Molecular marker technology has changed our view of the genome. While we have been able to construct crosses and monitor linkage for nearly a century, now we have the unprecedented ability to routinely monitor segregation at an effectively unlimited number of loci in any reasonably designed population. RFLPs, AFLPs, microsatellites, STSs, SCARs and RAPDs are now routinely used to monitor genome-wide linkage disequilibrium. Since it became possible to scan an entire genome, it has become routine to compile enormous segregation datasets. These huge datasets then demanded analysis. Doing two point tests by hand became a lost art.
Below is a genetics dataset derived by the North American Barley Genome Mapping Project. The dataset is formatted to run under Mapmaker and Mapmaker/QTL. The top line describes the type of population being analyzed (in this case a simple backcross population). The structure of the dataset is described in the second line. In this case, there are 150 individuals in the population which have been assayed for genotype at 435 loci. At the end of the dataset are appended 20 trait datasets. In each of these a phenotypic value is assigned to each of the 150 doubled haploids used in this experiment.
data type f2 backcross150 435 20 0 symbols A=A B=H
*Nar1 ABBBAABBABBABBBBBBABAABAABABBABAABA AAABAABABBAABBBBBAAABBABABABBBAABABABBAAABBBBAAAAABABAA BABABAAAAAAAAAA AABBABABBAABBBABAABBBBABBAAABBBBBBA BAAAABABAA
*Ale BABBAAABBABBAAAAABBAAABAAABAAAABBBAABAAABBBBBBAAAAA---- ----ABABBAAAABBAABAAAB-AABBBABBBBAAAABAAAAAAB-BBAAAAAAB BABBBBAABABAAABBBABAABAAAAAABBBABBABBBAB
*Dhn6 AAABAAAABBAA-ABBBBBABABAAABAAAABBABBBBBAABBBABBBA--ABAB ABABBAAABABBBAABAAAB ABABAAAAAAABAAABABBAABABA BAABABAABAAAABBBAAABAAAAA BAABBAAABBBBBBABABBBBAAAB
*Nar7 AABBAAAAAAABBBAAAAABBBBBBABBBBAABBBABBAAAAAAA ABBBA ---------ABAAAAAABBBABBABABBBABAAABAAABBBAABBABBABABAB BBAAAABABBAABBABAAABA BBABAAABBBBBABBABBABBAABB
*Glx ABBBBBAABBAA--BABABABAABABAAABAAAABBBABABAAAABBBBABAAAA ABABBABBABBBBBBBBBABBABAAABBABAAABBAAABAAAAAABAAAAABBAA ABBBAABBABBBBAABAABBABABBBBBBBAABABBBAB-
*ABC451 AAABABAABBABABABABAAAAAAABBAABBBAAAABAABBBBAAAABABAAAABABAABAB-ABABBBABBBABBABA-AAABAABABBAABABABBBABAABBB-AAAB ABAA--AAABABAAABBABBABA-ABAAAAABABBAAAB
*ABG452 BAAAAABABB-BABBAABAAABBABAABABABABBBBBBBABBAAAAABABBBBB BABABAABBBBBBBBBABBABBBA-AABAABAABABABBABBBBBAAAABB-BBAA AAAB--BBABAAAABB-ABBBBB-AAABBBBABBBABAB
*ABG453 ABABAABBABBABBAABBABAABBAABABABABBABABBBABBABAABABAAAAB AAAABBABAAABAAABBBAABBBAAAABB-ABABABBBBABABBABAABBBBAABB AAAAAAABBBBABBBABABBBBBABBBBAABABABAABB
*ABC454 BAABAB-AABABABABBABAAAABBBBAAABBAAAABABBBBBAAAAAABAAAAB ABBBAABAABABBBBBAAAAAABAAAAABBABABBBABABABBBBBBBBBBAAAAB ABAAAAABABAAABAABBBBABAABBAAAAABABBAAAA
*ABC455 AAAABABABAABBAABAABBBBBAAAAAABAABABABBBABBBAABAABAAAABB ABBBAAABABBBBA-AABBBAAAABAAAA-BBABAAAAA-AAABABABABBAAAAB BBBBAAAAAAABAABABBABBABAA-BABBAAB-AABBA
*PSR128 BABBAAABBABAAAAAABBAAABBAABAAAABBBAABAAAABABBBAAAAAABAA ABAABBB-BAAAABBBABAAABBABBBBABABBAABABAAAAAABBBAAAAABABB ABBABAABAAAABBBBABAABAAABAABBBABB-B-BAB
*PSR156 ABAAABBBABBBAABABBABAAABBABABBBABBABABBBBBBABABBABAAAAA BABABBAAAABBABABBBAABBBAAAAABAABABABBBBABABBABAABBBBAAAB AAABAAABBBBABBBABABBBBAABABAAABAB-BABBB
*ABG458 ABBBBBBAABBABBBAAB-BBBB-BABBABAABBBAABABBAAAAAABAAAABBA ABBAABA-BBAAABBABBABAABBAAAA-BAAABBB-ABBAABBBAAAABBAABAB ABBBAAABAAABBABBBAAAABABBBBBBABAABBAABB
*ABG459 BAABABBABBABABABBABAAAA-BBBAAABBAAAAAABBBBBBAAAABBAAAAB ABBBAABAABABBBBBAAAABABAAAAABBABABBBABABBABBBABBBBBAAAAB ABAAAAAAABAAABAABBBAABAABBAAAAABABBAAAA
*ABG460 ABAABBBAABAAAABBBAABBABBBABBBBABBBBBABABBBBABABBBAAAAAB AABAABB-AAABABAABBAABABB-AABBBABBBAAABBABAAABBAABBB-ABAB ABAB--AABBBABBBBBABBAAB-BBBAAABBBABAABA
*Prx2 AAABBAA-AA-B--ABA-B-BBAABAAAAABABBAAAAAAAAABBAAABBABAAB ABBABAABAAAAAAAAAABAAABAABAABBAABABBBABAABBBBBAAAAAABAAA BAAABAAABBBBBBAABBBABABAAABBBAABBAAABBA
*Brz ABBABBB-BA-B-BABAABABBABAAAABBAABABABBBABBAAABBABAAAABB ABABBABBABBBBABABBABBA--AA-BABBBAB-AAABAAAABBB-B-BBBBAA BBBBBAAAAABBBAABAABBABABBBBBBBBABB-AAB--
*iEst5 ABBBBBAABBAAAABABABABAABABAA-BAAAABBBABABA---BB-BABAAAA ABABBABBABBBBBBBBBABBABBAABBABAAAB-AAABAAAAAABAAAAABBAAA BBBAABBABBBBAABAAB-ABABBBBBBBAABABBBABB
*iEst9 BBBAAAABBABBBABABBBBAAABBBAAAABBBBBAAABBBBAABAAABBAAABB ABABAAABAABABBABBAABABBBBAABABBBABABBBBBAAABBBAABAABBABB ABBBBBBBABABAABBAAABABABAABAAABBAABBBBA
*iPgd2 BABBBBBAABBBABBBBABBAABBBAABAAAAAABBAABAABAABABABABABAB AABABBABAABAAAABBAABBBBBBABBAABBABABABBBAABABBBBABBABABA BABABAABABBBBABABBBBBAAABAAAABBAAAAAAAA
*RbcS BAABABAABBBABBABBABBAABBBBBABABBBAAAAABBBBBBAABABBAAAAB ABBBAAAAABABABBAAAAABA-BAABABAABAABAABABBABBBABBBBABBBAA BBAAAAAAABAAABAABBBAABAABAAAAAABABBBBAA
*Bmy1 ABBBBAB------AA------BABBBABBBBABBBABABABABABBABAAABBBB AABBBABAAAABABBBABABAAAAABAAAABBBAAABAAAAAABBBBAABBAAAA ABBAAABBBAABABABAAABABBBBBBBBBBABBBABAA-
*Bmy2 BAA-ABA------BA------AAA--BAAABBAABABAABBBBAAAABABAAAAB AB--BABBABABABBBBAABAA-A---ABBABABBAABABABBBABABBBBAAA- BABAAAAAAABAAAAAABABBABAABBABAAABABBAAA-
*Amy1 AABBAAAA-----BAAAAABBBBBBABABBAABBBABBAAAABABABBBAAABAB BBBAABAAAAABBBBABBABAB-BABAAABAAAABBAABBABBAB-BABB-A-A-B ABB-ABBABAAABABBABAAABBBBBBBBABBABBAAB-
*Lth ABB-AAB-A-----BBBBBBAABAABABBABAABAAAABAABABBAABBBBBAAA BBABABABBBBBBABABBAA-----AAAAABA-AABABA-AAAA-A-AAAABBBA AABBAAB-BABAAB-BBABBABABBABBBABA-BABABA-
*ABC302 BABBAAABBABAAAAAABBAAABBAABAAAABBBAABAAAABABBBAAAAAABAA ABAABBBBBAAAABBBABAAABBAABBBABABBAABABAAAAAABBBBAAAABA-B ABBABAABAAAABBBBABAABAAABAABBBABBABBBAB
*PSR167B AB-BB-B-------B-A-ABBBBBBABBABAAB-BAABABBAAAAAABAAAABBA ABBAABAABBAABBBABBAAAA---AAAABAA-BBBAAB-AABBB-AAAB-A-B-B ABB-AAABAAABB-BBBAAAABABBBB-BABAABBAAB-
*PSR167 ABBBAAB------BB---BBAABAABABBABAA-AAAABAABABBAABBBBBAAA BBABABABBBBBBABABBAAAB---AAAAABA-AABABABAAAAAABAAA-B-B-A ABB-AB-BABAAB-BBABBABABBABB-ABA-BABABA-
*Hor1 ABABAABABB-BBBBAABBBABABBAAABBABAAABABBBABAABABBAABABBB BABBBABBBAAAAABBBBABABBABABBAABBAAABBBBBABBBAAABABBBBBAA ABBBBAABAABAABBBAAAAAAAAAABABABBBAABBAA
*Hor2 ABABBABA-B-BBBBA-BBBABABBAAABBAAAAABAABABBAABABBAAAABAA BABABABBBAAAAABBBBABAB-ABAB-BABBAABBBBBBABBB-BABABBBBBAA ABBBAAABBABAABBBABAAAAAAAABABABBBAABBA-
*Ubi1 AAB-BAB----B-A-AA--BBBBAAABBABAABABAABBABBBBABBABAAAABB AABBBAABABBBBAABABBBBAA-BBAAABBBABAAAAAABAAAABABBBBAAABB BBBA-AAAAAABA-BABAABBAAABBABBAAABAAABA-
*PSR154 AA--A---------A----ABBAAB--ABAABA-BABAAAAABABAABBAAABAB BBBBABAAAAABABBABBBBAB--BBAAAAAAAAABAABBABBBAABABBBBBAA BABBAABBABAAABABBABAAABBBBBBBAABBAABAABB
*Ica1 B-AAA-----ABBBAAA-AAABBBBAABBBABAABBBBBBABAABAABBABBBBB BABBBAABBBBBAABBABBBBBBAAABBAABBABABABBABBBBAAABABBBBBA AABABBBBBABAAABBBAABBBBBAAABABBBBBBBABAA
*Cxp3 ABBBAAB-AB-A-BBBBBABAABBAA-B-BBAA--AAAABABABBAABB--BAAA ABAAABABBBAABABBBBAAAB---AAAAAAAAAABABBBAABBBAAAAAAA-BAB ABBAA---ABABBABBABBAABBBBBBBAAAAABBABA-
*Ltp1 BABBAAA-AAABAAAAAABAAABBABBABAABBBAABAAABBBBBAAAABAABAA BAAAAAAABBAAAAABAABABABBAABBBBBBBBAAAABAAABAABABBAAAAAAB ABBBBAABABAAABBBABAABAAAAAABBAAABAABBAB
*Prx1A A-BBBBA----A-ABAB---BAABA-AAABAAA-BBBAB-BAAAABBBBABAAAA ABABBABBABBBBABBBBABBA-AAABBABAA-BBAAABAAAAAA-AAAA-B-A-A BBB--BBABBBBAABAABBABABBBBB-BAA-ABBBAB-
*ABG312 BBBBBB-A--A-AA--B---BAB--B-AABAAAABBBBB-BAAAABBBBABBAAA ABABBABB-BBBBBBBBBAAABABAABBABA--BBAABB-BAAA-BAAB-ABBBAA BBBAA-BAABB---BAABBAB-BBB-AABAABAABBABB
*mSrh BABAAAABBABABAAABBBBAAABABBAAAABABAABAABAAAAABAAABAAAAA ABABABBBBAAAAAABAAAAABBBABABABBBBAABABABAAABBBBBAABBBABB ABBABAABAAAABBBBABAABAAAABABBBABBABBAAA
*mPub AAABAAAABBBABBAABBAAAAAAAABAAABBBBABAAABBBBABAAAABABABB BAAABBBBAAAABAAAAABABBBBBBBBBAABBBAABBBAABBBABBBABAAABBA BBAABBBAABAABABBBAAAABBBABABBABAABBBAAB
*PSR106 ABBBBABA-BBABBBAABABAABBBABBBBAABBBABAABABABAAABBABBBAA ABAAABAABBAABABBBBAAABBBAAAAAAAAABBBAABBAABBBAAAABBAABAB ABBBAAABABABBABBBBAAABABBBBBBABAABBABBB
*PSR106B ABBBBA-B-BABBBB-A-BBBBBBB-BAAB-ABABBABBBBBBBBBBABBABBAB BBBBAAAABBAABAABAAAAAABBBBAAAABAABAABBBBBAABAAAAABAABBA A BBBAAA-ABBBBABABAAAAABBABBBBBAAABBAABAB
*ksuA3A BABBAAA-AAABAAAAAABAAABBABBABAABBBAABAAABBBBBAAAABAABAA AAAAAAABBAAAAABAABABABBA-BBBBBBBBAAAABAAABAABABBAAAAAABB ABBBBAABABAAABBBABAABAAAAAABBAAABAABBAB
*ksuA3B ABBBABB-AABBBBAAABABBBBBBABBABAABBBAABABBAAAAAABAAAABBA BBBAABAABBAABBBABBAAAABBABAAABAAABBBAABBAABB-AAAABBAAAAB ABBBAAABAAABBABBBAAAABABBBABBABAABAAABB
*ksuA3C BBBAABB--BAAAABABBABBBABBABABBBABBABBBABBBBABABBBAAAAAA BABABBBAAABBABABBBAABABAAA-ABAABABABABBABAABABAABBBBABAB ABABAAAABBBABBBBBBBBBAAABABAAABABABABBB
*ksuA3D ---BAA--AAABBBA-A--BBABB-ABBBBAABBBAABAAAAAAAAA--AAABAA BBBAABAABBAABBBABBABA----B-AAB-B-BBB-AB-ABBABABABBBA-AAB ABBAAA-AAAAAB-BB-BAAABBB-BABBA-AABAAABB
*ksuD17 ABBBA----------------ABBBABBBBA---B-ABAABAAAAAABBAAAB BABBBAABAABBAABBBABBABABBBABAAABABABBBAABBAABABAAAABBAAA ABABBAAAAAAAABBABBBAAAABABBBABBABAABAAABB
*Cab1 ABAAAAABAABB-ABABBBBAAABBBAABBBABBBAAABBBAABBABABBAAABB AAABAAABAABABBBBABABABBBBAABAABBABABBBBBAABABBAA-AABBABA ABBBBAABABABAABBBBABABBBBABAAABBAABBBB-
*Cab2 AABBBBA-B--B-BABBBBBABBBB-BB------BBBBBBAAAABAAABAAAAAB AABABBBAAABAAAABBAABB---BBBBAAABAB-B-BBBA-BABB-A-BBABABA BBAA-BBBAABBA-BABABBAAAABAAAABB-AA-AA--
*ABC307A BAAAABBAABBBABBBBABBAABBBAABAAABBBBABBBAABAABABABABABAB AABABBABAABBABAAAABBBBBABABBAABBABABABBAABBABBBBAABABAAA BABABAABABAABABABBBBBAABBAAAABBABAAAAAA
*ABC307B ABABA--B-BBAB-ABBBABAABB-ABA--BABBABABABABBABAAAABABAAB AAAABBABAAABAAABBBAABBBAAAABBAABABAABBB-BABAABAABBB-AABB BAAAAA-BABA-BBBABAAABBBABABB-BBABABAABB
*ksuH11 -BBBB---------------BBAB-BABBBBABBBABABABABABBABA-ABB BBAABBB-BA-AABABBA-BABAAAAABAAAABBBAAABAAAAAAB--BAABBAAA ABBBAAA-BBAABABABAAABAB-BBBBBBBBABBBABAAA
*WG420 ABBBBABBABABBAABAABBBBBBBABAABBABABBABBBBBABBBBABA-BBAB B-BBBAABABBBBA-BAAA-AABABBBAAABBABAABAAABAAAABAABBAAAAAA BBBABAAAABBBABBBAAABBBBABBBBBAAABBAABAB
*CDO475 A--BBBB------AA-BA-AAAABAAAAABAAABBBBABABAAAABBABABAAAA BBABBABBABBBAABBBBABBA-----B-BAA-BBAAABAAAAAA-AAAAABBA-A BBB--B-ABBBBA-BAABBABABBBBBBB-ABABBBBB-
*BCD351e BABAAAABBABA-AAABBBBAAABABBAAAABABAABABBAAAAABAAABAAAAA AB-BA-B--AAAA---AAA-AB-BBBABABBBBAABABABAAABBBBBAABBBABB ABBABAABAAAABBBBABAABAAAABABBBABBABBAAA
*BCD351F BAABABAABBBABBABBABBAABBBBBABABBBAAAAABBBBBBAABABBAAAAB ABBBAABAABABAB-AAAABBABBAABABAA-AABAABABB-BBBABBBBAABAAA BBAAAAAAABAAABAABBBAABAABAAAA-ABABBBB--
*BCD351C BAAAAABABBABABBAABAAABBABAABABABABBBBBBBABBAAAAABABBBBB BABABAABBBBBAB-BABBBBBBAAAABAABAABABABBABBBBBAAAABBABBAA AAABBBBBABAAAABBBABBBBBBAAABBBBABBBABAB
*BCD351D AAABAAAABBAAB-BBBBAABAAABABAAAABBAABBABBABBBABBBBBBABAA ABABBBABAABBBA-BABABABBBAABAAAABAAABABBAABABABAABBBAABBA AABBBAAABAABAABAABAAAABBBBBBABABABAAAAA
*WG789A ABBBBBBABBAAAAAABABAAAABAAAAABAAABBBBABABAAAABBBB-BAAAA BBABBABBABBBBABBBBABBABAAABBABAAABBAAABAAAAAABAAAAABBAAA BBBAABBABBBBAABAABBABABBBBBBBAABABBBBBB
*WG789B BAAAAABABBABABBAABAAABBABAABABABABBBBBBBABBAAAAAB-BBBBB BABABAABBBBBABBBABBBBBBAAAABAABAABABABBABBBBBAAAABBABBAA AAABBBBBABAAAABBBABBBBBBAAABBBBABBBABAB
*BCD828 BBBAABBBABAAAAB-BB-BBBABBABABBBABBABBBABBBBABABBBAAAAAA BABABBBAAABBABABBBAABBBAAAAABAABABABABBABAABABAABBBBAAAB ABABAAAABBBABBBBBBBBBAAABABAAABABABABBB
*Gln2 AAABABBBAABAABBBABBABAABBBAAABBABBAABAABAABBAAAAABBBAAB BBABAABAAAAAAAABABAABA-ABAABBABBAABBAAAABBBBBBAAAAAAABAA AAAABAABBBBBABAABBBAAAAAAAABBAABBAAAABB
*BCD298B ABBBBAABABABBABBAABBBBBBBBBAABBABABBABBBB-BBBBBABBABBAB BBBBAAAABBAABAABAAAAAABBBBAAAABAABAABBBBBAABAAA-ABAABBAA BBBAAAAABBBBABABAAAAABBABBBBBAAABBAABAB
*Chs1A BAABAAA----A-BA--------BBBBABABB-AAAAABBBBBBAABABAAAAAB ABBBABAAABAAABBAAAAABABBAA-ABAAB-A-AAAABAABBBABBBBABAB- ABBAABBBAAABBABABBBBAABAABAAAB-ABAABBBA-
*Chs1b BAABAAA----A-BA--------BBBBABABB-AAAAABBBBBBAABABAAAAAB ABBBBBAAABAAABBAAAAABABBAA-ABAAB-A-AAAABAABBBABBBBABAB- ABBAABBBAAABBABABBBBAABAABAAAB-ABAABBBA-
*Chs3 --ABAAB------BB--------BB-AABBAB-AABABBBAB--BABBAABABBB BABBBABBBAAAAABBBBABABBA-A-B-ABB-A-BBBBBA--BAAAB-BBBBB- AABBBBAABAABAABBBAAAAAAAAAABABA--BA-BBA-
*ABC305 ABBBBABAABABBABAAABBBBBAAABBABBABABAABBABBBBBBBABAABAAB AABBBAABABBBBAABAABAAAAABBBAABBBABAAAAAABAAAABABBBBAAABA BBBABAAAABBBABBBAAABBBAABBABBAAABBAABAA
*ksuA1A ABBABBB-BBABAABAAABAABABAAAABBAABBBBBABABAAAABBABAAAAAB BBABBABBABBBAABABBABBABAAABBABBBABBAAABAAAAABBABAABBBAAB BBBBAAAAABBBAABAABBABABBBBBBBBABBBBBBBB
*ksuA1B B-BAA---BABABAA-B-B- AAABABBAAAABABAABAABAAAAABAAABAAAAAABABABBBBAAAAAABAAAA ABBBABABABB-BAABABABAAABBBBBAABBBABBABBABAABAAAABBBBABA ABAAAABABBBABBABBAAA
*His3A ABBBBBA-BB-A--BABABABAABABAAABAAABBBBABABAAAABBBBABAAAA ABABBABBABBBBABBBBABBA-AAABBABAAABBAAABAAAAA-BAAAA-BBAAA BBBAABBABBBBA-BAABBABABBBBBBBAABABBBAB-
*Pgk2A AAAAAAB-BB-A-ABBBA-ABABAAABAAAABBABBBBBAABBBABBBABBABAB ABABBAAABABBAAABAAABAAAB-A-AAABB-A-BABBAABABBBAABABAABAA AABBBAAABAABAABAABBAAABBBBBBABABBBBBAA-
*Pgk2B ABBBBAB--B-B-AAB---BBBBAAABBABBABABAABBABBBBBBBABAABABB AABBBAABABBBBAABAABAAAAA---AABBB-B-AAAAABAAAABABBBBAAABA BBBABAAAABBBA-BBAAABBBAABBABB-AABAAABA-
*ksuD22 AAAAABBBABAAAABBABAABAABBBBABBBBABAABABBABABAAABABABAAB BBABAABAAAABABABABABBAAABAABBABBAABBAAABBABBBBAAAAAAABAA A-AAAAABBBABABAABBBAA-AAABABBAAABAAAAA-
*ABG366 ABAABABAAAABBAABBAAAABBABBAABAAABABBBBAABBBBBAABBAABBBB AABBBABAAABBAABBAAABAAAAAB-AAAAABABABABAA-BABB-AABAAAAAA -AA-AABAA-BB-BAAAAAB-AAABABAAABA-------
*ABG356 BAABABAA---B-BA-----BAAAABBAABBBAABABAABBBBB-AABABAAAAB ABAA-ABBABABABBBBBABAA------BBAB-BBAABA-ABBBABABBBBAAAA BA-AA--AAABAAAAAABABBA-AABBA-A-A--------
*ksuD14C AAB-BABB--A-BAABA-BBBBBBBABAABBABABBABBBBBABBBBABAABBAB BABBBAABABBBBAABAAAAAABA-B-AAABBABAABAAABAAAABAABBAABAAA BBBABAAAABBBABBBAAABBBBABBBBBAAABBAABAB
*ABG377 ABABABBBABBBBAAABBABAABBAABABABABB-BABBBABBABABBABAAAAA BABABBABAABBABABBBAABBBAAA-ABAABABABBBBAB-BBABAABBBBAAAB A-ABAA-BBBBABBBABABBBBBABABAAABAB--AABB
*ABG358 BAABABBABBABABABBABAAABBBBBAAABBBAAAAABBBBBBAAAABBAAAAB ABBBAABAABABABBBAAABBABBAAAABBABAABBABABBABBBABBBBAABAAB A-AAAAAAABAAABAABBBAABAABBAAAAABABBAAAA
*CDO99 B-AAAABABBA-BB--A--B-BBBB--BBBABAAABBBBBABAABABBAABBBBB BABBBAABBABBAABBBBBBBBBABA-BAABB-BABABBBABBBAAABABBBBBAA ABBBBBBBAABAABBBAAABBBBAAABABBBBBBABBAA
*CDO348B BABBAAABB-BBAAAAABB-AABBAA-AAAABBBAABAAABBBBBBAAAAAABAA ABAAABBBBAAAABBAABAAABBAABBBABBBBAAAABAAAAAABABBAAAAAAB B ABBBBAABABAAABBBABAABAAAAAABBBABBABBBAB
*Pcr1 AAABABABAA-BA-BBABBABBAABBAAAABABBAAAAAAAAABBAAABBABAAB BBABAABAAAAAAAAAABAABBAABAABBAABAABBABAABBBBBBABAAAAAAA A BAAABAAABBBBBBAABBBABABAAABBBAABBAAABBB
*Pcr2 BAAAB-B-BB-B--BAABAAABBABAABABABABBBBBBBABBAAAAABABB-B- BA-A---BBBBBAB--A-BBBBB-AAABAABAABABABBABBBBBAAAABBABBAA AAABBBBBABAAAABBBABBBBBBAAABBBB-BBBABA-
*BCD129 ABBBBBAABBAAAABABABABAAAABAAABAAAABBBABABAAAABBBBABBAAA ABABBABBABBBBBBBBB-BBBABAABBABAAABBAABAABAAA-BAABAABBAAA BBBAABBABBBBAABAABBAB-BBBBABBAABABBBABB
*Rrn1 ABBBABBAAABABBAAA-ABBBBBB-BBABAABBBAABABBAAAAAABAAAABBA ABBAABAABBAABBBABBAAAABBAB-AABAAABBBAABBAABBBAAAABBAAAAB ABBBAAABAAABBABBBAAAABABBBABBABAABAAABB
*ABR315 -A-AAAAABBAABABBBABABABAAABAAAABBABBB--AABBBBBBBBBBABAB ABABBAAABABBAAABAAABAABBAAAAAABB-A-BABBAABA-BBAABABA-BAA A-BBBAAABAABAABAABBAAABBBBBBABABBBBBA--
*ksuF2A B--AA---------------ABBA-AABABA---BBBBBBABBAAA-ABABBB BBBA-ABAABBBBBABBBABBBB-BAAAAB-ABA--ABABBABBBBBAAAABBAB- -AAAABBBBBA-AAA-BBBABBBBBAAAABB-BABBBABA-
*ksuF2B BBBAA----------------BABBABABBBABBABBBABBBBABABBBAAAA AABAB-BBBAAABBABABBBA-BA---A-ABA-B-B-BABB-BAABABAABBBBAB -BABABAAAABBBABBBBBBBBBAAABABAA-BABABABB-
*ABC306 BAA-ABA----B--AB----BAAAABBAAABBAABABAABBBBAAAABABAAAAB ABAABABBABABABBBBBABAABABAAABBAB-BBAABABABBBABABBBBAAAAB ABAAAAAAABAAA-AABABBABAABBABAAABABBAAA-
*Amy2 AAAAAABABBBBBABAAABBBBBAAAABABAABABABBBABBBAABAABAAAABB ABABAAABABBBBAAAABBBAAAABAAAABBBABAAAAAAAAABABABABBAAAB B BBBBAAAAAAABABBABAABBABAABBABBAABAAABBA
*CDO373 A-ABAB-B--B-A-B-A---BAAB---AABB-B-AA----------A---BBAAB BB-BA-BAAA-AAAABAB--BAAABAABBABBAABBAAAABBBB-BAAAAAAABA AAAAAB-ABBBBBABAABBBAA-AAAAABBAABBAAAABB
*ksuF15 A-ABAB-A--A-AA-------AABB--AABBBAAAABABBABAAAAABABAAAAB BBAABABBAAABABABBAABBABA----BABB-ABAAAABB--BAAAABBBA-AA BAAAA----ABABA-ABBABAABAAABAAAAAABBAAAAB
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*PhoPdRes 46 78 115 63 52 51 51.5 110 57.5 44 77 45.5 99 50.5 102.5 51 58.5 85 50 56 89.5 86.5 52 54 48 62 106.5 88.5 90 78.5 64.5 59 54 - 65.5 93.5 74.5 78 51 56.5 50.5 47.5 56 72 82.5 88 78 91 47.5 66 99.5 112.5 71.5 114 57 105 55 47 57 67.5 85.5 42.5 65 70 66 73 54.5 107 50.5 53 60 74 78.5 82 - 47.5 118 42 57 84 110.5 72 75 - 49 74 44 107 64 54.5 48 106 50.5 75 50 85 85.5 45 59 48 61 44.5 46 63.5 57 64.5 100 54 134.5 61 56 73 53 76 91.5 91 111.5 56 68 90.5 48 83 102.5 75 68 73.5 53.5 -35 45.5 41 71 76.5 59 92.5 101.5 57 79.5 102 71 79.5 87 113 60 82.5 52 67 104.5 66.5 101 84
*aa1 37.4 28.0 36.2 25.3 25.2 28.2 27.1 28.3 33.0 28.3 30.0 28.5 27.7 32.9 29.7 29.8 29.2 23.5 26.4 26.4 28.6 37.5 30.1 30.2 30.8 29.1 28.1 22.2 24.8 30.8 24.4 30.1 32.0 27.6 36.1 21.7 34.3 27.7 19.0 24.3 24.1 28.9 27.8 15.4 30.6 26.2 22.9 25.1 28.0 26.9 17.2 21.4 39.1 26.4 26.0 22.1 27.5 23.1 27.5 30.5 33.1 37.8 42.8 24.7 28.3 27.6 27.9 28.0 27.1 26.9 34.4 27.3 28.5 29.7 31.9 30.9 31.0 32.5 32.3 35.9 31.7 28.4 30.9 24.7 22.8 35.6 48.6 31.1 32.0 24.4 25.8 26.8 28.4 33.9 26.9 27.1 29.2 26.0 27.0 28.6 38.3 27.0 30.0 30.8 33.2 36.8 23.1 28.4 21.5 42.7 32.7 37.7 33.0 28.8 32.4 26.6 26.3 23.4 38.1 29.5 28.2 29.4 26.1 25.2 21.9 26.6 25.3 31.0 42.8 26.7 28.7 26.8 20.3 25.9 24.0 25.2 27.5 26.7 35.2 27.7 40.4 32.3 24.8 25.7 22.7 30.5 20.9 23.5 29.9 32.4
*aa4 28.9 25.0 26.0 25.6 24.5 28.2 27.7 25.6 32.0 36.4 25.7 26.6 32.7 33.3 30.6 35.1 28.9 26.6 32.8 35.1 30.3 26.7 27.4 31.6 31.3 31.4 31.3 25.5 23.3 28.7 24.4 28.8 34.4 23.9 27.3 24.2 34.3 26.4 25.9 29.2 33.0 33.4 30.8 25.3 24.3 24.3 27.0 26.1 29.2 28.3 23.3 21.1 23.7 26.1 31.2 21.1 30.6 27.8 26.8 35.3 26.7 29.8 31.7 22.7 26.1 25.8 29.2 27.3 24.9 26.2 30.6 26.9 28.2 26.1 33.9 24.0 30.5 32.6 30.2 31.8 26.1 27.5 26.1 25.4 25.4 27.8 39.4 23.7 30.9 28.9 28.6 25.1 32.3 29.9 31.7 21.7 21.7 27.3 28.9 29.3 32.3 25.9 34.7 34.6 35.8 35.1 27.8 27.3 29.1 31.0 34.1 33.4 35.4 32.3 32.9 26.7 29.8 26.1 24.9 26.8 26.2 26.2 31.1 28.0 23.7 33.6 31.3 30.8 31.3 27.6 25.6 25.3 25.7 27.0 26.4 31.9 27.4 25.6 24.3 22.5 30.5 25.3 27.0 24.6 28.0 29.0 24.9 24.9 24.9 24.3
*dp1 95.00 68.00 70.00 71.00 60.00 84.00 64.00 74.00 98.00 95.00 105.00 81.00 105.00 85.00 74.00 71.00 73.00 64.00 78.00 72.00 68.00 107.00 80.00 59.00 75.00 58.00 80.00 55.00 71.00 69.00 57.00 70.00 55.00 62.00 89.00 72.00 83.00 99.00 50.00 49.00 74.00 103.00 75.00 55.00 111.00 60.00 68.00 68.00 101.00 69.00 49.00 49.00 94.00 62.00 59.00 86.00 61.00 81.00 52.00 77.00 90.00 78.00 122.00 86.00 82.00 85.00 65.00 76.00 52.00 68.00 61.00 73.00 88.00 75.00 95.00 76.00 94.00 72.00 82.00 105.00 77.00 84.00 69.00 70.00 69.00 76.00 99.00 81.00 90.00 74.00 92.00 63.00 65.00 87.00 77.00 49.00 105.00 77.00 61.00 54.00 97.00 70.00 72.00 78.00 87.00 117.00 61.00 88.00 63.00 91.00 91.00 103.00 123.00 97.00 100.00 74.00 55.00 49.00 101.00 79.00 77.00 66.00 55.00 63.00 84.00 87.00 93.00 59.00 127.00 60.00 80.00 58.00 35.00 61.00 46.00 55.00 64.00 65.00 84.00 80.00 92.00 77.00 55.00 78.00 50.00 82.00 46.00 74.00 65.00 69.00
*dp4 58.00 57.00 54.00 57.00 52.00 56.00 60.00 65.00 88.00 106.00 49.00 76.00 86.00 96.00 70.00 62.00 41.00 53.00 84.00 84.00 88.00 72.00 80.00 57.00 53.00 53.00 84.00 54.00 48.00 55.00 40.00 66.00 62.00 50.00 52.00 62.00 60.00 71.00 63.00 58.00 94.00 151.00 73.00 57.00 66.00 52.00 62.00 60.00 71.00 68.00 51.00 41.00 56.00 55.00 65.00 81.00 86.00 71.00 52.00 69.00 65.00 49.00 95.00 78.00 67.00 61.00 56.00 72.00 52.00 79.00 61.00 76.00 76.00 61.00 108.00 60.00 92.00 87.00 64.00 83.00 58.00 77.00 63.00 71.00 48.00 63.00 99.00 49.00 78.00 89.00 79.00 49.00 99.00 78.00 93.00 45.00 79.00 90.00 62.00 55.00 80.00 56.00 106.00 80.00 93.00 82.00 62.00 73.00 78.00 68.00 90.00 59.00 104.00 96.00 72.00 61.00 73.00 50.00 55.00 67.00 63.00 54.00 63.00 59.00 65.00 89.00 95.00 71.00 72.00 49.00 69.00 51.00 55.00 59.00 55.00 61.00 64.00 53.00 60.00 47.00 66.00 57.00 66.00 64.00 65.00 71.00 56.00 59.00 59.00 63.00
*hd1 156.50 149.50 150.00 157.00 149.50 161.00 164.00 148.50 163.50 161.50 155.50 155.50 149.00 161.00 149.50 158.00 158.50 144.50 158.00 160.00 145.00 148.50 157.50 160.50 158.50 158.50 155.50 150.00 149.50 146.00 156.50 157.50 158.50 149.50 147.00 148.50 144.00 148.50 159.50 156.00 158.00 152.00 156.00 159.00 149.50 149.50 148.50 143.00 161.50 154.50 149.50 149.00 147.50 148.50 155.50 154.50 159.00 159.50 161.00 146.50 149.50 163.00 148.00 148.50 163.00 147.50 158.50 151.50 159.00 159.50 151.50 147.00 146.00 150.00 154.00 164.00 149.50 156.50 161.00 146.00 149.00 150.00 150.00 159.00 162.50 148.00 151.50 150.00 144.50 157.00 157.50 149.00 148.50 147.00 158.00 159.00 145.50 157.00 155.00 158.50 143.00 165.00 159.50 156.50 158.00 144.00 150.00 164.00 148.50 148.00 150.00 149.50 148.00 148.00 147.50 148.00 149.50 151.00 148.50 149.50 156.00 149.50 150.00 150.00 163.00 157.50 149.00 151.50 162.50 154.00 144.50 149.00 156.50 148.50 153.00 159.00 145.00 149.50 146.00 150.00 148.50 149.00 154.50 148.00 162.50 160.00 147.50 164.50 150.00 149.00
*hd2 178.00 176.50 175.00 182.00 170.50 182.00 182.00 171.00 183.50 182.00 172.50 185.50 174.00 185.00 174.50 178.00 182.00 170.00 182.00 182.00 169.50 175.00 182.00 183.50 182.00 180.00 178.00 175.00 174.50 169.50 180.00 180.00 182.00 174.50 169.00 174.50 169.50 171.00 182.00 180.00 180.00 178.50 178.00 183.50 175.00 175.00 175.00 169.00 182.00 178.00 175.00 176.50 173.00 175.00 175.00 178.00 182.00 182.00 183.50 170.00 176.00 182.00 169.50 176.50 183.50 174.50 178.00 178.00 182.00 182.00 174.50 171.00 169.00 175.00 178.00 185.00 175.00 182.00 185.00 169.00 174.50 175.00 175.00 182.00 182.00 174.50 176.50 174.50 169.00 182.00 182.00 172.50 178.00 172.50 182.00 182.00 169.50 180.00 178.00 180.00 170.00 185.00 182.00 178.00 178.00 169.00 175.00 185.00 174.50 171.00 175.00 174.50 180.00 177.00 174.00 172.50 176.50 176.50 172.50 175.00 178.00 175.50 175.00 175.00 183.50 172.50 175.00 175.00 182.00 177.00 171.00 174.50 180.00 174.50 178.00 182.00 169.00 175.00 169.00 176.50 174.50 174.00 178.00 172.50 182.00 182.00 174.50 185.00 175.00 174.50
*ht1 113.50 94.50 88.00 107.50 77.00 113.50 119.00 96.50 112.00 106.50 110.50 97.50 71.50 107.50 80.50 94.00 105.00 96.00 95.00 113.00 89.50 82.00 90.50 114.50 103.00 102.00 108.00 88.00 94.00 80.50 102.00 92.50 112.00 102.50 75.00 93.50 86.50 84.00 102.50 105.50 113.00 93.00 103.00 107.00 91.00 89.50 93.00 84.50 116.00 91.50 92.50 90.50 71.00 81.00 88.00 95.00 109.00 107.50 96.50 94.00 94.50 119.00 73.00 87.00 98.50 75.50 103.50 80.00 121.00 108.00 88.50 89.50 94.00 82.00 98.50 99.00 92.50 113.00 103.00 74.50 84.00 86.00 90.00 123.50 101.50 72.50 90.50 97.00 83.00 106.00 124.50 83.50 96.00 91.00 98.00 109.00 85.00 92.50 109.50 116.50 85.50 110.50 117.00 94.00 107.00 69.50 88.50 105.50 99.50 81.00 107.00 88.00 86.50 96.00 81.00 85.50 88.50 91.00 80.50 85.00 107.50 81.50 86.00 102.50 122.50 107.00 99.50 108.00 120.50 104.50 75.00 86.00 98.00 80.50 83.50 121.50 76.00 79.00 70.00 84.50 82.50 84.50 102.50 91.50 95.00 106.00 85.50 120.50 99.50 95.50
*ht2 85.00 82.50 85.00 95.00 75.00 107.50 102.50 95.00 92.50 92.50 85.00 82.50 60.00 85.00 90.00 75.00 87.50 87.50 90.00 87.50 77.50 80.00 90.00 105.00 100.00 87.50 85.00 77.50 87.50 75.00 85.00 92.50 87.50 97.50 70.00 87.50 85.00 87.50 80.00 85.00 100.00 92.50 87.50 97.50 87.50 92.50 85.00 77.50 82.50 87.50 77.50 75.00 80.00 80.00 77.50 90.00 87.50 102.50 77.50 85.00 95.00 107.50 75.00 70.00 77.50 77.50 95.00 70.00 102.50 87.50 90.00 85.00 87.50 80.00 75.00 100.00 87.50 100.00 90.00 80.00 85.00 87.50 85.00 107.50 90.00 80.00 85.00 92.50 80.00 90.00 100.00 90.00 92.50 90.00 85.00 100.00 77.50 90.00 87.50 92.50 72.50 87.50 95.00 80.00 77.50 80.00 90.00 97.50 95.00 75.00 82.50 77.50 97.50 77.50 90.00 85.00 80.00 80.00 90.00 82.50 90.00 95.00 75.00 90.00 110.00 80.00 80.00 90.00 95.00 90.00 72.50 85.00 80.00 85.00 67.50 87.50 72.50 77.50 80.00 82.50 75.00 75.00 87.50 85.00 87.50 97.50 87.50 97.50 85.00 87.50
*lg2 5.0 30.0 30.0 0.0 10.0 5.0 0.0 70.0 0.0 0.0 25.0 15.0 0.0 0.0 45.0 0.0 20.0 35.0 0.0 5.0 20.0 0.0 0.0 10.0 20.0 10.0 10.0 5.0 10.0 10.0 20.0 0.0 0.0 35.0 5.0 30.0 15.0 10.0 0.0 15.0 0.0 0.0 0.0 0.0 35.0 10.0 35.0 0.0 0.0 10.0 15.0 10.0 0.0 5.0 5.0 30.0 0.0 0.0 0.0 40.0 40.0 0.0 10.0 10.0 0.0 30.0 0.0 15.0 0.0 0.0 20.0 20.0 10.0 15.0 5.0 0.0 45.0 15.0 5.0 15.0 15.0 20.0 30.0 15.0 5.0 15.0 20.0 30.0 10.0 0.0 10.0 30.0 25.0 35.0 0.0 10.0 10.0 20.0 0.0 10.0 0.0 0.0 0.0 50.0 0.0 10.0 30.0 5.0 50.0 35.0 0.0 5.0 15.0 5.0 55.0 35.0 25.0 25.0 30.0 30.0 20.0 35.0 20.0 45.0 10.0 15.0 20.0 15.0 10.0 20.0 15.0 15.0 5.0 20.0 10.0 0.0 0.0 35.0 25.0 10.0 10.0 25.0 0.0 10.0 0.0 0.0 15.0 10.0 15.0 5.0
*lg3 80.0 50.0 10.0 30.0 30.0 60.0 0.0 70.0 0.0 60.0 0.0 0.0 0.0 50.0 70.0 0.0 70.0 60.0 20.0 0.0 70.0 60.0 0.0 70.0 60.0 0.0 20.0 0.0 0.0 60.0 90.0 50.0 0.0 50.0 0.0 70.0 0.0 0.0 0.0 50.0 0.0 0.0 70.0 0.0 40.0 50.0 50.0 50.0 40.0 40.0 40.0 70.0 70.0 0.0 0.0 80.0 60.0 0.0 0.0 0.0 50.0 20.0 0.0 80.0 0.0 80.0 50.0 0.0 50.0 0.0 60.0 70.0 40.0 50.0 20.0 30.0 60.0 30.0 0.0 80.0 0.0 0.0 80.0 50.0 0.0 0.0 40.0 70.0 30.0 0.0 50.0 80.0 80.0 70.0 0.0 70.0 20.0 20.0 50.0 0.0 0.0 0.0 20.0 50.0 60.0 0.0 0.0 0.0 40.0 40.0 20.0 0.0 50.0 0.0 60.0 80.0 30.0 0.0 0.0 70.0 0.0 70.0 70.0 70.0 30.0 20.0 70.0 50.0 40.0 0.0 0.0 20.0 0.0 80.0 30.0 50.0 0.0 80.0 0.0 30.0 0.0 70.0 0.0 30.0 70.0 20.0 50.0 0.0 60.0 0.0
*me1 72.60 73.60 76.00 73.30 74.50 71.60 76.40 72.60 77.20 76.80 75.90 76.00 75.40 78.30 77.30 74.10 69.60 77.10 74.10 76.00 75.80 77.40 78.20 77.50 75.70 74.10 75.30 75.10 75.60 76.60 71.50 77.90 78.80 74.80 75.90 76.50 75.20 75.50 78.10 77.00 75.10 79.10 77.60 73.70 75.20 74.60 75.60 74.20 71.00 75.60 73.60 73.20 78.60 76.20 76.60 73.70 77.90 76.70 79.10 75.60 76.10 75.60 83.00 75.50 77.30 74.90 76.00 75.00 75.50 78.20 78.10 74.90 75.90 76.20 75.90 74.20 75.30 75.70 75.50 76.60 73.80 76.40 74.30 74.60 72.40 77.60 82.60 74.70 75.30 75.90 75.10 73.40 76.90 79.20 75.50 80.40 72.30 74.60 77.70 78.60 77.80 74.40 77.90 74.60 76.10 76.60 73.20 74.20 75.80 77.40 76.40 77.50 75.80 73.90 75.60 74.10 74.50 74.60 76.60 75.40 76.10 76.70 76.70 72.30 71.60 76.80 74.90 78.50 73.10 74.10 73.90 74.80 75.30 75.60 74.50 75.00 74.50 71.80 75.80 76.50 78.00 76.90 77.40 74.60 75.80 73.80 76.10 76.70 76.10 76.00
*me4 74.80 71.30 72.70 71.10 73.80 74.20 74.00 72.40 76.90 75.50 74.50 73.80 75.50 74.70 74.00 74.80 75.60 73.30 75.10 75.50 72.00 73.40 73.80 73.70 74.10 73.30 71.40 72.30 72.50 74.10 71.90 73.10 75.50 72.60 72.90 74.00 73.60 74.80 75.10 74.60 74.70 74.10 72.70 73.20 72.60 72.50 75.20 74.20 74.90 75.00 71.90 71.90 71.90 73.20 74.90 72.40 74.20 75.00 74.70 73.90 73.60 74.30 71.60 71.60 72.50 74.00 74.20 74.00 72.60 73.70 74.90 71.50 74.50 73.50 72.70 72.40 75.00 73.30 75.80 74.10 70.80 73.30 73.70 72.70 73.60 73.60 77.80 71.70 75.60 74.60 74.00 73.80 76.70 74.80 75.20 72.60 72.10 74.60 76.80 75.70 75.60 74.20 74.30 74.70 75.90 76.30 73.70 71.80 74.50 73.40 74.50 76.30 76.30 74.50 76.10 73.80 75.20 73.50 72.80 73.10 74.40 72.70 75.00 72.30 71.30 76.60 75.10 74.10 75.00 74.30 72.00 73.20 73.10 75.00 75.20 73.70 72.60 74.20 72.30 74.60 76.40 74.90 75.90 73.80 74.00 73.50 74.90 76.60 74.90 71.90
*bp1 16.3 11.5 12.5 13.9 11.2 14.6 9.4 12.5 11.0 13.3 13.5 12.5 13.0 10.6 8.9 13.0 14.0 11.7 13.0 10.2 9.9 12.5 9.4 9.9 11.6 12.8 14.2 12.2 12.7 10.0 14.0 10.5 10.0 12.5 13.3 11.2 14.7 14.6 9.7 9.7 13.4 11.2 13.2 12.6 11.6 11.5 11.2 11.9 14.8 11.6 11.5 12.0 10.4 11.2 12.3 12.6 9.8 11.6 8.7 13.3 12.6 11.6 14.7 12.2 12.2 12.7 12.4 11.5 12.5 9.4 9.8 11.3 12.4 9.8 14.9 13.3 12.0 13.0 12.1 10.3 13.5 11.4 12.0 12.1 13.5 9.3 9.3 12.9 12.8 11.7 11.6 11.6 10.6 10.5 11.4 8.3 14.9 13.3 10.6 9.0 11.9 13.9 10.1 13.0 13.4 14.2 11.4 13.2 10.6 12.1 12.9 12.2 15.4 14.5 11.5 13.1 11.5 9.7 13.4 10.0 13.4 10.4 10.6 12.3 12.8 12.8 12.6 9.6 14.6 13.1 13.7 11.3 11.5 12.2 10.5 13.8 13.5 12.6 13.2 11.3 12.0 12.8 11.0 14.1 13.5 14.7 12.0 11.1 11.7 13.2
*bp4 11.1 11.5 12.1 14.6 11.2 10.6 11.1 11.3 13.6 13.6 10.1 10.5 10.9 12.0 10.2 13.1 10.6 11.6 11.5 10.4 13.2 12.1 13.5 11.3 10.9 12.3 14.6 11.3 12.6 11.8 11.5 13.3 12.7 12.3 13.6 10.9 13.4 11.2 12.1 11.1 13.3 16.4 13.4 12.3 11.5 12.3 10.7 12.3 10.9 11.8 10.7 10.7 12.3 11.9 12.4 11.5 11.7 11.4 11.2 12.8 11.0 11.5 14.5 12.6 13.4 10.6 12.2 11.2 12.7 13.0 12.3 12.7 12.1 10.8 15.8 12.3 11.2 13.6 10.9 11.2 13.3 12.6 11.4 12.2 10.9 12.3 11.9 12.7 11.7 11.7 10.5 10.4 11.6 10.1 10.8 10.7 12.9 11.5 10.0 10.4 11.5 12.0 12.1 11.9 12.2 11.3 8.8 12.1 10.5 11.0 11.7 9.6 11.9 9.7 9.0 10.3 11.1 9.4 10.7 9.6 11.0 10.6 9.8 9.6 11.1 10.3 9.7 10.5 9.5 10.4 11.6 9.8 11.9 9.5 9.7 11.7 11.8 8.0 11.8 9.6 9.7 8.7 10.3 11.2 13.3 12.2 10.7 9.5 9.0 13.0
*yld1 4610.80 5159.00 4701.60 5296.90 4883.30 4681.50 4930.30 4691.60 5411.30 5041.30 5108.60 5643.30 4923.60 5145.60 4452.80 5031.20 3279.00 5582.80 5488.60 4520.00 4436.00 5001.00 6275.60 4072.70 3114.30 4859.70 5401.20 6117.50 4846.30 3860.90 4143.40 5175.80 4735.30 4678.10 4341.80 4651.20 4311.50 5824.90 5929.20 5192.70 4308.20 4567.10 5296.90 5942.60 5747.60 6009.90 5683.70 5034.60 3797.00 5683.70 5872.00 5744.20 4160.20 4489.80 6057.00 5616.40 5273.40 5572.70 4079.50 5192.70 5125.40 3813.80 4832.80 6077.20 5438.20 4072.70 4701.60 5179.20 4701.60 5730.80 4415.80 5276.70 5290.20 4960.60 4136.60 2441.60 5088.40 4967.30 3719.60 4671.40 4970.70 5626.50 5159.00 4459.50 5680.30 4510.00 4039.10 5048.10 4587.30 5381.00 4775.60 5148.90 5798.00 4281.30 5845.10 4136.60 4469.60 5710.60 5626.50 5259.90 4856.40 4382.20 5239.70 4563.80 4362.00 5108.60 4896.70 4099.60 5165.80 5286.80 5199.40 5337.30 3598.50 4641.10 4029.00 5394.50 5804.80 5861.90 5085.00 4140.00 5549.20 4789.10 5508.80 4869.80 3531.30 5212.80 5263.30 4129.90 3195.00 4264.40 3719.60 5421.40 6009.90 5290.20 4906.80 4738.60 5122.00 3931.50 2596.30 5687.00 5219.60 5031.20 6009.90 4610.80 5616.40 3790.20 5370.90 3390.00 5293.60 5522.30
*yld2 6836.70 5791.70 6108.30 6028.30 6723.30 5698.30 5550.00 5271.70 7665.00 5716.70 6523.30 5218.30 7323.30 5693.30 7215.00 4255.00 5453.30 5270.00 6275.00 5050.00 5518.30 5530.00 6256.70 4891.70 5133.30 5361.70 4276.70 5951.70 5091.70 5095.00 4868.30 6575.00 5311.70 5608.30 5343.30 5775.00 4380.00 6356.70 6223.30 5348.30 4615.00 4435.00 5455.00 6163.30 4301.70 5741.70 5436.70 4965.00 5573.30 6118.30 6540.00 5271.70 4461.70 6460.00 6576.70 5670.00 5731.70 5341.70 5743.30 5765.00 5466.70 5378.30 5346.70 5096.70 5926.70 6190.00 6283.30 6370.00 5818.30 5691.70 5550.00 5058.30 5506.70 6400.00 4616.70 4365.00 5905.00 5335.00 6021.70 6401.70 5288.30 6643.30 6713.30 4711.70 6431.70 6880.00 6005.00 6130.00 5600.00 5816.70 5381.70 6183.30 5661.70 6363.30 6056.70 5681.70 5291.70 6936.70 6820.00 6858.30 4433.30 4491.70 5973.30 6110.00 4768.30 5783.30 6345.00 6601.70 6568.30 6861.70 5503.30 6646.70 5808.30 6366.70 6365.00 6370.00 6473.30 6538.30 5198.30 5555.00 5386.70 5065.00 7206.70 7763.30 5168.30 4945.00 5201.70 5401.70 5381.70 5938.30 4556.70 7088.30 4991.70 6040.00 5763.30 4811.70 4936.70 5596.70 5915.00 5568.30 6561.70 5186.70 6330.00 5741.70 4421.70 5761.70 5775.00 6413.30 6050.00 5500.00 ************************************************************************ * Output from: Wed Sep 20 19:33:46 1995 * * * * MAPMAKER/EXP * * (version 3.0b) * * * ************************************************************************
data from 'SM434.DAT' are loaded
F2 backcross data (150 individuals, 434 loci)
'photo' is on: file is 'WEDNIGHT.OUT'
7> group 9.0
Linkage Groups at min LOD 9.00, max Distance 50.0
group1= ABG452 iPgd2 Hor1 Hor2 Ica1 Cab2 ABC307A BCD351C WG789B Chs3
CDO99 Pcr2
ksuF2A ABG373 ABG464 BCD98 Hor5 Glb1 ABC152B His4A Dor2 ABC160 Aga7
CDO105B
ABC164 ABG494 Act8 ABA002 ABA004 Aga6 ABG387a ABG022B ABG500a ABR337
ABG702
His3B MWG800 RisBPP16 ABG059 AtpbA ABC257 cMWG733 cMWG706a MWG706B
MWG837 MWG912
ABC261 ABG074 ABG055 MWG635C ABC322B BCD340A MWG938 MWG042A
KFP153B
8> group 9.0 20
error in sequence: that group is not defined
9> sequence group1
sequence #20= group1
10> group 9.0 25
Linkage Groups at min LOD 9.00, max Distance 25.0
group1= ABG452 iPgd2 Hor1 Hor2 Ica1 Cab2 ABC307A BCD351C WG789B Chs3
CDO99 Pcr2
ksuF2A ABG373 ABG464 BCD98 Hor5 Glb1 ABC152B His4A Dor2 ABC160 Aga7
CDO105B
ABC164 ABG494 Act8 ABA002 ABA004 Aga6 ABG387a ABG022B ABG500a ABR337
ABG702
His3B MWG800 RisBPP16 ABG059 AtpbA ABC257 cMWG733 cMWG706a MWG706B
MWG837 MWG912
ABC261 ABG074 ABG055 MWG635C ABC322B BCD340A MWG938 MWG042A
KFP153B -------
group2= Rrn1 ABG466 ABG474 WG223b ABC152A ABG20 Nir ABG378 ABG379
ABC163 ABA006
ABR331 ABC169B Ubi4 ABC170A ABC170B ABR335 ABG387b ABG388 ABG001
ABC175 His3D
Ubi5 ABG062 MWG820 MWG620 cMWG652a bBE54B B12DA BCD340E CDO497
MWG934 MWG663_2
MWG684A MWG684B
11> sequence group1
sequence #21= group1
12> order
Linkage Groups at min LOD 3.00, max Distance 50.0
Starting Orders: Size 5, Log-Likelihood 3.00, Searching up to 50 subsets
Informativeness: min #Individuals 1, min Distance 0.9
Placement Threshold-1 3.00, Threshold-2 2.00, Npt-Window 7 ==================================================================== ===========
Linkage group 1, 55 Markers:
7 ABG452 20 iPgd2 29 Hor1 30 Hor2 33 Ica1
48 Cab2 49 ABC307A 56 BCD351C 59 WG789B 65 Chs3
78 CDO99 81 Pcr2 85 ksuF2A 92 ABG373 96 ABG464
115 BCD98 138 Hor5 141 Glb1 149 ABC152B 156 His4A
160 Dor2 175 ABC160 177 Aga7 192 CDO105B 196 ABC164
199 ABG494 203 Act8 206 ABA002 207 ABA004 228 Aga6
235 ABG387a 247 ABG022B 270 ABG500a 273 ABR337 278 ABG702
284 His3B 304 MWG800 317 RisBPP16 332 ABG059 340 AtpbA
342 ABC257 356 cMWG733 358 cMWG706a 359 MWG706B 363 MWG837
365 MWG912 367 ABC261 370 ABG074 373 ABG055 378 MWG635C
394 ABC322B 395 BCD340A 407 MWG938 411 MWG042A 432 KFP153B
Most informative subset: 432 20 407 373 33 48 49 370 358 65 356 367 411 92 96
115 394 141 332 156 340 175 177 192 196 317 304 206 207 228 235 247 270 273 278
284
Searching for a unique starting order containing 5 of 36 informative loci...
Got one at log-likelihood 12.11
Placing at log-likelihood threshold 3.00...
Start: 247 175 156 284 358
Npt-13: 247 (160) 175 156 284 358
Npt-22: 247 (304) 160 175 156 284 358
Npt-13: 247 304 (141) 160 175 156 284 358
Npt-3: 247 304 141 160 175 156 284 (49) 358
Npt-33: 247 (273) 304 141 160 175 156 284 49 358
Npt-End: (196) 247 273 304 141 160 175 156 284 49 358
Npt-3: 196 (149) 247 273 304 141 160 175 156 284 49 358
Npt-4: 196 149 (317) 247 273 304 141 160 175 156 284 49 358
Npt-31: 196 149 317 (81) 247 273 304 141 160 175 156 284 49 358
Npt-End: 196 149 317 81 247 273 304 141 160 175 156 284 49 358 (356)
Npt-8: 196 149 317 81 247 273 304 141 160 175 156 284 49 358 (20) 356
Npt-End: 196 149 317 81 247 273 304 141 160 175 156 284 49 358 20 356 (365)
Npt-4: 196 149 317 81 247 273 304 141 160 175 156 284 49 358 20 356 (206) 365
Npt-13: 196 149 317 81 247 273 304 141 160 175 156 284 49 358 20 356 (394) 206
365
Npt-11: 196 149 317 81 247 273 304 141 160 175 156 284 49 358 20 356 (340) 394
206 365
Npt-16: 196 149 317 81 247 273 304 141 160 175 156 284 49 358 20 356 340 (278)
394 206 365
Npt-20: 196 149 317 81 247 273 304 141 160 175 156 284 49 358 20 356 340 278
394 206 (177) 365
Npt-23: 196 149 317 81 247 273 304 141 160 175 156 284 49 358 20 356 340 278
394 206 (48) 177 365
Npt-End: (270) 196 149 317 81 247 273 304 141 160 175 156 284 49 358 20 356 340
278 394 206 48 177 365
Npt-End: (115) 270 196 149 317 81 247 273 304 141 160 175 156 284 49 358 20 356
340 278 394 206 48 177 365
Npt-15: 115 (33) 270 196 149 317 81 247 273 304 141 160 175 156 284 49 358 20
356 340 278 394 206 48 177 365
Npt-End: (29) 115 33 270 196 149 317 81 247 273 304 141 160 175 156 284 49 358
20 356 340 278 394 206 48 177 365
Npt-10: 29 (78) 115 33 270 196 149 317 81 247 273 304 141 160 175 156 284 49
358 20 356 340 278 394 206 48 177 365
Npt-20: 29 (207) 78 115 33 270 196 149 317 81 247 273 304 141 160 175 156 284
49 358 20 356 340 278 394 206 48 177 365
Npt-20: 29 (65) 207 78 115 33 270 196 149 317 81 247 273 304 141 160 175 156
284 49 358 20 356 340 278 394 206 48 177 365 *** break ***
13>
13>
13> list loci Error Linkage Haplotype
Num Name Genotypes Prob Chrom Group Group Class New?
7 ABG452 143 1.00% - group1 - - -
20 iPgd2 150 1.00% - group1 - - -
29 Hor1 149 1.00% - group1 - - -
30 Hor2 143 1.00% - group1 - - -
33 Ica1 143 1.00% - group1 - - -
48 Cab2 125 1.00% - group1 - - -
49 ABC307A 150 1.00% - group1 - - -
56 BCD351C 149 1.00% - group1 - - -
59 WG789B 149 1.00% - group1 - - -
65 Chs3 117 1.00% - group1 - - -
78 CDO99 139 1.00% - group1 - - -
81 Pcr2 133 1.00% - group1 - - -
85 ksuF2A 117 1.00% - group1 - - -
92 ABG373 148 1.00% - group1 - - -
96 ABG464 145 1.00% - group1 - - -
115 BCD98 150 1.00% - group1 - - -
138 Hor5 141 1.00% - group1 - - -
141 Glb1 150 1.00% - group1 - - -
149 ABC152B 149 1.00% - group1 - - -
156 His4A 134 1.00% - group1 - - -
160 Dor2 145 1.00% - group1 - - -
175 ABC160 147 1.00% - group1 - - -
177 Aga7 135 1.00% - group1 - - -
192 CDO105B 90 1.00% - group1 - - -
196 ABC164 149 1.00% - group1 - - -
199 ABG494 145 1.00% - group1 - - -
203 Act8 145 1.00% - group1 - - -
206 ABA002 146 1.00% - group1 - - -
207 ABA004 122 1.00% - group1 - - -
228 Aga6 83 1.00% - group1 - - -
235 ABG387a 131 1.00% - group1 - - -
247 ABG022B 141 1.00% - group1 - - -
270 ABG500a 146 1.00% - group1 - - -
273 ABR337 129 1.00% - group1 - - -
278 ABG702 143 1.00% - group1 - - -
284 His3B 141 1.00% - group1 - - -
304 MWG800 145 1.00% - group1 - - -
317 RisBPP16 148 1.00% - group1 - - -
332 ABG059 142 1.00% - group1 - - -
340 AtpbA 150 1.00% - group1 - - -
342 ABC257 144 1.00% - group1 - - -
356 cMWG733 150 1.00% - group1 - -
358 cMWG706a 146 1.00% - group1 - - -
359 MWG706B 88 1.00% - group1 - - -
363 MWG837 146 1.00% - group1 - - -
365 MWG912 148 1.00% - group1 - - -
367 ABC261 148 1.00% - group1 - - -
370 ABG074 115 1.00% - group1 - - -
373 ABG055 99 1.00% - group1 - - -
378 MWG635C 124 1.00% - group1 - - -
394 ABC322B 147 1.00% - group1 - - -
395 BCD340A 133 1.00% - group1 - - -
407 MWG938 150 1.00% - group1 - - -
411 MWG042A 147 1.00% - group1 - - -
432 KFP153B 99 1.00% - group1 - - -
14> sequence 29 65 207 78 115 33 270 196 149 317 81 247 273 304 141 160 175 156
284
49 358 20 356 340 278 394 206 48 177 365
sequence #22= 29 65 207 78 115 33 270 196 149 317 81 247 273 304 141 160 175 156
284 49 358 20 356 340 278 394 206 48 177 365
15> map ==================================================================== ===========
Map:
Markers Distance
29 Hor1 0.0 cM
65 Chs3 7.7 cM
207 ABA004 10.9 cM
78 CDO99 0.0 cM
115 BCD98 12.0 cM
33 Ica1 7.2 cM
270 ABG500a 8.7 cM
196 ABC164 1.4 cM
149 ABC152B 1.4 cM
317 RisBPP16 2.0 cM
81 Pcr2 0.0 cM
247 ABG022B 3.5 cM
273 ABR337 5.7 cM
304 MWG800 2.7 cM
141 Glb1 0.0 cM
160 Dor2 9.0 cM
175 ABC160 14.2 cM
156 His4A 9.0 cM
284 His3B 3.6 cM
49 ABC307A 12.6 cM
358 cMWG706a 7.5 cM
20 iPgd2 4.2 cM
356 cMWG733 6.4 cM
340 AtpbA 2.0 cM
278 ABG702 6.4 cM
394 ABC322B 3.2 cM
206 ABA002 2.4 cM
48 Cab2 3.2 cM
177 Aga7 2.4 cM
365 MWG912 ----------
149.3 cM 30 markers log-likelihood= -369.84 ==================================================================== ===========
16> make chromosome chrom5a
chromosomes defined: leah1a chrom5a
17> anchor chrom5a
Hor1 - anchor locus on chrom5a
Chs3 - anchor locus on chrom5a
ABA004 - anchor locus on chrom5a
CDO99 - anchor locus on chrom5a
BCD98 - anchor locus on chrom5a
Ica1 - anchor locus on chrom5a
ABG500a - anchor locus on chrom5a
ABC164 - anchor locus on chrom5a
ABC152B - anchor locus on chrom5a
RisBPP16 - anchor locus on chrom5a
Pcr2 - anchor locus on chrom5a
ABG022B - anchor locus on chrom5a
ABR337 - anchor locus on chrom5a
MWG800 - anchor locus on chrom5a
Glb1 - anchor locus on chrom5a
Dor2 - anchor locus on chrom5a
ABC160 - anchor locus on chrom5a
His4A - anchor locus on chrom5a
His3B - anchor locus on chrom5a
ABC307A - anchor locus on chrom5a
cMWG706a - anchor locus on chrom5a
iPgd2 - anchor locus on chrom5a
cMWG733 - anchor locus on chrom5a
AtpbA - anchor locus on chrom5a
ABG702 - anchor locus on chrom5a
ABC322B - anchor locus on chrom5a
ABA002 - anchor locus on chrom5a
Cab2 - anchor locus on chrom5a
Aga7 - anchor locus on chrom5a
MWG912 - anchor locus on chrom5a
chromosome chrom5a anchor(s): iPgd2 Hor1 Ica1 Cab2 ABC307A Chs3 CDO99 Pcr2
BCD98
Glb1 ABC152B His4A Dor2 ABC160 Aga7 ABC164 ABA002 ABA004 ABG022B
ABG500a ABR337
ABG702 His3B MWG800 RisBPP16 AtpbA cMWG733 cMWG706a MWG912 ABC322B
18> framework chrom5a
setting framework for chromosome chrom5a... ==================================================================== ===========
chrom5a framework:
Markers Distance
29 Hor1 0.0 cM
65 Chs3 7.7 cM
207 ABA004 10.9 cM
78 CDO99 0.0 cM
115 BCD98 12.0 cM
33 Ica1 7.2 cM
270 ABG500a 8.7 cM
196 ABC164 1.4 cM
149 ABC152B 1.4 cM
317 RisBPP16 2.0 cM
81 Pcr2 0.0 cM
247 ABG022B 3.5 cM
273 ABR337 5.7 cM
304 MWG800 2.7 cM
141 Glb1 0.0 cM
160 Dor2 9.0 cM
175 ABC160 14.2 cM
156 His4A 9.0 cM
284 His3B 3.6 cM
49 ABC307A 12.6 cM
358 cMWG706a 7.5 cM
20 iPgd2 4.2 cM
356 cMWG733 6.4 cM
340 AtpbA 2.0 cM
278 ABG702 6.4 cM
394 ABC322B 3.2 cM
206 ABA002 2.4 cM
48 Cab2 3.2 cM
177 Aga7 2.4 cM
365 MWG912 ---------- 149.3 cM 30 markers log-likelihood= -369.84 ==================================================================== ===========
19> save chrom5a
saving genotype data in file 'CHROM5A.DAT'... ok
saving map data in file 'CHROM5A.MAP'... ok
20> sequence 30 56 65 92 96 138 192 199 203 245 247 332 342 359 363 370 373 378 395
407 411 432
sequence #23= 30 56 65 92 96 138 192 199 203 245 247 332 342 359 363 370 373 378
395 407 411 432
21> list loci Error Linkage Haplotype
Num Name Genotypes Prob Chrom Group Group Class New?
30 Hor2 143 1.00% - group1 - - -
56 BCD351C 149 1.00% - group1 - - -
65 Chs3 117 1.00% chrom5a group1 - - -
92 ABG373 148 1.00% - group1 - - -
96 ABG464 145 1.00% - group1 - - -
138 Hor5 141 1.00% - group1 - - -
192 CDO105B 90 1.00% - group1 - - -
199 ABG494 145 1.00% - group1 - - -
203 Act8 145 1.00% - group1 - - -
245 ABG019 128 1.00% - group5 - - -
247 ABG022B 141 1.00% chrom5a group1 - - -
332 ABG059 142 1.00% - group1 - - -
342 ABC257 144 1.00% - group1 - - -
359 MWG706B 88 1.00% - group1 - - -
363 MWG837 146 1.00% - group1 - - -
370 ABG074 115 1.00% - group1 - - -
373 ABG055 99 1.00% - group1 - - -
378 MWG635C 124 1.00% - group1 - - -
395 BCD340A 133 1.00% - group1 - - -
407 MWG938 150 1.00% - group1 - - -
411 MWG042A 147 1.00% - group1 - - -
432 KFP153B 99 1.00% - group1 - - -
22> del 192 359 373 432 370 65 378
sequence #24= 30 56 92 96 138 199 203 245 247 332 342 363 395 407 411
23> order
Linkage Groups at min LOD 3.00, max Distance 50.0
Starting Orders: Size 5, Log-Likelihood 3.00, Searching up to 50 subsets
Informativeness: min #Individuals 1, min Distance 0.9
Placement Threshold-1 3.00, Threshold-2 2.00, Npt-Window 7 ==================================================================== ===========
Linkage group 1, 7 Markers:
30 Hor2 138 Hor5 203 Act8 332 ABG059 363 MWG837
407 MWG938 411 MWG042A
Most informative subset is too small...
Searching for a starting order containing 5 of all 7 loci...
Failed to find a starting order at log-likelihood threshold 3.00. ==================================================================== ===========
Linkage group 2, 7 Markers:
56 BCD351C 92 ABG373 96 ABG464 199 ABG494 247 ABG022B
342 ABC257 395 BCD340A
Most informative subset: 56 92 96 395 247 342
Searching for a unique starting order containing 5 of 6 informative loci...
Failed to find a starting order at log-likelihood threshold 3.00.
Searching for a starting order containing 5 of all 7 loci... *** break ***
24> list chromosomes
Chromosome: #Total #Frame #Anchors #Placed #Unique #Region
leah1a 16 16 0 0 0 0
chrom5a 30 30 0 0 0 0
Total: 46 46 0 0 0 0
25> sequence chrom5a
sequence #25= chrom5a: assigned
26> map ==================================================================== ===========
Map:
Markers Distance
20 iPgd2 94.5 cM
29 Hor1 38.4 cM
33 Ica1 121.5 cM
48 Cab2 53.1 cM
49 ABC307A 127.4 cM
65 Chs3 19.5 cM
78 CDO99 35.6 cM
81 Pcr2 36.4 cM
115 BCD98 47.5 cM
141 Glb1 8.9 cM
149 ABC152B 36.8 cM
156 His4A 24.8 cM
160 Dor2 8.5 cM
175 ABC160 72.2 cM
177 Aga7 119.7 cM
196 ABC164 151.4 cM
206 ABA002 129.7 cM
207 ABA004 59.0 cM
247 ABG022B 10.9 cM
270 ABG500a 15.4 cM
273 ABR337 115.9 cM
278 ABG702 36.9 cM
284 His3B 44.9 cM
304 MWG800 7.7 cM
317 RisBPP16 126.1 cM
340 AtpbA 6.4 cM
356 cMWG733 12.3 cM
358 cMWG706a 44.3 cM
365 MWG912 11.6 cM
394 ABC322B ---------- 1617 cM 30 markers log-likelihood= -1008.00 ==================================================================== ===========
27> sequence 29 65 207 78 115 33 270 196 149 317 81 247 273 304 141 160 175 156
284
49 358 20 356 340 278 394 206 48 177 365
sequence #26= chrom5a: 29 65 207 78 115 33 270 196 149 317 81 247 273 304 141
160 175 156 284 49 358 20 356 340 278 394 206 48 177 365
28> map ==================================================================== ===========
Map:
Markers Distance
29 Hor1 0.0 cM
65 Chs3 7.7 cM
207 ABA004 10.9 cM
78 CDO99 0.0 cM
115 BCD98 12.0 cM
33 Ica1 7.2 cM
270 ABG500a 8.7 cM
196 ABC164 1.4 cM
149 ABC152B 1.4 cM
317 RisBPP16 2.0 cM
81 Pcr2 0.0 cM
247 ABG022B 3.5 cM
273 ABR337 5.7 cM
304 MWG800 2.7 cM
141 Glb1 0.0 cM
160 Dor2 9.0 cM
175 ABC160 14.2 cM
156 His4A 9.0 cM
284 His3B 3.6 cM
49 ABC307A 12.6 cM
358 cMWG706a 7.5 cM
20 iPgd2 4.2 cM
356 cMWG733 6.4 cM
340 AtpbA 2.0 cM
278 ABG702 6.4 cM
394 ABC322B 3.2 cM
206 ABA002 2.4 cM
48 Cab2 3.2 cM
177 Aga7 2.4 cM
365 MWG912 ----------
149.3 cM 30 markers log-likelihood= -369.84 ==================================================================== ===========
29> try 30
Hor2
----------
| 0.00 |
Hor1 | |
|-19.56 |
Chs3 | |
|-12.38 |
ABA004 | |
|-21.46 |
CDO99 | |
|-49.42 |
BCD98 | |
|-35.78 |
Ica1 | |
|-48.29 |
ABG500a | |
|-48.28 |
ABC164 | |
|-62.70 |
ABC152B | |
|-62.69 |
RisBPP16 | |
|-60.90 |
Pcr2 | |
|-65.27 |
ABG022B | |
|-57.24 |
ABR337 | |
|-53.37 |
MWG800 | |
|-59.19 |
Glb1 | |
|-66.07 |
Dor2 | |
|-48.38 |
ABC160 | |
|-42.01 |
His4A | |
|-47.41 |
His3B | |
|-56.78 |
ABC307A | |
|-43.70 |
cMWG706a | |
|-48.64 |
iPgd2 | |
|-55.08 |
cMWG733 | |
|-52.08 |
AtpbA | |
|-60.39 |
ABG702 | |
|-52.12 |
ABC322B | |
|-57.82 |
ABA002 | |
|-59.07 |
Cab2 | |
|-57.22 |
Aga7 | |
|-58.53 |
MWG912 | |
|-22.01 |
|----------|
INF |-22.20 |
----------
BEST -390.69
30> photo
'photo' is on: file is 'WEDNIGHT.OUT'
31> place 30
error: Bad value for multipoint likelihood threshold
32> try 56 92 96
BCD351C ABG373 ABG464 --------------------------------
|-43.03 -41.45 -36.58 |
Hor1 | |
|-81.74 -81.46 -76.62 |
Chs3 | |
|-64.04 -66.53 -61.39 |
ABA004 | |
|-56.11 -63.34 -57.28 |
CDO99 | |
|-71.54 -83.13 -76.81 |
BCD98 | |
|-42.48 -63.53 -55.96 |
Ica1 | |
|-30.49 -69.91 -58.95 |
ABG500a | |
| -6.82 -68.28 -55.17 |
ABC164 | |
| -3.78 -82.11 -67.61 |
ABC152B | |
| 0.00 -82.12 -66.14 |
RisBPP16 | |
| -0.23 -80.40 -64.01 |
Pcr2 | |
| -4.82 -84.77 -69.11 |
ABG022B | |
| -6.76 -76.77 -59.65 |
ABR337 | |
|-15.06 -72.93 -52.66 |
MWG800 | |
|-25.29 -78.88 -54.43 |
Glb1 | |
|-33.23 -85.78 -58.67 |
Dor2 | |
|-25.91 -67.26 -33.93 |
ABC160 | |
|-39.63 -58.80 0.00 |
His4A | |
|-58.41 -62.15 -0.44 |
His3B | |
|-72.32 -71.13 -22.87 |
ABC307A | |
|-62.92 -55.77 -23.37 |
cMWG706a | |
|-71.59 -56.24 -42.88 |
iPgd2 | |
|-77.80 -55.94 -53.62 |
cMWG733 | |
|-74.17 -42.89 -54.57 |
AtpbA | |
|-82.54 -44.01 -65.37 |
ABG702 | |
|-74.31 -31.10 -58.51 |
ABC322B | |
|-79.88 -29.23 -65.27 |
ABA002 | |
|-81.09 -23.35 -68.46 |
Cab2 | |
|-79.10 -10.71 -67.24 |
Aga7 | |
|-80.67 -1.57 -69.07 |
MWG912 | |
|-44.13 0.00 -34.90 |
|--------------------------------|
INF |-44.25 -41.92 -36.76 |
--------------------------------
BEST -370.44 -372.47 -376.72
33> place 56
error: Bad value for multipoint likelihood threshold
34> place 92
error: Bad value for multipoint likelihood threshold
35> place 96
error: Bad value for multipoint likelihood threshold
36> try 138 199 203 245 247
Hor5 ABG494 Act8 ABG019 ABG022B
------------------------------------------------------
| 0.00 -41.96 0.00 -0.07 -41.73 |
Hor1 | |
|-22.00 -80.73 -21.12 -40.39 -80.82 |
Chs3 | |
|-14.32 -63.05 -13.66 -25.64 -63.83 |
ABA004 | |
|-22.07 -55.07 -21.92 -22.69 -56.62 |
HDO99 | |
|-48.47 -70.42 -49.40 -42.75 -72.57 |
BCD98 | |
|-33.78 -42.22 -35.34 -22.92 -43.97 |
Ica1 | |
|-44.93 -30.46 -47.36 -28.80 -32.73 |
ABG500a | |
|-44.93 -6.82 -47.09 -26.94 -12.37 |
ABC164 | |
|-59.50 -3.78 -61.36 -40.56 -11.26 |
ABC152B | |
|-59.44 0.00 -61.36 -40.54 -8.13 |
RisBPP16 | |
|-57.65 -0.23 -59.58 -38.76 zero |
Pcr2 | |
|-62.01 -4.82 -63.94 -43.14 0.00 |
ABG022B | |
|-54.01 -6.76 -55.94 -35.14 zero |
ABR337 | |
|-50.13 -15.05 -52.07 -31.28 -12.87 |
MWG800 | |
|-55.97 -25.28 -57.88 -37.09 -25.55 |
Glb1 | |
|-62.87 -33.22 -64.75 -43.96 -31.57 |
Dor2 | |
|-45.18 -26.03 -47.06 -26.26 -24.73 |
ABC160 | |
|-38.84 -40.54 -40.68 -19.83 -39.58 |
His4A | |
|-44.25 -57.97 -46.09 -25.27 -56.09 |
His3B | |
|-53.66 -71.34 -55.49 -34.69 -70.11 |
ABC307A | |
|-40.89 -61.87 -42.63 -22.29 -61.21 |
cMWG706a | |
|-46.26 -70.47 -47.91 -28.37 -69.70 |
iPgd2 | |
|-52.48 -76.56 -54.22 -34.28 -75.68 |
cMWG733 | |
|-49.16 -72.94 -51.01 -30.44 -72.12 |
AtpbA | |
|-57.39 -81.33 -59.22 -38.65 -80.68 |
AMBG702 | |
|-49.10 -73.12 -50.91 -30.23 -72.55 |
ABC322B | |
|-54.74 -78.74 -56.55 -35.61 -78.11 |
ABA002 | |
|-55.98 -79.93 -57.81 -37.02 -79.32 |
Cab2 | |
|-54.13 -78.02 -55.97 -35.18 -77.35 |
Aga7 | |
|-55.41 -79.57 -57.26 -36.55 -78.91 |
MWG912 | |
|-18.84 -42.97 -20.68 0.00 -42.34 |
|------------------------------------------------------|
INF |-19.03 -43.04 -20.86 -0.06 -42.42 |
------------------------------------------------------
BEST -393.25 -370.44 -392.62 -408.30 -369.86
37> try 342 363 395 407 411
ABC257 MWG837 BCD340A MWG938 MWG042A
------------------------------------------------------
|-41.17 0.00 -37.12 0.00 0.00 |
Hor1 | |
|-80.62 -4.55 -77.24 -21.74 -13.26 |
Chs3 | |
|-65.86 -3.15 -62.62 -14.07 -8.23 |
ABA004 | |
|-62.37 -18.85 -59.70 -22.05 -19.95 |
CDO99 | |
|-82.47 -50.11 -79.69 -49.42 -49.40 |
BCD98 | |
|-63.40 -39.75 -59.88 -35.29 -37.47 |
Ica1 | |
|-69.61 -56.46 -65.85 -47.58 -52.42 |
ABG500a | |
|-67.65 -60.06 -64.10 -47.53 -54.12 |
ABC164 | |
|-81.59 -76.56 -77.88 -61.73 -69.63 |
ABC152B | |
|-81.51 -76.59 -77.92 -61.73 -69.65 |
RisBPP16 | |
|-79.64 -74.69 -76.18 -59.96 -67.82 |
Pcr2 | |
|-84.01 -79.07 -80.51 -64.32 -72.19 |
ABG022B | |
|-75.22 -71.35 -72.46 -56.31 -64.32 |
ABR337 | |
|-70.62 -67.90 -68.56 -52.44 -60.58 |
MWG800 | |
|-76.07 -74.11 -74.46 -58.25 -66.46 |
Glb1 | |
|-82.38 -81.20 -81.36 -65.12 -73.36 |
Dor2 | |
|-61.57 -63.53 -62.95 -47.42 -55.67 |
ABC160 | |
|-45.77 -57.17 -54.20 -41.04 -49.29 |
His4A | |
|-41.61 -62.65 -57.90 -46.45 -54.72 |
His3B | |
|-42.91 -72.12 -67.21 -55.85 -64.12 |
ABC307A | |
|-17.40 -59.46 -51.90 -43.15 -51.18 |
cMWG706a | |
| 0.00 -65.07 -51.79 -48.68 -56.47 |
iPgd2 | |
| -2.51 -71.13 -52.88 -54.82 -62.59 |
cMWG733 | |
|-18.01 -67.76 -39.95 -51.42 -59.43 |
AtpbA | |
|-36.93 -75.98 -40.73 -59.64 -67.65 |
ABG702 | |
|-34.92 -67.64 -28.39 -51.33 -59.21 |
ABC322B | |
|-46.73 -73.20 -26.80 -56.94 -64.75 |
ABA002 | |
|-51.76 -74.36 -23.17 -58.17 -65.83 |
Cab2 | |
|-54.29 -72.35 -10.76 -56.30 -63.91 |
Aga7 | |
|-58.64 -73.66 -1.60 -57.58 -65.25 |
MWG912 | |
|-33.25 -37.19 0.00 -21.01 -29.09 |
|------------------------------------------------------|
INF |-41.91 -37.57 -37.48 -21.22 -29.52 |
------------------------------------------------------
BEST -371.28 -376.22 -372.39 -393.77 -384.57
38> map
====================================================================
===========
Map:
Markers Distance
29 Hor1 0.0 cM
65 Chs3 7.7 cM
207 ABA004 10.9 cM
78 CDO99 0.0 cM
115 BCD98 12.0 cM
33 Ica1 7.2 cM
270 ABG500a 8.7 cM
196 ABC164 1.4 cM
149 ABC152B 1.4 cM
317 RisBPP16 2.0 cM
81 Pcr2 0.0 cM
247 ABG022B 3.5 cM
273 ABR337 5.7 cM
304 MWG800 2.7 cM
141 Glb1 0.0 cM
160 Dor2 9.0 cM
175 ABC160 14.2 cM
156 His4A 9.0 cM
284 His3B 3.6 cM
49 ABC307A 12.6 cM
358 cMWG706a 7.5 cM
20 iPgd2 4.2 cM
356 cMWG733 6.4 cM
340 AtpbA 2.0 cM
278 ABG702 6.4 cM
394 ABC322B 3.2 cM
206 ABA002 2.4 cM
48 Cab2 3.2 cM
177 Aga7 2.4 cM
365 MWG912 ----------
149.3 cM 30 markers log-likelihood= -369.84 ==================================================================== ===========
39> sequence all
sequence #27= all
warning: marker(s) listed in sequence multiple times...
40> group 7.0
warning: marker(s) listed in sequence multiple times... extras deleted
Linkage Groups at min LOD 7.00, max Distance 50.0
group1= Nar1 Nar7 ABG458 Amy1 Lth PSR167B PSR167 PSR154 Cxp3 PSR106
ksuA3B
ksuA3D ksuD17 Rrn1 ABG466 ABG474 WG223b ABC152A ABG20 Nir ABG378
ABG379 ABC163
ABA006 ABR331 ABC169B Ubi4 ABC170A ABC170B ABR335 ABG387b ABG388
ABG001 ABC175
His3D Ubi5 ABG062 MWG820 MWG620 cMWG652a bBE54B B12DA BCD340E
CDO497 MWG934
MWG663_2 MWG684A MWG684B -------
group2= Ale PSR128 ABC302 Ltp1 mSrh ksuA3A BCD351e ksuA1B CDO348B ABG473
WG530
WG541 Rrn2 BG123b CDO749 Adh6 WG364 ABR313 ABC483 WG889 CDO57B
ABA001 ABC168
Ubi2 ABR336 ABG497 Dor5 ABG395 CDO669B ABG705 ABC706 MWG522 ABG708
MWG502 ABC717
ABG316B ABG064 ABG069 B12DB MWG2040B MWG583 MWG042C MWG920_1 -------
group3= Dhn6 Bmy1 ksuH11 BCD351D Pgk2A ABG366 ABR315 BCD265B ABG472
iAco2
WG1026B WG464 BCD402B CDO669 Adh4 ABG484 WG114 BCD453B ABG313B
ABA003 ABG003
ABG498 ABG054 ABG394 ABG397 ABG500b TubA1 WG622 bAL882 ABC303
cMWG652B bAP91
MWG058 bBE54A MWG634 iHxk2 ABG319A ABG319C B32E MWG635a ABC321
MWG077 -------
group4= Glx ABC455 Brz iEst5 Ubi1 Prx1A ABG312 PSR106B WG420 CDO475
WG789A
BCD298B ABC305 ksuA1A His3A Pgk2B ksuD14C BCD129 Amy2 ABG461 ABC465
WG719 PSR129
CDO673 ABG476 Chi1 Adh7 Tha ABC151 ABC154A Plc Dor4B ABC156d ABC158
ABR303
ABR329 ABG380 WG834 WG380A ABC310b Cat3 ABC167a ABC169A dRpg1 ABG011
ABG022A
ABA301 ABC154B ABG701 ABG704 ABG652 MWG010B ABC308 bBE54E RisP103
MWG089 iPgd1A
MWG036B MWG813B MWG706C MWG836 MWG003 ABG320 MWG635B ABG075
MWG911 MWG555a
ABC322A BCD340C BCD340D ABC255 YAtp57A ABC254 MWG042B AdhIntro
MWG851a dSbl -------
group5= ABC451 ABG453 ABC454 PSR156 ABG459 ABG460 Prx2 RbcS Bmy2 mPub
ksuA3C
ABC307B BCD351F BCD828 Gln2 Chs1A Chs1b ksuD22 ABG356 ABG377 ABG358
Pcr1 ksuF2B
ABC306 CDO373 ksuF15 ABG462 ABC468 WG516 ABG471 iBgl BG123a WG996
WG645 Glb3
Glb4 Adh5 Adh8 Pox ABC152D ABC153 BCD410 Dor4A WG110 ABC156A ABC156C
CDO537
CDO64 CDO588 ABG4 ABC157 ABC161 ABC162 Prx1B CDO474c CDO113B His4B
ABG313A
ABC165 ABC166 ABG495B ABA005 ABG002 ABG014 ABR320 ABC167B ABC171
ABC172 ABR334
CDO474B ABG389 ABG005 ABG008 ABG019 Rrn5S1 Crg3A Crg3B ABC174 ABC176
ABA303
Rrn5S2 ABG058 ABG396 BCD131 ABG398 ABG399 ABG499 ABR338 ABG057
ABG703A ABG703b
ABA302 ABG010 His3C ABG654 MWG838 MWG503 cMWG682 MWG902 MWG858
MWG950 ABG315
bBE54C bBE54D ABG316A MWG584 ABG316C ABG316D ABG316E ABG317A
ABG317B ABG318 B15C
AtpbB cMWG691 MWG571B MWG571C MWG571a ABG319B cMWG720 ABG070
MWG798B ABC252
ABG065A ABG072 MWG520A MWG520B MWG878 MWG555b MWG064 MWG680
MWG557 ABC323 F3hA
MWG497 MWG041 -------
group6= ABG452 iPgd2 Hor1 Hor2 Ica1 Cab2 ABC307A BCD351C WG789B Chs3
CDO99 Pcr2
ksuF2A ABG373 ABG464 BCD98 Hor5 Glb1 ABC152B His4A Dor2 ABC160 Aga7
CDO105B
ABC164 ABG494 Act8 ABA002 ABA004 Aga6 ABG387a ABG022B ABG500a ABR337
ABG702
His3B MWG800 RisBPP16 ABG059 AtpbA ABC257 cMWG733 cMWG706a MWG706B
MWG837 MWG912
ABC261 ABG074 ABG055 MWG635C ABC322B BCD340A MWG938 MWG042A
KFP153B -------
group7= iEst9 Cab1 ABG463 WG644 CDO484 WG908 ABC309 CDO504 ABC482
ABC155 ABC310A
ABG495A ABG496 ABG390 ABG391 ABG707 ABG712 ABG314A ABG314B MWG514B
MWG813a
MWG877 MWG851b MWG851C MWG851D -------
unlinked= MWG798a BCD340B KFP153A F3hB
41> sequence group7
sequence #28= group7
42> list loci
Error Linkage Haplotype
Num Name Genotypes Prob Chrom Group Group Class New?
19 iEst9 150 1.00% - group7 - - -
47 Cab1 147 1.00% - group7 - - -
95 ABG463 149 1.00% - group7 - - -
107 WG644 146 1.00% - group7 - - -
124 CDO484 143 1.00% - group7 - - -
125 WG908 150 1.00% - group7 - - -
129 ABC309 147 1.00% - group7 - - -
131 CDO504 143 1.00% - group7 - - -
144 ABC482 142 1.00% - group7 - - -
163 ABC155 148 1.00% - group7 - - -
194 ABC310A 141 1.00% - group7 - - -
200 ABG495A 136 1.00% - group7 - - -
233 ABG496 141 1.00% - group7 - - -
239 ABG390 150 1.00% - group7 - - -
240 ABG391 141 1.00% - group7 - - -
294 ABG707 143 1.00% - group7 - - -
307 ABG712 138 1.00% - group7 - - -
319 ABG314A 150 1.00% - group7 - - -
320 ABG314B 150 1.00% - group7 - - -
330 MWG514B 150 1.00% - group7 - - -
354 MWG813a 146 1.00% - group7 - - -
357 MWG877 150 1.00% - group7 - - -
424 MWG851b 149 1.00% - group7 - - -
425 MWG851C 149 1.00% - group7 - - -
426 MWG851D 149 1.00% - group7 - - -
43> group 7.0 20
Linkage Groups at min LOD 7.00, max Distance 20.0
group1= iEst9 Cab1 ABG463 WG644 CDO484 WG908 ABC309 CDO504 ABC482
ABC155 ABC310A
ABG495A ABG496 ABG390 ABG391 ABG707 ABG712 ABG314A ABG314B MWG514B
MWG813a
MWG877 MWG851b MWG851C MWG851D
44> group 8.0 15
error in sequence: that group is not defined
45> sequence group1
sequence #29= group1
46> group 8.0 15
Linkage Groups at min LOD 8.00, max Distance 15.0
group1= iEst9 Cab1 ABG463 WG644 CDO484 WG908 ABC309 CDO504 ABC482
ABC155 ABC310A
ABG495A ABG496 ABG390 ABG391 ABG707 ABG712 ABG314A ABG314B MWG514B
MWG813a
MWG877 MWG851b MWG851C MWG851D -------
group2= PSR167B ksuA3B ksuA3D ksuD17 Rrn1 ABG474 WG223b ABG20 ABG379
ABC163
ABA006 ABR331 ABC169B Ubi4 ABC170B ABR335 ABG388 ABG001 ABC175 Ubi5
MWG820 B12DA
BCD340E CDO497 MWG684B -------
group3= PSR167 Cxp3 ABG466 ABC152A ABG378 His3D ABG062 MWG620
cMWG652a MWG663_2 -------
group4= PSR154 Nir ABC170A bBE54B MWG934 MWG684A -------
group5= PSR106 ABG387b
47> sequence all
sequence #30= all
warning: marker(s) listed in sequence multiple times...
48> group 7.0
warning: marker(s) listed in sequence multiple times... extras deleted
Linkage Groups at min LOD 7.00, max Distance 50.0
group1= Nar1 Nar7 ABG458 Amy1 Lth PSR167B PSR167 PSR154 Cxp3 PSR106
ksuA3B
ksuA3D ksuD17 Rrn1 ABG466 ABG474 WG223b ABC152A ABG20 Nir ABG378
ABG379 ABC163
ABA006 ABR331 ABC169B Ubi4 ABC170A ABC170B ABR335 ABG387b ABG388
ABG001 ABC175
His3D Ubi5 ABG062 MWG820 MWG620 cMWG652a bBE54B B12DA BCD340E
CDO497 MWG934
MWG663_2 MWG684A MWG684B -------
group2= Ale PSR128 ABC302 Ltp1 mSrh ksuA3A BCD351e ksuA1B CDO348B ABG473
WG530
WG541 Rrn2 BG123b CDO749 Adh6 WG364 ABR313 ABC483 WG889 CDO57B
ABA001 ABC168
Ubi2 ABR336 ABG497 Dor5 ABG395 CDO669B ABG705 ABC706 MWG522 ABG708
MWG502 ABC717
ABG316B ABG064 ABG069 B12DB MWG2040B MWG583 MWG042C MWG920_1 -------
group3= Dhn6 Bmy1 ksuH11 BCD351D Pgk2A ABG366 ABR315 BCD265B ABG472
iAco2
WG1026B WG464 BCD402B CDO669 Adh4 ABG484 WG114 BCD453B ABG313B
ABA003 ABG003
ABG498 ABG054 ABG394 ABG397 ABG500b TubA1 WG622 bAL882 ABC303
cMWG652B bAP91
MWG058 bBE54A MWG634 iHxk2 ABG319A ABG319C B32E MWG635a ABC321
MWG077 -------
group4= Glx ABC455 Brz iEst5 Ubi1 Prx1A ABG312 PSR106B WG420 CDO475
WG789A
BCD298B ABC305 ksuA1A His3A Pgk2B ksuD14C BCD129 Amy2 ABG461 ABC465
WG719 PSR129
CDO673 ABG476 Chi1 Adh7 Tha ABC151 ABC154A Plc Dor4B ABC156d ABC158
ABR303
ABR329 ABG380 WG834 WG380A ABC310b Cat3 ABC167a ABC169A dRpg1 ABG011
ABG022A
ABA301 ABC154B ABG701 ABG704 ABG652 MWG010B ABC308 bBE54E RisP103
MWG089 iPgd1A
MWG036B MWG813B MWG706C MWG836 MWG003 ABG320 MWG635B ABG075
MWG911 MWG555a
ABC322A BCD340C BCD340D ABC255 YAtp57A ABC254 MWG042B AdhIntro
MWG851a dSbl -------
group5= ABC451 ABG453 ABC454 PSR156 ABG459 ABG460 Prx2 RbcS Bmy2 mPub
ksuA3C
ABC307B BCD351F BCD828 Gln2 Chs1A Chs1b ksuD22 ABG356 ABG377 ABG358
Pcr1 ksuF2B
ABC306 CDO373 ksuF15 ABG462 ABC468 WG516 ABG471 iBgl BG123a WG996
WG645 Glb3
Glb4 Adh5 Adh8 Pox ABC152D ABC153 BCD410 Dor4A WG110 ABC156A ABC156C
CDO537
CDO64 CDO588 ABG4 ABC157 ABC161 ABC162 Prx1B CDO474c CDO113B His4B
ABG313A
ABC165 ABC166 ABG495B ABA005 ABG002 ABG014 ABR320 ABC167B ABC171
ABC172 ABR334
CDO474B ABG389 ABG005 ABG008 ABG019 Rrn5S1 Crg3A Crg3B ABC174 ABC176
ABA303
Rrn5S2 ABG058 ABG396 BCD131 ABG398 ABG399 ABG499 ABR338 ABG057
ABG703A ABG703b
ABA302 ABG010 His3C ABG654 MWG838 MWG503 cMWG682 MWG902 MWG858
MWG950 ABG315
bBE54C bBE54D ABG316A MWG584 ABG316C ABG316D ABG316E ABG317A
ABG317B ABG318 B15C
AtpbB cMWG691 MWG571B MWG571C MWG571a ABG319B cMWG720 ABG070
MWG798B ABC252
ABG065A ABG072 MWG520A MWG520B MWG878 MWG555b MWG064 MWG680
MWG557 ABC323 F3hA
MWG497 MWG041 -------
group6= ABG452 iPgd2 Hor1 Hor2 Ica1 Cab2 ABC307A BCD351C WG789B Chs3
CDO99 Pcr2
ksuF2A ABG373 ABG464 BCD98 Hor5 Glb1 ABC152B His4A Dor2 ABC160 Aga7
CDO105B
ABC164 ABG494 Act8 ABA002 ABA004 Aga6 ABG387a ABG022B ABG500a ABR337
ABG702
His3B MWG800 RisBPP16 ABG059 AtpbA ABC257 cMWG733 cMWG706a MWG706B
MWG837 MWG912
ABC261 ABG074 ABG055 MWG635C ABC322B BCD340A MWG938 MWG042A
KFP153B -------
group7= iEst9 Cab1 ABG463 WG644 CDO484 WG908 ABC309 CDO504 ABC482
ABC155 ABC310A
ABG495A ABG496 ABG390 ABG391 ABG707 ABG712 ABG314A ABG314B MWG514B
MWG813a
MWG877 MWG851b MWG851C MWG851D -------
unlinked= MWG798a BCD340B KFP153A F3hB
49> sequence group7
sequence #31= group7
50> order
Linkage Groups at min LOD 3.00, max Distance 50.0
Starting Orders: Size 5, Log-Likelihood 3.00, Searching up to 50 subsets
Informativeness: min #Individuals 1, min Distance 0.9
Placement Threshold-1 3.00, Threshold-2 2.00, Npt-Window 7 ==================================================================== ===========
Linkage group 1, 25 Markers:
19 iEst9 47 Cab1 95 ABG463 107 WG644 124 CDO484
125 WG908 129 ABC309 131 CDO504 144 ABC482 163 ABC155
194 ABC310A 200 ABG495A 233 ABG496 239 ABG390 240 ABG391
294 ABG707 307 ABG712 319 ABG314A 320 ABG314B 330 MWG514B
354 MWG813a 357 MWG877 424 MWG851b 425 MWG851C 426
MWG851D
Most informative subset: 19 425 95 107 124 125 424 131 144 163 194 200 357 354
240 294 307 330 320
Searching for a unique starting order containing 5 of 19 informative loci...
Got one at log-likelihood 6.49
Placing at log-likelihood threshold 3.00...
Start: 200 144 240 124 354
Npt-1: 200 144 240 (239) 124 354
Npt-1: 200 144 240 239 124 (95) 354
Npt-4: 200 (47) 144 240 239 124 95 354
Npt-5: 200 47 (163) 144 240 239 124 95 354
Npt-End: (125) 200 47 163 144 240 239 124 95 354
Npt-7: 125 (357) 200 47 163 144 240 239 124 95 354
Npt-End: 125 357 200 47 163 144 240 239 124 95 354 (426)
Npt-1: 125 357 200 47 163 144 240 239 124 95 354 (425) 426
Npt-1: 125 357 200 47 163 144 240 239 124 95 354 (320) 425 426
Npt-End: (330) 125 357 200 47 163 144 240 239 124 95 354 320 425 426
Npt-5: 330 (131) 125 357 200 47 163 144 240 239 124 95 354 320 425 426
Npt-1: 330 131 (19) 125 357 200 47 163 144 240 239 124 95 354 320 425 426
Npt-5: 330 131 (107) 19 125 357 200 47 163 144 240 239 124 95 354 320 425 426
Npt-7: 330 131 107 (307) 19 125 357 200 47 163 144 240 239 124 95 354 320 425
426
No unique placements for 6 remaining markers
Map:
Markers Distance
330 MWG514B 9.3 cM
131 CDO504 4.4 cM
107 WG644 3.5 cM
307 ABG712 3.5 cM
19 iEst9 2.7 cM
125 WG908 5.6 cM
357 MWG877 4.5 cM
200 ABG495A 7.7 cM
47 Cab1 0.0 cM
163 ABC155 6.4 cM
144 ABC482 5.7 cM
240 ABG391 2.8 cM
239 ABG390 7.9 cM
124 CDO484 2.8 cM
95 ABG463 3.5 cM
354 MWG813a 1.4 cM
320 ABG314B 2.8 cM
425 MWG851C 2.8 cM
426 MWG851D ----------
77.1 cM 19 markers log-likelihood= -235.11
Markers placed relative to above map:
330 131 107 307 19 125 357 200 47 163 144 240 239 124
:--9-:--4-:--3-:--3-:--3-:--6-:--4-:--8-:--0-:--6-:--6-:--3-:--8-:
424 2 ...:....:....:....:....:....:....:....:....:....:....:....:....:....:
319 2 ...:....:....:....:....:....:....:....:....:....:....:....:....:....:
129 2 ...:....:....:....:....:....:....:....:....:....:....:....:....:....:
194 2 ...:....:....:....:....:....:....:....:....:....:....:....:..*.:.**.:
294 2 ...:....:....:....:....:....:....:....:....:....:....:....:.**.:..*.:
233 2 ...:....:....:....:....:....:....:....:.**.:....:..*.:....:....:....:
124 95 354 320 425 426
:--3-:--3-:--1-:--3-:--3-:
424 2 :....:....:....:....:..*.:**.
319 2 :....:....:..*.:.**.:....:...
129 2 :....:....:..*.:.**.:....:...
194 2 :....:....:....:....:....:...
294 2 :....:....:....:....:....:...
233 2 :....:....:....:....:....:... -------------------------------------------------------------------------------
Placing at log-likelihood threshold 2.00...
Start: 330 131 107 307 19 125 357 200 47 163 144 240 239 124 95 354 320 425
426
Npt-5: 330 131 107 307 19 125 357 200 (233) 47 163 144 240 239 124 95 354 320
425 426
No unique placements for 5 remaining markers
Map:
Markers Distance
330 MWG514B 9.3 cM
131 CDO504 4.4 cM
107 WG644 3.5 cM
307 ABG712 3.5 cM
19 iEst9 2.7 cM
125 WG908 5.6 cM
357 MWG877 4.5 cM
200 ABG495A 6.8 cM
233 ABG496 0.7 cM
47 Cab1 0.0 cM
163 ABC155 6.4 cM
144 ABC482 5.7 cM
240 ABG391 2.8 cM
239 ABG390 7.9 cM
124 CDO484 2.8 cM
95 ABG463 3.5 cM
354 MWG813a 1.4 cM
320 ABG314B 2.8 cM
425 MWG851C 2.8 cM
426 MWG851D ----------
76.9 cM 20 markers log-likelihood= -236.54
Markers placed relative to above map:
330 131 107 307 19 125 357 200 233 47 163 144 240 239
:--9-:--4-:--3-:--3-:--3-:--6-:--4-:--7-:--1-:--0-:--6-:--6-:--3-:
424 2 ...:....:....:....:....:....:....:....:....:....:....:....:....:....:
129 2 ...:....:....:....:....:....:....:....:....:....:....:....:....:....:
319 2 ...:....:....:....:....:....:....:....:....:....:....:....:....:....:
194 2 ...:....:....:....:....:....:....:....:....:....:....:....:....:..*.:
294 2 ...:....:....:....:....:....:....:....:....:....:....:....:....:.**.:
239 124 95 354 320 425 426
:--8-:--3-:--3-:--1-:--3-:--3-:
424 2 :....:....:....:....:....:..*.:**.
129 2 :....:....:....:..*.:.**.:....:...
319 2 :....:....:....:..*.:.**.:....:...
194 2 :.**.:....:....:....:....:....:...
294 2 :..*.:....:....:....:....:....:...
order1= MWG514B CDO504 WG644 ABG712 iEst9 WG908 MWG877 ABG495A
ABG496 Cab1
ABC155 ABC482 ABG391 ABG390 CDO484 ABG463 MWG813a ABG314B MWG851C
MWG851D
other1= MWG851b ABC309 ABG314A ABC310A ABG707 ==================================================================== ===========
51> sequence 330 131 107 307 19 125 357 200 233 47 163 144 240 239 124 95 354 320
425 426
sequence #32= 330 131 107 307 19 125 357 200 233 47 163 144 240 239 124 95 354
320 425 426
52> map ==================================================================== ===========
Map:
Markers Distance
330 MWG514B 9.3 cM
131 CDO504 4.4 cM
107 WG644 3.5 cM
307 ABG712 3.5 cM
19 iEst9 2.7 cM
125 WG908 5.6 cM
357 MWG877 4.5 cM
200 ABG495A 6.8 cM
233 ABG496 0.7 cM
47 Cab1 0.0 cM
163 ABC155 6.4 cM
144 ABC482 5.7 cM
240 ABG391 2.8 cM
239 ABG390 7.9 cM
124 CDO484 2.8 cM
95 ABG463 3.5 cM
354 MWG813a 1.4 cM
320 ABG314B 2.8 cM
425 MWG851C 2.8 cM
426 MWG851D ----------
76.9 cM 20 markers log-likelihood= -236.54 ==================================================================== ===========
53> make chromosome chromx
chromosomes defined: leah1a chrom5a chromx
54> anchor chromx
MWG514B - anchor locus on chromx
CDO504 - anchor locus on chromx
WG644 - anchor locus on chromx
ABG712 - anchor locus on chromx
iEst9 - anchor locus on chromx
WG908 - anchor locus on chromx
MWG877 - anchor locus on chromx
ABG495A - anchor locus on chromx
ABG496 - anchor locus on chromx
Cab1 - anchor locus on chromx
ABC155 - anchor locus on chromx
ABC482 - anchor locus on chromx
ABG391 - anchor locus on chromx
ABG390 - anchor locus on chromx
CDO484 - anchor locus on chromx
ABG463 - anchor locus on chromx
MWG813a - anchor locus on chromx
ABG314B - anchor locus on chromx
MWG851C - anchor locus on chromx
MWG851D - anchor locus on chromx
chromosome chromx anchor(s): iEst9 Cab1 ABG463 WG644 CDO484 WG908 CDO504
ABC482
ABC155 ABG495A ABG496 ABG390 ABG391 ABG712 ABG314B MWG514B
MWG813a MWG877
MWG851C MWG851D
55> framework chromx
setting framework for chromosome chromx... ==================================================================== ===========
chromx framework:
Markers Distance
330 MWG514B 9.3 cM
131 CDO504 4.4 cM
107 WG644 3.5 cM
307 ABG712 3.5 cM
19 iEst9 2.7 cM
125 WG908 5.6 cM
357 MWG877 4.5 cM
200 ABG495A 6.8 cM
233 ABG496 0.7 cM
47 Cab1 0.0 cM
163 ABC155 6.4 cM
144 ABC482 5.7 cM
240 ABG391 2.8 cM
239 ABG390 7.9 cM
124 CDO484 2.8 cM
95 ABG463 3.5 cM
354 MWG813a 1.4 cM
320 ABG314B 2.8 cM
425 MWG851C 2.8 cM
426 MWG851D ----------
76.9 cM 20 markers log-likelihood= -236.54 ==================================================================== ===========
56> help chromosome
unrecognized command or help topic: 'chromosome'
Type 'help' for a list of commands and topics.
Type 'help Type 'help 57> help make chromosome
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MAKE CHROMOSOME Command
Description: Specify the Name(s) or Chromosome(s)
Help Topic: (6) Genome Analysis Features
Argument: The 'make chromosome' command declares one or more named chromosomes
to exist. (Upon creation, no markers are assigned to the new
chromosome). There is presently no way to completely undo the 'make
chromosome' command -- once declared, a chromosme exists until the data
file is re-prepared. Luckily, "extra" chromosomes may be safely
ignored if no loci are assigned to them.
====================================================================
=========
58> help framework
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=========
FRAMEWORK Command
Description: Set the Framework Map Order for a Chromosome
Help Topic: (6) Genome Analysis Features
Argument: MAPMAKER/EXP Commands and Options:
(1) GENERAL INFORMATION ON MAPMAKER VERSION 3.0:
about mapmaker.............License and Contact Information for MAPMAKER
release notes..............Information on the Release Notes
starting mapmaker..........How to Start MAPMAKER and Available Options
tutorial...................Information on the MAPMAKER Tutorial
entering commands..........How to Type Commands Into MAPMAKER
abbreviating commands......How to Abbreviate Commands You Type
keyboard editing...........Editing Commands and Sequences Using the Keyboard
postscript output..........What to Do With MAPMAKER PostScript Graphic Output
(2) BASIC MAPMAKER COMMANDS:
help (?)...................Read On-Line Help Information
photo......................Begin Saving MAPMAKER Output to a Text File
prepare data (pd)..........Prepares a New Data Set for Analysis
load data (ld).............Load Data Set for Analysis
save data..................Save Status, Mapping Results, etc.
quit (q)...................Quit from a MAPMAKER Session
(3) SEQUENCE COMMAND AND RELATED FEATURES:
sequence (s)...............Select the Loci and Order(s) You Wish to Analyze
history (h)................List Previous Sequences
expand sequence (x)........Set the Sequence, Expanding Names
insert (i).................Insert a Marker into the Sequence
append (a).................Append Marker(s) to the End of the Sequence
delete (d).................Deletes a Marker or Markers from the Sequence
edit sequence (e)..........Edit a Sequence Using the Keyboard
let (l)....................Name a Sequence
names (n)..................List the Named Sequences
forget named sequence......Erase a Named Sequence
translate (t)..............Show the Names and Numbers of Loci in the Sequence
(4) TWO-POINT (PAIRWISE) ANALYSIS COMMANDS:
two point..................Compute Pairwise Distances and LOD Scores
lod table..................Print All Two-Point Data for the Current Sequence
big lods...................List Linked Pairs of Markers in Sequence
near.......................List Markers in Sequence Near Other Marker(s)
links......................Find Any Markers Near Given Marker(s)
pairwise...................Print Two-Point Data Between Sequence and Other Loci
group......................Separate Markers in Sequence into Linkage Groups
default linkage criteria...LOD and Distance Thresholds for Two-Point Linkage
suggest subset.............Find Highly-Informative Well-Spaced Markers
informativeness criteria...Criteria for Finding Highly-Informative Markers
(5) MULTIPOINT ANALYSIS COMMANDS:
map (m)....................Compute and Print a Maximum Likelihood Map
draw map...................Compute and Draw a Maximum Likelihood Map
compare (c)................Compare Likelihoods of Many Map Orders
try........................Insert Markers into an Order and Compare Likelihoods
ripple.....................Test a Map Order by Permuting Local Orders
order......................Automatically Build Map Orders from Scratch
build......................Sequentially Add New Markers into a Known Map Order
multipoint criteria........Mapping Criteria for 'Order', 'Build', etc.
(6) GENOME ANALYSIS FEATURES:
make chromosome............Specify the Name(s) or Chromosome(s)
assign.....................Assign Markers to a Chromosome by Linkage
attach.....................Assign Markers to a Chromosome, Regardless
unassign...................Unassign Markers from All Chromosomes
anchor.....................Specify the Anchor Loci for a Chromosome
framework..................Set the Framework Map Order for a Chromosome
place......................Place Markers Relative to a Chromosome Framework
together...................Places Loci Together into the Framework
list loci (ll).............List Various Facts about Some Loci
list status (ls)...........List Mapping Status for Some Loci
list chromosomes (lc)......List the Number of Markers Mapped to Each Chromosome
list assignments (la)......List the Markers Assigned to Each Chromosome
draw chromosome............Draw Frameworks and Placements in PostScript
draw all chromosomes.......Draw All Frameworks and Placements in PostScript
age........................Declare Markers as 'Old' or 'New'
class......................Declare the Class for Markers
make class.................Define New Class(es) of Markers
(7) SYSTEMATIC ERROR DETECTION MECHANISM:
error detection............Turn the Typing Error Detection Mechanism On/Off
error probability..........Apriori Probability of Genotyping Error
error thresholds...........LOD-Error Thresholds for Candidate Errors
genotypes..................Display a Map at the Individual Crossover Level
(8) THREE-POINT ANALYSIS MECHANISM:
use three point............Whether Three-Point Analysis Will Be Used
three point................Pre-Compute Three-Point Log-Likelihoods
triple linkage criteria....Linkage Criteria for 'Three Point' Triples
triple exclusion criteria..Log-Likelihood Thresholds for Excluding a Triple
triple error detection.....Error Detection Option for Three-Point Analysis
forget three point.........Forget Pre-Computed Three-Point Likelihoods
(9) JOINING HAPLOTYPES IN LARGE DATA SETS:
join haplotypes............Collect Unseparated Markers into Haplotype Groups
list haplotypes (lh).......List Haplotype Groups for Certain Loci
restore haplotypes.........Un-Join Particular Haplotype Groups
(10) MAPMAKER PARAMETERS AND OPTIONS:
print names................Display Locus Names Instead of Numbers
print maps.................Print All Maps for Placed Markers
tolerance..................Convergence Tolerance
auto save data.............Automatically Save Data
units......................Units of Map Distance, Either cM or RF
centimorgan function.......Default Map Function, Either Haldane or Kosambi
more mode..................Enable Pauses after Each Screen of Output
(11) MISCELLANEOUS COMMANDS:
previous commands (p)......Review and Re-enter Previous Commands
review output..............Review Previous MAPMAKER Output
change directory (cd)......Change Default Directory Used by MAPMAKER
run........................Accept Commands from an Input File
time.......................Print Current Time
comment....................Enter a Comment into the Transcript
remark.....................Same as 'Comment'
system.....................Run System Command(s) Without Quitting MAPMAKER
import data................Load Data from a Database
export data................Save Data to a Database
wizard mode................Danger Will Robinson, Danger!
61> help
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=========
MAPMAKER/EXP Commands and Options:
(1) GENERAL INFORMATION ON MAPMAKER VERSION 3.0:
about mapmaker.............License and Contact Information for MAPMAKER
release notes..............Information on the Release Notes
starting mapmaker..........How to Start MAPMAKER and Available Options
tutorial...................Information on the MAPMAKER Tutorial
entering commands..........How to Type Commands Into MAPMAKER
abbreviating commands......How to Abbreviate Commands You Type
keyboard editing...........Editing Commands and Sequences Using the Keyboard
postscript output..........What to Do With MAPMAKER PostScript Graphic Output
(2) BASIC MAPMAKER COMMANDS:
help (?)...................Read On-Line Help Information
photo......................Begin Saving MAPMAKER Output to a Text File
prepare data (pd)..........Prepares a New Data Set for Analysis
load data (ld).............Load Data Set for Analysis
save data..................Save Status, Mapping Results, etc.
quit (q)...................Quit from a MAPMAKER Session
(3) SEQUENCE COMMAND AND RELATED FEATURES:
sequence (s)...............Select the Loci and Order(s) You Wish to Analyze
history (h)................List Previous Sequences
expand sequence (x)........Set the Sequence, Expanding Names
insert (i).................Insert a Marker into the Sequence
append (a).................Append Marker(s) to the End of the Sequence
delete (d).................Deletes a Marker or Markers from the Sequence
edit sequence (e)..........Edit a Sequence Using the Keyboard
let (l)....................Name a Sequence
names (n)..................List the Named Sequences
forget named sequence......Erase a Named Sequence
translate (t)..............Show the Names and Numbers of Loci in the Sequence
(4) TWO-POINT (PAIRWISE) ANALYSIS COMMANDS:
two point..................Compute Pairwise Distances and LOD Scores
lod table..................Print All Two-Point Data for the Current Sequence
big lods...................List Linked Pairs of Markers in Sequence
near.......................List Markers in Sequence Near Other Marker(s)
links......................Find Any Markers Near Given Marker(s)
pairwise...................Print Two-Point Data Between Sequence and Other Loci
group......................Separate Markers in Sequence into Linkage Groups
default linkage criteria...LOD and Distance Thresholds for Two-Point Linkage
suggest subset.............Find Highly-Informative Well-Spaced Markers
informativeness criteria...Criteria for Finding Highly-Informative Markers
(5) MULTIPOINT ANALYSIS COMMANDS:
map (m)....................Compute and Print a Maximum Likelihood Map
draw map...................Compute and Draw a Maximum Likelihood Map
compare (c)................Compare Likelihoods of Many Map Orders
try........................Insert Markers into an Order and Compare Likelihoods
ripple.....................Test a Map Order by Permuting Local Orders
order......................Automatically Build Map Orders from Scratch
build......................Sequentially Add New Markers into a Known Map Order
multipoint criteria........Mapping Criteria for 'Order', 'Build', etc.
(6) GENOME ANALYSIS FEATURES:
make chromosome............Specify the Name(s) or Chromosome(s)
assign.....................Assign Markers to a Chromosome by Linkage
attach.....................Assign Markers to a Chromosome, Regardless
unassign...................Unassign Markers from All Chromosomes
anchor.....................Specify the Anchor Loci for a Chromosome
framework..................Set the Framework Map Order for a Chromosome
place......................Place Markers Relative to a Chromosome Framework
together...................Places Loci Together into the Framework
list loci (ll).............List Various Facts about Some Loci
list status (ls)...........List Mapping Status for Some Loci
list chromosomes (lc)......List the Number of Markers Mapped to Each Chromosome
list assignments (la)......List the Markers Assigned to Each Chromosome
draw chromosome............Draw Frameworks and Placements in PostScript
draw all chromosomes.......Draw All Frameworks and Placements in PostScript
age........................Declare Markers as 'Old' or 'New'
class......................Declare the Class for Markers
make class.................Define New Class(es) of Markers
(7) SYSTEMATIC ERROR DETECTION MECHANISM:
error detection............Turn the Typing Error Detection Mechanism On/Off
error probability..........Apriori Probability of Genotyping Error
error thresholds...........LOD-Error Thresholds for Candidate Errors
genotypes..................Display a Map at the Individual Crossover Level
(8) THREE-POINT ANALYSIS MECHANISM:
use three point............Whether Three-Point Analysis Will Be Used
three point................Pre-Compute Three-Point Log-Likelihoods
triple linkage criteria....Linkage Criteria for 'Three Point' Triples
triple exclusion criteria..Log-Likelihood Thresholds for Excluding a Triple
triple error detection.....Error Detection Option for Three-Point Analysis
forget three point.........Forget Pre-Computed Three-Point Likelihoods
(9) JOINING HAPLOTYPES IN LARGE DATA SETS:
join haplotypes............Collect Unseparated Markers into Haplotype Groups
list haplotypes (lh).......List Haplotype Groups for Certain Loci
restore haplotypes.........Un-Join Particular Haplotype Groups
(10) MAPMAKER PARAMETERS AND OPTIONS:
print names................Display Locus Names Instead of Numbers
print maps.................Print All Maps for Placed Markers
tolerance..................Convergence Tolerance
auto save data.............Automatically Save Data
units......................Units of Map Distance, Either cM or RF
centimorgan function.......Default Map Function, Either Haldane or Kosambi