| Gene alias | Chrom. | Start | End | Num. of lncRNAs |
|---|---|---|---|---|
| Tcacao Thecc1EG046393 | cacao1chloroplast | 68025 | 68579 | 1 |
| Tcacao Thecc1EG046394 | cacao1chloroplast | 70996 | 71292 | 1 |
| Tcacao Thecc1EG046415 | cacao1chloroplast | 117611 | 117946 | 1 |
| Tcacao Thecc1EG046420 | cacao1chloroplast | 135987 | 136483 | 1 |
| Tcacao Thecc1EG046421 | cacao1chloroplast | 137525 | 138797 | 1 |
| Tcacao Thecc1EG000004 | scaffold_1 | 16143 | 17240 | 1 |
| Tcacao Thecc1EG000018 | scaffold_1 | 72783 | 81691 | 1 |
| Tcacao Thecc1EG000022 | scaffold_1 | 94846 | 95345 | 1 |
| Tcacao Thecc1EG000058 | scaffold_1 | 230231 | 231698 | 1 |
| Tcacao Thecc1EG000064 | scaffold_1 | 252838 | 253439 | 1 |
| Tcacao Thecc1EG000088 | scaffold_1 | 366617 | 367574 | 1 |
| Tcacao Thecc1EG000094 | scaffold_1 | 397391 | 397743 | 1 |
| Tcacao Thecc1EG000104 | scaffold_1 | 432946 | 433948 | 1 |
| Tcacao Thecc1EG000120 | scaffold_1 | 484233 | 484697 | 1 |
| Tcacao Thecc1EG000129 | scaffold_1 | 507603 | 507966 | 1 |
| Tcacao Thecc1EG000143 | scaffold_1 | 573104 | 574637 | 1 |
| Tcacao Thecc1EG000175 | scaffold_1 | 686226 | 688036 | 1 |
| Tcacao Thecc1EG000180 | scaffold_1 | 700582 | 701118 | 1 |
| Tcacao Thecc1EG000184 | scaffold_1 | 714460 | 715669 | 1 |
| Tcacao Thecc1EG000194 | scaffold_1 | 749172 | 750102 | 1 |
| Tcacao Thecc1EG000195 | scaffold_1 | 750174 | 751477 | 1 |
| Tcacao Thecc1EG000196 | scaffold_1 | 752988 | 753487 | 1 |
| Tcacao Thecc1EG000205 | scaffold_1 | 798722 | 800078 | 1 |
| Tcacao Thecc1EG000261 | scaffold_1 | 1061386 | 1064360 | 1 |
| Tcacao Thecc1EG000269 | scaffold_1 | 1101061 | 1101562 | 1 |
| Tcacao Thecc1EG000281 | scaffold_1 | 1167514 | 1169095 | 1 |
| Tcacao Thecc1EG000315 | scaffold_1 | 1297883 | 1298301 | 1 |
| Tcacao Thecc1EG000319 | scaffold_1 | 1311167 | 1312425 | 1 |
| Tcacao Thecc1EG000323 | scaffold_1 | 1323939 | 1325149 | 1 |
| Tcacao Thecc1EG000335 | scaffold_1 | 1374604 | 1375342 | 1 |
| Tcacao Thecc1EG000363 | scaffold_1 | 1484789 | 1485222 | 1 |
| Tcacao Thecc1EG000375 | scaffold_1 | 1538659 | 1539761 | 1 |
| Tcacao Thecc1EG000379 | scaffold_1 | 1558679 | 1559535 | 1 |
| Tcacao Thecc1EG000381 | scaffold_1 | 1559830 | 1564041 | 1 |
| Tcacao Thecc1EG000384 | scaffold_1 | 1567435 | 1568574 | 1 |
| Tcacao Thecc1EG000396 | scaffold_1 | 1617318 | 1619448 | 1 |
| Tcacao Thecc1EG000397 | scaffold_1 | 1619039 | 1620296 | 1 |
| Tcacao Thecc1EG000403 | scaffold_1 | 1659410 | 1663453 | 1 |
| Tcacao Thecc1EG000422 | scaffold_1 | 1725173 | 1728436 | 1 |
| Tcacao Thecc1EG000434 | scaffold_1 | 1778584 | 1779653 | 1 |
| Tcacao Thecc1EG000448 | scaffold_1 | 1847247 | 1848376 | 1 |
| Tcacao Thecc1EG000457 | scaffold_1 | 1882326 | 1883964 | 1 |
| Tcacao Thecc1EG000462 | scaffold_1 | 1895942 | 1897108 | 1 |
| Tcacao Thecc1EG000476 | scaffold_1 | 1957837 | 1960057 | 1 |
| Tcacao Thecc1EG000477 | scaffold_1 | 1962659 | 1963244 | 1 |
| Tcacao Thecc1EG000478 | scaffold_1 | 1971983 | 1974558 | 1 |
| Tcacao Thecc1EG000487 | scaffold_1 | 2010551 | 2013761 | 1 |
| Tcacao Thecc1EG000493 | scaffold_1 | 2032451 | 2033002 | 1 |
| Tcacao Thecc1EG000507 | scaffold_1 | 2081291 | 2082051 | 1 |
| Tcacao Thecc1EG000527 | scaffold_1 | 2195103 | 2196533 | 1 |