The rice chloroplast genome (NC_001320) and the rice mitochondrial genome (BA000029) were aligned to the Rice Genome Annotation Project pseudomolecules (release 6.1) using NUCMER (min cluster size 300bp, %identity > 90%).
Organellar Type: M - Mitochondrion C - Chloroplast
| Chr | end5 | end3 | Organellar
Type | Organellar
Align |
| Chr1 | 7760728 | 7763448 | C | 12512-15231 |
| Chr1 | 18682959 | 18683363 | M | 241431-241835 |
| Chr1 | 18683376 | 18683852 | M | 288390-288866 |
| Chr1 | 18684888 | 18685708 | M | 300809-301629 |
| Chr1 | 33496935 | 33503846 | C | 71460-78370 |
| Chr1 | 33504256 | 33505135 | C | 16301-15422 |
| Chr1 | 33508287 | 33510036 | C | 15418-13668 |
| Chr1 | 33511620 | 33515191 | C | 21960-25531 |
| Chr1 | 33511620 | 33515191 | M | 291673-288120 |
| Chr1 | 33521493 | 33529036 | C | 36762-44314 |
| Chr1 | 33532770 | 33533625 | C | 55592-54737 |
| Chr1 | 33548313 | 33551954 | M | 226353-222721 |
| Chr1 | 33552135 | 33553698 | C | 53116-54666 |
| Chr1 | 33553696 | 33556513 | C | 30299-27483 |
| Chr1 | 33556552 | 33558742 | C | 60054-62240 |
| Chr1 | 33558748 | 33562986 | C | 49583-45314 |
| Chr1 | 33565811 | 33572056 | C | 8101-14346 |
| Chr1 | 33572056 | 33573870 | C | 55827-57651 |
| Chr1 | 33577045 | 33578480 | C | 57647-59079 |
| Chr1 | 33581383 | 33586511 | M | 387766-382638 |
| Chr1 | 38268622 | 38272182 | C | 62500-58937 |
| Chr1 | 39115484 | 39116064 | M | 301322-300743 |
| Chr1 | 39116067 | 39116489 | M | 212192-212615 |
| Chr1 | 39118872 | 39119259 | M | 313788-314174 |
| Chr1 | 39119667 | 39119981 | M | 169264-168950 |
| Chr1 | 39122823 | 39123124 | M | 184764-184463 |
| Chr1 | 39126431 | 39127095 | M | 230440-229776 |
| Chr1 | 39350369 | 39350851 | M | 244741-245223 |
| Chr1 | 41493766 | 41494228 | M | 316628-317090 |
| Chr1 | 41720795 | 41721145 | C | 52589-52239 |
| Chr1 | 42111417 | 42112257 | M | 177155-176315 |
| Chr2 | 2392407 | 2393045 | M | 299906-300553 |
| Chr2 | 11194475 | 11195154 | M | 266482-267163 |
| Chr2 | 13297302 | 13300072 | C | 112891-110120 |
| Chr2 | 14244391 | 14249405 | C | 108752-113760 |
| Chr2 | 14252737 | 14254757 | C | 28622-26602 |
| Chr2 | 14254866 | 14259389 | C | 62135-57611 |
| Chr2 | 14259678 | 14261180 | C | 19789-21291 |
| Chr2 | 14261190 | 14265315 | C | 26501-30629 |
| Chr2 | 14265307 | 14283777 | C | 25383-6890 |
| Chr2 | 14265307 | 14269734 | M | 288268-292678 |
| Chr2 | 14269796 | 14271705 | M | 292677-294586 |
| Chr2 | 22317516 | 22318228 | M | 403054-403766 |
| Chr3 | 13642489 | 13642803 | M | 247610-247924 |
| Chr3 | 13644534 | 13644950 | M | 257992-258395 |
| Chr3 | 19974521 | 19974991 | C | 106040-105570 |
| Chr3 | 25244152 | 25247909 | C | 106500-102747 |
| Chr3 | 31802223 | 31803417 | M | 191009-189815 |
| Chr3 | 31810765 | 31811083 | M | 88264-88582 |
| Chr3 | 31811526 | 31814118 | C | 50356-52947 |
| Chr4 | 9088270 | 9099554 | C | 90116-101391 |
| Chr4 | 9088270 | 9100825 | C | 125002-112456 |
| Chr4 | 9100820 | 9105377 | C | 4867-310 |
| Chr4 | 9105485 | 9111401 | C | 41322-47252 |
| Chr4 | 9116765 | 9130612 | C | 32100-45962 |
| Chr4 | 9132593 | 9138214 | C | 80593-86223 |
| Chr4 | 9132593 | 9138214 | C | 134525-128895 |
| Chr4 | 9138229 | 9159660 | C | 91896-70494 |
| Chr4 | 9138229 | 9149529 | C | 123222-134525 |
| Chr4 | 9159843 | 9168007 | C | 85281-93449 |
| Chr4 | 9159843 | 9168007 | C | 129837-121669 |
| Chr4 | 9168084 | 9193006 | C | 5287-30253 |
| Chr4 | 9181738 | 9188486 | M | 294586-287933 |
| Chr4 | 9193149 | 9205704 | C | 86711-99269 |
| Chr4 | 9193149 | 9205704 | C | 128407-115849 |
| Chr4 | 16117124 | 16117567 | M | 212779-212337 |
| Chr4 | 23459264 | 23460003 | C | 21036-20297 |
| Chr4 | 23459406 | 23460003 | M | 292677-293274 |
| Chr4 | 23460000 | 23461576 | C | 3148-4725 |
| Chr4 | 23462832 | 23465171 | C | 84893-87233 |
| Chr4 | 23462832 | 23465171 | C | 130225-127885 |
| Chr4 | 23474043 | 23474470 | C | 26634-26207 |
| Chr4 | 32687565 | 32692572 | M | 268620-273647 |
| Chr4 | 32693504 | 32698261 | M | 262601-257824 |
| Chr4 | 32698262 | 32701127 | M | 307350-310221 |
| Chr4 | 32701124 | 32703132 | M | 310420-312464 |
| Chr5 | 12829572 | 12834795 | C | 74627-79854 |
| Chr5 | 12922037 | 12924902 | C | 21083-23944 |
| Chr6 | 12504799 | 12510187 | M | 135819-141160 |
| Chr6 | 12508180 | 12514816 | M | 44620-51268 |
| Chr6 | 12522736 | 12526127 | M | 192621-196013 |
| Chr6 | 12526936 | 12532400 | M | 196532-202010 |
| Chr6 | 12532400 | 12535838 | M | 202618-206048 |
| Chr6 | 23562362 | 23591838 | C | 79402-49919 |
| Chr6 | 28179111 | 28183317 | C | 104816-109022 |
| Chr7 | 12657996 | 12662079 | C | 109910-105819 |
| Chr7 | 14229365 | 14243753 | C | 94983-80593 |
| Chr7 | 14229365 | 14243753 | C | 120135-134525 |
| Chr7 | 27974246 | 27978877 | C | 76162-80807 |
| Chr8 | 12122 | 12762 | M | 224270-224906 |
| Chr8 | 9242600 | 9248562 | C | 100087-94131 |
| Chr8 | 9242600 | 9248562 | C | 115031-120987 |
| Chr8 | 9248562 | 9283597 | C | 93839-58806 |
| Chr8 | 9248562 | 9261813 | C | 121279-134525 |
| Chr8 | 12795578 | 12796023 | M | 240308-239863 |
| Chr8 | 22319839 | 22323017 | C | 3179-1 |
| Chr8 | 22323018 | 22325063 | C | 80593-82638 |
| Chr8 | 22323018 | 22325063 | C | 134525-132480 |
| Chr9 | 2493742 | 2496244 | C | 68703-71205 |
| Chr9 | 4673606 | 4678865 | M | 413357-408105 |
| Chr9 | 4690178 | 4696087 | M | 408105-402189 |
| Chr9 | 4696035 | 4698571 | M | 336260-338795 |
| Chr9 | 7176997 | 7177700 | M | 234925-234236 |
| Chr9 | 14504285 | 14509718 | C | 83053-77612 |
| Chr9 | 16535859 | 16536834 | M | 70607-71562 |
| Chr9 | 21929739 | 21930339 | C | 61558-62158 |
| Chr9 | 22733175 | 22733571 | M | 286235-286632 |
| Chr10 | 6206126 | 6207003 | C | 1832-2714 |
| Chr10 | 10719096 | 10736014 | C | 97525-80593 |
| Chr10 | 10719096 | 10736014 | C | 117593-134525 |
| Chr10 | 10736015 | 10837297 | C | 1-101391 |
| Chr10 | 10816507 | 10849764 | C | 134525-101278 |
| Chr10 | 14463903 | 14464522 | M | 329444-330063 |
| Chr10 | 19999494 | 19999874 | M | 325847-325463 |
| Chr10 | 20380194 | 20391156 | C | 89623-100575 |
| Chr10 | 20380194 | 20391156 | C | 125495-114543 |
| Chr10 | 20391155 | 20413167 | C | 51105-29085 |
| Chr10 | 22373427 | 22377739 | C | 11168-6854 |
| Chr11 | 14085346 | 14085831 | C | 70526-71015 |
| Chr11 | 16462608 | 16462952 | M | 261995-262339 |
| Chr12 | 5607898 | 5614870 | C | 48881-55839 |
| Chr12 | 5614872 | 5634531 | C | 98923-118635 |
| Chr12 | 5634529 | 5647871 | C | 58232-71624 |
| Chr12 | 8534810 | 8536693 | M | 255958-254056 |
| Chr12 | 8536696 | 8537306 | M | 253417-254029 |
| Chr12 | 8543166 | 8545759 | M | 73149-75644 |
| Chr12 | 8554515 | 8556951 | M | 208666-206227 |
| Chr12 | 8556994 | 8557840 | M | 206045-205199 |
| Chr12 | 8557840 | 8558993 | M | 205310-204127 |
| Chr12 | 11084561 | 11085663 | C | 57538-56425 |
| Chr12 | 11085721 | 11087521 | C | 110803-109009 |
| Chr12 | 11280128 | 11286592 | C | 45647-52118 |
| Chr12 | 13339650 | 13339980 | M | 239336-239006 |
| Chr12 | 13348481 | 13348828 | M | 312285-311938 |
| Chr12 | 13354726 | 13355147 | M | 173335-172914 |
| Chr12 | 13355150 | 13355573 | M | 271556-271979 |
| Chr12 | 13372913 | 13373310 | M | 175885-175487 |
| Chr12 | 13380655 | 13381007 | M | 285585-285937 |
| Chr12 | 13385787 | 13386116 | M | 299719-299390 |
| Chr12 | 13401449 | 13401866 | M | 225662-226079 |
| Chr12 | 13402569 | 13403141 | M | 262401-262973 |
| Chr12 | 13405380 | 13405793 | M | 327659-327246 |
| Chr12 | 13407673 | 13408105 | M | 242642-243074 |
| Chr12 | 13409875 | 13410199 | M | 89385-89708 |
| Chr12 | 20423792 | 20431305 | M | 174769-182286 |
| Chr12 | 20431307 | 20436595 | M | 336511-341789 |
| Chr12 | 20445315 | 20458205 | M | 177831-190726 |
| Chr12 | 20458205 | 20458567 | M | 317744-317382 |
| Chr12 | 20469288 | 20473350 | M | 317387-313326 |
| Chr12 | 20473344 | 20513744 | M | 92237-51835 |
| Chr12 | 20503188 | 20503637 | M | 294215-294664 |
| Chr12 | 20514863 | 20526607 | M | 51835-40090 |
| Chr12 | 20520064 | 20526607 | M | 141160-134617 |
| Chr12 | 20539213 | 20557277 | M | 165156-183215 |
| Chr12 | 20569360 | 20592211 | M | 183215-206048 |
| Chr12 | 20592251 | 20594554 | M | 206227-208532 |
| Chr12 | 20594560 | 20598311 | M | 212838-216589 |
| Chr12 | 20598313 | 20608151 | M | 275717-285572 |
| Chr12 | 20600946 | 20613151 | M | 409281-421493 |
| Chr12 | 20616586 | 20635603 | M | 273647-254621 |
| Chr12 | 20636877 | 20641573 | M | 165156-169849 |
| Chr12 | 20641573 | 20647382 | M | 169992-175799 |
| Chr12 | 20658118 | 20672185 | M | 175799-189870 |
| Chr12 | 20891726 | 20896176 | C | 104515-100066 |
| Chr12 | 20894850 | 20896176 | C | 113727-115052 |
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