AllegroMCODE Plugin Results -Date: 27 Dec, 2013 11:27:40 AM -Network Identifier: proper_above35seq_id_paralog_pairs_overlap100.csv -Parameters: Node Scoring: Include Loops:false, Degree Cutoff:2 Cluster Finding: Node Score Cutoff: 0.2, K-Core: 2, Max. Depth from Seed: 100 Post-Processing: From Selection: false, Haircut: true, Fluff: false -Clusters: Id Rank Score Nodes Edges Node IDs 1 1 31.303 66 2066 Rv0109, Rv0124, Rv0159c, Rv0160c, Rv0278c, Rv0279c, Rv0297, Rv0532, Rv0578c, Rv0742, Rv0746, Rv0747, Rv0754, Rv0832, Rv0833, Rv0834c, Rv0872c, Rv0977, Rv0978c, Rv0980c, Rv1067c, Rv1068c, Rv1087, Rv1091, Rv1172c, Rv1214c, Rv1243c, Rv1325c, Rv1396c, Rv1441c, Rv1450c, Rv1452c, Rv1468c, Rv1651c, Rv1759c, Rv1768, Rv1803c, Rv1818c, Rv1840c, Rv1983, Rv2126c, Rv2162c, Rv2340c, Rv2396, Rv2487c, Rv2490c, Rv2591, Rv2615c, Rv2634c, Rv2741, Rv2853, Rv3097c, Rv3344c, Rv3345c, Rv3367, Rv3388, Rv3507, Rv3508, Rv3511, Rv3512, Rv3514, Rv3590c, Rv3595c, Rv3653, Rv0151c, Rv1430 2 2 20.556 45 925 Rv2352c, Rv0305c, Rv0355c, Rv0388c, Rv0442c, Rv0755c, Rv0878c, Rv1135c, Rv1753c, Rv1918c, Rv2108, Rv2356c, Rv3135, Rv3347c, Rv3350c, Rv3533c, Rv2608, Rv1802, Rv3159c, Rv2892c, Rv1787, Rv1790, Rv1917c, Rv3343c, Rv1039c, Rv1548c, Rv3558, Rv0915c, Rv1361c, Rv1705c, Rv1706c, Rv1789, Rv1801, Rv1807, Rv1808, Rv1809, Rv2768c, Rv2770c, Rv3125c, Rv3136, Rv3144c, Rv3478, Rv3532, Rv3539, Rv3621c 3 3 7.5 16 120 Rv0796, Rv1369c, Rv1756c, Rv1764, Rv2106, Rv2167c, Rv2279, Rv2355, Rv2479c, Rv2649, Rv2814c, Rv3185, Rv3187, Rv3326, Rv3380c, Rv3475 4 4 7.5 16 120 Rv0795, Rv1370c, Rv1757c, Rv1763, Rv2105, Rv2168c, Rv2278, Rv2354, Rv2480c, Rv2648, Rv2815c, Rv3184, Rv3186, Rv3325, Rv3381c, Rv3474 5 5 6.5 14 91 Rv0145, Rv0146, Rv0281, Rv0725c, Rv0726c, Rv0731c, Rv0830, Rv0893c, Rv1729c, Rv1889c, Rv1896c, Rv3399, Rv3767c, Rv3787c 6 6 5.8 15 87 Rv1662, Rv0405, Rv1180, Rv1527c, Rv1661, Rv1664, Rv2048c, Rv2382c, Rv2931, Rv2932, Rv2933, Rv2934, Rv2940c, Rv2947c, Rv3825c 7 7 4.5 10 45 Rv0404, Rv1185c, Rv1521, Rv1529, Rv1925, Rv2930, Rv2941, Rv2950c, Rv3801c, Rv3826 8 8 4 9 36 Rv0491, Rv0602c, Rv0757, Rv0903c, Rv0981, Rv1027c, Rv1033c, Rv3246c, Rv3765c 9 9 3.5 8 28 Rv1047, Rv1199c, Rv2512c, Rv2666, Rv3023c, Rv3115, Rv3431c, Rv3640c 10 10 3.5 8 28 Rv0469, Rv0470c, Rv0503c, Rv0642c, Rv0643c, Rv0644c, Rv0645c, Rv3392c 11 11 3.333 9 30 Rv0094c, Rv1128c, Rv1148c, Rv1587c, Rv1702c, Rv1945, Rv3467, Rv1588c, Rv3466 12 12 2.5 6 15 Rv1758, Rv1984c, Rv2301, Rv3451, Rv3452, Rv3724B 13 13 2.5 6 15 Rv2832c, Rv3758c, Rv2397c, Rv3102c, Rv1238, Rv2038c 14 14 2.5 6 15 Rv0606, Rv0922, Rv2791c, Rv2885c, Rv2978c, Rv3827c 15 15 2.5 6 15 Rv0605, Rv0921, Rv2792c, Rv2886c, Rv2979c, Rv3828c 16 16 2.5 6 15 Rv0402c, Rv0450c, Rv0507, Rv0676c, Rv1557, Rv2339 17 17 2.429 7 17 Rv0386, Rv0890c, Rv0891c, Rv0894, Rv1358, Rv1359, Rv2488c 18 18 2.333 6 14 Rv1350, Rv2766c, Rv1941, Rv2002, Rv2857c, Rv3559c 19 19 2.333 6 14 Rv0336, Rv0393, Rv0397, Rv0515, Rv2100, Rv3776 20 20 2 5 10 Rv3714c, Rv1073, Rv1482c, Rv3517, Rv3555c 21 21 2 5 10 Rv0291, Rv1796, Rv3449, Rv3883c, Rv3886c 22 22 2 5 10 Rv0271c, Rv3061c, Rv3560c, Rv3562, Rv3573c 23 23 1.5 4 6 Rv3734c, Rv3740c, Rv2285, Rv3480c 24 24 1.5 4 6 Rv1996, Rv2005c, Rv2026c, Rv2623 25 25 1.5 4 6 Rv1755c, Rv2349c, Rv2350c, Rv2351c 26 26 1.5 4 6 Rv1318c, Rv1319c, Rv1320c, Rv3645 27 27 1.5 4 6 Rv1261c, Rv1558, Rv3178, Rv3547 28 28 1.5 4 6 Rv0973c, Rv2501c, Rv2967c, Rv3285 29 29 1.5 4 6 Rv0953c, Rv2161c, Rv3072c, Rv3079c 30 30 1.5 4 6 Rv0859, Rv1074c, Rv3546, Rv3556c 31 31 1.5 4 6 Rv0617, Rv2494, Rv2530c, Rv3320c 32 32 1.5 4 6 Rv0609, Rv0624, Rv1982c, Rv2759c 33 33 1.5 4 6 Rv3764c, Rv0600c, Rv0758, Rv1032c 34 34 1.5 4 6 Rv0565c, Rv3083, Rv3741c, Rv3854c 35 35 1.5 4 6 Rv0403c, Rv0451c, Rv0506, Rv0677c 36 36 1.5 4 6 Rv0229c, Rv0301, Rv2546, Rv2757c 37 37 1.5 4 6 Rv0220, Rv1426c, Rv2284, Rv2485c 38 38 1.5 4 6 Rv0172, Rv0592, Rv1969, Rv3496c 39 39 1.5 4 6 Rv0170, Rv0590, Rv1967, Rv3498c 40 40 1.5 4 6 Rv0168, Rv0588, Rv1965, Rv3500c 41 41 1.5 4 6 Rv0167, Rv0587, Rv1964, Rv3501c 42 42 1.5 4 6 Rv0129c, Rv1886c, Rv3803c, Rv3804c 43 43 1.5 4 6 Rv0116c, Rv0192, Rv1433, Rv2518c 44 44 1.4 5 7 Rv0851c, Rv1245c, Rv3057c, Rv3085, Rv1882c 45 45 1.25 4 5 Rv0217c, Rv1400c, Rv2970c, Rv1399c 46 46 1.25 4 5 Rv0222, Rv0675, Rv1136, Rv2486 47 47 1.25 4 5 Rv0223c, Rv0458, Rv0768, Rv2858c 48 48 1.25 4 5 Rv0065, Rv0549c, Rv0960, Rv1720c 49 49 1.2 5 6 Rv0014c, Rv0015c, Rv1746, Rv2088, Rv2176 50 50 1 3 3 Rv0073, Rv0655, Rv2564 51 51 1 3 3 Rv3814c, Rv3815c, Rv3816c 52 52 1 3 3 Rv3793, Rv3794, Rv3795 53 53 1 3 3 Rv3728, Rv3239c, Rv2333c 54 54 1 3 3 Rv2247, Rv3280, Rv3799c 55 55 1 3 3 Rv2032, Rv3127, Rv3131 56 56 1 3 3 Rv2028c, Rv2624c, Rv3134c 57 57 1 3 3 Rv1962c, Rv3384c, Rv3408 58 58 1 3 3 Rv1708, Rv3213c, Rv3918c 59 59 1 3 3 Rv1701, Rv2309c, Rv2894c 60 60 1 3 3 Rv1479, Rv3164c, Rv3692 61 61 1 3 3 Rv1477, Rv1478, Rv1566c 62 62 1 3 3 Rv1365c, Rv1904, Rv2638 63 63 1 3 3 Rv1194c, Rv1453, Rv2370c 64 64 1 3 3 Rv1183, Rv1522c, Rv3823c 65 65 1 3 3 Rv1182, Rv3820c, Rv3824c 66 66 1 3 3 Rv1077, Rv1336, Rv2334 67 67 1 3 3 Rv1034c, Rv2961, Rv3387 68 68 1 3 3 Rv1009, Rv1884c, Rv2389c 69 69 1 3 3 Rv0092, Rv0103c, Rv0969 70 70 1 3 3 Rv0892, Rv1393c, Rv3049c 71 71 1 3 3 Rv0866, Rv3119, Rv3323c 72 72 1 3 3 Rv0864, Rv3111, Rv3324c 73 73 1 3 3 Rv0854, Rv0856, Rv0857 74 74 1 3 3 Rv0815c, Rv3117, Rv3283 75 75 1 3 3 Rv0778, Rv2266, Rv3545c 76 76 1 3 3 Rv0741, Rv1313c, Rv3798 77 77 1 3 3 Rv0663, Rv0711, Rv3299c 78 78 1 3 3 Rv0597c, Rv3179, Rv3294c 79 79 1 3 3 Rv0595c, Rv0627, Rv0665 80 80 1 3 3 Rv0571c, Rv2030c, Rv2143 81 81 1 3 3 Rv0547c, Rv1543, Rv3391 82 82 1 3 3 Rv0504c, Rv0635, Rv0637 83 83 1 3 3 Rv0391, Rv1079, Rv3340 84 84 1 3 3 Rv0346c, Rv1704c, Rv2127 85 85 1 3 3 Rv0285, Rv1386, Rv3022A 86 86 1 3 3 Rv0277c, Rv0749, Rv2872 87 87 1 3 3 Rv0261c, Rv0267, Rv2329c 88 88 1 3 3 Rv0248c, Rv1552, Rv3318 89 89 1 3 3 Rv0174, Rv0594, Rv1971 90 90 1 3 3 Rv0173, Rv0593, Rv1970 91 91 1 3 3 Rv0136, Rv0568, Rv3685c 92 92 1 3 3 Rv0068, Rv0439c, Rv2263 93 93 1 3 3 Rv1266c, Rv3689, Rv3494c 94 94 1 4 4 Rv0560c, Rv2675c, Rv3699, Rv1377c