Table 2. Alignment co-ordinates and sequences of putative stem-loop structures that appear to have undergone inversion in Polystachya.
| Loop | Alignment co-ordinates | Sequence (majority) | Sequence (minority) | Substitutions before/after inversion reverted | Sequences (minority) |
|---|---|---|---|---|---|
| A | 74,660–74,678 | TCTATCTA-GAA-TAGATAGA | TCTATCTA-TTC-TAGATAGA | 3/0 | bicolor, concreta7, concreta9, tesselata1, melanantha, Phalaenopsis |
| B | 88,106–88,142 | GGCCCAATCTTTC-TTTTTTTGAGGA-AAAGATTGGGCC | GGCCCAATCTTTC-TCCTCAAAAAAA-AAAGATTGGGCC | 8/0 | humbertii2, oreocharis1, tsinjoarivensis2, melanantha |
| C | 90,456–90,496 | AGTAAGAACTCAGCG-GGGTAAGGCCT-CGCTGAGTTCTTACT | AGTAAGAACTCAGCG-AGGCCTTACCC-CGCTGAGTTCTTACT* | 7/0 | eurychila |
| D | 94,175–94,222 | ATTGAAGTAATGAGCCC-CAAGATGAATATGA-GGGCTCATTACTTCAAT | ATTGAAGTAATGAGCCC-TCATATTCATCTTG-GGGCTCATTACTTCAAT | 8/0 | humbertii1, steudneri |
| E | 94,679–94,717 | GTATCTAAGGAAGATCC-AAAGG-GGATCTTCCTTAGATAC | GTATCTAAGGAAGATCC-CTTCT-GGATCTTCCTTAGATAC | 5/2 | estrelensis12, estrelensis13, estrelensis14, eurychila, concreta7, concreta8, golungensis, oreocharis1, melanantha, humbertii1, Phalaenopsis |
| F | 97,230–97,258 | AACGTCCAGTG-CCAAAGT-CACTGAATGGG | ^CCCATTCAGTG-ACTTTGG-CACTGAATGGG | 6/0 | All 13 sequences of the estrelensis clade (cartooned in Figs. 2 and 4) |
| G | 104,698–104,730 | ATTCAATTCTTC-ATTCTTTCAA-GAAGAATGAAT | ATTCAATTCTTC-ATGAAAGAAA- GAAGAATGAAT | 6/0 | foliosa1, foliosa2, odorata1, odorata2, Phalaenopsis |
| H | 106,618–106,650 | ATTCATTCTTCAT-GAAAGA-ATGAAGAATTGAAT | ATTCATTCTTCAT-TCTTTC-ATGAAGAATTGAAT | 6/0 | foliosa1, foliosa2, odorata1, odorata2, Phalaenopsis |
Notes:
The loops that appear to have undergone inversions are underlined. Bolded bases would be treated as phylogenetically informative if the alignment does not take into account the inversion. Bases not involved in stem formation are in subscript.
*
Occurs in only one sequence.
^
Only the sequences with the inversion appear to form the stem in this case.