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1 = (% style="color: rgb(0,51,102);" %)Statistical population genetics, Spring 2016(%%) =
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6 **Teacher:** (% style="color: rgb(0,0,255);" %)[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Sirkka-Liisa Varvio>>doc:mathstatHenkilokunta.Varvio, Sirkka-Liisa]](%%)
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8 **Scope:** 5-10 cr, this means that a student can take either 5 cr or 10 cr
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10 **Type and prerequisites:** Intermediate / advanced studies in statistics. For other students: background from at least basic probability calculus and statistical inference courses needed.
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12 **Teaching: **The course consists of lectures, discussions, tutorials during computer sessions, assignments initiated during the sessions and completed during student´s own, additional, time. The spirit of the course is  learning by doing: data-analysis, exercises by pen-and-paper, simulations and reading scientific papers, rather than listening lectures.
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14 **Time schedule: **Period III, Thursdays 14-19 in computer class C128, Exactum, Kumpula is a 5 cr module. Each session will start by a (~~2 hours) lecture and/or tutorial for assignments. Another 5 cr module in period IV, time schedule will be negotiated during the III-period**.**
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16 **Passing the course:
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19 * Weekly assignment sets / home-exercise sets. You can perform these so that you form groups of 2-4 students.
20 * Three assignment sets will be pen-and-paper exercises, including some simulations and literature references, getting familiar with scientific articles, one is a data-analysis exercise. There is also to possibility write an essay instead of data-analysis.
21 * Home-exam will be given 3. March and answer submission (to Moodle) deadline will be 14. March.
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28 === (% style="color: rgb(0,0,255);" %)//[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)STAGE_MOODLE>>url:https://moodle.helsinki.fi/course/view.php?id=19624||shape="rect"]]//(%%) ===
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31 (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)This is course working area for assignment solutions and reports, discussions, questions, etc.  The link (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(255, 0, 0)" %)is now open.(% style="color: rgb(0,51,102);" %)
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37 (% style="color: rgb(0,51,102);" %)**Week 1**
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39 * (% style="color: rgb(0,51,102);" %)**Topic: **P(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)robability calculus and basic statistics applied on genetic problems
40 * (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102)" %)**Lecture material including the first assignment set: **(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 0, 255)" %)//[[(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Basic concepts: Probability, inheritance, population genetics>>attach:Basic concepts_ Probability inheritance population genetics.pdf]]//**
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42 * (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)//[[(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Link to a simple simulation program>>url:http://www.radford.edu/%7Ersheehy/Gen_flash/popgen/||shape="rect"]]//
43 * (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102)" %)**Background literature: **(% style="color: rgb(0,0,255);" %)__
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45 ** (% style="color: rgb(0,0,255);" %)//[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)A century of Hardy Weinberg equilibrium>>attach:mathstatKurssit.Biometry and bioinformatics III, spring 2014.WebHome@A century of Hardy Weinberg equilibrium.pdf]]//(%%)//,
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47 ** (% style="color: rgb(0,0,255);" %)// [[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)LD_understanding the evolutionary past and mapping the medical future>>attach:mathstatKurssit.Biometry and bioinformatics III, spring 2014.WebHome@LD_understanding the evolutionary past and mapping the medical future.pdf]]//(%%)//[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %) >>url:http://www.radford.edu/~~rsheehy/Gen_flash/popgen/||shape="rect"]]//(%%)
48 (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)**
49 **
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53 **~ (% style="color: rgb(0,51,102);" %)Week 2(%%)**
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55 * **Topic:**(% style="color: rgb(0,51,102);" %)  (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)Classical population genetics - selection, mutations, drift are the evolutionary factors in terms of population genetics. How has the understanding of genetic polymorphisms evolved, introduction to (human) genetic polymorphisms
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57 * **Lecture material including the second assignment set: **(% style="color: rgb(0,0,255);" %)//[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Modelling selection, mutation, drift>>attach:Modelling selection, mutation, drift.pdf]]//(%%)//**
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59 * **Background literature:**(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 255)" %)// [[(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %) >>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Revising human mutation rate, understanding human evolution.pdf]]//
60 ** (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 255)" %)//[[(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Revising human mutation rate, understanding human evolution>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Revising human mutation rate, understanding human evolution.pdf]]//(%%)//[[(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %),>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Human genomic disease variants, A neutral evolutionary explanation.pdf]]//
61 ** (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 255)" %)//[[(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Human genomic disease variants, A neutral evolutionary explanation>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Human genomic disease variants, A neutral evolutionary explanation.pdf]]//
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65 **~ (% style="color: rgb(0,51,102);" %)Week 3(%%)**(% style="color: rgb(0,51,102);" %) (% style="color: rgb(0,0,0);" %)
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67 * (% style="color: rgb(0,0,0);" %)**Topic: **Coalescence theory in population genetics: relating theory to data. 
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69 * (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %) (% style="color: rgb(0,51,102);" %)**Lecture material and assignment set 3:  **(% style="color: rgb(0,0,255);" %)//[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Coalescence theory and selection tests,>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Coalescence theory and selection tests.pdf]]//(%%)// [[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)An illustrative guest lecture on coalescence>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@An illustrative guest lecture on coalescence.pdf]](%%), [[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Assignment set 3>>attach:Assignment set 3.pdf]](%%)
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71 * (% style="color: rgb(0,51,102);" %)**Background literature:**
72 ** (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 255)" %)//[[(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Kingman´s Coalescence paper>>attach:mathstatKurssit.Biometry and bioinformatics III, spring 2014.WebHome@Kingman´s Coalescence paper.pdf]]//
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76 **~ (% style="color: rgb(0,51,102);" %)Weeks 4(%%)**(% style="color: rgb(0,51,102);" %), **5**
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78 (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)There will not be a session 18. Feb. and there is more information in Moodle! To compensate this, there will be sessions Mon 22. Feb. 12-14, Wed 24. Feb. 12-14 and Thu 25. Feb 14-18. These sessions will not include any lectures, just practical advise for those who want to come. You can also ask for help by Moodle, or by email (sirkka-liisa.varvio at helsinki.fi)
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81 * (% style="color: rgb(0,51,102);" %)**Choose one assignment. **(% style="color: rgb(0,0,0);" %)4.1. and 4.2. are data-analysis assignments, by using the software (% style="color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 51, 102); color: rgb(0, 0, 255)" %)[[(% style="color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)DnaSP 5.10.1>>url:http://http//www.ub.edu/dnasp/||shape="rect"]](%%) ((% style="color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 0); color: rgb(0, 0, 255)" %)[[(% style="color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Manual)>>attach:mathstatKurssit.Biometry and bioinformatics III, spring 2014.WebHome@DnaSP Manual.pdf]](% style="color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 0)" %) to get familiar with  polymorphisms (% style="color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 51, 102); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 0)" %)as well as some key concepts. If you don´t want to do practical data-analysis, choose 4.3. and write an essay. (% style="color: rgb(0,51,102);" %)** **(%%)
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83 * (% style="color: rgb(0,0,255);" %)//**[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Assignment 4.1.>>attach:Assignment 4.1.pdf]](%%)**//(%%)//** **//(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)
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88 (% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %) (% style="color: rgb(0,0,255);" %)[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)HLA_DRB1_freqtable.xlsx>>attach:mathstatKurssit.Biometry and bioinformatics III, spring 2014.WebHome@HLA_DRB1_freqtable.xlsx]](%%) , [[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)HLA_DRB1_alleles.txt>>attach:mathstatKurssit.Biometry and bioinformatics III, spring 2014.WebHome@HLA_DRB1_alleles.txt]](%%)  (% style="color: rgb(0, 0, 255); color: rgb(0, 0, 0)" %)(Note that you don´t need these two files as the population sample files are ready for analyses)
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90 *** (% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %) (% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255)" %)[[(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Czech.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Czech.txt]](% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %),  [[(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Portug.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Portug.txt]](%%), [[(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Swed.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Swed.txt]](%%), [[(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Bari.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Bari.txt]](%%), [[(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Chile.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Chile.txt]](%%), [[(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Xavant.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Xavant.txt]](%%), [[(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Camero.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Camero.txt]](%%), [[(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Oromo.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Oromo.txt]](%%), [[(% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Pygmi.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Pygmi.txt]]
91 * (% style="color: rgb(0,0,255);" %)//**[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Assignment 4.2.>>attach:Assignment 4.2.pdf]](%%)**//
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93 *** (% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %) (% style="color: rgb(0,0,255);" %)[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)USA_before_vacc.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@USA_before_vacc.txt]](%%), [[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)USA_after_vacc.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@USA_after_vacc.txt]](%%), [[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Skand_before_vacc.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Skand_before_vacc.txt]](%%), [[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Skand_after_vacc.txt>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Skand_after_vacc.txt]](% style="color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 0); color: rgb(0, 0, 255)" %)
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97 * (% style="color: rgb(0,0,255);" %)//[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Natural selection and infectious diseases in human populations>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Natural selection and infectious diseases in human populations.pdf]]//
98 * (% style="color: rgb(0,0,255);" %)//[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Recent human adaptation, genomic approaches, interpretations and insights>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Recent human adaptation, genomic approaches, interpretations and insights.pdf]]//
99 * (% style="color: rgb(0,0,255);" %)//[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans.pdf]]//
100 * (% style="color: rgb(0,0,255);" %)//[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Molecular sprandels, tests of adaptation at the genetic level>>attach:mathstatKurssit.Statistical genetics, spring 2015.WebHome@Molecular sprandels, tests of adaptation at the genetic level.pdf]]//
101 * (% style="color: rgb(0,0,255);" %)//[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Selective sweeps in dogs>>attach:Dog_PNAS-2016-Marsden-152-7.pdf]]//
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109 **~ (% style="color: rgb(0,51,102);" %)Week 6(%%)**(% style="color: rgb(0,51,102);" %)
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111 * (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)Home-exam will be given in March 4., deadline for submitting the answers March 14.(% style="color: rgb(0,51,102);" %)
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116 **~ (% style="color: rgb(0,51,102);" %)Period IV, the other 5 cr part of the course(%%)**(% style="color: rgb(0,51,102);" %)
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122 == (% style="color: rgb(0,0,255);" %)[[(% style="color: rgb(0, 0, 255); color: rgb(0, 0, 255)" %)Registration>>url:https://oodi-www.it.helsinki.fi/hy/opintjakstied.jsp?html=1&Tunniste=57734||shape="rect"]](%%) ==
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125  (% style="color: rgb(96,96,96);" %)Did you forget to register? (%%)[[What to do?>>url:https://wiki.helsinki.fi/display/mathstatOpiskelu/Kysymys4||style="text-decoration: underline;" shape="rect"]]
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