REPuter Results - Calculated Repeats Format: Size Pos_1 Type Size_2 Pos_2 Distance E-Value # /vol/reputer/bin/repfind -f -h 3 -l 16 /spool/reputer/_1052605368_7162/sequence.fna # 103432 -3 16 /spool/reputer/_1052605368_7162/sequence.fna 5604 35643 F 5604 46488 -3 0.00e+00 5319 41629 F 5319 52477 -3 0.00e+00 5214 41914 F 5214 52762 -3 0.00e+00 5144 43148 F 5144 53996 -3 0.00e+00 4966 36284 F 4966 47129 -3 0.00e+00 4617 42937 F 4617 53785 -3 0.00e+00 3638 31659 F 3638 42499 -3 0.00e+00 3638 31659 F 3638 53347 -3 0.00e+00 3620 31678 F 3620 53366 -3 0.00e+00 3620 31678 F 3620 42518 -3 0.00e+00 3202 32097 F 3202 42937 -3 0.00e+00 2991 32308 F 2991 53996 -3 0.00e+00 2968 32334 F 2968 43174 -3 0.00e+00 2968 32334 F 2968 54022 -3 0.00e+00 2282 19120 F 2282 23899 -3 0.00e+00 2020 19055 F 2020 23834 -3 0.00e+00 1949 18988 F 1949 23767 -3 0.00e+00 1935 35649 F 1935 57342 -3 0.00e+00 1741 20100 F 1741 24879 -3 0.00e+00 1481 36104 F 1481 57797 -3 0.00e+00 1480 46949 F 1480 57797 -3 0.00e+00 1301 47129 F 1301 57977 -3 0.00e+00 1269 18830 F 1269 23609 -3 0.00e+00 942 20938 F 942 25717 -3 0.00e+00 940 97622 F 940 102403 -3 0.00e+00 940 22213 F 940 26995 -3 0.00e+00 931 97633 F 931 102414 -3 0.00e+00 926 97640 F 926 102421 -3 0.00e+00 897 21076 F 897 25855 -3 0.00e+00 885 5733 F 885 8118 -3 0.00e+00 879 36710 F 879 58403 -3 0.00e+00 879 47555 F 879 58403 -3 0.00e+00 875 5753 F 875 8138 -3 0.00e+00 864 5765 F 864 8150 -3 0.00e+00 843 5787 F 843 8172 -3 0.00e+00 812 21403 F 812 26182 -3 0.00e+00 679 31654 F 679 53342 -3 0.00e+00 679 31654 F 679 42494 -3 0.00e+00 429 41217 F 429 52064 -1 2.01e-246 395 18233 F 395 23013 -3 1.27e-220 373 35276 F 373 56966 0 8.13e-216 373 35276 F 373 46118 0 8.13e-216 373 21842 F 373 26621 -2 5.08e-210 358 18629 F 358 23408 -3 1.79e-198 334 21881 F 334 26660 -1 2.46e-189 326 18728 F 326 23507 -3 2.49e-179 325 18794 F 325 23573 -3 9.86e-179 299 41347 F 299 52194 0 2.90e-171 293 18335 F 293 23115 -2 4.57e-162 265 18363 F 265 23143 -1 6.81e-148 Here is the intervals of the REPuter result. The format is as follows:left1 right1 left2 right2. 5733 6618 8118 9003 5753 6628 8138 9013 5765 6629 8150 9014 5787 6630 8172 9015 18233 18628 23013 23408 18335 18628 23115 23408 18363 18628 23143 23408 18629 18987 23408 23766 18728 19054 23507 23833 18794 19119 23573 23898 18830 20099 23609 24878 18988 20937 23767 25716 19055 21075 23834 25854 19120 21402 23899 26181 20100 21841 24879 26620 20938 21880 25717 26659 21076 21973 25855 26752 21403 22215 26182 26994 21842 22215 26621 26994 21881 22215 26660 26994 22213 23153 26995 27935 31654 32333 53342 54021 31654 32333 42494 43173 31678 35298 53366 56986 31678 35298 42518 46138 32097 35299 42937 46139 32308 35299 53996 56987 32334 35302 43174 46142 32334 35302 54022 56990 35276 35649 56966 57339 35276 35649 46118 46491 35649 37584 57342 59277 36104 37585 57797 59278 36710 37589 58403 59282 41217 41646 52064 52493 41347 41646 52194 52493 46949 48429 57797 59277 47129 48430 57977 59278 47555 48434 58403 59282 97622 98562 102403 103343 97633 98564 102414 103345 97640 98566 102421 103347 Here are the repeats I think in the sequences according to REPuter. [ 5733, 6630] == [ 8118, 9015] [18233,23153] == [23013,27935] [31654,35649] == [42494,46491] == [53342,57339] [35649,36103] == [57342,57796] [36104,37589] == [46949,57342] == [57797,59282] [41217,41646] == [52064,52493] [97622,98566] == [102403,103347] The length of the genome repeated twice. (897+4920+455+429+944)*2/103432 = 0.1478 The length of the genome repeated three times. (3995+1485)*3/103432 = 0.1589