Table 3. Ranking and comparison of p-distances and differences in the four plastid genome pairs.
| Pyrus | Cymbidium | Oenothera | Olea | |||||||||||||
| Rank | Region | Aligned length [bp] | PICs (SNPs/Indels) | p-distance [*10−3] | Region | Aligned length [bp] | PICs (SNPs/Indels) | p-distance [*10−3] | Region | Aligned length [bp] | PICs (SNPs/Indels) | p-distance [*10−3] | Region | Aligned length [bp] | PICs (SNPs/Indels) | p-distance [*10−3] |
| 1 | psbB–psbT | 184 | 6 (5/1) | 37.88 | trnP–psaJ | 366 | 6 (5/1) | 14.04 | ycf1–ndhF | 381 | 15 (9/6) | 36.73 | trnG–trnR | 170 | 5 (4/1) | 23.81 |
| 2 | psbI–trnS | 149 | 4 (3/1) | 22.06 | ndhF–rpl32 | 259 | 4 (3/1) | 13.04 | psbJ–psbL | 134 | 2 (2/0) | 14.93 | psbC–trnS | 243 | 6 (5/1) | 21.1 |
| 3 | ndhC–trnV | 760 | 24 (12/12) | 20.34 | trnK–rps16 | 613 | 17 (7/10) | 12.15 | rps4–trnT | 332 | 5 (4/1) | 12.16 | trnR–atpA | 112 | 3 (2/1) | 18.02 |
| 4 | trnR–atpA | 909 | 20 (10/10) | 13.61 | psaJ–rpl33 | 629 | 8 (6/2) | 9.93 | trnG–trnfM | 172 | 3 (2/1) | 11.9 | trnS–trnG | 715 | 12 (10/2) | 14.33 |
| 5 | ndhF–rpl32 | 1078 | 20 (12/8) | 11.41 | rps19–psbA | 345 | 4 (3/1) | 8.7 | ndhG–ndhI | 408 | 5 (4/1) | 9.9 | accD–psaI | 702 | 11 (10/1) | 14.27 |
| 6 | rpl36–rps8 | 459 | 5 (5/0) | 10.89 | rps19–trnH | 122 | 1 (1/0) | 8.2 | accD–psaI | 577 | 6 (5/1) | 8.68 | ycf15–trnL | 354 | 5 (5/0) | 14.12 |
| 7 | trnK–rps16 | 974 | 9 (8/1) | 8.38 | petA–psbJ | 635 | 6 (5/1) | 7.9 | trnQ–psbK | 355 | 6 (3/3) | 8.52 | psbA–trnH | 447 | 8 (6/2) | 13.51 |
| 8 | trnQ–rps16 | 905 | 10 (6/4) | 8.3 | ndhD–psaC | 129 | 1 (1/0) | 7.75 | ndhF–rpl32 | 932 | 7 (7/0) | 8.26 | rps4–trnT | 326 | 5 (4/1) | 12.31 |
| 9 | psbA–trnH | 268 | 6 (2/4) | 7.81 | psbC–trnS | 146 | 1 (1/0) | 6.85 | trnQ–accD | 2615 | 23 (12/11) | 5.59 | trnG–trnM | 174 | 2 (2/0) | 11.49 |
| 10 | trnL–trnF | 403 | 4 (3/1) | 7.59 | rrn4.5–rrn5 | 168 | 1 (1/0) | 5.95 | rps12–clpP | 397 | 4 (2/2) | 5.13 | psbB–psbT | 186 | 2 (2/0) | 10.75 |
| 11 | ndhJ–ndhK | 137 | 1 (1/0) | 7.3 | clpP intron 2 | 676 | 5 (4/1) | 5.93 | rps16–rbcL | 976 | 8 (4/4) | 5.06 | trnT–psbD | 1322 | 15 (14/1) | 10.6 |
| 12 | rpl14–rpl16 | 145 | 2 (1/1) | 6.99 | trnL–ccsA | 180 | 1 (1/0) | 5.56 | atpI–rps2 | 216 | 1 (1/0) | 4.63 | trnK–rps16 | 899 | 12 (9/3) | 10.06 |
| 13 | trnD–trnY | 448 | 4 (3/1) | 6.79 | ndhE–ndhG | 185 | 1 (1/0) | 5.41 | rps2–rpoC2 | 219 | 2 (1/1) | 4.59 | rps2–rpoC2 | 209 | 4 (2/2) | 9.66 |
| 14 | psbM–trnD | 1235 | 11 (8/3) | 6.51 | trnS–psbZ | 230 | 1 (1/0) | 4.35 | trnP–psaJ | 515 | 4 (2/2) | 4.37 | trnS–rps4 | 314 | 3 (3/0) | 9.55 |
| 15 | trnW–trnP | 156 | 1 (1/0) | 6.41 | ndhG–ndhI | 233 | 1 (1/0) | 4.29 | trnI–ycf2 | 462 | 2 (2/0) | 4.33 | psbN–psbH | 105 | 1 (1/0) | 9.52 |
| 16 | rpl16 intron | 1003 | 9 (6/3) | 6.01 | trnK–psbA | 257 | 1 (1/0) | 3.89 | atpH–atpI | 939 | 5 (4/1) | 4.26 | trnD–trnY | 107 | 2 (1/1) | 9.43 |
| 17 | ycf4–cemA | 526 | 3 (3/0) | 5.7 | trnS–rps4 | 287 | 1 (1/0) | 3.48 | trnK intron 5′ | 249 | 2 (1/1) | 4.03 | psbM–trnD | 657 | 7 (6/1) | 9.15 |
| 18 | rbcL–accD | 569 | 6 (3/3) | 5.33 | rpl16 intron | 1191 | 9 (4/5) | 3.46 | petN–psbM | 926 | 3 (3/0) | 3.24 | trnQ–psbK | 335 | 5 (3/2) | 9.01 |
| 19 | trnT–trnL | 1241 | 8 (6/2) | 4.94 | trnT–trnL | 610 | 4 (2/2) | 3.36 | psaA–ycf3 | 669 | 3 (2/1) | 3.01 | atpI–rps2 | 222 | 2 (2/0) | 9.01 |
| 20 | psaI–ycf4 | 413 | 4 (2/2) | 4.89 | atpI–rps2 | 300 | 1 (1/0) | 3.33 | trnS–psbZ | 348 | 1 (1/0) | 2.87 | atpF intron | 697 | 7 (6/1) | 8.62 |
| 21 | rps8–rpl14 | 207 | 2 (1/1) | 4.83 | psbB–psbT | 323 | 1 (1/0) | 3.1 | trnK–rps16 | 758 | 4 (2/2) | 2.67 | petN–psbM | 1171 | 12 (10/2) | 8.62 |
| 22 | rpl33–rps18 | 218 | 2 (1/1) | 4.67 | trnQ–psbK | 348 | 1 (1/0) | 2.87 | petD intron | 761 | 3 (2/1) | 2.65 | trnK–psbA | 236 | 2 (2/0) | 8.47 |
| 23 | trnS–trnG | 651 | 3 (3/0) | 4.62 | ycf4–cemA | 728 | 3 (2/1) | 2.75 | trnS–trnG | 788 | 2 (2/0) | 2.54 | ndhF–rpl32 | 479 | 4 (4/0) | 8.37 |
| 24 | rps16 intron | 909 | 7 (4/3) | 4.48 | rps4–trnT | 367 | 2 (1/1) | 2.74 | trnG intron | 804 | 4 (2/2) | 2.5 | psbI–trnS | 120 | 1 (1/0) | 8.33 |
| 25 | petD–rpoA | 225 | 1 (1/0) | 4.48 | trnT–psbD | 947 | 2 (2/0) | 2.11 | psaI–ycf4 | 412 | 5 (1/4) | 2.45 | petG–trnW | 121 | 1 (1/0) | 8.26 |
| 26 | atpF–atpH | 451 | 3 (2/1) | 4.44 | atpB–rbcL | 960 | 3 (2/1) | 2.11 | psbE–petL | 984 | 4 (2/2) | 2.05 | rps14–psaB | 122 | 1 (1/0) | 8.2 |
| 27 | trnM–atpE | 242 | 2 (1/1) | 4.29 | petN–trnD | 1020 | 2 (2/0) | 1.96 | trnT–trnL | 1114 | 4 (2/2) | 1.89 | psaA–ycf3 | 741 | 6 (6/0) | 8.1 |
| 28 | psaJ–rpl33 | 472 | 4 (2/2) | 4.29 | trnE–trnT | 1216 | 3 (2/1) | 1.68 | trnT–psbD | 1441 | 6 (2/4) | 1.43 | trnK intron 5′ | 268 | 3 (2/1) | 7.49 |
| 29 | rpoB–trnC | 1216 | 8 (5/3) | 4.13 | psaA–ycf3 | 638 | 1 (1/0) | 1.57 | ycf3 intron 2 | 720 | 1 (1/0) | 1.39 | rpl32–trnL | 835 | 10 (6/4) | 7.26 |
| 30 | trnL intron | 514 | 3 (2/1) | 3.9 | rpoB–trnC | 1461 | 3 (2/1) | 1.38 | petB intron | 775 | 4 (1/3) | 1.34 | ndhC–trnV | 1119 | 12 (8/4) | 7.24 |
The regions are sorted according to p-distances.