Input Data File: C:\...\5GenomesAligned_CovMasked.fas
 Number of sequences: 5    Number of sequences used: 5
 Selected region: 1-2199798   Number of sites: 2199798
 Total number of sites (excluding sites with gaps / missing data): 2193978

 Number of polymorphic (segregating) sites, S: 10580

 Estimate of the recombination parameter, R (or C) (Hudson 1987)
    Variance of the sample distribution of Kij, Sk^2: 12610170.000
    Estimate of Theta, per gene: 4519.800
    Value of the function g(C,n): 0.6172
    Estimate of R, per gene: 1.3
    Estimate of R, between adjacent sites: 0.0000
       Average nucleotide distance between the most distant sites: 2196554.00

 Minimum number of recombination events (Hudson and Kaplan 1985)
    Sites segregating for three or four nucleotides were not considered
          Site positions:  880984 882475 992968 993180 1049745 1080716 1623768 1881493
    Number of pairwise comparisons analyzed: 55878306
    Number of pairs of sites with four gametic types: 81299
       (Only the first 500 have been displayed)
          (4096,65040)  (4096,65621)  (4096,94226)  (4096,138047)  (4096,138064)
          (4096,223713)  (4096,444977)  (4096,447787)  (4096,447939)  (4096,495910)
          (4096,495943)  (4096,499626)  (4096,499639)  (4096,499640)  (4096,666889)
          (4096,689423)  (4096,774025)  (4096,783579)  (4096,834086)  (4096,878868)
          (4096,880942)  (4096,930284)  (4096,959472)  (4096,971220)  (4096,971495)
          (4096,972447)  (4096,975051)  (4096,975123)  (4096,975277)  (4096,975297)
          (4096,976467)  (4096,978224)  (4096,983054)  (4096,993530)  (4096,1053322)
          (4096,1053324)  (4096,1053348)  (4096,1053400)  (4096,1080725)  (4096,1080726)
          (4096,1121204)  (4096,1160500)  (4096,1160502)  (4096,1160660)  (4096,1173970)
          (4096,1177745)  (4096,1202448)  (4096,1212984)  (4096,1214066)  (4096,1214134)
          (4096,1214467)  (4096,1215365)  (4096,1215413)  (4096,1231882)  (4096,1250954)
          (4096,1250960)  (4096,1250961)  (4096,1250962)  (4096,1250964)  (4096,1289185)
          (4096,1292874)  (4096,1292886)  (4096,1292889)  (4096,1292977)  (4096,1479599)
          (4096,1479608)  (4096,1497490)  (4096,1500069)  (4096,1500076)  (4096,1500085)
          (4096,1543603)  (4096,1578293)  (4096,1599708)  (4096,1618218)  (4096,1618319)
          (4096,1632866)  (4096,1632931)  (4096,1634358)  (4096,1744411)  (4096,1744483)
          (4096,1777119)  (4096,1777137)  (4096,1780019)  (4096,1780037)  (4096,1797456)
          (4096,1820815)  (4096,1832431)  (4096,1856617)  (4096,1894901)  (4096,1899751)
          (4096,1956260)  (4096,2056961)  (4096,2070742)  (4096,2089672)  (4096,2103582)
          (4096,2104321)  (4096,2104472)  (4096,2104475)  (4096,2104596)  (4096,2106073)
          (4096,2106077)  (4096,2121578)  (4096,2153711)  (4616,138047)  (4616,138064)
          (4616,248305)  (4616,449373)  (4616,499626)  (4616,591582)  (4616,880942)
          (4616,1053286)  (4616,1053296)  (4616,1053322)  (4616,1053324)  (4616,1053348)
          (4616,1053400)  (4616,1080725)  (4616,1080726)  (4616,1280112)  (4616,1292874)
          (4616,1292886)  (4616,1292889)  (4616,1292977)  (4616,1500069)  (4616,1500076)
          (4616,1500085)  (4616,1622959)  (4616,1623004)  (4616,1632866)  (4616,1744483)
          (4616,2115111)  (7677,65040)  (7677,65621)  (7677,94226)  (7677,138047)
          (7677,138064)  (7677,223713)  (7677,444977)  (7677,447787)  (7677,447939)
          (7677,495910)  (7677,495943)  (7677,499626)  (7677,499639)  (7677,499640)
          (7677,666889)  (7677,689423)  (7677,774025)  (7677,783579)  (7677,834086)
          (7677,878868)  (7677,880942)  (7677,930284)  (7677,959472)  (7677,971220)
          (7677,971495)  (7677,972447)  (7677,975051)  (7677,975123)  (7677,975277)
          (7677,975297)  (7677,976467)  (7677,978224)  (7677,983054)  (7677,993530)
          (7677,1053322)  (7677,1053324)  (7677,1053348)  (7677,1053400)  (7677,1080725)
          (7677,1080726)  (7677,1121204)  (7677,1160500)  (7677,1160502)  (7677,1160660)
          (7677,1173970)  (7677,1177745)  (7677,1202448)  (7677,1212984)  (7677,1214066)
          (7677,1214134)  (7677,1214467)  (7677,1215365)  (7677,1215413)  (7677,1231882)
          (7677,1250954)  (7677,1250960)  (7677,1250961)  (7677,1250962)  (7677,1250964)
          (7677,1289185)  (7677,1292874)  (7677,1292886)  (7677,1292889)  (7677,1292977)
          (7677,1479599)  (7677,1479608)  (7677,1497490)  (7677,1500069)  (7677,1500076)
          (7677,1500085)  (7677,1543603)  (7677,1578293)  (7677,1599708)  (7677,1618218)
          (7677,1618319)  (7677,1632866)  (7677,1632931)  (7677,1634358)  (7677,1744411)
          (7677,1744483)  (7677,1777119)  (7677,1777137)  (7677,1780019)  (7677,1780037)
          (7677,1797456)  (7677,1820815)  (7677,1832431)  (7677,1856617)  (7677,1894901)
          (7677,1899751)  (7677,1956260)  (7677,2056961)  (7677,2070742)  (7677,2089672)
          (7677,2103582)  (7677,2104321)  (7677,2104472)  (7677,2104475)  (7677,2104596)
          (7677,2106073)  (7677,2106077)  (7677,2121578)  (7677,2153711)  (7689,138047)
          (7689,138064)  (7689,248305)  (7689,449373)  (7689,499626)  (7689,591582)
          (7689,880942)  (7689,1053286)  (7689,1053296)  (7689,1053322)  (7689,1053324)
          (7689,1053348)  (7689,1053400)  (7689,1080725)  (7689,1080726)  (7689,1280112)
          (7689,1292874)  (7689,1292886)  (7689,1292889)  (7689,1292977)  (7689,1500069)
          (7689,1500076)  (7689,1500085)  (7689,1622959)  (7689,1623004)  (7689,1632866)
          (7689,1744483)  (7689,2115111)  (7924,138047)  (7924,138064)  (7924,248305)
          (7924,449373)  (7924,499626)  (7924,591582)  (7924,880942)  (7924,1053286)
          (7924,1053296)  (7924,1053322)  (7924,1053324)  (7924,1053348)  (7924,1053400)
          (7924,1080725)  (7924,1080726)  (7924,1280112)  (7924,1292874)  (7924,1292886)
          (7924,1292889)  (7924,1292977)  (7924,1500069)  (7924,1500076)  (7924,1500085)
          (7924,1622959)  (7924,1623004)  (7924,1632866)  (7924,1744483)  (7924,2115111)
          (8451,65040)  (8451,65621)  (8451,94226)  (8451,138047)  (8451,138064)
          (8451,223713)  (8451,444977)  (8451,447787)  (8451,447939)  (8451,495910)
          (8451,495943)  (8451,499626)  (8451,499639)  (8451,499640)  (8451,666889)
          (8451,689423)  (8451,774025)  (8451,783579)  (8451,834086)  (8451,878868)
          (8451,880942)  (8451,930284)  (8451,959472)  (8451,971220)  (8451,971495)
          (8451,972447)  (8451,975051)  (8451,975123)  (8451,975277)  (8451,975297)
          (8451,976467)  (8451,978224)  (8451,983054)  (8451,993530)  (8451,1053322)
          (8451,1053324)  (8451,1053348)  (8451,1053400)  (8451,1080725)  (8451,1080726)
          (8451,1121204)  (8451,1160500)  (8451,1160502)  (8451,1160660)  (8451,1173970)
          (8451,1177745)  (8451,1202448)  (8451,1212984)  (8451,1214066)  (8451,1214134)
          (8451,1214467)  (8451,1215365)  (8451,1215413)  (8451,1231882)  (8451,1250954)
          (8451,1250960)  (8451,1250961)  (8451,1250962)  (8451,1250964)  (8451,1289185)
          (8451,1292874)  (8451,1292886)  (8451,1292889)  (8451,1292977)  (8451,1479599)
          (8451,1479608)  (8451,1497490)  (8451,1500069)  (8451,1500076)  (8451,1500085)
          (8451,1543603)  (8451,1578293)  (8451,1599708)  (8451,1618218)  (8451,1618319)
          (8451,1632866)  (8451,1632931)  (8451,1634358)  (8451,1744411)  (8451,1744483)
          (8451,1777119)  (8451,1777137)  (8451,1780019)  (8451,1780037)  (8451,1797456)
          (8451,1820815)  (8451,1832431)  (8451,1856617)  (8451,1894901)  (8451,1899751)
          (8451,1956260)  (8451,2056961)  (8451,2070742)  (8451,2089672)  (8451,2103582)
          (8451,2104321)  (8451,2104472)  (8451,2104475)  (8451,2104596)  (8451,2106073)
          (8451,2106077)  (8451,2121578)  (8451,2153711)  (8909,138047)  (8909,138064)
          (8909,248305)  (8909,449373)  (8909,499626)  (8909,591582)  (8909,880942)
          (8909,1053286)  (8909,1053296)  (8909,1053322)  (8909,1053324)  (8909,1053348)
          (8909,1053400)  (8909,1080725)  (8909,1080726)  (8909,1280112)  (8909,1292874)
          (8909,1292886)  (8909,1292889)  (8909,1292977)  (8909,1500069)  (8909,1500076)
          (8909,1500085)  (8909,1622959)  (8909,1623004)  (8909,1632866)  (8909,1744483)
          (8909,2115111)  (10776,138047)  (10776,138064)  (10776,248305)  (10776,449373)
          (10776,499626)  (10776,591582)  (10776,880942)  (10776,1053286)  (10776,1053296)
          (10776,1053322)  (10776,1053324)  (10776,1053348)  (10776,1053400)  (10776,1080725)
          (10776,1080726)  (10776,1280112)  (10776,1292874)  (10776,1292886)  (10776,1292889)
          (10776,1292977)  (10776,1500069)  (10776,1500076)  (10776,1500085)  (10776,1622959)
          (10776,1623004)  (10776,1632866)  (10776,1744483)  (10776,2115111)  (11993,138047)
          (11993,138064)  (11993,248305)  (11993,449373)  (11993,499626)  (11993,591582)
          (11993,880942)  (11993,1053286)  (11993,1053296)  (11993,1053322)  (11993,1053324)
          (11993,1053348)  (11993,1053400)  (11993,1080725)  (11993,1080726)  (11993,1280112)
          (11993,1292874)  (11993,1292886)  (11993,1292889)  (11993,1292977)  (11993,1500069)
          (11993,1500076)  (11993,1500085)  (11993,1622959)  (11993,1623004)  (11993,1632866)
          (11993,1744483)  (11993,2115111)  (12228,138047)  (12228,138064)  (12228,248305)
          (12228,449373)  (12228,499626)  (12228,591582)  (12228,880942)  (12228,1053286)
          (12228,1053296)  (12228,1053322)  (12228,1053324)  (12228,1053348)  (12228,1053400)
          (12228,1080725)  (12228,1080726)  (12228,1280112)  (12228,1292874)  (12228,1292886)
          (12228,1292889)  (12228,1292977)  (12228,1500069)  (12228,1500076)  (12228,1500085)

    Minimum number of recombination events, Rm: 113
    Recombination has been detected between sites:
          (57143,65040)  (65040,65621)  (65621,71273)  (86734,94226)  (94226,95196)
          (137418,138047)  (138064,139211)  (201229,223713)  (223713,226032)  (247543,248305)
          (248305,249284)  (440704,444977)  (447939,449373)  (449373,453062)  (490468,495910)
          (497690,499626)  (499626,500464)  (589643,591582)  (591582,596513)  (661739,666889)
          (666889,668099)  (680368,689423)  (689423,702044)  (767842,774025)  (774025,775129)
          (780261,783579)  (783579,783801)  (827476,834086)  (834086,853121)  (869174,878868)
          (878868,879212)  (879766,880942)  (880942,880959)  (928498,930284)  (930284,934511)
          (948084,959472)  (959472,962733)  (966403,971220)  (978224,981526)  (981526,983054)
          (983054,987495)  (989113,993530)  (993530,996459)  (1053184,1053286)  (1053400,1057065)
          (1080641,1080725)  (1080726,1081234)  (1118344,1121204)  (1121204,1132855)  (1160295,1160500)
          (1160660,1167298)  (1172040,1173970)  (1177745,1178720)  (1202321,1202448)  (1202448,1204359)
          (1207704,1212984)  (1215413,1231882)  (1277069,1280112)  (1280112,1280244)  (1288259,1289185)
          (1289336,1292874)  (1292889,1292977)  (1292977,1293717)  (1477837,1479599)  (1479608,1487685)
          (1496112,1497490)  (1497490,1497508)  (1499638,1500069)  (1500085,1500167)  (1512132,1543603)
          (1543603,1549874)  (1550841,1578293)  (1578293,1599708)  (1599708,1605282)  (1616622,1618218)
          (1618319,1622032)  (1622959,1623004)  (1623004,1623302)  (1631168,1632866)  (1632866,1632931)
          (1634358,1635215)  (1744251,1744411)  (1744483,1748374)  (1759136,1777119)  (1780037,1797456)
          (1797456,1810403)  (1814664,1820815)  (1832431,1856617)  (1856617,1858630)  (1893920,1894901)
          (1894901,1898478)  (1898934,1899751)  (1899751,1925849)  (1932522,1956260)  (1956260,1983979)
          (2056415,2056961)  (2056961,2056973)  (2066986,2070742)  (2070742,2075988)  (2079857,2089672)
          (2089672,2092016)  (2092496,2103582)  (2103582,2104321)  (2104321,2104472)  (2104596,2105237)
          (2105237,2106073)  (2106077,2109021)  (2112983,2115111)  (2115111,2115804)  (2119592,2121578)
          (2121578,2124215)  (2151816,2153711)  (2153711,2160293)