C. Bibliographie-[-abajian-abajian, Sputnik, 1994.

P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila, Nature, vol.437, issue.7062, p.437114952, 2005.
DOI : 10.1038/nature04107

. Angers, . Bernatchez, B. Angers, and L. Bernatchez, Complex evolution of a salmonid microsatellite locus and its consequences in inferring allelic divergence from size information, Molecular Biology and Evolution, vol.14, issue.3, p.230238, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025759

. Baer, Mutation rate variation in multicellular eukaryotes: causes and consequences, Nature Reviews Genetics, vol.2, issue.8, p.61931, 2007.
DOI : 10.1038/nrg2158

D. Balding, Forensic applications of microsatellite markers, Microsatellites evolution and applications, 1999.

S. R. Eddy, Automated de novo identication of repeat sequence families in sequenced genomes, Genome Res, issue.8, p.12126976, 2002.

. Batzer, . Deininger, M. A. Batzer, and P. L. Deininger, ALU REPEATS AND HUMAN GENOMIC DIVERSITY, Nature Reviews Genetics, vol.3, issue.5, p.3709, 2002.
DOI : 10.1038/nrg798

. Batzer, Standardized nomenclature for Alu repeats, Journal of Molecular Evolution, vol.22, issue.1, p.36, 1996.
DOI : 10.1007/BF00163204

. Batzer, Dispersion and insertion polymorphism in two small subfamilies of recently amplied human alu repeats, J Mol Biol, vol.247, issue.3, p.41827, 1995.

G. I. Bell and J. Jurka, The Length Distribution of Perfect Dimer Repetitive DNA Is Consistent with Its Evolution by an Unbiased Single-Step Mutation Process, Journal of Molecular Evolution, vol.44, issue.4, p.41421, 1997.
DOI : 10.1007/PL00006161

G. Benson, Tandem repeats nder : a program to analyze dna sequences, Nucleic Acids Res, vol.27, issue.2, p.57380, 1999.

S. Blanquart, Reconstruction phylogénétique par analyse bayésienne des séquences moléculaires, 2007.

J. D. Boeke, Lines and alusthe polya connection, Nat Genet, vol.16, issue.1, p.67, 1997.

. Brohede, J. Ellegren-]-brohede, and H. Ellegren, Microsatellite evolution: polarity of substitutions within repeats and neutrality of flanking sequences, Proceedings of the Royal Society B: Biological Sciences, vol.266, issue.1421, pp.266825-266858, 1421.
DOI : 10.1098/rspb.1999.0712

J. F. Brookeld, The generation of sequence similarity in sines and lines, Trends in Genetics, vol.9, issue.2, p.3838, 1993.

. Buard, . Jereys, J. Buard, and A. J. Jereys, Big, bad minisatellites, Nature Genetics, vol.13, issue.4, p.3278, 1997.
DOI : 10.1093/hmg/6.1.129

E. Buschiazzo and N. J. Gemmell, The rise, fall and renaissance of microsatellites in eukaryotic genomes, BioEssays, vol.499, issue.10, p.2810401050, 2006.
DOI : 10.1002/bies.20470

P. Calabrese and R. Durrett, Dinucleotide Repeats in the Drosophila and Human Genomes Have Complex, Length-Dependent Mutation Processes, Molecular Biology and Evolution, vol.20, issue.5, p.715725, 2003.
DOI : 10.1093/molbev/msg084

. Castelo, TROLL--Tandem Repeat Occurrence Locator, Bioinformatics, vol.18, issue.4, p.634636, 2002.
DOI : 10.1093/bioinformatics/18.4.634

. Chakraborty, Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci, Proceedings of the National Academy of Sciences, vol.94, issue.3, p.9410416, 1997.
DOI : 10.1073/pnas.94.3.1041

G. K. Macavoy and E. S. , Microsatellites : consensus and controversy, Comp Biochem Physiol B Biochem Mol Biol, vol.126, issue.4, pp.45576-154, 2000.

. Charlesworth, The evolutionary dynamics of repetitive DNA in eukaryotes, Nature, vol.371, issue.6494, p.37121520, 1994.
DOI : 10.1038/371215a0

. Coenye, T. Vandamme-]-coenye, and P. Vandamme, Characterization of Mononucleotide Repeats in Sequenced Prokaryotic Genomes, DNA Research, vol.12, issue.4, p.221233, 2005.
DOI : 10.1093/dnares/dsi009

. Cordaux, Retrotransposition of Alu elements: how many sources?, Trends in Genetics, vol.20, issue.10, p.204647, 2004.
DOI : 10.1016/j.tig.2004.07.012

. Cornuet, Inference on microsatellite mutation processes in the invasive mite, Varroa destructor, using reversible jump Markov chain Monte Carlo, Theoretical Population Biology, vol.69, issue.2, p.12944, 2006.
DOI : 10.1016/j.tpb.2005.07.005

URL : https://hal.archives-ouvertes.fr/hal-00161097

. Coward, . Drablos, E. Coward, and F. Drablos, Detecting periodic patterns in biological sequences, Bioinformatics, vol.14, issue.6, p.14498507, 1998.
DOI : 10.1093/bioinformatics/14.6.498

. Deininger, Master genes in mammalian repetitive dna amplication, Trends Genet, vol.8, issue.9, p.30711, 1992.

O. Delgrange and E. Rivals, STAR: an algorithm to Search for Tandem Approximate Repeats, Bioinformatics, vol.20, issue.16, p.20281220, 2004.
DOI : 10.1093/bioinformatics/bth335

URL : https://hal.archives-ouvertes.fr/lirmm-00108544

. Desmarais, Local Mutagenic Impact of Insertions of LTR Retrotransposons on the Mouse Genome, Journal of Molecular Evolution, vol.46, issue.13, p.66275, 2006.
DOI : 10.1007/s00239-005-0301-2

URL : https://hal.archives-ouvertes.fr/halsde-00341020

T. Dettman, J. R. Dettman, and J. W. Taylor, Mutation and Evolution of Microsatellite Loci in Neurospora, Genetics, vol.168, issue.3, p.168123148, 2004.
DOI : 10.1534/genetics.104.029322

H. Dewannieux, M. Dewannieux, and T. Heidmann, Role of poly(A) tail length in Alu retrotransposition, Genomics, vol.86, issue.3, p.37881, 2005.
DOI : 10.1016/j.ygeno.2005.05.009

D. Dieringer and C. Schlotterer, Two Distinct Modes of Microsatellite Mutation Processes: Evidence From the Complete Genomic Sequences of Nine Species, Genome Research, vol.13, issue.10, 2003.
DOI : 10.1101/gr.1416703

. Dirienzo, Mutational processes of simple-sequence repeat loci in human-populations, p.155, 1994.

. Dokholyan, Distributions of Dimeric Tandem Repeats in Non-coding and Coding DNA Sequences, Journal of Theoretical Biology, vol.202, issue.4, p.27382, 2000.
DOI : 10.1006/jtbi.1999.1052

S. Doolittle, W. F. Doolittle, and C. Sapienza, Selsh genes, the phenotype paradigm and genome evolution, Nature, issue.5757, p.2846013, 1980.

L. Duret, Evolution of synonymous codon usage in metazoans, Current Opinion in Genetics & Development, vol.12, issue.6, p.640649, 2002.
DOI : 10.1016/S0959-437X(02)00353-2

URL : https://hal.archives-ouvertes.fr/hal-00427267

R. C. Edgar and E. W. Myers, PILER: identification and classification of genomic repeats, Bioinformatics, vol.21, issue.Suppl 1, pp.152-158, 2005.
DOI : 10.1093/bioinformatics/bti1003

W. Ehrlich, M. Ehrlich, and R. Y. Wang, 5-Methylcytosine in eukaryotic DNA, Science, vol.212, issue.4501, p.21213507, 1981.
DOI : 10.1126/science.6262918

E. Eickbush, T. Eickbush, and D. Eickbush, Transposable elements, Evolution . Encyclopedia of Life Science, 2005.

M. Eickbush, T. Eickbush, and H. Malik, Origins and Evolution of Retrotransposons, Mobile DNA, p.11111144, 2001.
DOI : 10.1128/9781555817954.ch49

H. Ellegren, Heterogeneous mutation processes in human microsatellite dna sequences, Nat Genet, vol.24, issue.4, p.4002, 2000.

H. Ellegren, Microsatellite mutations in the germline: implications for evolutionary inference, Trends in Genetics, vol.16, issue.12, p.5518, 2000.
DOI : 10.1016/S0168-9525(00)02139-9

H. Ellegren, Microsatellites: simple sequences with complex evolution, Nature Reviews Genetics, vol.164, issue.6, p.43545, 2004.
DOI : 10.1016/S0379-0738(01)00564-3

. Estoup, Microsatellite variation in honey bee (apis mellifera l.) populations : hierarchical genetic structure and test of the innite allele and stepwise mutation models, Genetics, issue.2, p.14067995, 1995.

I. Falush, D. Falush, and Y. Iwasa, Size-Dependent Mutability and Microsatellite Constraints, Molecular Biology and Evolution, vol.16, issue.7, pp.960966-156, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026185

. Feng, Human L1 Retrotransposon Encodes a Conserved Endonuclease Required for Retrotransposition, Cell, vol.87, issue.5, pp.905-916, 1996.
DOI : 10.1016/S0092-8674(00)81997-2

H. Ferguson, D. O. Ferguson, and W. K. Holloman, Recombinational repair of gaps in dna is asymmetric in ustilago maydis and can be explained by a migrating dloop model, Proceedings of the National Academy of Sciences of the United States of America, p.9354195424, 1996.

A. J. Flavell, Retroelements, reverse transcriptase and evolution, Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, vol.110, issue.1, p.315, 1995.
DOI : 10.1016/0305-0491(94)00122-B

A. Formosa, T. Formosa, and B. M. Alberts, Dna-synthesis dependent on genetic-recombination -characterization of a reaction catalyzed by puried bacteriophage-t4 proteins, Cell, issue.5, p.47793806, 1986.

C. Fu, Y. X. Fu, and R. Chakraborty, Simultaneous estimation of all the parameters of a stepwise mutation model, Genetics, vol.150, issue.1, p.48797, 1998.

. Garza, Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size, Mol Biol Evol, vol.12, issue.4, p.594603, 1995.

. Gelfand, TRDB--The Tandem Repeats Database, Nucleic Acids Research, vol.35, issue.Database, pp.80-87, 2007.
DOI : 10.1093/nar/gkl1013

. Goeau, Life with 6000 genes, Science, issue.5287, pp.274546-5637, 1996.

A. J. Gordon, Microsatellite birth register, Journal of Molecular Evolution, vol.45, issue.3, p.337338, 1997.

T. Gregory, Genome size evolution in animals, editor, The evolution of the genome, 2005.

. Haag-liautard, Direct estimation of per nucleotide and genomic deleterious mutation rates in drosophila, Nature, issue.7123, pp.445825-157, 2007.

B. Harr and C. Schlotterer, Long microsatellite alleles in drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide underrepresentation, Genetics, issue.3, p.155121320, 2000.

. Harr, Conservation of locusspecic microsatellite variability across species : a comparison of two drosophila sibling species, d. melanogaster and d. simulans, Mol Biol Evol, vol.15, issue.2, p.17684, 1998.

. Harr, Removal of Microsatellite Interruptions by DNA Replication Slippage: Phylogenetic Evidence from Drosophila, Molecular Biology and Evolution, vol.17, issue.7, p.1710019, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026381

C. Hartl, D. Hartl, and A. Clark, Principles of Population Genetics, 1997.

P. J. Hastings, Recombination in the eukaryotic nucleus, BioEssays, vol.103, issue.2-3, p.6164, 1988.
DOI : 10.1002/bies.950090206

P. Henderson, S. T. Henderson, and T. D. Petes, Instability of simple sequence DNA in Saccharomyces cerevisiae., Molecular and Cellular Biology, vol.12, issue.6, p.12274957, 1992.
DOI : 10.1128/MCB.12.6.2749

. Huang, Mutation Patterns at Dinucleotide Microsatellite Loci in Humans, The American Journal of Human Genetics, vol.70, issue.3, p.62534, 2002.
DOI : 10.1086/338997

. Jarne, Microsatellites, transposable elements and the X chromosome, Molecular Biology and Evolution, vol.15, issue.1, p.2834, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025844

. Jarne, P. Lagoda-]-jarne, and P. J. Lagoda, Microsatellites, from molecules to populations and back, Trends in Ecology & Evolution, vol.11, issue.10, p.11424429, 1996.
DOI : 10.1016/0169-5347(96)10049-5

J. Jurka, Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons, Proceedings of the National Academy of Sciences, vol.94, issue.5, p.18727, 1997.
DOI : 10.1073/pnas.94.5.1872

P. Jurka, J. Jurka, and C. Pethiyagoda, Simple repetitive DNA sequences from primates: Compilation and analysis, Journal of Molecular Evolution, vol.46, issue.2, p.1206, 1995.
DOI : 10.1007/BF00167107

. Kapitonov, . Jurka, V. Kapitonov, and J. Jurka, The age of Alu subfamilies, Journal of Molecular Evolution, vol.26, issue.1, p.5965, 1996.
DOI : 10.1007/BF00163212

. Katti, Dierential distribution of simple sequence repeats in eukaryotic genome sequences, Mol Biol Evol, issue.7, pp.1811617-158, 2001.

M. Kimura, Genetic variability maintained in a nite population due to mutational production of neutral and nearly neutral isoalleles, Genet Res, vol.11, issue.3, p.24769, 1968.

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., p.11120, 1980.
DOI : 10.1007/BF01731581

. Kimura, . Crow, M. Kimura, and J. F. Crow, The number of alleles that can be maintained in a nite population, Genetics, vol.49, p.72538, 1964.

. Kimura, . Ohta, M. Kimura, and T. Ohta, Stepwise mutation model and distribution of allelic frequencies in a nite population, Proc Natl Acad Sci, issue.6, p.75286872, 1978.

. Klinman, Immune Recognition of Foreign DNA, Immunity, vol.11, issue.2, p.1239, 1999.
DOI : 10.1016/S1074-7613(00)80087-4

. Kolpakov, mreps : Ecient and exible detection of tandem repeats in dna, Nucleic Acids Res, issue.13, p.3136728, 2003.

R. Kolpakov and G. Kucherov, Finding approximate repetitions under hamming distance, Theoretical Computer Science, vol.303, issue.1, p.135156, 2003.
DOI : 10.1007/3-540-44676-1_14

URL : https://hal.archives-ouvertes.fr/inria-00100491

. Krakauer, . Plotkin, D. C. Krakauer, and J. B. Plotkin, Redundancy, antiredundancy, and the robustness of genomes, Proceedings of the National Academy of Sciences, vol.99, issue.3, p.9914059, 2002.
DOI : 10.1073/pnas.032668599

C. Krawczak, M. Krawczak, and D. N. Cooper, The human gene mutation database, Trends in Genetics, vol.13, issue.3, p.121122, 1997.
DOI : 10.1016/S0168-9525(97)01068-8

. Kruglyak, Distribution and Abundance of Microsatellites in the Yeast Genome Can Be Explained by a Balance Between Slippage Events and Point Mutations, Molecular Biology and Evolution, vol.17, issue.8, p.1712109, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026404

. Lai, . Sun, Y. L. Lai, and F. Z. Sun, The Relationship Between Microsatellite Slippage Mutation Rate and the Number of Repeat Units, Molecular Biology and Evolution, vol.20, issue.12, pp.202123-2131, 2003.
DOI : 10.1093/molbev/msg228

. Landau, An algorithm for approximate tandem repeats, J Comput Biol, vol.8, issue.1, pp.118-159, 2001.

. Lander, Initial sequencing and analysis of the human genome, Nature, vol.6, issue.6822, p.409860921, 2001.
DOI : 10.1038/35057062

. Leclercq, Detecting microsatellites within genomes: significant variation among algorithms, BMC Bioinformatics, vol.8, issue.1, p.125, 2007.
DOI : 10.1186/1471-2105-8-125

URL : https://hal.archives-ouvertes.fr/lirmm-00193269

. Leitch, Evolution of DNA Amounts Across Land Plants (Embryophyta), Annals of Botany, vol.95, issue.1, p.207217, 2005.
DOI : 10.1093/aob/mci014

. Levinson, . Gutman, G. Levinson, and G. A. Gutman, High frequencies of short frameshifts in poly-ca/tg tandem repeats borne by bacteriophage m13 in escherichia coli k, p.12, 1987.

. Levinson, . Gutman, G. Levinson, and G. A. Gutman, Slipped-strand mispairing : a major mechanism for dna sequence evolution, Mol Biol Evol, vol.4, issue.3, p.20321, 1987.

W. Li, Molecular evolution The origins of genome architecture, 1997.

. Malpertuy, Analysis of Microsatellites in 13 Hemiascomycetous Yeast Species: Mechanisms Involved in Genome Dynamics, Journal of Molecular Evolution, vol.56, issue.6, p.5673041, 2003.
DOI : 10.1007/s00239-002-2447-5

G. Marais, Les eets pervers du sexe sur l'évolution des génomes, 2002.

. Mcgill, Coconversion of anking sequences with homothallic switching, Cell, vol.57, issue.3, p.459467, 1989.

. Messer, . Arndt, P. W. Messer, and P. F. Arndt, The Majority of Recent Short DNA Insertions in the Human Genome Are Tandem Duplications, Molecular Biology and Evolution, vol.24, issue.5, p.11907, 2007.
DOI : 10.1093/molbev/msm035

. Messier, The birth of microsatellites, Nature, vol.381, issue.6582, p.381483, 1996.
DOI : 10.1038/381483a0

. Mikkelsen, Initial sequence of the chimpanzee genome and comparison with the human genome, Nature, issue.7055, p.4376987, 2005.

. Morgulis, WindowMasker: window-based masker for sequenced genomes, Bioinformatics, vol.22, issue.2, p.134141, 2006.
DOI : 10.1093/bioinformatics/bti774

. Moxon, Adaptive evolution of highly mutable loci in pathogenic bacteria, Current Biology, vol.4, issue.1, p.2433, 1994.
DOI : 10.1016/S0960-9822(00)00005-1

C. Nachman, M. W. Nachman, and S. L. Crowell, Estimate of the mutation rate per nucleotide in humans, Genetics, vol.156, issue.1, p.297304, 2000.

. Nadir, Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications., Proceedings of the National Academy of Sciences, vol.93, issue.13, p.9364705, 1996.
DOI : 10.1073/pnas.93.13.6470

. Noor, Evolutionary History of Microsatellites in the Obscura Group of Drosophila, Molecular Biology and Evolution, vol.18, issue.4, p.5516, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003834

. Oakes, A unique conguration of genome-wide dna methylation patterns in the testis, Proc Natl Acad Sci, vol.104, issue.1, p.22833, 2007.

K. Ohta, T. Ohta, and M. Kimura, Model of mutation appropriate to estimate number of electrophoretically detectable alleles in a nite population, Genetical Research, vol.22, issue.2, p.201204, 1973.

C. Orgel, L. E. Orgel, and F. H. Crick, Selsh dna -the ultimate parasite, Nature, issue.5757, p.284604607, 1980.

H. Paques, F. Paques, and J. E. Haber, Multiple pathways of recombination induced by double-strand breaks in saccharomyces cerevisiae, Microbiology and Molecular Biology Reviews, vol.63, issue.2, p.349, 1999.

N. Payseur, B. A. Payseur, and M. W. Nachman, Microsatellite variation and recombination rate in the human genome, Genetics, issue.3, p.15612851298, 2000.

T. D. Petes, Meiotic recombination hot spots and cold spots, Nature Reviews Genetics, vol.97, issue.5, p.3609, 2001.
DOI : 10.1038/35072078

. Podlutsky, Spectrum of point mutations in the coding region of the hypoxanthine- guanine phosphoribosyltransferase (hprt) gene in human T-lymphocytes in vivo, Carcinogenesis, vol.19, issue.4, p.55766, 1998.
DOI : 10.1093/carcin/19.4.557

. Price, Whole-genome analysis of Alu repeat elements reveals complex evolutionary history, Genome Research, vol.14, issue.11, p.14224552, 2004.
DOI : 10.1101/gr.2693004

. Primmer, . Ellegren, C. R. Primmer, and H. Ellegren, Patterns of molecular evolution in avian microsatellites, Molecular Biology and Evolution, vol.15, issue.8, p.159971008, 1998.
DOI : 10.1093/oxfordjournals.molbev.a026015

. Primmer, Directional evolution in germline microsatellite mutations, Nature Genetics, vol.2, issue.4, p.3913, 1996.
DOI : 10.1038/ng0896-391

G. Pupko, T. Pupko, and D. Graur, Evolution of Microsatellites in the Yeast Saccharomyces cerevisiae: Role of Length and Number of Repeated Units, Journal of Molecular Evolution, vol.48, issue.3, p.483136, 1999.
DOI : 10.1007/PL00006474

R. , D. Richard, G. F. Dujon, and B. , Distribution and variability of trinucleotide repeats in the genome of the yeast saccharomyces cerevisiae, Gene, vol.174, issue.1, p.16574, 1996.

R. , D. Richard, G. F. Dujon, and B. , Trinucleotide repeats in yeast, Res Microbiol, vol.148, issue.9, p.73144, 1997.

G. F. Richard and F. Paques, Mini- and microsatellite expansions: the recombination connection, EMBO reports, vol.88, issue.2, p.1226, 2000.
DOI : 10.1093/embo-reports/kvd031

. Rolfsmeier, Mismatch Repair Blocks Expansions of Interrupted Trinucleotide Repeats in Yeast, Molecular Cell, vol.6, issue.6, p.15017, 2000.
DOI : 10.1016/S1097-2765(00)00146-5

. Rolfsmeier, M. L. Lahue-]-rolfsmeier, and R. S. Lahue, Stabilizing Effects of Interruptions on Trinucleotide Repeat Expansions in Saccharomyces cerevisiae, Molecular and Cellular Biology, vol.20, issue.1, pp.173-80, 2000.
DOI : 10.1128/MCB.20.1.173-180.2000

. Rose, O. Falush-]-rose, and D. Falush, A threshold size for microsatellite expansion, Molecular Biology and Evolution, vol.15, issue.5, p.6135, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025964

. Rossi, Evidence for rolling-circle replication in a major satellite dna from the south american rodents of the genus ctenomys, Mol Biol Evol, vol.7, issue.4, p.34050, 1990.

. Rubinsztein, Microsatellite evolutionevidence for directionality and variation in rate between species, Nat Genet, vol.10, issue.3, p.33743, 1995.

. Sainudiin, Microsatellite Mutation Models: Insights From a Comparison of Humans and Chimpanzees, Genetics, vol.168, issue.1, p.38395, 2004.
DOI : 10.1534/genetics.103.022665

. Schug, Mutation and evolution of microsatellites in Drosophila melanogaster, Genetica, pp.102-1031, 1998.
DOI : 10.1007/978-94-011-5210-5_29

. Schug, The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster, Molecular Biology and Evolution, vol.15, issue.12, pp.15175160-163, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025901

. Schug, Low mutation rates of microsatellite loci in Drosophila melanogaster, Nature Genetics, vol.135, issue.1, p.99102, 1997.
DOI : 10.1038/ng0197-99

. Shriver, Vntr allele frequency distributions under the stepwise mutation model : a computer simulation approach, Genetics, vol.134, issue.3, p.98393, 1993.

. Sibly, A maximum-likelihood approach to tting equilibrium models of microsatellite evolution, Molecular Biology and Evolution, vol.18, issue.3, p.413417, 2001.

. Smit, Repeatmasker, 1996.

. Smith, K. N. Smith, and A. Nicolas, Recombination at work for meiosis, Current Opinion in Genetics & Development, vol.8, issue.2, 1998.
DOI : 10.1016/S0959-437X(98)80142-1

. Smith, . Waterman, T. F. Smith, and M. S. Waterman, Identication of common molecular subsequences, J Mol Biol, vol.147, issue.1, p.1957, 1981.

W. Sokol, K. A. Sokol, and C. G. Williams, Evolution of a triplet repeat in a conifer, Genome, vol.48, issue.3, p.4841726, 2005.
DOI : 10.1139/g05-004

W. Stephan, Recombination and the evolution of satellite DNA, Genetical Research, vol.106, issue.03, p.16774, 1986.
DOI : 10.1146/annurev.ge.14.120180.001005

. Strand, Destabilization of tracts of simple repetitive dna in yeast by mutations aecting dna mismatch repair, Nature, issue.6443, p.3652746, 1993.

I. Tachida, H. Tachida, and M. Iizuka, Persistence of repeated sequences that evolve by replication slippage, Genetics, vol.131, issue.2, p.4718, 1992.

D. Tautz, Notes on the denition and nomenclature of tandemly repetitive dna sequences, Exs, vol.67, p.218, 1993.

. Tautz, Cryptic simplicity in DNA is a major source of genetic variation, Nature, vol.2, issue.6080, p.3226526, 1986.
DOI : 10.1038/322652a0

. Taylor, The death of a microsatellite: a phylogenetic perspective on microsatellite interruptions, Molecular Biology and Evolution, vol.16, issue.4, pp.56772-164, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026138

. Toth, Microsatellites in dierent eukaryotic genomes : survey and analysis, Genome Res, issue.7, p.1096781, 2000.

S. Trivedi, Comparison of simple sequence repeats in 19 archaea, Genet Mol Res, vol.5, issue.4, p.74172, 2006.

. Valdes, Allele frequencies at microsatellite loci : the stepwise mutation model revisited, Genetics, issue.3, p.13373749, 1993.

. Volfovsky, A clustering method for repeat analysis in dna sequences, Genome Biol, vol.2, issue.8, p.27, 2001.

A. Vowles, E. J. Vowles, and W. Amos, Evidence for Widespread Convergent Evolution around Human Microsatellites, PLoS Biology, vol.11, issue.8, p.199, 2004.
DOI : 10.1371/journal.pbio.0020199.sg005

A. Vowles, E. J. Vowles, and W. Amos, Quantifying ascertainment bias and species-specic length dierences in human and chimpanzee microsatellites using genome sequences, Mol Biol Evol, vol.23, issue.3, p.598607, 2006.

J. B. Walsh, Persistence of tandem arrays : implications for satellite and simple-sequence dnas, Genetics, vol.115, issue.3, p.55367, 1987.

. Wang, Comparison of bisulfite modification of 5-methyldeoxycytidine and deoxycytidine residues, Nucleic Acids Research, vol.8, issue.20, pp.4777-90, 1980.
DOI : 10.1093/nar/8.20.4777

. Watson, . Crick, J. D. Watson, and F. H. Crick, Molecular structure of nucleic acids ; a structure for deoxyribose nucleic acid, Nature, issue.4356, p.1717378, 1953.

W. Weber, J. L. Weber, and C. Wong, Mutation of human short tandem repeats, Human Molecular Genetics, vol.2, issue.8, p.11231128, 1993.
DOI : 10.1093/hmg/2.8.1123

. Webster, Microsatellite evolution inferred from human- chimpanzee genomic sequence alignments, Proceedings of the National Academy of Sciences of the United States of America, p.9987488753, 2002.
DOI : 10.1073/pnas.122067599

. Wexler, Finding approximate tandem repeats in genomic sequences, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, p.12928942, 2005.
DOI : 10.1145/974614.974644

. Whittaker, Likelihood-based estimation of microsatellite mutation rates, Genetics, vol.164, issue.2, p.781787, 2003.

. Wierdl, Microsatellite instability in yeast : dependence on the length of the microsatellite) :76979. References 1. Consortium IHGS: Initial sequencing and analysis of the Human Genome, Genetics Nature, vol.146, issue.36822, pp.409860-921, 1997.

H. Ellegren, Microsatellites: simple sequences with complex evolution, Nature Reviews Genetics, vol.164, issue.6, pp.435-480, 2004.
DOI : 10.1016/S0379-0738(01)00564-3

A. Benet and G. Molla, d(GAmiddle dotTC)n microsatellite DNA sequences enhance homologous DNA recombination in SV40 minichromosomes, Nucleic Acids Research, vol.28, issue.23, pp.4617-4639, 2000.
DOI : 10.1093/nar/28.23.4617

P. Martin, K. Makepeace, S. Hill, D. Hood, and E. Moxon, Microsatellite instability regulates transcription factor binding and gene expression, Proceedings of the National Academy of Sciences, vol.102, issue.10, pp.3800-3804, 2005.
DOI : 10.1073/pnas.0406805102

E. Moxon, P. Rainey, M. Nowak, and R. Lenski, Adaptive evolution of highly mutable loci in pathogenic bacteria, Current Biology, vol.4, issue.1, pp.24-33, 1994.
DOI : 10.1016/S0960-9822(00)00005-1

M. Mitas, Trinucleotide repeats associated with human disease, Nucleic Acids Research, vol.25, issue.12, pp.2245-54, 1997.
DOI : 10.1093/nar/25.12.2245

I. Arzimanoglou, F. Gilbert, and H. Barber, Microsatellite instability in human solid tumors, Cancer, vol.55, issue.10, pp.1808-1828, 1998.
DOI : 10.1002/(SICI)1097-0142(19980515)82:10<1808::AID-CNCR2>3.0.CO;2-J

P. Jarne and P. Lagoda, Microsatellites, from molecules to populations and back, Trends in Ecology & Evolution, vol.11, issue.10, pp.424-433, 1996.
DOI : 10.1016/0169-5347(96)10049-5

B. Harr and C. Schlötterer, Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide underrepresentation, Genetics, vol.155, issue.3, pp.1213-1233, 2000.

J. Jurka and C. Pethiyagoda, Simple repetitive DNA sequences from primates: Compilation and analysis, Journal of Molecular Evolution, vol.46, issue.2
DOI : 10.1007/BF00167107

T. Pupko and D. Graur, Evolution of Microsatellites in the Yeast Saccharomyces cerevisiae: Role of Length and Number of Repeated Units, Journal of Molecular Evolution, vol.48, issue.3, pp.313-319, 1999.
DOI : 10.1007/PL00006474

M. Katti, P. Ranjekar, and V. Gupta, Differential Distribution of Simple Sequence Repeats in Eukaryotic Genome Sequences, Molecular Biology and Evolution, vol.18, issue.7, pp.1161-1168, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003903

S. Kruglyak, R. Durrett, M. Schug, and C. Aquadro, Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations, Proceedings of the National Academy of Sciences, vol.95, issue.18, pp.9510774-9510782, 1998.
DOI : 10.1073/pnas.95.18.10774

D. Dieringer and C. Schlötterer, Two distinct modes of microsatellite mutation processes: evidence from the complete 40 Rivals E: A Survey on Algorithmic Aspects of Tandem Repeats Evolution, International J of Foundations of Computer Science, vol.15, issue.2, pp.225-257, 2004.

E. Rivals and G. Kucherov, Algorithmes d'analyse de séquences en bioinformatique Périodicité et répétitions Université Montpellier II Finding approximate repetitions under Hamming distance, Theor Comp, vol.303, pp.135-56, 2003.

V. Fischetti, G. Landau, P. Sellers, and J. Schmidt, Identifying periodic occurences of a template with applications to protein structure, Information Processing Letters, vol.45, issue.1, pp.11-18, 1993.
DOI : 10.1016/0020-0190(93)90245-5

T. Smith and M. Waterman, Identification of common molecular subsequences, Journal of Molecular Biology, vol.147, issue.1, pp.195-202, 1981.
DOI : 10.1016/0022-2836(81)90087-5

J. Jurka, Repbase Update: a database and an electronic journal of repetitive elements, Trends in Genetics, vol.16, issue.9, pp.9418-9438, 2000.
DOI : 10.1016/S0168-9525(00)02093-X

E. Rivals, M. Dauchet, J. Delahaye, and O. Delgrange, Compression and genetic sequence analysis, Biochimie, vol.78, issue.5, pp.315-337, 1996.
DOI : 10.1016/0300-9084(96)84763-8

M. Morgante, M. Hanafey, and W. Powell, Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes, Nature Genetics, vol.30, issue.2
DOI : 10.1038/ng822

A. Goffeau, B. Barrell, H. Bussey, R. Davis, B. Dujon et al., Life with 6000 Genes, Science, vol.274, issue.5287, pp.2751051-2751053, 1997.
DOI : 10.1126/science.274.5287.546

J. Galagan, The genome sequence of the filamentous fungus Neurospora crassa, Nature, vol.422, issue.6934, pp.859-68, 2003.
DOI : 10.1038/nature01554

M. Adams, S. Celniker, R. Holt, C. Evans, and G. Jea, The Genome Sequence of Drosophila melanogaster, Science, vol.287, issue.5461, pp.2185-95, 2000.
DOI : 10.1126/science.287.5461.2185

R. Sokal and F. Rohlf, Biometry : the principles and practice of statistics in biological research W.H. Freeman, 1995.