Table 2.
Features of LIMP repeats identified in the L. incisa mitochondrial genome
| LIMP # | Centera | Structureb | Total length (nt) | Stem length (bp) | Palindromic regionc(nt) | Imperfect genomic readsd | ΔG RNA hairpin (kcal.mol−1)e | transcriptome coveragef |
|---|---|---|---|---|---|---|---|---|
| 1 | 33 | 5;+;4 | 52 | 20 | 52 | 0;6 | −30.60 | low (19) |
| 2 | 2152 | 8;+;6 | 77 | 30 | 77 | 18;5 | −49.70 | NO (2) |
| 3 | 7742 | 7;+;8 | 82 | 35 | 82 | 0;11 | −63.00 | NO (1) |
| 4 | 10697 | 8;-;7 | 82 | 35 | 82 | 0;6 | −61.20 | NO (0) |
| 5 | 14093 | 8;-;9 | 92 | 40 | 96 | 9;7 | −77.60 | NO (1) |
| 6 | 15481 | 7;+;10 | 92 | 35 | 92 | 1;2 | −66.60 | NO (1) |
| 7 | 16799 | 10;-;9 | 102 | 45 | 102 | 4;12 | −80.00 | NO (1) |
| 8 | 17732 | 8;+;9 | 92 | 40 | 96 | 20;5 | −76.80 | NO (0) |
| 9 | 18115 | 7;-;8 | 82 | 35 | 86 | 12;0 | −68.20 | NO (0) |
| 10 | 23885 | 3;-;2 | 32 | 10 | 74 | 1;0 | −55.20 | normal (145) |
| 11 | 29424 | 3;-;9 | 67 | 15 | 67 | 1;6 | −27.40 | normal (47) |
| 12 | 32075 | 11;+;13 | 127 | 55 | 127 | 27;12 | −101.70 | NO (1) |
| 13 | 43731 | 3;+;3 | 37 | 15 | 37 | 4;0 | −21.70 | normal (83) |
| 14 | 50059 | 12;-;8 | 107 | 40 | 107 | 1;7 | −70.40 | NO (5) |
| 15 | 55976 | 4;+;13 | 92 | 20 | 96 | 8;10 | −48.00 | low (13) |
| 16 | 59523 | 5;-;5 | 57 | 25 | 57 | 0;0 | −41.30 | low (18) |
| 17 | 60233 | 8;-;7 | 82 | 35 | 82 | 0;1 | −61.20 | NO (1) |
| 18 | 66788 | 7;-;9 | 87 | 35 | 87 | 4;9 | −63.10 | NO (1) |
| 19 | 67694 | 9;+;8 | 92 | 40 | 92 | 14;6 | −68.20 | NO (1) |
| average: | 80.7 | 31.8 | 83.7 | −59.6 | ||||
| total: | 1533 | 605 | 1591 | 124;105 |
aposition of first nt of first T-unit
bnumber of A-units; type of loop; number of T-units
cincluding additional nucleotides extending the stem, see Fig. 2a
dreads showing a change in the number of A-units; of T-units
eincluding extension of palindrome for #5, 8, 9 and 10
fcoverage level (number of reads at position of lowest coverage; 5 or below is considered an interruption)