATGGGGACTGCTTTTCGTNATAAGCCTTGTAGNACTATTTGACT   SEQ ID NO: 289               MER66I   CTGGGCCCCTTAGATCAGGTATCCAGAGATTTTTACTCCTCCGGTGCTAG   SEQ ID NO: 290               LTR37A   TTCCTTCCCCCACTGTGGAAAAAGCCAGTTTTGCNTCYATTTGCAAATTC   SEQ ID NO: 291               LTR37B   GGGAATGTACCTNTGTTGACTTTGCTATTTACTATTTGATTAGGGCCCAG   SEQ ID NO: 292               CHARLIE5   ACGTTTTCTCACCGATATCACACTGCATATGAACAAGCTAAATTTGAAGC   SEQ ID NO: 293               TIGGER5   TTAAGGTAGGCTAGGCTAAGCTATGATGTTCGGTAGGTTAGGTGTATTAA   SEQ ID NO: 294               TIGGER5_A   GGTTTCTACTGAATGTGTATCGCTTTCGCACCATCGTAAAGTTGAAAAAT   SEQ ID NO: 295               TIGGER5_B   GTTTACCCTCGTGATCGCGCGGCTGACTGGGARCTGCGGYTCACTGYCGC   SEQ ID NO: 296               LTR38   ATCTCCCATCTGCTAGCATTTGATTAATAAAGCTGCTTTCCTTTCACCAC   SEQ ID NO: 297               LOOPER   ATGACAGTTGATGAGCAGTTAGTTGCATTCAAAGGATATTGCCCATTTCG   SEQ ID NO: 298               HERVK22I   GCGCCTGACAGACCTGTTGCTGCACACATCTGTACTCTTCAATCAACAAA   SEQ ID NO: 299               MER51I   ACCACCCCTGGTCATTAAGGAGCTACCCTGTCTCCATTAGAHAGAGCAGG   SEQ ID NO: 300               MLT1I   GAGCAGAGCCCCAGCCGACCCGCGATGGACATGTAGCATGAGCAAGAAAT   SEQ ID NO: 301               LTR41   AGGGGTAGTGGCTGCTCCTTATATCTGCTATTCCTATATTCTTTAGAGTT   SEQ ID NO: 302               MER52A   CAATAAAGCTCCTCTTCGCCTTGCTCACCCTCCACTTGTCCGCGTACCTC   SEQ ID NO: 303               MER52B   TCTCCTCTGAGCTGTTCTATCGCTCAATAAAGCTCCTCTTCATCTTGCTC   SEQ ID NO: 304               MER52C   AGGATGGCCAGAGGACAAAGRGGGCAGAGAGACAATGGGACWGGATGACC   SEQ ID NO: 305               MER94   GCCTGGGACAGTCCTGGTTTATRCCTGTTGTCCTGGCGTAATTATTAATA   SEQ ID NO: 306               CHARLIE6   GAGGGGNAACCACACAAAAAGAGNAGGCTAATAAGTTGGCCAAAATAAGC   SEQ ID NO: 307               LTR39   TTTCTCCCGCTGCAAAATCTCGGTGTSGATGTTTGGTTTTACTGCGCCGG   SEQ ID NO: 308               LTR40A   TCTCTGACCCAGGAGTCTCGTGTCTTCTGCCAGCATCCATGAAACTGTGG   SEQ ID NO: 309               LTR40B   TCTCTGACCCAGGAGTCTCATGTCTTCTGCCAGCATCCATGAAACTGTGG   SEQ ID NO: 310               HERVL_40   TGCTTGGATGTCCTGTTGATAGTAGCCTTAATTAAATGCTNTATGAGACA   SEQ ID NO: 311               LTR9B   GTGTCGTTTTATCTAAATCGGCGCGAGGACCAAGGACCCTGGTGTTCCTC   SEQ ID NO: 312               HUERS-P3   CTCCAAATGGTGCTGCAGACCGAACCACACATAGACACGCCATTCTTCCA   SEQ ID NO: 313               HUERS-P3B   GAGATSAAATCAAAATCATTGACAGGCTCAGGGAAAATGCCGGCTTCAGC   SEQ ID NO: 314               HUERS-P2   TAGACACAGGNAAGAGACCTGGGAAGCTTNAGTAGCCACCGTGTAAGCCC   SEQ ID NO: 315               LTR20B   TTCGCTCCAACCTCACCCTTTGTGTCCATGCTCCTTAATTTTCTTGGTCG   SEQ ID NO: 316               HERVG25   CTRAGRACCCTTAAACCAGCCTCRRGARAARTCCTAACTGCTGTTNCCTA   SEQ ID NO: 317               LTR42   CTTCTTTCTTTGGAATCCCAACTGGCCCCATCTCAGGANGGTTTGGGGYA   SEQ ID NO: 318               LTR43   TTCYTTTGCAATAAATTRCTCTATGCTGCATCTCCTTTGCTGTGTGTCTC   SEQ ID NO: 319               LTR44   GTGTGTCTTCCCAGGTCAATCCTCACATTTGGCTTCCAATAAACCTTTAT   SEQ ID NO: 320               MER95   GTCTCCCGGTTCGCGARCTGTWCTTTCTCTYATTGTATGCACAATAAACT   SEQ ID NO: 321               L1MC5   TAAATGACACCATRGGGATGCAATCAGCAAAATCCAGACTGTGGGAAACT   SEQ ID NO: 322               MLT1J   ATGGAGCAGAGCTGCCATACCAGCCCTGGACTGCCTACCTCTAGACTTCT   SEQ ID NO: 323               HERVFH21   CAAGACATGATGCTACTCCAAGAATACCGACGGCTCCAGGAACAGCAGTC   SEQ ID NO: 324               ZOMBI_C   AAACTCATTTGGCAGCAAAACCTGACCTGAACTGATATGAGGCTATTTAT   SEQ ID NO: 325               MER96   AATTTAAGGAGGCACTCACTCTCAGGGTCGTGCAAGTGCAGGGTCGGCAT   SEQ ID NO: 326               LTR45   GCCCACCTCCTGTCTCCTTGCTGGCCGGTTTTGCAATAAAGCCTTTCTTT   SEQ ID NO: 327               LTR46   TCTGGCATTAAGCTGGTCCCCCACYTYYRCAGGTTTTNTGCTGGATATAA   SEQ ID NO: 328               MER99   GCTTTCAACTTGATGTCAGTGGATTCCTTCGAATCAGTAATGTCTCTATG   SEQ ID NO: 329               RICKSHA   AATACGGTTCGTCTGCTCATAACTGTTATACCCGTGCGACTGTCATTAGT   SEQ ID NO: 330               MER96B   CTCAGGCTCCAGTATGAGTNGACACTGCACAGTTRCTGATCCTGTATTTA   SEQ ID NO: 331               MLT1K   TCTTGCCACCACGNGGAGAGAGCCTGCCTGAGAATGAAGCCAACACAGAG   SEQ ID NO: 332               HERVK3I   CCCTTGGACCAGTCTAAAGCACCACATTAACATCTTATATGTAGTCCTTG   SEQ ID NO: 333               LTR22A   CGCTGCATACCTGTGTCTGAGTACTCATTTCATCCATCGGTCGGCCAGGG   SEQ ID NO: 334               LTR47A   ACACAGACGTGGCTTCTGTTTGTAAGTCCCTATTAAATGTTTCTTTCTGA   SEQ ID NO: 335               LTR47B   TCCTTCTGCGTTTGGGGGTCATTTTGCATATACGGCCCTTTCACGAAACA   SEQ ID NO: 338               MER101   TTCGTTTTACACCGAAGGCTGCATCTCCCCGGTTTGCAAACTGTTCACTG   SEQ ID NO: 337               LTR48   CAGTTCATTTCAGCAAACCTTCAGAGGGGACAGAGGGGAAGCTTTCCTTT   SEQ ID NO: 338               LTR48B   TAATCATTCTCCTCTGTGATTCCCCCATGCTATGCACGTTAAAATAAATT   SEQ ID NO: 339               LTR49   TGCCTTTTGTCAGTTGATTTTTCAGCGAACCTTCAGAGGGCGAAGGGGAA   SEQ ID NO: 340               LTR8A   CTCTTTCTTTATTGCAATGCCATGGTCTTTGTCTGTGCAGCGGGCAGGAA   SEQ ID NO: 341               MER41E   GTAGAAGCCCCAAACCCYMTTGGCGCAACTCWCTCTCTTGAGTATGCCCG   SEQ ID NO: 342               MLT2E   TCCCCCCTCCAGACCTTCACTTCCCCAGCTCCTCCCACAATTGTATAAGG   SEQ ID NO: 343               LTR50   TCTCTGTTAAAATAACTGGTGTGGTTTCTGTCTTCTCCTGACTGGACCCT   SEQ ID NO: 344               LTR51   TCTTTGAAGAGAGAGCGCCTTTGGTCTATGCCAGAGACTATCTCTTCCCA   SEQ ID NO: 345               MER103   GTGCATTGTGAATCTCCAAGAGGGGAAATATAGTATGCAGTRTTTCCCAA   SEQ ID NO: 346               MER104   TTAACATCTCTGAAATCGGGATGCATCTTACAATCGATGGCATGTCATAG   SEQ ID NO: 347               CHESHIRE_A   ACAACGGCAGAGTTGAGTAGTTGCGACAGAGACCGTATGGCCCGCAAAGC   SEQ ID NO: 348               CHESHIRE_B   ACAACGGCAGAGTTGAGTAGTTGCGACAGAGACCGTATGGCCCGCAAAGC   SEQ ID NO: 349               HUERS-P1   ATCTGCTCTTCGCCTTGCCCAGAGACCCCACTGTGAATTACCATTTGGAG   SEQ ID NO: 350               LTR45B   GTATTGGCTTCGCATCAGGCAGCAGNNAGCCCATTGATTGCTTRGTAACA   SEQ ID NO: 351               LTR52   ATACCCTCTTGGTGTGTGTGTGGCATCATCAGTCTTAACATCCAAACCAA   SEQ ID NO: 352               MER105   GCCCTAAGGCATCCATTGTATGTAATGAATTAACTTCTCTCCTATGCATC   SEQ ID NO: 353               LTR53   CATCTGTCCAGTGTTGGGTGTCATGTGTTTARCCATCCCCATAACCCTAG   SEQ ID NO: 354               LTR54   TATAAAGCCAACCTCCTCTGCTCAGCTCATYGGAACACTCATTCTATTTT   SEQ ID NO: 355               MER106   TGTGGTATTAAAATTTCATGGNGGGGGGGGGTGATTAGGAAAAAAATGTC   SEQ ID NO: 356               MER107   TTCTACCTTATCACTAGAGACAGAAACTAAAACCATGGCTTCAGGCTGCT   SEQ ID NO: 357               MER44B   ACTTAATAATGGCCCCAAAGCGCAAGAGTAGTGATGCTGGCATATTGTTA   SEQ ID NO: 358               MER61I   CTACTGACAGCAGGGGAGATAGGGCATACGTGGGTAGAGCGGATAATTCC   SEQ ID NO: 359               HERVL68   CCCTGGAAGGCTTTCAGGTCAGCTTCAACTTACTGGCCAGAGTTGTGCTG   SEQ ID NO: 360               MER83B   CCTCTTTGCAGACAGCCCCTTCTCTGCTGTGCTGCCCGTTGCAACCTTGC   SEQ ID NO: 361               MER83C   GCACGTAGCCCCCTCCAGTACAACCCTATAAAACTTCCCTCCAGCCCCTG   SEQ ID NO: 362               MLT1L   GAAAGAACCTGGGTCCTTGATGATATCGTTGAGCCGCTGAATTAACCAAC   SEQ ID NO: 363               MLT2F   ATCAGACGCARAGACAACAGCCTTACAGAGACTGCTTAACCAGCTCCCAC   SEQ ID NO: 364               LTR55   TCATATCTTTTTCCTTGATCAGCCCCCAAATCCCTTRAACCCCCTTCACA   SEQ ID NO: 365               LTR56   CTCTTTTTTGCCTTTAAAAATCCACTTGTAACTGCTGCTAATTGGAGTGT   SEQ ID NO: 366               LTR57   GAGTGCCCTGTATGTAAGTCCTAATAAACTCATCTACTTATCAAGCTGGA   SEQ ID NO: 367               LTR58   AGCCGCAAGCCTATTAAACCTTGCCTGAGAAAATCGGTTTGGCCTGGTGT   SEQ ID NO: 368               LTR59   ATTTTTCCTRGRTGTGCCCTCAAGCTGGCTCAGTAAACCTCGATGNTTTG   SEQ ID NO: 369               MER4BI   CTGANAGGATAAAGATACCTCGTGACAAAGCCTCCTGGGTATAATACTCC   SEQ ID NO: 370               MER50I   AAAATGGCTTCCCTGGGTTCTTCCCTTTTTAGGCCCACTTGTTAGTCTCC   SEQ ID NO: 371               LOR1I   TCCAATTACAGGTGTGACGTTTTCATTCCTCATCATTATCCCACAACGCC   SEQ ID NO: 372               LTR26E   TCGGTGTATTGACTTGCCGCGCATCGGGCAACAAACCTATTACGGTCACA   SEQ ID NO: 373               LTR16A1   CTGCCCTATCCTGCTTCCCTCACTCCCTTACAAGTTTCTCCTGAGAGCAC   SEQ ID NO: 374               LTR24B   TCTTTGGAATCTGTGYTTCCNGGGTGGNCCATCNTCAAACTTTGCACTTG   SEQ ID NO: 375               LTR16D   CCCGCTCCTGCTCCCTCCCCTTTTATCTTTCACAGGNTTTCCCCTAATAA   SEQ ID NO: 376               LTR60   CTTCAARAAAAATCYGACATCATAAAAACCCCGTGCAGACTCTCAGGGCT   SEQ ID NO: 377               MLT1E1   GTAGGCAGAATTCTAAGATGGCCCCCAAGATTCCCACCCCCTGGTGTACA   SEQ ID NO: 378               MLT1J1   TAGCCAACGGAATGTAAGCAGAAGTGATGTGCGCCACTTCCAGGCCTGGC   SEQ ID NO: 379               MLT1J2   CCTGAGTCACTACNTGGAGGAGAGCCACCCACACCCGACCAGAACCCNCA   SEQ ID NO: 380               LTR1B   TCRGCTRGGGRCRGTCAGAGARGAGNTCAGCCGCTGGAYNGCCAAACTCC   SEQ ID NO: 381               MER109   TGTCCRTCATTNCTGGCATNGTCAGGACTAGGTAMGGTCTCGDCCAACTG   SEQ ID NO: 382               MLT1E2   GCCCCCCAAAGATGTCCATGCCCTAATCCCTGGAACCTGTGAATATGTTA   SEQ ID NO: 383               LTR22B   CACTGGCTGGTCGGCAACTGTTTACAGCACTCTCCTGGGAGTCTGTAAGC   SEQ ID NO: 384               MLT1G1   TTTCCAAAGATGGCCGCAACAATATCTCCCATCCCACATGCTCTTCTTAC   SEQ ID NO: 385               L1MCC_5   GCCCATTTCCAGGCATAAATACTATTTACCTCAGTCTCTACTGTTCTTCT   SEQ ID NO: 386               MER110   CTCGCCTCACTGTGCCCACCAATCCAAAGCTATTATGTCATAAACTCTGC   SEQ ID NO: 387               HERVK11I   CAAAGAATCCTGCGTCAAAATCGAGAGAACGAACAAGCCTTCATCGCCAT   SEQ ID NO: 388               HERVK14I   AATAAAAAGGCTGGACAAGATATATGGTGGAGGGATGCACATACAAAGAG   SEQ ID NO: 389               HERVK13I   CAGGCGTCTCCACGGAGTCCAATGAAAAACTCGAAGCCAGCGACAAGCAA   SEQ ID NO: 390               HERVK14CI   CTCATAGCTCCTATAATGCCATTGAACACCAGTGAGAGACGATTAGACGT   SEQ ID NO: 391               LTR14C   ACCGCCACTGCTACACATCTTATCGAATGACTCACGAGTTCTCCTTCACT   SEQ ID NO: 392               LTR61   ATCCACTGAGCTGGTGCGTACCTTAAAATAAATAACAATCCTCCTGTATT   SEQ ID NO: 393               HERV49I   CTCAATTTGTTTTCTCCCCTCCTTTGCCTATCTCTATCTAACAACCTCTA   SEQ ID NO: 394               HERV15I   ATAGAGGCAGTAGTAACCCGAAACACTACCATGCTATTGACGGCATTAAC   SEQ ID NO: 395               LTR62   CAAANATGTGTGGACCTGGITATCTCTGAGCTTGCRCTGCTCACGACACA   SEQ ID NO: 396               LTR64   GGCTATAGGCNTYCCTCAGTCTACAGTCCTCAGTAAGACTTCTGAATAAA   SEQ ID NO: 397               MER112   CCAGACCAGTGGCTTTCAAACTTTTTTTGACTATGACCCACAGTAAGAAA   SEQ ID NO: 398               MER113   AAGCACCAAACTGAGACTTTCTCCTTGATGTAATCAGAAGGATTGAAAGA   SEQ ID NO: 399               MER110A   TTACCCAATCCTAATCAAGCCCCTACATTGAAAGACCTGCCTTAAATCAG   SEQ ID NO: 400               LTR33A   CTTCTTGCTGTTGCTAATCTCTGGGTTGCCTCACCATTGNTTCCCTGTTT   SEQ ID NO: 401               MLT1F1   CCCCGGCCGACATCTTGACTGCAACCTCATGAGAGACCCTGAGCCAGAAC   SEQ ID NO: 402               SATR1   ACACCCCCCCCSTACVCCCACMCCCCCTGTGATATTGTTCGTAATATCCA   SEQ ID NO: 403               MER115   TTTAAATATTTAGACATATGGTATGTGGGCCTCCATTTGTACTCTTGCCC   SEQ ID NO: 404               MER117   GCACAGGAGGGGGAAGTAGCAGCANATATGCTATGTATTTGCCATCCCTG   SEQ ID NO: 405               MER20B   TAGGTGCAAGCATCTGACTACTTCATTATGTCTTCTAGTGTAGTCATGCC   SEQ ID NO: 406               LTR65   TCCATGGTTCCTCTGGTGTGCAGTCTCCCTCATTGCAATAAGTCAATAAA   SEQ ID NO: 407               LTR38B   TGAAGYGGTTGCTTTGGATAGGAATCYGGCCRCTTCCCCATTACTAGTTT   SEQ ID NO: 408               CR1_HS   GGATTGACAGCAGATCAMGGGAAGTGATTATACCCCTTTACAATGCCTTG   SEQ ID NO: 409               L1ME4   GTGGGATGGACAGGGATGGGAGGGACTGACTTTTCACTGTATACCTTTTT   SEQ ID NO: 410               MLT1H1   TGGACCCTCCAGACCAGCCCATCTGCCAGCTGAATACCACTGAGTGACCT   SEQ ID NO: 411               LTR2B   GGGACAGAAATTGTGCACTCGGGGAGCTCGGATTTTAAGGCAGTAGCTTG   SEQ ID NO: 412               MER101B   CCAGAAACCACCTCCCCACAAGCCCACTAGAAACAAACATCTGACAGAGA   SEQ ID NO: 413               MER45R   TAGCCNATAAAATACTCTTAACAGCTCCAGNAACAGTTGCATCAGCAGAA   SEQ ID NO: 414               MLT1G2   TTTAAAACATGGCCGCAAATTCTTTGACACTCCTCTCATTGAGANGTGGG   SEQ ID NO: 415               MSTA1   CTTGCTTCCTCTCTCACCATGTGATCTCTGCACACGCTGGCTCCCCTTCC   SEQ ID NO: 416               LTR6A   GAATTCGTCTCAAAGTGTGGCGTTTCTCTATAACTCGCTCGGTTACAACA   SEQ ID NO: 417               L3   GGTCTGGAAACCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTT   SEQ ID NO: 418               LTR66   TGCCATTTACGTGGGATAAAGCTTGTTTACCCTTAAAGGTATTGTGTGTG   SEQ ID NO: 419               PRIMA41   ACCTTTTGTCGGAACTCGGAGTTATGAACGACCCTCACCATACCGATGCT   SEQ ID NO: 420               MARNA   TATNGCCTCCCAAGGTGACTACTTTGAAGGGGACAACACTCATTTGGATG   SEQ ID NO: 421               MER119   TTACTGAGACACTAAGGGCGCCGTGAACCGAGAAAGTTTGGGAACCTCTG   SEQ ID NO: 422               LTR67   GTTCTCCAGCCCTCCCGGAGATTCTGTGAGCTACCCAATATCCTTTAATA   SEQ ID NO: 423               L1M3DE_5   CGGGCNGATTGGTGAGATCCNTCTCCTACACGAGGCCAGTCTGACAAGAC   SEQ ID NO: 424               RICKSHA_0   CTCTTATGGACTATCTGCGTGCAATTGCCCATAATCTATCCCTGTAATAT   SEQ ID NO: 425               MER4E   AGGGGTCTGGGGAGTCATGCCCTACAAACCATAAATTCTCATCAGATGGG   SEQ ID NO: 426               MER104A   ACCTTTCGCGTTTCAGTTAACAAACCATTTAAGGACCATTTGAGGAAGGA   SEQ ID NO: 427               LTR40C   TGCTCATGCTGCTTGCTGTGYCATGAGTAATAAAGTCCTTTGTCTCTGAC   SEQ ID NO: 428               LTR54B   TGCTCAAGCTACTTTACAAAAGCCAAACTGCTCTGCCATGCCCAGCGGAG   SEQ ID NO: 429               MIR3   GGAAGCAGTATGGTATAGTGGAAAGAACAACTGGACTAGGAGTCAGGAGA   SEQ ID NO: 430               MLT1G3   CCAGCTGTCAAGTCATCCCCAGCCTCTNNCAGYCMTCCCCAGCCTTCAAG   SEQ ID NO: 431               MSTA2   CCACTTCCCCTTTGACCTTCTCTGCCATGTTATGATGCAGCATGAAAGCC   SEQ ID NO: 432               L1MD1_5   TTTGAGAACTGAACTAAAGGATAGACCACTACCCAGGTCCCAGACTGGCC   SEQ ID NO: 433               LTR10E   ARTGCTAATTTTTCTTTGCAGCACCGAGGAACAAGCATTCTGTTTCTAAA   SEQ ID NO: 434               LTR24C   TCTCTGGAGTCTGTGTTTCCTGAATGGCCATTCCCAGCTTTTNACTTGAA   SEQ ID NO: 435               MLT1C1   TGGAGTGATGCAGCCATAAGCCAAGGAATGCCAGCAGCCAAGCCACCAGA   SEQ ID NO: 436               MSTD   GTGGGTTTGTTATAAAAGNAAGTTCGGCCCCCTTTTGCTCTCTCNCTCTC   SEQ ID NO: 437               LTR68   ATCTTTACGTCATATACATTTCCATGTCTCAGGAGGCTAGGGCTTTTTAC   SEQ ID NO: 438               L1MED_5   TAAAAACCCAGTGGATAGGTNAAACAGCAGATTAGANACAGCTGAAGAGA   SEQ ID NO: 439               L1ME5   ACTGAAAGGAAATATACACCAAAATGTTAACAGTGGTTATCTCTGGGTGG   SEQ ID NO: 440               TIGGER6A   TAGAAGAAATAGCTGACCGTGGGAATGTTGACACTGCCGCCATTTGAGAG   SEQ ID NO: 441               MER51C   AGACCAAATCCTTCATCCAGATAAGGGGTAGCCAATAGAACCTCAAAAAG   SEQ ID NO: 442               LTR6B   CCGGCTAAATAAACGGACTCTTAATTCGTCTCAAAGTGTGGCGTTTTCTC   SEQ ID NO: 443               MER21A   TCCACAGTTCCTGGCTCATAACTCCCATAGCCCTTGTTACAGTCTTTTGT   SEQ ID NO: 444               MER34B   CCACAAGTTGCTGCCCCTAGAGACTCAAAGTCCTTTTCCTTTGTCTTGTC   SEQ ID NO: 445               LTR3B   AGTTTCTTTTGTCTTAAGTTTTCATTTCTGCGTTCGTCCCCCTTCGTTCA   SEQ ID NO: 446               MER54A   AGGCGGTTGTATAAGGCAGATATCTGGATCGACCACATTGAGGAACTGGG   SEQ ID NO: 447               MER74C   GCCTTTCATCTATCCGAGTGTCANTGTGTTGTGTCCCGCCATCAAAAGAA   SEQ ID NO: 448               ERVL   AAGAGTAAACATCACTCAAGGACTTTACCTCCTCTTCTCGGGAAGGGGTT   SEQ ID NO: 449               HERVL74   AAATACCCCNAATAATTGATGTCAAAACTGACGTCAAGACANAAAGGGGT   SEQ ID NO: 450               MER83AI   TAAGTCCCAACTCAGGGATTTAGGTCCACGTAACCTCCTGACCGACTAAC   SEQ ID NO: 451               MER83BI   TCTCCGATGAGTTCTTTCCTCCAGCAAGATCCAATATCCTAAGTCCCACA   SEQ ID NO: 452               MER84I   ATTTTCCCTTTCTTGAGACCCCAATAGGCAGCAGGTAGACATGAGCATGG   SEQ ID NO: 453               LTR75   TAATAAACTGTCTGAATCTAAAAGTGGCTCGTTGTATCTTTACCAGCCGA   SEQ ID NO: 454               L1PA7_5   CACCGAGCTAGCTGCAGGAGTTTTTTTTTTTCGTACCCCAGTGGCGCCTG   SEQ ID NO: 455               L1PA13_5   CTTTAGCCCTAGGGGAACTGTCGGACCTGAACTCTGCAGGGCGGTCTTGC   SEQ ID NO: 456               L1M1_5   AAGAAACAAATAACATACAATGGAGCTCCAATACGTCTGGCAGCAGACTT   SEQ ID NO: 457               L1M2A_5   CATGTCAGACCCGACACCAAGAGGGATCCCCTCGGCTAAGTCTCCCCATT   SEQ ID NO: 458               L1M1B_5   CCCATTCGGGACGGGCAGCGCTCTGATTGTTTACTAGAGCCGAGGCAAAC   SEQ ID NO: 459               L1MB3_5   AAAGGGGTGGGGATGGAGCTGTAAAGGAGCAGAGTTTTTGTATGTTATTG   SEQ ID NO: 460               L1MDB_5   CACAAAAGTAGGCCAGGACCTGCATGCTAAACCTAAACAGGGTGACTGCC   SEQ ID NO: 461               L1HS   CACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGGGGGAG   SEQ ID NO: 462               L1PA3   AACACATGGACACAGGAAGGGGAACATCACACTCTGGGGACTGTTGTGGG   SEQ ID NO: 463               L1PA4   AACACATGGACACAGGAAGGGGAACATCACACACCGGGGCCTGTTGTGGG   SEQ ID NO: 464               L1PA5   GAACACTTGGACACAGGAAGGGGAACATCACACACCGGGGCCTGTTGTGG   SEQ ID NO: 465               L1PA6   GAGAAATACCTAATGTAAATGACGAGTTGATGGGTGCAGCAAACCAACAT   SEQ ID NO: 466               L1PA8   AGGACAAATACCTAATGCATGCGGGGCTTAAAACCTAGATGACGGGTTGA   SEQ ID NO: 467               L1PA10   ATAGCTAATGCATGCTGGGCTTAATACCTAGGTGATGGGTTGATAGGTGC   SEQ ID NO: 468               L1PA12   CTTAATACCTGGGTGATGAAATAATCTGTACAACAAACCCCCATGACACA   SEQ ID NO: 469               L1PA13   TACCTGGGTGATGAAATAATCTGTACAACAAACCCCCATGACACAAGTTT   SEQ ID NO: 470               L1PA14   GGGAGAGGAGCAGAAAAGATAACTATTGGGTACTGGGCTTAATACCTGGG   SEQ ID NO: 471               L1PA16   TGGGTGATGGGATCATTCGTACCCCAAACCTCAGCATCACGCAATATACC   SEQ ID NO: 472               L1PB2   ATCTCAGAAATCACCACTAAAGAACTTATCCATGTAACCAAAAACCACCT   SEQ ID NO: 473               L1PB4   KTACACTAAAAGCCCAGACTTCACCACTACGCAATATATCCATGTAACAA   SEQ ID NO: 474               L1MA1   ATTCTCCATGATGTGCTTATTTCACATTGCATGCCTGTATCAAAACATCT   SEQ ID NO: 475               L1MA3   GCTGGGAAGGGTAGTGGGGTGGGGGGGAAGTGGGGATGGTTAATGGGTAC   SEQ ID NO: 476               L1MA4   GGAGGGGGGGAATGAAGAGAGGTTGGTTAATGGGTACAAAAATACAGTTA   SEQ ID NO: 477               L1MA4A   GAGGACTTGAAATGTTCCCAACACATAGAAATGATAAATACTCGAGGTGA   SEQ ID NO: 478               L1MA5A   TGGGAAGGGTAGGGGGAAGGGGGGGATAGGGAGAGATTTGTTAAAGGATA   SEQ ID NO: 479               L1MA6   ATAGGAGGAATAAGTTCTGGTGTTCTATTGCACAGTAGGGTGACTATAGT   SEQ ID NO: 480               L1MA7   ATGGGGAGATGTTGGTCAAAGGGTACAAAGTTTCAGTTAGACAGGAGGAA   SEQ ID NO: 481               L1MA8   TGCTNATGGTCCCATGACTGGCCACTCTGTGAACACAGTAAACAAGTTTG   SEQ ID NO: 482               L1MB1   GAAATGGGGAGTTGCTGTTCAATGGGTATAAAGTTTCAGTTATGCAAGAT   SEQ ID NO: 482               L1MB2   GGGTATAGAGTTTCAGTTTTGCAAGATGAAAAAGTTCTGGAGATCGGTTG   SEQ ID NO: 484               L1MB4   TGGTGATGGTTGCACAACAMTGTGAATGTACTTAATGCCACTGAATTGTA   SEQ ID NO: 485               L1MB5   AGGGGGAATGGGGAGTGACTGCTTAATGGGTACGGGGTTTCCTTTTGGGG   SEQ ID NO: 486               L1MB8   GGAATGGGGAGTGACTGCTAATGGGTACGGGGTTTCTTTTGGGGGTGATG   SEQ ID NO: 487               L1ME1   GGTGGGGGNAGGGGATTGACTACAAAGGGGCATGAGGGAACTTTTTGGGG   SEQ ID NO: 488               L1ME3   ATAGTGGTTACCTTTGGGGAGGGTTATTGACTGGGAAGGGGCATGAGGGA   SEQ ID NO: 489               L1ME4A   GACTGGAAGGAAATACACCAAAATGTTAACAGTGGTTATCTCTGGGTGGT   SEQ ID NO: 490               L1MC1   TTGATAGTGGGGGAGGCTGTGCATGTGTGGGGGCAGGGGGTATATGGGAA   SEQ ID NO: 491               L1MD3   ACCCATAACCCCAGTCTAATCATGAGAAAACATCAGACAAACCCAAATTG   SEQ ID NO: 492               HAL1B   AGAGGAGAGGTGGAAGGAAGTATGAGAGTGCTAATNTCCTCATCTTTCAT   SEQ ID NO: 493               L1MA9_5   AGACCCAGGGTTCAGGCCTGTCCCAGTAGACCCCAGCACTAGGCTAGTCC   SEQ ID NO: 494               L1MDA_5   AAGAAGGAATCTTGGAACATCAGGAAGGAAGAAAGAACATAGTAAGAAGC   SEQ ID NO: 495               L1MEB_5   GGCAGAAACTGGAGGGGAGTCGACACCTGGAAGAAGGGAATWGCACGGAG   SEQ ID NO: 496               TIGGER5A   TTAAGGTAGGCTAGGCTAAGCTATGATGTTCGGTAGGTTAGGTGTATTAA   SEQ ID NO: 497               TIGGER6B   AGGCAACCCCATCAAGAACTTANGCGAAAAAAGATGTAGGATCACAAAGT   SEQ ID NO: 498               TIGGER7   TCGGATGGAACGCAGCATTAAAGTCACCCATATGATCAATGAAGGATTAC   SEQ ID NO: 499               MER44D   CCTCACTTCATCTCATCACGTAGGCATTTATCATCTCACATCTATCACAA   SEQ ID NO: 500               MER69C   ATCGACGAAGATAACATAAAACTCATAATACGCCACTACAACGAGGACAT   SEQ ID NO: 501               MER106B   TATTTATGTTTGATCCTCAGTGCTTTGTGTGACTTGGGCTTTGAGAATTA   SEQ ID NO: 502               CHARLIE2A   GATTGGTTTGACAATGAGGACTGGCTTTGCCAATTAGGTTATATGGCAGA   SEQ ID NO: 503               CHARLIE2B   TTAATNCACCTTTTGTAAGCCCTATACTTACTAGTGGCCCAATACCTTCT   SEQ ID NO: 504               CHARLIE7   ACTTAGAACCAGACCTTCGAATCGCTGTATCACAAAGTGTTAAACCAAGA   SEQ ID NO: 505               CHARLIE8   ATTTATGTTACCTGCCTGGCCCCTGTAGGCATTTGAGTTTGCGACCCCTG   SEQ ID NO: 506               CHARLIE8A   ATTTATGTTACCTGCCTGGCCCCTGTAGGCATTTGAGTTTGCGACCCCTG   SEQ ID NO: 507               MER63D   ACAATGTAACGGCTACAGACACGACACACTTTTAAGTTTAATCTGCATTA   SEQ ID NO: 508               MER97A   TGTTAAAAAATGATCCGCTCTGGGTGTCGAATACGCTAGGTACGCCACTG   SEQ ID NO: 509               MER97B   CCAGTGGTATGNTTTWGTAGTTGCCTAAATTGTACCTTTTGCAGACGTTT   SEQ ID NO: 510               MER97C   TGTTAAAAAATGATCCGCTCTGGGTGTCGAATACGCTAGGTACGCCACTG   SEQ ID NO: 511               MER6B   GTTCTTGGAAACTGCGACTTTAAGCGAAACGACGTACAGCAGGTCCTCGA   SEQ ID NO: 512               ZAPHOD   ATTGCCGGCCCATCAACAGAACACCCAGACATGTGCAATAATAATTAAAT   SEQ ID NO: 513               TIGGER9   GCCAGTCAGATTTCACGGCANTGCCAATGTTTCTGTCTGTACAGCGNTGT   SEQ ID NO: 514               HERVL66I   CTCCTGTGCTTACCCTGTATCTGTAATCTATATCAACTATGCCTTCCCCA   SEQ ID NO: 515               THE1A   TTTATCAGGGGTTTCCGCTTTTGCTTCTTCCTCATTTTCCTCTTGCCGCC   SEQ ID NO: 516               THE1C   GTGTCCCCACCCAAATCTCATCTTGAATTGTAGTTCCCATAATCCCCACG   SEQ ID NO: 517               MSTB   TGTTAGTTCACGCGAGATCTGGTTGTTTAAAAGAGTNTGGCACCTCCCCC   SEQ ID NO: 518               MSTB1   CTTCCTCTCTCGCCATGTGATCTCTGCACACGCCGGCTCCCCTTCACCTT   SEQ ID NO: 519               MLT1AR   TCAGTCTGCTCCCTATCTTCGGCTGCCCGTTTAGNTGTGGCTCAAGTGGG   SEQ ID NO: 520               MLT1CR   AAGGTGCGGCCTGGTTTCTCCTTGCTGCTTATAGTAAAATGCGAGAGGAA   SEQ ID NO: 521               MER104B   CCTTTCGCGTTTCAGTTAACAAACCATTTAAGGACCATTTGAGGAAGGAA   SEQ ID NO: 522               MER104C   TGAAGGCAGGAGAAATTGCCNAATCCCNCGGAATAGATGAAAGAAATTTC   SEQ ID NO: 523               HSTC2   TNATGTAGACTCCTTCGCAAGACTCCATCAGCGAACCATTTGACACTTTT   SEQ ID NO: 524               L2A   ACGCTCTTCCCCCAGATATCCACGTGGCTSGCTCCYTCACCTCMTTCAGG   SEQ ID NO: 525               L2B   CCTGCCACTCTGGGTTATMATTGTCTGTKNGCANGTCTGTCTCCCCCACT   SEQ ID NO: 526               MER51D   TTTGTTTGGGACACCAAGAGCCTGGAACTGCACRGCACCAKCTGGTAACA   SEQ ID NO: 527               MER5C   TGGACCAGTGCTAGTCTGCAAACTGTTTGTTACCAGTCCATGATAAGATA   SEQ ID NO: 528               HERVK11DI   CCCGGTGCTGAAGTTTTAGACGGTATCTCTGAGGGGTTATCTAATCTCAA   SEQ ID NO: 529               LTR69   GAAAAGTCGCCCCTGGGGAAGCTGGTTAACTAGGACCACCCAAGACCCCC   SEQ ID NO: 530               HERV30I   AAAAAAGGAGCTTGAACACTCAGAACCCTGAAATATGTTTAACCAATGGA   SEQ ID NO: 531               HERV19I   CATAGCAGGAATAATGGTTACTAACAGAAAATAACACATGGGCCTTTCCA   SEQ ID NO: 532               LTR19C   TCACTCTGTGTGTGTGTGTCCGCGACCTCGATCTCCTTGGCCGTGAGACC   SEQ ID NO: 533               HERV46I   ACCCACTGCTTCAAAACCCAAACCCTGATTACAGCNCCCCTATTCGGCAG   SEQ ID NO: 534               HERV52I   TNAATAAGACATGGCACATTTCAGTCATCCATCAAACATCAGGGGTGAAT   SEQ ID NO: 535               MER89I   GCTTCTGCGCAGCCGCTCTCTCATCAGATGATCGCCATGATGATACAACA   SEQ ID NO: 536               MER110I   GACAATGGTCTNTCCTTCAGNTCGGGNTGAAGAATGACCAAAGGAGAAAT   SEQ ID NO: 537               MER21I   ATCCTTGTTTCGNGTAAGGGAATTCAGTGGTTGGAAANCAGGGAGTGGCC   SEQ ID NO: 538               PABL_AI   GCGCTCAAAGGGTGAGTTAACTGGATCGTATGCCGGGAGCCTATTGTTTT   SEQ ID NO: 539               PABL_BI   CTCGCGGTCCTGGCCATCCTTGNAGGCATGGGCATAACGTTATGTTGTGG   SEQ ID NO: 540               MERS2AI   ACNCCCANGGGATTATCTACTCCCCTAAACAGCTATCTCTCTTCTAAAGT   SEQ ID NO: 541               HERV57I   AGCCATGGCTATACGTTATAGACCTGTATAGTTCTTCCCCTCATACCCTA   SEQ ID NO: 542               MER70I   GGGCATATGAAATGGACTAGCTTTGCTAAGGGGGATATCTGGGTTGGGGG   SEQ ID NO: 543               HERV38I   CGGGATCGGTTTGGAGTGCTCCGTCTGCATCGGATCCGTCTGTGTTTGTG   SEQ ID NO: 544               L1M2B_5   CTTTCCCTACCCACTGCCACTACNYCTGACTCTGGGGCCAAAGCACATGC   SEQ ID NO: 545               L1M2C_5   ACACCCCAATGAACTGACACCAAGACCCATTTATACAAATAAGTTTTTCC   SEQ ID NO: 546               HERVFH191   CTGGAGCAGTCCTCCAAAATAGACGGGGATTAGATCTTATAACGGCTGAA   SEQ ID NO: 547               HERV70_I    CTCAGTGGCAGATGGTAGAGGTCAAGAGAGGANGGACACTAGCAACCAGG   SEQ ID NO: 548               LTR70   TCTTTGCTCCCAGGTTAYAATCCTNAAGCTTGRCCCAAATAAACTGTCTA   SEQ ID NO: 549               MER120   AGATGTGGATACTCAAGATTTCTATTGGGGAAAACTGTGGTCCTTAGTAA   SEQ ID NO: 550               REP522   TGTATTGCTGGCAGCAGTGAGGTGGGTTAAGGGTGCTATCCGGGGCTGCA   SEQ ID NO: 551               LTR71A   TTAAAAGTCTCGCTTCCACTGTTCTTCGTGTCTCTGAGTCCATTCTTTGG   SEQ ID NO: 552               LTR71B   CATTAAAAGTCTCACTTTCGCTGTTCTCCGGGTCTCTGAGTCCATTCTTT   SEQ ID NO: 553               LTR12B   CCCACCAGAAGGAAGAAACTCCGGACACATCTGAACATCTGAAGGAACAA   SEQ ID NO: 554               MER121   AGACACTTTTTTCCCCCTTAATTTTTAAACCCATGTGTATTTCAAGGGAA   SEQ ID NO: 555               MER122   TGCAGTTGGTGGCGACAGAGACTGTAGTGTGGCTGGAGTGGTAGGAAGGG   SEQ ID NO: 556               LTR7A   AAAGCTTTATTGCTCACACAAAGCCTGTTTGGTGGTCTCTTCACACGGAC   SEQ ID NO: 557               LTR7B   ACAGCCTTGTTGCTCACACAAAGCCTGTTTGGTGGTCTCTTCACACGGAC   SEQ ID NO: 558               MER51E   GATTAGGCAGCAYACAGGCCACATCCTCACTCCTGTGATAACAAGACAGA   SEQ ID NO: 559               MER41F   CAGGAGAATAGAAAATTCCAGGCAGCAGTTTCACATGACTAGCAAAAGGA   SEQ ID NO: 560               LTR2C   AAGATAAATAGCCAGACAACCTTGGCACCACCACCYGGCCCTAGGAGTTA   SEQ ID NO: 561               LTR38C   ACACCTCACTCTTGTTATTTTGGCTTCTTTCTACAAGCGGCAAGCAGCYG   SEQ ID NO: 562               LTR72   AACCTGTATTCTCATGGAGAGTCGTTTGTTACTCACCAGGYGAATRAACC   SEQ ID NO: 563               MER65D   TAAAAGCTTCCCTTTACCCTCCCCTCTTCAGATGCATCTGTGGCTTGCCA   SEQ ID NO: 564               ALR1   TGAGGCCTTCGTTGGAAACGGGATTTCTTCATATAATGCTAGACAGAAGA   SEQ ID NO: 565               LTR1C   GGTTCCAGCATTCATTCGCTCCGGTTCCCGCACTCACTCGCTTGCATGCT   SEQ ID NO: 566               LTR45C   TCTCACAAGCAGAGGGAGTTTCAGCATTTCAGCAAGTTGTTTCTTTTCTT   SEQ ID NO: 567               LTR76   GATGTTAAGTCTGCTGGGTCTGAGTGCACTCAATAAAAGATCCTCCTGTT   SEQ ID NO: 568               MER72B   TTTCACAATGCATCCCTTCCTAAAAACTGACCACCATCTCTGGACTGGTT   SEQ ID NO: 569               ALR2   GTGAAGGGATATTTGGGAGCTCATTGAGGCCTATGGTGAAAAAGAAAATA   SEQ ID NO: 570               LTR1D   GTTCCAGCACTCATGCACTCCAGTTCCCACCTCGTTCACTCACATGCTCC   SEQ ID NO: 571               MER34C   TCCTGGTCACCTCCCCATAACTGGCCTTCCCCACACCCTTCTTTCTTTGT   SEQ ID NO: 572               MER50B   ACTCCCTAAACACACTGCGCGTGCTCAATTCCCAAGGGTAAGGAGGGCAC   SEQ ID NO: 573               HERVP71A_1   AATTGTGGCAGGAGTCTTAACAGCAGTGGGATGTTGTATTATCCCTTGTG   SEQ ID NO: 574               LTR27B   TTTGCCCACCCTTTCCCGATTGATTCTTTCTGAATAATGCCTTTTAACCA   SEQ ID NO: 575               LTR12C   CACCAGAAGGAAGAAACTCCGAACACATCCGAACATCAGAAGGAACAAAC   SEQ ID NO: 576               LTR43B   CAGTCGGTGCTGTCTCACYYTTGAGCAGCCNYGCTCTGACTCAGCTGTCA   SEQ ID NO: 577               LTR72B   CCCTTGTTAAATCCTCCTTGGTTGTGGTCATTGGACTGTCACCTGCCAAG   SEQ ID NO: 578               LTR77   GGGACAAGAACTCAGACCTTGCTAAACTAAGGAGTAAGAAGACTGCAACA   SEQ ID NO: 579               L1PREC1   GTCAAAGTGCTTCATTAAATGGGTCCTGTTCCCTGTGCCACCCAACTGGG   SEQ ID NO: 580               MER2B   TCATTCACGTGGATTCAATGTAGTACTYGGTGTATGGCAAATTCAAGTTT   SEQ ID NO: 581               MER93B   CTATAAAAGCCTCCCCCTTGCATTCCCTCGGTGGAGCTCCCGAACCACTT   SEQ ID NO: 582               SATR2   TGTACACCCTGTGATATTATTCGTAATATCCTAGGGGGATGTTACTCCTA   SEQ ID NO: 583               GOLEM_C   GGGNAAATGANTGATATTCAGTAATGGTGCTGGGACATTTGGTTTTCCAT   SEQ ID NO: 584               MLT1A   CCCCTCTAGAGGATGCAGCATWCAAGGYGCCATCTTGGAAGCAGAGASCA   SEQ ID NO: 585               L1PREC2   TGGCTGAACACTCCCAGTAACAGTGGCTCTGCGTTTCTCGGAGGTGGAGC   SEQ ID NO: 586               BLACKJACK   CATCCAAACAAGCTGCGATATTCTACCCAACGATATAGAAGCTGTAGTTG   SEQ ID NO: 587               L1M2A1_5   GCCCACCCAACCCATCACAGCTTCCAGCAACACCAACATGGACTGCTTGG   SEQ ID NO: 588               MLT1E1A    TGGAAGAGGATTCTAAGCCTCAGATGAGAACACAGCCCTAGCCAACACCT   SEQ ID NO: 589               MER4E1   TTCTTCCAGACCCTCCCAATCCTAAAGAGATTAACTAAGATCTGAATAGG   SEQ ID NO: 590               PRIMA4_I   CGTGACCTCCTAGGATGAGCCTTCCTAGTGATGTGGGACCTAAAACTTCT   SEQ ID NO: 591               PRIMA4_LTR   TTTAAATTTGGAGCCCTCAAAATCATCTTCGGAGAAAGGCATAGACCTGT   SEQ ID NO: 592               L1M4B   AAAACAANCACNANGAGCCGGGGGNGGGGAATCAGTATCCAGAGTTGCTA   SEQ ID NO: 593               L1PA14_5   CACACAGACAGCAGATTAGGGCTAACCTGGCAAGGATACAGCTTGTCTGC   SEQ ID NO: 594               LTR13A   TCTCTTTGTCTTGTGTCTTTATTTATTACAATCTCTCGTCTCCGCACACG   SEQ ID NO: 595               HAL1C   AACCACAACATNAGAGGACCCANCACTCCTCCTACCACCAAAACAAAACC   SEQ ID NO: 596               HERVIP10F   AGAGGCTCATAGAAATGGCACTTACTAAAACCTCCCTTAACTATCCTCCA   SEQ ID NO: 597               MLT1F2   CNGATCCTCCCCTCNAGTTGAGCCTTGAGATGAGACTGCAGTCCTGGCTG   SEQ ID NO: 598               MLT1FR   TTTGGACCCCCAAAATTCTACTGGCAGGAAGCAGGCTGAGAAAACTACTC   SEQ ID NO: 599               HERVIP10FH   CAGAGGCTCATAAAAACGGCACTTACTAAAACCTCCCTTAACTATCCTCC   SEQ ID NO: 600               LTR10F   TTCCCTCCCTTGTCCAGGTGTGCGCTCACCATTGCTCCATCTGTGAGGGT   SEQ ID NO: 601               MER34B_I   CTAAAGACACTTTGTGCTCAGACCTAGAAATCTTCTCAATTGGCTGCCAT   SEQ ID NO: 602               MER57A_I   CTGGAAGGCCTATGCACCTAATAATAGAACCTCATGTATCTTCCGCTACT   SEQ ID NO: 603               PRIMAX_I   AATTAACCAAGGCTTTTAAAATTCCTTGGCCAAAAGCTCTTCCATTGGTT   SEQ ID NO: 604               MER75B   CATTTCCCGTTTGCCCCAAGAATACTCTTGTCTCTAATCCTAATGTAACA   SEQ ID NO: 605               MLT2B3   CCCAGGTGGTTTGGCATTTGATTAGAATGATTGGGCTGCCCCAGGTGTGT   SEQ ID NO: 606               MER66C   AGGATCTGGTCCAGACAGGATAAAGTGAAGAAACNRGCAGGAACCAGCAG   SEQ ID NO: 607               MER52D   CACNGCTCCACACCTGRCTTNNCCTTGGCAGGNNTGGATCNAGGNCCTTG   SEQ ID NO: 608               MER41G   TGCTTTGCAATAAAAGCTTCTTGCCTTTCGCTTCATTCTGACTCATCCCT   SEQ ID NO: 609               MER21C   AGGAGCATCTTTTGTTCTAATATTTGGTCTTTGACCCTAGTTCCTGACAC   SEQ ID NO: 610               LTR20C   CCAACCTCACCCTTTGTGTCCATGCTCCTTAATTTTCTTGGTTGTGAGAC   SEQ ID NO: 611               L1PBA1_5   TCTGTTTGCGGGAGAAGTTTCTGACTTTACCTGGAGCTGAGTCAAKTTAG   SEQ ID NO: 612               L1MB4_5   AATCTCATGTCAAAAAAACACTAGCTGAACACAAGCTAAGGAACAGAGAC   SEQ ID NO: 613               LTR73   TTGACACTCACTTTCGGTTTTGTGTATTGGCTTCGTGACACCAAACAGGG   SEQ ID NO: 614               HARLEQUINLTR   GGGAGGAGACCACCCCTCATATTGTCTTATGCCCAATTTCTGCCTCCAAA   SEQ ID NO: 615               LTR12D   CACCAGAAGGAAGAAACTCCGGACACATCTGAACATCTGAAGGAACAAAC   SEQ ID NO: 616               LTR12E   CACTCCTGAAGTCAGCGAGACCACGAACCCACCGGGAGGAACAAACAACT   SEQ ID NO: 617               MLT2B4   GTAAGAGAGAATTCCTCCTGCCTGACTGCCTTTGAACTGGGACATCGGTC   SEQ ID NO: 618               MER9B   TAACAACATGTTTTTGCTCGCAGATAACAGCCAGAGCCTGTTTCTCTRCT   SEQ ID NO: 619               SVA2   GAAGTGACAGCCTTGTGTGTGATCTTTCTGCCCTCCCCAAGTTTGCATTT   SEQ ID NO: 620               HERV39   TCTTGCTGCTAAAACTGCATACAACAGCCACCCAGCCAAGAGGAATTAAT   SEQ ID NO: 621               MLT1H2   CCCAGCTGCCATGCTAAAAGAAGCTCAGGCTAGACTATTGGATGATGAGA   SEQ ID NO: 622               LTR10G   GCTGAGAAAACTTTTGCCTGAGTGCTGGTTTCACTTTGCGGCACCAAGCA   SEQ ID NO: 623               MER4A1   CAGAAACTCAAAAGAATGCAAGGATTTGTCTCTCACCTACCTGTGACCTG   SEQ ID NO: 624               MER4D1   CTCTAGTATAGCATCACATGACAGATAGCAGGCCCTGAAAGAAATCAAAG   SEQ ID NO: 625               THE1D   CNTCTCTCTCCTGCCGCCTTGTGAAGAAGGTGCTTGCTTCCCCTTTGCCT   SEQ ID NO: 626               LTR5B   CCTCCGTATGCTGAGCGCCGGTCCCCTGGGCCCACTGTTCTTTCTCTATA   SEQ ID NO: 627               MER46   TTGAGTATCCCTTATCCAAAATGCTTGGGACCAGAAGTGTTTCGGATTTC   SEQ ID NO: 628               CHARLIE4   GTGACTCCACATGTTAATGGTCTTATTCAAGCTAAGCAGCATCTACTATC   SEQ ID NO: 629               CHARLIE9   CGTTGCAACGTGCACAGTTCATGCTAAGGATCCGTGCGATGCACTCTGAT   SEQ ID NO: 630               TIGGER8   NGTCNATTGTTTGACTTTCACACATTCGACTTCCATACACGTTTTCAGGA   SEQ ID NO: 631               MER5A1   TACTGAATCAGAATCTGCGTTTTAACAAGATCCCCAGGTGATTCATATGC   SEQ ID NO: 632               KANGA2_A   TTGGCCANAAACTTTTNTTGAATCTTCTCATTGGGAAAAATTGGGAGATC   SEQ ID NO: 633               FORDPREFECT   TTCACGTGCACTGATTGGACAATAAACAAATACGTAAGTACCTCTTCTCT   SEQ ID NO: 634               FORDPREFECT_A   ACTTAGAAAATTTCGAGGAAGGCACTCCAAAGCACGGGGTCCCCTGAGGC   SEQ ID NO: 635               LTR16E   ACGCATCACCTTGCATTGCTTCCCATCCTTCCCTGCCTCACTTCCCTTTT   SEQ ID NO: 636               L1PA17_5   CGAAGCCAAACGATCATACACAACATACACCACAGTCATACCCTCAAGGG   SEQ ID NO: 637               CHARLIE10   AGTAGCGCTGTCATCAATCCAACCTAGATTAGATAAGTTAACAAGCAAGA   SEQ ID NO: 638               THE1B   CGCCATGATTGTGAGGCCTCCCCAGCCATGTGGAACTGTGAGTCCATTAA   SEQ ID NO: 639               MSTA   ATGATTGTAAGTTTCCTGAGGCCTCCCCAGAAGCCGAGCAGATGCCAGCA   SEQ ID NO: 640               MSTC   ATGCGGCCCCTCGACCTTGGACTTCCCAGCCTCCAGAACTGTAAGAAATA   SEQ ID NO: 641               MLT1A   GCCGTCTACGAACCAGGGAATGAGCCCTCACCAGAAACTGAATCTGCCGG   SEQ ID NO: 642               MLT1B   GCCATCTACAAGCCAAGGAGAGAGGCCTCAGAAGAAACCAACCCTGCCGA   SEQ ID NO: 643               MLT1C   CATGGAACAGATTCTCCCTCACAGCCCTCAGAAGGAACCAACCCTGCCGA   SEQ ID NO: 644               MLT1D   TAGCCCAGTGAGACCCATTTCGGACTTCTGACCTCCAGAACTGTAAGATA   SEQ ID NO: 645               MLT1E   TTGTGAGACCCTGAAGCAGAGGACCCAGCTAAGCTGTGCCCGGACTCCTG   SEQ ID NO: 646               MLT1F   CATCTTGACTGCAACCTCATGAGAGACCCTGAGCCAGAACCACCCAGCTA   SEQ ID NO: 647               MLT2A1   GTTCTTCAGTTTTGGGACTCGGACTGGCTCTCCTTGCTCCTCAGCTTGCA   SEQ ID NO: 648               MLT2B2   TCACGTGAGCCAATTCCCCTAATAAATCYCYTCTATCCATCCTATTGGTT   SEQ ID NO: 649               MLT2C2   CCACAATCGCGTGAGCCAATTCCTTAAAATAAATCTCTCTCTACACACAC   SEQ ID NO: 650               MLT2D   TCTGCCTGCCTGATNGTCTTCGAACTGGAATATCAGCTCTGCGGATTTTG   SEQ ID NO: 651               MER4A   TAAAASCAAGCTGTRCCCCGACCACCTTGGGCACATGTCGTCAGGACCTC   SEQ ID NO: 652               MER4B   CTAAAATGTATAAAASCAAGCTGTRCCCCGACCACCTTGGGCACATGTKG   SEQ ID NO: 653               MER4C   ATTGAAGCCCTCAAAATCATCTTTGGAGAAAGGCACAGACCACAGATGTT   SEQ ID NO: 654               MER9   GCTGTGAGACCCCTGATTCCCACTTCACACCTCTATATTTCGTGTGTGTG   SEQ ID NO: 655               MER11A   CACGGTCCTACCGATATGTGATGTCACCCCYGGAGGCCCAGCTGTAAAAT   SEQ ID NO: 656               MER11B   CCGGATRCCCAGCTTTAAAATTTCTCTCTTTTGTACTCTGTCCCTTTATT   SEQ ID NO: 657               MER39   GGTCTTTGGGTCTTCATTTCTGAAGGCTCCCATGTCACGTAAAACTTTGA   SEQ ID NO: 658               MER48   TGTTGTTGTGGACGCGCTCTCGGGGTTSGAACCGAYACAAGARCCTTACA   SEQ ID NO: 659               LOR1   TCTTCCTTGGCAATAMTYRTTGTCTCAGTGATTGGCTTTCTGTGCAGTGA   SEQ ID NO: 660               MER49   TGCGGGATGGCCACCTTGCAGGCTGTAACCCTTTATAAGAAATAAAGTCT   SEQ ID NO: 661               MER39B   TGCCTTTTCTCCWATTAATCTGCCTTTTGTSAGTTGATTTTTCAGTGAAM   SEQ ID NO: 662               MER61   AAGCCTAAWTTTTCGTGGCCGTGTGACAAGGACCCCGTCTTTAGCTGAAC   SEQ ID NO: 663               MER31   CCTGTACCTATCGCAATGGTCCTGAATAAAGTCTGCCTTACCGTGCTTTA   SEQ ID NO: 664               MER34   GCCGGAAACTCTAAGAGGGTAGAGGWAAAATTTTTCCTTCYCTNCCATGG   SEQ ID NO: 665               MER41C   TTTACACTGTGGAATCACCCTGAATTCTTTCTTGCATGAGATCCAAGAAC   SEQ ID NO: 666               MER50   TGCTCTAAAACTTGCCTCGGTCTCTTTTTCTGCCTTATGCCCCTCAGTCG   SEQ ID NO: 667               MER65A   GAATATGCACATAGTTTACTATGGCACGCGTATTCCCATTGCAATGCTCT   SEQ ID NO: 668               MER65B   GTGTATGCCCCAAATTGCAATTCTGTTCTTCACATGTTATTCCCAAATAA   SEQ ID NO: 669               MER66A   AGCCGCTTCAATAAAAGTTGCTGTCTAATACCACCARCTCGCCCTTGAAT   SEQ ID NO: 670               MER66B   GTGTATGCCCCAAATTGCAATTCTGTTCTTCACATGTTATTCCCAAATAA   SEQ ID NO: 671               MER67A   ATTCTCCCTTTAAAACGCCCAGTCACCTCTGCACAAATCGAAGCTGAGCT   SEQ ID NO: 672               MER67B   CCTCATTCTCCCTTTAAAACGCCCAGTCACCTCTGCACAAATTGGAATGG   SEQ ID NO: 673               MER67C   TAGCAGATTGCCTGTGATGCGCATCACATTCTGGTTTAATGCTTATTCAA   SEQ ID NO: 674               MER68A   CCTGTGAGTCCTCCTAGCGAATCACCGAACCTGGGGGTGGTCTTGGGAAC   SEQ ID NO: 675               MER68B   TTCCCTTTGCTGATCTTGCCGTGTATCCTTACNRTGTCGCTGTAATAAAT   SEQ ID NO: 676               MER70A   TGTTCTGTCTCACCGGACTCAGACAAGTTGGTAACCAGTGCACAGTGAAC   SEQ ID NO: 677               MER70B   TCNGACCCCTATTCCTGGTGGTTGGCATAGTGATGATCTTTGCTATTCTC   SEQ ID NO: 678               MER72   GCTGCAACCCTTTATGAGAAATAAAGCTCTCCTTTCCAAATTTATGAACC   SEQ ID NO: 679               MER73   GGTGACGGGGTACGACTGGGTTTCAAACAACTTATGTCAGGCCTAAAAAT   SEQ ID NO: 680               MER74   AAGCATGATTAATACAAKYTGGTCTGTGATGAACGGATGCCAAATAGWCG   SEQ ID NO: 681               MER76   TGTTGCCTTAATCGGCTNCTCTGACACCCGGCAGCTCAGCTCTCTCTCCA   SEQ ID NO: 682               MER77   CTTCTAGCGAATCACTGAACCTGAGGGTGGTCTTGGGGACCCCCGACACA   SEQ ID NO: 683               MLT1G   GCGTCTTGACTGCGCCGATACCACGTGGGACAGAGAWGAACTRCCCAGCT   SEQ ID NO: 884               PABL_A   AATAAAAACTCTCTTCCTCCCCAGTTCATCTGCATCTCGTTATTGGGCCA   SEQ ID NO: 685               PABL_B   CCAGTTCATCTGCATCTCGTTATTGGGCCACGAGAATAAGCAGCCCGACC   SEQ ID NO: 686               MER41D   ATAAACTTGCTCTTCTCACTGTACTCCGCAACTCGCCTTGAATTCCTTCC   SEQ ID NO: 687               MER51A   CTCTGCTTTTGTTGCTTCATTCTTTCCTTGCTTTGTTTGTGCGTTTTGTC   SEQ ID NO: 688               MER51B   CTCTGCTTTTGTTGCTTCATTCTTTCCTTGCTTTGTTTGTGCGTTTTGTC   SEQ ID NO: 689               MER57A   ATCTTCTACCACATGGCTGCACTGGAGTCTCTGAACCTACTCTGGTTCTG   SEQ ID NO: 690               MER57B   TATAAATTTGTTCCGACCACGAGGCATCCCTGGAGTCTCTCTGAATCTGC   SEQ ID NO: 691               MER65C   ACCTCCAACCTTCTCTTTGTTC1TTGGACATACCGAAGACCACCTGGTCT   SEQ ID NO: 692               MER83   ACAACTGTCTTGGTAAATTATTTTTACCTCCCGCGCCACCGGCCCCAGAT   SEQ ID NO: 693               MER54   TGAAAGATACACTGTAAACACCCACAACCAMCTTCCCTGGAGCCCCATCA   SEQ ID NO: 694               MER87   ACTTACTGGCTGTCGWGCGGTGAGCAGTACCAGCTTTGGATTCAGTTACA   SEQ ID NO: 695               MER74A   AATGGCAGTCGTCTCCTGATCTGTTGGCCTTACCATACCTGAATAATAAT   SEQ ID NO: 696               MER74B   CTTTTCAATGGCAGTCGTCTCCTGATCTGTTGGCCTTACCATACCTSAAT   SEQ ID NO: 697               MER88   AGGGGAACTTGTGGCAGGGACCAGCCTTATCACACTGGTGCACCTGGTCA   SEQ ID NO: 698               MER54B   AGCCATTTGGGTGTGGTGTAGAACTGGAAACTGTGTCAAGGGTGACTGAG   SEQ ID NO: 699               MER31A   AAATTCCCACTTGCCCATGCTGTATTCGGAGTTGAGCCCAATCTCTCTCC   SEQ ID NO: 700               MER31B   TCCCCACTTGTCCTTGCTGTATTCGGAGTTGAGCCCAATCTCTCTCCCCT   SEQ ID NO: 701               MER67D   ATCCACCTGCCTTTTGTTTCAGNGGAGTTGAGTTCAANCTCTAACCCCTA   SEQ ID NO: 702               MER11C   TTGTACTCTGTCCCTTTATTTCTCAAGCCAGCCGACGCTTAGGGAAAATA   SEQ ID NO: 703               MER11D   ACTATCTTGTGTGTGTCTATTATTTCTCAACCTGCCGATCCGCCTAGGAG   SEQ ID NO: 704               MER61B   CGCCCAATAAATTCTGCTCCTCACCCTTCAATGTGTCCGCGWGCCTAATC   SEQ ID NO: 705               MER61C   GKGACAAGAACCCGGGTTTTAGCTGAACTAAGGAGCAAAATYCTGCAWCA   SEQ ID NO: 706               MER92A   GTTCCTGAGGTCGGAGCGTTCTCCCTATTGCAATAGTCTTTTTGAATAAA   SEQ ID NO: 707               MER92B   TTCTGCCTGAACTTTGAGATGCTTGCAGATCTTATGGTCAGAGCGTTCTC   SEQ ID NO: 708               MER92C   TATCTACCCCTTCCTATAAAAGTCCAAGGCAAAACCACCCTGCCGAGACA   SEQ ID NO: 709               MER93   CTTCCTCATNCACCYTATAAAAGCCTTTCCTTCAAGCCCCTCCGGCGGAG   SEQ ID NO: 710               MLT1H   CACAGATGCATGAGGGAGCCCAGCCGAGACCAGAAGAACCACCCAGCTGA   SEQ ID NO: 711               MER89   AAGCTCTGAATAAATAGCCTTTGCTTGTTCTCATTTGGKTGGTCTTCATT   SEQ ID NO: 712               MER90   CCTCGCTGCARCGAGCAATAAACCCAACTTGTTCAACCACAGGTGTGTTC   SEQ ID NO: 713               MLT2A2   TGTGGGACTTCACCTTGTGATCGTGTGAGTCAATACTCCTTAATAAACTC   SEQ ID NO: 714               MLT1I   GAGCAGAGCCCCAGCCGACCCGCGATGGACATGTAGCATGAGCAAGAAAT   SEQ ID NO: 715               MER52B   GCCACAGAGGTTTCCGGCCAGAAAAGCGACACCCCAAGGATCCCATGACA   SEQ ID NO: 716               MER52C   ACACTAAATAAAGCTCTTCTTCGTCTTCTTCACCCTTCACTTGTCTGCGT   SEQ ID NO: 717               MER95   TTGARGTCTCCCGGTTCGCGARCTGTWCTTTCTCTYATTGTATGCACAAT   SEQ ID NO: 718               MLT1J   ATGGAGCAGAGCTGCCATACCAGCCCTGGACTGCCTACCTCTAGACTTCT   SEQ ID NO: 719               MLT1K   AGCTACCCCTGGACTTTTCAGTTACGTGAACCAATAAATTCCCTTTTTTG   SEQ ID NO: 720               MER101   TTCGTTTTACACCGAAGGCTGCATCTCCCCGGTTTGCAAACTGTTCACTG   SEQ ID NO: 721               MER41E   TTTCTGACTCATCCTTGAATTCCTTCTCGCGATGGTGTCAAGAGCCTGGA   SEQ ID NO: 722               MLT2E   TCCCCCCTCCAGACCTTCACTTCCCCAGCTCCTCCCACAATTGTATAAGG   SEQ ID NO: 723               MLT1E1   TGATTTCAGCCTTGTGAGACCCTGAGCAGAGGACCCAGCTAAGCCGTGCC   SEQ ID NO: 724               MLT1J1   AGCCACTGTACATTTTGGGGTTTATTTGTTACAGCAGCTAGCGTTACCTT   SEQ ID NO: 725               MLT1J2   CCTGAGTCACTACNTGGAGGAGAGCCACCCACACCCGACCAGAACCCNCA   SEQ ID NO: 726               MLT1E2   TTGATTTCGGCCTTGTGAGACCCTGAGCAGAGAACCCAGCCGAGCCCACC   SEQ ID NO: 727               MLT1G1   TGCCCAAATTGCAGATTCGTGAGCAAAATAAATGATTGTTGTTGTTTTAA   SEQ ID NO: 728               MER110   CTCAGCTTTGCTTGATCAACAGGTTTTNTTTTCTGGTGGTCTTTTTGGGG   SEQ ID NO: 729               MER110A   TGGTGCTCYCCCTTACCACAGTAAGCAATAAACTCAGCTTTGTCTTATCA   SEQ ID NO: 730               MLT1F1   GAGAGACCCTGAGCCAGAACCACCCAGCTAAGCTGCTCCCGAATTCCTGA   SEQ ID NO: 731               MER101B   GGCTGTGTCTCCCTGGTTTGCAAACTGTTCACTGGAATAAACTCTCCTCC   SEQ ID NO: 732               MLT1G2   CCCTGCTGTGCCCTGTCCGAATTCCTGACCCACAGAATCCGTGAGCATAA   SEQ ID NO: 733               MSTA1   AGATGCTCGCACCATGCTTTTTGTCCAGCCAGCAGAAYTATGAGCCAAAT   SEQ ID NO: 734               MLT1G3   AGCCTTCAAGTCTTCCCAGCTGAGGCCCCAGACATCATGGAGCAGAGAGC   SEQ ID NO: 735               MSTA2   TGCCCTTGAACTTCCCAGCCTGCAGAACCATGAGCTAAATAAACCTCTTT   SEQ ID NO: 736               MLT1C1   GCCTCCAGAGGGAGCATGGCCCTGCTGACACCTTKGATTTCAGCCCAGTG   SEQ ID NO: 737               MSTD   GATGACGCAGCAAGAAGGCCCTCACCAGATGCCGGCNCCWTGATCTTGGA   SEQ ID NO: 738               MER51C   TCTCGCTTTAATAAATTCCTGCTTTCGCTGCTTCGTTCCTGTGTTTCATT   SEQ ID NO: 739               MER21A   TGGTGTGAGAGCAGAGGAAAAACACGGTTTGAGAGAGTTTTCCCGAAACA   SEQ ID NO: 740               MER34B   TCTGTCTTTTGTTACAGGGGTCTATTCCAACTAAGAACTTATGAGGGTTG   SEQ ID NO: 741               MER54A   TATCTGGATCGACCACATTGAGGAACTGGGAGGAGGCGGAGAACTGGAAA   SEQ ID NO: 742               MER74C   GCCTTTCATCTATCCGAGTGTCANTGTGTTGTGTCCCGCCATCAAAAGAA   SEQ ID NO: 743               THE1A   CTCATTTTCCTCTTGCCGCCGCCATGTAAGAAGTGCCTTTCGCCTCCCGC   SEQ ID NO: 744               THE1C   ATGTGAAGAAGGACGTGTTTGCTTCCCCTTCCGCCATGATTGTAAGTTTC   SEQ ID NO: 745               MSTB   ATGATTGNAAGCTTCCTGAGGCCTCACCAGAAGCCGAGCAGATGCCGGCG   SEQ ID NO: 746               MSTB1   GCCATGCTTCTTGTACAGCCTGCAGAACCGTGAGCCAAATAAACCTCTTT   SEQ ID NO: 747               MER51E   CTGTGGAGTGTACTTTCGCTTCAATAAATCTGTGCTTTCGTTACTNCGTT   SEQ ID NO: 748               MER41F   TGGGTGGCACCACAGTTCCGAGAAATCTTCACCTTTTTCCAGGAATCTTC   SEQ ID NO: 749               MER65D   TAAAAGCTTCCCTTTACCCTCCCCTCTTCAGATGCATCTGTGGCTTGCCA   SEQ ID NO: 750               MER72B   TCCTTTTACCCCTCCCTCAAAGTGCTTTGCTCTCAGCTTCTGCCAGAGGC   SEQ ID NO: 751               MER34C   TTGTTACAGGGGTCTGTCCCAGCTAAGAACTATGAAGGGTAGAGAGAAAA   SEQ ID NO: 752               MER50B   GATATGCCGCYGGTAACTCAGGGTAACTCGGATCTCTTCCACCGGTAACA   SEQ ID NO: 753               MER93B   CTATAAAAGCCTCCCCCTTGCATTCCCTCGGTGGAGCTCCCGAACCACTT   SEQ ID NO: 754               MLT1A1   CATCTTGGAAGCAGAGASCAGGCCCTCACCAGACACCAAACCTGCTGGNA   SEQ ID NO: 755               MLT1E1A   CTTGTGAGACCCTGAGCAGAGGACCCAGCTAAGCTGTGCCCAGACTCCTG   SEQ ID NO: 756               MER4E1   TCACGGGCCATGGTCACTCATATTTGGCTCAGAATAAATCTCTTCAAATA   SEQ ID NO: 757               PRIMA4_LTR   TTTAAATTTGGAGCCCTCAAAATCATCTTCGGAGAAAGGCATAGACCTGT   SEQ ID NO: 758               MLT1F2   ACACCTTGATTGCAGCCTTGTGAGAGACCCTGAGCCAGAAGACCCAACTA   SEQ ID NO: 759               MLT2B3   CTTCTCAGCCTCCATAATCAAGTGAGCCAATTCCCCTAATAAATCCCTTC   SEQ ID NO: 760               MER66C   GAGCAGTACCGTTCAATAAAAGATTGCTGTCTAACACCACTGGCTCACCC   SEQ ID NO: 761               MER52D   CTCAGGCAAAGGHACCACHGGHCACAGAGGTTTCTGGCCAGAAAAGBGAC   SEQ ID NO: 762               MER41G   TGCTTTGCAATAAAAGCTTCTTGCCTTTCGCTTCATTCTGACTCATCCCT   SEQ ID NO: 763               MER21C   TGTGGGATCTGATGCTAACTCCAGGGTAGATAGTGTCAGAATTGAATTAA   SEQ ID NO: 764               MLT2B4   CCTGGGTCTCCAGCTTGCCAACTCACCCTGCAGATCTTGGGACTTCTCAG   SEQ ID NO: 765               MER9B   TAAATATGTGGGTCAAACTCTGTTTGTGGCTCTCAGCTCTGAAGGCTGTT   SEQ ID NO: 766               MLT1H2   TACACCATGTGGAGCAGAAGAACCACCCAGCTGAGCCCAGCCAACACAGA   SEQ ID NO: 767               MER4A1   AAAACCAAGCTGTGCTCTGACCACCTTGGGCACATGTCGTCAGGACCTCC   SEQ ID NO: 768               MER4D1   TCANAGGCCATGGTCACTCATATTTGGCTCAGAATAAATCTCTTCAAATA   SEQ ID NO: 769               THE1D   TGCTTGCTTCCCCTTTGCCTTCTGCCATGATTGTAAGTTTCCTGAGGCCT   SEQ ID NO: 770                  
 
         [0031]     The expression and methylation patterns of the present invention can be evaluated by utilizing high-density arrays or microarrays. As defined herein, “microarray” can be a chip, a glass slide or a nylon membrane comprising different types of material, such as, but not limited to, nucleic acids, proteins or tissue sections. By utilizing microarray technology, a plurality of transposable element sequences from transposable element families can be analyzed simultaneously to obtain expression and/or methylation patterns. One of skill in the art can design a microarray chip or glass slide that contains the representative nucleic acid sequences of all of the members of a particular transposable element family or the nucleic acid sequences of select members of a particular transposable element family. A chip can also contain the nucleic acid sequences of selected transposable elements from one or more families. Array design will vary depending on the transposable element families and the sequences from these families being analyzed. One of skill in the art will know how to design or select a chip that contains the transposable element sequences associated with a cell at a particular stage of pluripotency. Such microarray chips can be obtained from commercial sources such as Affymetrix, or the microarray chips can be synthesized. Methods for synthesizing such chips containing nucleic acid sequences are known in the art. See, for example, U.S. Pat. No. 6,423,552, U.S. Pat. No. 6,355,432 and U.S. Pat. No. 6,420,169 which are hereby incorporated in their entireties by this reference.  
         [0032]     The present invention also provides microarray slides or chips comprising transposable element sequences or fragments thereof from transposable element families.  
         [0033]     As stated above, a microarray slide or chip can contain the representative nucleic acid sequences of all of the members of one or more transposable element families or the nucleic acid sequences of select members of one or more transposable element families. The present invention also provides for a kit comprising a microarray slide or chip of the present invention for determining the stage of pluripotency of a cell. Utilizing the methods of the present invention, a chip(s) or glass slide(s) that specifically detect a cell&#39;s stage or type of pluripotency can be synthesized. For example, if it is known that transposable element sequences from fifty families are expressed in a fully pluripotent stem cell, a chip that contains the necessary transposable element sequences from these fifty families can be synthesized, such that one of skill in the art can utilize a kit, containing this chip, for detecting and staging fully pluripotent stem cells. Similarly, utilizing the expression patterns of transposable element sequences characteristic of cells that are partially pluripotent (e.g., capable of differentiating into a type of brain or neural cell but not into liver cells), it is possible to manufacture a kit containing a chip comprising the transposable element sequences in order to diagnose and stage cells possessing this degree of developmental potential.  
         [0034]     Microarray techniques would be known to one of skill in the art. For example, U.S. Pat. No. 6,410,229 and U.S. Pat. No. 6,344,316, both hereby incorporated by this reference, describe methods of monitoring expression by hybridization to high density nucleic acid arrays. For example, one skilled in the art would first produce fluorescent-labeled cDNAs from mRNAs isolated from stem cells. A mixture of the labeled cDNAs from the stem cells is added to an array of oligonucleotides representing a plurality of known transposable elements, as described above, under conditions that result in hybridization of the cDNA to complementary-sequence oligonucleotides in the array. The array is then examined by fluorescence under fluorescence excitation conditions in which transposable element polynucleotides in the array that are hybridized to cDNAs derived from the stem cells can be detected and quantified.  
         [0035]     The expression patterns of the present invention can also be determined by assaying for mRNA transcribed from transposable elements, in situ hybridization and Northern blotting and assaying for proteins expressed from a mRNA. Particular protein products translated from mRNAs transcribed by transposable element genes can be detected by utilizing immunohistochemical techniques, ELISA, 2-D gels, mass spectrometry, Western blotting, and enzyme assays.  
         [0036]     In the present invention, patterns of expression can include one, two, three, four, five, six, seven, eight, nine, ten, twenty or more families of transposable elements and at least one, two, three, four, five, ten, fifteen, twenty, twenty-five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members of each transposable element family are being analyzed. For example, the present invention provides for the determination of an expression pattern of one family of transposable elements in which one, two, three, four, five, ten, fifteen, twenty, twenty five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members of a transposable element family are analyzed. The present invention also provides for the determination of an expression pattern of two families, wherein one, two, three, four, five, ten, fifteen, twenty, twenty five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members are analyzed for each family. Similarly, the invention provides for the determination of an expression pattern of three families, wherein one, two, three, four, five, ten, fifteen, twenty, twenty five fifty, one hundred, two hundred, three hundred, four hundred, five hundred, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members are analyzed for each family. Similarly, the invention provides for the determination of an expression pattern of multiple families, for example, 10, 20, 30, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650 or 700 families wherein one, two, three, four, five, ten, fifteen, twenty, twenty five fifty, one hundred, two hundred, three hundred, four hundred, five hundred, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members are analyzed for each family.  
         [0037]     By utilizing the methods of the present invention, a reference expression pattern can be obtained for fully pluripotent stem cells, as well as for cells that have a lesser degree of developmental potential (reduced pluripotency). Therefore, the present invention provides a method of assigning an expression pattern of transposable elements to a fully pluripotent stem cell comprising: a) determining expression of one or more families of transposable elements in a fully pluripotent stem cell and assigning the expression pattern obtained from step a) to the cell.  
         [0038]     The present invention also provides a method of assigning an expression pattern of transposable elements to a pluripotent stem cell comprising: a) determining expression of one or more families of transposable elements in a pluripotent stem cell and assigning the expression pattern obtained from step a) to the cell.  
         [0039]     Also provided by the present invention is a method of assigning an expression pattern of transposable elements to a differentiated cell comprising: a) determining expression of one or more families of transposable elements in a differentiated cell and assigning the expression pattern obtained from step a) to the cell.  
         [0040]     The present invention also provides a method of determining the developmental potential of a cell comprising: a) determining expression of one or more families of transposable elements in a cell to obtain an expression pattern; b) matching the expression pattern of step a) with a known expression pattern for a cell and c) determining the level of developmental potential of a cell based on matching of the expression pattern of a) with a known expression pattern for a cell with a specific level of developmental potential.  
         [0041]     In the methods of the present invention, the expression pattern obtained from a sample of cells taken from a subject can be obtained from outside sources, such as a testing laboratory or a commercial source. Therefore, the step of obtaining the expression pattern can be performed by one skilled artisan and the step of comparing the expression pattern can be performed by a second skilled artisan. Thus, the present invention provides a method of determining the developmental potential of a cell comprising a) matching a test transposable element expression pattern of a cell with a known expression pattern for a cell at a specific stage of developmental potential; and b) determining the developmental potential of a cell based on matching of the test expression pattern of a cell with a known expression pattern for a cell at a specific stage of developmental potential.  
         [0042]     For example, one of skill in the art can obtain a fertilized oocyte derived pluripotent stem cell and determine the expression pattern of one or more transposable element families. By determining which transposable elemnt families are expressed as well as which members of these transposable element families are expressed, one of skill in the art can assign this pattern to a fertilized oocyte derived pluripotent stem cell. This can be done for another stem cell with a more limited developmental potential than a fertilized oocyte, for example, a stem cell derived from a brain, such that a library of expression patterns are readily available not only to identify a cell with fully pluripotent or pluripotent potential but to determine the stage of pluripotency, i.e., level of developmental potential. Similarly, this can be done for stem cells derived from any tissue, or for oocytes in which a nucleus derived from a differentiated cell has been introduced to determine the degree to which that nucleus has reacquired pluripotency. By determining the expression patterns of transposable elements in cells with different stages of pluripotency, the skilled artisan can determine which transposable element families and which members of these families are markers of the developmental potential of cells.  
         [0043]     Such libraries of expression patterns are useful for determining the developmental potential of stem cells. For example, a nucleus from a fully differentiated cell from a patient with Parkinson&#39;s disease can be transplanted into an enucleated oocyte. Once the expression patterns of putative stem cells descendent from this oocyte are determined according to the methods of the present invention, this expression pattern can be compared to a library of expression patterns to determine the level of pluripotency associated with the expression pattern. Once this is determined, a decision can be made with regard to the potential of these stem cells to regenerate appropriate neural cells if implanted in the patient&#39;s brain. The present methods will also be useful in evaluating the effectiveness of various treatments in stimulating stem cells to develop or, conversely, to monitor the effectiveness of treatments to stimulate determined and/or differentiated cells to regain pluripotency. For example, a sample of partially or fully differentiated neural cells could be treated in vitro with oocyte cellular extracts or other chemicals, small molecules, peptides, growth factors, etc. designed to reprogram differentiated cells to regain full or partial pluripotency. Expression patterns can be obtained from these treated cells and compared to expression patterns pre-established to be characteristic of pluripotent stem cells. Since the skilled artisan will have reference patterns for the fully differentiated cell, as well- as, reference patterns for a a fully pluripotent stem cell and stem cells of more limited pluripotency, changes in transposable element expression after treatment can be monitored to determine if the treatment results in a transposable element expression pattern which more closely resembles a fully pluripotent or pluripotent stem cell.  
         [0044]     For example, if before treatment, certain families and members of these families are expressed, and after treatment, more families and/or members of these families are expressed, it can be said that this particular treatment is effective in increasing the developmental potential of the cell or in reprogramming the differentiated cell to become pluripotent. In some instances, effective treatments may involve decreasing the expression of certain transposable elements and increasing the expression of others. Therefore, once libraries of expression patterns are established from untreated differentiated cells, one of skill in the art will know whether or not treatment is effective in a particular cell lineage by comparing the expression pattern of a sample from samples of cells at different stages of treatment, with reference patterns established for the fully pluripotent stem cells. If a treatment is not successful in a particular cell lineage, the skilled artisan will recognize this by noting that the expression pattern is not changing as expected, and other dosages, or treatments can be employed.  
         [0045]     Therefore, the present invention also provides a method of identifying a factor that increases the developmental potential of a cell comprising: a) determining expression of one or more families of transposable elements, in a cell to obtain a first expression pattern; b) administering a putative factor that increases developmental potential to the cells; c) determining expression of one or more families of transposable elements in a cell after administration of the factor to obtain a second expression pattern; and d) comparing the second expression pattern with the first expression pattern such that if the differences between the expression patterns can be correlated with an increase in developmental potential, the factor increases the developmental potential of the cell. The changes observed between expression patterns can vary depending on the type of differentiated cell.  
         [0046]     In some instances, effective treatment of a cell, i.e., increasing the developmental potential of a cell, will result in fewer transposable elements being expressed in the second expression pattern as compared to the first expression pattern. In other instances, there may be more transposable elements expressed in the second expression pattern as compared to the first expression pattern.  
         [0047]     The expression patterns of the present invention can also be used in combination with other diagnostic markers of genomic reprogramming, such as the loss of expression of genes known to be characteristically and specifically expressed in specific types of differentiated cells. The expression patterns of the present invention can also be used with methylation patterns and/or chromatin status patterns to assess the developmental potential of any type of cell.  
         [0000]     Analysis of Methylation Patterns  
         [0048]     The present invention also provides methods of assessing methylation status of transposable element sequences and its role in development. Thus, also provided by the present invention is a method of determining a methylation pattern of one or more families of transposable elements in a cell comprising determining methylation of one or more families of retroviral elements. By analyzing global methylation patterns of transposable elements, one of skill in the art can assign particular methylation patterns to the various stages of developmental potential of a cell. These methylation patterns can be utilized with the expression patterns and chromatin status patterns described herein to assess the developmental potential of a cell or cells.  
         [0049]     In the present invention, methylation patterns can include one, two, three, four, five, six, seven, eight, nine, ten, twenty or more families of transposable elements and at least one, two, three, four, five, ten, fifteen, twenty, twenty-five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred members, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members of each transposable element family. For example, the present invention provides for the determination of a methylation pattern of one family of transposable elements in which one, two, three, four, five, ten, fifteen, twenty, twenty five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred members, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members of the transposable element family are analyzed. The present invention also provides for the determination of a methylation pattern of two families, wherein one, two, three, four, five, ten, fifteen, twenty, twenty five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred members, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members are analyzed for each family. Similarly, the invention provides for the determination of a methylation pattern of three families, wherein one, two, three, four, five, ten, fifteen, twenty, twenty five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred members, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members are analyzed for each family. Similarly, the invention provides for the determination of an methylation pattern of multiple families, for example, 10, 20, 30, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650 or 700 families wherein one, two, three, four, five, ten, fifteen, twenty, twenty five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members are analyzed for each family.  
         [0050]     By utilizing the methods of the present invention, a reference methylation pattern can be obtained for fully pluripotent stem cells, as well as for. cells that have more limited developmental potential (reduced pluripotency). Therefore, the present invention provides a method of assigning a methylation pattern of transposable elements to a fully pluripotent stem cell comprising: a) determining methylation of one or more families of transposable elements in a fully pluripotent stem cell and assigning the expression pattern obtained from step a) to the cell.  
         [0051]     The present invention also provides a method of assigning a methylation pattern of transposable elements to a pluripotent stem cell comprising: a) determining methylation of one or more families of transposable elements in a pluripotent stem cell and assigning the methylation pattern obtained from step a) to the cell.  
         [0052]     Also provided by the present invention is a method of assigning a methylation pattern of transposable elements to a differentiated cell comprising: a) determining methylation of one or more families of transposable elements in a differentiated cell and assigning the methylation pattern obtained from step a) to the cell.  
         [0053]     The present invention also provides a method of determining the developmental potential of a cell comprising: a) determining methylation of one or more families of transposable elements in a cell to obtain a methylation pattern; b) matching the methylation pattern of step a) with a known methylation pattern for a cell and c) determining the level of developmental potential of a cell based on matching of the expression pattern of a) with a known methylation pattern for a cell with a specific level of developmental potential.  
         [0054]     In the methods of the present invention, the methylation pattern obtained from a sample cell taken from a subject can be obtained from outside sources, such as a testing laboratory or a commercial source. Therefore, the step of obtaining the methylation pattern can be performed by one skilled artisan and the step of comparing the methylation pattern can be performed by a second skilled artisan. Thus, the present invention provides a method of establishing the developmental potential of a cell or cells comprising: a), matching a test transposable element methylation pattern of a cell with a known methylation pattern for a cell with a specific level of developmental potential; and b) determining the level of developmental potential of the cell based on matching of the test methylation pattern with a known methylation pattern for a cell with a specific level of developmental potential.  
         [0055]     For example, one of skill in the art can obtain a fertilized oocyte derived pluripotent stem cell and determine the methylation pattern of one or more transposable element families. By determining which transposable element families are methylated as well as which members of these transposable element families are methylated, one of skill in the art can assign this pattern to a fertilized oocyte derived pluripotent stem cell. This can be done for another stem cell with a more limited developmental potential than a fertilized oocyte, for example, a stem cell derived from a brain, such that a library of methylation patterns are readily available to not only to identify a cell with pluripotent potential but to determine the stage of pluripotency, i.e., level of developmental potential. Similarly, this can be done for stem cells derived from any tissue, or for oocytes in which a nucleus derived from a differentiated cell has been introduced to determine the degree to which that nucleus has reacquired pluripotency. By determining the methylation patterns of retrolements in cells with different stages of pluripotency, the skilled artisan can determine which transposable element families and which members of these families are markers of the level of pluripotency and developmental potential of cells.  
         [0056]     Such libraries of methylation patterns are useful for determining the developmental potential of stem cells. For example, a nucleus from a filly differentiated cell from a patient with Parkinson&#39;s disease can be transplanted into an enucleated oocyte. Once the methylation pattern of putative stem cells descendent from this oocyte is determined according to the methods of the present invention, this methylation pattern can be compared to a library of methylation patterns to determine the level of pluripotency associated with the methylation pattern. Once this is determined, a decision can be made with regard to the potential of these stem cells to regenerate appropriate neural cells if implanted in the patient&#39;s brain. The present methods will also be useful in evaluating the effectiveness of various treatments in stimulating stem cells to develop or, conversely, to monitor the effectiveness of treatments to stimulate determined and/or differentiated cells to regain pluripotency. For example, a sample of partially or fully differentiated neural cells could be treated in vitro with oocyte cellular extracts or other chemicals, small molecules, peptides, growth factors etc. designed to reprogram differentiated cells or to increase pluripotency. Methylation patterns can be obtained from these treated cells and compared to methylation patterns pre-established to be characteristic of pluripotent stem cells. Since the skilled artisan will have reference patterns for the fully differentiated cell, as well as a fully pluripotent stem cell and stem cells of more limited pluripotency, changes in transposable element methylation after treatment can be monitored to determine if the treatment results in a transposable element methylation pattern that more closely resembles the methylation pattern for a pluripotent stem cell.  
         [0057]     For example, if before treatment, certain families and members of these families are methylated, and after treatment, fewer families and/or members of these families are methylated, it can be said that this particular treatment is effective in increasing the developmental potential of the cell or in reprogramming the differentiated cell to become pluripotent. In some instances, effective treatments may involve decreasing the methylation of certain transposable elements and increasing the methylation of others. Therefore, once libraries of methylation patterns are established from untreated differentiated cells, one of skill in the art will know whether or not treatment is effective in a particular cell lineage by comparing the methylation pattern of a sample from samples of cells at different stages of treatment, with reference patterns established for the fully pluripotent stem cells. If a treatment is not successful in a particular cell lineage, the skilled artisan will recognize this by noting that the methylation pattern is not changing as expected, and other dosages, or treatments can be employed.  
         [0058]     Therefore, the present invention also provides a method of identifying a factor that increases the developmental potential of a cell comprising: a) determining methylation of one or more families of transposable elements in a cell to obtain a first methylation pattern; b) administering a putative factor that increases developmental potential to the cells; c) determining methylation of one or more families of transposable elements in the cell after administration of the factor to obtain a second expression pattern; and d) comparing the second methylation pattern with the first methylation pattern such that if the differences between the methylation patterns can be correlated with an increase in developmental potential, the factor increases the developmental potential of the cell. The changes observed between expression patterns can vary depending on the type of differentiated cell.  
         [0059]     In some instances, an effective treatment will result in fewer transposable elements being methylated in the second methylation pattern as compared to the first methylation pattern. In other instances, there may be more transposable elements methylated in the second pattern as compared to the first methylation pattern.  
         [0060]     The methylation patterns of the present invention can also be used in combination with other diagnostic markers of genomic reprogramming, such as the loss of methylation of genes known to be characteristically and specifically expressed in specific types of differentiated cells (e.g the differentiated liver cell marker DDP IV-dipeptidyl peptidase-see Oh et al. 2000 Hepatocyte growth factor induces differentiation of adult rat bone marrow cells into a hepatocyte lineage in vitro.  Biochem. Biophys. Res. Commun.  279: 500-504).  
         [0061]     Methods of measuring methylation are known in the art and include, but are not limited to methylation-specific. PCR, methylation microarray analysis, use of a methyly binding column and ChIP (a chromatin immunoprecipitation approach) analysis. Methylation can also be monitored by digestion of nucleic acid sequences with methylation sensitive and non-sensitive restriction enzymes followed by Southern blotting or PCR analysis of the restriction products (See Takai et al. “Hypomethylation of LINE1 retrotransposon in human hepatocellular carcinomas, but not in surrounding liver cirrhosis”  Jpn J. Clin. Oncol.  30(7) 306-309). One of skill in the art could also utilize methods in which genomic DNA is digested followed by PCR. (See, for example, Cartwright et al., “Analysis of Drosophila chromatin structure in vivo” Methods in Enzymology, Vol. 304)  
         [0062]     Methylation-specific PCR (MSP) technology utilizes the fact that DNA in humans is methylated mainly at certain cytosines located 5′ to guanosine. This occurs especially in GC-rich regions, known as CpG islands. To distinguish the methylation state of a sequence, MSP relies on differential chemical modification of cytosine residues in DNA. Treament with sodium bisulfite converts unmethylated cytosine residues into uracil, leaving the methylated cytosines unchanged. This modification thus creates different DNA sequences for methylated and unmethylated DNA. PCR primers can then be designed so as to distinguish between these different sequences. Two sets of primers (and additional control sets of primers) are designed: one set with sequences annealing to unchanged (methylated in the genomic DNA) cytosines and the other set with sequences annealing to the altered (unmethylated in the genomic DNA) cytosines. A comparison of PCR results using the two sets of primers reveals the methylation state of a PCR product. If the primer set with the altered sequence gives a PCR product, then the indicated cytosine was unmethylated. If the primer set with the unchanged sequence gives a PCR product, then the cytosines were methylated and thus protected from alteration. Evron et al. (“Detection of breast cancer cells in ductal lavage fluid by methylation-specific PCR,”  Lancet  2001, 357: 1335-1336) describes the use of MSP to detect breast cancer and is hereby incorporated in its entirety by this reference.  
         [0063]     To use a microarray to study transposable element methylation, one of skill in the art would select for methylated and unmethylated DNA from total genomic DNA. The selectively isolated DNA is then hybridized to the transposable element array either directly or after amplification and patterns are compared between various cell types/tissue types as described earlier in the patent application.  
         [0064]     There are several approaches for selecting methylated DNA. One method is chromatin immunoprecipitation (ChIP). Another method utilizes a column binding approach and a third option involves ligation of adapters to fragmented genomic DNA and methylation-specific restriction digestion of the ligation products followed by PCR amplification.  
         [0065]     In all cases, the selected DNA fragments are labeled by incorporation of dNTPs coupled with fluorescent dyes (for example Cy3 or Cy5 coupled dNTPs) and hybridization to the microarray is performed according to standard protocols. One of skill in the art could utilize the BioPrime DNA labeling system from Life Technologies or other kits available for such labeling.  
         [0066]     As stated above, microarray techniques would be known to one of skill in the art. For example, U.S. Pat. No. 6,410,229 and U.S. Pat. No. 6,344,316, both hereby incorporated by this reference, describe methods of hybridizing nucleic acids to high density nucleic acid arrays. For example, one skilled in the art would first produce fluorescent-labeled DNA isolated from the tissue of interest. A batch of labeled genomic/amplified genomic DNAs representing either one sample or a mixture of two samples from the tissue sources of interest is added to an array of oligonucleotides representing a plurality of known transposable elements, as described above, under conditions that result in hybridization of the DNAs to complementary-sequence oligonucleotides in the array. The array is then examined by fluorescence under fluorescence excitation conditions in which transposable element oligonucleotides in the array that are hybridized to genomic/amplified genomic DNAs derived from the tissue of interest can be detected and quantified.  
         [0067]     ChIP technology involves in vivo formaldehyde cross-linking of DNA and associated proteins in intact cells, followed by selective immunoprecipitation of protein-DNA complexes with specific antibodies. Such an approach allows detection of any protein at its in vivo binding site directly. In particular, proteins that are not bound directly to DNA or that depend on other proteins for binding activity in vivo can be analyzed by this method. Since methylation involves methylation complexes that involve numerous proteins which interact with DNA, by utilizing ChIP technology, methylation complexes can be cross-linked to transposable element sequences to which they are bound and then an antibody specific to one of the proteins (i.e, one of the proteins involved in the methylation complex, such as methyltransferase or a protein having a methyl binding site, for example, MBD1) can be utilized to immunoprecipitate the methylation complex-DNA bound sequence. The complex can then be chemically released and the transposable element sequence to which it was bound can be identified. For references describing ChIP technology, see Orlando (“Mapping chromosomal proteins in vivo by formaldehyde crosslinked-chromatin immunoprecipitation,”  TIBS  2000, 25:99-104) and Kuo et al. (“In Vivo Cross-Linking and Immunoprecipitation for Studying Dynamic Protein:DNA Associations in a Chromatin Environment,” 1999, 19: 425-433) both of which are incorporated in their entireties by this reference.  
         [0068]     Formaldehyde crosslinking followed by chromatin immunoprecipitation is reviewed in Orlando 2000. By addition of formaldehyde to live tissue/cells, DNA and nearby proteins are cross-linked in vivo, followed by sonication of the tissue/cell suspension. The DNA is fragmented in the process. Antibodies recognizing methyl-binding proteins are added and the immune complexes are collected, thereby precipitating methylated DNA with associated proteins. DNA without methyl-binding proteins will be collected from the supernatant. The cross-linking step is then reversed for both fractions, followed by a DNA purification step. The isolated DNA can be ligated to linker oligonucleotides and amplified by PCR. Fluorescence labeling and hybridization is then performed as described above.  
         [0069]     The column binding approach is used to select for methylated DNA after genomic DNA extraction. The column contains methyl-CpG-binding proteins, for example the methyl-binding domain of rat MeCP2, covalently linked to a histidine tag, then attached to a Ni-agarose matrix. Fragmented genomic DNA (digested with restriction enzymes, for example MseI) is run through the column. The column retains DNA containing methylated cytosines, unmethylated DNA is collected from the flow-through. Retained methylated DNA is recovered from the column. (Cross, S. H., Charlton, J. A., Nan, X. and Bird, A. P. (1994) Purification of CpG islands using a methylated DNA binding column.  Nat Genet.,  6, 236-244 and Brock, Huang, Chen and Johnson (2001) A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP).  Nucleic Acids Research, l vol. 29, no.24). The isolated DNA can be ligated to linker oligonucleotides and amplified by PCR. Fluorescence labeling and hybridization is then performed as described above.  
         [0070]     Linker ligation/Methylation-specific restriction/PCR can also be utilized. The methods of the present invention can utilize a modified version of DMH (Differential Methylation Hybridization) (References: Huang et al. ‘Methylation profiling of CpG islands in human breast cancer cells’  Human Molecular Genetics  1999, Vol.8, No.3 and Yan et al. ‘Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays’  Cancer Research  2001, 61, 8375-8380). Genomic DNA is digested with MseI. Then, the ends of the resulting fragments are ligated to linker oligonucleotides. Ligated fragments undergo restriction digestion with methylation-sensitive enzymes BstUI and/or HpaII, followed by PCR amplification of undigested fragments. Fluorescence labeling and hybridization is then performed as described above.  
         [0071]     A COT-1 subtractive hybridization step can be utilized at some point before labeling the DNA to separate out the highly repetitive sequences from the sample (See Craig et al. ‘Removal of repetitive sequences from FISH probes using PCR-assisted affinity chromatography’  Human Genetics  1997, Vol. 100, 472-476).  
         [0072]     Another technique, methylation-specific oligonucleotide (MSO) microarray, uses bisulfite-modified DNA as a template for PCR amplification, resulting in conversion of unmethylated cytosine, but not methylated cytosine, into thymine within CpG islands of interest. The amplified product, therefore, may contain a pool of DNA fragments with altered nucleotide sequences due to differential methylation status. A test sample is hybridized to a set of olignonucleotide arrays that discriminate between methylated and unmethylated cytosine at specific nucleotide positions, and quantitative differences in hybridization are determined by fluorescence analysis. For examples of methylation microarray techniques see Gitan et al. (“Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis,”  Genome Res.  2002, 12: 158-164.), Shi et al. (“Oligonucleotide-based microarray for DNA methylation analysis: Principles and applications,”  J. Cell Biochem.  2003, 88: 138-143.), Yan et al. (“Applications of CpG island microarrays for high-throughput analysis of DNA methylation,”  J. Nutr.  2002, 132: 2430S-2434S), Wei et al. (“Methylation microarray analysis of late-stage ovarian carcinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers,” Clin Cancer Res. 2002, 8: 2246-2252.), all of which are incorporated herein, in their entireties, by this reference.  
         [0000]     Analysis of Chromatin Status  
         [0073]     The present invention also provides methods of assessing the chromatin status of transposable element sequences and its role in the developmental potential of cells. These chromatin status patterns can be used in combination with transposable element expression patterns and/or methylation patterns described herein to assess the developmental potential of cells. One of the skill in the art would know how to assess chromatin status by methods standard in the art. See Orlando (“Mapping chromosomal proteins in vivo by formaldehyde crosslinked-chromatin immunoprecipitation,”  TIBS  2000, 25:99-104) and Kuo et al. (“In Vivo Cross-Linking and Immunoprecipitation for Studying Dynamic Protein:DNA Associations in a Chromatin Environment,” 1999, 19: 425-433) both of which are incorporated in their entireties by this reference.  
         [0074]     Thus, the present invention provides a method of assigning a chromatin status pattern of transposable elements to the level of developmental potential of a cell comprising: a) determining chromatin status of one or more families of transposable elements; and b) assigning the chromatin status pattern obtained from step a) to the level of developmental potential of a cell.  
         [0075]     As utilized herein, “chromatin status” refers to the chromosomal structure or the chromosomal accessibility or the ability of restriction enzymes to access a transposable element sequence or a fragment thereof. Therefore, chromatin status patterns can contain sequences that are accessible to restriction enzymes and sequences that are not accessible to restriction enzymes.  
         [0076]     The present invention also provides a method of determining the developmental potential of a stem cell comprising: a) determining chromatin status of one or more families of transposable elements in a stem cell to obtain a chromatin status pattern; b) matching the chromatin status pattern of step a) with a known chromatin status pattern for a cell at different stages of developmental potential ranging from a filly pluripotent stem cell to a fully differentiated cell and; c) determining the developmental potential of the stem cell based on matching the chromatin status pattern of a) with a known chromatin status pattern for a cell at a specific developmental stage.  
         [0077]     In the present invention, chromatin status patterns can include one, two, three, four, five, six, seven, eight, nine, ten, twenty or more families of transposable elements and at least one, two, three, four, five, ten, fifteen, twenty, twenty-five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred members, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members of each transposable element family. For example, the present invention provides for the determination of a chromatin status pattern of one family of transposable elements in which one, two, three, four, five, ten, fifteen, twenty, twenty five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred members, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members of the transposable element family are analyzed. The present invention also provides for the determination of a chromatin status pattern of two families, wherein one, two, three, four, five, ten, fifteen, twenty, twenty five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred members, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members are analyzed for each family. Similarly, the invention provides for the determination of a methylation pattern of three families, wherein one, two, three, four, five, ten, fifteen, twenty, twenty five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred members, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members are analyzed for each family. Similarly, the invention provides for the determination of an chromatin status pattern of multiple families, for example, 10, 20, 30, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650 or 700 families wherein one, two, three, four, five, ten, fifteen, twenty, twenty five, fifty, one hundred, two hundred, three hundred, four hundred, five hundred, one thousand, two thousand, three thousand, four thousand, five thousand, six thousand, seven thousand, eight thousand, nine thousand, ten thousand, twenty thousand, fifty thousand, one hundred thousand, two hundred thousand, three hundred thousand, four hundred thousand or five hundred thousand members are analyzed for each family.  
         [0078]     By utilizing the methods of the present invention, a reference chromatin status pattern can be obtained for fully pluripotent stem cells, as well as for cells that have more limited developmental potential (reduced pluripotency). Therefore, the present invention provides a method of assigning a chromatin status pattern of transposable elements to a fully pluripotent stem cell comprising: a) determining chromatin status of one or more families of transposable elements in a fully pluripotent stem cell and assigning the chromatin status pattern obtained from step a) to the cell.  
         [0079]     The present invention also provides a method of assigning a chromatin status pattern of transposable elements to a pluripotent stem cell comprising: a) determining chromatin status of one or more families of transposable elements in a pluripotent stem cell and assigning the chromatin stauts pattern obtained from step a) to the cell.  
         [0080]     Also provided by the present invention is a method of assigning a chromatin status pattern of transposable elements to a differentiated cell comprising: a) determining chromatin status of one or more families of transposable elements in a differentiated cell and assigning the chromatin status pattern obtained from step a) to the cell.  
         [0081]     The present invention also provides a method of determining the developmental potential of a cell comprising: a) determining chromatin status of one or more families of transposable elements in a cell to obtain a chromatin status pattern; b) matching the chromatin status pattern of step a) with a known chromatin status pattern for a cell and c) determining the level of developmental potential of a cell based on matching of the expression pattern of a) with a known chromatin status pattern for a cell with a specific level of developmental potential.  
         [0082]     In the methods of the present invention, the chromatin status pattern obtained from a sample cell taken from a subject can be obtained from outside sources, such as a testing laboratory or a commercial source. Therefore, the step of obtaining the chromatin status pattern can be performed by one skilled artisan and the step of comparing the chromatin status pattern can be performed by a second skilled artisan. Thus, the present invention provides a method of establishing the developmental potential of a cell or cells comprising: a) matching a test transposable element chromatin status pattern of a cell with a known chromatin status pattern for a cell with a specific level of developmental potential; and b) determining the level of developmental potential of the cell based on matching of the test chromatin status pattern with a known chromatin status pattern for a cell with a specific level of developmental potential.  
         [0083]     For example, one of skill in the art can obtain a fertilized oocyte derived pluripotent stem cell and determine the chromatin status pattern of one or more transposable element families. By determining which transposable element families are methylated as well as which members of these transposable element families are methylated, one of skill in the art can assign this pattern to a fertilized oocyte derived pluripotent stem cell. This can be done for another stem cell with a more limited developmental potential than a fertilized oocyte, for example, a stem cell derived from a brain, such that a library of chromatin status patterns are readily available to not only to identify a cell with pluripotent potential but to determine the stage of pluripotency, i.e., level of developmental potential. Similarly, this can be done for stem cells derived from any tissue, or for oocytes in which a nucleus derived from a differentiated cell has been introduced to determine the degree to which that nucleus has reacquired pluripotency. By determining the chromatin status patterns of retrolements in cells with different stages of pluripotency, the skilled artisan can determine which transposable element families and which members of these families are markers of the level of pluripotency and developmental potential of cells.  
         [0084]     Such libraries of chromatin status patterns are useful for determining the developmental potential of stem cells. For example, a nucleus from a fully differentiated cell from a patient with Parkinson&#39;s disease can be transplanted into an enucleated oocyte. Once the chromatin status pattern of putative stem cells descendent from this oocyte are determined according to the methods of the present invention, this chromatin status pattern can be compared to a library of chromatin status patterns to determine the level of pluripotency associated with the chromatin status pattern. Once this is determined, a decision can be made with regard to the potential of these stem cells to regenerate appropriate neural cells if implanted in the patient&#39;s brain. The present methods will also be useful in evaluating the effectiveness of various treatments in stimulating stem cells to develop or, conversely, to monitor the effectiveness of treatments to stimulate determined and/or differentiated cells to regain pluripotency. For example, a sample of partially or fully differentiated neural cells could be treated in vitro with oocyte cellular extracts or other chemicals, small molecules, peptides, growth factors etc. designed to reprogram differentiated cells or to increase pluripotency. Chromatin status patterns can be obtained from these treated cells and compared to chromatin status patterns pre-established to be characteristic of pluripotent stem cells. Since the skilled artisan will have reference patterns for the fully differentiated cell, as well as a fully pluripotent stem cell and stem cells of more limited pluripotency, changes in transposable element chromatin status after treatment can be monitored to determine if the treatment results in a transposable element chromatin status pattern that more closely resembles the chromatin status pattern for a pluripotent stem cell.  
         [0085]     For example, if before treatment, certain families and members of these families are methylated, and after treatment, fewer families and/or members of these families are methylated, it can be said that this particular treatment is effective in increasing the developmental potential of the cell or in reprogramming the differentiated cell to become pluripotent. In some instances, effective treatments may involve decreasing the chromatin status of certain transposable elements and increasing the chromatin status of others. Therefore, once libraries of chromatin status patterns are established from untreated differentiated cells, one of skill in the art will know whether or not treatment is effective in a particular cell lineage by comparing the chromatin status pattern of a sample from samples of cells at different stages of treatment, with reference patterns established for the fully pluripotent stem cells. If a treatment is not successful in a particular cell lineage, the skilled artisan will recognize this by noting that the chromatin status pattern is not changing as expected, and other dosages, or treatments can be employed.  
         [0086]     Also provided by the present invention is a method of identifying a cellular differentiation induction factor comprising: a) determining chromatins status of one or more families of transposable elements in a stem cell to obtain a first chromatin status pattern; b) administering a putative induction factor to the cell; c) determining the chromatin status of one or more families of transposable elements in the cell after administration of the putative induction factor to obtain a second chromatin status pattern; and d comparing the second chromatin status pattern with the first chromatin status pattern such that if there is a change in the second chromatin status pattern as compared to the first chromatin status pattern, the induction factor is a cellular differentiation induction factor.  
         [0087]     Further provided by the present invention is a method of identifying a factor that increases the developmental potential of a cell comprising: a) determining chromatin status of one or more families of transposable elements in a differentiated cell to obtain a first chromatin status pattern; b) administering a putative factor that increases developmental potential to the cell; c) determining expression of one or more families of transposable elements in the cell after administration of the putative factor to obtain a second chromatin status pattern; and d) comparing the second chromatin status pattern with the first chromatin status pattern such that if there is a change in the second chromatin status pattern as compared to the first chromatin status pattern, the factor is effective in increasing the developmental potential of the cell.  
         [0088]     In some instances, an effective treatment will result in fewer transposable elements being accessible to restriction enzymes in the second chromatin status pattern as compared to the first chromatin status pattern. In other instances, there may be more transposable elements accessible to restriction enzymes in the second pattern as compared to the first chromatin status pattern.  
         [0089]     The chromatin status patterns of the present invention can also be used in combination with other diagnostic markers of genomic reprogramming, such as the loss of methylation of genes known to be characteristically and specifically expressed in specific types of differentiated cells (e.g the differentiated liver cell marker DDP IV-dipeptidyl peptidase—see Oh et al. 2000 Hepatocyte growth factor induces differentiation of adult rat bone marrow cells into a hepatocyte lineage in vitro.  Biochem. Biophys. Res. Commun.  279: 500-504).  
         [0090]     The present invention also provides a computer system comprising a) a database including records comprising a plurality of reference retroelement expression patterns, and associated developmental potential information; and b) a user interface capable of receiving a selection of one or more test retroelement expression patterns for use in determining matches between a test retroelement expression pattern and a reference retroelement expression pattern, and displaying the records associated with matching expression patterns. The computer systems of the present invention can also include a database including records comprising a plurality of reference methylation patterns, and associated developmental potential information, b) a user interface capable of receiving a selection of one or more test methylation patterns for use in determining matches between a test methylation pattern and the reference methylation pattern, and displaying the records associated with matching expression patterns. Also provided is a computer system comprising a) a database including records comprising a plurality of reference chromatin status patterns, and associated developmental potential information; and b) a user interface capable of receiving a selection of one or more test chromatin status patterns for use in determining matches between a test chromatin status pattern and a reference chromatin status pattern, and displaying the records associated with matching expression patterns.  
         [0091]     It will be appreciated by those skilled in the art that expression patterns, methylation patterns and/or chromatin status patterns identified in cells as described by the present invention can be stored, recorded, and manipulated on any medium which can be read and accessed by a computer. As used herein, the words “recorded” and “stored” refer to a process for storing information on a computer medium. A skilled artisan can readily adopt any of the presently known methods for recording information on a computer readable medium to generate a list of sequences comprising one or more of the nucleic acids of the invention. Another aspect of the present invention is a computer readable medium having recorded thereon at least 2, 5, 10, 15, 20, 25, 30, 50, 100, 200, 250, 300, 400, 500, 1000, 2000, 3000, 4000 or 5000 expression patterns, methylation patterns and/or chromatin status patterns of the invention or patterns identified from cells.  
         [0092]     Computer readable media include magnetically readable media, optically readable media, electronically readable media and magnetic/optical media. For example, the computer readable media may be a hard disc, a floppy disc, a magnetic tape, CD-ROM, DVD, RAM, or ROM as well as other types of other media known to those skilled in the art.  
         [0093]     Embodiments of the present invention include systems, particularly computer systems which contain the sequence information described herein. As used herein, “a computer system” refers to the hardware components, software components, and data storage components used to store and/or analyze the expression patterns of the present invention or other expression patterns. The computer system preferably includes the computer readable media described above, and a processor for accessing and manipulating the data.  
         [0094]     Preferably, the computer is a general purpose system that comprises a central processing unit (CPU), one or more data storage components for storing data, and one or more data retrieving devices for retrieving the data stored on the data storage components. A skilled artisan can readily appreciate that any one of the currently available computer systems are suitable.  
         [0095]     In one particular embodiment, the computer system includes a processor connected to a bus which is connected to a main memory, preferably implemented as RAM, and one or more data storage devices, such as a hard drive and/or other computer readable media having data recorded thereon. In some embodiments, the computer system further includes one or more data retrieving devices for reading the data stored on the data storage components. The data retrieving device may represent, for example, a floppy disk drive, a compact disk drive, a magnetic tape drive, a hard disk drive, a CD-ROM drive, a DVD drive, etc. In some embodiments, the data storage component is a removable computer readable medium such as a floppy disk, a compact disk, a magnetic tape, etc. containing control logic and/or data recorded thereon. The computer system may advantageously include or be programmed by appropriate software for reading the control logic and/or the data from the data storage component once inserted in the data retrieving device.  
         [0096]     In some embodiments, the computer system may further comprise an expression pattern comparer for comparing the expression pattern(s) stored on a computer readable medium to expression pattern(s) stored on a computer readable medium. An “expression pattern comparer” refers to one or more programs which are implemented on the computer system to compare a nucleotide sequence with other nucleotide sequences. Similarly, programs capable of comparing methylation status patterns and chromatin status patterns are also contemplated by the present invention.  
         [0097]     This invention also provides for a computer program that correlates expression patterns with a particular level of developmental potential. Similarly, the present invention also provides a computer program that correlates methylation patterns with a particular level of developmental potential. Also provided is a computer program that correlates chromatin status with a particular level of developmental potential. The computer programs of this invention can optionally include treatment options for cells, such that one of skill in the art would be able to treat cells and modulate the developmental stage of the cell.  
         [0098]     Throughout this application, various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains.  
         [0099]     It will be apparent to those skilled in the art that various modifications and variations can be made in the present invention without departing from the scope or spirit of the invention. Other embodiments of the invention will be apparent to those skilled in the art from consideration of the specification and practice of the invention disclosed herein. It is intended that the specification and examples be considered as exemplary only, with a true scope and spirit of the invention being indicated by the following claims.