Table 3.
Long repeat sequences in A. sinensis chloroplast genome.
| id | Repeat Start 1 | Type | Size(bp) | Repeat Start 2 | Mismatch(bp) | E-value | Gene | Region |
|---|---|---|---|---|---|---|---|---|
| 1 | 1471 | F | 41 | 71846 | −3 | 4.26E-10 | IGS | LSC |
| 2 | 1480 | F | 41 | 71855 | −3 | 4.26E-10 | IGS | LSC |
| 3 | 1574 | F | 163 | 71953 | −3 | 1.00E-81 | IGS | LSC |
| 4 | 1587 | F | 156 | 71966 | −3 | 1.44E-77 | IGS | LSC |
| 5 | 8609 | F | 31 | 37664 | −3 | 1.88E-04 | IGS | LSC |
| 6 | 41152 | F | 41 | 43376 | −2 | 1.09E-11 | psaB(CDS); psaA(CDS) | LSC |
| 7 | 46415 | F | 36 | 101941 | −1 | 1.64E-10 | ycf3(intron); IGS | LSC; IRA |
| 8 | 46415 | F | 36 | 124843 | −3 | 2.92E-07 | ycf3(intron); ndhA(inton) | LSC; SSC |
| 9 | 46424 | F | 30 | 101950 | −1 | 5.59E-07 | ycf3(intron); IGS | LSC; IRA |
| 10 | 70177 | F | 30 | 70366 | −3 | 6.81E-04 | accD(CDS) | LSC |
| 11 | 70195 | F | 67 | 70273 | −2 | 6.54E-27 | accD(CDS) | LSC |
| 12 | 70195 | F | 36 | 70291 | −2 | 8.60E-09 | accD(CDS) | LSC |
| 13 | 70199 | F | 53 | 70259 | −1 | 1.40E-20 | accD(CDS) | LSC |
| 14 | 70218 | F | 34 | 70260 | −1 | 2.47E-09 | accD(CDS) | LSC |
| 15 | 70260 | F | 31 | 70296 | −1 | 1.44E-07 | accD(CDS) | LSC |
| 16 | 95892 | F | 31 | 95928 | −3 | 1.88E-04 | ycf2(CDS) | IRA |
| 17 | 96540 | F | 31 | 150227 | −3 | 1.88E-04 | ycf15(CDS) | IRA; IRB |
| 18 | 97906 | F | 30 | 148863 | −2 | 2.43E-05 | IGS | IRA; IRB |
| 19 | 101938 | F | 41 | 124840 | −2 | 1.09E-11 | IGS; ndhA(intron) | IRA; SSC |
| 20 | 112678 | F | 31 | 112720 | 0 | 1.55E-09 | IGS | IRA |
| 21 | 113385 | F | 55 | 113454 | 0 | 5.52E-24 | IGS | IRA |
| 22 | 118510 | F | 64 | 118590 | −1 | 4.04E-27 | ccsA(CDS) | SSC |
| 23 | 119996 | F | 32 | 120064 | −3 | 5.20E-05 | IGS | SSC |
| 24 | 131641 | F | 30 | 131707 | −3 | 6.81E-04 | ycf1(CDS) | SSC |
| 25 | 132792 | F | 31 | 132831 | −2 | 6.50E-06 | ycf1(CDS) | SSC |
| 26 | 133153 | F | 39 | 133216 | −3 | 5.85E-09 | ycf1(CDS) | SSC |
| 27 | 133168 | F | 38 | 133231 | −1 | 1.08E-11 | ycf1(CDS) | SSC |
| 28 | 133282 | F | 62 | 133351 | 0 | 3.37E-28 | ycf1(CDS) | SSC; IRB |
| 29 | 150839 | F | 31 | 150875 | −3 | 1.88E-04 | ycf2(CDS) | IRB |
| 30 | 8610 | I | 30 | 47858 | −1 | 5.59E-07 | IGS | LSC |
| 31 | 37665 | I | 30 | 47858 | −3 | 6.81E-04 | IGS | LSC |
| 32 | 46415 | I | 36 | 144821 | −1 | 1.64E-10 | ycf3(intron); IGS | LSC; IRB |
| 33 | 46424 | I | 30 | 144818 | −1 | 5.59E-07 | ycf1(CDS) | LSC; IRB |
| 34 | 89862 | I | 30 | 156882 | −3 | 6.81E-04 | ycf2(CDS) | IRA; IRB |
| 35 | 89886 | I | 30 | 156906 | −3 | 6.81E-04 | ycf2(CDS) | IRA; IRB |
| 36 | 94593 | I | 38 | 152149 | −2 | 6.00E-10 | ycf2(CDS) | IRA; IRB |
| 37 | 94611 | I | 38 | 152167 | −2 | 6.00E-10 | ycf2(CDS) | IRA; IRB |
| 38 | 95892 | I | 31 | 150839 | −3 | 1.88E-04 | ycf2(CDS) | IRA; IRB |
| 39 | 95900 | I | 41 | 150839 | 0 | 1.48E-15 | ycf2(CDS) | IRA; IRB |
| 40 | 95918 | I | 41 | 150857 | 0 | 1.48E-15 | ycf2(CDS) | IRA; IRB |
| 41 | 95928 | I | 31 | 150875 | −3 | 1.88E-04 | ycf2(CDS) | IRA; IRB |
| 42 | 112668 | I | 41 | 134047 | −1 | 1.82E-13 | IGS | IRA; IRB |
| 43 | 112668 | I | 62 | 134047 | −2 | 5.73E-24 | IGS; ycf1(CDS),IGS | IRA; IRB |
| 44 | 112678 | I | 31 | 134047 | 0 | 1.55E-09 | IGS | IRA; IRB |
| 45 | 112689 | I | 62 | 134068 | −2 | 5.73E-24 | IGS | IRA; IRB |
| 46 | 112699 | I | 31 | 134047 | −1 | 1.44E-07 | IGS | IRA; IRB |
| 47 | 112710 | I | 41 | 134089 | −1 | 1.82E-13 | IGS | IRA; IRB |
| 48 | 112720 | I | 31 | 134089 | 0 | 1.55E-09 | IGS | IRA; IRB |
| 49 | 112720 | I | 31 | 134068 | −1 | 1.44E-07 | IGS | IRA; IRB |
| 50 | 113385 | I | 70 | 133274 | −1 | 1.08E-30 | IGS; ycf1(CDS) | IRA |
| 51 | 113454 | I | 55 | 133358 | 0 | 5.52E-24 | IGS; ycf1(CDS) | IRA; SSC |
| 52 | 113526 | I | 530 | 117403 | 0 | 0.00E+00 | IGS,rpl(CDS) | IRA; SSC |
| 53 | 124840 | I | 41 | 144819 | −2 | 1.09E−11 | ndhA(CDS,intron); IGS | SSC; IRB |
| 54 | 59836 | T | 31 | 59866 | 0 | 1.55E-09 | rps18 | LSC |
| 55 | 112668 | T | 41 | 112710 | −1 | 1.82E−13 | IGS | IRA |
| 56 | 118496 | T | 78 | 118576 | −3 | 1.61E−31 | IGS | SSC |
| 57 | 132782 | T | 41 | 132821 | −3 | 4.26E−10 | ycf1(CDS) | SSC |
| 58 | 133193 | T | 44 | 133235 | 0 | 2.31E−17 | ycf1(CDS) | SSC |
| 59 | 133274 | T | 70 | 133343 | −1 | 1.08E-30 | ycf1(CDS) | SSC; IRB |
| 60 | 134047 | T | 41 | 134089 | −1 | 1.82E-13 | IGS | IRB |
F, Forward; I, Inverted; T, Tandem; IGS, intergenic space.